From 5ec7858e9e2f547e7f9f0288d27fe8b4d28a29a7 Mon Sep 17 00:00:00 2001 From: michael-petersen Date: Thu, 8 May 2025 14:51:01 +0100 Subject: [PATCH] some top-level cosmetic changes --- AUTHORS | 13 - COPYING | 674 ---- ChangeLog | 7084 ----------------------------------------- Exception.H | 104 - NEWS | 13 - Paper/paper/paper.pdf | Bin 363396 -> 363497 bytes README.md | 1 + 7 files changed, 1 insertion(+), 7888 deletions(-) delete mode 100644 AUTHORS delete mode 100644 COPYING delete mode 100644 ChangeLog delete mode 100644 Exception.H delete mode 100644 NEWS diff --git a/AUTHORS b/AUTHORS deleted file mode 100644 index f0fedbd14..000000000 --- a/AUTHORS +++ /dev/null @@ -1,13 +0,0 @@ -Original author ---------------- - -Martin D. Weinberg - -The following people have contributed code ------------------------------------------- - -The following people have offered fixes ---------------------------------------- - -Enrico Vesperini -Jun-Hwan Choi diff --git a/COPYING b/COPYING deleted file mode 100644 index 3877ae0a7..000000000 --- a/COPYING +++ /dev/null @@ -1,674 +0,0 @@ - GNU GENERAL PUBLIC LICENSE - Version 3, 29 June 2007 - - Copyright (C) 2007 Free Software Foundation, Inc. - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - - Preamble - - The GNU General Public License is a free, copyleft license for -software and other kinds of works. - - The licenses for most software and other practical works are designed -to take away your freedom to share and change the works. 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If not, see . - -Also add information on how to contact you by electronic and paper mail. - - If the program does terminal interaction, make it output a short -notice like this when it starts in an interactive mode: - - Copyright (C) - This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. - This is free software, and you are welcome to redistribute it - under certain conditions; type `show c' for details. - -The hypothetical commands `show w' and `show c' should show the appropriate -parts of the General Public License. Of course, your program's commands -might be different; for a GUI interface, you would use an "about box". - - You should also get your employer (if you work as a programmer) or school, -if any, to sign a "copyright disclaimer" for the program, if necessary. -For more information on this, and how to apply and follow the GNU GPL, see -. - - The GNU General Public License does not permit incorporating your program -into proprietary programs. If your program is a subroutine library, you -may consider it more useful to permit linking proprietary applications with -the library. If this is what you want to do, use the GNU Lesser General -Public License instead of this License. But first, please read -. diff --git a/ChangeLog b/ChangeLog deleted file mode 100644 index d0c59cd62..000000000 --- a/ChangeLog +++ /dev/null @@ -1,7084 +0,0 @@ -Changelog -========= - - -(unreleased) ------------- - -Fix -~~~ -- Forgot to assign IP to cuIonElement structure fields. [Martin D. - Weinberg] - -Other -~~~~~ -- Clean up messages in CMakeLists.txt and add SLURM support library - where needed. [mdw] -- Added nvToolsExt library as needed. [Martin D. Weinberg] -- Adjusted CMake config for CUDA extra libraries and removed automake, - autoconf cruft. [Martin D. Weinberg] -- Updated autogen.sh for CMake. [Martin D. Weinberg] -- Added extra CUDA lib to CUDA_LIBRARIES. Added doxygen detection and - configuration. [Martin D. Weinberg] -- Fix linking problem on unity. [Martin D. Weinberg] -- EXP library changed from libexp to libEXP to prevent target conflict - with exp executable. Missing EXP reference added to utils - directories as necessary. [Martin D. Weinberg] -- Added missing EXP globals. [Martin D. Weinberg] -- Configuration updates based on Robert Blackwell's start on the port - from automake/conf to CMake. - Added CMakeLists.txt configuration to - all missing directories. - Added install targets. - Tweaked the - main HDF5 configuration at the top level. - All libraries are now - shared. - Added toggles for user modules (USER_ENABLED and USER_ALL) - [Martin D. Weinberg] -- Change header format to system from local. [Martin D. Weinberg] -- Add config_cmake.h.in (was .gitignore(d)...) [Robert Blackwell] -- Remove FindMKL and do general cleanup of main CMakeLists.txt. [Robert - Blackwell] -- Merge remote-tracking branch 'origin/Eigen' into cmake. [Robert - Blackwell] -- Check in double exponential test. [michael_petersen] -- Fix the mean mass computation. [Martin D. Weinberg] -- Fixed a failed merge. [Martin D. Weinberg] -- Remove debugging line. [Martin D. Weinberg] -- Merge branch 'Eigen' of https://bitbucket.org/mdweinberg/exp into - Eigen. [mdw] -- Merge branch 'Eigen' of https://bitbucket.org/mdweinberg/exp into - Eigen. [Martin D. Weinberg] -- Cleanup in forcetest2. [michael_petersen] -- Update for Trace mean-mass ICs. [Martin D. Weinberg] -- Merge branch 'Eigen' of https://bitbucket.org/mdweinberg/exp into - Eigen. [Martin D. Weinberg] -- Merge of current version, replacing test code. [Martin D. Weinberg] -- Make pair count consistent with detailed balance. [mdw] -- Implemented NoCool option. [mdw] -- Restored the mean-mass option. [mdw] -- Added an explicit energy conservation algorithm for effective particle - masses; this will require changing the equilibrium IC conditions. - [mdw] -- Version update and some cruft removal. [mdw] -- Turn off cell count debugging output. [mdw] -- Additional fixes to algorithm implementation. [Martin D. Weinberg] -- More debugging output for new kinetic algorithm. [Martin D. Weinberg] -- Added main parameter parsing for double exponential conditioning - function. [Martin D. Weinberg] -- Added double exponential conditioning function. [Martin D. Weinberg] -- Fix n_p loops. [Martin D. Weinberg] -- Additional XC_DEEP* reporting. [Martin D. Weinberg] -- Additional XC_DEEP* reporting. [Martin D. Weinberg] -- Additions to XC_DEEP* output. [mdw] -- An additional improvement to Makefile.am for libtool building; - hopefully we will not need this much longer. [Martin D. Weinberg] -- Add restricted range to halocoef. [Martin D. Weinberg] -- Add restricted range to diskcoef. [Martin D. Weinberg] -- Promoted to Eigen; untested. [Martin D. Weinberg] -- Fixed some fencepost errors in DEBUG tests. [Martin D. Weinberg] -- Fixed some fencepost errors in test routine. [Martin D. Weinberg] -- Remove unused ECUT_DF from DiskHalo2.H. [Martin D. Weinberg] -- Add some sane defaults in localmpi.H so one node works without - initialization as a fall back. [Martin D. Weinberg] -- Remove unused ECUT_DF option. [Martin D. Weinberg] -- White-space ormatting changes only. [Martin D. Weinberg] -- Allow parallelization for numproc>NDP in DiskHalo2. Checked with - numproc=32 for NDP=16. [Martin D. Weinberg] -- Fix typo in diagnostic output. [Martin D. Weinberg] -- Removing default std namespace for consistency. [Martin D. Weinberg] -- Promote FDIST and FDISTC are classes to set default num values. - [Martin D. Weinberg] -- Added reporting of start position for >0 in epitable. [Martin D. - Weinberg] -- Improve epitable range checks. [mdw] -- Remove duplicated diagnostic output. [Martin D. Weinberg] -- Update mpi detection logic. [Martin D. Weinberg] -- Remove creation of shared libraries and add DSMC build. [Robert - Blackwell] -- Merge remote-tracking branch 'origin/Eigen' into cmake. [Robert - Blackwell] -- Cruft removal from SLGridMP2.cc; added Luan's latest UserAddMass - version; fixed fence-post errors in slcheck. [Martin D. Weinberg] -- Changed Eigen read/write strategy in SphereSL. [Martin D. Weinberg] -- Fence-post error fix in SphericalOrbit. [Martin D. Weinberg] -- Change Eigen view for testing; add some iostream checks. [Martin D. - Weinberg] -- Merged UserSat.cc. [mdw] -- Merge branch 'Eigen' of https://bitbucket.org/mdweinberg/exp into - Eigen. [mdw] -- Some additional UserSat tests. [Martin D. Weinberg] -- Add satellite mass column to UserSat log file. [mdw] -- Switch MatrixXd to Matrix3d for Euler rotations. [mdw] -- Missing index increment. [Martin D. Weinberg] -- Implementation for a more sane rmin, rmax logic. [Martin D. Weinberg] -- Fix the SLGridSph signature confusion caused by Analysis routines - using the old constructor calls; enforce grid radii in SphereSL. - [Martin D. Weinberg] -- Remove override for modelfile name. [Martin D. Weinberg] -- Change default name from mssaprof to haloprof. [Martin D. Weinberg] -- Remove control cruft. [Martin D. Weinberg] -- Missing dimensions in center variable. [mdw] -- Fix fence-post error in frequency access. [mdw] -- Cuda implementation of UserSat; comments. [Martin D. Weinberg] -- Preliminary implementation of UserSat for cuda. [Martin D. Weinberg] -- Fixed a fence-post error in the 3-vector. [Martin D. Weinberg] -- Fixed fence-post errors and a bunch to list counting error. [Martin D. - Weinberg] -- Comments only. [Martin D. Weinberg] -- Need to clear particle vector before add_particle call. [Martin D. - Weinberg] -- Add radial offsets for fmax table. [Martin D. Weinberg] -- Added buffered block writes to Particle to speed up PSQ. [Martin D. - Weinberg] -- Forgot to reset new counters. [Martin D. Weinberg] -- Added the YAML version of coefficient dumps to SphereSL. [Martin D. - Weinberg] -- Changed default halo particle type to 'dark' [Martin D. Weinberg] -- Code clean-up only; no functional changes. [Martin D. Weinberg] -- Added a reconstruction check on halo fields. [Martin D. Weinberg] -- Fix fence-post error in SphereSL leftover from Eigen conversion; fix - default file constructor for PSPout and PSPspl. [Martin D. Weinberg] -- Fix missing default limit flags for orders. [Martin D. Weinberg] -- Remove init index cruft from haloprof2. [Martin D. Weinberg] -- Add main 'exp' library to cmake. [Robert Blackwell] -- Add CUDA CMake build support for exputil. [Robert Blackwell] -- Add fortran as a cmake project language. [Robert Blackwell] -- Add lots of dependency checks to cmake and generate config.h. [Robert - Blackwell] -- Add cmake skeleton and rudimentary build of exputil. [Robert - Blackwell] -- Add yaml-cpp submodule. [Robert Blackwell] -- Added filePrefix specification to the fileNameCreator instances in - diskprof and haloprof. [Martin D. Weinberg] -- Merge branch 'Eigen' of https://bitbucket.org/mdweinberg/exp into - Eigen. [Martin D. Weinberg] -- Missing removal of PSP.H from pcatest in Analysis. [mdw] -- Problem in Eigen binary writes using .data() for some reason; - reverting to original method. [Martin D. Weinberg] -- Fix YAML difference parser. [Martin D. Weinberg] -- Add some error handing on file failure to diskprof and haloprof. - [Martin D. Weinberg] -- Remove lingering reference to localmpi.cc. [mdw] -- Remove the copy of header.cc from src; this kludge is no longer - necessary. [mdw] -- PSP now needs header.H from src so add -I flag in utils/PhaseSpace. - [mdw] -- Change DSMC libraries to shared for consistency with libexp. [Martin - D. Weinberg] -- Configure DSMC by default for testing. [Martin D. Weinberg] -- More fixes for standalone consistency with main EXP libraries. [Martin - D. Weinberg] -- Try to get Makefile.am order for shared library correct. [Martin D. - Weinberg] -- More clean up for standalone integration. [Martin D. Weinberg] -- MPI synchronization fix. [Martin D. Weinberg] -- Mistakenly used a 6 rather than 5 character index filed for PSP. - Fixed default directories in haloprof2.cc and diskprof2.cc. [Martin D. - Weinberg] -- Preliminary implementation of a general phase-space-reading class. - [Martin D. Weinberg] - - Still needs lots of work. PSP is fully implemented. Gadget HDF5 - seems to work but does not include all of the essential features, such - as reading multiple files per snapshot, in particular. -- Added Iterable class. [Martin D. Weinberg] -- Just some formatting clean up. [Martin D. Weinberg] -- Reorganize EXP executable into a driver and exp library. [Martin D. - Weinberg] -- Remove all C limits cruft and use C++ limits instead. [Martin D. - Weinberg] -- Deprecate all but one variant of haloprof and diskprof; add optional - radial order (and harmonic order) rangle restrictions on field - evaluation. [Martin D. Weinberg] -- Turn off verbose coefficient diagnostics. [mdw] -- Fence post error in GPU table assignment fixed. [mdw] -- Added toggle for verbose coefficient printing in cuda. [mdw] -- Merge branch 'Eigen' of https://bitbucket.org/mdweinberg/exp into - Eigen. [mdw] -- Added library flags for boost.random, following Mike's sugggestion. - Mike: please check that this helps. [Martin D. Weinberg] -- Pushed coefficient debug checks to their own member function. [Martin - D. Weinberg] -- Merge branch 'Eigen' of https://bitbucket.org/mdweinberg/exp into - Eigen. [mdw] -- Add option for Chebyshev smoothing for Abel transform in DF. [Martin - D. Weinberg] -- Fencepost errors in cuda to cpu coefficient mapping. [Martin D. - Weinberg] -- Additional fixes and debug output for gendisk2. [Martin D. Weinberg] -- Merge branch 'Eigen' of https://bitbucket.org/mdweinberg/exp into - Eigen. [mdw] -- Allow for multiple smoothing types. [Martin D. Weinberg] -- Merge branch 'Eigen' of https://bitbucket.org/mdweinberg/exp into - Eigen. [mdw] -- Change default DF interpolation for testing. [Martin D. Weinberg] -- Merge branch 'Eigen' of https://bitbucket.org/mdweinberg/exp into - Eigen. [mdw] -- Another FP error and additional clean up. [Martin D. Weinberg] -- Merge branch 'Eigen' of https://bitbucket.org/mdweinberg/exp into - Eigen. [mdw] -- Restore global iteration counter. [Martin D. Weinberg] -- Merge branch 'Eigen' of https://bitbucket.org/mdweinberg/exp into - Eigen. [mdw] -- A few more fence post fixes; comment changes and range checks in - distf/dfde/d2fde2. [Martin D. Weinberg] -- Merge branch 'Eigen' of https://bitbucket.org/mdweinberg/exp into - Eigen. [mdw] -- Changes to MPI for Eigen objects. [Martin D. Weinberg] -- Additional spline checks. [Martin D. Weinberg] -- Commented out deep debug. [Martin D. Weinberg] -- Merge branch 'Eigen' of https://bitbucket.org/mdweinberg/exp into - Eigen. [mdw] -- One additional verbose output removal. [Martin D. Weinberg] -- Fence post fixes. [Martin D. Weinberg] -- Additional fence post fixes. [mdw] -- Remove verbose output. [Martin D. Weinberg] -- Fix fencepost errors in cylindrical basis construction. [Martin D. - Weinberg] -- Make the eigtest routine work using Eigen. [Martin D. Weinberg] -- Yet more fencepost error fixes. [Martin D. Weinberg] -- More fencepost error fixes. [Martin D. Weinberg] -- More minor fixes for random_gen, localmpi, etc. [Martin D. Weinberg] -- Still more updates for boost.random and replace PSP2.H by PSP.H. [mdw] -- More updates for boost.random. [mdw] -- Additional fixed for boost.random. [Martin Weinberg] -- Missing commit of separate implemenation for boost.special. [Martin D. - Weinberg] -- More fence-post error fixes. [Martin D. Weinberg] -- Added the global instance of the boost.random generator for stand- - alone drivers. These global variables should go into a header, I - suppose. [Martin D. Weinberg] -- Removed old GNU random classes and replaced them with boost.random. - Removed the expgnu library. [Martin D. Weinberg] -- Some fencepost error fixes. [Martin D. Weinberg] -- Version bump. [Martin D. Weinberg] -- Minor CUDA update for Eigen::Vector3d. [Martin D. Weinberg] -- Added complete set of files for Vector/Matrix --> Eigen translation. - [Martin D. Weinberg] - - This code fully compiles without error but almost certainly does NOT work. -- Additional updates. [Martin D. Weinberg] - - - Vector/Matrix->Eigen changes that I missed on the first round - - Some additional .h to .H and cruft removal -- Removed old Vector/Matrix classes along with a pile of other bad - cruft. [Martin D. Weinberg] - - The code compiles from start to finish but I almost certainly have - introduced a variety of bugs and problems. This will take some time - to test, verify, and sort out. -- Corrected electron scattering mass in accum-trace-scatter algorithm. - [Martin D. Weinberg] -- Added stop signal for off-grid interpolation in playback. [Martin D. - Weinberg] -- Make YAML headers in spherical basis coefficient files the default. - [Martin D. Weinberg] -- Failsafe to prevent an infinite loop. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Need strncpy for coefficient file read. [mdw] -- Minor fixes for playback on GPU side. [Martin D. Weinberg] -- Needed for strncpy function. [Martin D. Weinberg] -- Allow for both old and new cylindrical coefficient header types in - read for playback. [Martin D. Weinberg] -- Some fixes for playback. [Martin D. Weinberg] -- Check for eof when reading coefficieints. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Reference 'comp' should be 'tcomp' [mdw] -- Don't use COV frame for KE for 1 particle components. [Martin D. - Weinberg] -- Fix force references. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- More commenting. [Martin D. Weinberg] -- More cudaAware overrides to prevent GPU device fetches when there are - not wanted. [Martin D. Weinberg] -- Addition cudaAware restriction for force evaluation. [Martin D. - Weinberg] -- Version bump. [mdw] -- Move particles to cuda for level computation when force is not cuda - aware. [mdw] -- An additional check for whether cuda is used for all interacting - components. [mdw] -- Simplify logic for interactions with cuda. [mdw] -- Revert ParticleToCuda and CudaToParticle restrictions. [mdw] -- Spelling change in comments only. [Martin D. Weinberg] -- Draft suppression of CPU<-->GPU particle exchange for no native - implementation. [Martin D. Weinberg] -- Comments only. [Martin D. Weinberg] -- Implemented the Miyamoto-Nagai particles in the Point class; ifxed a - parameter swap in the UserMNdisk routine (oops) [Martin D. Weinberg] -- Removed uninitialized variables from UserAddMass as a test. Luan may - wish to study and implement the changes. Not that I suspect any - problems here to be honest. [Martin D. Weinberg] -- Bumped up the default DATTRIB_CUDA value from 4 to 12 for H+He DSMC - tests. [mdw] -- Removed duplicated storage allocation check for variance computation; - not hurting anything but unnecessary. [mdw] -- Fixed uninitialized pca counter variables which was leading to - failure. Oops. Not sure how those/when the default initialization got - dropped. [mdw] -- Clear use list. [mdw] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Some formatting for clarity and three 'breaks' changed to 'continues' - [mdw] -- Change default output prefix. [Martin D. Weinberg] -- Toggle off some verbose debugging. [Martin D. Weinberg] -- Update for cuda compilation but use_cuda=false. [Martin D. Weinberg] -- Check for sampT allocation. [Martin D. Weinberg] -- More sanity checks for coef2. [mdw] -- Cherry picked from 'massevo' branch. [mdw] -- Sanity check on reduction in coef2 for sampT>0. [mdw] -- Zero use counter before fork. [Martin D. Weinberg] -- Fix flag for pcavar storage initialization. [Martin D. Weinberg] -- Upgraded error messages. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Make sampT=1 the default to match defSampT in AxisymmetricBasis and - EmpCylSL. [mdw] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Attempt to accommodate the older HDF5 API. [Martin Weinberg] -- Remove unneccessary count field from vtk file names. [Martin D. - Weinberg] -- Add some file exception handling to Coef readers. [Martin D. Weinberg] -- Add new simple routines for producing VTK profiles from coefficient - files. These still need testing. [Martin D. Weinberg] -- Change name from Coefs to CylCoefs for syntatic symmetry. [Martin D. - Weinberg] -- Minor changes for additional diagnostics. [Martin D. Weinberg] -- Remove test variance trim. [Martin D. Weinberg] -- Additional diagnostic fields. [Martin D. Weinberg] -- Fix mutex unlock misordered line. [Martin D. Weinberg] -- Improve center component output formatting. [Martin D. Weinberg] -- Give the user some feedback for a center override. [Martin D. - Weinberg] -- Added expansion and reconstruction center options. I haven't check - this, so le t me know if there are any problems. [Martin D. Weinberg] -- Allow all m values to be summed in trim. [Martin D. Weinberg] -- Change test array normalization. [Martin D. Weinberg] -- Change default on snr reorder. [Martin D. Weinberg] -- Add |evec|^2 to output. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Set defSampT unconditionally. [mdw] -- Improve warning message for T>=sampT. [mdw] -- Documentation changes only. [Martin D. Weinberg] -- Set default variance sample size to 1 for Cuda efficiency. [Martin D. - Weinberg] -- Version change. [Martin D. Weinberg] -- Additional comments. [Martin D. Weinberg] -- Made CPU and GPU versions consistent; additional comments. [Martin D. - Weinberg] -- Remove debug chatter; some additional comments. [Martin D. Weinberg] -- Removed T_coef in favor of T_covr for both sample and mean variance - computation; fixed typo kernel for variance computation. [Martin D. - Weinberg] -- Removed T_coef in favor of T_covr for both sample and mean variance - computation. [Martin D. Weinberg] -- Added a positive variance sanity check; simplifed normalization of - variance. [Martin D. Weinberg] -- A few more minor updates to variance tapering; checked cuda code - successfully with both versions 11.1 and 11.3. [Martin D. Weinberg] -- Updates for internal variance smoothing computation. [Martin D. - Weinberg] -- Move exp_version() back into parse so that timestamp is kept up to - date. [Martin D. Weinberg] -- Some clean up for variance code; change variance to full population - rather than 1-particle variance for consistency. [Martin D. Weinberg] -- Fix mistaken restriction introduced in multistep update. [Martin D. - Weinberg] -- Undefined default value for subsampling. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [mdw] -- Some updates for variance trimming. [Martin D. Weinberg] -- Convert bootstrap to report 1-particle covariance using CLT scaling. - [Martin D. Weinberg] -- Add conversion to 1-particle covariance. [mdw] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Fix norm constants. [mdw] -- Added missing new line. [Martin D. Weinberg] -- Added density-only cross validation for Sphere. [Martin D. Weinberg] -- Corrected 4pi factors. [Martin D. Weinberg] -- Propagate user SEED to AxiSymModel. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [mdw] -- Added orthgonal slice options for field output. [Martin D. Weinberg] -- Remove Lmax>=1 restriction. [Martin D. Weinberg] -- Allow mmax=0 evaluation. [Martin D. Weinberg] -- Allow rank=1 vectors and matricies. [Martin D. Weinberg] -- Updated cross-validation code for weighted trunction. [mdw] -- Add version of halo coefficient reader that prints out cosine and sine - coefficients together. [mdw] -- Change for mass norm in get_trimmed. [mdw] -- Change default number of eigenvalues; add total power diagnostics. - [mdw] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [mdw] -- Restriction so that lmax=0 does not fail. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Documentation only. [Martin D. Weinberg] -- Remove variance of mean S/N scaling and leave pure sample variance S/N - instead. [mdw] -- Add radial order cut experiment; leaving the code but this does not - seem promising. [mdw] -- Scale from standard covariance to match bootstrap covariance for - testing. [mdw] -- Allow user to modify sampT from the sqrt(N) default. [mdw] -- Add power diagnostic in trim. [Martin D. Weinberg] -- Updates for mass and variance scaling. [mdw] -- Generalize bootstrap variance scaling for arbitrary partitioning, not - only sqrt. [mdw] -- Clean up norms for SNR smoothing. [mdw] -- Clean up norms for SNR smoothing. [mdw] -- Added toggle for verbose covariance output. [mdw] -- Remove debug and add L1 & L2 restriction to surface reconstruction. - [mdw] -- Add differenced images for SNR trim. [Martin D. Weinberg] -- Removed unused variable. [Martin D. Weinberg] -- Checks okay; remove debugging output. [mdw] -- Add phi averaging and parallelization for evaluation loop. [mdw] -- Set nodd and neven to zero when not set; doesn't matter for anything. - [mdw] -- New style YAML header caches are now default. [mdw] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [mdw] -- Remove covariance computation. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [mdw] -- Added EmpCylSL expansion for testing. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [mdw] -- Test k-d nn density map. [Martin D. Weinberg] -- Updates for k-d NN density estimate. [Martin D. Weinberg] -- Add mass/weightt accumulation to nearestN in k-d interface. [Martin D. - Weinberg] -- Minor updates and testing code. [mdw] -- Use ball density estimate by default. [Martin D. Weinberg] -- Added local density estimation using a k-d nearest N neighbor search. - [Martin D. Weinberg] -- Updates for KL bootstrap amplitude. [Martin D. Weinberg] -- Updated versions of KL analysis. [Martin D. Weinberg] -- Fix index overwrite detected by nvcc 11.3. [Martin D. Weinberg] -- Include the spherical harmonic prefactor in dump_coefs output to - simply power computation. [Martin D. Weinberg] - - The YAML stanza will now contain the {normed: true} tag to indicate this to readers -- Name change in default files. [Martin D. Weinberg] -- Missing check for SPL in init phase space. [Martin D. Weinberg] -- Use com0 for local centering in the cuda Orient implementation for - consistency with the cpu implementation. [mdw] -- Noticed typo in nsiz computation which ended up dividing bunch size by - numprocs twice; it should not matter in practice. [mdw] -- Merge branch 'CUDA_DEVEL' into devel. [mdw] - - Devel is currently deprecated owing the many fixes to both timestepping and - cuda implementation. After the merge, CUDA_DEVEL will be discarded or - repurposed. -- Fix restriction of grid indices in the coordinate kernel which was - truncating at NUMX-1 and NUMY-1 rather than NUMX and NUMY. [mdw] -- Get true grid radius directly from EmpCylSL; clean up mixture factor - application for future use; move interpolation constants of loop and - designate them constexpr. [mdw] -- Add member function to get Rtable size. [mdw] -- Add debug off-grid warning. [mdw] -- Get true grid radius directly from EmpCylSL; clean up mixture factor - application for future use; move interpolation constants of loop and - designate them constexpr. [mdw] -- Just cosmetic white space. [mdw] -- Floor timestep as done in CPU version; no evidence that this has - effected anything so far . . . [mdw] -- Fixed to centering algorithm on GPU. [mdw] -- Use regime interpolation and potential value. [mdw] -- Version bump for ID. [mdw] -- Make vertical quantile histogram consistently oriented with density - and surface histograms. [mdw] -- Left justify header. [mdw] -- -v output is now the default for -h, so consolidate. [mdw] -- Put GPU device constant reporting at VERBOSE>4; I'm tired of seeing - the clutter in the stdout. [mdw] -- Also change PID info stanza printed at top of log for cosmetic - consistency. [mdw] -- Minor typo fix. [mdw] -- Cosmetic changes to stdout EXP intialization for consistency; while - I'm waiting . . . [mdw] -- Added an additional debugging field for checking; checks okay and - disabled; updated for mdrft. [mdw] -- Added an additional debugging field for checking; checks okay and - disabled. [mdw] -- Comment the change from diagnostic output at mstep==0 to - mstep+1==Mstep. [Martin D. Weinberg] -- Simply adjust call logic and put reporting at mstep=Mstep rather than - mstep=0. [Martin D. Weinberg] -- Made a new variable for mstep+1 to help with notation. [Martin D. - Weinberg] -- Fix multistep for this method. [Martin D. Weinberg] -- Swap option parsing with EXP welcome header. [Martin D. Weinberg] -- Version bump. [Martin D. Weinberg] -- Make percentages in timer output more readable using boost::format - (until C++20 std::format is available) [Martin D. Weinberg] -- Cleaned up notation for computing coefficients on drifted step. - [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [mdw] -- Minor correction to mainpage document. [Martin D. Weinberg] -- Fix +1 fencepost error; this explains why my interpolation had a - pattern with mstep. [mdw] -- Added some additional debug output only. [Martin D. Weinberg] -- Removed 'tstp'; added automatic branch, commit, and compile time to - stdout. [mdw] -- Minor changes for clarity: use component rather than cC for orient and - center vector; use mfirst[mstep] rather than passed mlevel value. - [mdw] -- Additional comment. [mdw] -- More comments; adjusted mstep for final kick. [mdw] -- After a bunch more algorithm checking, I believe that this is now - implemented as intended. The major changes are fixing the drifted - step coefficient interpolation. The original step.cc implementation - was correct, just a bit confusing in retrospect since the positions - have drifted past the velocities so one has to be careful to keep - track of that in the multstep coefficient interpolation. In - particular: the position in the interpolation is "mstep+1" not - "mstep". Added a bit more clarification in the comments. The - evolution still need to be testing and compared. [mdw] -- Return to the original step strategy but put the coefficient - interpolation offset into the coefficient interpolation code, rather - than step.cc. [mdw] -- Clean up the comments only. [mdw] -- Proposed fencepost error fix for multistep algorithm. Also added some - additional comments about what's going on in this implementation. - [Martin D. Weinberg] -- Fixed the weird multistep issue; downward level changes need to be - limited to the minimum active level or coefficient updates will be - discarded and only included at the next computation on the target - particle's new level. This is broken in both the CUDA and CPU code. - I doubt it matter much except under usual circumstances, such as very - large values of multistep. [mdw] -- Attempt to remove deprecated PhaseSpace class utilities. [Martin D. - Weinberg] -- Update diskprof2 for PSP2 (OUT & SPL) input. [Martin D. Weinberg] -- Formatting fix to timer output. [mdw] -- Add system time to step timer output. [mdw] -- Changed 'samplesize' to 'samplesz' for compactness; added some header - documentation. [Martin D. Weinberg] -- Override sqrt(N) subsample size. [Martin D. Weinberg] -- Fixes to variance computation. [Martin D. Weinberg] -- Restored 'printf' lines for deep debugging but unused by default. - [Martin D. Weinberg] -- Added a flattened covariance matrix to Cuda for noise computation. - [Martin D. Weinberg] -- Add helper member to get variance matrix from Cuda. [Martin D. - Weinberg] -- Enforce nintsub >=0 to prevent user from causing divide_by_zero. - [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Okay, found the source of the CUDA multilevel implementation at long - last! [mdw] - - Sigh. That took a really long time. - - o Embarassingly, it was a typo: the multistep short range needed to be - [mlevel, mlevel] rather than [mlevel, multistep]. I think I had that - last range in my head from the coefficient implementation. - - o This deserves a version bump. And the whole thing needs to be - tested now. -- Remove the cuda override debugging which is cumbersome and not much - help anyhow. [mdw] -- Some extra comments only. [mdw] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Override coefficient and accelration for testing based on a boolean - toggle. [mdw] -- Comment changes only. [mdw] -- Remove commented cruft for clarity. [mdw] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Replace the 'compute' argument with 'false' in the coefficient - adjustment kernel call. [Martin D. Weinberg] -- Replace the 'compute' argument with 'false' in the coefficient - adjustment kernel call. [Martin D. Weinberg] -- Use the native operator< rather than custom pairLess functor. [Martin - D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Change routine name to cuda_zero_coefs() [Martin D. Weinberg] -- Change routine name to cuda_zero_coefs() [Martin D. Weinberg] -- Removed old comment. [Martin D. Weinberg] -- A few more error checks for insurance. [Martin D. Weinberg] -- Fixes for compilation without cuda enviroment. [Martin D. Weinberg] -- Check that npart < I._s not P._s, although I._s should equal P._s, so - it should not matter. [Martin D. Weinberg] -- Remove blank source file; some minor clean ups. [Martin D. Weinberg] -- Routine name changes to prevent me from getting confused. [mdw] -- Test coefficient zeroing logic. [Martin D. Weinberg] -- Some additional comments only. [Martin D. Weinberg] -- Comments only. [Martin D. Weinberg] -- Use /usr/bin/env to find python executable in a module environment. - [mdw] -- Forget to commit this source file. [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [mdw] -- Attempt to fix compilation problems on Unity by adding cuda support to - libexputil. [mdw] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Put Emacs mode tag at top of file for detection. [Martin D. Weinberg] -- Implemented Orient on the GPU device. [Martin D. Weinberg] -- Try to incorporate CPU<-->GPU fetch logic. [Martin D. Weinberg] -- Change preprocessor config flag for consistency. [Martin D. Weinberg] -- Range fix for level indicies. [Martin D. Weinberg] -- Name change for routine only. [Martin D. Weinberg] -- Fix for move of sledge.f. [Martin D. Weinberg] -- Reorganize names of fix_position routines. [Martin D. Weinberg] -- Move sledge.f to exputil. [Martin D. Weinberg] -- Clean fix_positions organization. [Martin D. Weinberg] -- Minor clean up; still need to cudaize orient. [Martin D. Weinberg] -- Reverted; there was no gaff in device copy; try kernel updates with - pointer rather than reference. [Martin D. Weinberg] -- Comments only. [Martin D. Weinberg] -- Only update particle levels at or above current level; won't save much - time but . . . [Martin D. Weinberg] -- Gaff in host to dev copy sequence fixed. [Martin D. Weinberg] -- Only need to compute difference matrices for mfirst[mstep] since other - changes are discarded until multistepping hits the lower particle - level. [Martin D. Weinberg] -- Don't call CudaGetLevelRange for multistep=0; no big deal; should save - a tiny chuck of time. [Martin D. Weinberg] -- Remove commented lines. [Martin D. Weinberg] -- Additional comment only. [Martin D. Weinberg] -- Additional tweaks to UserTestCuda. [Martin D. Weinberg] -- Restore the mlevel restrictions in coefficient updates to test the old - code. [Martin D. Weinberg] -- Get a little fancier with output control and parameters. [Martin D. - Weinberg] -- User test routine that implements a CUDA kernel. [Martin D. Weinberg] -- Documentation version bump. [Martin D. Weinberg] -- Change default double attributes from 12 to 4. [Martin D. Weinberg] -- Use local header reads to prevent confusion. [Martin D. Weinberg] -- Clean up fractional time for easier to read output. [Martin D. - Weinberg] -- New test implementation using various CUDA constructs to allow or - coefficient update on the device. [Martin D. Weinberg] - - - Version bump - - The adjust step is no longer the bottle neck - - Version should be algorithmically identical to the original version - - Still needs work to compare with original version - - Speed up is a factor 20x over the original version with a single node test -- Yet more comments. [Martin D. Weinberg] -- Additional comments only. [Martin D. Weinberg] -- Allow host and device calls in structure for future use. [Martin D. - Weinberg] -- Variable name change for clarity. [Martin D. Weinberg] -- Update for index indirection. [Martin D. Weinberg] -- Need to use kernel rather than thrust for indirection. [Martin D. - Weinberg] -- Variable name change for clarity. [Martin D. Weinberg] -- Replace multiple thrust::reduce with a single cuda kernel in - cuda_fix_positions. [Martin D. Weinberg] -- Removed cruft. [Martin D. Weinberg] -- Implementation of indirect indexing. [Martin D. Weinberg] -- Added relative fractions to step timing. [Martin D. Weinberg] -- Fix typo in dynA computation. [Martin D. Weinberg] -- Additional timing diagnostics; use thrust rather than kernel for level - update (doesn't matter much) [Martin D. Weinberg] -- Code clean-up: use reference to cudaParticle and not pointer - (equilvalent code but easier to read) [Martin D. Weinberg] -- Remove restriction in differ list to >=mfirst[mstep] [Martin D. - Weinberg] -- Remove restriction in differ list to >=mfirst[mstep] [Martin D. - Weinberg] -- Do not check levlist when using cuda. [Martin D. Weinberg] -- Remove redundant particle copies. [Martin D. Weinberg] -- Something strange about limiting coefficient difference matrix to - mfirst[mstep] and above; this commit changes that which seems to be - what I originally intended (???) [Martin D. Weinberg] -- Go back to per component stream selection. [Martin D. Weinberg] -- Remove test timer. [Martin D. Weinberg] -- Missing check for use_cuda in ParticlesToCuda. [Martin D. Weinberg] -- Use differ matrices. [Martin D. Weinberg] -- A few additional time stepping tests; implemented level output from - GPU; something is still broken in acceleration or updates. [Martin D. - Weinberg] -- Move CUDA device context assignment to the top level; it doesn't make - sense for Component to assign context. Allow component to query and - cache device #. [Martin D. Weinberg] -- Updates for level sort and range split. [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Split sort and range finding for levels. [Martin D. Weinberg] -- New routines for computing multistep time steps on the CUDA device. - [Martin D. Weinberg] -- Constant printing change only. [Martin D. Weinberg] -- Fixed mistake in coordinate addressing; only affected diagnostic - output. [Martin D. Weinberg] -- Fix cuda-free compilation. [Martin D. Weinberg] -- Save some updates including a preliminary implementation of the update - step; needs more debugging. [Martin D. Weinberg] -- Preliminary start on adjust step, but this version is broken. [Martin - D. Weinberg] -- Partially working implementation with multistep=0 only. [Martin D. - Weinberg] -- Add particle use counter correctly for cudaCylinder. [Martin D. - Weinberg] -- Partial implementation of a CUDA-only EXP. [Martin D. Weinberg] -- Begin implemented an ondevice EXP version. [Martin D. Weinberg] -- Use /usr/bin/env to find python executable in a module environment. - [mdw] -- Test for CUDA implementation of DSMC with CPU implementation. [Martin - D. Weinberg] -- Compliing implementation of CUDA Trace algorithm; still needs testing. - [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Add a cuda mem copy timer diagnostic. [Martin D. Weinberg] -- Updates to CUDA trace DSMC implementation. Note to self: still will - not work so do not use it. [Martin D. Weinberg] -- Documentation changes only. [Martin D. Weinberg] -- Prevent overflow and underflow in tau computation by checking for - large tau value first, and adding intermediate check for minimum tau - value. [mdw] -- Fixes for energy conservation in Coulombic scattering routine. [Martin - D. Weinberg] -- Comments only. [Martin D. Weinberg] -- Add default python path back into libtool script. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Improve pair selection in accumTraceScatter. [mdw] -- Zero charge check for mean charge computation. [mdw] -- Comments and minor updates. [Martin D. Weinberg] -- Energy bookkeeping update for recombination using newRecombAlg. - [Martin D. Weinberg] -- Fix GauntFF database initialization error. [Martin D. Weinberg] -- Fix diagnostic exit message. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Added rejected fraction to output file. [mdw] -- Add sanity check for dimension of PNG diagnostic output. [mdw] -- Fix output formating and a few mistakes in KL bunch assignment. [mdw] -- Fix minSNR lower bound check and trimmed coefficient cacheing. [Martin - D. Weinberg] -- Fix minSNR lower bound check. [Martin D. Weinberg] -- Fix minSNR lower bound check. [Martin D. Weinberg] -- Changes to progress labeling only. [Martin D. Weinberg] -- Draft implementation for KL analysis. [Martin D. Weinberg] -- Preliminary KL anaysis routine for Cylinder. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Remove a debug print statement. [mdw] -- Changes to allow SNR cuts for diskprof2 visualization. [mdw] -- Changes for external force time in multistepping. [Martin D. Weinberg] -- Minor fixes. [Martin D. Weinberg] -- Minor correction to coefficient trimming logic in EmpCylSL. [Martin D. - Weinberg] -- Used preprocessor to remove nintsub option by default. [Martin D. - Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- White space correction only. [Martin D. Weinberg] -- Version bump. [Martin D. Weinberg] -- Need to call output->Run(n) at end of multistep ladder. [Martin D. - Weinberg] -- Put output->Run at the beginning of the step. [Martin D. Weinberg] -- Fix ordering of time step increment and Output->Run call to get output - at the desired time step. [Martin D. Weinberg] -- Fix ordering of time step increment and Output->Run call to get output - at the desired time step. [Martin D. Weinberg] -- Whitespace and comments only. [Martin D. Weinberg] -- Whitespace and comments only. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Cleaned up MPI exits; added Hall shape exponent to the spherical - method. [Martin D. Weinberg] -- A few fixes for pca implementation. Still needs work so should not - yet be used. [Martin D. Weinberg] -- CuStream ring is causing trouble in the CUDA pca reduction. I - probably need some additional synchronization or perhaps I'm not using - streams correctly. Set to 1 as a work around (which seems to work). - Anyway, the pca cuda implementation is still unfinished and should not - be used for production. [Martin D. Weinberg] -- Formatting clean up only. [Martin D. Weinberg] -- Fix broken reporting of Hall method; doesn't change results, just log - file. [Martin D. Weinberg] -- Toggle on verbose output for spherical grid parameters in cuda. - [Martin D. Weinberg] -- Tag debug output with DEBUG as a reminder. [Martin D. Weinberg] -- Minor clean up to cross validation stuff. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [mdw] -- Not sure what happened, but this did not stick the first time. [mdw] -- Include eigen3 headers in nvcc compile flags. [Martin D. Weinberg] -- Remove thread number output test. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- The intended Thrust API works as of CUDA 11.1; adjusted workaround - logic accordingly. Fixed up a gaff in coefficient sizing introduced - as I started to implement EOF on the CUDA side. Currently testing but - good so far. [Martin D. Weinberg] -- Update draft implementation of EOF covariance for consistency to fix - indexing; additional output simplification and comments. [Martin D. - Weinberg] -- Comments, white space, name changes only. [Martin D. Weinberg] -- Changed class name chdata to new name atomicData in cuda members. - [Martin D. Weinberg] -- Clean up to output signaling for OutPS* classes and DSMC updates. - [Martin D. Weinberg] -- Test weighted scheme for Coulombic interactions. [Martin D. Weinberg] -- Fix weighting scheme for low ionization fraction. [Martin D. Weinberg] -- Fixed to charge and rate computation. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Comments only. [Martin D. Weinberg] -- Restore level computation at substeps; fix for doc dir scan in - configure.ac. [Martin D. Weinberg] -- Fixed typo in Ei/Ef ratio. [Martin D. Weinberg] -- A bit more clean up. [Martin D. Weinberg] -- Fixes to new Gaunt factor interpolation. [Martin D. Weinberg] -- Add van Hoof et al. Gaunt factor toggle. [Martin D. Weinberg] -- Unit fix in free-free cross secton. [Martin D. Weinberg] -- Implemented Karzas-Latter free-free cross section with modern Gaunt - factor approximation. [Martin D. Weinberg] -- Comment changes only. [Martin D. Weinberg] -- Added user settable NUMDF. [mdw] -- Add verbose output to VFLAG & 8. [mdw] -- Allow selection of gridded or ungridded cross sections. [Martin D. - Weinberg] -- Added quadrature to recombintation cross section to resolve - dielelectronic resonances. [Martin D. Weinberg] -- Added more comments. [Martin D. Weinberg] -- Remove ancient rcs id string. [Martin D. Weinberg] -- Fix MPI_Reduce misplacement! [Martin D. Weinberg] -- Formatting diffs only. [Martin D. Weinberg] -- Formatting diffs only. [Martin D. Weinberg] -- More chat suppression. [Martin D. Weinberg] -- Remove some of the insane verbosity in DiskHalo2 and initial2. [Martin - D. Weinberg] -- Version bump. [Martin D. Weinberg] -- More clean up for fudge factors and python calls. [Martin D. Weinberg] -- Add some exception handling for directory scan. [Martin D. Weinberg] -- Added some comments and corrections for energy units. Ratios now - check, but so far we are only exact for H and He. [Martin D. Weinberg] -- Added energy reweighting to bin center. [Martin D. Weinberg] -- Updates for ratio testing. [Martin D. Weinberg] -- Corrected file name convention. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Add runtag and prefix to coefficient output. [mdw] -- Allow a range of norders for reconstruction (e.g. even and odd) [mdw] -- Added preliminary test Badnell data reader. [Martin D. Weinberg] -- Allow colormap choice. [mdw] -- Added VTK output per rotated coefficient for diskeof. [Martin D. - Weinberg] -- Fixes for EOF conditioning tests. [mdw] -- Missing MPI reduction. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Fix restart logic. [mdw] -- Added EOF basis test for Cylinder. [Martin D. Weinberg] -- Added EOF basis test for Cylinder. [Martin D. Weinberg] -- Fix object count for Vector zero in expcoefT,T1,M,M1. [mdw] -- Missing reference make_shared creattion. [Martin D. Weinberg] -- Add member functions to Component to convert from local to global - coordinate system; convert particle positions and velocities in - UserAddMass to global coordinates. [Martin D. Weinberg] -- Version bump to mark changes (albeit very minor) to add - determine_fields_at_point to some basis classes. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [mdw] -- Accel is turned off if no basis forces are available; other minor - formatting changes. [mdw] -- Some header documentation only. [Martin D. Weinberg] -- Added toggle for initial acceleration from components. [Martin D. - Weinberg] -- Another typo fix: acceleration from each component needs to be - accumulated. [mdw] -- Typo fix. [mdw] -- Report accel components. [mdw] -- Minor changes to Mike's fix. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Draft zero acceleration multistep bypass. [Michael] -- Updates for accelration adding for UserAddMass. [Martin D. Weinberg] -- Added monopole initialization routine. [mdw] -- Return to mass-weighted variance for error analysis. [Martin D. - Weinberg] -- Revert covar computation. [mdw] -- White space change only. [Martin D. Weinberg] -- Error propagation for coefficients. [mdw] -- Merged Luan's UserAddMass code. [Martin D. Weinberg] -- Updates for cross validation. [mdw] -- Added varialble exponent to Hall smoothing function. [mdw] -- Fixed cache read error: all nodes read so do not reduce table entries - on reread. [mdw] -- White space change only. [mdw] -- Cleaned up expcoef interface; made algorithmic changes in error - analysis; fixed wrong Ylm coefficient in analysis routines. [Martin D. - Weinberg] -- Remove some default debugging output. [Martin D. Weinberg] -- Make SNR computation consistent between Spherical and Cylinder. - [Martin D. Weinberg] -- Updates for particle number tracking in noise computation. [Martin D. - Weinberg] -- Put priorty queue stuff in separate header. [Martin D. Weinberg] -- Sign change in Term 3. [Martin D. Weinberg] -- Fixed progress bar, 2nd try. [Martin D. Weinberg] -- Fixed progress bar. [Martin D. Weinberg] -- More updates for Cylinder cross validation; still needs more work. - [Martin D. Weinberg] -- Minor fixes and some additional debugging output. [Martin D. Weinberg] -- Added multipole version for Cylinder. [Martin D. Weinberg] -- Fixed typo in cross_validation_cyl.cc; added EVEN_M flag to Cylinder. - [Martin D. Weinberg] -- More debugging. [Martin D. Weinberg] -- Some additional debugging. [Martin D. Weinberg] -- More fixes for cross_validation_cyl speed up; added Progress.H to shut - up boost deprecation warnings. [Martin D. Weinberg] -- More updates for cross validation. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Fix/restore definition of global in exputil lib. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Added gdb_trace option. [Martin D. Weinberg] -- Fix header packing order for recon_bin. [Martin D. Weinberg] -- Implementation of cross validation algorithm for Cylinder; not tested - but it does compile. [Martin D. Weinberg] -- Reorder division by mass per bin. [Martin D. Weinberg] -- Added interpolation to ang mom grid. [Martin D. Weinberg] -- This script will be autogenerated by the application that needs it. - [Martin D. Weinberg] -- Added electron energy cutoff option. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Fixes for SNR log values in loop. [Martin D. Weinberg] -- Header for PNG image output. [Martin D. Weinberg] -- Rename of cross_validation for cylinder. [Martin D. Weinberg] -- Rename of cross_validation. [Martin D. Weinberg] -- Included Hall smoothing. [Martin D. Weinberg] -- Turn off debug output by default. [Martin D. Weinberg] -- Change norm for covariance, add resampling option for - checking/debugging, zero accumulators in snr loop in main, add PNG - eigenfunction output. [Martin D. Weinberg] -- Fixed total mass computation in the SphereSL analysis class. [Martin - D. Weinberg] -- Missing verbose switch. [Martin D. Weinberg] -- Fixed typo in truncation for S/N. [Martin D. Weinberg] -- Remove per-node output from main. [Martin D. Weinberg] -- Implement S/N cuts for total cross-validation. [Martin D. Weinberg] -- Added rscl option to SphereSL in utils/Analysis. [Martin D. Weinberg] -- Parallelized coefficient cross-validation. [Martin D. Weinberg] -- Added cross validation test code. [Martin D. Weinberg] -- Minor fix to collisional excitation line selection: wrong line energy - for selected cross section with grid version. [Martin D. Weinberg] -- Fix typo in error string only. [Martin D. Weinberg] -- Added logic to preserve the workaround for the Thrust binary search - bug when (if) it is fixed; this is all preprocessor so the code will - be indentical. [Martin D. Weinberg] -- Sanity check: don't call scatterPhotoTrace if weight=0. [Martin D. - Weinberg] -- Fix a few typos: workaround flag misspelled. [Martin D. Weinberg] -- Work around for bug in thrust::binary-search. It looks like this will - be fixed eventually; see https://github.com/NVIDIA/thrust/pull/1104. - [Martin D. Weinberg] -- Version bump. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Fix thrust calls from device, which is unsupported usage. [Martin D. - Weinberg] -- Updated configuration for C++-14 required for Cuda 11.x. [Martin D. - Weinberg] -- Added min/max positions. [Martin D. Weinberg] -- Put storage for gdb_trace into the exputil library. [Martin D. - Weinberg] -- Add histogram for Coulombic logarithm. [Martin D. Weinberg] -- Added additional config variables for logL scaling. [Martin D. - Weinberg] -- Fix header parameter order. [Martin D. Weinberg] -- Added logL and lambda_D diagnostics. [Martin D. Weinberg] -- Updates for new EmpCylSL headers. [Martin D. Weinberg] -- Custom change for hdf5 C++ libs; fix slshift issue. [Martin D. - Weinberg] -- Remove configure time git variables. [Martin D. Weinberg] -- Remove accidental leading character. [Martin D. Weinberg] -- Update configuration for automatic detection of HDF5. [Martin D. - Weinberg] -- Added some OpenMP thread control. [Martin D. Weinberg] -- Fix up eigen3 check comment. [mdw] -- Fix eigen include variable. [michael_petersen] -- Restored EVEN_M restriction. [Martin D. Weinberg] -- Completed draft version of frequency extractor. [Martin D. Weinberg] -- More updates: ready to test time grid construction. [Martin D. - Weinberg] -- Added new routine for estimating azimuthal and vertical oscillation - frequencies. [Martin D. Weinberg] -- Put coefficient headers and readers in their own sources. [Martin D. - Weinberg] -- Add sanity check for energy grids; thought I already did this, - honestly. [Martin D. Weinberg] -- Remove deprecated mean-mass algorithm to prevent further confusion. - [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Remove temporary store for recomb rates. [Martin D. Weinberg] -- Add grid toggle for recombination cross section. [Martin D. Weinberg] -- Fix header order. [Martin D. Weinberg] -- Cache output moved outside of temperature loop (oops) [Martin D. - Weinberg] -- Add standalone routine to make recombination cache files. [Martin D. - Weinberg] -- Added test for consistency of MDW and RJA implementations of 'fudge' - ratio. Added caching to MDW implementation. [Martin D. Weinberg] -- Whitespace changes only. [Martin D. Weinberg] -- Fixed weighting function. [Martin D. Weinberg] -- Fix to scale computation. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Add additional support libraries needed for some versions of hdf5. - [mdw] -- Allow for the more general case of serial or parallel hdf5. [mdw] -- Draft fix for FPE found by Becky Arnold. [Martin D. Weinberg] -- Add exponential disk basis for kinematic expansion. [Martin D. - Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Make it so the upper and lower limits of temperatures fudge factors - are calculated for are not hard coded. [r-j-arnold] -- In function that gets the fudge factor from the tables implement - conditions for if the temperature is outside those there are factors - calculated for. [r-j-arnold] -- Modify the function that gets the fudge factor to use interpolation - rather than the closest computed value. [r-j-arnold] -- Removed very old cruft, leaving the one non-system function. [Martin - D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [r-j-arnold] -- Make particles add themselves at the lowest multistep level in - UserAddMass. [Martin D. Weinberg] -- Fix source of immdiate FPE errors (negative T indecies) [r-j-arnold] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Remove double up of fudge factor application. [r-j-arnold] -- My take on Becky's fudge version. [Martin D. Weinberg] -- Clean up and corrections (?) for Ion-Electron ordering in radiative - recombination cross section. [Martin D. Weinberg] -- Cleaning and comment changes only. [Martin D. Weinberg] -- Missing constant declaration in correction_factors; version flag - update for CollideIon. [Martin D. Weinberg] -- Move Becky's recombination factors out of global name space. [Martin - D. Weinberg] -- Fix random number generation for multiple processes. [Martin D. - Weinberg] -- Add the script used to calculated what the fudge factors are. [r-j- - arnold] -- Made changes to the necessary files to implement the fudge factor. - [r-j-arnold] -- Add the files holding correction factors needed to fudge the ratios. - [r-j-arnold] -- Zero maccum in psp2bess and fix MPI logic in psp2interp. [Martin D. - Weinberg] -- Clean up only. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Missing type? [michael_petersen] -- Added additional comments and restored diagnostic output. [Martin D. - Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Add progress bar, check file range before starting, fix file name - construction from snapshot number. [Martin D. Weinberg] -- Added simple 2d density histogram for MSSA support. [Martin D. - Weinberg] -- Fixed typo in mass bin variable name. [Martin D. Weinberg] -- Append to existing coefficient file. [Martin D. Weinberg] -- Revert to original header with nmin. [Martin D. Weinberg] -- Make cmap vs {cmapr, cmapz} backwards compatible. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Add 3d DiskEval. [michael_petersen] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Typo in parameter reading from cylindrical cachefile fixed. [Martin D. - Weinberg] - - 'DENS' should have been 'dens' -- Update for MSSA radial basis range. [Martin D. Weinberg] -- Missing assignment of default model file for SLGridSph. [Martin D. - Weinberg] -- Version bump and a bit of simplification for git version reporting. - [Martin D. Weinberg] -- Update to simplify automatic git commit reporting in exp. [Martin D. - Weinberg] -- Fix progress bar after reordering MPI and OpenMP loops. [Martin D. - Weinberg] -- Documentation of 'easter egg' in header. [Martin D. Weinberg] -- Changed MPI and OpenMP parallelization strategy for pnum==1. [Martin - D. Weinberg] -- Some comments and updated norm constants in orthogonality check. - [Martin D. Weinberg] -- Some comments and updated norm constants in orthogonality check. - [Martin D. Weinberg] -- Allow compilation without OpenMP. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Just some additional comments. [Martin D. Weinberg] -- Variance debug test fix. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Add runtag to ortho check file. [Martin D. Weinberg] -- Check orthgonality after creation. [Martin D. Weinberg] -- Output variance matrices on VFLAG & 32. [Martin D. Weinberg] -- Additional comments in debugging routine. [Martin D. Weinberg] -- Added cylindrical basis orthogonality check for debugging. [Martin D. - Weinberg] -- Fix cuda constant typo. [Martin D. Weinberg] -- Updates to cuda for mapping change for Sphere. [Martin D. Weinberg] -- Updates to cuda for mapping change. [Martin D. Weinberg] -- Changes to coordinate mapping nomenclature in Cylinder and EmpCylSL; - lots of tiny changes to utilities. [Martin D. Weinberg] -- Add for strncpy. [Martin D. Weinberg] -- Add total density and potential to surface grids. [Martin D. Weinberg] -- Use doubles in FindPoint to enable large mesh sizes. [Martin D. - Weinberg] -- Try to fix histogram orientation and offset. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Do not read time and cylmass in binary for new-style eof header. - [Martin D. Weinberg] -- For consistency with everything else: define nmax limit be 1 + max - index. [Martin D. Weinberg] -- Return if requested eigenvalues is zero. [Martin D. Weinberg] -- Missing default initialization of EvenOdd. [Martin D. Weinberg] -- Removed some unused arrays intended for debugging. [Martin D. - Weinberg] -- Fix logic for M-SSA with groups rather than pairs. [Martin D. - Weinberg] -- Comments only. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Added some additional comments only. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Softened gravity clean up for Direct. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Std namespace specifications only. [Martin D. Weinberg] -- Comments only. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Looks like an MPI deadhang in OutAscii to me . . . draft fix. [Martin - D. Weinberg] -- Implement spline kernel for softened gravity. [Martin D. Weinberg] -- Add alternative output directory. [Martin D. Weinberg] -- Fixed typo in option string for outdir. [Martin D. Weinberg] -- Added output directory prefix. [Martin D. Weinberg] -- Draft code to generate coefficient files from PSP files. [Martin D. - Weinberg] -- Thought that I already fixed this typogit diff diskprof2.cc? [Martin - D. Weinberg] -- Merge branch 'devel' of bitbucket.org:mdweinberg/exp into devel. - [michael-petersen] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Bin boundary clean up. [Martin D. Weinberg] -- Update for multiple M values. [Martin D. Weinberg] -- Update for new cylindrical basis header. [Martin D. Weinberg] -- Update for new cylindrical basis header. [Martin D. Weinberg] -- Updates for density binning. [Martin D. Weinberg] -- Corrected typo. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Added additional YAML error capture. [Martin D. Weinberg] -- Fix null terminate in make_unique [Martin D. Weinberg] -- Missing MPI_Finalize added. [Martin D. Weinberg] -- For fields: we need to compute density*scalar. [Martin D. Weinberg] -- Variable name change for clarity. [Martin D. Weinberg] -- Comments only. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Fine grained progress report. [Martin D. Weinberg] -- Add range check. [Martin D. Weinberg] -- Norm fix. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Added support for YAML header coefficient files. [Martin D. Weinberg] -- Added new cache header option in gendisk2. [Martin D. Weinberg] -- Missing cstring header for strlen. [Martin D. Weinberg] -- Typo in YAML header. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Fix normalization in Bessel. [Martin D. Weinberg] -- Typo fix. [Martin D. Weinberg] -- More info in YAML headers. [Martin D. Weinberg] -- Fix progress bar. [Martin D. Weinberg] -- Added YAML support for read_eof_header. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Sanity check for mmax; additional guidance in output. [Martin D. - Weinberg] -- Sanity check for mmax. [Martin D. Weinberg] -- Added draft implementations of YAML headers for SphericalBasis coefs, - Cylinder coefs, and the EmpCylSL EOF basis; they can be enabled with - the NewCoefs and NewCache static bools. [Martin D. Weinberg] -- Minor clean up in VFLAG output stanzas. [Martin D. Weinberg] -- Missing EvenOdd debugging stanza for NaN; oops. [Martin D. Weinberg] -- Fix accel parameter in OutAscii. [michael-petersen] -- Add EvenOdd support in EmpCylSL for utils. [Martin D. Weinberg] -- Version bump and some additional comments in EmpCylSL. [Martin D. - Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Convert to MPI. [Martin D. Weinberg] -- Merge branch 'devel' of https://bitbucket.org/mdweinberg/exp into - devel. [Martin D. Weinberg] -- Suppress detailed errors unless verbose is set. [Martin D. Weinberg] -- Updates for computing a user-specified number of odd-parity EOF basis - functions. This is specified by the ncylodd to Cylinder, which results - in ncylorder-ncylodd even functions and ncylodd odd functions. If - ncylodd is unspecified or set to a value < 0, one gets the original - version in eigenfunction order. [Martin D. Weinberg] -- Return best value so far when iterations are exceeded. [Martin D. - Weinberg] -- Cache norm for Bessel expansion. [Martin D. Weinberg] -- Added Bessel fct kinetic routine. [Martin D. Weinberg] -- Memory mangement cleanup: removed pointers in favor of shared_ptr and - removed the elaborate delete stanzas in destructors. No changes to - algorithms. [Martin D. Weinberg] -- Remove EXP lib dependencies from hdf52accel. [Martin D. Weinberg] -- Switch from scaled to true relative force. [Martin D. Weinberg] -- Add hdf5 library detection. [Martin D. Weinberg] -- Don't ignore local m4 files. [Martin D. Weinberg] -- Added caching to DiskEval; added C++ version of hdf5 to accel for - speed. [Martin D. Weinberg] -- Use floats, not doubles for Gadget2. [Martin D. Weinberg] -- Switch to binary read. [Martin D. Weinberg] -- Add user-supplied output file name. [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' into devel. [Martin D. Weinberg] -- Added routine to do a force test from particle positions and - accelerations using DiskEval. [Martin D. Weinberg] -- Added routine to do a force test from particle positions and - accelerations using DiskEval. [Martin D. Weinberg] -- Version bump. [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' into CUDA. [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Fixed typo in storage initialization. [Martin D. Weinberg] -- Added the possibility of an upper ionization-state limit. [Martin D. - Weinberg] -- Remove implicit namespace declaration. [Martin D. Weinberg] -- Add coef stanza sanity check and remove some debug lines. [Martin D. - Weinberg] -- Add coef stanza sanity check and remove some debug lines. [Martin D. - Weinberg] -- Fixed coefficient order, oops. [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- More fixes to coefficient data base, although none seem to be the root - cause of the problem. [Martin D. Weinberg] -- Change memory management for coefficients. [Martin D. Weinberg] -- Added a few more playback bypass checks. [Martin D. Weinberg] -- Added a few more playback bypass checks. [Martin D. Weinberg] -- Missing multistep override for playback. [Martin D. Weinberg] -- Allow UserHalo to apply to all components or one at a time. [Martin D. - Weinberg] -- Regression for older OpenMP. [Martin D. Weinberg] -- Removed debugging cruft. [Martin D. Weinberg] -- Using fixed point floating for coefficient mapping. [Martin D. - Weinberg] -- Fix for setting cylmass manually. [Martin D. Weinberg] -- One more suppression of mulitstep update. [Martin D. Weinberg] -- White-space change only. [Martin D. Weinberg] -- Suppress multistep coefficient update for playback. [Martin D. - Weinberg] -- Allocate sin coefficients for m=0 for convenience. [Martin D. - Weinberg] -- Coefficient evaluation duplication fix. [Martin D. Weinberg] -- White space change and comments added only. [Martin D. Weinberg] -- Simplify coefMaster logic. [Martin D. Weinberg] -- Additional comments only. [Martin D. Weinberg] -- Change default to MPI coefficient communication. [Martin D. Weinberg] -- Added coefficient master node test. [Martin D. Weinberg] -- Remove substep output container '.'; that was an annoying bad idea. - [Martin D. Weinberg] -- Version bump. [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Added a few additional read checks. [Martin D. Weinberg] -- Draft implementation of coefficient playback. The tag 'playback: - file' in the force configuration indicates playback where 'file' is - the previously generated coefficient file for the basis. The lmax, - mmax, nmax parameters must match but no other sanity checking is - performed. Expect bugs. [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Indicate multistep output call with mstep>0 by '.' [Martin D. - Weinberg] -- Print step number only at the top of the multistep hierarchy. [Martin - D. Weinberg] -- Restore the actual file, not just .gitignore. [michael-petersen] -- Restore sledge.f, we need it! [michael-petersen] -- Added working directory support. [Martin D. Weinberg] -- Fixed broken bin indexing. [Martin D. Weinberg] -- Ring histogram code, previously in the MSSA branch. [Martin D. - Weinberg] -- Fix Makefile.am to reflect source renaming to prevent upper-lower case - confusion for some OS. [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Merged in pricewhelan/exp/ignore-file (pull request #9) [Adrian Price- - Whelan] - - Add .gitignore file and some file renames for OSX case insensitivity -- Renames for osx case insensitivity. [Adrian Price-Whelan] -- Ignore binary exec. [Adrian Price-Whelan] -- Add git ignore file for files generated during build process. [Adrian - Price-Whelan] -- Merged in pricewhelan/exp/typo (pull request #8) [Adrian Price-Whelan] - - Fix tiny typo in docstring -- Another typo. [Adrian Price-Whelan] -- Fix typo in docstring. [Adrian Price-Whelan] -- Add multistep output feature. [michael-petersen] -- Multistep output feature addition. [michael-petersen] -- One option for full multistep outputs. [michael-petersen] -- Merge branch 'CUDA_DEVEL' of bitbucket.org:mdweinberg/exp into msp. - [michael_petersen] -- Coef.H fix? [michael_petersen] -- Another old compiler work around. [Martin D. Weinberg] -- Simplify coefficient packing for PCs. [Martin D. Weinberg] -- Work arounds for old compliers. [Martin D. Weinberg] -- Fixes for eigen3 config and dropped pkg-config support from autoconf. - [Martin D. Weinberg] -- Updates to m4 files for boost config. [Martin D. Weinberg] -- Slight bump up of default knot number. [Martin D. Weinberg] -- Reduce default radial grid size a bit. [Martin D. Weinberg] -- Update default DiskEval parameters. [Martin D. Weinberg] -- Fixed fence-post error; force now check with M-N analytic formula - within a small fraction of a percent. [Martin D. Weinberg] -- Update for new version of DiskEval with x/(1-x) scaling. [Martin D. - Weinberg] -- Added an mapping from the semi-infinite to unit interval for grid and - quadrature in DiskEval; didn't help much, maybe a bit. [Martin D. - Weinberg] -- Merge local version. [Martin D. Weinberg] -- Include some of the utils directories in doxygen. [Martin D. Weinberg] -- Added analytic force evaluation for M-N disk. [Martin D. Weinberg] -- Formatted output change only. [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Resequence particles after external forces are finished; assign - nbodies in number update for simplicity. [Martin D. Weinberg] -- Fixed particle counter gaff in new version of get_particles; tests - okay under cuda. [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Merge branch 'NewParticles' into CUDA_DEVEL. [Martin D. Weinberg] -- A few more comments and simplification of vtan computation. [Martin D. - Weinberg] -- A few more comments only. [Martin D. Weinberg] -- Fix particle number bug in updated version of get_particles. [Martin - D. Weinberg] -- Output and file name fix. [Martin D. Weinberg] -- Added OpenMP to coefficient and orthogonal comptuation; let caller be - responsible for setting OpenMP parameters rather than DiskEval. - [Martin D. Weinberg] -- Use a different number of output grid points for 1d and 2d. [Martin D. - Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Missing conversion of nbodies_tot to CurTotal() [Martin D. Weinberg] -- Help string change only. [Martin D. Weinberg] -- Support for latest VTK versions. [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Missing conversion of nbodies_tot to CurTotal() [Martin D. Weinberg] -- Missing conversion of accum_cosN and accum_sinN. [Martin D. Weinberg] -- Fixed minor logic error in nbodies recomputation. [Martin D. Weinberg] -- Update default makeIon.config for Trace. [Martin D. Weinberg] -- Report true rmin and rmax rather than log(rmin) and log(rmax) [Martin - D. Weinberg] -- Added additional time control; start time and addition interval can - now be specified. Added additional documenation for doxygen web page. - [Martin D. Weinberg] -- Spelling changes, a few additions. [Martin D. Weinberg] -- Added missing news and recent changes file. [Martin D. Weinberg] -- Fix typo. [Martin D. Weinberg] -- Compute angular momemtum and velocity moments in local frame. [Martin - D. Weinberg] -- Added documentation for Component::GetNewPart and - Component::DestroyPart for user modules. [Martin D. Weinberg] -- Need to update index tables for load_balance if particles have been - added or destroyed. [Martin D. Weinberg] -- Add levlist support to load balancing. [Martin D. Weinberg] -- Fix error on zero-mass bin and int<->unsigned comparisons. [Martin D. - Weinberg] -- Updates for levlist registration. [Martin D. Weinberg] -- Updated algorithm for small numbers added particles. [Martin D. - Weinberg] -- Version bump. [Martin D. Weinberg] -- Modified nbodies_tot and nbodies assignments from Component to account - for variable particle numbers. [Martin D. Weinberg] -- Added draft version of particle spawning user routine. [Martin D. - Weinberg] -- Minor fixes to get_particles for index-free particle transport. - [Martin D. Weinberg] -- Updates for particle spawning and destroying. [Martin D. Weinberg] -- Fix return void* [Martin D. Weinberg] -- Changed relative force to that at a scale length and scale height. - [Martin D. Weinberg] -- Relative forces in radial direction based on midplane force at A; - Relative forces in vertical direction based on force at R, z=H. - [Martin D. Weinberg] -- Fixed up OpenMP support. [Martin D. Weinberg] -- Fixed up OpenMP support. [Martin D. Weinberg] -- Added merdional plane output. [Martin D. Weinberg] -- Added OpenMP support in DiskEval to make. [Martin D. Weinberg] -- Added explicit MN test for potential. [Martin D. Weinberg] -- Added progress bar. [Martin D. Weinberg] -- Version bump. [Martin D. Weinberg] -- Removed all those crazy pointer constructions. [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Added column header to output file. [Martin D. Weinberg] -- White space changes. [Martin D. Weinberg] -- Switch to make_shared. [Martin D. Weinberg] -- Only root node writes diagnostic output. Also note: the code will - exit if there are so few particles that some nodes have none. This - could be fixed but it is not worth it, at this point. [Martin - Weinberg] -- Added truncated disk density. [Martin D. Weinberg] -- Fixed NOUT logic for basis restriction. [Martin D. Weinberg] -- Added multipole evaluation of disk force and potential for checking - expansion. [Martin D. Weinberg] -- Added disk truncation to EOF conditioning function. [Martin D. - Weinberg] -- Print first 5 density basis functions. [Martin D. Weinberg] -- Check for YAML node in config. [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' into CUDA. [Martin D. Weinberg] -- Added generalized cored power-law profile for EOF construction. - [Martin D. Weinberg] -- Update coefficient check for EOF. [Martin D. Weinberg] -- Report more parameters. [Martin D. Weinberg] -- Just a spelling correction. [Martin D. Weinberg] -- Added radial scaling for deprojected mass distribution. [Martin D. - Weinberg] -- Report DiskType. [Martin D. Weinberg] -- Fixed typo for CMAP=2 vertical mapping. [Martin D. Weinberg] -- Fixed typo: RMIN should be a Rmin. [Martin Weinberg] -- Added some additional deprojection debugging. [Martin D. Weinberg] -- Attempt to restore prior behavior of CMAP for backward compatibility; - this requires a new variable CMAPTYPE. [Martin D. Weinberg] -- Fix switch statement for conditioning model. [Martin D. Weinberg] -- Updated CMAP for vertical mapping in EmpCylSL and added a power - mapping. [Martin D. Weinberg] -- Let CMAP turn off vertical scaling as well. [Martin D. Weinberg] -- Add potential output. [Martin D. Weinberg] -- Version bump. [Martin D. Weinberg] -- Change enum name to prevent confusion. [Martin D. Weinberg] -- Avoid recomputation of SphGridSL. [Martin D. Weinberg] -- Promoted SLGridSph *ortho to shared_ptr; fixed botched deprojection - model in initia2.cc. [Martin D. Weinberg] -- Read parameters directly from cachefile by default; this can be - overridden by the 'ignore' parameter, in which case the EOF will be - recomputed if the parameters do not match. [Martin D. Weinberg] -- Added comments only. [Martin D. Weinberg] -- Removed non-zero return codes to keep OpenMPI mpirun command from all - of its 'scary' chatter. [Martin D. Weinberg] -- Change default option names to something less confusing: the disk - basis conditioning model is now 'condition' and the deprojection disk - model is now 'deproject' [Martin D. Weinberg] -- Fixed typo in enum naming. [Martin D. Weinberg] -- Added Miyamoto-Nagai disk to initial2.cc DiskDens. [Martin D. - Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Allowed EmpModel to be chosen by option flag. [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Remove the vestigial PLUMMER variable. [Martin D. Weinberg] -- Version bump. [Martin D. Weinberg] -- Added custom spherical deprojection models to EmpCylSL. [Martin D. - Weinberg] -- Added 'long form' option to print out rates as well as ratio. [Martin - D. Weinberg] -- Added some additional comments; tests logarithmic scaling against - testRatio results for three different temperatures. [Martin D. - Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Log scale for energy grids. [Martin D. Weinberg] -- Added additional debugging diagnostics. [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Report progress by listing files as they are processed. [Martin D. - Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Added sincle char option flags. [Martin D. Weinberg] -- Fix typo in dens vtkFloatArray config. [Martin D. Weinberg] -- Some temporary deep checking for recombination coefficients. [Martin - D. Weinberg] -- Return correct (void *) [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Member to retrieve curent length scale. [Martin D. Weinberg] -- Added density estimation to vtu files. [Martin D. Weinberg] -- Added density estimation to vtu files. [Martin D. Weinberg] -- Draft implementation of a PSP to unstructured points converter. - [Martin D. Weinberg] -- This is old cruft and may be confusing some builds; removing it. - [Martin D. Weinberg] -- White space changes. [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Changes to diagnostic output only. [Martin D. Weinberg] -- Updated truncation and scaling logic. [Martin D. Weinberg] -- Open coefficient file for append. [Martin D. Weinberg] -- Updated for Plummer law fit and tabulated fit to particle - distribution. [Martin D. Weinberg] -- Fix error in particle map indexing. [Martin D. Weinberg] -- Check for zero mass bins and remove ptr to SLGridSph in favor of - shared pointer. [Martin D. Weinberg] -- Removed basis scale update and added temporal and spatial smoothing. - [Martin D. Weinberg] -- Added basis recomputation option; untested. [Martin D. Weinberg] -- Fixed wrong explanation in program_options description strings. - [Martin D. Weinberg] -- Capture return value from system() [Martin D. Weinberg] -- Updated TidalRadius routine. [Martin D. Weinberg] -- Version bump. [Martin D. Weinberg] -- Fix mistake in translation between zero energy and radius. [Martin D. - Weinberg] -- White-space changes only. [Martin D. Weinberg] -- Additional checks for empty components. [Martin D. Weinberg] -- Update for difference between SphericalBasis and SphereSL [should - change coefficient dump in SphericalBasis] [Martin D. Weinberg] -- White space change only. [Martin D. Weinberg] -- Added progress output for coefficients only. [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Fixes for consistency with exp_halo. [Martin D. Weinberg] -- Draft update of haloprof2 for generating coefficients from a series of - PSP file. [Martin D. Weinberg] -- Updates for total reconstruction for all triple groupings. [Martin D. - Weinberg] -- Fixed spherical radius for volume output. [Martin D. Weinberg] -- Update to halo MSSA rendering routine. [Martin D. Weinberg] -- Added support for halo MSSA. [Martin D. Weinberg] -- Remove old cylindrical header type. [Martin D. Weinberg] -- Fix up missing void* returns. [Martin D. Weinberg] -- Fix up missing void* returns. [Martin D. Weinberg] -- Changed header coefficient names to include SphericalBasis. [Martin D. - Weinberg] -- Added missing void pointer return. [Martin D. Weinberg] -- Read halo coefficients and make power plots. [Martin D. Weinberg] -- Change CHEBY=false by default. [Martin D. Weinberg] -- Removed dependence on case for GenDiskType comparison. [Martin D. - Weinberg] -- Added string selection for Jeans' variant selection. [Martin D. - Weinberg] -- Added a maximum energy to DF ratio computation to prevent negative - mass selection owing to potential tapirs in models. [Martin D. - Weinberg] -- Reverted change to array mapping (it was correct in the older commit) - [Martin D. Weinberg] -- Add basis compare member to header; missing from merge. [Martin D. - Weinberg] -- Repair OpenMP detection, the HAVE_OPENMP config.h flag was failing to - be set. [Martin D. Weinberg] -- Fix units in output recombination and ionization coefficients. [Martin - D. Weinberg] -- Revert all those debugging additions to EmpCylSL; got back further. - [Martin D. Weinberg] -- Revert all those debugging additions to EmpCylSL. [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Additional debugging tests. [Martin D. Weinberg] -- Parity checking for debugging. [Martin D. Weinberg] -- Added support routine to compure EOF tables. [Martin D. Weinberg] -- Added routine to compure EOF tables. [Martin D. Weinberg] -- Change to coefficient clear. [Martin D. Weinberg] -- Added leading zeros to frame counter. [Martin D. Weinberg] -- Removed deprecated config variables. [Martin D. Weinberg] -- Fixed write error in histogram data arrays. [Martin D. Weinberg] -- Flip x-y in VTK output. [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- White space changes and comments only. [Martin D. Weinberg] -- White space changes and comments only. [Martin D. Weinberg] -- Fixed histogram indexing. [Martin D. Weinberg] -- Write VTK output with tags. [Martin D. Weinberg] -- Enabled VTK output. [Martin D. Weinberg] -- Added haloprof version using PSP2. [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Add index and mass values to BAD MASS diagnostic output. [Martin D. - Weinberg] -- Added indx and mass value output to BAD MASS warning. [Martin D. - Weinberg] -- Version bump. [Martin D. Weinberg] -- Added test contraint for mmax. [Martin D. Weinberg] -- Simple fix to formatting. [Martin D. Weinberg] -- Test smoothing using log smoothing by Chebychev following Mike P. - [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- For MULTI mass, use DF=1 (Eddington) by default. [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Some minor checking for debugging. [Martin D. Weinberg] -- Added getK() to Ion to return speciesKey. [Martin D. Weinberg] -- Put limits on kappa/omega. [Martin D. Weinberg] -- Prevent sqrt(<0) in diagnostic output. [Martin D. Weinberg] -- Fixed out-of-bounds grid for halo mass table. [Martin D. Weinberg] -- Fixed EOL problem in halo bods read. [Martin D. Weinberg] -- Minor formating fixes. [Martin D. Weinberg] -- More changes to 'evolved' logic. [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Ascii coefficient dump. [Martin D. Weinberg] -- Space basis dump using mapped coordinates. [Martin D. Weinberg] -- More logic changes for evolved_halo flag. [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Component name key is 'compname' rather than 'comp_name' as listed in - the documentation; documentation is hereby fixed. [Martin D. Weinberg] -- New info lines. [Martin D. Weinberg] -- Fixed up logic errors in reading halo file for evolved_halo=true - option; some namespace clean up. [Martin D. Weinberg] -- Switched from pointers to shared pointers. [Martin D. Weinberg] -- More descriptive boolean name. [Martin D. Weinberg] -- Do not print particle index for 'input' style. [Martin D. Weinberg] -- Change Diskhalo2 and initial2 to allow for realizing a disk from a - previous halo body file. [Martin D. Weinberg] -- Updates to initial2.cc for halo body file bypass. [Martin D. Weinberg] -- Version bump. [Martin D. Weinberg] -- Provide column headers for EmpCylSL cache mismatch. [Martin D. - Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Added coordinate mapping toggle to SphericalSL. [Martin D. Weinberg] -- Ported to program_options. [Martin D. Weinberg] -- Ported to program_options. [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Tried making the code but got the error strncpy was not declared in - this scope with regards to the ascii2psp2.cc file. Added an extra - include to include it in the scope. [r-j-arnold] -- Check for exactly two file names on the command line. [Martin D. - Weinberg] -- Fix recomb.py. [Martin D. Weinberg] -- Added NCHEB setting; probably not really needed since CHEBY is rarely - used. [Martin D. Weinberg] -- Update for yaml_diff compilation on eagle. [Martin D. Weinberg] -- Use boost::program_options for option parsing. [Martin D. Weinberg] -- Use boost::program_options for option parsing. [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Fixed error in collision type diagnostic output. [Martin D. Weinberg] -- Error in token type fixed. [Martin D. Weinberg] -- Wrong data type for dbthresh and misspelling in PFbufsz. [Martin D. - Weinberg] -- Updated m4 boost macros. [Martin D. Weinberg] -- Added yaml_diff tool for comparing config files. [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' into CUDA. [Martin D. Weinberg] -- Added user-configurable center offset. [Martin D. Weinberg] -- Implemented a center offset for the surface histograms; not yet - configurable. [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Do file open check before closing to prevent stream exception. [Martin - D. Weinberg] -- Fix logic for file location. [Martin Weinberg] -- Added a version of ascii2psp, ascii2psp2, that adds YAML info from a - config file. [Martin D. Weinberg] -- Some minor cleanup. [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Fixed option help. [Martin D. Weinberg] -- Added additional runtime file checks. [Martin D. Weinberg] -- Switch order of autoconf commands. [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Added additional explanation about zero time. [Martin D. Weinberg] -- Comment changes only. [Martin D. Weinberg] -- Comment changes only. [Martin D. Weinberg] -- Version bump for changes to SPL/PSP. [Martin D. Weinberg] -- Don't open file if split list is empty in openNextBlob() [Martin D. - Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Updated restart file reading for split PSP (SPL) format. [Martin D. - Weinberg] -- Version bump for changes to OutputContainer to prevent multiple calls - at the same time. [Martin D. Weinberg] -- Differentiate initial time and restart time. [Martin D. Weinberg] -- Logic to prevent rerunning the run method of OutputContainer at the - same time step. [Martin D. Weinberg] -- Fixed bad edit with extra \} [Martin D. Weinberg] -- Removed debug lines. [Martin D. Weinberg] -- Missing broadcast of starting OutPSQ file to all nodes. [Martin D. - Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin Weinberg] -- Added YZ projected density. [Martin D. Weinberg] -- Updates for X-Z projections. [Martin D. Weinberg] -- Rewrite boost dependencies for eofbasis. [Martin D. Weinberg] -- Add mmin parameter. [Martin Weinberg] -- Add proper BOOST paths to eofbasis. [Martin Weinberg] -- Use VTK to make EOF basis images. [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Rewrote SPL file policy to remove leading path for blob files. [Martin - D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Check for trailing '/' in source directory specification. [Martin D. - Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Fix typo in comment. [Martin D. Weinberg] -- Added XZ projected density. [Martin D. Weinberg] -- Add eofbasis and fix empdump. [Martin D. Weinberg] -- Dump eof basis to VTK files. [Martin D. Weinberg] -- Added additional tests for options and input file existence. [Martin - D. Weinberg] -- Add argument processing in addition to amplitude. [Martin D. Weinberg] -- Added outfile name to pvd filename. [Martin Weinberg] -- Set 'indexing=true' by default. [Martin Weinberg] -- Remove unused global cuda constants. [Martin D. Weinberg] -- Fixes for PSPspl directory alternatives. [Martin Weinberg] -- Added directory rewriting for SPL files. [Martin D. Weinberg] -- Added volume and surface density computation for histogram. [Martin D. - Weinberg] -- Automatically select PSP or SPL based on file name. [Martin D. - Weinberg] -- 1D histogram of for PSP2. [Martin D. Weinberg] -- Converted to PSP2. [Martin D. Weinberg] -- PSPptr is now in PSP2.H. [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Comment changes only. [Martin D. Weinberg] -- Added profile routine for spherical model based on PSP2 class. [Martin - D. Weinberg] -- Removed some cruft. [Martin D. Weinberg] -- More implementations for new PSP2class. [Martin D. Weinberg] -- Removed debug line. [Martin D. Weinberg] -- Added cmd_file recording. [Martin D. Weinberg] -- Minor bug fixes. [Martin D. Weinberg] -- Ensure that ComponentHeader::info string is null terminated. [Martin - D. Weinberg] -- Version of diskprof2 that uses new PSP2 reader. [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Additional fixes to first-time logic for cuda_initialization. [Martin - D. Weinberg] -- Copy texture memory and coordinate mappings at beginning of each step. - Clearly, the cuda device has no per-class-instance isolation. [Martin - D. Weinberg] -- Test implementations for new PSP2 reader. [Martin D. Weinberg] -- Comment updates only. [Martin D. Weinberg] -- Update parameter description for Doxygen. [Martin D. Weinberg] -- Merged in fix_psp_io_bug (pull request #4) [r-j-arnold] - - Fix bug which made psp_io.py break if a component had no parameters. -- Fix bug which made psp_io.py break if a component had no parameters. - [r-j-arnold] -- Add genMakeIonconfig.py which autogenerates a makeIon.config file for - user-specified elements. [r-j-arnold] -- Added additional sanity checks for species_map for use_elc based on - particle attribute sizes. [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Added necessary global variables to Particle.cc for STANDALONE usage. - [Martin D. Weinberg] -- Removed deprecated variables. [Martin D. Weinberg] -- Added sanity checks for species_map based on particle attribute sizes. - [Martin D. Weinberg] -- Missing change of default setting of real4=true. [Martin D. Weinberg] -- Real4=true by default. [Martin D. Weinberg] -- Removed nagg from OutCHKPTQ. [Martin D. Weinberg] -- Updated logic for renaming, unlinking, and error messages. [Martin D. - Weinberg] -- Working but not yet producing exact values. [Martin D. Weinberg] -- Fixed range check and checkpoint logic. [Martin D. Weinberg] -- Additions for OutCHKPTQ, the split checkpoint output routine. [Martin - D. Weinberg] -- Split checkpoint file implementation. [Martin D. Weinberg] -- Name change from psp2whole to spl2psp. [Martin D. Weinberg] -- Version bump for new Output method. [Martin D. Weinberg] -- Added sequence ranges. [Martin D. Weinberg] -- Added some additional file state checking. [Martin D. Weinberg] -- Rename for consistency with file naming convention. [Martin D. - Weinberg] -- Added OutPSQ: routine to output PSP from each node and each component. - The entire PSP file is reassembled from these parts using the - psp2whole routine. [Martin D. Weinberg] -- Use std::tmpnam rather than tmpnam, with compiler warnings regardless. - [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Added some additional comments to the recomb.py routine. [Martin D. - Weinberg] -- Script should use python3 not python2. [Martin D. Weinberg] -- Removed used member variables: cache, Nmin, Nmax. [Martin D. Weinberg] -- Removed deprecated ConsAlgSplit. [Martin D. Weinberg] -- Comment out printing of python command line for ratios. [Martin D. - Weinberg] -- Quiet down ChiantiPy by piping stdout and stderr to /dev/null. [Martin - D. Weinberg] -- Use tmpnam(0) to construct the recombination rate temporary file. - [Martin D. Weinberg] -- Change graphics backend to prevent X11 issues. [Martin D. Weinberg] -- Added recombination coefficient ratio kludge. [Martin D. Weinberg] -- Added Python3 to shell string. [Martin D. Weinberg] -- Script to get ChiantiPy recombation rates. [Martin D. Weinberg] -- Removed the test key pseudoH. [Martin D. Weinberg] -- Routine to generate EXP vs Chianti thermal recombination coefficient - ratio. [Martin D. Weinberg] -- Added option to use hydrogenic recombination for all species. [Martin - D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Updated tasks. [Martin D. Weinberg] -- Added sanity check for element range. [Martin D. Weinberg] -- Added column labels. [Martin D. Weinberg] -- Use direct integration of Bethe-Heitler approximation to compute free- - free thermal emission for testing. [Martin D. Weinberg] -- Convert from mass probability to particle number for inelastic energy - computation for Trace method. [Martin D. Weinberg] -- Added inverse fine-structure-constant value. [Martin D. Weinberg] -- Fix particle number weighting in Trace routine for inelastic energy - contributions. [Martin D. Weinberg] -- Additions for emissivity test routines. [Martin D. Weinberg] -- Test routine for collisional emissivity; draft for free-free but this - is more complicated I fear, than the naivity of my implementation. - [Martin D. Weinberg] -- Fixed incorrect mode setting. Now use the mnemonic flags. [Martin D. - Weinberg] -- Fixes to script writing. [Martin D. Weinberg] -- Remove deprecated (and incorrect) electron scattering routines. - [Martin D. Weinberg] -- Removed deprecated electron scattering. [Martin D. Weinberg] -- Finish merge from BISECT to CUDA_DEVEL. [Martin D. Weinberg] -- Remove the MeanMass algorithm from both cpu and gpu code. [Martin D. - Weinberg] -- Removed TraceAccum flag and hardwired traceAccum algorithm. [Martin D. - Weinberg] -- Merge script-write from CUDA_DEVEL. [Martin D. Weinberg] -- A to-do list for DSMC implementation. [Martin D. Weinberg] -- Added NAME_ID and VERSION_ID to _description tag for output parameter - file; version bump. [Martin D. Weinberg] -- Update genIonization for ChiantiPy 0.9. [Martin D. Weinberg] -- Add VFKY toggle to YAML CollideIon database. [Martin D. Weinberg] -- A few more comments in Verner-Yakovlev initialize. [Martin D. - Weinberg] -- Added std::make_shared for clarity of intent. [Martin D. Weinberg] -- Some additional documentation. [Martin D. Weinberg] -- Added a TODO list for DSMC directory. [Martin D. Weinberg] -- DSMC version bump. [Martin D. Weinberg] -- Simply Verner-Yakovlev table broadcast. [Martin D. Weinberg] -- Clean out all deprecated submethods from Trace algorithm except for - TraceAccum. [Martin D. Weinberg] -- Write genIonization CHIANTI script if it does not exist in the working - directory. [Martin D. Weinberg] -- Make genIonization script a C++ string literal so user will have the - CHIANTI sript. [Martin D. Weinberg] -- Change recombination type to Verner and emit warning for other - choices. [Martin D. Weinberg] -- Use std::fill rather than a loop to remove name designations from - Verner-Yakovlev file. [Martin D. Weinberg] -- Fix test routines for new recombination implemenation. [Martin D. - Weinberg] -- Generalize the Verner method to include the full Verner and Yakovlev - cross section tables. [Martin D. Weinberg] -- Remove now unused gs_only parameter. [Martin D. Weinberg] -- Remove now unused gs_only parameter. [Martin D. Weinberg] -- The Verner and Yakovlev table. [Martin D. Weinberg] -- Some simplification for clarity in recomb XC. [Martin D. Weinberg] -- Added a new Verner flag for testing. [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' into CUDA. [Martin D. Weinberg] - - This includes recent changes for the recombination cross section computation. -- Fix some inverted statistical weights. [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Change default settings for KE_DEBUG and TraceAccum. [Martin D. - Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Change default to ground-state only in Recomb. [Martin D. Weinberg] -- Fixed Emin,Emax typo. [Martin D. Weinberg] -- Added probability based particle pair selection for - accumScatterTrace() [Martin D. Weinberg] -- Add random choice for accumScatterTrace pairs to prevent bias. [Martin - D. Weinberg] -- Minor updates for clarify and missing accumReset in - CollideIon::initialize_cell. [Martin D. Weinberg] -- More comments. [Martin D. Weinberg] -- Some additional comments. [Martin D. Weinberg] -- Draft version of TraceAccum implementation. [Martin D. Weinberg] -- Added Original split algorithm back and a new algorithm based on this - but for subsplits called New. [Martin D. Weinberg] -- Merged in documentation_update (pull request #3) [r-j-arnold] - - Documentation update -- README edited online with Bitbucket. [Martin Weinberg] -- README edited online with Bitbucket. [Martin Weinberg] -- Add information on downloading CHIANTI and modifying .bashrc to - readme. [Becky Arnold] -- Redo instructions on how to make and config. [Becky Arnold] -- Version bump for CollideIon. [Martin D. Weinberg] -- Changed the default ConsAlg method to Inert2. [Martin D. Weinberg] -- Mistake in range checking for ConsAlg method parsing. [Martin D. - Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Fix doc string. [Martin D. Weinberg] -- Rename of ConsAlg variants for consistency. [Martin D. Weinberg] -- Added labeling for ConsAlg on start up. [Martin D. Weinberg] -- Updated YAML doc strings for ConsAlg. [Martin D. Weinberg] -- Merge branch 'CUDA_DEVEL' of https://bitbucket.org/mdweinberg/exp into - CUDA_DEVEL. [Martin D. Weinberg] -- Updates for ConsAlg energy conservation algorithm for explicit - momentum conservation. [Martin D. Weinberg] -- Doc string change only. [Martin D. Weinberg] -- Added documentation/comments for the updated ENERGY_ES algorithms in - the Trace method. [Martin D. Weinberg] -- Fixes for momentum deferred-energy update. [Martin D. Weinberg] -- Added an additional energy conservation method for testing. [Martin D. - Weinberg] -- New energy conservation for sub-split particles in Trace method. Test - version with with both v1 and v2 adjustments coded. [Martin D. - Weinberg] -- Removed the minimum eps threshold in favor of not staging cross - sections if eps=0. Removed some debugging cruft. Added a check to - defer processing large negative energy excesses in scatterTrace. - [Martin D. Weinberg] -- Another conservation diagnostic test. [Martin D. Weinberg] -- More fixes to energy conservation diagnostics. [Martin D. Weinberg] -- Version bump for work on trace algorithm. [Martin D. Weinberg] -- Version bump. [Martin D. Weinberg] -- Improve energy conservation diagnostic for eta=0 cases. [Martin D. - Weinberg] -- Switch per-body diagnostic to acceptCount. [Martin D. Weinberg] -- Fix collision diagnostic for log file. [Martin D. Weinberg] -- Merge branch 'COM_TEST' of https://bitbucket.org/mdweinberg/exp into - COM_TEST. [Martin D. Weinberg] -- Fixes to energy conservation check for MeanMass method toggle. At - this point, the MeanMass method is likely to be deprecated and - removed. [Martin D. Weinberg] -- Use minimum floor for Pord weighting to prevent divide-by-zero - condition. [Martin D. Weinberg] -- Use minimum floor for Pord weighting to prevent divide-by-zero - condition. [Martin D. Weinberg] -- Additional TestSpread diagnostics. [Martin D. Weinberg] -- Typo in TestSpreadCount parameter parsing. [Martin D. Weinberg] -- Merge branch 'COM_TEST' into CUDA. [Martin D. Weinberg] -- Remove test upscale for trace method. [Martin D. Weinberg] -- Remove suppression of all inelastic but free-free and coll. excite for - testing. [Martin D. Weinberg] -- Restored orirginal eta dependence. [Martin D. Weinberg] -- Added TESTSPREAD and collsion type restriction for testing. [Martin D. - Weinberg] -- Fix dependencies for copied header files. [Martin D. Weinberg] -- Added UserMassEvo class for adjusting mass per particle for each - component. [Martin D. Weinberg] -- Added UserMassEvo class for adjusting mass per particle for each - component. [Martin D. Weinberg] -- Added upscale parameter for selection generation. [Martin D. Weinberg] -- Merge branch 'COM_TEST' of https://bitbucket.org/mdweinberg/exp into - COM_TEST. [Martin D. Weinberg] -- Fix typo in diagnostic interval logic and nvTrace labeling. [Martin D. - Weinberg] -- Added frational weighting test. [Martin D. Weinberg] -- Updates to set scale from UserTidalRad. [Martin D. Weinberg] -- Merge branch 'COM_TEST' of https://bitbucket.org/mdweinberg/exp into - COM_TEST. [Martin D. Weinberg] -- Set rtrunc in component. [Martin Weinberg] -- Update for a multiplicative factor for rtrunc. [Martin D. Weinberg] -- Update for a multiplicative factor for rtrunc. [Martin D. Weinberg] -- Fixed incorrect ordering of cov computation relative to pass=0 and - pass=1. [Martin D. Weinberg] -- Continued testing and debugging. [Martin Weinberg] -- Remove local acceleration from old COM system computation. [Martin - Weinberg] -- Added new test routine for active determination of tidal radius. - [Martin D. Weinberg] -- Remove Particle.H from utils/ICs before linking. [Martin D. Weinberg] -- Comment out FTGL support libraries for VTK in configure. [Martin D. - Weinberg] -- Another change to COM centering logic for orient: orient center should - always be computed relative to COM and IC should be ignored of - com_system is set. [Martin D. Weinberg] -- Fix Particle header copying logic. [Martin D. Weinberg] -- Fix typo: index q in freeze() should be n. [Martin D. Weinberg] -- Removed deprecated COM coordinate system everywhere in terms of the - newer on-the-fly coordinate computation. [Martin D. Weinberg] -- For pure H, recombination may invalidate scheduled electronic - interactions. Check and drop scattering events for this case. [Martin - D. Weinberg] -- Version bump for centering update. [Martin D. Weinberg] -- Added an 'Origin' centering scheme to Component as the default. - [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Fixed typo in ionization and recombination change in energy, as in CPU - version. [Martin D. Weinberg] -- Fixed typo in config parsing that should not have affected anything. - [Martin D. Weinberg] -- Fixed typo in ionization and recombination change in energy. [Martin - D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Change warning message for unassigned processes when using cuda. - [Martin D. Weinberg] -- Fix for equal species check. [Martin D. Weinberg] -- Fix minor typos in bunch host implementation. [Martin D. Weinberg] -- Fixes to cuda bunch allocation. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Draft changes for cuda particle allocation in bunches. [Martin D. - Weinberg] -- Remove test cruft and add additional diagnostics for collisional - excitation computation. [Martin D. Weinberg] -- Fix typo in com update (?) [Martin D. Weinberg] -- Remove old fac1, fac2 logic and try electron energy tests. [Martin D. - Weinberg] -- Remove some cruft from old energy adjustment. [Martin D. Weinberg] -- Version bump. [Martin D. Weinberg] -- Fix refactoring of Component initialization for cuda. [Martin D. - Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Remove weird energy conservation enforcement. [Martin D. Weinberg] -- Revert change to Pord. [Martin D. Weinberg] -- Changes to fix COM on restarts. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Fix electron mass handling in Pord for MeanMass. [Martin D. Weinberg] -- Energy diagnostic updates. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Fix typo. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Fixes to subdirectory toggles. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Continuing to fix this same typo (\!) [Martin D. Weinberg] -- Fix mistake in electron energy computation. [Martin D. Weinberg] -- Fix typo. [Martin D. Weinberg] -- Make cuda version consistent with cpu version; remove verbose debug - output for collision cross sections. [Martin D. Weinberg] -- YAML conversion to unsigned rather than uint_32. [Martin D. Weinberg] -- Fixed to SEED option in YAML config. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Changes to charge handling for testing mean-mass vs particle-spliting - algorithms. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Draft change to makeIonIC for mean-mass algorithm possible mistake. - [Martin D. Weinberg] -- Removed cruft; make electron mass threshold match CPU version. [Martin - D. Weinberg] -- Test to reconcile cuda with cpu version. [Martin D. Weinberg] -- Energy check updates. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Remove weighting test lines. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Added interaction diagnostic to ERROR output. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Missing changes to weights. [Martin D. Weinberg] -- Added setting of the ACG random number seed. [Martin D. Weinberg] -- Some additional KE tests. [Martin D. Weinberg] -- Missing fixes to weight factors and electron energy. [Martin D. - Weinberg] -- Diagnostic output clean up: print signed shorts. [Martin D. Weinberg] -- Updated for double and single counting in selection computation. - [Martin D. Weinberg] -- Corrections for subspecies weighting. [Martin D. Weinberg] -- Version bump. [Martin D. Weinberg] -- Revert centering changes. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Added Orient center to be preferredto comI center. [Martin D. - Weinberg] -- Prefer Orient center for com system origin, if available. [Martin D. - Weinberg] -- Fix weights for new refactoring test. [Martin D. Weinberg] -- Added copying rather than linking to automake for MacOS (?) [Martin D. - Weinberg] -- Exploring minor mistake in refactoring algorihtm. [Martin D. Weinberg] -- Some extra debugging info. [Martin D. Weinberg] -- Some extra debugging and variable changes when debug flags are used to - prevent stomping. [Martin D. Weinberg] -- Draft updates for com origin handling. [Martin D. Weinberg] -- Updated damping computation. [Martin D. Weinberg] -- Typo in center of velocity output computation. [Martin D. Weinberg] -- Updated fpetrap.h line number. [Martin D. Weinberg] -- Fix to XC cpp flag and default value for NTCnodb. [Martin D. Weinberg] -- Fix factor of two pair counting typo in generateSelectionTrace. - [Martin D. Weinberg] -- Changes to diagnostic output only. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Merge branch 'master' into CUDA. Orient.cc changes. [Martin D. - Weinberg] -- Merge branch 'master' into CUDA. Includes changes for compatibility - with MacOS. [Martin D. Weinberg] -- Updated psp_io.py from Mike P. [Martin D. Weinberg] -- Added a comment about the eof cache location. [Martin D. Weinberg] -- White-space changes for readability only. [Martin D. Weinberg] -- Added Miyamoto-Nagai external potential. [Martin D. Weinberg] -- Fixed typos in config files; added a bit more to README. [Martin D. - Weinberg] -- Fixes to examples and outdir locations for OrbDiag and - ComponentContainer levels file. [Martin D. Weinberg] -- Make output go to outdir. [Martin D. Weinberg] -- Remove exp extension namespace. [Martin D. Weinberg] -- Added additional variable for OpenMP library. [Martin D. Weinberg] -- Checks for OpenMP to allow OpenMP unaware compilers to work. [Martin - D. Weinberg] -- More replacements of values.h for cfloat or limits.h. [Martin D. - Weinberg] -- Removed unused code from expgnu. [Martin D. Weinberg] -- Replace iostream.h with iostream. [Martin D. Weinberg] -- Remove used file. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. Fix - parse.cc conflict. [Martin D. Weinberg] -- Changes integer to true booleans for yaml compatibility in examples - dir. [Martin Weinberg] -- Remove debug lines. [Martin Weinberg] -- Make cuda off by default. [Martin Weinberg] -- Allow either 'cuda' or 'use_cuda' key in global stanza. [Martin - Weinberg] -- Improved energy list merge algorithm. [Martin Weinberg] -- Removed legacy header cruft. [Martin D. Weinberg] -- Fix typo in vtk header location. [Martin D. Weinberg] -- A few minor updates for energy checking. [Martin D. Weinberg] -- Change 'use_cuda' to 'cuda' in yaml config. [Martin D. Weinberg] -- Fix tidal variable type in thread passing. [Martin D. Weinberg] -- Updates to Component for centering logic. [Martin Weinberg] -- Remove erroneous use_cuda flags from examples. [Martin Weinberg] -- Merge branch 'master' into CUDA. [Martin D. Weinberg] -- Change cuda to use_cuda in global stanza. [Martin Weinberg] -- Change cpp variable VERBOSE to VERBOSE_CTR to prevent stomping. - [Martin Weinberg] -- Bump up turn-off value for dynfracD to much larger value. [Martin - Weinberg] -- Merge branch 'CUDA' [Martin Weinberg] -- Change default names of input files. [Martin D. Weinberg] -- Fix energy conservation tests. [Martin D. Weinberg] -- Fix broken multistep reporting. [Martin D. Weinberg] -- Look for 'config.yml' if the YAML config is not specified. [Martin D. - Weinberg] -- Do not try to compile the documentation if doxygent is not found. - [Martin D. Weinberg] -- Fix erroneous cuda type in non-cuda code. [Martin D. Weinberg] -- Removed some verbose debug output with CPP directives. [Martin D. - Weinberg] -- Removed some verbose debugging output. [Martin D. Weinberg] -- Added spread deferred energy option as a configurable option. [Martin - D. Weinberg] -- Remove erroneous electron energy scaling. [Martin D. Weinberg] -- Changes to diagnostic output only. [Martin D. Weinberg] -- Mistake in refactoring loop, and missing neutral-electron cross - section. [Martin D. Weinberg] -- Fixed broken selection diagnostic reporting. [Martin D. Weinberg] -- Mistake in nocool correction. [Martin D. Weinberg] -- Removed erroneous no cool correction from energy increments and - decrements. [Martin D. Weinberg] -- Work around for bug in cuda compiler (swap template) and updates for - "no cooling" tests. [Martin D. Weinberg] -- White space change only. [Martin D. Weinberg] -- Added temperature and number fields. [Martin D. Weinberg] -- Make units consistent with Trace method. [Martin D. Weinberg] -- Added ion and electron energy quantiles. [Martin D. Weinberg] -- Added version of pspstat (pspstatT) for new trace method. [Martin D. - Weinberg] -- Added recombination energy conservation for NOCOOL mode. [Martin D. - Weinberg] -- Removed some debugging cruft. [Martin D. Weinberg] -- Removed duplicated pair selection keys. [Martin D. Weinberg] -- Version bump. [Martin D. Weinberg] -- Fixed missing factor of velocity in NTC pair selection algorithm. - [Martin D. Weinberg] -- Increased default energy grid spacing to decrease memory footprint. - [Martin D. Weinberg] -- Implemented refactored algorithm for cuda. [Martin D. Weinberg] -- NTC with no DB enabled by default. [Martin D. Weinberg] -- Code clean up; fixed up per species separation and collision pair - selection; simplified NTC logic a bit. [Martin D. Weinberg] -- Before restructuring CollideIon. [Martin D. Weinberg] -- Templetized NTC in preparation for per-state crossSection returns. - [Martin D. Weinberg] -- Added ionizate state excess handling as an option. [Martin D. - Weinberg] -- Added output for ionization coefficient tally. [Martin D. Weinberg] -- Increased default kmax value. [Martin D. Weinberg] -- Add cuda energy grid parameters to yaml config. [Martin D. Weinberg] -- Change parameter prefix to 'config' [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Updated usage options. [Martin D. Weinberg] -- Added/fixed help strings. [Martin D. Weinberg] -- Updated for current version. [Martin D. Weinberg] -- Change default param file from 'PARAM' to 'PARAM.yml' [Martin D. - Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Another minor format change. [Martin D. Weinberg] -- Output formatting change only. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Simplify VTK version logic. [Martin D. Weinberg] -- Add GIT info verbose option to EXP command line. [Martin D. Weinberg] -- Version bump. [Martin D. Weinberg] -- Reflect git branch and version in verbose flag to exp. [Martin D. - Weinberg] -- Simplify VTK version logic. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Fix VTK version switches in configure.ac. [Martin D. Weinberg] -- Added multiple file parsing. [Martin D. Weinberg] -- Remove test debug Debye length. [Martin D. Weinberg] -- MeanLambda should be inelastic part only. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Removed redundant def. [Martin D. Weinberg] -- Minor changes for debugging and energy conservation checking. [Martin - D. Weinberg] -- Minor fix to energy conservation test. [Martin D. Weinberg] -- Trying to find energy weirdness in cuda version. [Martin D. Weinberg] -- EXP version bump. [Martin D. Weinberg] -- Version bump. [Martin D. Weinberg] -- Added mean-mass computation to psp2histoT* routines. [Martin D. - Weinberg] -- Added version that combines mulitple PSP dumps. [Martin D. Weinberg] -- Throw std::runtime_error rather than std::string to get error printed - on traceback. [Martin D. Weinberg] -- Change default species file name to species.yml for consistence with - makeIonIC. [Martin D. Weinberg] -- Additional doxygen doc strings. [Martin D. Weinberg] -- Rewrote so messages appear on throw. [Martin D. Weinberg] -- Cruft removal and documentation changes. [Martin D. Weinberg] -- Some code readability improvements. [Martin D. Weinberg] -- Increase the maximum grid energy for cuda textures. [Martin D. - Weinberg] -- Updates to cross section tests. [Martin D. Weinberg] -- Documentation only. [Martin D. Weinberg] -- Typo: wrong data type for cuMinMass constant. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Added minimum mass for electron while using the MeanMass variant and - added an additional cuda device check before trying to initialize. - [Martin D. Weinberg] -- Allow multiple MPI processes to use the same GPU. [Martin D. Weinberg] -- Enabled 'ngpus' to be set. [Martin D. Weinberg] -- Some additional sanity checking and apply minimum mass threshold for - MeanMass algorithm. [Martin D. Weinberg] -- Added functions to gather collision type diagnostic output from the - GPU, removed dynamic heap allocation infavor of thrust_device storage, - improved energy conservation checking. [Martin D. Weinberg] -- Added functions to gather collision type diagnostic output from the - GPU, increased output width and removed '|' from *.ION_coll output, - improved energy conservation checking. [Martin D. Weinberg] -- Added functions to gather collision type diagnostic output from the - GPU. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Some additional comments; removal of the velocity upscaling for the - MeanMass algorithm, which is unnecessary and a mistake. [Martin D. - Weinberg] -- Suppress writing of YAML config to standard output unless VERBOSE >= - 7. [Martin D. Weinberg] -- Set nthrds=1 by default. [Martin D. Weinberg] -- Remove debug instance tracking. [Martin D. Weinberg] -- Found what appears to be a stream::close() bug when the stream is - dynamically constructed as a pointer. Work around: remove pointers. - [Martin D. Weinberg] -- Remove pointer to ofstream which seem to have a destructor bug GNU. - [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Removed bad cruft in Trace method that was breaking the heap. [Martin - D. Weinberg] -- Fixed typo in "escape" time step criterion, following Mike. [Martin D. - Weinberg] - - P's head up. -- Add exception handling to collide.effort open; don't persist ntcdb if - use_ntcdb==false. [Martin D. Weinberg] -- Typo fix: IT instead of IE. [Martin D. Weinberg] -- Corrections to number weightings for ionization state changes. [Martin - D. Weinberg] -- Add "nint" alternative to "freq" for setting nint parameter. [Martin - D. Weinberg] -- Minor changes to weightings in Trace method for consistency. [Martin - D. Weinberg] -- Fix initialization in Pord. [Martin D. Weinberg] -- Commented out per process cell count. [Martin D. Weinberg] -- Set KE1 and KE2 arrays to zero on construction. [Martin D. Weinberg] -- Added cell sum diagnostic for deep checking. [Martin D. Weinberg] -- Added divide by zero check for conservation weighting. [Martin D. - Weinberg] -- Formatting upgrades for XC_DEEP9. [Martin D. Weinberg] -- Output formatting change only. [Martin D. Weinberg] -- Debugging updates and bug fix. [Martin D. Weinberg] -- More debugging updates. [Martin D. Weinberg] -- Missing value of inverse molecular weight for ionization updates. - [Martin D. Weinberg] -- Removed some debug output. [Martin D. Weinberg] -- Possible fix to partInteractions main loop and some addition comments. - [Martin D. Weinberg] -- Some addition comments. [Martin D. Weinberg] -- Updates for deferred energy conservation reporting and debugging. - [Martin D. Weinberg] -- Documentation only. [Martin D. Weinberg] -- Updated to allow a multiple input file idiom, e.g.: -f `ls OUT.run.0*` - [Martin D. Weinberg] -- Version bump. [Martin D. Weinberg] -- Added cross-section counters using CUDA atomic operators. [Martin D. - Weinberg] -- Factored species updates from Pord structure. [Martin D. Weinberg] -- Turn off some deep debugging output by default. [Martin D. Weinberg] -- Updated to read yaml species definiton. [Martin D. Weinberg] -- Additional debugging output. [Martin D. Weinberg] -- Updates to elastic collisions. [Martin D. Weinberg] -- Fix typo in symbol memcopy. [Martin D. Weinberg] -- Added Recomb_IP to CollideIon class and apply toggle to cuda - implementation. [Martin D. Weinberg] -- Minor typo fix. [Martin D. Weinberg] -- Additional debugging output. [Martin D. Weinberg] -- Compute crm for cell; additional debugging output. [Martin D. - Weinberg] -- Added flag to use mean interaction velocity from current cell rather - than sample cell. [Martin D. Weinberg] -- Updates for IP values in cuda ion elements. [Martin D. Weinberg] -- Additional comments, removed some old debug output, fixed econs logic - to match serial version. [Martin D. Weinberg] -- Remove unnecessary sanity checks for DATTRIB length. [Martin D. - Weinberg] -- Fixes to energy updates and comment out some deep debugging output. - [Martin D. Weinberg] -- Comment out some deep debugging output. [Martin D. Weinberg] -- Fix logic in dattrib size check. [Martin D. Weinberg] -- Turn off reporting of parallel merge data size. [Martin D. Weinberg] -- Fix sanity check logic error and, add return error return value to - ParticleHtoD, and bump up default attribute size. [Martin D. Weinberg] -- Removed some debug cruft. [Martin D. Weinberg] -- Commented out verbose output. [Martin D. Weinberg] -- Fix typo. [Martin D. Weinberg] -- Enable NTC algorithm without database. [Martin D. Weinberg] -- Enable NTC algorithm without database. [Martin D. Weinberg] -- Forgot to check in changes here. [Martin D. Weinberg] -- Fix for consistency with fortran formats in CHIANTI. [Martin D. - Weinberg] -- Print out info about debug_wait on root node only. [Martin D. - Weinberg] -- Declare output stream outside of restriction to master node. [Martin - D. Weinberg] -- Fix misspelling. [Martin D. Weinberg] -- Version bump. [Martin D. Weinberg] -- Attempt to replace MPI_Abort() by 'MPI_Finalize(); exit()' when - possible. [Martin D. Weinberg] -- DSMC version # bump. [Martin D. Weinberg] -- Fix parsing of new CHIANTI scups files. [Martin D. Weinberg] -- Upgrade from CHIANTI version 7 to version 9. [Martin D. Weinberg] -- Set radiative recombination type before initialization (Duh\!) [Martin - D. Weinberg] -- Additional checks for valid spline vectors in CHIANTI. [Martin D. - Weinberg] -- Additional checks for valid spline vectors in CHIANTI. [Martin D. - Weinberg] -- Additional checks for valid spline vectors in CHIANTI. [Martin D. - Weinberg] -- Generalize spline dimension for CHIANTI fits. [Martin D. Weinberg] -- Fixed physical particle count evaluation and improved Elastic cross - section evalution. [Martin D. Weinberg] -- Added Elastic cross section checks. [Martin D. Weinberg] -- Minor mods to the 'pin' and 'extrapolate' modes for linear - interpolation. [Martin D. Weinberg] -- Debugging output. [Martin D. Weinberg] -- Added FPE trapping support, although the problem that prompted this - was in genIonRecomb which needs cuda initialization support to be used - with a cuda install. [Martin D. Weinberg] -- Turn off cell count output. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Added command line saving and additional output filename options. - [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Fixed typo on vtk file naming. [Martin D. Weinberg] -- Consistent naming and output for pca diagnostics. [Martin D. Weinberg] -- White space change for readability only. [Martin D. Weinberg] -- Added tk_type==None to Cylinder. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Add some temporary debug. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Clean up some old, unneccessary debugging output. [Martin D. Weinberg] -- Fix weights, oops. [Martin D. Weinberg] -- Refactored stride for cells and additional debugging output. [Martin - D. Weinberg] -- Fixes of neutral-ion weights. [Martin D. Weinberg] -- Fixes and updates. [Martin D. Weinberg] -- Added mssaprof diagnostic routine. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Changed cudaParticle references to pointers. [Martin D. Weinberg] -- Removed temporary debug output. [Martin D. Weinberg] -- Updated for setting coefficients from std::vectors. [Martin D. - Weinberg] -- White space change only. [Martin D. Weinberg] -- Fixes to per state numbers for inelastic energy loss/gain. [Martin D. - Weinberg] -- Added Nsel and Tau diagnostics to cuda routine. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Factored Coulombic FP algorithm from hard-inelastic scattering. - [Martin D. Weinberg] -- Refactored for separate Coulomb FP and hard-scattering algorithms. - [Martin D. Weinberg] -- Weight fix. [Martin D. Weinberg] -- Fixed bug in cuda particle key evaluation. [Martin D. Weinberg] -- Turn off extrapolation by default; additional debugging. [Martin D. - Weinberg] -- Added additional debug output. [Martin D. Weinberg] -- Debug output separator. [Martin D. Weinberg] -- Fix debug logic. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Minor clean up for clarity: add default argument for - adjust_multistep_level. [Martin D. Weinberg] -- Include switch between Coulombic and other dominating cross sections. - [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Comments only. [Martin D. Weinberg] -- Remove useless nbodmax sanity check. [Martin D. Weinberg] -- Cleaned up NTVX calls for cuda. [Martin D. Weinberg] -- Version bump. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Cleanup of multistep adjust variant. [Martin D. Weinberg] -- Added feature flat to put multistep adjustment outside of loop. - [Martin D. Weinberg] -- Fixed loop counter logic for new factoring. [Martin D. Weinberg] -- Removed Symmetric_Eigenvalue declarations. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Fixes to debug testing and sanity value checking. [Martin D. Weinberg] -- Missing default parameter. [Martin D. Weinberg] -- Fixed typo. [Martin D. Weinberg] -- Reversed loop order. [Martin D. Weinberg] -- Added new methods to Vector header. [Martin D. Weinberg] -- Output formatting change only. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Fix typo. [Martin D. Weinberg] -- Sanity check on kEi and kEe computation. [Martin D. Weinberg] -- Remove use_cuda; now in global.H. [Martin D. Weinberg] -- Added warning for incomplete convergence in dsyevd. [Martin D. - Weinberg] -- Added additional nan factor checking. [Martin D. Weinberg] -- Additional crs debugging checks toggled by DEBUG_CRS boolean. [Martin - D. Weinberg] -- Added an additional NaN debug statement. [Martin D. Weinberg] -- Change use_cuda logic. [Martin D. Weinberg] -- Updated for Eigen3 compilation of SVD routine. [Martin D. Weinberg] -- Added SVD method for symmetric eigenvalue problem in EmpCylSL. [Martin - D. Weinberg] -- Do not barf if YAML force parameters are missing. [Martin D. Weinberg] -- Fixed ignore_info YAML bug. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Added MPI error handler for debugging. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Added elapsed time to ComponentContainer timing output. [Martin D. - Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Minor updates in timer logic. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Fixed preprocessor for DSMC toggle. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Do not compile and include DSMC by default. [Martin D. Weinberg] -- Divide-by-zero check. [Martin D. Weinberg] -- Increase output precision. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Fixed unintialized coefficient accumulation for quadruature. [Martin - D. Weinberg] -- Use configure to toggle x86_64 specific FPU trapping. [Martin D. - Weinberg] -- Update for VTK 7.1 interface. [Martin D. Weinberg] -- Updated Component for ignore_info restart. [Martin D. Weinberg] -- Documentation only. [Martin D. Weinberg] -- Added runtag variable. [Martin D. Weinberg] -- Zero out character string for YAML conf to prevent EOF issues in - parser. [Martin D. Weinberg] -- Added mpicc and mpiCC to allow wrapper to find mpi.h. [Martin D. - Weinberg] -- Added mpicc and mpiCC to allow wrapper to find mpi.h. [Martin D. - Weinberg] -- Enable trapping with gdb wait. [Martin D. Weinberg] -- Extra diagnostics. [Martin D. Weinberg] -- Comment change only. [Martin D. Weinberg] -- Fixed global variable gaff when converting to boost::program_options. - [Martin D. Weinberg] -- Added progress bar for eof quadrature. [Martin D. Weinberg] -- Updated eof_generate timing diagnostics. [Martin D. Weinberg] -- Fixed split timer updates. [Martin D. Weinberg] -- Added OpenMP support for EmpCylSL. [Martin D. Weinberg] -- Fixed to parallel thread loop for local variables. [Martin D. - Weinberg] -- Added OpenMP support for EmpCylSL. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin Weinberg] -- Added override of .eof read-only enforcement. [Martin D. Weinberg] -- Version bump. [Martin Weinberg] -- Looks like the swap to the new vtk lib format needs to at version 7.0. - [Martin D. Weinberg] -- Add boost system libs to DSMC test routines. [Martin Weinberg] -- VTK 6.1 acts like VTK 6.0; change in configure.ac. [Martin Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin Weinberg] -- More fixes for missing boolean tags. [Martin D. Weinberg] -- Added rotation to orbit diagnostic output. Removed cruft. [Martin D. - Weinberg] -- Added orbit diagnostic output and fixed numdf omission for - SphericalTable df initialization. [Martin D. Weinberg] -- Added monopole computation for relative density field. [Martin D. - Weinberg] -- Added relative density field. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin Weinberg] -- Switch order of boost m4 checks. [Martin Weinberg] -- Multithread basis construction. [Martin D. Weinberg] -- Draft fix of parameter ignore for restart. [Martin D. Weinberg] -- Remove dynamically allocated temporary from coef kernels. [Martin D. - Weinberg] -- Added std::endl to YAML->string write to prevent char overrun on - parsing; this must be a libyaml-cpp bug. [Martin D. Weinberg] -- Missing equal sign in output. [Martin D. Weinberg] -- Only print EOF identification for log in root process. [Martin D. - Weinberg] -- Changed header labels it pcamat files to help prevent confusion. - [Martin D. Weinberg] -- Separate coefficient bootstrap variance from EOF variance - computations. [Martin D. Weinberg] -- Updates for VTK eof basis output. [Martin D. Weinberg] -- Fixes to EOF coefficient output. [Martin D. Weinberg] -- Added EOFTEST. [Martin D. Weinberg] -- Added convariance matrix to pcamat output files. [Martin D. Weinberg] -- Remove deep debug of cylmass accumulation. [Martin D. Weinberg] -- Convert use[] from C-style array to std::vector. [Martin D. Weinberg] -- Fixes for cylmass computation from cuda. [Martin D. Weinberg] -- Fixed typo in unimplemented mixture basis for cuda. [Martin D. - Weinberg] -- Fix level interpolation typo. [Martin D. Weinberg] -- Fixed a typo just introduced. [Martin D. Weinberg] -- Only zero bootstrap on level 0. [Martin D. Weinberg] -- Turn off coefficient dumping. [Martin D. Weinberg] -- Only zero bootstrap on level 0. [Martin D. Weinberg] -- Only zero bootstrap on level 0. [Martin D. Weinberg] -- Missing npca0 parsing. [Martin D. Weinberg] -- Fixed recently introduced error in particle indexing. [Martin D. - Weinberg] -- Need sum over levels for initial prestep. [Martin D. Weinberg] -- Removed commented debugging cruft. [Martin D. Weinberg] -- Removed duplicated inner level loop. [Martin D. Weinberg] -- Fixed one word tipsy mapping in PSP. [Martin D. Weinberg] -- Added VTK locations for non-standard installations. [Martin D. - Weinberg] -- Fix underrun in thrust::transform in bootstrap for small number of - particles per level. [Martin D. Weinberg] -- Comment out 'used' debugging lines. [Martin D. Weinberg] -- Remove unnecessary multistep reset. [Martin D. Weinberg] -- Separate coefficients from acceleration. [Martin D. Weinberg] -- Clean up multistep coefficient call duplication. [Martin D. Weinberg] -- Version bump. [Martin D. Weinberg] -- One more instance of multimap (see previous commit) [Martin D. - Weinberg] -- Use multimap instead of map to prevent replacing duplicate keys in S/N - sort. [Martin D. Weinberg] -- Updated examples directory for YAML config. [Martin D. Weinberg] -- Correct mlevel offset in cuda coefficient kernel. [Martin D. Weinberg] -- Removed a debug DoH copy. [Martin D. Weinberg] -- Additional comments. [Martin D. Weinberg] -- Npca0 parameter is the first pca step. [Martin D. Weinberg] -- Fixed reduce_by_key stride. [Martin D. Weinberg] -- Disable cudaParticle debugging dump. [Martin D. Weinberg] -- Do not call cuda routine for no particles. [Martin D. Weinberg] -- Do not call cuda routine for no particles. [Martin D. Weinberg] -- Show entire particle structure for debugging. [Martin D. Weinberg] -- Fixed SortByLevel ranges for coefficients and acceleration separately. - [Martin D. Weinberg] -- Needed special strided sum reduce for PCA accumulation. [Martin D. - Weinberg] -- Remove deep debug output. [Martin D. Weinberg] -- Put interpolation stepping grid into global. [Martin D. Weinberg] -- Fixed typo in pca inversion. [Martin D. Weinberg] -- More updates for PCA; changed historical versioned filename, - EmpOrth9thd.h/cc, to EmpCyLSL.h/cc. [Martin D. Weinberg] -- More updates for multistepping with pca. [Martin D. Weinberg] -- Debugging updates. [Martin D. Weinberg] -- Added missing LDFLAGS. [Martin D. Weinberg] -- Move 'compute' from static to variable. [Martin D. Weinberg] -- Remove coefJK. [Martin D. Weinberg] -- Minor adjustments to bootstrap variance for accuracy. [Martin D. - Weinberg] -- Updated pcalog labels for consistency between AxisymmetricBasis and - EmpCylSL. [Martin D. Weinberg] -- Fix norms for b_Hall and S/N. [Martin D. Weinberg] -- Fixed mismatched norms in S/N and b_Hall computation. [Martin D. - Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Fixes to Hall computation. [Martin D. Weinberg] -- Added used mass sumation. [Martin D. Weinberg] -- Added used mass sumation. [Martin D. Weinberg] -- Use compute flag for pca rather than (compute & (mlevel==0)) [Martin - D. Weinberg] -- White-space change for readability only. [Martin D. Weinberg] -- Fixed cumulative power computation in pca_hall. [Martin D. Weinberg] -- Fixed more minor mistakes. [Martin D. Weinberg] -- Fixed another typo. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Update pcalog output. [Martin D. Weinberg] -- Fixes for cuda and fixes to real-time Hall filtering. [Martin D. - Weinberg] -- Fixed file name typo. [Martin D. Weinberg] -- Additional info in sanity/error output. [Martin D. Weinberg] -- Allow a subvector to passed to kernel. [Martin D. Weinberg] -- Fixed diag headers. [Martin D. Weinberg] -- Version bump. [Martin D. Weinberg] -- Typo fix. [Martin D. Weinberg] -- Additional parameters to log file. [Martin D. Weinberg] -- Added pcadiag flag. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Missing return type in setTK. [Martin D. Weinberg] -- Added additional selection diagnostics. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Added some thresholding and nan testing in crossSectionTrace. [Martin - D. Weinberg] -- Big PCA clean-up and switched smoothing to modulus. [Martin D. - Weinberg] -- Fixes to Debye computation. [Martin D. Weinberg] -- Added Debye length estimate. [Martin D. Weinberg] -- Allow scalar and vectors in boffset and boxsize config. [Martin D. - Weinberg] -- Updated config for vector-valued boxsize and boffset; removed tubbe - and slab geometry parameters. [Martin D. Weinberg] -- Only call cuda initialize for GPU devices in use. [Martin D. Weinberg] -- Added contraint on number of GPU cards per node. [Martin D. Weinberg] -- Version bump. [Martin D. Weinberg] -- Updates for tk_type setting from yaml config. [Martin D. Weinberg] -- Move a diagnostic structure to global scope to prevent problems with - older g++ versions. [Martin D. Weinberg] -- Use explicit global namespace for isnan to no confuse older versions - of nvcc. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Fixed typo in component parameter parsing. [Martin D. Weinberg] -- Fixed parsing of consp and tidal with yaml. [Martin D. Weinberg] -- Partial implementation of oct-ree in cuda. [Martin D. Weinberg] -- Merge branch 'CUDA_YAML' into CUDA. [Martin D. Weinberg] -- Merge branch 'CUDA_YAML' of https://bitbucket.org/mdweinberg/exp into - CUDA_YAML. [Martin D. Weinberg] -- Draft changes to include covariance matrix in VtkPCA output. [Martin - D. Weinberg] -- Version bump. [Martin D. Weinberg] -- Merge branch 'CUDA_YAML' into CUDA. [Martin D. Weinberg] -- Added cuda implementation for Morton curve generation and sort. - [Martin D. Weinberg] -- Change defaults in pHOT algorithm selection; add additional timing - routines. [Martin D. Weinberg] -- Updates to prevent the needs for multiple pass link and install. - [Martin D. Weinberg] -- Fixed some MPI mistakes that were leading to stack smashing. [Martin - D. Weinberg] -- Updated species config using yaml rather than species.spec file. - [Martin D. Weinberg] -- Updated makeIon for yaml config output. [Martin D. Weinberg] -- Additional debugging. [Martin D. Weinberg] -- Revert to old key computation by default. [Martin D. Weinberg] -- Alternative, faster key computation. [Martin D. Weinberg] -- Fix typo in step size for elastic interpolation. [Martin D. Weinberg] -- Fix fencepost error in elastic interpolation. [Martin D. Weinberg] -- Added CUDA include flag to Makefile.am files. [Martin D. Weinberg] -- Comments only. [Martin D. Weinberg] -- Fixed logic for even-odd particle numbers per cell. [Martin D. - Weinberg] -- Added simpler support for uneven numbers of particles per cell. - [Martin D. Weinberg] -- Update for even and odd per cell particle count. [Martin D. Weinberg] -- Merge branch 'CUDA_YAML' of https://bitbucket.org/mdweinberg/exp into - CUDA_YAML. [Martin D. Weinberg] -- Added separate electron temp to config for Uniform Trace. [Martin D. - Weinberg] -- Fixed config parsing for new YAML db. [Martin D. Weinberg] -- Updates for TreeDSMC config parsing. [Martin D. Weinberg] -- Fixed ignore_info flag. [Martin D. Weinberg] -- Print YAML::Node on YAML::Exception. [Martin D. Weinberg] -- Removal of uint128 types. [Martin D. Weinberg] -- Use YAML rather than JSON. [Martin D. Weinberg] -- Update to allow YAML configuration to be updated at the top level. - [Martin D. Weinberg] -- Allow PSP.cc to try old style PSP info stanza if yaml parsing fails. - [Martin D. Weinberg] -- Override from PSP component parsing from YAML: ignore=true to use - default parameters from config file for old PSP and changing - parameters. [Martin D. Weinberg] -- Typos in paramater parsing. [Martin D. Weinberg] -- Fixed output format. [Martin D. Weinberg] -- Added component name to exception reporting. [Martin D. Weinberg] -- Emit YAML map in flow style. [Martin D. Weinberg] -- Added additional YAML handling to allow user to find config mistakes - more easily. [Martin D. Weinberg] -- Changed extension from .yaml to .yml for conventional consistency. - [Martin D. Weinberg] -- Added missing LDFLAGS for cuda. [Martin D. Weinberg] -- Merge branch 'CUDA_YAML' of https://bitbucket.org/mdweinberg/exp into - CUDA_YAML. [Martin D. Weinberg] -- Allow write_binary to change size of the header info string. [Martin - D. Weinberg] - - to accommodate a large parameter set. -- Allow write_binary to make a larger info string. [Martin D. Weinberg] -- Typo in name for cuda parameter. [Martin D. Weinberg] -- Turn off debugging output. [Martin D. Weinberg] -- Update YAML node on restart. [Martin D. Weinberg] -- Removed some debug lines and added some exception handling. [Martin D. - Weinberg] -- Updates for changed config format. [Martin D. Weinberg] -- Converted from component, output, externan maps to sequence to - preserve order. [Martin D. Weinberg] -- Whitespace only. [Martin D. Weinberg] -- Missing _LDFLAGS for boost. [Martin D. Weinberg] -- Remove references to config. [Martin D. Weinberg] -- Remove ParamDatabase header. [Martin D. Weinberg] -- Readability changes only. [Martin D. Weinberg] -- Removed ParamParse refs. [Martin D. Weinberg] -- Improved readability. [Martin D. Weinberg] -- Improved readability. [Martin D. Weinberg] -- Fixed wrong YAML::Node in Component parameter parsing. [Martin D. - Weinberg] -- Added YAML exception handling. [Martin D. Weinberg] -- Added some error handling for YAML. [Martin D. Weinberg] -- Version bump. [Martin D. Weinberg] -- Missing boost::program_options initialization. [Martin D. Weinberg] -- YAML flag in wrong place. [Martin D. Weinberg] -- Addded more yaml diagnostic. [Martin D. Weinberg] -- Fixed yaml library logic. [Martin D. Weinberg] -- Fixed for YAML. [Martin D. Weinberg] -- Swapped ProgramParam in favor of YAML config. [Martin D. Weinberg] -- Added YAML support. [Martin D. Weinberg] -- Added YAML library checking. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Fix MPI sequencing issue for histogram. [Martin D. Weinberg] -- Fixed definition of numZ for output. [Martin D. Weinberg] -- Added vertical position quantiles to surface output. [Martin D. - Weinberg] -- Updates for basis dump file naming (so that globbing gives numerical - order for viewing. [Martin D. Weinberg] -- Updates to EOF utilities. [Martin D. Weinberg] -- Updated filenames for basis dump. [Martin D. Weinberg] -- Routine to dump eof basis images. [Martin D. Weinberg] -- Added leading # to header lines in output. [Martin D. Weinberg] -- Fixed MeanMass logic, oops. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Fix incorrect comment only. [Martin D. Weinberg] -- Spelling in comment only. [Martin D. Weinberg] -- Version bump. [Martin D. Weinberg] -- Added no-cool option; fixed energy accounting, was missing - superparticle number conversion. [Martin D. Weinberg] -- Additional bug fixes; mostly units. [Martin D. Weinberg] -- Missing units from densQ. [Martin D. Weinberg] -- Remove temporary bypass of diagnostic computation. [Martin D. - Weinberg] -- Fixed diagnostic electron Tau accumulation. [Martin D. Weinberg] -- More information in exception message. [Martin D. Weinberg] -- Spelling correction in comment only. [Martin D. Weinberg] -- Moved to a single species array. [Martin D. Weinberg] -- Added additional NvToolExt timing markers; added flag to suppress GPU - computation in CollideIon for testing. [Martin D. Weinberg] -- Fixed typo on Ivel2, Evel2 access in kernel. [Martin D. Weinberg] -- Get the thrust vectors out of global scope to prevent seg fault on - global dtor call. [Martin D. Weinberg] -- Make fpe_trap grap INVALID FP only. [Martin D. Weinberg] -- Handle out of range values on diagnostic histogram. [Martin D. - Weinberg] -- Don't be chatty if there is no NTC database. [Martin D. Weinberg] -- Additional checks on values. [Martin D. Weinberg] -- Fixes to multi-module linking for nvcc. [Martin D. Weinberg] -- Refactoring of DSMC source organization to avoid dlopen() [Martin D. - Weinberg] -- Some additional debugging. [Martin D. Weinberg] -- Updates to dattrib array handling. [Martin D. Weinberg] -- White space change only. [Martin D. Weinberg] -- Updates for Cuda DSMC. [Martin D. Weinberg] -- Fixed typo for new recombination algorithm (not currently used) - [Martin D. Weinberg] -- Minor updates after visual pass. [Martin D. Weinberg] -- Comments only. [Martin D. Weinberg] -- Remove unused meanM array. [Martin D. Weinberg] -- Merge branch 'master' into CUDA. [Martin D. Weinberg] -- Preliminary implementation of CUDA DSMC; additional development will - take place on the CUDA branch. [Martin D. Weinberg] -- Fixed error in attribute loading logic for cuda ferry. [Martin D. - Weinberg] -- Added CUDA flags to Make as necessary. [Martin D. Weinberg] -- Added more debug info to dlopen(), e.g. so developer can see missing - symbols. [Martin D. Weinberg] -- Added SYNC/BARRIER/SYNC semantic to test NFS flushing. [Martin D. - Weinberg] -- Fixed restart semantics with MPI-IO parameters. [Martin D. Weinberg] -- More clean up of MPI-IO stuff. [Martin D. Weinberg] -- Minor updates to documentation and OutCHKPT consistency. [Martin D. - Weinberg] -- Fixed incorrect location for Indexing() definition in Component. - [Martin D. Weinberg] -- Wrong location for firsttime flag. [Martin D. Weinberg] -- Added index warning for MPI-IO PSP output. [Martin D. Weinberg] -- Updated to write non-sequenced checkpoints using MPI-IO. [Martin D. - Weinberg] -- Added particle buffer size parameter and choice between blocking and - non-blocking writes; not sure why one would use the former but kept - just in case. [Martin D. Weinberg] -- Modified error handler call for MPI-2 API. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Remove debugging cruft. [Martin D. Weinberg] -- Fix restart logic: for OutPSP, each node needs to know nbeg. [Martin - D. Weinberg] -- Updates to MPI-IO implementation: extra documentation, allow number of - aggregators to be set by user, renabled error return testing, disabled - debug dump frequency. [Martin D. Weinberg] -- White space change only. [Martin D. Weinberg] -- Additional notes on OutPSP. [Martin D. Weinberg] -- Additional notes on OutPSP. [Martin D. Weinberg] -- Fixed for MPI-IO with initial dump for testing. [Martin D. Weinberg] -- Version bump. [Martin D. Weinberg] -- White space change only. [Martin D. Weinberg] -- Offset updated in header call. [Martin D. Weinberg] -- Added help info. [Martin D. Weinberg] -- Stage bunches of particles for MPI_File_write. [Martin D. Weinberg] -- Some weird issue with MPI error capture in MPI_File_* [Martin D. - Weinberg] -- Added draft version of MPI PSP writing. [Martin D. Weinberg] -- Added template for reading disk coefficients. [Martin D. Weinberg] -- More fixes cuda/non-cuda toggle. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Changes for CUDA toggle. [Martin D. Weinberg] -- Simplify cuda toggles. [Martin D. Weinberg] -- Various updats for CUDA integration. [Martin D. Weinberg] -- Changes to accommodate DEBUG and CUDA. [Martin D. Weinberg] -- Updates to cross section structures. [Martin D. Weinberg] -- More interim changes to allow device implementation to be called from - cross section kernel. [Martin D. Weinberg] -- Clean up copied files. [Martin D. Weinberg] -- More cross section implementation; need a separate ion-electron cross - section kernel for efficiency, I believe. [Martin D. Weinberg] -- More cross section implementation. [Martin D. Weinberg] -- Working through cross section implementation; need to write a - collision type index function for cuda maptype. [Martin D. Weinberg] -- Half-written cuda port of CollideIon for Trace method. [Martin D. - Weinberg] -- Implemented all four key cross sections. [Martin D. Weinberg] -- Added collisional excitation to cuda test. [Martin D. Weinberg] -- Working version of free-free test routine. [Martin D. Weinberg] -- Updates for cuda cross section test; still more to go before a working - test. [Martin D. Weinberg] -- Add template for cuda cross section test. [Martin D. Weinberg] -- Updates for cuda. [Martin D. Weinberg] -- Fixes to debug output for container changes. [Martin D. Weinberg] -- Missing clean up of atomic_constants.* [Martin D. Weinberg] -- Fix pairs computation in Trace. [Martin D. Weinberg] -- Switch from maximum to mean cross section estimation; median would be - better, but much harder. [Martin D. Weinberg] -- Added parameter defaulting to true for EmpCylSL::setEven(...) [Martin - D. Weinberg] -- Added EVEN_M exclusion to Cylinder and EmpCylSL classes. [Martin D. - Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin Weinberg] -- Updated documentation for Output timer support. [Martin D. Weinberg] -- Added Output timer support using Timer.h class. [Martin D. Weinberg] -- Added EVEN_M toggle. [Martin D. Weinberg] -- Updated probability for number count in recombination and ionization. - [Martin D. Weinberg] -- Fixes for MeanMass recombA tabulation. [Martin D. Weinberg] -- Updated recombination coefficient computation for MeanMass. [Martin D. - Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Minor draft updates for cuda implementation of Ion. [Martin D. - Weinberg] -- Merge branch 'master' into CUDA. [Martin D. Weinberg] -- Begin implemented CUDA version of cross section evaluation. [Martin D. - Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Add default eof cache file. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- More doc updates. [Martin D. Weinberg] -- Additional documentation. [Martin D. Weinberg] -- Cross section timing routine for CPU. [Martin D. Weinberg] -- Cross section timing routine for CPU. [Martin D. Weinberg] -- Additional update. [Martin D. Weinberg] -- Thanks to CCA. [Martin D. Weinberg] -- Web page updates. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Select combinatoric number of pairs for meanmass trace. [Martin D. - Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin Weinberg] -- Added draft logo. [Martin D. Weinberg] -- Merge branch 'master' into CUDA. [Martin D. Weinberg] -- Change 'architectural' to 'code' [Martin D. Weinberg] -- Removed experimental .js script. [Martin D. Weinberg] -- Version bump. [Martin D. Weinberg] -- Merge branch 'CUDA' [Martin D. Weinberg] -- Zero counters in ParticleFerry when position is reset. [Martin D. - Weinberg] -- Example doc. [Martin D. Weinberg] -- Customize html output. [Martin D. Weinberg] -- More doc updates. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Threshold eigenvalues in PCA to prevent NaN Hall values. [Martin D. - Weinberg] -- Comment update. [Martin D. Weinberg] -- Comment about cache file generation. [Martin D. Weinberg] -- Added additional example files. [Martin D. Weinberg] -- Add additional warning about time to compute eof basis. [Martin D. - Weinberg] -- Forgot to add consolidated dsmc documentation. [Martin D. Weinberg] -- Fixed numbered list. [Martin D. Weinberg] -- Fixed typo. [Martin D. Weinberg] -- Web page updates. [Martin D. Weinberg] -- Swap named exceptions. [Martin Weinberg] -- Added sleep and flush to catch stanza in top-level error handler. - [Martin Weinberg] -- Comment updates. [Martin D. Weinberg] -- Comment updates. [Martin D. Weinberg] -- Remove final endl from error messages. [Martin D. Weinberg] -- Fix types. [Martin D. Weinberg] -- Make EXPException implementation header only. [Martin D. Weinberg] -- Version bump. [Martin D. Weinberg] -- Removed C-style exit() in favor of thrown exceptions. [Martin D. - Weinberg] -- Updates to navigation and added stubs for new sections to heop new - users. [Martin D. Weinberg] -- Doc update only. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Updates to output timing info. [Martin Weinberg] -- Remove old Timer.h C-style time implementation in favor std::chrono. - [Martin D. Weinberg] -- Update multistep timing diagnostics. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Test mean KE for Coulombic cross section. [Martin D. Weinberg] -- Missing mass accumulation in speciesGather. [Martin D. Weinberg] -- Added total step timer. [Martin D. Weinberg] -- Another fix to eta logic. [Martin D. Weinberg] -- Fixed eta computation (missing norm) [Martin D. Weinberg] -- Changes to comments only. [Martin D. Weinberg] -- More accurate temperature and energy computation. [Martin D. Weinberg] -- Comments only. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Fixed electron-electron diffusion coefficient. [Martin D. Weinberg] -- Zero out Z value to suppress warning message. [Martin D. Weinberg] -- Fixes for valgrind cleanliness. [Martin D. Weinberg] -- Added default null constructor to KeyConvert. [Martin D. Weinberg] -- Updates for version and Collide class name info. [Martin D. Weinberg] -- Fixed units in electron velocity for mean mass. [Martin D. Weinberg] - - electron-electron scattering. -- Minor updates and comments for Mean-Mass Algorithm. [Martin D. - Weinberg] -- Increaes the default MPI buffer sizxe. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Fixed missing LMAX entry in program options. [Martin D. Weinberg] -- More logic fixes to gendisk2. [Martin D. Weinberg] -- Fixed typo in stream class type. [Martin D. Weinberg] -- Allow cache file name to be specified. [Martin D. Weinberg] -- Updated control logic for cache files. [Martin D. Weinberg] -- More cleanup. [Martin D. Weinberg] -- More clean ups. [Martin D. Weinberg] -- Added multithreading to EmpCylSL and SphericalSL for gendisk. [Martin - D. Weinberg] -- Added a 'report' flag. [Martin D. Weinberg] -- Enforce minimum energy to prevent off grid evaluation. [Martin D. - Weinberg] -- Rewrote GridDebug stanzas for readability. [Martin D. Weinberg] -- Turn off GridDebug flag. [Martin D. Weinberg] -- Switch from map to vector for atomic_weights to improve performance. - [Martin D. Weinberg] -- Replaced std::map with std::vector for hCross. [Martin D. - Weinberg] -- Updated counter types for grid debugging. [Martin D. Weinberg] -- More cross section grid debugging info. [Martin D. Weinberg] -- Removed unused variables. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Added toggles for collisional excitation and ionization grids. [Martin - D. Weinberg] -- Rescale electron balistic velocity for cross section computation. - [Martin D. Weinberg] -- Turned off xs value debugging. [Martin D. Weinberg] -- Added cross section gridding for collisional excitation and - ionization. [Martin D. Weinberg] -- Updates for MeanMass algorithm for electrons. [Martin D. Weinberg] -- Fix particle number weighting. [Martin D. Weinberg] -- Another fix for mean-mass temperature computation. [Martin D. - Weinberg] -- Fix for mean-mass temperature computation. [Martin D. Weinberg] -- Fix for mean-mass temperature computation. [Martin D. Weinberg] -- Fixes for mean-mass initialization. [Martin D. Weinberg] -- Update for mean-mass algorithm. [Martin D. Weinberg] -- Added emacs C++ tags to cuda files. [Martin D. Weinberg] -- Added implementation of mean-mass algorithm. [Martin D. Weinberg] -- Minor fixes to trace version of histo output. [Martin D. Weinberg] -- Fixed electron prob for Coulombic scattering. [Martin D. Weinberg] -- Added variance computation to tau diagnostic output. [Martin D. - Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Updates for SSA wake info. [Martin D. Weinberg] -- Enabled setting coefficients in EmpCylSL. [Martin D. Weinberg] -- Added profile output using a time series of coefficients. [Martin D. - Weinberg] -- Adjustments to Makefile.am for consistency with Flatiron. [Martin - Weinberg] -- Simplified cuda SM string configuration. [Martin D. Weinberg] -- Added CUDA sm arch string to configuration. [Martin D. Weinberg] -- Added 'safe cuda call' for MPI. [Martin D. Weinberg] -- Updated diagnostic stdout info to include component name for cuda - init. [Martin D. Weinberg] -- Added additional cuda initialization checks. [Martin D. Weinberg] -- Additional limit checks. [Martin D. Weinberg] -- Fixed extremal values. [Martin D. Weinberg] -- Removed unused Bounds.cuH. [Martin Weinberg] -- Added additional lib paths for standard cuda installations in m4 - macro. [Martin Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Don't need the hand-rolled binary search any longer. [Martin D. - Weinberg] -- Launch a single thread to compute lower and upper bounds using thrust - on the user thread. [Martin D. Weinberg] -- Restore blocking on component streams until thrust binary search bug - is fixed. [Martin D. Weinberg] -- Use percentages for adjust stat output. [Martin D. Weinberg] -- Added a message pragma for the ZeroAcc return. [Martin D. Weinberg] -- Use non-blocking stream creation by default. [Martin D. Weinberg] -- Removed debugging cruft. [Martin D. Weinberg] -- Added CPP toggles for previously missed CUDA code. [Martin D. - Weinberg] -- Only node zero writes timing info. [Martin D. Weinberg] -- Added CPP timing toggle to Run() method. [Martin D. Weinberg] -- Added CPP timing toggle to Run() method. [Martin D. Weinberg] -- Removed commented out debugging. [Martin D. Weinberg] -- Fixes to PartPtr implementation. [Martin D. Weinberg] -- Version bump. [Martin D. Weinberg] -- Initial attempt at converting Particle to Particle shared pointers. - [Martin D. Weinberg] -- Remove erroneous resize of host_particles vector. [Martin D. Weinberg] -- Updated bunch size logic; this should have been done at the same time - as cudaSphericalBasis. [Martin D. Weinberg] -- Updates; still some error in SphericalBasis somewhere. [Martin D. - Weinberg] -- Added width control to particle output. [Martin D. Weinberg] -- Added reduced version of coefficient debugging output. [Martin D. - Weinberg] -- Decrease field width. [Martin D. Weinberg] -- Decrease field width. [Martin D. Weinberg] -- Added level to particle diagnostic output. [Martin D. Weinberg] -- Implementation of cyclic storage for asynchronous kernel computation. - [Martin D. Weinberg] -- Added flag to allow C++ constexpr in device code. [Martin D. Weinberg] -- Fixes to replace broken thrust upper/lower bound methods. [Martin D. - Weinberg] -- Remove broken copy constructors from circular iterator template. - [Martin D. Weinberg] -- Added upper/lower bounds routine because the thrust version does not - work with streams. [Martin D. Weinberg] -- Added comments. [Martin D. Weinberg] -- Commented out stream usage by thrust::binary_search routines, which - seem to be failing. [Martin D. Weinberg] -- Moved cuda implementation to cudaComponent.cu. [Martin D. Weinberg] -- Added circular/cyclic iterator template. [Martin D. Weinberg] -- Turn off texture debugging output. [Martin D. Weinberg] -- Added a templatized cyclical iterator. [Martin D. Weinberg] -- Updated ZeroPotAccel for CUDA, but include null return for now since - this duplicates effort on host. [Martin D. Weinberg] -- Test code for multiple streams to improve I/O concurrency. [Martin D. - Weinberg] -- Preliminary implementation of staging batches of particles for the - cuda device. [Martin D. Weinberg] -- Reordered NVCC_CXXFLAGS. [Martin D. Weinberg] -- Replace defines for machine constnats by constexpr. [Martin D. - Weinberg] -- Use configure variables for blas. [Martin D. Weinberg] -- Use std::numeric_limits instead of C defines. [Martin D. Weinberg] -- Missing support file for nv trace. [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Merge branch 'CUDA' of http://bitbucket.com/mdweinberg/EXP into CUDA. - [Martin D. Weinberg] -- Zero coefficients for zero-particle levels. [Martin D. Weinberg] -- Remove additional preprocessor in favor of _intended_ null - constructor. [Martin D. Weinberg] -- Need additional preprocessor logic to hide NV profiling. [Martin D. - Weinberg] -- Added missing CUDA local header. [Martin D. Weinberg] -- Added space reserve on CUDA board to reduce allocation volatility; - turn off coefficient debugging. [Martin D. Weinberg] -- Increased precision for table check; added epsilon based tolerance. - [Martin D. Weinberg] -- Increased precision for coefficient and acceleration test output; make - table radius check in cudaCylinder agree with CPU version. [Martin D. - Weinberg] -- Leave table comparison *on* for now. [Martin D. Weinberg] -- Added axis orientation correction to cudaCylinder. [Martin D. - Weinberg] -- Fixes for single/double precision switch. [Martin D. Weinberg] -- Old cruft removed. [Martin D. Weinberg] -- Several missed verbose output statements flagged. [Martin D. Weinberg] -- Range checks; fixed confusion in cudaCylinder over spherical and - cylindrical radius. [Martin D. Weinberg] -- Code clean up; added flag to suppress diagnostic table output. [Martin - D. Weinberg] -- Zero coefficient contribution from out-of-bounds particles. [Martin D. - Weinberg] -- Move allocation of device worksapce into calling class for efficiency. - [Martin D. Weinberg] -- White space changes only. [Martin D. Weinberg] -- Beginning of documents changes. [Martin D. Weinberg] -- Use sine/cosine recursion in spherical force. [Martin D. Weinberg] -- Fixed swapped real4/real8 statements in texture load. [Martin D. - Weinberg] -- Added switch for single/double precision. [Martin D. Weinberg] -- Fixed a texture lookup typo, implemented a full comparsion between - host and device table values, other minor clean up. [Martin D. - Weinberg] -- Removed shadowed parameters. [Martin D. Weinberg] -- Updates for double. [Martin D. Weinberg] -- Fixes for component interaction. [Martin D. Weinberg] -- Added various NVTX annotations for nvprof profiling. [Martin D. - Weinberg] -- Fix the intercomponent forces. [Martin D. Weinberg] -- Remove debug messages about level skipping. [Martin D. Weinberg] -- Fixed mistake in level specification for cuda coefficient - determination. [Martin D. Weinberg] -- Bug fixes and removal of debugging output. [Martin D. Weinberg] -- Another rework of intercomponent particle copying. [Martin D. - Weinberg] -- Suppress GPU timer if cuda is not used. [Martin D. Weinberg] -- Bumped up tolerance for Legendre derivatives, added switch to suppress - cuda methods even if cuda is available. [Martin D. Weinberg] -- Fixes for single-precision Legendre derivatives and intercomponent - interactions. [Martin D. Weinberg] -- Provide message on successful fpe isntall. [Martin D. Weinberg] -- Added particle count for coefficient determination. [Martin D. - Weinberg] -- Simplified timing output. [Martin D. Weinberg] -- Added switch for external potential accumulation. [Martin D. Weinberg] -- Additional timing diagnostics. [Martin D. Weinberg] -- Additional fixes and diagnostics; still seems to be a cuda memory - issue somewhere. [Martin D. Weinberg] -- Fixed coefficient logic. [Martin D. Weinberg] -- Fixes to scope and logic for live cuda candidate. [Martin D. Weinberg] -- Changes for CUDA force switch. [Martin D. Weinberg] -- Added energy histogram for trace species method. [Martin D. Weinberg] -- Updates for running CUDA coefficient and force determination *live - mode* [Martin D. Weinberg] -- Merge branch 'CUDA' of https://bitbucket.org/mdweinberg/exp into CUDA. - [Martin D. Weinberg] -- Turned off verbose debugging output. [Martin D. Weinberg] -- Compute cuda test before cpu test in SphericalBasis for force - comparison. [Martin D. Weinberg] -- Center fixes. [Martin D. Weinberg] -- Updates for Component centering on the CUDA side. [Martin D. Weinberg] -- Remove stray character. [Martin D. Weinberg] -- Modifications for 3D texture. [Martin D. Weinberg] -- Updates for candidate _real_ cuda implementation. [Martin D. Weinberg] -- Updates for candidate _real_ cuda implementation. [Martin D. Weinberg] -- White space change only. [Martin D. Weinberg] -- Flagged out debugging sanity checkes. [Martin D. Weinberg] -- Fixed typo in force evaluation. [Martin D. Weinberg] -- Comment out some debugging. [Martin D. Weinberg] -- White space change only. [Martin D. Weinberg] -- Version bump. [Martin D. Weinberg] -- Implementation of Cylinder coefficient accumulation and force - evaluation for testing and timing. [Martin D. Weinberg] -- Zero acceleration in cuda_particles for each component. [Martin D. - Weinberg] -- Added cuda compile flags, although not used in src/user at this point. - [Martin D. Weinberg] -- Preliminary CUDA implementation for the Cylinder class; untested, - compiles only. [Martin D. Weinberg] -- Additional force checks. [Martin D. Weinberg] -- Force evaluation and testing; moved global class instances into - main() to prevent breaking CUDA context which prevents profiling. - [Martin D. Weinberg] -- Implemented but did not test a force computation; coefficient - computation is working. [Martin D. Weinberg] -- Fixes to preliminary version; something odd with the thrust destructor - that needs to be fixed. [Martin D. Weinberg] -- Additional fixes and debugging; looks like I've messed up the Legendre - function computation. [Martin D. Weinberg] -- Added toggles for CUDA headers. [Martin D. Weinberg] -- Various dumb-ass workarounds for CUDA's lack of a viable linker for - device addresses. Sigh. [Martin D. Weinberg] -- Merge cuda timer into cudaUtil.H. [Martin D. Weinberg] -- Copy particles for testing fro host to cuda in SphericalBasis. [Martin - D. Weinberg] -- Initial implementation of a CUDA-based coefficient determination for - SphericalBasis for testing only; it compiles but almost sure has bugs. - [Martin D. Weinberg] -- Initial implementation of CUDA detection complete. [Martin D. - Weinberg] -- Stub for CUDA compilation test; to be removed later. [Martin D. - Weinberg] -- Added CUDA detection to configure. [Martin D. Weinberg] -- Updates for Ubuntu 18.04. [Martin D. Weinberg] -- Set precision for pcamat. [Martin D. Weinberg] -- Typo in pcamat header fixed. [Martin D. Weinberg] -- Added transformation matrix output. [Martin D. Weinberg] -- Added additional tests fields and cumulative var. [Martin D. Weinberg] -- Merge branch 'newTrace' of https://bitbucket.org/mdweinberg/exp into - newTrace. [Martin D. Weinberg] -- Added AlgOrth to scatterTrace. [Martin D. Weinberg] -- Change jackknife partition to modulus for better load balancing and - fix pca initialization logic. [Martin D. Weinberg] -- Change jackknife partition to modulus for better load balancing. - [Martin D. Weinberg] -- Remove redundant pcaorig flag. [Martin D. Weinberg] -- Missing toggle for Hall smoothing. [Martin D. Weinberg] -- Merge branch 'newTrace' of https://bitbucket.org/mdweinberg/exp. - [Martin D. Weinberg] -- Improved curve-fit, added datafile output. [Martin D. Weinberg] -- Added header for Eagle. [Martin D. Weinberg] -- Merge branch 'newTrace' of https://bitbucket.org/mdweinberg/exp into - newTrace. [Martin D. Weinberg] -- Changed diagnostic header only. [Martin D. Weinberg] -- Added coefficient smoothing type to Cylinder. [Martin D. Weinberg] -- PCA Hall computation updated for Cylinder. [Martin D. Weinberg] -- Added VTK coefficient output files to Cylinder. [Martin D. Weinberg] -- Merge branch 'newTrace' of https://bitbucket.org/mdweinberg/exp into - newTrace. [Martin D. Weinberg] -- Merge branch 'newTrace' of https://bitbucket.org/mdweinberg/exp into - newTrace. [Martin D. Weinberg] -- Merge branch 'newTrace' of https://bitbucket.org/mdweinberg/exp into - newTrace. [Martin D. Weinberg] -- Merge branch 'newTrace' of https://bitbucket.org/mdweinberg/exp into - newTrace. [Martin D. Weinberg] -- Added cstring header for memcpy. [Martin D. Weinberg] -- Merge branch 'newTrace' [Martin D. Weinberg] -- Added sequence # to reduced particle structure. [Martin D. Weinberg] -- Fixed new accumulate call with sequence # [Martin D. Weinberg] -- Merge branch 'newTrace' of https://bitbucket.org/mdweinberg/exp. - [Martin D. Weinberg] -- New jack knife variane estimate for Hall smoothing. [Martin D. - Weinberg] -- Merge branch 'newTrace' of https://bitbucket.org/mdweinberg/exp. - [Martin D. Weinberg] -- Clean-up of PCA algorithm. [Martin D. Weinberg] -- Additional exploration of basis map using Hall smoothing. [Martin D. - Weinberg] -- Added VTK output for PCA for tests and visualization. [Martin D. - Weinberg] -- Clean up electron temperature diagnostic output. [Martin D. Weinberg] -- Fix molecular weight computation for new version. [Martin D. Weinberg] -- Typo in electron mass, ooops. [Martin D. Weinberg] -- Cruft removal. [Martin D. Weinberg] -- Version bump. [Martin D. Weinberg] -- Merge of newTrace branch with master. [Martin D. Weinberg] -- Removed crufty SendParticle and RecvParticle routines from - ParticleFerry. [Martin D. Weinberg] -- Documentation changes only. [Martin D. Weinberg] -- Missing initialization of ParticleFerry from binary. [Martin D. - Weinberg] -- Return ParticleFerry to production, not debug status. [Martin D. - Weinberg] -- Remove MPI_Datatype in favor of raw byte buffer in ParticleFerry (BIG - CHANGE, needs testing) [Martin D. Weinberg] -- Fixed typo in CHIANI file suffix. [Martin D. Weinberg] -- Consolidation of CHIANTI filename parsing. [Martin D. Weinberg] -- Fix typo. [Martin D. Weinberg] -- Fixed typo in secondaryScatter. [Martin D. Weinberg] -- Merge branch 'newTrace' of https://bitbucket.org/mdweinberg/exp into - newTrace. [Martin D. Weinberg] -- Weighting update for secondaryScatter. [Martin D. Weinberg] -- Updated makeIon for logN abundance specification. [Martin D. Weinberg] -- Added electron to PeriodicTable as atomic number 0. [Martin D. - Weinberg] -- Fixed typo in MPI target for dumpFrontier; return pHOT flags to - production status. [Martin D. Weinberg] -- Updates to dumpFrontier. [Martin D. Weinberg] -- Add min/max to dumpFrontier. [Martin D. Weinberg] -- Added frontier diagnostic output. [Martin D. Weinberg] -- Added slab geometry. [Martin D. Weinberg] -- Put 'log' in field label when using logE option. [Martin D. Weinberg] -- Clear counters between files. [Martin D. Weinberg] -- Fixed output axis knots. [Martin D. Weinberg] -- Added PVD creation to psp2eHisto. [Martin D. Weinberg] -- Added option to scale logarithmically in energy. [Martin D. Weinberg] -- Fixed input flags. [Martin D. Weinberg] -- Merge branch 'newTrace' of https://bitbucket.org/mdweinberg/exp into - newTrace. [Martin D. Weinberg] -- Remove testing warnings and cruft from trace implementation. [Martin - D. Weinberg] -- Added psp2eHisto for processing a planar DSMC interface. [Martin D. - Weinberg] -- Updated makeIon for interface ICs. [Martin D. Weinberg] -- Updates for temperature overrides. [Martin D. Weinberg] -- Fixed typo in scatterTrace. [Martin D. Weinberg] -- Change reporting of rcmbScale. [Martin D. Weinberg] -- More updates to recombination count histogram. [Martin D. Weinberg] -- Updates to rcmbTotl implementation. [Martin D. Weinberg] -- Promoted rcmbTotl counter to double and added weights. [Martin D. - Weinberg] -- Merge branch 'newTrace' of https://bitbucket.org/mdweinberg/exp into - newTrace. [Martin D. Weinberg] -- Remove debug output. [Martin D. Weinberg] -- Fix MPI stupidity in rcmbTotlGet routine usage. [Martin D. Weinberg] -- More updates to recombination count histogram. [Martin D. Weinberg] -- Fixes for recombination count histogram. [Martin D. Weinberg] -- Merged fix to histogram trim for recombination distribution. [Martin - D. Weinberg] -- Added recombination count histogram. [Martin D. Weinberg] -- Log scale recombination energy. [Martin D. Weinberg] -- Added runtag to title. [Martin D. Weinberg] -- Fixed KE check for trace. [Martin D. Weinberg] -- Added comments. [Martin D. Weinberg] -- Additional comments and white space changes. [Martin D. Weinberg] -- Fixed journal reference. [Martin D. Weinberg] -- Added comments only. [Martin D. Weinberg] -- Fixes to normalization. [Martin D. Weinberg] -- Version of psp_dist that bins energy distribution in log E. [Martin D. - Weinberg] -- Version bump. [Martin D. Weinberg] -- Change to y-axis label. [Martin D. Weinberg] -- Merged scatterTrace methods. [Martin D. Weinberg] -- White-space change only; energy conservation checks okay. [Martin D. - Weinberg] -- Added energy conservation algorithm to Trace method. [Martin D. - Weinberg] -- Added algorithm test flags to JSON config file. [Martin D. Weinberg] -- Fixed elec_balance usage with TRACE_ELEC. [Martin D. Weinberg] -- Additional updates for electron energy tracking. [Martin D. Weinberg] -- Fixed logic in 'plotem' routine. [Martin D. Weinberg] -- Fixed typo in electron velocity dispersion computation. [Martin D. - Weinberg] -- Merge branch 'newTrace' of https://bitbucket.org/mdweinberg/exp into - newTrace. [Martin D. Weinberg] -- Added option for separate ionization equilibrium. [Martin D. Weinberg] -- Option to change % fraction scale. [Martin D. Weinberg] -- Fix stupid fencepost error. [Martin D. Weinberg] -- Plot binned distribution automatically; fixed type assignment. [Martin - D. Weinberg] -- Add plotting routine 'helper' for *.ION_coll files. [Martin D. - Weinberg] -- Added energy loss tabulation for NOCOOL. [Martin D. Weinberg] -- Version bump. [Martin D. Weinberg] -- Removed egrid and effsteps (cruft) [Martin D. Weinberg] -- A few updates to cache methods. [Martin D. Weinberg] -- Added log diags for Ion cache methods. [Martin D. Weinberg] -- Minor debug fixes to array cache version. [Martin D. Weinberg] -- Added grid eval for radiative recombination and free-free. [Martin D. - Weinberg] -- Added checks to NTC gather. [Martin D. Weinberg] -- Correction to electron temp computation. [Martin D. Weinberg] -- Added electron dispersion temperature to output. [Martin D. Weinberg] -- Temporary test non-dispersion based energy for electron temperature - computation. [Martin D. Weinberg] -- Merge branch 'newTrace' of https://bitbucket.org/mdweinberg/exp into - newTrace. [Martin D. Weinberg] - - Conflicts: - utils/PhaseSpace/pspstatS.cc -- Additional electron scattering diagnostic. [Martin D. Weinberg] -- Old unchecked-in update. [Martin D. Weinberg] -- Added some support for trace elements. [Martin D. Weinberg] -- Additional support for DSMC trace method. [Martin D. Weinberg] -- Added option to suppress inelastic upscaling. [Martin D. Weinberg] -- Allow collLim output for Trace method. [Martin D. Weinberg] -- Fix CS sanity check for use_ntcdb=false; only affects log output. - [Martin D. Weinberg] -- Allow suppression of ntc db for electrons, too. [Martin D. Weinberg] -- Fix logic error for ntc db suppression. [Martin D. Weinberg] -- Fixes to NTC no-database test. [Martin D. Weinberg] -- Add missing exclusions for use_ntbdb. [Martin D. Weinberg] -- Added ntcdb override. [Martin D. Weinberg] -- Include NTC parameters in initial parameter inventory. [Martin D. - Weinberg] -- Added additional quantile values. [Martin D. Weinberg] -- Version bump. [Martin D. Weinberg] -- Added user control NTC threshold. [Martin D. Weinberg] -- Fixes to NTC. [Martin D. Weinberg] -- Merge branch 'newTrace' of https://bitbucket.org/mdweinberg/exp into - newTrace. [Martin D. Weinberg] -- Added z=0.1 and z=1.1 toggle. [Martin D. Weinberg] -- Fix weighting error in recombA computation; StatsMPI class. [Martin D. - Weinberg] -- Version bump. [Martin D. Weinberg] -- Update trace algorithm for interaction counting. [Martin D. Weinberg] -- Removed deprecated dynamic exception specification. [Martin D. - Weinberg] -- Removed deprecated dynamic exception specification. [Martin D. - Weinberg] -- Removed deprecated dynamic exception specification. [Martin D. - Weinberg] -- Merge branch 'newTrace' of https://bitbucket.org/mdweinberg/exp into - newTrace. [Martin D. Weinberg] -- Version bump. [Martin D. Weinberg] -- Fixed error in update algorithm. [Martin D. Weinberg] -- Updated old version to read coefficient.dat file. Fixed doc string - typos. [Martin D. Weinberg] -- Fixes to electron EPSM. [Martin D. Weinberg] -- Added photoIB atomic number counts to output. [Martin D. Weinberg] -- Added total number of photoionized atoms to photoIB diagnostics for - comparison with ION_coll. [Martin D. Weinberg] -- Fixed initial cross section typo. [Martin D. Weinberg] -- Add BINARY archive by default. [Martin D. Weinberg] -- More updates to maxAge handling. [Martin D. Weinberg] -- Add value to adjust NTC::maxAge and toggle Collide::ageout. [Martin D. - Weinberg] -- Add flag to turn of ageOut by default. [Martin D. Weinberg] -- Added Mike P's new version. [Martin D. Weinberg] -- Simplified StatsMPI implementation. [Martin D. Weinberg] -- Upgrades for Python3. [Martin D. Weinberg] -- Upgrades for Python3. [Martin D. Weinberg] -- Added no-inline-small-functions option for boost::serialzation. - [Martin D. Weinberg] -- Log output labeling change only. [Martin D. Weinberg] -- Use updating function of std::map::erase. [Martin D. Weinberg] -- Turn off debugging output. [Martin D. Weinberg] -- Fix ageout() function. [Martin D. Weinberg] -- Remove verbose debug output. [Martin D. Weinberg] -- Fixed typo in ionization and recombination energy check. [Martin D. - Weinberg] -- Version bump. [Martin D. Weinberg] -- Add cache cleaning to NTC data base. [Martin D. Weinberg] -- Added some verbose debugging statements. [Martin D. Weinberg] -- Remove verbose debugging statement. [Martin D. Weinberg] -- Added some verbose debugging statements. [Martin D. Weinberg] -- Removed some deep debug statements and updated ntc selection for - electrons in finalize_cell. [Martin D. Weinberg] -- Fixed error in new quantile selection. Ooops! [Martin D. Weinberg] -- Debugging weird electron scattering problem still. [Martin D. - Weinberg] -- Added some deep debugging for electron scattering algorithms. [Martin - D. Weinberg] -- Merge branch 'newTrace' of https://bitbucket.org/mdweinberg/exp into - newTrace. [Martin D. Weinberg] -- Change output normalization. [Martin D. Weinberg] -- Missing factor of 4 for Coulombic cross section for electrons. [Martin - D. Weinberg] -- Fixed merge problems. [Martin D. Weinberg] -- Merged. [Martin D. Weinberg] -- Added CHIANTI solutions for coefficients. [Martin D. Weinberg] -- Update checks and output on photo IB equilbrium codes. [Martin D. - Weinberg] -- Rename weight variable for clarity. [Martin D. Weinberg] -- Merge branch 'newTrace' of https://bitbucket.org/mdweinberg/exp into - newTrace. [Martin D. Weinberg] -- This iteration method is stable for all densities. [Martin D. - Weinberg] -- Allow electron velocity position to vary. [Martin D. Weinberg] -- Enhance photoStat reporting. [Martin D. Weinberg] -- Fixed MPI typo; improved photoIB output control for stats. [Martin D. - Weinberg] -- Fixed minor bug. [Martin D. Weinberg] -- Updated photoStat accumulator. [Martin D. Weinberg] -- Added particle photon time stamps. [Martin D. Weinberg] -- Added per collision photoionization method. [Martin D. Weinberg] -- Diagnostic output for photo IB values. [Martin D. Weinberg] -- Merge branch 'newTrace' of https://bitbucket.org/mdweinberg/exp into - newTrace. [Martin D. Weinberg] -- New initialization mode for photoionization equilibrium tests. [Martin - D. Weinberg] -- Diagnostic output formating change only. [Martin D. Weinberg] -- Remove test output. [Martin D. Weinberg] -- Updated trace species histogram output. [Martin D. Weinberg] -- Clean up diagnostic counters on command. [Martin D. Weinberg] -- Merge branch 'newTrace' of https://bitbucket.org/mdweinberg/exp into - newTrace. [Martin D. Weinberg] -- Added trace fraction histogram for diagnostics. [Martin D. Weinberg] -- Clear diagnostic recomb counters after every step. [Martin D. - Weinberg] -- Added map clear and documentation to photoW. [Martin D. Weinberg] -- Remove debugging lines. [Martin D. Weinberg] -- Added diagnostic file for photoionization. [Martin D. Weinberg] -- Fixed typo. [Martin D. Weinberg] -- Merge branch 'newTrace' of https://bitbucket.org/mdweinberg/exp into - newTrace. [Martin D. Weinberg] - - Conflicts: - src/pCell.cc - src/user/Collide.cc -- Remove deep debug lines. [Martin D. Weinberg] -- Initialize cell time in infinite past. [Martin D. Weinberg] -- Add time stamp to cell interaction; better rounding for pair - generation. [Martin D. Weinberg] -- Time tracking for cell interactions. [Martin D. Weinberg] -- Added flag to dump PSP as in input file for EXP. [Martin D. Weinberg] -- Update for enum. [Martin D. Weinberg] -- Merge branch 'newTrace' of https://bitbucket.org/mdweinberg/exp into - newTrace. [Martin D. Weinberg] -- Restored the energy transfer Coulombic cross section scaling. [Martin - D. Weinberg] -- Fixed minimum Coulombic cross section default. [Martin D. Weinberg] -- Added per step mean electron MFP output; toggle minimum Coulombic - cross section to interparticle spacing (off by default now) [Martin D. - Weinberg] -- Added recombination energy histogram. [Martin D. Weinberg] -- Added multiple plot type selection. [Martin D. Weinberg] -- Allow more types of curve fitting. [Martin D. Weinberg] -- Recombination and photoionization cofficients can be written to - std::out for debugging. [Martin D. Weinberg] -- Fix up energy computation for 'interact' type. [Martin D. Weinberg] -- Add variable specification for Haart and Madau spectral flux form. - [Martin D. Weinberg] -- Make executable. [Martin D. Weinberg] -- Added plotting routine for combining energy distributions from PSP - files. [Martin D. Weinberg] -- Revert "Added interval reporting for diagDist" [Martin D. Weinberg] - - This reverts commit ad52d9a1b7827d5efd760d8cad18fb37acd3db1a. -- Revert "Added interval reporting for diagDist" [Martin D. Weinberg] - - This reverts commit 6b1b627fc5da2a8c89fd8e82342d5f20d2e41542. -- Added interval reporting for diagDist. [Martin D. Weinberg] -- Added interval reporting for diagDist. [Martin D. Weinberg] -- Output changes only. [Martin D. Weinberg] -- Missing endl. [Martin D. Weinberg] -- Add photoionization type to algorithm list. [Martin D. Weinberg] -- Use Haardt and Madau values at 1 Ryd. [Martin D. Weinberg] -- Quasar exponent and value following Haardt and Madau (2012) [Martin D. - Weinberg] -- Fixed photoionization overcounting by moving interaction to - finalize_cell. [Martin D. Weinberg] -- For recombination coefficient estimation. [Martin D. Weinberg] -- Added time-step diagnostics to photoionization. [Martin D. Weinberg] -- Added error checking output in tracePhotoScatter. [Martin D. Weinberg] -- Fixed energy conservation in scatterPhotoTrace. [Martin D. Weinberg] -- More updates for scatterPhotoTrace. [Martin D. Weinberg] -- Photoionization updates. [Martin D. Weinberg] -- Partial implementation of photoionization by a background. [Martin D. - Weinberg] -- Missing endl. [Martin D. Weinberg] -- Changed tolCS default. [Martin D. Weinberg] -- Make cross-section sanity check a configurable value. [Martin D. - Weinberg] -- Fix missing initialization. [Martin D. Weinberg] -- Fix typo. [Martin D. Weinberg] -- Additional selection debug counters. [Martin D. Weinberg] -- Fixed auto ptr problem that I introduced several days ago. [Martin D. - Weinberg] -- White space for readability. [Martin D. Weinberg] -- Remove some chatty debugging output. [Martin D. Weinberg] -- Turn off NTC dump for debugging by default. [Martin D. Weinberg] -- Added time stamps to NTC quantile data for improved synchronization. - [Martin D. Weinberg] -- Added dump() for debugging saved and restored values. [Martin D. - Weinberg] -- Set current time in serialized NTC db. [Martin D. Weinberg] -- Need #include for gcc 4.9. [Martin D. Weinberg] -- Doc changes. [Martin D. Weinberg] -- Attempt to fix NTC serialization logic error by putting Quantile - objects in a container for control. Needs debugging test. [Martin D. - Weinberg] -- Added Quantile container for improved Quantile serialization and - accuracy. [Martin D. Weinberg] -- Version bump. [Martin D. Weinberg] -- White space changes only. [Martin D. Weinberg] -- Correct number weighted fractions. [Martin D. Weinberg] -- Remove debugging cruft. [Martin D. Weinberg] -- Use number fraction not mass fraction in cross-section weighting. - [Martin D. Weinberg] -- Update to electron number count computation for Trace. [Martin D. - Weinberg] -- Changed default range for free-free wavelengths. [Martin D. Weinberg] -- Make mu scaling a parameter. [Martin D. Weinberg] -- Remove cruft from mu map tests. [Martin D. Weinberg] -- Updates to c_r upscaling based on interaction energy for subspecies. - [Martin D. Weinberg] -- Velocity factor updates based on subspecies reduced mass. [Martin D. - Weinberg] -- Double counting fix for Trace. [Martin D. Weinberg] -- Typo in parameter output fixed. [Martin D. Weinberg] -- Merge minor typo fix. [Martin D. Weinberg] -- Added random seed using /dev/urandom. [Martin D. Weinberg] -- Fixed missing brackets. [Martin D. Weinberg] -- Removed maxSelA and maxSelB in favor of a single collision per cell - value: maxSel. [Martin D. Weinberg] -- Change to add collision limiting to Trace method. [Martin D. Weinberg] -- Merge branch 'newTrace' of https://bitbucket.org/mdweinberg/exp into - newTrace. [Martin D. Weinberg] -- Added missing std header. [Martin D. Weinberg] -- Added trace-method sanity check on initialization. [Martin D. - Weinberg] -- Fixed typo in electron scattering seleection. [Martin D. Weinberg] -- MFPTS clean up. [Martin D. Weinberg] -- Roundoff sanity check (for single particle in sample cell) [Martin D. - Weinberg] -- More output diagnostics. [Martin D. Weinberg] -- Check load on nodes. [Martin D. Weinberg] -- Attempt to fix the serialization of enum class for c++11 by non- - intrusive serialization. [Martin D. Weinberg] -- Turn off timer output by default. [Martin D. Weinberg] -- White space clean up. [Martin D. Weinberg] -- Added some addition mutex locks for ntcdb. [Martin D. Weinberg] -- Added timing output option. [Martin D. Weinberg] -- Updated debugging. [Martin D. Weinberg] -- Merge branch 'newTrace' of https://bitbucket.org/mdweinberg/exp into - newTrace. [Martin D. Weinberg] -- Add mutex initializer to constructor. [Martin D. Weinberg] -- Consolidation of physical constant declaration. [Martin D. Weinberg] -- Remove OpenMP in favor of Pthreads to prevent confusion. [Martin D. - Weinberg] -- Merge branch 'newTrace' of https://bitbucket.org/mdweinberg/exp into - newTrace. [Martin D. Weinberg] -- Additional plotting diagnostics. [Martin D. Weinberg] -- Remove annoying debug warnings about uninitialized boxes. [Martin D. - Weinberg] -- Documentation changes only. [Martin D. Weinberg] -- Merge branch 'newTrace' of https://bitbucket.org/mdweinberg/exp into - newTrace. [Martin D. Weinberg] -- Updates to DSMC plotting diagnostics for trace method. [Martin D. - Weinberg] -- Fixed to NTCdb and crossIJ logic. [Martin D. Weinberg] -- Merge branch 'newTrace' of https://bitbucket.org/mdweinberg/exp into - newTrace. [Martin D. Weinberg] -- Removed debugging lines. [Martin D. Weinberg] -- Fixed energy scaling for CHIANTI comparison. [Martin D. Weinberg] -- Fixed output logic for timestep output. [Martin D. Weinberg] -- Merge branch 'newTrace' of https://bitbucket.org/mdweinberg/exp into - newTrace. [Martin D. Weinberg] -- Added additional debugging tools. [Martin D. Weinberg] -- Version bump. [Martin D. Weinberg] -- Fix to crossfac treatment for Trace method. [Martin D. Weinberg] -- Fix tree instance caching. [Martin D. Weinberg] -- Merge branch 'newTrace' of https://bitbucket.org/mdweinberg/exp into - newTrace. [Martin D. Weinberg] -- Added option for myid=0 only to wait on debug sleep loop. [Martin D. - Weinberg] -- Switch to suppress free-free cross section computation. [Martin D. - Weinberg] -- Added body index test to pHOT. [Martin D. Weinberg] -- Put timing info at end of top-level step. [Martin D. Weinberg] -- Updates to whole-step timing. [Martin D. Weinberg] -- Updated to conform to latest C++/C standards. [Martin D. Weinberg] -- Minor output adjustments for Trace method. [Martin D. Weinberg] -- Fixed loop error in traceCrossSection computation (oops) [Martin D. - Weinberg] -- Merge branch 'newTrace' of https://bitbucket.org/mdweinberg/exp into - newTrace. [Martin D. Weinberg] -- Fixed energy units for coulCrs. [Martin D. Weinberg] -- Added electron-ion collision energy histogram. [Martin D. Weinberg] -- Generalized the effective Coulombic scattering to allow better - selection statistics for collisional excitation. [Martin D. Weinberg] -- Added velocity independent Coulombic effective cross section. [Martin - D. Weinberg] -- Added a column to show energy lost to total KE for each channel. - [Martin D. Weinberg] -- Merge branch 'newTrace' of https://bitbucket.org/mdweinberg/exp into - newTrace. [Martin D. Weinberg] -- Remove redundant inverse energy scaling from the direct ionization - cross section computation. [Martin D. Weinberg] -- Add energy output to channel summary. [Martin D. Weinberg] -- Additional trace diagnostics. [Martin D. Weinberg] -- Changed temperature assignment override. [Martin D. Weinberg] -- Added Trace method temperature override. [Martin D. Weinberg] -- Change default units, temperature for Trace method should come from - config file for consistency. [Martin D. Weinberg] -- DSMC version bump. [Martin D. Weinberg] -- Merge branch 'newTrace' of https://bitbucket.org/mdweinberg/exp into - newTrace. [Martin D. Weinberg] -- Change output table in DSMC_log to list cumulated collisions. [Martin - D. Weinberg] -- Fixed lingering cruft from last merge. [Martin D. Weinberg] -- White space changes only. [Martin D. Weinberg] -- Merge branch 'newTrace' of https://bitbucket.org/mdweinberg/exp into - newTrace. [Martin D. Weinberg] -- Fixed erroneous sequence of diagnostic call in finalize_cell. [Martin - D. Weinberg] -- Updates to Trace algorithm; removed deep debug sanity checks. [Martin - D. Weinberg] -- Documentation update. [Martin D. Weinberg] -- Minor bug in effort analysis fixed. [Martin D. Weinberg] -- Trace method energy debug test. [Martin D. Weinberg] -- Additional diagnostics. [Martin D. Weinberg] -- Bug fix. [Martin D. Weinberg] -- Added deferred energy total to diagnostics. [Martin D. Weinberg] -- Added deferred energy count diagnostic. [Martin D. Weinberg] -- Print out full interact type. [Martin D. Weinberg] -- ID dominant inelastic type. [Martin D. Weinberg] -- Return MPI debugging in electronGather to 'off' by default. [Martin D. - Weinberg] -- Additional energy loss diagnostics to help identify the econs runaway. - [Martin D. Weinberg] -- Clean up and correct diagnostic stanza in inelasticTrace. [Martin D. - Weinberg] -- Additional cleaning and diagnostics for new Trace implementation. - [Martin D. Weinberg] -- Added histogram for KE/delE ratio. [Martin D. Weinberg] -- Level reporting update. [Martin D. Weinberg] -- Add protection for zero valued delE for spEmax computation. [Martin D. - Weinberg] -- Merge branch 'newTrace' of https://bitbucket.org/mdweinberg/exp into - newTrace. [Martin D. Weinberg] -- Updated diagnostic output and spEmax computation for Trace algorithm. - [Martin D. Weinberg] -- Merge branch 'newTrace' of https://bitbucket.org/mdweinberg/exp into - newTrace. [Martin D. Weinberg] -- Merge branch 'newTrace' of https://bitbucket.org/mdweinberg/exp into - newTrace. [Martin D. Weinberg] -- Additional comments; remove verbose debug. [Martin D. Weinberg] -- SpEmax computation must occur after scatterTrace. [Martin D. Weinberg] -- Remove NN in favor of N0 * TProb in Trace computation. [Martin D. - Weinberg] -- Flip ratio for spEmax. [Martin D. Weinberg] -- Include option for maximum energy loss per interaction for time step - selection inelasticTrace. [Martin D. Weinberg] -- Include option for maximum energy loss per interaction for time step - selection inelasticTrace. [Martin D. Weinberg] -- Included energy loss for time step selection inelasticTrace. [Martin - D. Weinberg] -- Fixed spProb computation for normalization subdominant interactions in - inelasticTrace. [Martin D. Weinberg] -- Remove no longer relevant prob check for inelasticTrace, since TProb - is now really a count which may be larger than one. [Martin D. - Weinberg] -- Fixed data type in std::accumulate. [Martin D. Weinberg] -- Merge branch 'newTrace' of https://bitbucket.org/mdweinberg/exp into - newTrace. [Martin D. Weinberg] -- Fix to inelastic rate computation. [Martin D. Weinberg] -- Merge branch 'newTrace' of https://bitbucket.org/mdweinberg/exp into - newTrace. [Martin D. Weinberg] -- Fixed the Kramers' cross section; allowed free-free wavenumber grid to - be changed on the fly; updated testCross.cc to include grid adjustment - for tuning. [Martin D. Weinberg] -- Added option to plot KE only. [Martin D. Weinberg] -- Slight rearrangement of energy conservation logic for inelasticTrace. - [Martin D. Weinberg] -- Added option for Econs/Etot ratios. [Martin D. Weinberg] -- Fixed interaction selection for Trace algorithm. [Martin D. Weinberg] -- Merge branch 'newHybrid' [Martin D. Weinberg] -- Added warnings if file is not found. [Martin D. Weinberg] -- Added warnings if file is not found. [Martin D. Weinberg] -- Minor fixes to main branch that were in the development branch. None - are critical but I want to move the minor bug fixes into the master - branch. Most of the changes are only relevant to DSMC. [Martin D. - Weinberg] -- Homogenize print dividers where possible. [Martin D. Weinberg] -- Species plotting for trace algorithm. [Martin D. Weinberg] -- Merge branch 'newHybrid' of https://bitbucket.org/mdweinberg/exp into - newHybrid. [Martin D. Weinberg] -- Removed excessW from Trace algorithm implementation. Added electron - scattering for Trace algorithm in finalize_cell. [Martin D. Weinberg] -- Removed scaled probability for Trace method. [Martin D. Weinberg] -- Typo/bug fix in the weight computation for a recombination update. - [Martin D. Weinberg] -- Fixed trace weight index arithmetic. [Martin D. Weinberg] -- Remove nselRat from trace algorithm cross section computation. [Martin - D. Weinberg] -- Fix typo (keyPos rather than use_key) [Martin D. Weinberg] -- Bug fix to Trace method species accumulation. [Martin D. Weinberg] -- Fixed typo in mol weight computation for Trace. [Martin D. Weinberg] -- Sanity check on keypos for thermal BC. [Martin D. Weinberg] -- Use Particle::defaultKey for Trace species key. [Martin D. Weinberg] -- Fixes to enable DSMC output for Trace method. [Martin D. Weinberg] -- Bump TreeDSMC version number. [Martin D. Weinberg] -- A few updates to Trace-method diagnostic output. [Martin D. Weinberg] -- Fix up molecular weight computations for energy conservation checks - for Trace method. [Martin D. Weinberg] -- Added use_cons to trace generation. [Martin D. Weinberg] -- Added variables for default number of integer and double attributes in - generated ICs. [Martin D. Weinberg] -- Implement molecular weight computation for Trace method. [Martin D. - Weinberg] -- Guard against zero dt value in multistep level computation. [Martin D. - Weinberg] -- Merge branch 'newHybrid' of https://bitbucket.org/mdweinberg/exp into - newHybrid. [Martin D. Weinberg] -- Merge branch 'newHybrid' of https://bitbucket.org/mdweinberg/exp into - newHybrid. [Martin D. Weinberg] -- Comments only. [Martin D. Weinberg] -- Added parameter to log file output. [Martin D. Weinberg] -- Typo in STANDLONE clause for Particle.{h,H} header. [Martin D. - Weinberg] -- Draft update of Trace algorithm based on port from recent version of - the Hybrid algorithm. [Martin D. Weinberg] -- Generalization of NTC::Interact. [Martin D. Weinberg] -- Added compile string. [Martin D. Weinberg] -- Test code and input file for Configuration.H. [Martin D. Weinberg] -- General boolean conversion in the property tree. [Martin D. Weinberg] -- White space changes. [Martin D. Weinberg] -- Additional TRACE_FRAC implementation. [Martin D. Weinberg] -- Added NO_EXACT flag to remove trace inequality owing to ionization - fraction. Ionization fraction determines the interaction rate. - [Martin D. Weinberg] -- Renamed SAME_TRACE_SUPP to TRACE_OVERRIDE. [Martin D. Weinberg] -- Merge branch 'newHybrid' of https://bitbucket.org/mdweinberg/exp into - newHybrid. [Martin D. Weinberg] -- Minor updates based on profiling. [Martin D. Weinberg] -- Merge branch 'newHybrid' of https://bitbucket.org/mdweinberg/exp into - newHybrid. [Martin D. Weinberg] -- Merge branch 'newHybrid' of https://bitbucket.org/mdweinberg/exp into - newHybrid. [Martin D. Weinberg] -- Particle caching of speciesKey. [Martin D. Weinberg] -- Added additional linewidth parameter. [Martin D. Weinberg] -- Makefile fix (for std=c++11) and version bump (owing to change from - rb_map to hash_map for Component::Particle structure. [Martin D. - Weinberg] -- Moved from map to unordered_map for Particles map for performance - testing. [Martin D. Weinberg] -- Energy conservation fixex. [Martin D. Weinberg] -- Merge branch 'newHybrid' of https://bitbucket.org/mdweinberg/exp into - newHybrid. [Martin D. Weinberg] -- Version bump. [Martin D. Weinberg] -- Added linewidth option. [Martin D. Weinberg] -- Merge branch 'newHybrid' of https://bitbucket.org/mdweinberg/exp into - newHybrid. [Martin D. Weinberg] -- Added pooled conservation of energy flag. [Martin D. Weinberg] -- Added additional test options. [Martin D. Weinberg] -- Deprecate qCrit option. [Martin D. Weinberg] -- Merge branch 'newHybrid' of https://bitbucket.org/mdweinberg/exp into - newHybrid. [Martin D. Weinberg] -- Added a suppression for ion-ion scatering in the Hybrid method. - [Martin D. Weinberg] -- Fixed minor mistake in debugging energy conservation accumulation. - [Martin D. Weinberg] -- Split radiative energy loss from deferred COM loss. [Martin D. - Weinberg] -- Updates for KE.Delta in mom cons method. [Martin D. Weinberg] -- Merge branch 'newHybrid' of https://bitbucket.org/mdweinberg/exp into - newHybrid. [Martin D. Weinberg] -- Added addition energy diagnostics. [Martin D. Weinberg] -- Add option for suppressing total E temperature in favor of dispersion - temperature. [Martin D. Weinberg] -- Added an addtional plot view. [Martin D. Weinberg] -- Set default Tmax=1.0e32. [Martin D. Weinberg] -- Merge branch 'newHybrid' of https://bitbucket.org/mdweinberg/exp into - newHybrid. [Martin D. Weinberg] -- Added additional specific views to *ION_coll data. [Martin D. - Weinberg] -- Added scripts to provide basic statistics on DSMC body files. [Martin - D. Weinberg] -- Clean up cruft only. [Martin D. Weinberg] -- Remove verbose debug output. [Martin D. Weinberg] -- Added diagnostic output for added tree branches. [Martin D. Weinberg] -- Don't add cells to the tree if they have no particles. [Martin D. - Weinberg] -- Add -delE to center-of-mass frame if delE<0. [Martin D. Weinberg] -- Added option to toggle channel selection strategy in Hybrid Method. - [Martin D. Weinberg] -- Debug checking for CProb. [Martin D. Weinberg] -- Reformatting of FPE user messages. [Martin D. Weinberg] -- Fixed for 3rd leading column in *ION_coll. [Martin D. Weinberg] -- Formatting change only. [Martin D. Weinberg] -- Added delE to scatter error output. [Martin D. Weinberg] -- Fixed sign mistake in energy conservation check. [Martin D. Weinberg] -- Stdout formatting change only. [Martin D. Weinberg] -- Attempt to fix COM energy decrement and conservation checks. [Martin - D. Weinberg] -- Additional FPU trap selection info to stdout. [Martin D. Weinberg] -- Added information strings to stdout for various fpe trap types. - [Martin D. Weinberg] -- Fall back to sane values in EPSM method for electrons. [Martin D. - Weinberg] -- Prevent divide by zero and sqrt(<0) for output diagnostics. [Martin D. - Weinberg] -- Added info about fpe_wait option to stdout. [Martin D. Weinberg] -- Three layers of spin wait warning. [Martin D. Weinberg] -- Version bump for FPE handling. [Martin D. Weinberg] -- Added ionization threshold for electron-electron scattering. [Martin - D. Weinberg] -- Fixed mistake in Pord helper class. [Martin D. Weinberg] -- Improve reporting frequency. [Martin D. Weinberg] -- Finished gdb-wait trap for floating-point exceptions. Will now test - by using. [Martin D. Weinberg] -- Deep debug for KE now enabled by KE_DEBUG flag. [Martin D. Weinberg] -- Fixed help strings. [Martin D. Weinberg] -- Remove some energy conservation debugging cruft. [Martin D. Weinberg] -- Debug fix. [Martin D. Weinberg] -- Debug fix. [Martin D. Weinberg] -- Debug fix. [Martin D. Weinberg] -- Merge branch 'newHybrid' of https://bitbucket.org/mdweinberg/exp into - newHybrid. [Martin D. Weinberg] -- Add BOOST_LDFLAGS to LDFLAGS variables for the main exp and user - modules. [Martin D. Weinberg] -- Minor fixes; energy conservation self-checks ahve been passed so far. - [Martin D. Weinberg] -- Still checking for energy conservation accuracy. [Martin D. Weinberg] -- More changes (actually a revert) to deferred energy. [Martin D. - Weinberg] -- New recomb algorithm test. [Martin D. Weinberg] -- Merge branch 'newHybrid' of https://bitbucket.org/mdweinberg/exp into - newHybrid. [Martin D. Weinberg] -- Restore initialization of I12 variable (editting mistake) [Martin D. - Weinberg] -- A few updates to conservation diagnostics. [Martin D. Weinberg] -- Remove NOCOOL restriction to finalize_cell Hybrid debugging output. - [Martin D. Weinberg] -- Change to energy accounting. [Martin D. Weinberg] -- Fixed sign error in deferred energy bookkeeping. No-energy-loss run - now conserves energy correctly. [Martin D. Weinberg] -- Fixes to new hybrid-method energy conservation scheme. [Martin D. - Weinberg] -- Info string change only. [Martin D. Weinberg] -- Deferred energy algorithm update. [Martin D. Weinberg] -- Updates for deferred energy consevation for order-unity valued - electron ionization fractions. [Martin D. Weinberg] -- Test new Vcom ExactE variant. [Martin D. Weinberg] -- More updates to Hybrid implementation for channel selection. [Martin - D. Weinberg] -- Merge branch 'newHybrid' of https://bitbucket.org/mdweinberg/exp into - newHybrid. [Martin D. Weinberg] -- Updated for latest version of doxygen. [Martin D. Weinberg] -- Fixes for MC in Hybrid test. [Martin D. Weinberg] -- Added MC selector for Hybrid interaction to prevent order unity trace - fraction. [Martin D. Weinberg] -- Merge branch 'newHybrid' of https://bitbucket.org/mdweinberg/exp into - newHybrid. [Martin D. Weinberg] -- Added back the AlgOrth option. [Martin D. Weinberg] -- Fixed typo. [Martin D. Weinberg] -- Merge branch 'newHybrid' of https://bitbucket.org/mdweinberg/exp into - newHybrid. [Martin D. Weinberg] -- Some cleaning up for readability. [Martin D. Weinberg] -- Merge branch 'newHybrid' of https://bitbucket.org/mdweinberg/exp into - newHybrid. [Martin D. Weinberg] -- Fixed to Hybrid method momentum conservation checks. [Martin D. - Weinberg] -- Routine to plot energy conservation quanties from *ION_coll file. - [Martin D. Weinberg] -- Remove vfac in favor for KE.vfac in scatterHybrid. [Martin D. - Weinberg] -- Removed the crufty InteractData structure; replaced by Pord. [Martin - D. Weinberg] -- Updated swapping logic and secondaryScatter for energy conservation - algorithm. [Martin D. Weinberg] -- Merge branch 'newHybrid' of https://bitbucket.org/mdweinberg/exp into - newHybrid. [Martin D. Weinberg] -- Merge branch 'newHybrid' of https://bitbucket.org/mdweinberg/exp into - newHybrid. [Martin D. Weinberg] - - Conflicts: - src/user/CollideIon.cc -- Updates to hybrid parameter handling. [Martin D. Weinberg] -- Version bump. [Martin D. Weinberg] -- Mostly debugged energy conservation algorithm. [Martin D. Weinberg] -- Additional output diagnostics for debugging. [Martin D. Weinberg] -- Updates to energy conservation check for new trace particle - implmentation of the Hybrid method. [Martin D. Weinberg] -- Updates to hybrid parameter handling. [Martin D. Weinberg] -- Updated for new partial trace implementation. [Martin D. Weinberg] -- Updated for new columns. [Martin D. Weinberg] -- Added momentum per cell enforcement for ExactE/Hybrid method. [Martin - D. Weinberg] -- Updated for dispersion temperature and energy output. [Martin D. - Weinberg] -- Updates for output of both total- and dispersion-based temperature and - energy fields. [Martin D. Weinberg] -- Plotting routines for both total- and dispersion-based temperature and - energy plots. [Martin D. Weinberg] -- Removed duplicate plot. [Martin D. Weinberg] -- Some additional diagnostic output and code cleaning. [Martin D. - Weinberg] -- Added a gdb wait handler for debugging: [Martin D. - Weinberg] -- Added FE flag report on SIFPE handler installation. [Martin D. - Weinberg] -- Cleaned up interface for collecting the gdb backtrace. [Martin D. - Weinberg] -- Version bump. [Martin D. Weinberg] -- Fixed equal species flag detection for hybrid method. [Martin D. - Weinberg] -- Added gdb-based backtrace handler to give line numbers for FPE errors; - global boolean flag: [Martin D. Weinberg] -- Changed channel diagnostic to accumulate total for each channel rather - than max prob. [Martin D. Weinberg] -- Merge current working version. [Martin D. Weinberg] -- Merged local changes. [Martin D. Weinberg] -- Updated for multichannel elastic and inelastic scattering for hybrid - algorithm. [Martin D. Weinberg] -- Merge branch 'newHybrid' of https://bitbucket.org/mdweinberg/exp into - newHybrid. [Martin D. Weinberg] -- White space change only. [Martin D. Weinberg] -- Updated Icont specialization. [Martin D. Weinberg] -- Fixed for gcc 4.x compiler. [Martin D. Weinberg] -- More tweaks to diagnostics for interaction types. [Martin D. Weinberg] -- Tweaks to diagnostics for interaction types. [Martin D. Weinberg] -- More diagnostics for interaction types. [Martin D. Weinberg] -- Updates for refactoring collision-type bookeeping. [Martin D. - Weinberg] -- Fixed error in ParamParse. [Martin D. Weinberg] -- Added missing upscale factor in inelastic rates for collisional - limiters. [Martin D. Weinberg] -- Merge branch 'newHybrid' of https://bitbucket.org/mdweinberg/exp into - newHybrid. [Martin D. Weinberg] -- Updated plotting routines. [Martin D. Weinberg] -- Merged changes. [Martin D. Weinberg] -- Merged changes. [Martin D. Weinberg] -- Added boost factor for inelastic collisions for testing. [Martin D. - Weinberg] -- Mistake in interaction probabilities fixed. [Martin D. Weinberg] -- Added randomization to interaction list to reprevent bias in - ionization-recombination. [Martin D. Weinberg] -- Fixed CE and CF cache for updated algorithm; still needs more work to - make it clean, but I want to test it first. [Martin D. Weinberg] -- Check for valid energy in electronic excitation or ionization - interaction. [Martin D. Weinberg] -- Test for parsing ION_coll files by column label. Updated for Python - argparse. [Martin D. Weinberg] -- Fixed mistake in neutral-proton elastic scattering. [Martin D. - Weinberg] -- Merge branch 'newHybrid' of https://bitbucket.org/mdweinberg/exp into - newHybrid. [Martin D. Weinberg] -- Added points to some lines to disambiguate. [Martin D. Weinberg] -- Missing reference in loop. [Martin D. Weinberg] -- Additional comments and diagnostics. [Martin D. Weinberg] -- Another energy handling update. [Martin D. Weinberg] -- Fixed scattering diagnostic and energy conversion to superparticle - units. [Martin D. Weinberg] -- Running now, let's try it on real data. [Martin D. Weinberg] -- First test version. [Martin D. Weinberg] -- Find *.species fields by column heading. [Martin D. Weinberg] -- Added log(Lambda) value to CollionIon config. [Martin D. Weinberg] -- Add diagnostics about EPSM cell counts. [Martin D. Weinberg] -- Fixes for EPSM algorithm for electron scattering. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Added a global 3d unit-vector generator. [Martin D. Weinberg] -- Fixed merge for electron EPSM. [Martin D. Weinberg] -- Added EPSM algorithm for electron scattering. [Martin D. Weinberg] -- Comment merge. [Martin D. Weinberg] -- Added swap template. [Martin D. Weinberg] -- Updated AlgOrth for parallel or zero norm components. [Martin D. - Weinberg] -- Addition test restrictions for unequal weight interactions. [Martin D. - Weinberg] -- Converted to energy per particle. [Martin D. Weinberg] -- Additional debug interaction methods, trace-species energy splitting, - and diagnostic output. [Martin D. Weinberg] -- White-space change only. [Martin D. Weinberg] -- Changed execute flag. [Martin D. Weinberg] -- Additional *.species plots. [Martin D. Weinberg] -- Updated hybrid electron dof logic. [Martin D. Weinberg] -- Added additional energy conservation algorithm. [Martin D. Weinberg] -- Added q threshold for electron scattering (for testing) [Martin D. - Weinberg] -- DebugFC diagnostics. [Martin D. Weinberg] -- Updated CollideIon electron energy for hybrid-model electronfraction. - [Martin D. Weinberg] -- Comments and white space. [Martin D. Weinberg] -- Added additional finalize_cell diagnostic output. [Martin D. Weinberg] -- Added finalize-cell diagnostics to CollideIon config. [Martin D. - Weinberg] -- Added timing for entire DSMC step. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Fixed timing accumulation in UserTreeDSMC. [Martin D. Weinberg] -- Updated elapsed timer computation. [Martin D. Weinberg] -- Additional comments in pCell. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- White space change only. [Martin D. Weinberg] -- Added comparison plotting script for per species data. [Martin D. - Weinberg] -- Fixed sample cell status reporting error; no bug in tree itself, just - in the tree diagnostics. [Martin D. Weinberg] -- Some optimizations for ALL of EXP to remove extraneous map searches - and save CPU time. [Martin D. Weinberg] -- Added collision limited for elastic Coulombic interactions. [Martin D. - Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Improvements to velocity extrema and estimates per cell. [Martin D. - Weinberg] -- Propagated collTnum time step choice to Collide main class from - CollideIon. [Martin D. Weinberg] -- Added collision count to time step adjustment based on collTnum target - accepted collisions per cell. [Martin D. Weinberg] -- Fixed error in Quantile communication. [Martin D. Weinberg] -- Fixed body list for sample cell. [Martin D. Weinberg] -- Fixed screwed-up merge with eagle. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Added ion-ion scattering xs. [Martin D. Weinberg] -- Typo in logL computation; erroneous atomic mass ratio? [Martin D. - Weinberg] -- Added debug flags to config. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Fixed typo. [Martin D. Weinberg] -- Check integrity of data lines (e.g. in case fs runs out of space) - [Martin D. Weinberg] -- Added neutron proton cross sections (implemented for H and He) [Martin - D. Weinberg] -- Update to n*sigma diagnostic computation. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] - - Conflicts: - utils/Analysis/ion_coll_number.py - utils/Analysis/ion_coll_ratio.py - utils/Analysis/ion_coll_smooth.py - utils/Analysis/ion_coll_time.py -- Change collision limiting logic to pure thresholding rather than - scaling. [Martin D. Weinberg] -- Updates for Efrac. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Taylor series convergence commented out. [Martin D. Weinberg] -- Report electron fraction for Hybrid method rather than electron - velocity ratio. [Martin D. Weinberg] -- Updates for electron fraction for ExactE (explicit energy - conservation) altorithm. [Martin D. Weinberg] -- Fixed wrong sign in deltaKE! Ooops. [Martin D. Weinberg] -- Updated electron mass computation for KE and added various consE - tests. [Martin D. Weinberg] -- Added Quantile test routine to the makefile. [Martin D. Weinberg] -- Added test routine for Quantile class. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Updated and checked Quantile class. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Fixed typo in static_cast for Quantile.cc. [Martin D. Weinberg] -- Promote variable types in Quantile to prevent integer wrapping. This - will probably need further improvement, alas. [Martin D. Weinberg] -- Suppress all electron distribution histograms by default. [Martin D. - Weinberg] -- Fewer histogram diagnostics by default. [Martin D. Weinberg] -- Turn off NTC diagnostics by default. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Added an approximate min/max velocity estimator rather than direct N^2 - algorithm. [Martin D. Weinberg] -- Fix repetative calls to tk::spline.set_points. This was a bug. - [Martin D. Weinberg] -- Remove interactive mode from script. [Martin D. Weinberg] -- Make Ncoll the default MFP estimator for time-step control. [Martin D. - Weinberg] -- Added an empirical MFP estimator for time step control. [Martin D. - Weinberg] -- Added missing static variable. [Martin D. Weinberg] -- Changed variable names to simplify usage. [Martin D. Weinberg] -- Added time-of-flight time step selection. [Martin D. Weinberg] -- Updated default writing of _description and _date strings into config. - [Martin D. Weinberg] -- Added the necessary and currently missing time-step assignment to - spTau for Hybrid method. [Martin D. Weinberg] -- Added a cooling per cell time step selection unified for all collision - algorithms. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Added additional read error diagnostics and distinguishing markers to - curves. [Martin D. Weinberg] -- Clean up and test for energy conservation. [Martin D. Weinberg] -- Adjustments to "ALWAYS_APPLY" logic. [Martin D. Weinberg] -- Updated for newest version of CollideIon. [Martin D. Weinberg] -- Clean up some of the energy conservation tests; still trying to ensure - full conservation for radiative energy loss. [Martin D. Weinberg] -- Added time scaling. [Martin D. Weinberg] -- Updates to collision info plotting script. [Martin D. Weinberg] -- Updated python scripts and BarrierWrapper backport. [Martin D. - Weinberg] -- Routine to parse *.ION_coll files for plotting. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- More diagnostics and algorithm tweaks to detect and prevent excess - energy runaway. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Added electronic potential to energy diagnostics in CollDiag. [Martin - D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Added template diagnostic printing of std::array. [Martin D. Weinberg] -- Added LOWESS smoothing to ion_coll_ratio.py plotting routine. [Martin - D. Weinberg] -- Added energy conservation field accumulation. [Martin D. Weinberg] -- Added inelastic energy scaling to test equipartition. [Martin D. - Weinberg] -- Updated DSMC processing scripts. [Martin D. Weinberg] -- Add toggle for gs_only variable for radiative recombination. [Martin - D. Weinberg] -- Added spectrum in wavelength option. [Martin D. Weinberg] -- Added contribution from each process to spectral output. [Martin D. - Weinberg] -- Typo in info string. [Martin D. Weinberg] -- Added spectral output for testing. [Martin D. Weinberg] -- More updates to separate the default singleton interaction channel - from the electron-electron interaction channel. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] - - Conflicts: - src/user/Collide.H -- Updates for electron type. [Martin D. Weinberg] -- Let electron flag be 0 rather than 65535; more intuitive it seems. - [Martin D. Weinberg] -- Typographical error. [Martin D. Weinberg] -- Change electron tag to avoid NTC sanity check warning. [Martin D. - Weinberg] -- Added ntcThresh local to Collide which is initialized by ntcThreshDef; - this allows ntcThresh to be adjusted or chosen by some algorithm in a - future implementation. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Fixed multiplicity "correction" for collisional excitation; Omega - includes ground-state multiplicity. [Martin D. Weinberg] -- Changed default wavenumber range to accommodate free-free up to approx - 10^7 degrees. [Martin D. Weinberg] -- Fixed cross-section collision type typographical error. [Martin D. - Weinberg] -- Added computed number density to output. [Martin D. Weinberg] -- Fixed typo in interaction type tag for free-free cross section. - [Martin D. Weinberg] -- Increased free-free partial cross section wavenumber range. [Martin D. - Weinberg] -- Explicit comments for derived system unit update after command-line - parameter read. [Martin D. Weinberg] -- Confusion between specified system length unit and pc; fixed. [Martin - D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Clean up some debugging output. Explicitly define free-free - wavenumber endpoints. [Martin D. Weinberg] -- Print tree volume into log file. [Martin D. Weinberg] -- Update tree volume when sides are set. [Martin D. Weinberg] -- WS fixes and added command line parsing to checkICweights.py. [Martin - D. Weinberg] -- More updates. [Martin D. Weinberg] -- Fix treeVol computation: local variable should be class variable. - [Martin D. Weinberg] -- Minor fixes to previous commit. [Martin D. Weinberg] -- Corrected computation of physical volumes from system pHOT tree - volume. Ooops. That's a factor of 8. [Martin D. Weinberg] -- Add subspecies interaction energies to eDistDBG distribution group. - [Martin D. Weinberg] -- Replace some "prob > 0" by "prob >= 0" for correctness, although - prob=0 should be suppressed by the current interaction selector, so - this for future insurace. [Martin D. Weinberg] -- Missing semicolon. [Martin D. Weinberg] -- Some additional comments to code. [Martin D. Weinberg] -- New analysis tools and minor production tweaks. [Martin D. Weinberg] -- Commit Mike P's psp_io, more selection collision diagnostic output. - [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Add missing dCross[id].clear() for Hybrid scheme. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Updates for psp2range. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Added psp field range utility. [Martin D. Weinberg] -- Version bump, for Component.cc change. [Martin D. Weinberg] -- Pretty printing change. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Restricted collision counting in hybrid to dominant interactions. - [Martin D. Weinberg] -- Updated sequence checking in Component::load_balance to use indx - rather than the long-time deprecated iattrib[0]. Did not check this - fix. [Martin D. Weinberg] -- Updated for energy conservation algorithm. [Martin D. Weinberg] -- Compute species and electron temperatures in pspstatS. [Martin D. - Weinberg] -- Merged change in scatter diagnostic print out. [Martin D. Weinberg] -- Updated pspstatS. [Martin D. Weinberg] -- Encode both elements in dominant interaction counts db. [Martin D. - Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Changed header name to something more descriptive - (GetWithDef-->InitContainer) [Martin D. Weinberg] -- More commenting. [Martin D. Weinberg] -- Added some comments. [Martin D. Weinberg] -- Change name of helper-class header. [Martin D. Weinberg] -- Fixed up gaffs in particle position encoding. [Martin D. Weinberg] -- Encoded particle ordering into dominant interaction diagnostic. - [Martin D. Weinberg] -- Need static_cast for std container wrapper. [Martin D. Weinberg] -- Added new default dominant interactio type counter for diagnostic - debugging. [Martin D. Weinberg] -- Add a template wrapper to implement an STL associative container with - a default value. [Martin D. Weinberg] -- Added diagnostic for ion_electron count for primary hybrid - interaction. [Martin D. Weinberg] -- Typo: multithread objects are ntcVal and wgtVal, not ntcSum and - wghtSum. [Martin D. Weinberg] -- Version bump. [Martin D. Weinberg] -- Limit size of NTC diagnostics using a circular buffer. [Martin D. - Weinberg] -- Removed unused variable Z. [Martin D. Weinberg] -- Added toggle to electron dist histogram debugging. [Martin D. - Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Example makeIon json config file. [Martin D. Weinberg] -- Updated energy conservation algorithm. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Added json parser to makeIonIC.cc. [Martin D. Weinberg] -- Generalized initialization scheme for two temperature gas to test - equilibration. [Martin D. Weinberg] -- More documentation and debugging output. [Martin D. Weinberg] -- Updated comment and whitespace formating only. [Martin D. Weinberg] -- Updated commenting. [Martin D. Weinberg] -- Minor cleanup in variable names for clarity. [Martin D. Weinberg] -- Make Interact a class and initialize all data. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Fixed typo. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Script to check energy conservation column in DSMC gas file. [Martin - D. Weinberg] -- Changed subspecies interaction probability from "weight" to "prob" for - better clarity. [Martin D. Weinberg] -- Cache assigned energy. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Another fixed subspecies implementation mistake. [Martin D. Weinberg] -- Fixed a typo in KE units. [Martin D. Weinberg] -- Fixed out-of-sync calls from generateSelectionHybrid Sub to cross- - section initialization for different ion values; this is inefficient - but can be fixed after testing. [Martin D. Weinberg] -- Comments only. [Martin D. Weinberg] -- Clean up cruft and improve energy diagnostics for accumulation of - subspecies interactions. [Martin D. Weinberg] -- A few more fixes to new subspecies implementation. [Martin D. - Weinberg] -- Adjusted energy weighting for subdominant species. Removed sum over - donor particle substates. [Martin D. Weinberg] -- Adjusted energy weighting for subdominant species. [Martin D. - Weinberg] -- Fix a few special cases that crashed the plotting scripts. [Martin D. - Weinberg] -- Write Tree DSMC version header into log. [Martin D. Weinberg] -- Additional autoconf clean up for VTK configuration. [Martin D. - Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Updated for Python script suffix addition. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Added logscale option to energy loss subplot. [Martin D. Weinberg] -- Additional fixes for VTK 6.x configuration. [Martin D. Weinberg] -- Updates for gcc 5 (using Ubuntu 16.04) [Martin D. Weinberg] -- Add version identifier to userinfo() output. [Martin D. Weinberg] -- Updated subspecies algorithm to ignore particle splitting, which is - already accounted for in the interaction density. [Martin D. Weinberg] -- A few minor clean ups to deferred energy gain/loss for subdominant - species; should not change results significantly. [Martin D. Weinberg] -- Updated and renamed Python scripts in Analysis to *.py. [Martin D. - Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Updated for electron energy distribution per element. [Martin D. - Weinberg] -- Added test routine for EnumBitset.H. [Martin D. Weinberg] -- Refactored subdominate species inelastic updates. [Martin D. Weinberg] -- Additional tests and updates for recombEquil() computations. [Martin - D. Weinberg] -- Add per ion energy distributions to DSMC_log. [Martin D. Weinberg] -- Replace ion_*_dist.py routines by a single ion_dist.py that takes each - of the three fields as an command-line parameter. [Martin D. Weinberg] -- A few more updates to Python plotting scripts for DSMC diagnostics. - [Martin D. Weinberg] -- Additional DSMC diagnostic visualization scripts. [Martin D. Weinberg] -- Fixed mass units for ion mass (missing factor of amu) [Martin D. - Weinberg] -- Fixed MPI tag inconsistency in eGather. [Martin D. Weinberg] -- Fixed typo in ion energy distribution output. [Martin D. Weinberg] -- Added ion energy distribution output. [Martin D. Weinberg] -- Added electron energy distribution print out. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Updates to normalization for ionization-recombination equilibrium and - added test for variable upper energy limit in thermal intergration. - [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Missing source file. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] - - Conflicts: - src/user/CollideIon.H -- Added initialization using native ionization and recombination cross - sections in thermal equilibrium. [Martin D. Weinberg] -- Added native ionization and recombination rate coefficients. [Martin - D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] - - Conflicts: - src/user/CollideIon.H -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] - - Conflicts: - src/user/CollideIon.H - src/user/CollideIon.cc -- Added code to compute ionization and recombination equilibrium for a - thermal gas. [Martin D. Weinberg] -- Added default values for p1 and p2 in KE_ constructor. [Martin D. - Weinberg] -- Updates for adding energy excess for trace interactions in hybrid - algorithm. [Martin D. Weinberg] -- Updated for extended ION_coll file format. [Martin D. Weinberg] -- Routine to plot electron energy diagnostics. [Martin D. Weinberg] -- Additional updates for electron velocity diagnostics. [Martin D. - Weinberg] -- Refactored hybrid method for new E_split method testing. [Martin D. - Weinberg] -- Sponsor update. [Martin D. Weinberg] -- Version bump. [Martin D. Weinberg] -- Updated main doc page. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] - - Conflicts: - src/user/Collide.cc - src/user/CollideIon.cc -- Additional CollideIon documentation. [Martin D. Weinberg] -- Additional debugging for electron scattering. [Martin D. Weinberg] -- Added config flag for fpe trapping (for debugging) rather than - requiring a recompile with -DDEBUG. [Martin D. Weinberg] -- Separate implementation of tk::spline to avoid use of anonymous - namespace. [Martin D. Weinberg] -- Updates for full interaction matrix rather than upper half. [Martin D. - Weinberg] -- Missing updates for subspecies. Ooops. [Martin D. Weinberg] -- Small changes in output energy diagnostics for accuracy. [Martin D. - Weinberg] -- Bug fix in Min/Mean/Max vel dif computation. [Martin D. Weinberg] -- Fixed units in min/mean/max velocity computation. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Implement Min/Mean/Max velocities for ion-electron interactions in - hybrid algorithm. [Martin D. Weinberg] -- Fixed formating for debug output. [Martin D. Weinberg] -- Fixed hybrid selection logic. [Martin D. Weinberg] -- Toggled off verbose cross-section debugging in hybrid algorithm. - [Martin D. Weinberg] -- Floor energy for hybrid cross section computation. [Martin D. - Weinberg] -- Fix for missing automatic entries in NTC database. [Martin D. - Weinberg] -- Fixed a few undefined variables in helper-class constructors. [Martin - D. Weinberg] -- Updates for rewritten hybrid algorithm. [Martin D. Weinberg] -- Fixed reduced mass in Coulombic cross section. [Martin D. Weinberg] -- Added more cross sections to testCrossSection test routine. [Martin D. - Weinberg] -- Removed factor of q from interaction weight in hybrid method. [Martin - D. Weinberg] -- Spelling error. [Martin D. Weinberg] -- Scaled up cross section to account for collisionally limited pair - selection. [Martin D. Weinberg] -- Added upscaling probabilities when collisions are limited in hybrid - method. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Changed std::vector to boost::circular_buffer for caching diagnostic - data. [Martin D. Weinberg] -- Add a missing carriage return; no change to code. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Added additional diagnostics. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Updates to BarrierWrapper output. [Martin D. Weinberg] -- Update for ionization and recombination cross sections. [Martin D. - Weinberg] -- Added error tolerance variable for energy conservation error - reporting. [Martin D. Weinberg] -- Added collision limit check for hybrid mode. [Martin D. Weinberg] -- Addition failure tests. [Martin D. Weinberg] -- Fixed return request list growth. [Martin D. Weinberg] -- Added increasing length delay to heavy-weight alarm in BarrierWrapper. - [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] - - Conflicts: - src/user/Ion.cc -- Added intential mistake to test code. [Martin D. Weinberg] -- Fixed misplaced {} in BarrierWrapper.H upon c++11 edit. [Martin D. - Weinberg] -- Code to test barrier wrapper. [Martin D. Weinberg] -- Additional documentation to Ion. [Martin D. Weinberg] -- Fixes to ExactE algorithm and lots of debugging output. [Martin D. - Weinberg] -- Added flag for recombination to ground state only in Verner cross - section. [Martin D. Weinberg] -- Fixed zero data problem. [Martin D. Weinberg] -- Added additional energy conservation debugging. [Martin D. Weinberg] -- Debugging problem in hybrid velocity update. [Martin D. Weinberg] -- Correct SAME_IONS_SCAT debugging in inelasticHybrid. [Martin D. - Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- More detail in electron temp sanity check. [Martin D. Weinberg] -- Fixed bugs introduced in hybrid method during debugging. [Martin D. - Weinberg] -- More fixes to finalize_cell with debugging info. [Martin D. Weinberg] -- Missing Hybrid test in finalize_cell. [Martin D. Weinberg] -- Updated electron scattering for hybrid-mode cross section computation. - [Martin D. Weinberg] -- Update electron temperature computation. [Martin D. Weinberg] -- Compute cross section from the ntcdb for the Hybrid method. [Martin D. - Weinberg] -- Compute effective cross section in each cell from the NTCdb. [Martin - D. Weinberg] -- Added global NTC distribution debugging diagnostic. [Martin D. - Weinberg] -- Added diagnostic print out for distribution of ratios of true cross - section to mean cross section. [Martin D. Weinberg] -- Print true bin edges rather than log bin edges when using log scaling. - [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Merged test version. [Martin D. Weinberg] -- Simplify electron temperature logic. [Martin D. Weinberg] -- Documentation updates and renumbered elec_elec from 300 to 7. [Martin - D. Weinberg] -- Added some doc strings and attempted to complete the use_cons - implementation for the hybrid method. [Martin D. Weinberg] -- Revert default electron mass to true electron mass. [Martin D. - Weinberg] -- Use Bodies() member of pCell to compute electron temperature in a - sample cell. [Martin D. Weinberg] -- Bump up the default number of integer attributes to hold speciesKey - and collision count (for debugging) [Martin D. Weinberg] -- Added test for hybrid species norm and fixed fencepost error in - ionization and recombination bookkeeping. [Martin D. Weinberg] -- Fix typo (and bug\!) [Martin D. Weinberg] -- Change from boost::tuple to std::tuple in Collide* [Martin D. - Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Fixed explicit energy conservation for hybrid algorithm. [Martin D. - Weinberg] -- Set interFlag for Hybrid method. [Martin D. Weinberg] -- Added interFlag to Hybrid algorithm. [Martin D. Weinberg] -- Revert previous MPI formatting. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Added correct size for specM communication. [Martin D. Weinberg] -- Updated method for computing table of hybrid species. [Martin D. - Weinberg] -- Added new routine to compute hybrid species fractions. [Martin D. - Weinberg] -- Fix normalization in species output. [Martin D. Weinberg] -- Remove cruft and a typo fix. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Fixed zero relative velocity handling. [Martin D. Weinberg] -- Updated output table for hybrid type. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Use size_t for species attribute counter. [Martin D. Weinberg] -- Additional debug diagnostics and fixes for species normalization for - hybrid algorithm. [Martin D. Weinberg] -- Disable deep debugging. [Martin D. Weinberg] -- Changed sample-cell logic to use new Bodies() method. Added - additional for the "hybrid" method. [Martin D. Weinberg] -- Set charge field to zero when generating ICs for the "hybrid" method. - [Martin D. Weinberg] -- Added temporary "hybrid" boolean to indicate hybrid method for - counting species. Need to find better, automatic way to do this. - [Martin D. Weinberg] -- Added additional sanity diagnostics. [Martin D. Weinberg] -- Added additional sanity diagnostics. [Martin D. Weinberg] -- Fixed sample-cell logic. [Martin D. Weinberg] -- Added additional sample-cell diagnostics. [Martin D. Weinberg] -- Debugging changes . . . still not there. [Martin D. Weinberg] -- Forgot to broadcast hybrid_pos. [Martin D. Weinberg] -- Fixed mistake in atomic number data type. [Martin D. Weinberg] -- Fixed reported location of nimax and ndmax. [Martin D. Weinberg] -- Increased limits in ParticleFerry.H. [Martin D. Weinberg] -- Added new hybrid type to CollideIon. [Martin D. Weinberg] -- Update initial condition routine for new hybrid type. [Martin D. - Weinberg] -- Fix the type coersion in xdr call. [Martin D. Weinberg] -- Add atomic database output member fct. [Martin D. Weinberg] -- Update interparticle spacing computation (although it will probably - only very rarely be needed) [Martin D. Weinberg] -- Again, didn't I just add these changes an hour ago??! Must have - overwritten them, so here they are again. [Martin D. Weinberg] -- Added atomic weights to PeriodicTable class. [Martin D. Weinberg] -- Again, didn't I just add these changes an hour ago??! Must have - overwritten them, so here they are again. [Martin D. Weinberg] -- Didn't I just add these same sanity checks an hour ago??! Must have - overwritten them, so here they are again. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Added before "Too many collisions" message. [Martin D. Weinberg] -- Revert "Fixed a few minor typos in the PeriodicTable class and added - additional sanity checking to the AtomicElement::set method" [Martin - D. Weinberg] - - This reverts commit 52e886dfeb511c9d7dba386dd45f2638212f8c41. -- Fixed a few minor typos and added additional sanity checking. [Martin - D. Weinberg] -- Added cross-section scaling to the configuration. [Martin D. Weinberg] -- Fixed up some white space and comments only. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Added user-suppled config file for CollideIon. [Martin D. Weinberg] -- Use periodic table db for storing cross section scales. [Martin D. - Weinberg] -- Added atomic data structure for future use. [Martin D. Weinberg] -- Updated for testing per-species cross-section scaling. [Martin D. - Weinberg] -- Updated interparticle spacing estimate per cell. [Martin D. Weinberg] -- Command-line-option clean up. [Martin D. Weinberg] -- Python routine to plot species fractions vs time or temp. [Martin D. - Weinberg] -- Apply the scaled cross section factor to particle interaction counts. - [Martin D. Weinberg] -- Fixed Particle.h/Particle.H header logic [again?] [Martin D. Weinberg] -- Test ratio of mean cell cross section to computed particle cross - section. [Martin D. Weinberg] -- Removed minor cruft. [Martin D. Weinberg] -- Final update for this branch before merge. [Martin D. Weinberg] -- Merge branch 'newQ' of https://bitbucket.org/mdweinberg/exp into newQ. - [Martin D. Weinberg] -- Changes to TopBase interface and RR computation. [Martin D. Weinberg] -- Fixed parallel test in testCrossSection. [Martin D. Weinberg] -- Use Hydrogenic cross sections for recombination to excited states. - [Martin D. Weinberg] -- Print NoDelC value on start-up. [Martin D. Weinberg] -- Added radiative recombination Gaunt factors. [Martin D. Weinberg] -- Minor changes for consistency. [Martin D. Weinberg] -- Fixed merge. [Martin D. Weinberg] -- Added Verner subroutine for photoionization cross sections. [Martin D. - Weinberg] -- Updated AxisymmetricBasis for correct ensemble coefficient variance. - [Martin D. Weinberg] -- Clean up diskprof tests; seems good to go. [Martin D. Weinberg] -- Added missing mutex initialization in EmpOrth9thd. [Martin D. - Weinberg] -- Added switch to compute sample variance rather than expectation - variance. [Martin D. Weinberg] -- Fixed up Particle.h/Particle.H issue in utils. [Martin D. Weinberg] -- Added header reading utility for eof cache. [Martin D. Weinberg] -- Fix to EmpOrth9thd for standalone behavior. [Martin D. Weinberg] -- PCA using expectation rather than sample variance. [Martin D. - Weinberg] -- Merge branch 'newQ' of https://bitbucket.org/mdweinberg/exp into newQ. - [Martin D. Weinberg] -- White space formatting changes only. [Martin D. Weinberg] -- Formatting changes in DSMC_spc_log. [Martin D. Weinberg] -- Added electron energy cloning on ionization (for testing only); and - added limits to plotSpecies.py. [Martin D. Weinberg] -- Added flag to suppress ionization, recombination, or both in weighted - method. [Martin D. Weinberg] -- Fixed logic in restriction to scattering only. [Martin D. Weinberg] -- Allow change in electron mass for testing. [Martin D. Weinberg] -- Cleaned up AlgOrth implementation for electron scattering. [Martin D. - Weinberg] -- Improved diagnostic output format. [Martin D. Weinberg] -- Merge branch 'newQ' of https://bitbucket.org/mdweinberg/exp into newQ. - [Martin D. Weinberg] -- Make electron energy conservation for scattering consistent with ions. - [Martin D. Weinberg] -- Merge branch 'newQ' of https://bitbucket.org/mdweinberg/exp into newQ. - [Martin D. Weinberg] -- Added excess diagnostics. [Martin D. Weinberg] -- Merge branch 'newQ' of https://bitbucket.org/mdweinberg/exp into newQ. - [Martin D. Weinberg] -- Fixed typo. [Martin D. Weinberg] -- Merge branch 'newQ' of https://bitbucket.org/mdweinberg/exp into newQ. - [Martin D. Weinberg] -- Added another energy conservation variant. [Martin D. Weinberg] -- Merge branch 'newQ' of https://bitbucket.org/mdweinberg/exp into newQ. - [Martin D. Weinberg] -- Update electron scattering for explicit energy conservation algorithm. - [Martin D. Weinberg] -- Merge branch 'newQ' of https://bitbucket.org/mdweinberg/exp into newQ. - [Martin D. Weinberg] -- More debugging of use_cons. [Martin D. Weinberg] -- Merge branch 'newQ' of https://bitbucket.org/mdweinberg/exp into newQ. - [Martin D. Weinberg] -- Merge branch 'newQ' of https://bitbucket.org/mdweinberg/exp into newQ. - [Martin D. Weinberg] -- Improved the TRACE_REAPPLY doc string. [Martin D. Weinberg] -- Merge branch 'newQ' of https://bitbucket.org/mdweinberg/exp into newQ. - [Martin D. Weinberg] - - Conflicts: - src/user/CollideIon.cc -- Added exact energy conservation trace algorithm option. [Martin D. - Weinberg] -- Fix inelasticWeight interaction type selection. [Martin D. Weinberg] -- Updates for splitting bookkeeping. [Martin D. Weinberg] -- Added delta KE in trace loss assignment by electrons and ions to main - algorithm. [Martin D. Weinberg] -- Delta KE in trace loss assignment by electrons and ions. [Martin D. - Weinberg] -- Separate scattering and inelastic reporting. [Martin D. Weinberg] -- Fix error in order of algorithm selection report. [Martin D. Weinberg] -- Added counter to count species id of collision pairs. [Martin D. - Weinberg] -- Fix energy conservation diagnostic when using TRACE_REAPPLY. [Martin - D. Weinberg] -- Added energy conservation label array to plotSpecies python module, - for convenience only. [Martin D. Weinberg] -- Added feature to immediately add splitting excess to COM. [Martin D. - Weinberg] -- Add electrone excess energy to the .species file. [Martin D. Weinberg] -- Added NTC distribution details for debugging. [Martin D. Weinberg] -- Fixes for new NTC selection algorithm. [Martin D. Weinberg] -- Added additional trace species debug option. [Martin D. Weinberg] -- Merge branch 'newQ' of https://bitbucket.org/mdweinberg/exp into newQ. - [Martin D. Weinberg] -- Change diagnostic percentiles for NTC sampling output. [Martin D. - Weinberg] -- Version bump for log file output. [Martin D. Weinberg] -- Minor fixes, new Quantile version seems ready to test. [Martin D. - Weinberg] -- Toggle interactive plot widget. [Martin D. Weinberg] -- Add new smoothing routines for collision type diagnosis. [Martin D. - Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] - - Conflicts: - src/user/Quantile.cc -- Added a termination hook to the ExternalForces collection. [Martin D. - Weinberg] -- Updates to NTC database to prevent MPI buffers from expanding. [Martin - D. Weinberg] -- Changed relaxtion quantile algorithm to P^2 quantile algorithm. - [Martin D. Weinberg] -- Rewrite quantile algorithm for NTC module. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Additional NTC diagnostic print out. [Martin D. Weinberg] -- Missing NTCFAC for electron scattering. [Martin D. Weinberg] -- Additional documentation for Collide. [Martin D. Weinberg] -- Add upscaling factor to NTC database. [Martin D. Weinberg] -- Add a single tag member to python module. [Martin D. Weinberg] -- Added test routine for reading SLGridSph cache. [Martin D. Weinberg] -- Limit collisional excitations to elements above fractional threshold. - [Martin D. Weinberg] -- Fixed meanF computation for Direct and Weight. [Martin D. Weinberg] -- Added suppression of collisional excitation if population is under a - given threshold. [Martin D. Weinberg] -- Make several of the plotting routines Python modules with - documentation that may be viewed with help() [Martin D. Weinberg] -- Simplify logic for Verner cross section bookkeeping, for future - reference; algorithm unchanged. [Martin D. Weinberg] -- Restore energy contribution from recombining electron for case without - electron subspecies only. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Looks like blunder in recombination energy assignment. [Martin D. - Weinberg] -- Removed dynfracR and changed the default value of dynfracD to 1000.0, - effectively disabling it for our standard simulation units. [Martin D. - Weinberg] -- Fix Verner charge offset. [Martin D. Weinberg] -- Increased default parameter line buffer in ParamParse from 512 to - 4096. [Martin D. Weinberg] -- Exposed verbose output control and interval variables in NTCdb as - global variables, settable by the user as ntc_verbose and ntc_chkpt, - respectively. [Martin D. Weinberg] -- Attempted fix for NTC serialization interval problem. [Martin D. - Weinberg] -- Formating updates for multistep level output. [Martin D. Weinberg] -- Merge branch 'testRV' [Martin D. Weinberg] -- Fixed bug in SLGridSph constructor call from Sphere class. [Martin D. - Weinberg] -- Changes to add r/v time step algorithm. [Martin D. Weinberg] -- Added new abbreviated particle transport class. This should insulate - the DiskHalo* codes from future changes to the Particle class. [Martin - D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Fixed index error in ionization stage naming for Verner cross section - database. [Martin D. Weinberg] -- Updates for new fields in CollideIon output files. [Martin D. - Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Added Python script for plotting psp2histoE output. [Martin D. - Weinberg] -- Added variable x-axis label. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Fixed preinstallation library flags in util Makefile.am. [Martin D. - Weinberg] -- Oops; captilized DOUBLE type. [Martin D. Weinberg] -- Should be passing shared pointer instead of raw pointer. Oops. - [Martin D. Weinberg] -- Updated energy loss algorithm for ionization to handle electron energy - loss owing to loss of electron from KE pool. [Martin D. Weinberg] -- Updates to enegy conservation algorithm. [Martin D. Weinberg] -- Update to Wa>Wb selection; not needed any longer. [Martin D. Weinberg] -- Fix typo (+ rather than +=) [Martin D. Weinberg] -- Fix dattrib read values from float (4-byte) PSP dump. [Martin D. - Weinberg] -- Add electron energy output. [Martin D. Weinberg] -- Energy conservation is fixed. [Martin D. Weinberg] -- Fixed up energy conservation for recombation without cooling for - testing. [Martin D. Weinberg] -- Added electron energy sharing for ionization interaction. [Martin D. - Weinberg] -- Added plotting/parsing utility for comparing mulitple *.species files. - [Martin D. Weinberg] -- Added additional debug lines to track down energy conservation - problem. [Martin D. Weinberg] -- Remove debugging tests from CollideIon. [Martin D. Weinberg] -- WIP on master: a34d8c5 Merge branch 'master' of - https://bitbucket.org/mdweinberg/exp. [Martin D. Weinberg] -- Allow threshold stopping to be toggled. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Removed the shared pointers from the NTC database to simply the - implementation and to reduce the size of the serialized version of the - database. Added a more stats to pspstatS. [Martin D. Weinberg] -- Script to plot energy contributions per species only. [Martin D. - Weinberg] -- Use the integrated differential free-free cross section. [Martin D. - Weinberg] -- Added globals for linking makegrid without VTK. Tested. [Martin - Weinberg [mdw@umass.edu]] -- Added cross section test routine; updated configure so that makegrid - will not be compiled if VTK is not available. [Martin D. Weinberg] -- Unset verbose debugging in electronGather() [Martin D. Weinberg] -- Fixed energy limit in Verner & Yakolev radiative recombination cross - section function. [Martin D. Weinberg] -- Added comments in the code about this change. [Martin D. Weinberg] -- Add parenthesis for disambiguation of the logic syntax. [Martin D. - Weinberg] -- Fix mistake in energy conservation check logic. [Martin D. Weinberg] -- Read cached json CollideIon config file on restart. [Martin D. - Weinberg] -- Increase default persistence interval to 10. [Martin D. Weinberg] -- Remove verbose debugging output from NTC.H. [Martin D. Weinberg] -- Needed to update ntcdb persistence to include the data from all nodes. - [Martin D. Weinberg] -- Serialize NTCdb for restarting. There may be other issues in - CollideIon that need attention as well. [Martin D. Weinberg] -- Fix restart problem for runtag.species file. [Martin D. Weinberg] -- Adjust Configuration.H for API change in Boost. [Martin D. Weinberg] -- Fix type mis-match in Configuration.event parsing. [Martin D. - Weinberg] -- Workaround for C++11 in property_tree xml reader/writer: use - std::string instead of char. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Added remaining CollideIon static parameters to json database. [Martin - D. Weinberg] -- Added json configuration parsing to CollideIon. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- An initial version of a JSON/XML parser for EXP. For the future . . . - [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Merge branch 'traceWeight' [Martin D. Weinberg] -- Merge branch 'traceWeight' [Martin D. Weinberg] - - Conflicts: - src/user/UserTreeDSMC.cc -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Fixed weighted species mass value. [Martin D. Weinberg] -- Added pspstatS: version of pspstat that prints gas species info. - [Martin D. Weinberg] -- Additional algorithm tweaking options for testing. [Martin D. - Weinberg] -- Additional fixes for direct method with electrons. [Martin D. - Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] - - Conflicts: - src/user/CollideIon.cc -- Add inelasticWeight algorithm flags to log. [Martin D. Weinberg] -- Enable use of direct algorithm with electron carriers. [Martin D. - Weinberg] -- Added ion and electron energies and temperatures for each type to - *.species file. [Martin D. Weinberg] -- Fixed blunder in use of "auto" loops: needed ref not copy. [Martin D. - Weinberg] -- Added debugging options as boolean flags. [Martin D. Weinberg] -- Added an alternative energy conservation algorithm for testing. - [Martin D. Weinberg] -- Momentum ratio distribution histogram for diagnostic debugging. - [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Add electron energy counter to dattrib. [Martin D. Weinberg] -- Tweak electron momemtum conservation algorithm for testing. [Martin D. - Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Fixed electron temperature, molecular weight error. [Martin D. - Weinberg] -- Fixed species reset error in specE diangostic. [Martin Weinberg] -- Want to see both specific and total electron energies for each - species. [Martin D. Weinberg] -- Merge with Eagle's copy. [Martin D. Weinberg] -- Reverted accidentally commited change made for testing only. [Martin - Weinberg] -- Compute electron energy per particle per element for equipartition - diagnostic. [Martin D. Weinberg] -- Clean up explicit electron energy conservation code. [Martin D. - Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Explicit electron scattering conservation algorithm. [Martin D. - Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] - - Conflicts: - src/user/CollideIon.cc -- Added trace species algorithm to electron scattering implementation. - [Martin D. Weinberg] -- Use boost filesystem to create debug files. [Martin D. Weinberg] -- More electron debugging tools. [Martin D. Weinberg] -- Additional tests for energy conservation in electron scattering - routine. [Martin D. Weinberg] -- Remove equal species debugging line. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Fix neutral-neutral trace energy conservation. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Missing factor 1/2 in electron energy. [Martin D. Weinberg] -- Fix merge conflict. [Martin D. Weinberg] -- Clean up electron energy computation per cell. [Martin D. Weinberg] -- Added electron molecular weight correction. [Martin D. Weinberg] -- Update electron energy units for output. Minor change to use_cons && - use_elec com algorithm. [Martin D. Weinberg] -- Added electron ensemble energy output. [Martin D. Weinberg] -- Add ion fractions to makeIon output. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] -- Updates for VTK in /usr/local. [Martin D. Weinberg] -- Added fix Coulombic logarithm factor. This could be computed from a - thermal estimate of the sample cell to derive the Debye radius . . . - maybe later. [Martin D. Weinberg] -- Merge changes for slurm detection back from traceWeight. Bump version - number: NEW MASTER IS 7.34. [Martin D. Weinberg] -- Merge branch 'traceWeight' [Martin D. Weinberg] -- Restore slurm detection for checkpoint timer. This somehow got lost - in the merge from traceWeight branch to master. [Martin D. Weinberg] -- Merge branch 'master' of https://bitbucket.org/mdweinberg/exp. [Martin - D. Weinberg] - - Conflicts: - src/user/UserTreeDSMC.cc -- Roll back c++11 changes in this branch, mistakenly committed. [Martin - D. Weinberg] -- Minor updates to master after merging traceWeight. [Martin D. - Weinberg] -- Additional comments in configure.ac. Removed testing cruft from - CollideIon.cc. [Martin D. Weinberg] -- Remind user to add -Wno-literal-prefix to reduce chattiness. [Martin - D. Weinberg] -- Updates for latest version of VTK (to be used on updated Eagle - cluster). [Martin D. Weinberg] -- Merge local changes. [Martin D. Weinberg] -- Added scattering counters for diagnosis. [Martin D. Weinberg] -- If libslurm is in the path, attempt to find remaining job time using - the slurm api. Otherwise, look for pbs. [Martin D. Weinberg] -- Implement slurm lib checkpoint timer functionality. [Martin D. - Weinberg] -- Updates for consistence between Direct and Weight methods for - electrons. [Martin D. Weinberg] -- Fixed typo in electron NTC diagnostics. [Martin D. Weinberg] -- Added some comment text; set all test debugging in inelasticWeight - OFF. [Martin D. Weinberg] -- Added electron NTC diagnostic output. [Martin D. Weinberg] -- Compute electron scattering separately from ions. [Martin D. Weinberg] -- Remove the trace species rejection test. [Martin D. Weinberg] -- Added new collision limited electron algorithm. [Martin D. Weinberg] -- Allow variable electron scattering algorithm (to ameliorate high - electron collision frequency). [Martin D. Weinberg] -- Fixed energy conservation check in inelasticTrace. [Martin D. - Weinberg] -- Merge branch 'traceWeight' of https://bitbucket.org/mdweinberg/exp - into traceWeight. [Martin D. Weinberg] -- Repaired energy conservation for electrons. [Martin D. Weinberg] -- Merge branch 'traceWeight' of https://bitbucket.org/mdweinberg/exp - into traceWeight. [Martin D. Weinberg] -- Minor cleaning. [Martin D. Weinberg] -- Start to clean up unneccessary debugging code. [Martin D. Weinberg] -- Deal with no-electron condition. [Martin D. Weinberg] -- Added separate electron and ion energy change diagnostic - distributions. [Martin D. Weinberg] -- Turn off verbose debugging, add banner warnings in log if experimental - algorithms are in use. [Martin D. Weinberg] -- Merge branch 'traceWeight' of https://bitbucket.org/mdweinberg/exp - into traceWeight. [Martin D. Weinberg] - - Conflicts: - utils/PhaseSpace/Makefile.am -- Merge branch 'traceWeight' of https://bitbucket.org/mdweinberg/exp - into traceWeight. [Martin D. Weinberg] -- Added scattering only option to CollideIon. [Martin D. Weinberg] -- Changes to Direct method to enable use_elec option. [Martin D. - Weinberg] -- Changes to direct method based on the use_elec enhancement. [Martin D. - Weinberg] -- Changed point and line types. [Martin D. Weinberg] -- Turn off cross-section debugging. [Martin D. Weinberg] -- Generalized psp2histoE to compute ion and electron temperatures. - Added plotting scripts to Analyzie for use with psp2histoE. [Martin D. - Weinberg] -- Routine for computing electron energy distribution. [Martin D. - Weinberg] -- Minor clean up. [Martin D. Weinberg] -- Allow multiple files to be parsed. [Martin D. Weinberg] -- Debugged species histogram. [Martin D. Weinberg] -- Add species to psp2histo1d. [Martin D. Weinberg] -- Fixed minor mistake in generateSelectionWeight. Not expecting this to - matter that much, but will test. [Martin D. Weinberg] -- Allow NOCOOL to be set in CollideIOn. [Martin D. Weinberg] -- Bump version number. [Martin D. Weinberg] -- Added setting memory limits and simply using system values without - reporting. [Martin D. Weinberg] -- Added equipartition flag. Fixed typo in equipartition algorithm. - [Martin D. Weinberg] -- Merge branch 'traceWeight' of https://bitbucket.org/mdweinberg/exp - into traceWeight. [Martin D. Weinberg] -- Code for enforcing equipartition of paired electrons and ions. [Martin - D. Weinberg] -- Merge branch 'traceWeight' of https://bitbucket.org/mdweinberg/exp - into traceWeight. [Martin D. Weinberg] -- Changed coefficient for Kramers cross section. [Martin D. Weinberg] -- Version bump. [Martin D. Weinberg] -- Merge branch 'traceWeight' of https://bitbucket.org/mdweinberg/exp - into traceWeight. [Martin D. Weinberg] -- Updated intialization output, identifying collision and rr types. - [Martin D. Weinberg] -- Fixed typo in vfac definition for inelasticWeight(). [Martin D. - Weinberg] -- Fixed broken vfac logic. [Martin D. Weinberg] -- Remove confusing vi definition in inelasticWeight in favor of direct - energy ratio. [Martin D. Weinberg] -- Separate ion vfac and electron vfac. [Martin D. Weinberg] -- More simplification of radiative cross section setting. [Martin D. - Weinberg] -- Debugged dynamic rr cross-section setting. [Martin D. Weinberg] -- Allow runtime selection of rad. recomb. cross-section types for - testing. [Martin D. Weinberg] -- Added radiative recombination cross section selection and reporting. - [Martin D. Weinberg] -- Track electron temperature. [Martin D. Weinberg] -- Updates to list analysis and increase field with in run.species - output. [Martin D. Weinberg] -- Increase output field width for run.species file. [Martin D. Weinberg] -- Restored omitted trace weight factor from collision probability. - [Martin D. Weinberg] -- Turn off NTC debugging by default. [Martin D. Weinberg] -- Fix energy logic in weighted routine. [Martin D. Weinberg] -- Fixes to diagnostics for better resolution. [Martin D. Weinberg] -- Removed deep debugging lines; no longer needed. [Martin D. Weinberg] -- Fixes to interface (which was breaking the algorithm owing to change - from pHOT to pCell passing). [Martin D. Weinberg] -- A few minor typos fixed in generateSelectionWeight(). [Martin D. - Weinberg] -- Additional comments. [Martin D. Weinberg] -- More debugging output. [Martin D. Weinberg] -- Added per species number count plots. [Martin D. Weinberg] -- Added circular_buffer for electron energy gain/loss diagnostic output. - [Martin D. Weinberg] -- Merge branch 'traceWeight' of https://bitbucket.org/mdweinberg/exp - into traceWeight. [Martin D. Weinberg] -- Merge branch 'traceWeight' of https://bitbucket.org/mdweinberg/exp - into traceWeight. [Martin D. Weinberg] - - Conflicts: - src/user/CollideIon.cc -- Too many std::endl in distribution outout. [Martin D. Weinberg] -- Added electron energy loss/gain diagnostic output. [Martin D. - Weinberg] -- Added trim to AsciiHisto. [Martin D. Weinberg] -- Fixed typographical mistake in velocity ratio. [Martin D. Weinberg] -- Added CL/MFP diagnostic distribution output. [Martin D. Weinberg] -- Sqrt wrong order in computing elecV and ionV diagnostics. [Martin D. - Weinberg] -- Fix typos in including AsciiHisto. [Martin D. Weinberg] -- Make this templated. [Martin D. Weinberg] -- Added ascii histogram distribution for electron and ions. [Martin D. - Weinberg] -- Update to fix typo in new IC version. [Martin D. Weinberg] -- Minor changes to weight version of selection member. [Martin D. - Weinberg] -- Added electron species. [Martin D. Weinberg] -- Report d(KE) in system units, not physical units. [Martin D. Weinberg] -- Remove the deque in favor of single element entry; uses less memory - and not subject to huge heap size for poor DSMC parameter choice. - [Martin D. Weinberg] -- Still another unit fix. Sigh. [Martin D. Weinberg] -- Added signal emission for too many NTC trials per cell. [Martin D. - Weinberg] -- More blunders in implementation of new algorithm fixed. Mostly - confused units. [Martin D. Weinberg] -- Fixed mistake in cell species iteration. [Martin D. Weinberg] -- Fix diagnostic mean-free path computation for consistency with trace - weight algorithm. [Martin D. Weinberg] -- Added comments to NTC.H only. [Martin D. Weinberg] -- Change "round" to "floor" to prevent oob in pcent vector. [Martin D. - Weinberg] -- Minor clean up of intialization array specification. [Martin D. - Weinberg] -- Change to running quantile rather than sorted quantile. [Martin D. - Weinberg] -- Quantile implementation for NTC product estimate. [Martin D. Weinberg] -- Changed NTC cell statistics from max to avg. [Martin D. Weinberg] -- Minor cleaning up. [Martin D. Weinberg] -- Update to generateSelectionWeight for consistency with standard NTC - algorithm. [Martin D. Weinberg] -- Added default NTC value setting from UserTreeDSMC. [Martin D. - Weinberg] -- Added larger prior value returned VelCrsAvg() before empirical - estimation is available. [Martin D. Weinberg] -- Change label again. [Martin D. Weinberg] -- Change output label for third tuple in NTCitem. [Martin D. Weinberg] -- Only log crat if we have a ntcF value above threshold. [Martin D. - Weinberg] -- CRAT debugging. [Martin D. Weinberg] -- Turn off reporting of VelCrs stanza after maxrpt outputs. [Martin D. - Weinberg] -- Fixed NTC accumulation logic. Shouldn't matter all that much. [Martin - D. Weinberg] -- Removed NTC structures from pCell/sCell classes and moved them to - Collide (where they belong!) This also fixes issues with pHOT - reconstruction. [Martin D. Weinberg] -- Rewrote _max structures. [Martin D. Weinberg] -- Fixed introduced mistake in species loop. [Martin D. Weinberg] -- Additional debugging in CollideIon. Surpress plotting columns with - *_E labels in *.species table. [Martin D. Weinberg] -- Minor changes to cross section accounting. [Martin D. Weinberg] -- Merge branch 'traceWeight' of https://bitbucket.org/mdweinberg/exp - into traceWeight. [Martin D. Weinberg] -- Removed ionization energy from radiative cooling increment. Fixed - density mistake in "weight" version of makeIon. [Martin D. Weinberg] -- Test suppression of equlibrium velocity. [Martin D. Weinberg] -- Added dof flag. [Martin D. Weinberg] -- Added dof logic back to code. [Martin D. Weinberg] -- Fixed energy leak, now try a full run. [Martin D. Weinberg] -- Removed spurious comments. [Martin D. Weinberg] -- Implemented const pointer interface for Collide class. [Martin D. - Weinberg] -- Change Collide interface to use const pointers to prevent stupid - mistakes. [Martin D. Weinberg] - - Merge branch 'traceWeight' of https://bitbucket.org/mdweinberg/exp into traceWeight - - Conflicts: - src/user/CollideIon.cc -- Minor rewrite of the Weight version (but now it's not conserving - energy correctly and I need to look at this in more detail). [Martin - D. Weinberg] -- Add reduced mass including electron as an interal subspecies. [Martin - D. Weinberg] -- Updates to diagnostic weights. [Martin D. Weinberg] -- Use reduced mass to compute equipartition electron velocity for - collision. [Martin D. Weinberg] -- Make selection algorithma gree with written notes (trace.pdf). [Martin - D. Weinberg] -- Merge branch 'traceWeight' of https://bitbucket.org/mdweinberg/exp - into traceWeight. [Martin D. Weinberg] -- Another few bugs squashed; main fix: using Direct cross section - computation insteead of Weight cross section computation. [Martin D. - Weinberg] -- Merge branch 'traceWeight' of https://bitbucket.org/mdweinberg/exp - into traceWeight. [Martin D. Weinberg] - - Conflicts: - src/user/CollideIon.cc -- Updates to fix mistake in super-particle interaction number. [Martin - D. Weinberg] -- Merge branch 'traceWeight' of https://bitbucket.org/mdweinberg/exp - into traceWeight. [Martin D. Weinberg] -- Added missing ZMList declaration. [Martin D. Weinberg] -- Merge branch 'traceWeight' of https://bitbucket.org/mdweinberg/exp - into traceWeight. [Martin D. Weinberg] -- Merge branch 'traceWeight' of https://bitbucket.org/mdweinberg/exp - into traceWeight. [Martin D. Weinberg] -- Fix species output file for weight method. [Martin D. Weinberg] -- A bit of cruft removal. [Martin D. Weinberg] -- Cleaned up molecular weight computatation from gas sample cell. - [Martin D. Weinberg] -- Fixed molecular weight computation. [Martin D. Weinberg] -- Added some debugging diagnostics. [Martin D. Weinberg] -- A few minor bug fixes. [Martin D. Weinberg] -- Implemented a hybrid trace particle scheme (more or less following - Boyd's conservative trace particle method). New scheme labeled - "weight" in enum selector. [Martin D. Weinberg] -- Regressed ratio changes in favor of direct cross section computation - for each trace component. [Martin D. Weinberg] -- Fixed sign blunder in Verner cross section. [Martin D. Weinberg] -- Updates for Verner radiative cross sections. [Martin D. Weinberg] -- Adding Verner cross section approximation. [Martin D. Weinberg] -- Merge branch 'c++11rc' of https://bitbucket.org/mdweinberg/exp into - c++11rc. [Martin D. Weinberg] - - Conflicts: - src/user/CollideIon.cc -- Updates of gas scripts for new output format with weightings. [Martin - D. Weinberg] -- Additional updates to trace algorithm. [Martin D. Weinberg] -- Another change to cross section weighting algorithm. [Martin D. - Weinberg] -- Test version using mean densities (not working as well as the old - original algorithm alas). Check in for a record of these changes. - [Martin D. Weinberg] -- Test an alternative refactored algorithm for trace particle - interactions. [Martin D. Weinberg] -- Compute mass-fraction weights in interaction sequence rather than - initially. [Martin D. Weinberg] -- Merge branch 'c++11rc' of https://bitbucket.org/mdweinberg/exp into - c++11rc. [Martin D. Weinberg] - - Conflicts: - src/user/CollideIon.cc -- Changed diagnostic fraction accumulation from pairs to number. [Martin - D. Weinberg] -- Fixed typo in energy per interaction computation. Ooops. [Martin D. - Weinberg] -- Another update to species counting. [Martin D. Weinberg] -- Clean up. Still need to remove verbose debugging stuff (or at least - turn it off). [Martin D. Weinberg] -- Test for pure mass fraction scheme. Needs to be clean up. [Martin D. - Weinberg] -- Fixes to new trace species scheme: added mean mass fraction as global - variable. [Martin D. Weinberg] -- More diagnostics and a bug fix introduced earlier today. [Martin D. - Weinberg] -- Turned off deep debugging for now. [Martin D. Weinberg] -- Fixed a particle mass bug. [Martin D. Weinberg] -- More erase removal in favor of clear(). [Martin D. Weinberg] -- Remove erase statements in favor of clear statements for containers. - [Martin D. Weinberg] -- Additional diagnostic info. [Martin D. Weinberg] -- Added some debugging to trace map. [Martin D. Weinberg] -- More updates to CollideIon trace species excess algorithm. [Martin D. - Weinberg] -- Keep excess list for ionizaton and recombination. [Martin D. Weinberg] -- Turn off debug diagnostic. [Martin D. Weinberg] -- Version bump. [Martin D. Weinberg] -- Maybe a bug in ionization/recombination trace logic? Check this. - [Martin D. Weinberg] -- Merge branch 'c++11rc' of https://bitbucket.org/mdweinberg/exp into - c++11rc. [Martin D. Weinberg] - - Conflicts: - utils/Analysis/ion_rate - utils/ICs/SphericalSL.h -- More C++ 11 updates. Fixed (regress) change to cross section booking - in CollideIon. [Martin D. Weinberg] -- Additional C++ 11 updates for iterators. [Martin D. Weinberg] -- Fixed minor iterator problem. [Martin D. Weinberg] -- Changed to auto iterator style for clarity. Needs to be tested. - [Martin D. Weinberg] -- Fixed a broken instance for loop that should have been an iterator for - loop. [Martin D. Weinberg] -- Changed iterators to auto. Test i1==i2 change. [Martin D. Weinberg] -- Added scripts that plot CHIANTI estimates. [Martin D. Weinberg] -- Fixed bad code in Z,C to name conversion. [Martin D. Weinberg] -- Update for nonstandard boost lib location. [Martin D. Weinberg] -- A few more minor changes for C++-11. [Martin D. Weinberg] -- Update for C++-11 compliance. [Martin D. Weinberg] -- Added version of plotting routine that plots Chianti estimate using - PyChianti. [Martin D. Weinberg] -- Attempt to speed up CollideIon by caching Cspline instances in the Ion - instance instead of recreating on each call. Fixed to constructor - ambiguity in SLGridSph. [Martin D. Weinberg] -- Fix for spherical cache file overwrite by cylindrical basis - generation. [Martin D. Weinberg] -- Deprecated the stripped down Particle.h structure in favor of the full - Particle.H structure to prevent confusion. Should not affect - performance in any significant way (I hope). [Martin D. Weinberg] -- Add monopole mass computation to multimass coordinate generation - routine. [Martin D. Weinberg] -- Fix bug in positioning file pointer. [Martin D. Weinberg] -- Deprecated the "stripped-down" version of the Particle structure to - prevent confusion. The performance hit should be minor (I hope). - [Martin D. Weinberg] -- Position the file stream pointer inside of GetParticle by default. - [Martin D. Weinberg] -- Updated blas and lapack m4 macros. [Martin D. Weinberg] -- Remove C and Z fields from lightweight Particle class. [Martin D. - Weinberg] -- Additional comments only. [Martin D. Weinberg] -- Merge branch 'ExpION' of https://bitbucket.org/mdweinberg/exp into - ExpION. [Martin D. Weinberg] - - Conflicts: - src/user/Collide.cc -- Added minimum time interval for effort reporting. [Martin D. Weinberg] -- Version bump. [Martin D. Weinberg] -- Rewrite of the heavy-weight BarrierWrapper. Incorpored BWData class - definition into BarrierWrapper.H. [Martin D. Weinberg] -- Additional BarrierWrapper debugging. [Martin D. Weinberg] -- Merge branch 'ExpION' of https://bitbucket.org/mdweinberg/exp into - ExpION. [Martin D. Weinberg] -- Fixes to tree update ordering and diagnostic return from - Collide::collide() [Martin D. Weinberg] -- Merge branch 'ExpION' of https://bitbucket.org/mdweinberg/exp into - ExpION. [Martin D. Weinberg] -- Suppress diagnostic accumulation for empty levels in pHOT hierarchy. - [Martin D. Weinberg] -- Change collide.effort file writing to MPI data gather with writing - from root node. [Martin D. Weinberg] -- Use energy/volume in *.ION_coll. [Martin D. Weinberg] -- Added log scale option for energy-loss plots. [Martin D. Weinberg] -- Additional fixes for multiple timestep algorithm. [Martin D. Weinberg] -- Reenable multiple time steps. [Martin D. Weinberg] -- Removed _debug suffixes; who needs those extra characters? [Martin D. - Weinberg] -- Comments, cruft removal, and fix to *.species logic for proper - restarts. [Martin D. Weinberg] -- Added marker size flag. [Martin D. Weinberg] -- Merge branch 'ExpION' of https://bitbucket.org/mdweinberg/exp into - ExpION. [Martin D. Weinberg] -- Updated and added new analysis programs and scripts. [Martin D. - Weinberg] -- Version bump. [Martin D. Weinberg] -- O Restored the templated version Cspline and updated Ion and - interactSelect accordingly o Added python analysis scripts/programs - for CollideIon diagnostics to Analysis directory. [Martin D. Weinberg] -- Print mass fractions not number fractions for species output using - direct DSMC scheme in CollideIon. [Martin D. Weinberg] -- O Fixed mistake in interaction rate for "off diagnonal" species o - Updated comments accordingly. [Martin D. Weinberg] -- O Added molecular weight value for temperature computation o Corrected - typo in mean molecular weight evaluation o Fixed missing - syncrhonization of di_head in Ion class o Renamed the template version - of Cspline and hard-coded a double-double implementation. [Martin D. - Weinberg] -- Added diagnostic output of array sizes on mismatch. [Martin D. - Weinberg] -- Let root node do the data base reads and send db to remaining nodes. - [Martin D. Weinberg] -- Additional comments for trace method. [Martin D. Weinberg] -- Some code cleaning. [Martin D. Weinberg] -- Removed debug lines. Free-free stuff appears to be fixed. More tests - still needed. [Martin D. Weinberg] -- Merge branch 'ExpION' of https://bitbucket.org/mdweinberg/exp into - ExpION. [Martin D. Weinberg] -- Experiment with differing energy grid range. [Martin D. Weinberg] -- Fix mistakes in Greene's statement of the Elwert-Bethe cross section. - [Martin D. Weinberg] -- Try Greene's version of the Elwert approx. [Martin D. Weinberg] -- Merge branch 'ExpION' of https://bitbucket.org/mdweinberg/exp into - ExpION Rename some routines for clarity. [Martin D. Weinberg] -- Attempt to fix blunders in FF cross section selection. [Martin D. - Weinberg] -- Simplified inelasticTrace() logic by removing tdelE. [Martin D. - Weinberg] -- Fixes to output formating. [Martin D. Weinberg] -- Merge branch 'ExpION' of https://bitbucket.org/mdweinberg/exp into - ExpION. [Martin D. Weinberg] -- Added temperature to ION_coll output. [Martin D. Weinberg] -- Whitespace for readability only. [Martin D. Weinberg] -- Playing with double counting factor in interaction rate. [Martin D. - Weinberg] -- Merge branch 'ExpION' of https://bitbucket.org/mdweinberg/exp into - ExpION. [Martin D. Weinberg] - - Conflicts: - src/user/CollideIon.cc -- Merge branch 'ExpION' of https://bitbucket.org/mdweinberg/exp into - ExpION. [Martin D. Weinberg] -- Added column indices to .ION* output. [Martin D. Weinberg] -- Updates to *ION* output. [Martin D. Weinberg] -- Added column index headers to *ION* debug files. [Martin D. Weinberg] -- Missing keyPos initialization in Component stream constructor. [Martin - D. Weinberg] -- Fixed double-counting book keeping in interaction rate. [Martin D. - Weinberg] -- Fixed numerical error in cross section unit conversion in TopBase. - Looks good to go now. [Martin D. Weinberg] -- Added TopBase cross section evalution. [Martin D. Weinberg] -- Merge branch 'ExpION' of https://bitbucket.org/mdweinberg/exp into - ExpION. [Martin D. Weinberg] -- Cleaned up testing cruft in radiative recombination cross section - routines. [Martin D. Weinberg] -- Additional comments and cruft removal. [Martin D. Weinberg] -- Updated numerical value of Mewe (typo from Brandt's version it - appears). [Martin D. Weinberg] -- Updated the Mewe computation. [Martin D. Weinberg] -- Bug fix to Kramers. Need to fix Mewe and retry. [Martin D. Weinberg] -- Added summation over levels in Kramers. [Martin D. Weinberg] -- Need to add sum over levels to Kramer's cross section with Milne - relation. [Martin D. Weinberg] -- Added Kramers b-f cross section with Milne f-b rule. [Martin D. - Weinberg] -- Added additional documentation for new class members. Still need to - update Kramers relation to include Milne relation. [Martin D. - Weinberg] -- Added Milne-based radiative recombination cross section. [Martin D. - Weinberg] -- Refactor storage of CHIANTI data. [Martin D. Weinberg] -- Still experimenting with recombination cross section. Will implement - an explicit Milne relation version. [Martin D. Weinberg] -- Clean up some cruft. Need to study ionization and recombination cross - sections. [Martin D. Weinberg] -- Revise diagnostic temperature computation. [Martin D. Weinberg] -- Bump version #. [Martin D. Weinberg] -- Missing index increment in temperature diagnostic estimate. [Martin D. - Weinberg] -- Remove deprecated local fft library. [Martin D. Weinberg] -- - Fixed previous cruft left over from Brandt's changes to the phase- - space record - More diagnostics and bug fixes to Trace. [Martin D. - Weinberg] -- Fixed bug in collisional cross-section data passing. [Martin D. - Weinberg] -- Updates to ionization/recombination weight changes. [Martin D. - Weinberg] -- Added changes to weight computation again. [Martin D. Weinberg] -- More work on weight computation and update. [Martin D. Weinberg] -- Updates for new trace-species algorithm. [Martin D. Weinberg] -- Merge branch 'traceSpecies' of https://bitbucket.org/mdweinberg/exp - into traceSpecies. [Martin D. Weinberg] - - Conflicts: - src/user/CollideIon.cc -- Recombination/Ionization account seems to be off . . . needs more - work. [Martin D. Weinberg] -- Tweaks to algorithm rates for testing. [Martin D. Weinberg] -- - Fixed inverse molecular weight necessary to compute number densities - for cross sections. - Minor documentation fixes and cruft - removal. [Martin D. Weinberg] -- Changed mass weighting to number weighting in cross section - computation for trace algorithm. [Martin D. Weinberg] -- Looks like a mistake in E_rel energy that would effect Helium (as - observed in tests). Test a fix. [Martin D. Weinberg] -- Fixed typo in inelastic energy accumulation for trace algorithm. - [Martin D. Weinberg] -- Remove deprecated "deltaE" variable in CollionIon. [Martin D. - Weinberg] -- One more precision bump on printSpecies output. [Martin D. Weinberg] -- Bumped up precision in species output. [Martin D. Weinberg] -- Missing particle weight update (oops!) [Martin D. Weinberg] -- Minor change to species diagnostics; code cleaning and output - precision change for readability. [Martin D. Weinberg] -- Fixed specM construction for trace fraction diagnostics. [Martin D. - Weinberg] -- Include dynamical molecular weight computation. [Martin D. Weinberg] -- Adjusted trace species rates to account for corss sections of both - interactors. [Martin D. Weinberg] -- Another missed instance of unsigned rather than double. Initialized - some variables to shut up the compiler. [Martin D. Weinberg] -- Forgotten update to variable type in collDiag MPI reduction. [Martin - D. Weinberg] -- Make sure selectInteract does not call for spline for fewer than 3 - points. [Martin D. Weinberg] -- Need to instantiate collide before calling gatherSpecies. [Martin D. - Weinberg] -- Blunder in nsel assignment fixed. [Martin D. Weinberg] -- Bug fixes in implementation. [Martin D. Weinberg] -- More fixes to trace algorithm. Using probabilities rather than MC - interactions for trace components. [Martin D. Weinberg] -- A few minor fixes in degree-of-freedom handling for Trace Algorithm. - [Martin D. Weinberg] -- Continued revisions and implementation of Trace Species Algorithm. - [Martin D. Weinberg] -- Continuing to implement Trace Particle scheme. [Martin D. Weinberg] -- Preliminary attempt at trace species implementation. [Martin D. - Weinberg] -- Some additional comments; turned off verbose cross-section debugging - by default. [Martin D. Weinberg] -- Merge branch 'ExpION' of https://bitbucket.org/mdweinberg/exp into - ExpION. [Martin D. Weinberg] -- More work on elastic scattering branches. [Martin D. Weinberg] -- Remove debugging flags for production. [Martin D. Weinberg] -- Multithreading fixes and mnemonics for interaction types using enums. - [Martin D. Weinberg] -- Updated energy accounting bug in collisional cross-section vector. - [Martin D. Weinberg] -- Replace accidentally deleted blocks of code in the cross-section - computation. [Martin D. Weinberg] -- Fixes to cross section formula. [Martin D. Weinberg] -- Removed E_thermal stuff. Makes no sense to me. [Martin D. Weinberg] -- Merge branch 'ExpION' of https://bitbucket.org/mdweinberg/exp into - ExpION. [Martin D. Weinberg] -- Collect mean collision energy per particle, not super particle. - [Martin D. Weinberg] -- Merge branch 'ExpION' of https://bitbucket.org/mdweinberg/exp into - ExpION. [Martin D. Weinberg] -- Fix divide-by-zero in ION energy diagnostic when no interactions exist - for a particular specie. [Martin D. Weinberg] -- Added collision diagnostics for each ion species (for debugging). - Removed verbose pHOT_cell* files by default. Set DEBUG_EXTRA=true to - restore old behavior. [Martin D. Weinberg] -- Merge branch 'ExpION' of https://bitbucket.org/mdweinberg/exp into - ExpION. [Martin D. Weinberg] -- Added separate electron velocity upscale factors for each super - particle. [Martin D. Weinberg] -- Comments only. [Martin D. Weinberg] -- Minor bug fixes. [Martin D. Weinberg] -- More updates to COM energy distribution. [Martin D. Weinberg] -- Restored per-node list of ionizatoin states on start-up. [Martin D. - Weinberg] -- Updated comments. [Martin D. Weinberg] -- Forgot C update in particle key. [Martin D. Weinberg] -- Missing assignment of use_key fixed. [Martin D. Weinberg] -- Additional comments. [Martin D. Weinberg] -- Cleaned up species map construction. [Martin D. Weinberg] -- Merge branch 'speciesAttribute' of - https://bitbucket.org/mdweinberg/exp into speciesAttribute. [Martin D. - Weinberg] -- Fix MPI mistake in species diagnostic gather in UserTreeDSMC. [Martin - D. Weinberg] -- White space changes only, for readibility. [Martin D. Weinberg] -- Removed out-of-order warning. [Martin D. Weinberg] -- More sanity checks on particle position flags. [Martin D. Weinberg] -- Removed some cruft. [Martin D. Weinberg] -- Get species key column from Component. [Martin D. Weinberg] -- Remove Z,C fields from Particle. [Martin D. Weinberg] -- Merge branch 'ExpION' of https://bitbucket.org/mdweinberg/exp into - ExpION. [Martin D. Weinberg] -- Forgot electron speed correction to effective cross section. Now - included. [Martin D. Weinberg] -- Restored Brandt's "asserts" for debugging. [Martin D. Weinberg] -- Tests of recombination cross section with Spitzer formula. [Martin D. - Weinberg] -- Minor fixes. [Martin D. Weinberg] -- Merge branch 'ExpION' of https://bitbucket.org/mdweinberg/exp into - ExpION. [Martin D. Weinberg] - - Conflicts: - src/user/Collide.cc - src/user/CollideIon.cc -- Updated scattering cross sections. [Martin D. Weinberg] -- Fixed indexing bug in selecting particles for interaction. [Martin D. - Weinberg] -- Fixed goof in body indexing for cell collision selection. [Martin D. - Weinberg] -- Cross-section computation simplification. [Martin D. Weinberg] -- Simplified initial per cell total cross section computation. [Martin - D. Weinberg] -- Fixed up a few minor mistakes. [Martin D. Weinberg] -- Updated ICs for internal energy variable. [Martin D. Weinberg] -- Updates for internal energies. Still need to update IC code. [Martin - D. Weinberg] -- Update for internal energy computation (NOT DONE) [Martin D. Weinberg] -- Fixed counter diagnostics. [Martin D. Weinberg] -- Test of full cross-section*v algorithm. [Martin D. Weinberg] -- Split inelastic and cross section computations for DSMC particle - selection. [Martin D. Weinberg] -- Need to add cross section average for DSMC particle selection - algorithm. [Martin D. Weinberg] -- Fix mass assignment blunder in makeIonIC.cc. [Martin D. Weinberg] -- Removed W1,W2 weights. [Martin D. Weinberg] -- Typo: mistakenly included reciprocal of statistical weights. [Martin - D. Weinberg] -- Added statistical weight member function to Collide class. [Martin D. - Weinberg] -- More typo fixes (oops). [Martin D. Weinberg] -- More work on collision selection rules. [Martin D. Weinberg] -- Typo in mean molecular weight computation. [Martin D. Weinberg] -- Fixed broken mean molecular weight for temperature diagnostic. [Martin - D. Weinberg] -- Cruft removal and changes to selection logic. [Martin D. Weinberg] -- No need to compute scattering cross sections twice. Combined into one - initial computation for each pair. [Martin D. Weinberg] -- Remove tests with boosted electron velocity (just curious). [Martin D. - Weinberg] -- Merge branch 'ExpION' of https://bitbucket.org/mdweinberg/exp into - ExpION. [Martin D. Weinberg] -- Separate interaction energy and shareable energy. [Martin D. Weinberg] -- Added geometric cross section from computed atomic radii. [Martin D. - Weinberg] -- Merge branch 'ExpION' of https://bitbucket.org/mdweinberg/exp into - ExpION. [Martin D. Weinberg] -- Revert to "pure" DSMC with statistical weights for multimass issues. - [Martin D. Weinberg] -- Merge branch 'ExpION' of https://bitbucket.org/mdweinberg/exp into - ExpION. [Martin D. Weinberg] -- Cruft removal and more comments. [Martin D. Weinberg] -- Turn off cross-section debugging (the default setting). [Martin D. - Weinberg] -- Formatting changes only. [Martin D. Weinberg] -- Take ratio of final cross section to initial cross section in - write_cross_debug() [Martin D. Weinberg] -- Fix cross-section debugging thread issue. [Martin D. Weinberg] -- Logic error fix in write_cross_debug() [Martin D. Weinberg] -- Added cross-section debugging code for testing scattering vs total - cross section. [Martin D. Weinberg] -- Updated totalCrossSection to return the total scattering cross - section. [Martin D. Weinberg] -- Missing hsdiam factor from Collide constructors. [Martin D. Weinberg] -- More cruft removal. [Martin D. Weinberg] -- More documentation and cruft removal. Question about collFrac in - comments. [Martin D. Weinberg] -- Added diamfac parameter and hard-sphere parameter to all Collide - classes for consistency with CBA. Removed multiple accounting for - scattering cross sections. [Martin D. Weinberg] -- Some minor cruft removal. [Martin D. Weinberg] -- Added additional unit conversion constants to UserTreeDSMC - instantiation info. [Martin D. Weinberg] -- Print mass fractions in each species. [Martin D. Weinberg] -- More debugging cruft removal. [Martin D. Weinberg] -- Added additional documentation. [Martin D. Weinberg] -- Rad recomb loses the electron KE. [Martin D. Weinberg] -- Removed more cruft. Fixed error, that I introduced, in cross section - scaling. [Martin D. Weinberg] -- Forgot the energy unit scaling. [Martin D. Weinberg] -- Another fix to energy per dof computation. [Martin D. Weinberg] -- Remove some of the chatty output. [Martin D. Weinberg] -- Missing Elastic.cc in source list for libdsmc. [Martin D. Weinberg] -- Merge branch 'ExpION' of https://bitbucket.org/mdweinberg/exp into - ExpION. [Martin D. Weinberg] -- Try new c.o.m. energy computation. [Martin D. Weinberg] -- Added Elastic scattering cross section implementation to CollideIon. - [Martin D. Weinberg] -- Merge branch 'ExpION' of https://bitbucket.org/mdweinberg/exp into - ExpION. [Martin D. Weinberg] -- Changes to diagnostics. Need to include total cross section. [Martin - D. Weinberg] -- Fix up Analysis routines for new Particle definition. More decrufting - of CollideIon. [Martin D. Weinberg] -- Test routine for Elastic.cc. [Martin D. Weinberg] -- Added elastic scattering data base. Still needs to be integrated with - the CollideIon class. [Martin D. Weinberg] -- Make sure that diagnostic debug file for CollideIon is opened for - appending. [Martin D. Weinberg] -- Fixed MPI_IN_PLACE mistake (oops, how many times have I done this??!) - [Martin D. Weinberg] -- A few minor fixes to the MPI sync for CollideIon diagnostics. [Martin - D. Weinberg] -- Merge branch 'ExpION' of https://bitbucket.org/mdweinberg/exp into - ExpION. [Martin D. Weinberg] -- Added MPI stuff for CollideIon diagnostics. Added missing variables - for linking to makeIon. [Martin D. Weinberg] -- Merge branch 'ExpION' of https://bitbucket.org/mdweinberg/exp into - ExpION. [Martin D. Weinberg] -- Updates including changing Z, C from unsigned char to unsigned short - and updates to diagnostic output in CollideIon. [Martin D. Weinberg] -- Merge branch 'ExpION' of https://bitbucket.org/mdweinberg/exp into - ExpION. [Martin D. Weinberg] - - Conflicts: - utils/ICs/Makefile.am -- Updates for latest version of CHIANTI. [Martin D. Weinberg] -- Use "unsigned short" rather than "unsigned char"; too many - difficulties in native char conversion. Fix up to CollideIon - interaction selection logic. [Martin D. Weinberg] -- Merge branch 'ExpION' of https://bitbucket.org/mdweinberg/exp into - ExpION. [Martin D. Weinberg] -- More updates to initialization routine. [Martin D. Weinberg] -- Updates to makeIonIC. [Martin D. Weinberg] -- Merge branch 'ExpION' of https://bitbucket.org/mdweinberg/exp into - ExpION. [Martin D. Weinberg] -- Added plasma DSMC initialization test code. Still to be debugged. - [Martin D. Weinberg] -- Attempted to recast all int --> unsigned char for Z and C. More - comments and cruft removal. Removed implicit namespace declarations - for clarity. [Martin D. Weinberg] -- Made a full pass through Brandt's code, added comments, changed some - data types and containers for efficiency. [Martin D. Weinberg] -- Added a page for Ion implementation details. [Martin D. Weinberg] -- Added some more documentation and performed a little clean-up on - Brandt's coding style. [Martin D. Weinberg] -- Spell checked. [Martin D. Weinberg] -- Fixed the formating for Brandt's documentation. [Martin D. Weinberg] -- Missing doc file from Brandt's tree. [Martin D. Weinberg] -- Merge of Brandt Gaches new source tree. [Martin D. Weinberg] -- Call every force class independent of the number of particles in the - current process at the current level. This is a slight increase in - CPU time but allows the correct operation of routines that do not - separate into coefficient evaluation and force evaluation steps. - [Martin Weinberg] - - Changed the name of the SatFix proxy which was being missed under the - Debian Wheezy compile for some reason. Is this a namespace problem? - Or a linking problem? Not sure. -- Remove deprecated libeigen from configure.ac. [Martin D. Weinberg] -- Attempted to recast all int --> unsigned char for Z and C. More - comments and cruft removal. Removed implicit namespace declarations - for clarity. [Martin D. Weinberg] -- Made a full pass through Brandt's code, added comments, changed some - data types and containers for efficiency. [Martin D. Weinberg] -- Added a page for Ion implementation details. [Martin D. Weinberg] -- Added some more documentation and performed a little clean-up on - Brandt's coding style. [Martin D. Weinberg] -- Spell checked. [Martin D. Weinberg] -- Fixed the formating for Brandt's documentation. [Martin D. Weinberg] -- Missing doc file from Brandt's tree. [Martin D. Weinberg] -- Merge of Brandt Gaches new source tree. [Martin D. Weinberg] -- Remove the deprecated ICs directory from the ExpMPI repository and - promote all directories to the top level. [Martin D. Weinberg] -- Remove old CVS directory; I don't even recall how to use CVS. [Martin - D. Weinberg] -- Fixing rare bug in repartition cell exchange. [weinberg] -- Improvements to particle/cell handling. Tried and hopefully succeeded - in finding a bug that seems to occur for dense gridding that I beleive - was due to multiple body-cell pairs that were not correctly identified - with the correct particle sequence id. Testing now. [weinberg] -- A few minor bug fixes. [weinberg] -- Added counts to shocktube trace. [weinberg] -- Allow parsing of both command line global options and file option - file. [weinberg] -- More clean ups based on g++-4.7.3 to get to the current C++ standard. - [weinberg] -- Missing helper class defs for BarrierWrapper. [weinberg] -- A bit of clean up and more comments. [weinberg] -- Fixed typo in binary particle write routine. [weinberg] -- Added variable, aindex, for toggle use of sequence variable for input - ascii file. [weinberg] -- Move particle reads and write from Component to Particle class. - [weinberg] -- More minor fixes. [weinberg] -- Fixed that tiny and irrelevant, but hard to find bug in the - multithreaded version. [weinberg] -- Updates for new PSP version. [weinberg] -- Added header label. [weinberg] -- Fixed mistake in UserEBar filenaming and makegrid option parsing. - [weinberg] -- Fixed iterator problem in Output for arrays. Added separate time - scale coefficient for escape time scale. [weinberg] -- Updates for C++ ANSI. Fixed typo in time step computation. [weinberg] -- Bump version # [weinberg] -- Fixes to psp utilities for real4 and real8 types. Fix to multiple - species cross section initialization. [weinberg] -- Clarified debugging options by placing global variables governing - these options at the top of the source file. [weinberg] -- BarrierWrapper updates for debugging MPI synchronization. The - BarrierWrapper can now be turned on and off in the global stanza of - the input file. The wrapper will report long barrier waits and - attempt to detect synchronization problems. [weinberg] -- Missing new source file. [weinberg] -- Remove some verbose debugging output. [weinberg] -- Bump version # [weinberg] -- More changes for float and double fields in PSP output files. - [weinberg] -- Updates for real4 and real8 types in phase-space output. [weinberg] -- OutPS* will write floats rather than doubles. [weinberg] -- Updated PSP classes for double and single precision output. [weinberg] -- A few fixes for DEBUG output in pHOT and UserTreeDSMC. [weinberg] -- Fix m4 macros for latest autoconf. [weinberg] -- Fix a few minor goofs. [weinberg] -- Added addtional documentation. [weinberg] -- Draft refactorization of the Collide routines. [weinberg] -- More edits. [weinberg] -- Some refactoring updates. [weinberg] -- Interim update; still refactoring. [weinberg] -- Version bump. [weinberg] -- Fixes and enhancements to multistep diagnostics. Comments only in - AxisymmetricBasis. [weinberg] -- PCA fixes. Seems to be working for the sphere. All that I tested. - [weinberg] -- Fix typo. [weinberg] -- Changed name from selector to pca throughout. Provided comments in - pca diagnostic output and check for <0 eigenvalues. [weinberg] -- Fixes for mstep fencepost orientation. [weinberg] -- Some fixes and updates for PCA. [weinberg] -- Mstep order change for testing. [weinberg] -- Removed the erroneous posnsync option altogether. [weinberg] -- Comments only. [weinberg] -- Added output fraction parsing script. [weinberg] -- Minor updates. [weinberg] -- Add additional output precision. [weinberg] -- Make the code work (again) for a single species. [weinberg] -- Simple box statistics. [weinberg] -- Another typo!!! [weinberg] -- Again. [weinberg] -- Multispecies bug in pCell total accumulation fixed. [weinberg] -- Debugged the _new_ debugging output in UserTreeDSMC. [weinberg] -- Typo fix. [weinberg] -- Consistent counting for collisions. [weinberg] -- Multiple species update for DSMC. [weinberg] -- Eliminate computation of coefficients for multilevel timesteps if - there are no particles at current or higher time step levels. - [weinberg] -- Add default mass fractions. [weinberg] -- Additional diagnostic routine, restrict_order, in EmpOrth9thd.cc. Fix - restart error in UserSNheat. [weinberg] -- Added coefficient output. [weinberg] -- Make Jeans initialization the default method. Fixed a profile_diag - linear/log switch. [weinberg] -- Added multimass time-step level info to OrbTrace. [weinberg] -- Revert the last mistaken change. [weinberg] -- Fixed typo. [weinberg] -- Added diagnostics. Removed a check that was causing erroneous values - of kappa. [weinberg] -- Fixed added all versions of disk generation (jeans with asymmetric - drift, jeans without asymmetric drift and epicyclic). Fixed missing - assignments in one version of the constructor. [weinberg] -- Make sure gen_point uses a different random seed on each node. - [weinberg] -- Force mass conservation for multimass. [weinberg] -- Added mass ratio to debug output. [weinberg] -- Remove the epsilon from time step checking. [weinberg] -- Make profiles based on time intervals rather than step counts. - [weinberg] -- Cleaned up a few mistakes. Should be ready to go. [weinberg] -- Routine to spit out spherical table computed for each step. [weinberg] -- Added missing source; fixed an MPI error in MPIAllreduce. [weinberg] -- Additional verbose diagnostics. [weinberg] -- Added missing storage allocations to arrays for the frequency - computation in one of the constructors. Uncommented the terms that - evaluate the forces from the fields rather than the monopole terms. - Fixed usage error in MPI_Allreduce. [weinberg] -- Added number counts per bin to makegrid. [weinberg] -- Needed to zero out mm0. [weinberg] -- Missing synchronization statement. [weinberg] -- Fixed boo boo in heating computation. [weinberg] -- Stochastic star formation + SN generator for gas. [weinberg] -- Forgot return value for read_eof_header. [weinberg] -- Only read the header in empinfo. [weinberg] -- Fixed up Makefile for Analysis dir. [weinberg] -- Initialize a EMP ortho instance from a save/cache file. [weinberg] -- Left in an mistaken output line in binary file output. [weinberg] -- Missing source check in. [weinberg] -- Fixed typos in option list. [weinberg] -- Missing boost include path flag. [weinberg] -- Add boost program options. [weinberg] -- Added makegrid routine to utils/Analysis tree. [weinberg] -- Updates for Ubuntu 11.04. [weinberg] -- Clean out some cruft. [weinberg] -- Include extra checks on radial gridding and additional energy - diagnostics. [weinberg] -- Deal with the ordering problem introduced by the "indexing" option. - [weinberg] -- Undefined variable in Cylinder due to the MixtureBasis stuff. Sigh . - . . [weinberg] -- Example input and model files. [weinberg] -- Allow user to choose cmap option for Cylinder. [weinberg] -- Fixed more missing global variables (outdir and runtag). [weinberg] -- Missing globals. [weinberg] -- Update for indexing. [weinberg] -- Tag the tracefiles by run id. [weinberg] -- Additional global debugging functions. [weinberg] -- Generalized sanity check for CollideLTE. Changed default parameter - for cooling computation time step. [weinberg] -- Updates for additional particle info. [weinberg] -- Add more particle info to pspinfo. [weinberg] -- Formatting changes only. [weinberg] -- Added shearing sheet equations. [weinberg] -- Documentation update and fix fence post error (!) [weinberg] -- Removed debug line. [weinberg] -- Header output. [weinberg] -- A few code clean-ups. No bug fixes. [weinberg] -- Use vector spatial IC rather than R_p in y-dir only. [weinberg] -- M user/UserTreeDSMC.cc M user/LinearOrbit.cc M - user/UserTreeDSMC.H. [weinberg] -- Additional doc. Remove diamCBA. [weinberg] -- Added total (large) step timing diagnostics. [weinberg] -- Fixed up the timing routines for clarity. Reset the timers outside of - the myid=0 stanza in t UserTreeDSMC (a bug in the diagnostic routine - but will not have affected the resutls). [weinberg] -- White space changes only. [weinberg] -- Clean up TwoCenter center assignment logic and renamed MultiCenter to - EJcom. [weinberg] -- Additional diagnostics, update COM per level during level - readjustment. [weinberg] -- Generalized for multicenter disk and cylinder components. [weinberg] -- Recent minor changes. [weinberg] -- Included dynamical friction in UserSatWake orbit. [weinberg] -- Allow m=0 contribution. [weinberg] -- Make explicit temporary in tranpose for both Vector and CVector. - [weinberg] -- Fix up error in Transpose, sigh. [weinberg] -- More updates for UserSatWake (still appears to be a bug somewhere) - [weinberg] -- More updates for satellite-induced halo wake. [weinberg] -- Added backtraces for Vector, Matrix, CVector, CMatrix errors. - [weinberg] -- More fixes. [weinberg] -- Fixes for UserSatWake. Ready to try! [weinberg] -- Added multiple M harmonics. [weinberg] -- Fixed additional references to Complex class. [weinberg] -- Renamed Complex to KComplex. Removed UnboundCoefs in favor of - TimeSeries Coefs and updated UserSatWake accordingly. [weinberg] -- More fixes for QP disk generation. [weinberg] -- Added monopole approximation. [weinberg] -- Added new disk IC generator. [weinberg] -- R-z histograms for gas. [weinberg] -- Uncommented axisymmetric drift computation (now default). [weinberg] -- Only print out timing info for epsm when epsm is used. Generalize and - renamed gasprof to psphisto. [weinberg] -- Added cooling enhancement factor for testing. [weinberg] -- Added computation for gas disk profiles. [weinberg] -- Better duplication diagnostics (fixed the bug in the old version that - was giving a false positive). Changed flags to production values. - [weinberg] -- Added post-partition effort-based load-balance check. [weinberg] -- White space typo fix. [weinberg] -- Added new timer. [weinberg] -- Fixed bug (I'm pretty sure now) in pCell::findSampleCell() [weinberg] -- Typo fix. [weinberg] -- A few more fixes to sanity checks. [weinberg] -- More fixes. [weinberg] -- Some fix ups. [weinberg] -- Back to standard octree . . . [weinberg] -- Additional timing diagnostics. [weinberg] -- Increased ascii body file buffer size. [weinberg] -- Attempts to improve DSMC efficiency. [weinberg] -- Additional diagnostics and MPI_Allgatherv timing test. [weinberg] -- Simple gas profile histogram generator. [weinberg] -- Check in merged branch. [weinberg] -- Initial addition of asymmetric drift computation for initial condition - generation. [weinberg] -- Added an additional wait timer for debugging. [weinberg] -- Updated timing algorithm in pHOT to include cell partition overhead. - Fixed but in diagnostic output in DiskHalo2 that could cause routine - to address uninitialized arrays. [weinberg] -- Added example gas analysis routine. [weinberg] -- Some extra diagnostics; clean effort variable before each step. - [weinberg] -- Error in ascii format documentation. [weinberg] -- Added total effort to particle number report. [weinberg] -- Moved configure.in to configure.ac. Added stubs for Hansung Gim to - add bar triggering routines. [weinberg] -- Update input/output paths. Improved epicylic freq determination by - using a Chebyshev fit for computing numerical derivatives. [weinberg] -- Fix bug in V_phi computation. [weinberg] -- Prefix model files with homedir. [weinberg] -- Found/fixed bug for NOCOOL mode. [weinberg] -- Clean up some cruft, relax diagnostic output criteria. [weinberg] -- Cleaned up key partioning implementation and diagnostics. [weinberg] -- Made bits per dimension ("nbits" variable) a global variable. Included - sanity checks for packing in a key_type variable. [weinberg] -- Additional sanity check; added comment for maximum bits in native type - length. [weinberg] -- Additional bug fixes for the direct integration cooling calculation. - [weinberg] -- Explicit solution of cooling equation. [weinberg] -- Absolute value for Strouhal number computation. [weinberg] -- Reduce the DSMC diagnostic output. [weinberg] -- Working version at this point. [weinberg] -- Added attribute array construction for tipsy input. [weinberg] -- Added Knudsen and Strouhal number computation. [weinberg] -- Added debug barrier calls to pHOT routines. [weinberg] -- Source for MPI_Barrier debugging routine. [weinberg] -- Added MPI_Barrier location debugging routine. [weinberg] -- Increase the field width for ascii output. [weinberg] -- Bump up the verbosity level for CHKPT output. [weinberg] -- Updates to UserSlabHalo. [weinberg] -- Added lapack-3 detection; removed comment cruft from UserPeriodic. - [weinberg] -- UserPeriodic updates; needs to be tested. [weinberg] -- Fixed offset bug. [weinberg] -- Added vacuum boundary condition. [weinberg] -- Removed the barrier from ComponentContainer timings. Bumped the - version #. [weinberg] -- Additional (semi-final) timing and partition balancing fixes. - [weinberg] -- Added work-effort based HOT partioning. Required adding an "effort" - field to the particle structure. [weinberg] -- Partition by effort weighting by cells. [weinberg] -- Added additional timing diagnostics. [weinberg] -- Removed lapack detection cruft in favor of the ACX_LAPACK and ACX_BLAS - macros. [weinberg] -- Enable restarts for OutFrac diagnostics. Update autogen.sh for - automatic configuration of lapack. [weinberg] -- Bug fix for xi domain (oops!!) [weinberg] -- Added "time only" option. [weinberg] -- Upgrades to disk ic code. [weinberg] -- IC updates. [weinberg] -- Upgrade gendisk2 to use generate_eof. [weinberg] -- Missing Lapack wrapper. [weinberg] -- Added missing m4 directory. [weinberg] -- Bug fix. [weinberg] -- Updates including new EmpCylSL changes. [weinberg] -- EmpOrth9thd changes ported from Orbit/EOF. [weinberg] -- Added eof preconditioning routine. [weinberg] -- Attempted fix for restart bug in Orient. [weinberg] -- Boundary defaults changed for SL. Better latels on level diags for - new DT scheme. [weinberg] -- Fix SL limits for non-cuspy, homogeneous core model. [weinberg] -- Typo in diagnostic output fixed. [weinberg] -- Improved the time step algorithm: spatial scale is now the "scale - height" of the gravitational potential. [weinberg] -- Added GPTL calls for timing. Enabled by the --enable-gptl flag to - configure. Created the typedef PartMapItr for map::iterator. [weinberg] -- Timing updates. [weinberg] -- Added GPTL stubs for debugging timing performance. [weinberg] -- Restart updates. Changed default NICE value to 0. [weinberg] -- Updates to spherical shell force routine. [weinberg] -- Added a spherical shells routine. [weinberg] -- Added level counter for DSMC diagnostics. Fixed blunder in cooling - rate. [weinberg] -- Added slab analysis routine, checkpoint timer code. [weinberg] -- Add Slab external potential module. [weinberg] -- Checkpoint timer class. Still testing. As of this point, the class - does what it is supposed but does not initiate any action, only prints - diagnostics. [weinberg] -- Updates to checkpointing class and diagnostic output. [weinberg] -- Fixes to unordered_map vs. hash_map selection. [weinberg] -- Updated hash_map -> unordered map. [weinberg] -- Attempt to improve sampling rate computation for gas particle - partition. [weinberg] -- Extra diagnostics for pHOT. Updates for shadow satellite. [weinberg] -- Separate gas and stellar disk scale lengths. [weinberg] -- Debugged outdir enhancements. Found and finxed minor interpolation - bug in EllipsoidForce. [weinberg] -- Added outer radius variable parameter to uniform gas disk generation. - [weinberg] -- Fixed up a minor logic problem. [weinberg] -- Attempt to improve output directory handling. [weinberg] -- Clean up UserPST code. Missing scaling for scale height in particle - generation. [weinberg] -- Removed defunct reference to PSTDisk. [weinberg] -- Added Piner-Stone-Teuben initial condition generator and User routine - for external force. [weinberg] -- Added force computation. [weinberg] -- Added disk potential solver test routine. [weinberg] -- Add inertial output by default. [weinberg] -- Fix the com-system mistake found by Jun-Hwan (sorry about that) - [weinberg] -- Added center of acceleration output. Fixed frame of reference issues - in multistep timestep selection. [weinberg] -- Add verbose output option for eof accumulation. [weinberg] -- Fixed up com_log error in current time parsing. [weinberg] -- PSP analysis routines. [weinberg] -- Missing file from last check in. [weinberg] -- Added disk wake analysis routine (not completely debugged yet). - [weinberg] -- Added tree parition load balancing. [weinberg] -- Removed some redudancies from pHOT and additional diagnostics. - [weinberg] -- Added smoothing at monopole boundary to Cylinder force grid. - [weinberg] -- Enable compulsive FPE trapping only with DEBUG compile flag set. - [weinberg] -- Removed the non-working multistep_com_dt option. [weinberg] -- Added support for multimass gas disk. [weinberg] -- Changed EPSMratio (epsm parameter in UserTreeDSMC) to mean the - threshold in collisions per particle above which we use EPSM. - [weinberg] -- Fixed an EPSM bug. [weinberg] -- Additional sanity checks. [weinberg] -- Fix string length for processor name. [weinberg] -- Fix out-of-bounds errors for diagnostic output. [weinberg] -- Temperature diagnostics for CollideLTE.cc. [weinberg] -- Added node list and removed diagnostic output files from pCell, by - default. [weinberg] -- Added a variable, centerlevl, to specify the multistep levels to - compute the center positions. [weinberg] -- Fix duplication in Orient log entries. [weinberg] -- Fixed level list reported. [weinberg] -- Some level list logic problems; attempting to debug these. [weinberg] -- Remove extraneous diagnostic timers. [weinberg] -- Turn off time step debugging. [weinberg] -- Fixed recently introduced bug in multistepping for Cylinder. - [weinberg] -- Another fix to empty root nodes in oct-tree. [weinberg] -- Turn off the extra coefficient debugging output. [weinberg] -- Attempt to handle empty root nodes in pHOT.cc and pCell.cc. Output - format change only in multistep.cc. [weinberg] -- Handle zero values. [weinberg] -- More zero value tests on diagnostic distributions to prevent divide by - zeros. [weinberg] -- Check for zero T and n0. [weinberg] -- Cosmetic white-space change and additional comments. [weinberg] -- Added multistep_reset to EmpOrth9thd. Turned off some debug output. - [weinberg] -- Remove multistep_swap routines. Interpolation control should now be - implemented internal to the force routine. [weinberg] -- Formating and diagnostic changes. [weinberg] -- Clean up interdependency loops in header files. [weinberg] -- Implemented thread timing routines in PotAccel. Can be used for any - force . . . [weinberg] -- Added thread timer to ComponentContainer. Moved thread class - instances into ComponentContaier data rather than globals. [weinberg] -- Fixed a few threading blunders in Cylinder introduced for multistep - treatment. [weinberg] -- Updates to allow Cylinder for self_consistent=0 work correctly. - [weinberg] -- Changes to integrate multimass in DiskHalo for IC generation. - [weinberg] -- Only compute level counters for diagnostic output once per step. Add - expansion image output to gendisk2. [weinberg] -- Some fixes to !self_consistent logic. [weinberg] -- Remove deprecated ctrlev flag. [weinberg] -- Removed mstep test from fix_positions. [weinberg] -- COM and COV evaluations moved to largest multistep. [weinberg] -- Orient accumulate member only called at the end of a multistep. - [weinberg] -- Fix bug in UserStat (fencepost error when particle list changed) and a - small change to the COM updates (still TO BE tested). [weinberg] -- ANSI C++ header updates; check for both g2c and gfortran libraries. - [weinberg] -- ANSI C++ heder updates. [weinberg] -- Fixed bad logic in com multistep update. [weinberg] -- Another missing file! [weinberg] -- One more missing file. [weinberg] -- Missing file! [weinberg] -- Minor bug fixes for UserSatWake (and some older multistep ones, too) - [weinberg] -- Code for imposing satellite halo perturbations. [weinberg] -- Module for compute the contribution of rotation force. [jhchoi] -- Add extend point mass falg. [jhchoi] -- Add extend point mass falg. [jhchoi] -- Fix bug for twocenter centering. [jhchoi] -- Fix twocenter bug by swapping mixture and Cmixture. [jhchoi] -- Comments and fixed diagnostic output counter. [weinberg] -- Code clean up. [weinberg] -- Attempt fix for Orient restart. Change default eigen analysis - algorithm. [weinberg] -- Documentation for the VERBOSE flag. [weinberg] -- Fixed up the SatFix routine for new particle map. Added some - additional debug output to Direct (only used if DEBUG preprocessor - flag is defined). [weinberg] -- Erroneous line in Component destructor removed. Fencepost error in - OrbTrace fixed. [weinberg] -- Added damping to orient calculation. [weinberg] -- Additional comments. Fix up Orient for multistep restarts. [weinberg] -- Cruft removed from pHOT.cc: we will use Alltoall reduction, rather - than individual sends to let the MPI implementation deal with the - optimization. [weinberg] -- Additional adjustTree options. [weinberg] -- Separate compile flags for pHOT. [weinberg] -- Added copy constructore to Timer, Attempted to optimized - pHOT::adjustTree. Added additional timers to ComponentContainer. - [weinberg] -- Removed the "maxlev" parameter which was a bad idea both because it - didn't save much CPU time and because it was confusing to implement - and maintain. Added multiple levels to COM/COV/angmom tracking per - component. [weinberg] -- Diag output updates. [weinberg] -- Updates for maxlev consistency. [weinberg] -- Fixed bug in stellar disk eval. [weinberg] -- Added constant scale heigh and fixed isothermal gas disk solution. - [weinberg] -- Fix velocity units. [weinberg] -- Mistake in linear interpolation (typo of course). [weinberg] -- Fix to isothermal gas sphere; fixes to diagnostic output. [weinberg] -- Added routines for isothermal gas sphere test. [weinberg] -- Flip a few diagnostic ratios. [weinberg] -- More diagnostic tests. [weinberg] -- Removed plethora of step-tagged files in favor of single files with - multiple stanzas. [weinberg] -- Additional diagnostics. [weinberg] -- Fixed a fencepost error in particle exchange, added multiple time step - control to the Direct force method, added the beginnings of global - exception handler. [weinberg] -- Comments only. [weinberg] -- Additional diagnostics. [weinberg] -- Yet more cooling updates and diags. [weinberg] -- Another excess energy algorithm fix up. [weinberg] -- Fixed up a bunch of inconsistencies in the total energy conservation - with cooling. [weinberg] -- Remove debug output. [weinberg] -- Fix typo that was causing an error in threaded computation of the - cooling time step. [weinberg] -- Correct sign error in Excess register. [weinberg] -- Diagnostics for excess energy registers. [weinberg] -- Added collusional excess energy calculation to EPSM part of DSMC - algorithm. [weinberg] -- More informative labels from Component output (cosmetic change). - [weinberg] -- Addtional documentation and diagnostic output fix ups. [weinberg] -- Cosmetic fixes only . . . [weinberg] -- Change Ecurr computation from minimum to mean. [weinberg] -- Updates for multistepping with TwoCenter classes. [weinberg] -- Looking for Orient bug while multstepping. [weinberg] -- Added maximum level for center and orient computation. [weinberg] -- Fixed multistep problem in Cylinder. [weinberg] -- Fix gendisk and eof logic in Cylinder. [weinberg] -- Additional timng diagnostics, using MPIScatter rather than - MPIAllreduce to exchange particle send and receive lists. SVD updates - for EmpOrth9thd. [weinberg] -- Additional timers, updates to gendisk2. [weinberg] -- Comment out the nonblocking send and receives which seem to be slower - than the blocking ones! [weinberg] -- Updated exchange algorithm to improving speed. Still needs more - improvements. [weinberg] -- Additional logic changes for multisteppng. [weinberg] -- Fixed maxlev logic bug in EmpOrth9thd. [weinberg] -- Fixed debug lines in pHOT.cc. [weinberg] -- Evaluate acceleration before centering in ComponentContainer. - [weinberg] -- Output level info at end of step not beginning. [weinberg] -- Fixed cooling excess logic and periodic bc logic, both of which had a - few inconsistencies. [weinberg] -- Fixed an initialization typos in Collide.cc Attempted fix to the - excess internal energy calculation. [weinberg] -- Repaired synchronization bug in spreadOOB. [weinberg] -- Added more debug and fixed up non-blocking send logic. [weinberg] -- Additional fix ups to partioning out-of-bounds particles. [weinberg] -- Additional debug diagnostics. Improvement to HeatCool interpolation - (added log scale). [weinberg] -- Another bug fix in out-of-bounds algorithm. [weinberg] -- More updates for handling out-of-bounds particles. [weinberg] -- Fixed bug in out-of-bounds list deletion for spreadOOB. [weinberg] -- Cleaned up logic for out of bounds particles. [weinberg] -- Added partition and tracking for out-of-bounds particles. [weinberg] -- Changes to pHOT for out of bounds particles. [weinberg] -- Fixed but in pCell, remove cell from frontier in RemoveAll method. - [weinberg] -- Rewrite adjustTree for full tree repair. [weinberg] -- Streamline timestep computation for DSMC. [weinberg] -- Add destructor. [weinberg] -- Fixed Makefile. [weinberg] -- Missing updates on last check in. [weinberg] -- Missing Makefile.am. [weinberg] -- Test routine for HeatCool with table interpolation. Tests OK! - [weinberg] -- Cooling table cache, timing and time routines for HeatCool. [weinberg] -- Added cooling computaton timer. [weinberg] -- Add additional timing diagnostics. Add flags to bypass MFP statistics - acquisition. [weinberg] -- Do full "Hamiltonian" updates only at levels below maxlev. [weinberg] -- Added output intervals to Orient. [weinberg] -- More fixups in DSMC tree. [weinberg] -- Only run and report diagnostics every nsteps instead of cumulatively - and reporting every nsteps. [weinberg] -- Diagnostics stepping in Collide rather than diag on every step. - [weinberg] -- Just cleanup and additional comment lines. [weinberg] -- Updates in pHOT adjustTree update logic. Added transaction list - rather than three separate lists. [weinberg] -- Updates to adjustTree routine for tree repair. [weinberg] -- Attempt (not finished) to add tree adjustments to DSMC to accelerate - time stepping for very dense cells. [weinberg] -- More bug fixes. [weinberg] -- Fix up circular velocity bug for gas. [weinberg] -- Changed to logarithmic gridding in z direction for density table for - gas. [weinberg] -- Fixed mistake in assigning gas mass. [weinberg] -- Header and implementation for inverse normal distribution. [weinberg] -- Multistep fixes in Cylinder. Added gas disk generation code in utils. - [weinberg] -- Added comment lines only. [weinberg] -- Missing initialization of time step counter. [weinberg] -- Added diagnostics. [weinberg] -- Updates for carrying scale information for multistep in particle - class. [weinberg] -- Bug fixes to memory growth in diagnostic accumulation routines. - [weinberg] -- Additional multistep diagnostics. [weinberg] -- Fixed bug in multistep tracking. [weinberg] -- Updates to fix a minor bug in diagnostic reporting in Collide. - [weinberg] -- Added simple routine to apply a constant acceleration. [weinberg] -- Fixed errors in jitter algorithm. [weinberg] -- Fixed logic error in order of diagnostic output depending on whether - or not mfpstat is selected. [weinberg] -- Subtract additional artificial Coriolis force due to artificial - rotation. Also the flag to set the radius only in which the particle - is affected by the rotation. [jhchoi] -- Fixed a timestep bug in UserTreeDSMC. [weinberg] -- Add periodic boundary condition routine for trying shocktube test with - ExpMPI. [weinberg] -- Rotating satellite module. [jhchoi] -- Added flags to some of the diagnostic output (default to false). - [weinberg] -- Additiona DSMC debugging and diagnostics. [weinberg] -- Still debugging DSMC: a few minor bug fixes and lots more diagnostics. - [weinberg] -- Fix restart bug in pHOT initialization. [weinberg] -- Change the EPSM trigger from MFP ratio to collision count ratio. - [weinberg] -- Still more DSMC diagnostics. [weinberg] -- Additional DSMC diagnostic output. [weinberg] -- More DSMC debugging. [weinberg] -- Updated threaded code to bypass pthread create for nthrds=1. - Additional fixes to DSMC. [weinberg] -- Additional diagnostics for debugging. [weinberg] -- Remove char[] in favor of char*. Change MPI strategy for Repartition - in pHOT. [weinberg] -- Debugged new version of HOT for exp code, added global variable to - change ParticleFerry buffer size at runtime. [weinberg] -- Added multistep logic for non-gravitational processes. [weinberg] -- Fixed volume bug (using int rather than unsigned long long, ooops). - [weinberg] -- Added more collision diagnostics. [weinberg] -- Updated for latest changes in DSMC and replaced deprecated char string - references with const char references. [weinberg] -- Fixes to PhaseSpace utilities and cooling. [weinberg] -- Fixed error in Cylinder for external forces (wrong coordinate system). - [weinberg] -- Fixed bug in Cylinder for external force evalution (wrong coordinate - system for forces) [weinberg] -- Fixed OrbTrace and added more debugging diagnostics. [weinberg] -- Debug diagnostics and fixes for multistepping with intercomponent - interactions. [weinberg] -- Switch over from a vector to a map for particle indexing in - preparation for DSMC. [weinberg] -- Need to integrate oct-tree partition into Component class. [weinberg] -- Upgrade Timer class, more changes to DSMC. Ready for a full test. - [weinberg] -- Reconcile int and unsigned ints. [weinberg] -- Interface EXP and ParticleFerry. [weinberg] -- Missing file: Timer.h. [weinberg] -- Initial version of DSMC module. [weinberg] -- Added routine to convert tipsy binary in "standard" format to PSP - format. [weinberg] -- Improved accuracy of numerical derivative; streamlined interface for - interpolation. [weinberg] -- Minor change to avoid crash for satellite mass loss test. [jhchoi] -- Added parameter to set fraction of monopole mass. [weinberg] -- Implement self-consistent potential for new bar routine. [weinberg] -- Fixed bug for exponential denstiy profile. [weinberg] -- Full documentation of ellisoidal potential. [weinberg] -- Added documentation for web page. [weinberg] -- Remove a debugging statement. [weinberg] -- Remove unintialized variable that was setting amp to zero. [weinberg] -- Type on quadrupole formula (jeez!) [weinberg] -- Fixed typo in level list output. [weinberg] -- Fixed typos in output diagnostics and rho0 computation for expon=1. - [weinberg] -- Bar code with explicit computation of quadrupole potential from an - ellipsoidal mass distribution. [weinberg] -- Changed from "soft" flag to hardness exponent "alpha" in UserEBar. - [weinberg] -- More multithreading adjustments to improve efficiency. [weinberg] -- Multithreding updates to multistep code. [weinberg] -- Debug fixes (typos etc.) for level list implementation. [weinberg] -- Added level lists for particle loops. [weinberg] -- Streamlined implementation of multithreading incr_position and - incr_velocity. [weinberg] -- Added multithreading to incr_position and incr_velocity. [weinberg] -- More fix ups of bar force routines for multistepping. [weinberg] -- Fixed centering error in bar monopole for multistepping. [weinberg] -- Additions for keeping track of level populations. [weinberg] -- Changed return type for standalone usage. [weinberg] -- Changed multistep from int to unsigned. [weinberg] -- Added routine to test energy and angular momentum conservation per - particle. [weinberg] -- Fixed a delete bug that was preventing a clean exit. [weinberg] -- Beta version of multiple time stepping. [weinberg] -- A few minor bug fixes. [weinberg] -- Fixed a few typos. [weinberg] -- Fixed typo in mail subject. [weinberg] -- Added direct simulation monte carlo (DSMC) code to src/user. - [weinberg] -- Minor fix to diagnostic output formating. [weinberg] -- ID process on exit. [weinberg] -- Fix errors in destructors for clean termination. [weinberg] -- Attempt to find destruction bug in EXP exit; bump up version # - [weinberg] -- Upgrades: remove #pragma implementation directives, added flag to not - follow bar linear momentum to fix centering at origin. [weinberg] -- One addition to SatelliteOrbit to allow adjusting the number of - iterations for orbit determination. Fix typo in number of nodes - computation in UserEBarS updating pattern speed evolution. [weinberg] -- Add a flattening halo models scheme. [jhchoi] -- Flattening halo models. [jhchoi] -- Cosmetic updates (diagnostic output and doxygen documentation) - [weinberg] -- Added updated mail command (to try to fix erroneous mail messages on - commit) [weinberg] -- Added a module to fix Point particles to given orbits. Fixed - deallocation bug in ExternalCollection (attempt to close loaded - libraries before removing class instances). [weinberg] -- Changed mail command in loginfo. [weinberg] -- Added orbit finding routine to SatelliteOrbit and upgraded UserSat. - [weinberg] -- *** empty log message *** [jhchoi] -- Fixed restart bug (I hope). [weinberg] -- Minor updates for debugging OpenMPI finalize. [weinberg] -- Minor fixes, updates. [weinberg] -- Fix threading problem (an non-reentrant call) in UserWake. [weinberg] -- Changes needed to incorporate wake module. [weinberg] -- Record contribution to bar torque from each component. [weinberg] -- BarRun output to include torque computed from particle forces. - [weinberg] -- Add column #s to OUTLOG. [weinberg] -- Another bug fix for SatFix. [weinberg] -- Debugged SatFix for a single satellite pair. [weinberg] -- Rewrite algorithm in SatFix. [weinberg] -- Bar method that computes torque self consistently using Newton's 3rd - Law. [weinberg] -- Generalized SatFix for any even number of particles. [weinberg] -- Fix minor typo. [weinberg] -- Bump version ID. [weinberg] -- Added a way to artifically change the total angular momentum of the - bar (e.g. to increase the available angular momentum reservoir). - [weinberg] -- Minor error for Iz in satellite Iz is MASS*LENGTH*LENGTH but Iz was - MASS*LENGTH*LENGTH*omega !!!! [jhchoi] -- Minor error for Iz in satellite Iz is MASS*LENGTH*LENGTH but Iz was - MASS*LENGTH*LENGTH*omega !!!! [jhchoi] -- Update to remove cruft needed for gcc version <= 3.3. [weinberg] -- Add mssing argument in initialization (read omega) [jhchoi] -- Add mssing argument in initialization (read omega) [jhchoi] -- Minor changes and add fixed satellite omega. [jhchoi] -- Minor change and add fixed satellite omega. [jhchoi] -- Fix bug on computing minJ and maxJ. [jhchoi] -- Correct errors on computing minJ and maxJ. [jhchoi] -- Improved when a root is on a limits. [jhchoi] -- Minor updates. [weinberg] -- Enabled new-style info format strings. [weinberg] -- Updates Cylinder for consistency with gendisk. [weinberg] -- Minor documentation updates. [weinberg] -- Added some additional documentation. [weinberg] -- Allow logarithmic coordinate scaling as well as algebraic coordinate - scaling for SL basis grid. [weinberg] -- Fix ups for 64-bit. [weinberg] -- Some clean-up for gcc 7.1 and a tiny update for AMD 64bit (fortran - argument passing) [weinberg] -- Added more parameter value output on initialization. [weinberg] -- Some additional debug lines. [weinberg] -- Added a debug output line (no logic changes). [weinberg] -- Minor updates. [weinberg] -- Suppress warnings about virtual constructors. [weinberg] -- Removed orphaned variables in UserResPotOrb. [weinberg] -- Fixed minor typos. [weinberg] -- Updated documentation. [weinberg] -- Minor fixes. [weinberg] -- Added ResPot routines for a predescribed orbit. [weinberg] -- Fix restart bug in Component; remove more cruft in Cylinder. - [weinberg] -- Restored freeze lines in SphericalBasis and SphericalBasisMixtureSL. - [weinberg] -- Extra diagnostics. [weinberg] -- Missing file. [weinberg] -- Fixed erroneous range check. [weinberg] -- Multiple minor updates for consistency. [weinberg] -- Restart supprot in Orient and additional documenatation. [weinberg] -- Initial condition documenatation. [weinberg] -- Missing file. [weinberg] -- Added gendisk to util directory. [weinberg] -- Added summary statistics utility. [weinberg] -- Added header to Orient file. [weinberg] -- Added monopole flag to SphericalBasis. Fixed restart problem in - UserBar. [weinberg] -- Updates for ANSI compatbility (now compiles gcc 4.0) [weinberg] -- Fixed up documentation in headers. Changed ResPot error string - declaration. CVS. [weinberg] -- A few (very minor) updates in headers for gcc-3.4. [weinberg] -- Update for subset of particles in expansion. [weinberg] -- Update version id. [weinberg] -- Update version and timestamp. [weinberg] -- Minor updates for eqmotion=0. [weinberg] -- Removed radial limits; let ResPot instance take care of this. - [weinberg] -- Provide fine tuning over grid limits. [weinberg] -- Fixed typo in mapping for points off of model grid. [weinberg] -- Minor typos fixed. [weinberg] -- Minor output fix up. [weinberg] -- Fixed error logging. [weinberg] -- Added mutex to random # generation (not sure these routines are - reentrant) [weinberg] -- Files for UserResPotN. [weinberg] -- Minor changes. [weinberg] -- Fix bug in flagging logic. [weinberg] -- Update to fix minor vr, vt range bug. [weinberg] -- Separate out copious debug output. [weinberg] -- Updated single resonance module. Version updated for minor bug fixes. - [weinberg] -- Typo. [weinberg] -- Fixed another interface bug. [weinberg] -- Fix typo. [weinberg] -- Changes to com_system itnerface. [weinberg] -- Fixed PS dump signal logic and ResPot integration. [weinberg] -- Fix typo. [weinberg] -- Candidate fix to coordinate interface in SphericalBasisMixtureSL.cc. - [weinberg] -- Error in Component::Local. [weinberg] -- Changes for new interface in SphericalBasisMixtureSL. [weinberg] -- Removed expansion from ResPot, fixed SphericalBasis interface (I hope) - [weinberg] -- Added dump ps on HUP. [weinberg] -- Documentation updates only. [weinberg] -- More documentation. [weinberg] -- Fixed up "-d", default global parameter print out. [weinberg] -- Added a bit of fluff. [weinberg] -- Tweaks to parse routine (beautification mostly) [weinberg] -- Do not include self energy in potential for direct summation. - [weinberg] -- Comment out debugging lines. [weinberg] -- Checked in changes for UserResPotN. [weinberg] -- Fixed logic for external particle acceleration computation. [weinberg] -- Make utility library static. [weinberg] -- Repairs to Makefile. [weinberg] -- Changes to user to reconcile command library and Makefile. [weinberg] -- Updated info for current "release" [weinberg] -- Merging NewC branch onto HEAD at version 6.0. [weinberg] -- Merge from NewC back to HEAD. [weinberg] -- Erroneous call to freeze in particle phase space integration. - [weinberg] -- Minor bug fixes. [weinberg] -- Fix bugs that JunHwan found. [weinberg] -- Added momentum conservation to com system. [weinberg] -- Fix up documentation. [weinberg] -- More twiddles to deal with com_system. [weinberg] -- Minor fixes and a bit of extra debug info in log files. [weinberg] -- More fixes for system com. [weinberg] -- Orient bug fix. [weinberg] -- Fix bug. [weinberg] -- Minor fix. [weinberg] -- Added COM system log file diagnostic to Component. [weinberg] -- Forgot this file! [weinberg] -- Fix OutLog. [weinberg] -- Updated phase space writing routines. [weinberg] -- Changes for center of mass system coordinates. [weinberg] -- Minor fixes and additional diagnostics. [weinberg] -- Fixed minor bug in UserHalo. [weinberg] -- Fix ComponentContainer bug. Added UserHalo. [weinberg] -- For including a background spherical halo potential. [weinberg] -- Fix order of fix_position call. [weinberg] -- Added log file for center. Changed a few docs. [weinberg] -- Added constant velocity center in Orient. Documentation update. - [weinberg] -- Added velocity IC to Orient. [weinberg] -- Missing file . . . [weinberg] -- Test routine for ResPot. [weinberg] -- Minor fixes to utils. ResPot updates. [weinberg] -- Backport update for r_circ determination. [weinberg] -- More respot updates. [weinberg] -- Scope of Omega vs omega variables was incorrect. Both should be class - variables. [weinberg] -- Updates for ResPot default parameters. [weinberg] -- Change name of global variable from "mapping" to "eqmotion" [weinberg] -- Update for mapping routine. [weinberg] -- Fix ups in orbit class for ResPot and UserResPot. [weinberg] -- Fixed bad porting typo in gknots-->LegeQuad. [weinberg] -- Added orbital element test routine (and missing localmpi header) - [weinberg] -- Fixed a few more typos. [weinberg] -- A few bugs fixed in ResPot. [weinberg] -- New version of ResPot. [weinberg] -- Change linear frequency time dependence rather than erf() [weinberg] -- Updated to allow a frequency shift with time. [weinberg] -- Moved from src. [weinberg] -- Moved from src. [weinberg] -- Moved biorth computation to exputil. [weinberg] -- Needed for UserResPot. [weinberg] -- Updates for rearranging sledge compilations in makefiles. [weinberg] -- Add method that applies no force. [weinberg] -- Added null force method. [weinberg] -- Add NUME and NUMK grid parameters to UserResPot. [weinberg] -- Some bugs found. [weinberg] -- Missing file. [weinberg] -- More parameter fix ups. [weinberg] -- Add parameters for bar shape. [weinberg] -- Fix error velocity unit vectors. [weinberg] -- Updates to utils and new user method (UserResPot) [weinberg] -- Added option to have particles ignore bar monopole. [weinberg] -- Fix recentering on restart bug. [weinberg] -- Fix bug in loop counter. [weinberg] -- Fix up bug in omega.dat reading. [weinberg] -- Version of EBar that includes a Omega vs T table. [weinberg] -- Fixed typo. [weinberg] -- Added sanity check for SEQCHECK. [weinberg] -- Fixed bug in Orient centering on restart. Use mnemonics for UserSat. - [weinberg] -- Backported extremal checks from C++mdw libs. [weinberg] -- Update time stamp. [weinberg] -- Print out list of user routines. Use mutex for orb in UserTorque. - [weinberg] -- Fixed factory initialization for user routines to obey ANSI scoping - rules. [weinberg] -- Change file name parameters. [weinberg] -- Added User routine to add torque to phase space from E-J image. - [weinberg] -- Fixed Orient bug: user specified center was not initialized before the - first step. [weinberg] -- Fixed typo for integer attributes. [weinberg] -- Fixed up autogen.sh for new versions of auto*tools. [weinberg] -- Added missing namespace statements for std as required. [weinberg] -- Remove deprecated macro. [weinberg] -- Restored previous computation of diffusion coefficients (which was - correct). [weinberg] -- Added some debug stuff. [weinberg] -- Backwards compatbility to gcc 2.95. [weinberg] -- Fix typo in ParamParse. [weinberg] -- Fix nonexistent directories & old files. [weinberg] -- Generalization of ParseParams. CVS - ---------------------------------------------------------------------- - [weinberg] -- Addded "new_item" member. [weinberg] -- Bumped up version #. Fixed bug in diffusion coefficient. [weinberg] -- Fixed missing definition and doc string. [weinberg] -- Updated doxygen comments. [weinberg] -- ANSI and Libtool updates. [weinberg] -- Added a bit more documenation. [weinberg] -- Fix interpolation fencepost error. [weinberg] -- Typo in debug output. [weinberg] -- Fixed cruft in parser. [weinberg] -- Set grid size in scale units. [weinberg] -- Fixed description in doc. [weinberg] -- Record debug flag in log. [weinberg] -- A few minor clean ups. [weinberg] -- Made debug switch a parameter. [weinberg] -- Augment debug routine for smaller spatial window. [weinberg] -- Bug fix. [weinberg] -- Z force sign error for monopole approx. [weinberg] -- More debug enhancements. [weinberg] -- More thorough debug routine. [weinberg] -- Bug fix. [weinberg] -- Changed integration variable for exponential disk potential. - [weinberg] -- Fixed output routine bug. [weinberg] -- Added more parameters to log file info line. [weinberg] -- Add genTable call to constructor. [weinberg] -- Added UserDisk: a user module for a thin exponential disk. [weinberg] -- Made a user potential for a thin exponential disk. [weinberg] -- Fixed bug in Orient which allowed the differenced energy gradient to - latch at zero. [weinberg] -- Itsy bitsy formating change. [weinberg] -- Make rcylmin and rcylmax settable again. [weinberg] -- Fixed initial center specification bug. [weinberg] -- Fix typo in revised Orient code. [weinberg] -- Allow initial center to be passed to Orient. [weinberg] -- Fixed bug (typo in particle postions) [weinberg] -- Documentation update (only) [weinberg] -- Moved freeze code into component class so that each component could - have different "tidal" radii. [weinberg] -- Update OutLog for per component KE in component's center of velocity - frame. [weinberg] -- Override end-point classification for SL problem. [weinberg] -- Let Orient read log file to get initial center (even on a new run) - [weinberg] -- Triaxial external logarithmic potential. [weinberg] -- Fixed monopole=0 bug. [weinberg] -- Fixed blunder in code without monopole. [weinberg] -- Changed diag text. [weinberg] -- Remove unneeded header finding code. [weinberg] -- Fixed missing lines in file renaming. [weinberg] -- Added restart info . . . [weinberg] -- Allow monopole to be turned on and off. [weinberg] -- Fix production options. [weinberg] -- Specific autogen.sh for buzzard's auto* versions. [weinberg] -- Updated version number. [weinberg] -- Merged ANSI branch back to head!! [weinberg] -- Fixed help documentation. [weinberg] -- Added one-dimensional biorthogonal function check. [weinberg] -- Added centering from component->center. [weinberg] -- Added diverge flags. [weinberg] -- Fix minor debug output fencepost error. [weinberg] -- Added facility to use a time-dependent quadrupole from an input table. - [weinberg] -- Additional checks and diagnostics. [weinberg] -- Overload RegisterComponent in SphereTwoCenter to assign the component - pointer to the the SphericalBasisMixtureSL instances as well as the - SphereTwoCenter instance. [weinberg] -- Need to register containing component with each SphereSL in - SphereTwoCenter. [weinberg] -- Minor fix of slcheck in MPI mode. [weinberg] -- Fixed missing initialization for default adiabatic variables on - restart. [weinberg] -- Fix undefined "time" variable in Component. Reference in Adiabatic() - to "time" should be "tpos". [weinberg] -- Updated massmodel to included changes to more recent - SphericalModelTable. Use unevenly space grid by default. [weinberg] -- Updated massmodel from newer SphericalModelTable. Use uneven spaced - table by default. [weinberg] -- Added support for the DIVERGE option in SphericalModelTable. - [weinberg] -- Documentation update. [weinberg] -- Added Adiabatic member to Component class. Specifying either the - "ton" or "twid" component will now enable adiabatic per particle mass - turn on. [weinberg] -- Get mail when repository changes . . . [weinberg] -- Add flag to toggle energy centering to include/exclude kinetic energy - and include/exclude external potential. [weinberg] -- Changed Orient to include external potential using the EJext flag. - [weinberg] -- Added axis ratios as input variables. [weinberg] -- Updated ChangeLog from cvs log. [weinberg] -- Added kludge to use last minimum energy value as center. [weinberg] -- Simplied selection of boolean values in initialize(). [weinberg] -- Changed parameters: barmass is now the total mass of the bar. - Amplitude is the fraction of the quadrupole presented (relative to the - fit to the ellipoid with mass "barmass" [weinberg] -- Fix use_external bug. [weinberg] -- Replace hardwired bratio and cratio by variable values. [weinberg] -- Fixed (evil) typo in sychronize_velocity argument (was -1) [weinberg] -- Added doc on rs parameter. Added forgotten factor of mfactor. - [weinberg] -- Missing argument in write_ascii call. [weinberg] -- Added method to output ascii format phase-space structure. [weinberg] -- This should do it on the formula. [weinberg] -- One more time on the TeX formula. [weinberg] -- Documentation fix (TeX error) [weinberg] -- Added power-law exponent to argument of erf in mixture function. - [weinberg] -- Incorrect member called in top level SphereTwoCenter force call. - [weinberg] -- Added force output to slshift. [weinberg] -- Added new two-center routines to Makefile. [weinberg] -- Added routines to implement the two center kludge. [weinberg] -- Updated UserDiffRot to print initial distribution of dynamical times. - Added -D_REENTRANT to CXXFLAGS and CFLAGS (should make this a global - option somehow). [weinberg] -- Fixed fence-post error in particle indexing. [weinberg] -- Fix dynamical time computation bug in UserDiffRot and null termination - in filename construction in OutPSN. [weinberg] -- Fixed bug in dynamical time calculation. [weinberg] -- Added option to avoid particles. [weinberg] -- Added routine to randomize line of nodes. [weinberg] -- Changed defaults for Phi and Theta quadrature. [weinberg] -- Fixed factor of two between coefficients and evaluation routines. - [weinberg] -- Normalization fix. [weinberg] -- Update to norm of coefficients. [weinberg] -- Added coefficient dump to Reconstruct class. [weinberg] -- Additional documentation and "-h" help. Added 4Pi normalization for - potential/density. [weinberg] -- Missing file from previous check in. [weinberg] -- Added help stanza. [weinberg] -- Added test program to explore required basis parameters for a central - shift of an input spherical model. [weinberg] -- Fixed bug in bar output in cases where angmname is not set. [weinberg] -- Debugged algorithm to choose nbeg on restart. [weinberg] -- Add automatic file number detection on restart. [weinberg] -- Updated a few of the Output routines to deal automatically with - restarting. [weinberg] -- Fixed mistake in myid* assignment: look unassigned myid1 before myid0. - [weinberg] -- Fixed bug in debug output (sigh). [weinberg] -- Fixed bug in component name search. Changed verbose output only for - master node (n0). [weinberg] -- Added routine to enforce mirror image of phase space for two - satellites. [weinberg] -- Make doc the last target in case doxygen is not installed. [weinberg] -- Added variable monopole mass. [weinberg] -- Generalized UserBar to separate angmom and centering targets. - [weinberg] -- Document debug members. [weinberg] -- Added doxygen documentation. [weinberg] -- Separate ang mom and centering targets. [weinberg] -- Added MONOPOLE to id string for log file. [weinberg] -- Additional documentation. [weinberg] -- Bug fixes. [weinberg] -- Added force routines for homogeneous ellipsoid. [weinberg] -- Added flag to use even angular L terms only. [weinberg] -- Added bar potential including a monopole term. [weinberg] -- Allow a fresh start from an arbitrary time (using the "time" parameter - in the global section). [weinberg] -- Forgot to set time . . . [weinberg] -- Fix component count in get_particles for nodes with zero particles. - Now uses NULL pointer to signal end of particle list rather than - returned number in the current packet. [weinberg] -- Improve restart logic. Add component parameter cacheing. Allow user - to change component string on the fly. Old PhaseSpace parsing should - be compatable. Not caching cparam was an oversight (read BUG). - [weinberg] -- Improve restart logic. [weinberg] -- Added additioal info for Orient diag. [weinberg] -- Added additional debug info. Fixed minor indexing bug in OrbTrace. - [weinberg] -- Make sure that Ecurr and target number are parallelized. [weinberg] -- Changes to implement/debug Orient code. [weinberg] -- Added adiabatic turn on for particles. [weinberg] -- Fix up the Hall smoothing for the cylinder. [weinberg] -- Repaired the screwed up cmap tag. [weinberg] -- Documented the new "slcheck" routine. [weinberg] -- Removed debugging source. [weinberg] -- Remove duplicated files. [weinberg] -- Reorganization of utils directory. Addition of SL checking utility. - [weinberg] -- Added support for Hall smoothing. Doc update in headers. [weinberg] -- Updated & debugged. [weinberg] -- Changes to UserDiffuse algorithm and log output. [weinberg] -- Changes to log output only. [weinberg] -- Kludge to let angular momenta of particles diffuse on energy surface. - [weinberg] -- Changed the variable from shallow to soft. [weinberg] -- Updated bar to use either hard or soft form of the bar potential. - [weinberg] -- Remove debug line from UserBar. [weinberg] -- Add angular momentum computation to component; needed by UserBar. - [weinberg] -- Fix typo . . . [weinberg] -- Don't overwrite existing OUT files. Doc string update in - SphericalBasis.H. [weinberg] -- Fix bugs that Kelly found . . . [weinberg] -- Added Interaction print out to logfile (stdout). Minor cosmetic - changes to improve readability. [weinberg] -- Removed deprecated classes from library (String & Regex). Fixed but - in OutCoef. [weinberg] -- Add end of file warning to verbose output only. [weinberg] -- Don't compile Regex (seems to have problems with global constructors) - [weinberg] -- Improved error handling for corrupted (e.g. truncated) psp files. - [weinberg] -- Fix initialization bug in total number of bodies. [weinberg] -- Eliminate multiple messages about on start up. - [weinberg] -- Consolidated psp functionality to a single class and reimplemented the - utilities. [weinberg] -- Updated gendisk with smoothing of disk potential field for epicylic - frequency computation. [weinberg] -- Added various range checks. [weinberg] -- Write time at current position step rather than latest of position and - velocity steps. [weinberg] -- Added requisite commas in configure file. [weinberg] -- Add verbose debugging flag. [weinberg] -- Added a few additional checks and protection against fluctuations at - center due to lack of particles. [weinberg] -- Prevent extrapolation in radius in epicylic table. [weinberg] -- Fix up velocity syncrhonization in phase space output routines. - [weinberg] -- Add sychronize velocity routine to global header file. [weinberg] -- Forgot to resychronize phase-space dumps. [weinberg] -- Parameter and help-text update. [weinberg] -- Make parameters consistent. [weinberg] -- Routine to dump each component to an ascii per-component file. - [weinberg] -- Change default parameter values. [weinberg] -- Changed error messages to make more descriptive on warning rather than - error. [weinberg] -- Fix error in detecting the existence of the processor.rates file. - [weinberg] -- Added additional usage help. [weinberg] -- Parameter fix ups. [weinberg] -- Minor bug in output basis routine CVSCVS: Committing in . [weinberg] -- Add norder as parameter. [weinberg] -- Strip leading spaces from parsed tokens. [weinberg] -- More debug output. [weinberg] -- Label change. [weinberg] -- Changes to diagnostic output. [weinberg] -- Add additional debug . . . [weinberg] -- For simplicity. [weinberg] -- Mistakenly added files. [weinberg] -- Initial revision. [weinberg] -- Remove rcylmin and rcylmax from user key=value access. [weinberg] -- Coordinate mapping in SLGridSph should always be on in EmpCylSL. - [weinberg] -- Start updating the NEWS file. [weinberg] -- Remove requirement for processor.rates file. [weinberg] -- Updated to remove cmap from global variable of SLGrid* classes. - [weinberg] -- Change delimiters to comma. [weinberg] -- Change parameter delimiter to comma. [weinberg] -- Coefficient output routines. [weinberg] -- Fix up for Cylinder scaling and OutCoef. [weinberg] -- Updates for Output & OrbTrace. [weinberg] -- Added u, v, w to the trace. [weinberg] -- Fix fence point error on some force loops. [weinberg] -- Make OrbTrace tied to a specific component. [weinberg] -- Fixed error in particle indexing for small numbers of particles. - Added debug lines to Direct. [weinberg] -- Fix error in center determination. [weinberg] -- Normalization fix up (?) [weinberg] -- Write to bar state file on first step. [weinberg] -- Fixes to UserBar for multiple components. [weinberg] -- More updates. [weinberg] -- More additions. [weinberg] -- Fix typo. [weinberg] -- Added FAQ. [weinberg] -- Documentation update. [weinberg] -- Added draft of a quick start document. [weinberg] -- Added "outpsn" to OutputContainer. [weinberg] -- Phase space output with one file per dump. [weinberg] -- Add code to stop reading but not abort if damaged header if found. - [weinberg] -- Documentation updates. [weinberg] -- Use most recent bar potential model in UserBar. [weinberg] -- Make sure OUT.bak char string is null terminated. [weinberg] -- Updated userinfo message. [weinberg] -- Add missing header file. [weinberg] -- Allow for fixed corotation fraction or fixed pattern speed. Update - parameters from U* to mnemonics. [weinberg] -- Updated to scan src/user for header files. [weinberg] -- COM and COV is current multipled by mass value!! Fixed. [weinberg] -- Add comment character to final header line. [weinberg] -- Fixed parameter parsing bug. [weinberg] -- Updated OrbTrace. [weinberg] -- Fix up documentation error. [weinberg] -- Update documenation strings. Remove unneeded files. [weinberg] -- Replaced by EmpOrth9thd. [weinberg] -- Fixed doxygen doc bug. [weinberg] -- Added a few fix ups and eliminated a bit of cruft in the global - stanza. [weinberg] -- Fix up to make sure OutCHKPT can be instantiated. Update some doc - files. [weinberg] -- Documenation for utility programs. [weinberg] -- Fixed up component method for binary restarts. [weinberg] -- Added check point output method (untested) [weinberg] -- Added *unoptimized* utility to split out a single phase space dump. - [weinberg] -- Add use_external clause. [weinberg] -- Added parameter list to doc. [weinberg] -- Added some doc. [weinberg] -- A few more updates to Direct. Seems to be working now. - ---------------------------------------------------------------------- - [weinberg] -- One more doc update. [weinberg] -- Updated documenation and removed unnecessary code. [weinberg] -- A bit more code clean up. [weinberg] -- Finished Direct method; needs testing. [weinberg] -- Mistake in fields_cyl: accumulated_eval returns forces not potential - gradients. [weinberg] -- Fix error in column header. [weinberg] -- Have Basis define the field evaluation members rather than - AxisymmetricBasis. This allows UserBar to cast the force for both - Spherical and Cylindrical types to a Basis abstract interface. - ---------------------------------------------------------------------- - [weinberg] -- Shorted column names. [weinberg] -- Fix up column headers to hold component names. [weinberg] -- Fix bug in self_consistent logic for Cylinder class. Updates to - EmpOrth9 (changed disk deprojection to improve accuracy of density) - [weinberg] -- Interaction should not recompute coefficients! May need to be changed - for a few other methods. Will check. [weinberg] -- Wrong asymptotic monopole condition for cylinder. [weinberg] -- Minor bug fixes, parameter changes. [weinberg] -- Redefine get_com_component to private member. [weinberg] -- Update for new EmpOrth9thd source. [weinberg] -- Lots of minor bug fixes. [weinberg] -- Changed ps2tispy to psp2tipsy. Name change only. [weinberg] -- Update for new version of disk expansion. [weinberg] -- New example directory with one example. [weinberg] -- Append to current rates file. Remove some debugging lines. [weinberg] -- Missing file. [weinberg] -- Get rid of duplicate files and directories. [weinberg] -- Ok. [weinberg] -- Try to fix up main branch repository. [weinberg] -- Replace repository (sigh) [weinberg] -- Reversion to previous version. [weinberg] -- New version. [weinberg] -- Release of reorganized version of code. [weinberg] -- Merged reoranized branch on to trunk. [weinberg] -- C++ routines updated for consistency with LAM 6.3.2. Needed to take - the expand.h out of C linkage. Updated Makefile to point at LAM - 6.3.2. [weinberg] -- Debug code for single point mass particle. [weinberg] -- Check in the version.h to update the date. [weinberg] -- *** empty log message *** [weinberg] -- Update version to include ID and date. [weinberg] -- Neglected to include print out of some cylindrical grid parameters. - [weinberg] -- Fixed up bug in defining edge of cylindrical grid. [weinberg] -- Initialization of coefficients on restart was being skipped, - erroneously. [weinberg] -- Fixed logic for restarting: no com or cov centering on restart. - [weinberg] -- Included exterior multipole solution in Sturm-Liouville potential and - force evaluation. [weinberg] -- Old version of routine, never finished, never used. [weinberg] -- Initial checkin. [weinberg] -- Initial checkin. [weinberg] -- Updated makefile to include String. [weinberg] -- Added Gamma variates class to random number generators based on TOMS - 599. [weinberg] -- Forgot this in initial load of repository. [weinberg] -- Initial entry of EXP code into repository. [weinberg] -- Removed junk list of files. [weinberg] -- GNU libg++ random and string classes. [weinberg] -- New repository initialized by cvs2svn. [(no author)] - - diff --git a/Exception.H b/Exception.H deleted file mode 100644 index 3e2ea198b..000000000 --- a/Exception.H +++ /dev/null @@ -1,104 +0,0 @@ -// -*- C++ -*- - -#ifndef EXPException_h -#define EXPException_h - -#include -#include -#include - - -/** Defines an Error Handler base class EXPException to handle - exceptions -*/ -class Exception : public std::exception -{ -public: - //! Generic exception - explicit Exception(std::string exceptionname, std::string message, - std::string sourcefilename, int sourcelinenumber); - - //! Copy constructor - Exception(const Exception& e); - - //! Destructor. - virtual ~Exception() {} - - //! Returns an error message suitable for printing to the user. - std::string getErrorMessage(); - - /** Returns a pointer to the (constant) error description. - * @return A pointer to a const char*. The underlying memory - * is in posession of the Exception object. Callers must - * not attempt to free the memory. - */ - virtual const char* what() const throw (){ - return getErrorMessage().c_str(); - } - - -protected: - //! Protected so it is only called by properly implemented classes. - Exception(string sourcefile, int linenumber); - - //! Friendly name of the exception. - std::string exceptionname; - - //! Error message describing the error in more detail. - std::ostringstream errormessage; - -protected: - //! Source file where throw occured. - std::string sourcefilename; - - //! Line number of throw. - int sourcelinenumber; -}; - - -//! Used when execution reaches a point it should not reach. -class InternalError : public Exception -{ -public: - //! Use this when you reach an unexpected state. - //@{ - InternalError(std::string sourcefilename, int sourcelinenumber); - - InternalError(std::string msg, - std::string sourcefilename, int sourcelinenumber); - - InternalError(int err, std::string msg, - std::string sourcefilename, int sourcelinenumber); - //@} -}; - - -//! Handles open file related exceptions. -class FileOpenException : public Exception -{ -public: - //! Reports filename, errno error, and location of throw - FileOpenException(std::string filename, int errno_, - std::string sourcefilename, int sourcelinenumber); -}; - -//! Handle file creation related exceptions. -class FileCreateException : public Exception -{ -public: - //! Reports filename, errno error, and location of throw - FileCreateException(std::string filename, int errno_, - std::string sourcefilename, int sourcelinenumber); -}; - -//! Handle file format related exceptions for DataStreams -class FileFormatException : public Exception -{ -public: - //! Constructor: supply diagnostic message - FileFormatException(std::string message, - std::string sourcefilename, int sourcelinenumber); -}; - - -#endif diff --git a/NEWS b/NEWS deleted file mode 100644 index 069aa416f..000000000 --- a/NEWS +++ /dev/null @@ -1,13 +0,0 @@ -2005-03-23 Major release with new centering changes, incorporation of - center of mass methods into Component class, many bug fixes, - fixed scaling problem in Cylindrical basis, etc. - -2002-07-10 Fixed a minor problem with OutCoef. Added log files - diagnostics to Interaction list. - -2002-06-05 All lists of keyword=value pairs are now comma delimited - rather than space delimited - -2002-06-07 Removed dependence on a "processor.rates" file. 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