Handle Spherical SL solutions for large harmonic orders

doc/exp.cfg

@@ -964,6 +964,8 @@ INPUT                  = ./intro.doc \
                          ../include \
                          ../src \
                          ../src/user \
+			 ../exputil \
+			 ../expui \
                          ../utils/ICs \
                          ../utils/Analysis \
                          ../utils/PhaseSpace
@@ -1788,7 +1790,7 @@ FORMULA_MACROFILE      =
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-USE_MATHJAX            = NO
+USE_MATHJAX            = YES
 
 # With MATHJAX_VERSION it is possible to specify the MathJax version to be used.
 # Note that the different versions of MathJax have different requirements with
@@ -1948,7 +1950,7 @@ EXTRA_SEARCH_MAPPINGS  =
 # If the GENERATE_LATEX tag is set to YES, doxygen will generate LaTeX output.
 # The default value is: YES.
 
-GENERATE_LATEX         = NO
+GENERATE_LATEX         = YES
 
 # The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. If a
 # relative path is entered the value of OUTPUT_DIRECTORY will be put in front of

exputil/SLGridMP2.cc

@@ -2907,7 +2907,8 @@ void SLGridSlab::compute_table(struct TableSlab* table, int KX, int KY)
 		<< std::setw( 5) << iflag[i]
 		<< std::endl;
 
-      if (VERBOSE && iflag[i] != 0) {
+
+  if (VERBOSE && iflag[i] != 0) {
 
 	if (iflag[i] > -10) {
 	  cout << std::setw(14) << "x"

src/AxisymmetricBasis.H

@@ -4,43 +4,45 @@
 #include <Basis.H>
 #include <Eigen/Eigen>
 
-//! Defines a basis-based potential and acceleration class
-/*! Configurable parameters are:
+/** @class AxisymmetricBasis
+    @brief Defines a basis-based potential and acceleration class
 
-  @param Lmax  is the maximum spherical harmonic order
+    @details **YAML configuration**
 
-  @param Mmax  is the maximum cylindrical harmonic order
+    @param Lmax  is the maximum spherical harmonic order
 
-  @param nmax  is the maximum radial order
+    @param Mmax  is the maximum cylindrical harmonic order
 
-  @param dof   is the dimensionality of the basis
+    @param nmax  is the maximum radial order
 
-  @param npca  is the frequency for pca analyses
+    @param dof   is the dimensionality of the basis
 
-  @param npca0 is the number of steps to skip before the first pca analysis
+    @param npca  is the frequency for pca analyses
 
-  @param pcavar boolean turns on pca analyses
+    @param npca0 is the number of steps to skip before the first pca analysis
 
-  @param pcaeof boolean turns on emperical function recomputation
+    @param pcavar boolean turns on pca analyses
 
-  @param pcadiag boolean turns on diagnostic pca output
+    @param pcaeof boolean turns on emperical function recomputation
 
-  @param pcavtk boolean prints out visualizable representations of pca info
+    @param pcadiag boolean turns on diagnostic pca output
 
-  @param hexp is the Hall smoothing exponent
+    @param pcavtk boolean prints out visualizable representations of pca info
 
-  @param samplesz is the number of subsamples for pca variance
-  analysis (default: 1). Value 0 means use sqrt number of particles
+    @param hexp is the Hall smoothing exponent
 
-  @param vtkfreq is the frequency for printing pca variance analysis info
+    @param samplesz is the number of subsamples for pca variance
+    analysis (default: 1). Value 0 means use sqrt number of particles
 
-  @param tksmooth is the S/N for Hall truncation for VarianceCut method
+    @param vtkfreq is the frequency for printing pca variance analysis info
 
-  @param tkcum is the cumulative fraction eigenvalue power for truncation for CmululativeCut method
+    @param tksmooth is the S/N for Hall truncation for VarianceCut method
 
-  @param tk_type is the smoothing type, one of: Hall, VarianceCut, CumulativeCut, VarianceWeighted
+    @param tkcum is the cumulative fraction eigenvalue power for truncation for CmululativeCut method
 
-  @param subsamp true sets partition variance computation (default: false)
+    @param tk_type is the smoothing type, one of: Hall, VarianceCut, CumulativeCut, VarianceWeighted
+
+    @param subsamp true sets partition variance computation (default: false)
 */
 class AxisymmetricBasis : public Basis
 {

src/Cube.H

@@ -18,7 +18,36 @@
 #include <cudaMappingConstants.cuH>
 #endif
 
-//! Periodic cube basis
+/** @class Cube
+
+    @brief Periodic cube basis
+
+    @details **YAML configuration**
+
+    @param nminx is the minimum absoulte value of the wave number in
+    the x direction (default: 0)
+
+    @param nminy is the minimum absoulte value of the wave number in
+    the y direction (default: 0)
+
+    @param nminz is the minimum absoulte value of the wave number in
+    the z direction (default: 0)
+
+    @param nmaxx is the maximum absoulte value of the wave number in
+    the x direction (default: 16)
+
+    @param nmaxy is the maximum absoulte value of the wave number in
+    the y direction (default: 16)
+
+    @param nmaxz is the maximum absoulte value of the wave number in
+    the z direction (default: 16)
+
+    @param method string sets the evaluation method for the CUDA
+    kernel.  Available methods are: all, full, 3d which compute all
+    dimensions at once and planes, axes, and 1d which compute wave
+    vectors by plane.  This may be extended to specific algorithms in
+    the future.  This does nothing for the CPU-only computation.
+*/
 class Cube : public PotAccel
 {
 

src/Cylinder.H

@@ -22,10 +22,11 @@
 
 class MixtureBasis;
 
-/** This routine computes the potential, acceleration and density 
+/** @class Cylinder
+    @brief This routine computes the potential, acceleration and density 
     using the Cylindrical biorthogonal expansion 
 
-    Configuration parameters:
+    @details **YAML configuration**
 
     @param rcylmin is the minimum cylindrical grid radius in scale-length units
 
@@ -35,7 +36,9 @@ class MixtureBasis;
 
     @param hcyl is the scale height
 
-    @param lmax is the maximum spherical harmonic index for EOF construction
+    @param lmaxfid is the maximum spherical harmonic index for EOF construction
+
+    @param nmaxfid is the maximum radial index for EOF construction
 
     @param mmax is the maximum azimuthal order for the resulting basis
 
@@ -87,24 +90,34 @@ class MixtureBasis;
 
     @param snr is the signal-to-noise prefactor for sharpness computation
 
-    @param evcut is the cumulative trim remainder on the covariance eigenvalues (default: -1, which implies no trimming).  Set to small positive value for trimming.
+    @param evcut is the cumulative trim remainder on the covariance
+    eigenvalues (default: -1, which implies no trimming).  Set to
+    small positive value for trimming.
 
     @param try_cache false suppresses cache reading on restart (default: true)
 
     @param EVEN_M true uses even harmonic orders only
 
-    @param cmap is the coordinate mapping type (deprecated but kept for backward consistency)
+    @param cmap is the coordinate mapping type (deprecated but kept
+    for backward consistency)
 
     @param cmapr is the radial coordinate mapping type
 
     @param cmapz is the vertical coordinate mapping type
 
-    @param self_consistent set to false turns off potential expansion; only performed the first time
+    @param self_consistent set to false turns off potential expansion;
+    only performed the first time
 
-    @param playback file reads a coefficient file and uses it to compute the basis function output for resimiulation
+    @param playback file reads a coefficient file and uses it to
+    compute the basis function output for resimiulation
 
-    @param python is the file name of Python module which supplies the 'disk_density' function for conditioning the cylindrical basis.  A non-null string triggers the use of the Python interpreter to evaluate the target density function.
+    @param pyname is the file name of Python module which supplies the
+    'disk_density' function for conditioning the cylindrical basis.  A
+    non-null string triggers the use of the Python interpreter to
+    evaluate the target density function.
 
+    @param dumpbasis set to true dumps the basis to a file for
+    diagnostic examination (default: false)
 */
 class Cylinder : public Basis
 {

src/FlatDisk.H

@@ -13,47 +13,59 @@ typedef std::shared_ptr<BiorthCyl> CylPtr;
 #include <cudaUtil.cuH>
 #endif
 
-/** Computes the potential, acceleration and density using an empirical
-    function analysis for a flat Bessel basis and a target density
+/** @class FlatDisk
 
-    Parameters
+    @brief Computes the potential, acceleration and density using an
+    empirical function analysis for a flat Bessel basis and a target
+    density
 
-    \param rcylmin is the minimum value in the table for the 
+    @details **YAML configuration**
+
+    @param rcylmin is the minimum value in the table for the 
     radial basis functions (default is 0.0)
 
-    \param rcylmax is the maximum value in the table for the 
+    @param rcylmax is the maximum value in the table for the 
     radial basis functions in acyltbl units (default is 10.0)
 
-    \param scale is the expansion factor to get the physical scale from
+    @param scale is the expansion factor to get the physical scale from
     the internal scale (default is 0.01)
 
-    \param mmax is the maximum azimuthal order
+    @param mmax is the maximum azimuthal order
 
-    \param numx is the number of grid points in the scaled radial direction
+    @param numx is the number of grid points in the scaled radial direction
 
-    \param numy is the number of grid points in the scaled vertical direction
+    @param numy is the number of grid points in the scaled vertical direction
 
-    \param knots is the number of quadrature points for EmpCyl2d
+    @param knots is the number of quadrature points for EmpCyl2d
 
-    \param logr scales the EmpCyl2d grid logarithmically
+    @param logr scales the EmpCyl2d grid logarithmically
 
-    \param model name for conditioning the new basis using EmpCyl2d (default: expon)
+    @param model name for conditioning the new basis using EmpCyl2d
+    (default: expon)
 
-    \param biorth is the biorthogonal basis set used by EmpCyl2d for conditioning (default: bess)
+    @param biorth is the biorthogonal basis set used by EmpCyl2d for
+    conditioning (default: bess)
 
-    \param background sets a fixed monopole potential and force for the model.  Used for stability analysis of disks with active and inactive tapers, following Zang
+    @param background sets a fixed monopole potential and force for
+    the model.  Used for stability analysis of disks with active and
+    inactive tapers, following Zang
 
-    \param nmaxfid is the maximum radial order for the basis used by EmpCyl2d for conditioning
+    @param nmaxfid is the maximum radial order for the basis used by
+    EmpCyl2d for conditioning
 
-    \param numr is the number of grid points in the radial direction for the numerical basis in EmpCyl2d
+    @param numr is the number of grid points in the radial direction
+    for the numerical basis in EmpCyl2d
 
-    \param NQDHT is the number of grid points for the numerical Hankel transform
+    @param NQDHT is the number of grid points for the numerical Hankel transform
 
-    \param diskconf is a YAML configuration for the target disk model in EmpCyl2d
+    @param diskconf is a YAML configuration for the target disk model
+    in EmpCyl2d
 
-    \param cachename is the name of the cache file for the newly constructed basis
+    @param cachename is the name of the cache file for the newly
+    constructed basis
 
-    \param dumpbasis provides the user with a ascii table of the basis potential-density pairs
+    @param dumpbasis provides the user with a ascii table of the basis
+    potential-density pairs
 */
 class FlatDisk : public PolarBasis 
 {

src/Sphere.H

@@ -13,16 +13,16 @@ typedef std::shared_ptr<SLGridSph> SLGridSphPtr;
 #include <cudaUtil.cuH>
 #endif
 
-/** Computes the potential, acceleration and density using the Sturm
+/** @class Sphere
+    @brief Computes the potential, acceleration and density using the Sturm
     Liouville direct solution
 
-    \param rmin is the minimum value in the table for the 
-    radial basis functions (default is 0.001)
+    @details **YAML configuration**
 
-    \param rmapping is the halo scale length (default is 0.067*rmax).  This
+    @param rmapping is the halo scale length (default is 0.067*rmax).  This
     is used to for the coordinate mapping  (see below).
 
-    \param cmap should be 1 for algebraic coordinate scaling, 2 for log
+    @param cmap should be 1 for algebraic coordinate scaling, 2 for log
     coordinate scaling, 0 for no scaling as follows: 
     \f[ 
     x = {r/r_s-1 \over r/r_s+1} 
@@ -37,12 +37,34 @@ typedef std::shared_ptr<SLGridSph> SLGridSphPtr;
     better choice.  Logarithmic scaling will insist that the
     <code>rmin>0</code>.
 
-    \param numr is the number radial coordinate knots in the table 
-    (default is 1000)
+    @param numr is the number radial coordinate knots in the table 
+    (default: 2000)
 
-    \param diverge sets the power law extrapolation of a cusp profile
+    @param nums is the number of bins in the empirical mass array
+    (default: 2000)
 
-    \param dfac is the inverse slope of the power law
+    @param noff is the offset into the empirical mass array for
+    computing upper and lower grid boundaries (default: 32)
+
+    @param diverge set to true means assume a cuspy profile
+
+    @param dfac is the power of the "divergent" cusp
+
+    @param modelname is the file containing the input background model profile
+
+    @param cachename is the name for the SL grid cache file
+
+    @param dtime is the interval between basis recomputations (<=0 for never)
+
+    @param diverge sets the power law extrapolation of a cusp profile
+
+    @param dfac is the inverse slope of the power law
+
+    @param logr set to true uses a logarithmic spacing for the
+    empirical radial grid (default: false)
+
+    @param plummer set to true uses a Plummer-model fit to the
+    empirical mass array to make basis model (default: true)
 */
 class Sphere : public SphericalBasis 
 {
@@ -119,16 +141,6 @@ public:
       @param c0 is the instantiating caller (Component)
       @param conf passes any parameters to basis instance (rsphSL, rmin and numr
       @param m allows the spherical basis to be used for multiple center expansions 
-
-      Input line parameters include:
-      @param rmapping is the radius for coordinate scaling
-      @param numr is the number of radial grid points
-      @param cmap set to true for scaling coordinates from the semi-infinite to finite segment
-      @param diverge set to true means assume a cuspy profile
-      @param dfac is the power of the "divergent" cusp
-      @param modelname is the file containing the input background model profile
-      @param cachename is the name for the SL grid cache file
-      @param dtime is the interval between basis recomputations (<=0 for never)
   */
   Sphere(Component* c0, const YAML::Node& conf, MixtureBasis* m=0);