From e8a2fbeaa60bae0e780d55f0fc8feae63a9ed863 Mon Sep 17 00:00:00 2001 From: Jinzhe Zeng Date: Wed, 12 Oct 2022 21:12:48 -0400 Subject: [PATCH 01/10] migrate from setup.py to pyproject.toml (#366) --- README.md | 11 ++---- plugin_example/pyproject.toml | 16 ++++++++ plugin_example/setup.py | 12 ------ pyproject.toml | 59 ++++++++++++++++++++++++++++++ setup.py | 69 ----------------------------------- 5 files changed, 79 insertions(+), 88 deletions(-) create mode 100644 plugin_example/pyproject.toml delete mode 100644 plugin_example/setup.py create mode 100644 pyproject.toml delete mode 100644 setup.py diff --git a/README.md b/README.md index 5d8214b27..a5ad27bd3 100644 --- a/README.md +++ b/README.md @@ -259,11 +259,8 @@ If a valence of 3 is detected on carbon, the formal charge will be assigned to - # Plugins -One can follow [a simple example](plugin_example/) to add their own format by creating and installing plugins. It's critical to add the [Format](dpdata/format.py) class to `entry_points['dpdata.plugins']` in `setup.py`: -```py - entry_points={ - 'dpdata.plugins': [ - 'random=dpdata_random:RandomFormat' - ] - }, +One can follow [a simple example](plugin_example/) to add their own format by creating and installing plugins. It's critical to add the [Format](dpdata/format.py) class to `entry_points['dpdata.plugins']` in [`pyproject.toml`](plugin_example/pyproject.toml): +```toml +[project.entry-points.'dpdata.plugins'] +random = "dpdata_random:RandomFormat" ``` diff --git a/plugin_example/pyproject.toml b/plugin_example/pyproject.toml new file mode 100644 index 000000000..d8652bd2d --- /dev/null +++ b/plugin_example/pyproject.toml @@ -0,0 +1,16 @@ +[build-system] +requires = ["setuptools>=45"] +build-backend = "setuptools.build_meta" + +[project] +name = "dpdata_random" +version = "0.0.0" +description = "An example for dpdata plugin" +dependencies = [ + 'numpy', + 'dpdata', +] +readme = "README.md" + +[project.entry-points.'dpdata.plugins'] +random = "dpdata_random:RandomFormat" diff --git a/plugin_example/setup.py b/plugin_example/setup.py deleted file mode 100644 index 031afb60f..000000000 --- a/plugin_example/setup.py +++ /dev/null @@ -1,12 +0,0 @@ -from setuptools import setup - -setup( - name="dpdata_random", - packages=['dpdata_random'], - entry_points={ - 'dpdata.plugins': [ - 'random=dpdata_random:RandomFormat' - ] - }, - install_requires=['dpdata', 'numpy'], -) diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 000000000..6cc28717b --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,59 @@ +[build-system] +requires = ["setuptools>=45", "setuptools_scm[toml]>=6.2"] +build-backend = "setuptools.build_meta" + +[project] +name = "dpdata" +dynamic = ["version"] +description = "Manipulating data formats of DeePMD-kit, VASP, QE, PWmat, and LAMMPS, etc." +authors = [ + {name = "DeepModeling"}, + {name = "Han Wang", email = "wang_han@iapcm.ac.cn"}, +] +license = {file = "LICENSE"} +classifiers = [ + "Programming Language :: Python :: 3.6", + "License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)", +] +dependencies = [ + 'numpy>=1.14.3', + 'monty', + 'scipy', + 'h5py', + 'wcmatch', + 'importlib_metadata>=1.4; python_version < "3.8"', +] +requires-python = ">=3.6" +readme = "README.md" +keywords = ["lammps", "vasp", "deepmd-kit"] + +[project.urls] +Homepage = "https://github.com/deepmodeling/dpdata" +documentation = "https://docs.deepmodeling.com/projects/dpdata" +repository = "https://github.com/deepmodeling/dpdata" + +[project.entry-points.console_scripts] +dpdata = "dpdata.cli:dpdata_cli" + +[project.optional-dependencies] +ase = ['ase'] +amber = ['parmed'] +pymatgen = ['pymatgen'] +docs = [ + 'sphinx', + 'recommonmark', + 'sphinx_rtd_theme>=1.0.0rc1', + 'numpydoc', + 'm2r2', + 'deepmodeling-sphinx>=0.1.1', + 'sphinx-argparse', +] + +[tool.setuptools.packages.find] +include = ["dpdata*"] + +[tool.setuptools.package-data] +dpdata = ['*.json'] + +[tool.setuptools_scm] +write_to = "dpdata/_version.py" diff --git a/setup.py b/setup.py deleted file mode 100644 index 4407c625d..000000000 --- a/setup.py +++ /dev/null @@ -1,69 +0,0 @@ -# -*- coding: utf-8 -*- - -from os import path -import setuptools - -readme_file = path.join(path.dirname(path.abspath(__file__)), 'README.md') -try: - from m2r import parse_from_file - readme = parse_from_file(readme_file) -except ImportError: - with open(readme_file) as f: - readme = f.read() - -# install_requires = ['xml'] -install_requires=['numpy>=1.14.3', 'monty', 'scipy', 'h5py', 'wcmatch', 'importlib_metadata>=1.4; python_version < "3.8"'] - -setuptools.setup( - name="dpdata", - use_scm_version={'write_to': 'dpdata/_version.py'}, - setup_requires=['setuptools_scm'], - author="Han Wang", - author_email="wang_han@iapcm.ac.cn", - description="Manipulating data formats of DeePMD-kit, VASP, QE, PWmat, and LAMMPS, etc.", - long_description=readme, - long_description_content_type="text/markdown", - url="https://github.com/deepmodeling/dpdata", - packages=['dpdata', - 'dpdata/vasp', - 'dpdata/lammps', - 'dpdata/md', - 'dpdata/deepmd', - 'dpdata/qe', - 'dpdata/siesta', - 'dpdata/gaussian', - 'dpdata/cp2k', - 'dpdata/xyz', - 'dpdata/pwmat', - 'dpdata/amber', - 'dpdata/fhi_aims', - 'dpdata/gromacs', - 'dpdata/abacus', - 'dpdata/rdkit', - 'dpdata/plugins', - 'dpdata/pymatgen', - ], - package_data={'dpdata':['*.json']}, - classifiers=[ - "Programming Language :: Python :: 3.6", - "License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)", - ], - keywords='lammps vasp deepmd-kit', - install_requires=install_requires, - extras_require={ - 'ase': ['ase'], - 'amber': ['parmed'], - 'pymatgen': ['pymatgen'], - 'docs': [ - 'sphinx', - 'recommonmark', - 'sphinx_rtd_theme>=1.0.0rc1', - 'numpydoc', - 'm2r2', - 'deepmodeling-sphinx>=0.1.1', - 'sphinx-argparse', - ], - }, - entry_points={"console_scripts": ["dpdata = dpdata.cli:dpdata_cli"]}, -) - From bc6508bae9b8f3ef9f35199519c0f2c4c05ef473 Mon Sep 17 00:00:00 2001 From: pxlxingliang <91927439+pxlxingliang@users.noreply.github.com> Date: Sat, 29 Oct 2022 21:18:10 +0800 Subject: [PATCH 02/10] fix(abacus): do not collect the unconverged structure for AIMD (#368) --- dpdata/abacus/md.py | 19 + tests/abacus.md.unconv/INPUT | 30 + tests/abacus.md.unconv/OUT.ABACUS/MD_dump | 176 + .../OUT.ABACUS/running_md.log | 5035 +++++++++++++++++ tests/abacus.md.unconv/STRU | 30 + tests/abacus.md.unconv/water_coord | 30 + tests/abacus.md.unconv/water_force | 30 + tests/abacus.md.unconv/water_virial | 30 + tests/test_abacus_md.py | 38 +- 9 files changed, 5417 insertions(+), 1 deletion(-) create mode 100644 tests/abacus.md.unconv/INPUT create mode 100644 tests/abacus.md.unconv/OUT.ABACUS/MD_dump create mode 100644 tests/abacus.md.unconv/OUT.ABACUS/running_md.log create mode 100644 tests/abacus.md.unconv/STRU create mode 100644 tests/abacus.md.unconv/water_coord create mode 100644 tests/abacus.md.unconv/water_force create mode 100644 tests/abacus.md.unconv/water_virial diff --git a/dpdata/abacus/md.py b/dpdata/abacus/md.py index 020f968b5..253e48a2f 100644 --- a/dpdata/abacus/md.py +++ b/dpdata/abacus/md.py @@ -3,6 +3,7 @@ import numpy as np from .scf import ry2ev, bohr2ang, kbar2evperang3, get_block, get_geometry_in, get_cell, get_coords import re +import warnings # Read in geometries from an ABACUS MD trajectory. # The atomic coordinates are read in from generated files in OUT.XXXX. @@ -80,6 +81,10 @@ def get_energy(outlines, ndump, dump_freq): if nenergy%dump_freq == 0: energy.append(float(line.split()[-2])) nenergy+=1 + elif "!! convergence has not been achieved" in line: + if nenergy%dump_freq == 0: + energy.append(np.nan) + nenergy+=1 assert(ndump == len(energy)), "Number of total energies in running_md.log = %d. Number of frames in MD_dump = %d. Please check."%(len(energy), ndump) energy = np.array(energy) return energy @@ -113,6 +118,20 @@ def get_frame (fname): with open(os.path.join(path_out, "running_md.log"), 'r') as fp: outlines = fp.read().split('\n') energy = get_energy(outlines, ndump, dump_freq) + + unconv_stru = '' + for i,iene in enumerate(energy): + if np.isnan(iene): + coords = np.delete(coords,i-ndump,axis=0) + cells = np.delete(cells,i-ndump,axis=0) + force = np.delete(force,i-ndump,axis=0) + stress = np.delete(stress,i-ndump,axis=0) + energy = np.delete(energy,i-ndump,axis=0) + unconv_stru += "%d " % i + ndump = len(energy) + if unconv_stru != '': + warnings.warn(f"Structure %s are unconverged and not collected!" % unconv_stru) + for iframe in range(ndump): stress[iframe] *= np.linalg.det(cells[iframe, :, :].reshape([3, 3])) if np.sum(np.abs(stress[0])) < 1e-10: diff --git a/tests/abacus.md.unconv/INPUT b/tests/abacus.md.unconv/INPUT new file mode 100644 index 000000000..d4f1574ec --- /dev/null +++ b/tests/abacus.md.unconv/INPUT @@ -0,0 +1,30 @@ +INPUT_PARAMETERS +calculation md +ntype 2 +nbands 8 + +ecutwfc 50.000000 +scf_thr 1.000000e-07 +scf_nmax 100 + +basis_type lcao +dft_functional lda +gamma_only 1 + +mixing_type pulay +mixing_beta 0.400000 +smearing_method gaussian +smearing_sigma 0.020000 + +cal_force 1 +cal_stress 1 + +md_type 0 +md_nstep 10 +md_tfirst 10 +md_dt 1 +chg_extrap second-order + +deepks_scf 1 +deepks_bandgap 0 +deepks_model model.ptg diff --git a/tests/abacus.md.unconv/OUT.ABACUS/MD_dump b/tests/abacus.md.unconv/OUT.ABACUS/MD_dump new file mode 100644 index 000000000..fb5e1b4e2 --- /dev/null +++ b/tests/abacus.md.unconv/OUT.ABACUS/MD_dump @@ -0,0 +1,176 @@ +MDSTEP: 0 +LATTICE_CONSTANT: 1.889726125458 +LATTICE_VECTORS + 14.524509151052 0.000000000000 0.000000000000 + -0.014055052628 15.127720223676 0.000000000000 + -0.442369434823 0.417648184158 14.953520775918 +VIRIAL (KBAR) + 0.117880839971 0.348548064508 0.269730962791 + 0.348548064508 -1.559580670587 -1.949852828444 + 0.269730962791 -1.949852828444 -2.332929959367 +INDEX LABEL POSITIONS FORCE (eV/Angstrom) + 0 H 10.872796345708 0.993283528438 3.293903479774 0.203673227663 -0.476188513340 -0.673198308232 + 1 H 10.341931867316 14.686041612304 2.160229648207 -0.497679578285 3.938931579746 4.649209009347 + 2 O 10.133374044868 0.350751910571 3.193008852361 0.294006350622 -3.462743066406 -3.976010701114 + + +MDSTEP: 1 +LATTICE_CONSTANT: 1.889726125458 +LATTICE_VECTORS + 14.524509151052 0.000000000000 0.000000000000 + -0.014055052628 15.127720223676 0.000000000000 + -0.442369434823 0.417648184158 14.953520775918 +VIRIAL (KBAR) + -0.052861928550 0.190313757600 0.235641072577 + 0.190313757600 -1.590040770984 -1.856968175095 + 0.235641072577 -1.856968175095 -2.206369542675 +INDEX LABEL POSITIONS FORCE (eV/Angstrom) + 0 H 10.875596899173 0.988023063544 3.294283265923 -0.254022717293 -0.877700208440 -0.747314202230 + 1 H 10.340932440770 14.707241014770 2.180444767744 -0.497860772145 3.864467170520 4.570589962154 + 2 O 10.131572917949 0.334812972999 3.172413946676 0.751883489438 -2.986766962080 -3.823275759924 + + +MDSTEP: 2 +LATTICE_CONSTANT: 1.889726125458 +LATTICE_VECTORS + 14.524509151052 0.000000000000 0.000000000000 + -0.014055052628 15.127720223676 0.000000000000 + -0.442369434823 0.417648184158 14.953520775918 +VIRIAL (KBAR) + -0.316210888687 -0.207283827612 0.007046496091 + -0.207283827612 -1.346616360903 -1.287258423394 + 0.007046496091 -1.287258423394 -1.415183801991 +INDEX LABEL POSITIONS FORCE (eV/Angstrom) + 0 H 10.875946508110 0.974294086278 3.287452572336 -1.045230179415 -1.628147086821 -0.958970724628 + 1 H 10.335129392135 14.765726825200 2.244759338627 -0.207420915322 2.933943064626 3.340010877721 + 2 O 10.137026357647 0.290056139835 3.114930069379 1.252651094738 -1.305795977804 -2.381040153093 + + +MDSTEP: 3 +LATTICE_CONSTANT: 1.889726125458 +LATTICE_VECTORS + 14.524509151052 0.000000000000 0.000000000000 + -0.014055052628 15.127720223676 0.000000000000 + -0.442369434823 0.417648184158 14.953520775918 +VIRIAL (KBAR) + -0.260134638405 -0.993002747244 -0.895525915647 + -0.993002747244 0.262836092646 1.051311229863 + -0.895525915647 1.051311229863 1.805220211014 +INDEX LABEL POSITIONS FORCE (eV/Angstrom) + 0 H 10.866211187568 0.944855891202 3.271369225774 -1.519717284879 -2.134878371745 -1.173199796326 + 1 H 10.327325037621 14.852520858530 2.341300087841 2.109118093970 -3.394877057008 -5.282580352734 + 2 O 10.154566032703 0.232700301582 3.034472666728 -0.589400809091 5.529755428753 6.455780149060 + + +MDSTEP: 4 +LATTICE_CONSTANT: 1.889726125458 +LATTICE_VECTORS + 14.524509151052 0.000000000000 0.000000000000 + -0.014055052628 15.127720223676 0.000000000000 + -0.442369434823 0.417648184158 14.953520775918 +VIRIAL (KBAR) + 0.504846487933 -0.963922770050 -1.396738517223 + -0.963922770050 2.096159352353 2.997442421390 + -1.396738517223 2.997442421390 4.270661113979 +INDEX LABEL POSITIONS FORCE (eV/Angstrom) + 0 H 10.841812836866 0.894819268862 3.243966231690 -0.065851648219 -0.473828154419 -0.442665692581 + 1 H 10.339870561687 14.906559335828 2.386871728651 4.482678409108 -9.390324011782 -13.734305291761 + 2 O 10.166418859339 0.228698446623 3.016304020001 -4.416826760889 9.864152166202 14.176970984342 + + +MDSTEP: 5 +LATTICE_CONSTANT: 1.889726125458 +LATTICE_VECTORS + 14.524509151052 0.000000000000 0.000000000000 + -0.014055052628 15.127720223676 0.000000000000 + -0.442369434823 0.417648184158 14.953520775918 +VIRIAL (KBAR) + 2.301988732603 2.106077476560 0.632201255105 + 2.106077476560 1.094304604347 -0.313178332666 + 0.632201255105 -0.313178332666 -0.819241722779 +INDEX LABEL POSITIONS FORCE (eV/Angstrom) + 0 H 10.816779114892 0.840210903747 3.212292166621 6.855059278224 5.454541643043 1.016758449181 + 1 H 10.395667320285 14.869995037486 2.299927582003 -0.960810002863 1.486842944666 2.333454697801 + 2 O 10.135655822714 0.319871110080 3.134922231718 -5.894249275361 -6.941384587709 -3.350213146982 + + +MDSTEP: 6 +LATTICE_CONSTANT: 1.889726125458 +LATTICE_VECTORS + 14.524509151052 0.000000000000 0.000000000000 + -0.014055052628 15.127720223676 0.000000000000 + -0.442369434823 0.417648184158 14.953520775918 +VIRIAL (KBAR) + 0.224387150431 1.128837044998 1.081862730682 + 1.128837044998 -0.268818497136 -1.093793836625 + 1.081862730682 -1.093793836625 -2.004917355086 +INDEX LABEL POSITIONS FORCE (eV/Angstrom) + 0 H 10.857886603488 0.838230819836 3.190428320831 1.363129257990 1.501361774798 0.692219305499 + 1 H 10.442193679586 14.847776580413 2.235497831256 -2.370639635238 2.295060837375 4.247420933792 + 2 O 10.048021974818 0.344069651064 3.221215828255 1.007510377248 -3.796422612173 -4.939640239291 + + +MDSTEP: 7 +LATTICE_CONSTANT: 1.889726125458 +LATTICE_VECTORS + 14.524509151052 0.000000000000 0.000000000000 + -0.014055052628 15.127720223676 0.000000000000 + -0.442369434823 0.417648184158 14.953520775918 +VIRIAL (KBAR) + -1.914534915401 0.160753699840 1.525216417878 + 0.160753699840 -0.780431878582 -0.977244043867 + 1.525216417878 -0.977244043867 -2.191357680684 +INDEX LABEL POSITIONS FORCE (eV/Angstrom) + 0 H 10.912146278758 0.850736662489 3.175243370290 -2.896292249377 -0.849289935513 1.095057694700 + 1 H 10.465846863187 14.847702075120 2.212049427419 -2.832220895025 2.019939251673 4.270685618311 + 2 O 9.970109115947 0.331638313704 3.259849182634 5.728513144402 -1.170649316160 -5.365743313011 + + +MDSTEP: 8 +LATTICE_CONSTANT: 1.889726125458 +LATTICE_VECTORS + 14.524509151052 0.000000000000 0.000000000000 + -0.014055052628 15.127720223676 0.000000000000 + -0.442369434823 0.417648184158 14.953520775918 +VIRIAL (KBAR) + -2.513125907165 -0.154419226124 1.580371274213 + -0.154419226124 -0.825335562412 -0.815094290966 + 1.580371274213 -0.815094290966 -2.050106792249 +INDEX LABEL POSITIONS FORCE (eV/Angstrom) + 0 H 10.938461005959 0.855048109998 3.170624111252 -3.822684404614 -1.352624889240 1.151176221490 + 1 H 10.462173292782 14.867117004122 2.229806840379 -2.984053847480 1.788365306177 4.125001485576 + 2 O 9.947467959151 0.307911937194 3.246711028711 6.806738252094 -0.435740416937 -5.276177707066 + + +MDSTEP: 9 +LATTICE_CONSTANT: 1.889726125458 +LATTICE_VECTORS + 14.524509151052 0.000000000000 0.000000000000 + -0.014055052628 15.127720223676 0.000000000000 + -0.442369434823 0.417648184158 14.953520775918 +VIRIAL (KBAR) + -1.921730659733 -0.250128628384 1.045305625840 + -0.250128628384 -0.550642430618 -0.443385704265 + 1.045305625840 -0.443385704265 -1.253788166285 +INDEX LABEL POSITIONS FORCE (eV/Angstrom) + 0 H 10.927892467255 0.846308722497 3.177112004724 -3.263179899026 -1.178327094849 0.932844111407 + 1 H 10.429708004337 14.903787020423 2.287364433146 -2.485295875334 1.119241763062 3.025686004957 + 2 O 9.990501786298 0.279981308393 3.182665542472 5.748475774360 0.059085331787 -3.958530116363 + + +MDSTEP: 10 +LATTICE_CONSTANT: 1.889726125458 +LATTICE_VECTORS + 14.524509151052 0.000000000000 0.000000000000 + -0.014055052628 15.127720223676 0.000000000000 + -0.442369434823 0.417648184158 14.953520775918 +VIRIAL (KBAR) + 0.125490523345 -0.470583331016 -0.646063109567 + -0.470583331016 0.977542641385 1.479381534553 + -0.646063109567 1.479381534553 2.154282026823 +INDEX LABEL POSITIONS FORCE (eV/Angstrom) + 0 H 10.885839055837 0.826200216607 3.192600467891 -0.652935734428 0.144670019023 0.624517068595 + 1 H 10.373263276599 14.951256068815 2.374115432862 1.613773327904 -3.964330561830 -5.728774672298 + 2 O 10.088999925455 0.252620765891 3.080426079588 -0.960837593476 3.819660542807 5.104257603703 + + diff --git a/tests/abacus.md.unconv/OUT.ABACUS/running_md.log b/tests/abacus.md.unconv/OUT.ABACUS/running_md.log new file mode 100644 index 000000000..cb5231730 --- /dev/null +++ b/tests/abacus.md.unconv/OUT.ABACUS/running_md.log @@ -0,0 +1,5035 @@ + + WELCOME TO ABACUS v3.0 + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 8 + Start Time is Fri Oct 28 10:37:22 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + DRANK = 1 + DSIZE = 8 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + The esolver type has been set to : ksdft_lcao + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = H + atom label for species 2 = O + lattice constant (Bohr) = 1.88973 + lattice constant (Angstrom) = 1 + + READING ATOM TYPE 1 + atom label = H + L=0, number of zeta = 2 + L=1, number of zeta = 1 + number of atom for this type = 2 + start magnetization = FALSE + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = O + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + TOTAL ATOM NUMBER = 3 + + CARTESIAN COORDINATES ( UNIT = 1.88973 Bohr ). + atom x y z mag vx vy vz + tauc_H1 10.8727963457 0.993283528438 3.29390347977 0 0 0 0 + tauc_H2 10.3419318673 14.6860416123 2.16022964821 0 0 0 0 + tauc_O1 10.1333740449 0.350751910571 3.19300885236 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: H_gga_6au_60Ry_2s1p.orb + orbital file: O_gga_6au_60Ry_2s2p1d.orb + + Volume (Bohr^3) = 22172.5176163 + Volume (A^3) = 3285.62419713 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +14.5245091511 +0 +0 + -0.0140550526276 +15.1277202237 +0 + -0.442369434823 +0.417648184158 +14.9535207759 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0688491424805 +6.39672274884e-05 +0.00203497496722 + +0 +0.0661038137415 -0.00184626337762 + +0 -0 +0.0668738830798 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is H_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is O_ONCV_PBE-1.0.upf + pseudopotential type = NC + exchange-correlation functional = PBE + nonlocal core correction = 0 + valence electrons = 6 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + + In Pseudopot_upf::read_pseudo_header : dft_functional from INPUT does not match that in pseudopot file + Please make sure this is what you need + XC functional updated to : lda + exchange-correlation functional = LDA + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 200 + [fft grid for charge/potential] = 128, 144, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 72, 64 + nbxx = 36864 + nrxx = 294912 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1059123 + number of sticks = 12499 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 1562 132390 + 2 1562 132390 + 3 1563 132391 + 4 1563 132391 + 5 1562 132390 + 6 1562 132390 + 7 1562 132390 + 8 1563 132391 + --------------- sum ------------------- + 8 12499 1059123 + number of |g| = 124423 + max |g| = 18.0911730027 + min |g| = 0.00474434963522 + + SETUP THE ELECTRONS NUMBER + electron number of element H = 1 + total electron number of element H = 2 + electron number of element O = 6 + total electron number of element O = 6 + occupied bands = 4 + NLOCAL = 23 + NBANDS = 8 + NBANDS = 8 + DONE : SETUP UNITCELL Time : 0.0987153092179 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0991557371016 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup numerical orbitals: | + | This part setup: numerical atomic orbitals, non-local projectors | + | and neutral potential (1D). The atomic orbitals information | + | including the radius, angular momentum and zeta number. | + | The neutral potential is the sum of local part of pseudopotential | + | and potential given by atomic charge, they will cancel out beyond | + | a certain radius cutoff, because the Z/r character. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP ONE DIMENSIONAL ORBITALS/POTENTIAL + delta k (1/Bohr) = 0.01 + delta r (Bohr) = 0.01 + dr_uniform (Bohr) = 0.001 + rmax (Bohr) = 30 + kmesh = 711 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 601 0.01 6 1 1 + 2 0 1 601 0.01 6 1 1 + 3 1 0 601 0.01 6 1 1 + 4 1 1 601 0.01 6 1 1 + 5 2 0 601 0.01 6 1 1 + DESCRIPTOR L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 205 0.01 2.04 0.405 1 + 2 0 1 205 0.01 2.04 0.101 1 + 3 1 0 205 0.01 2.04 0.189 1 + 4 1 1 205 0.01 2.04 0.0659 1 + 5 2 0 205 0.01 2.04 0.11 1 + 6 2 1 205 0.01 2.04 0.0466 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 4 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 1 + trace_loc_row dimension = 23 + trace_loc_col dimension = 23 + nloc = 72 + Initialize the descriptor index for DeePKS (lcao line) + lmax of descriptor = 2 + nmax of descriptor= 2 + total basis (all atoms) for descriptor= + Type 1 number_of_atoms 2 + Type 2 number_of_atoms 1 + descriptors_per_atom 18 + total_descriptors 54 + DONE : INIT CHARGE Time : 1.57 (SEC) + + init_chg = atomic + DONE : INIT POTENTIAL Time : 4.4493 (SEC) + + + ------------------------------------------- + STEP OF MOLECULAR DYNAMICS : 0 + ------------------------------------------- + searching radius is (Bohr)) = 12.01 + searching radius unit is (Bohr)) = 1.88973 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 6 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 6 + pnum = 2 + prow = 0 + pcol = 2 + nRow_in_proc = 12 + nCol_in_proc = 6 + pnum = 3 + prow = 0 + pcol = 3 + nRow_in_proc = 12 + nCol_in_proc = 5 + pnum = 4 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 6 + pnum = 5 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 6 + pnum = 6 + prow = 1 + pcol = 2 + nRow_in_proc = 11 + nCol_in_proc = 6 + pnum = 7 + prow = 1 + pcol = 3 + nRow_in_proc = 11 + nCol_in_proc = 5 +receiver_size is 529 ; receiver_size of each process is: +72 72 72 60 66 66 66 55 +sender_size is 302 ; sender_size of each process is: +72 72 72 50 0 0 0 36 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 302 + sender_size = 302 + last sender_buffer = 0.000228498 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 4.1469e-05 + + Density error is 0.215551670516 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 302 + sender_size = 302 + last sender_buffer = 0.000434249282145 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000162124929476 + + Density error is 0.111411353552 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 302 + sender_size = 302 + last sender_buffer = 0.000443877018971 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000180194960199 + + Density error is 0.0707925955392 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 302 + sender_size = 302 + last sender_buffer = 0.00050099701803 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000240183215032 + + Density error is 0.0048756009633 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 302 + sender_size = 302 + last sender_buffer = 0.000478170151511 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000224066377643 + + Density error is 0.00166678072552 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 302 + sender_size = 302 + last sender_buffer = 0.000472736097633 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000220633672259 + + Density error is 0.000450591596517 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 302 + sender_size = 302 + last sender_buffer = 0.000473022689523 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000221212357895 + + Density error is 8.87538780553e-05 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 302 + sender_size = 302 + last sender_buffer = 0.000473012898172 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000221137913467 + + Density error is 2.71962286254e-05 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 302 + sender_size = 302 + last sender_buffer = 0.000472989998119 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000221121976389 + + Density error is 7.07506529074e-06 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 302 + sender_size = 302 + last sender_buffer = 0.000472998128219 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000221127907626 + + Density error is 5.3396753095e-07 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 302 + sender_size = 302 + last sender_buffer = 0.000472998596312 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000221128485462 + + Density error is 2.09429973819e-07 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 12-------------------------------- + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = 1 + number of non-zero elements in sender_buffer = 302 + sender_size = 302 + last sender_buffer = 0.000472998601303 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000221128462355 + + Density error is 2.7186595854e-08 + + charge density convergence is achieved + final etot is -464.873809909 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 +0.20367321 -0.47618848 -0.67319826 + H2 -0.49767955 +3.9389313 +4.6492087 + O1 +0.29400633 -3.4627428 -3.9760104 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +0.117881 +0.348548 +0.269731 + +0.348548 -1.559581 -1.949853 + +0.269731 -1.949853 -2.332930 + TOTAL-PRESSURE: -1.258210 KBAR + + + ------------------------------------------------------------------------------------------------ + Energy Potential Kinetic Temperature Pressure (KBAR) + -17.083696 -17.083791 +9.5004463e-05 +10 -1.2573695 + ------------------------------------------------------------------------------------------------ + +output Pressure for check! +Virtual Pressure is -1.2573695 Kbar +Virial Term is -1.2582099 Kbar +Kenetic Term is +0.00084041896 Kbar + + + ><><><><><><><><><><><><><><><><><><><><><>< + + MD STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + ++0.118671 +0.34830674 +0.27013745 ++0.34830674 -1.5588633 -1.9506966 ++0.27013745 -1.9506966 -2.3319162 + + + + ------------------------------------------- + STEP OF MOLECULAR DYNAMICS : 1 + ------------------------------------------- + NEW-OLD atomic charge density approx. for the potential ! + searching radius is (Bohr)) = +12.01 + searching radius unit is (Bohr)) = +1.88973 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +6 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +6 + pnum = +2 + prow = +0 + pcol = +2 + nRow_in_proc = +12 + nCol_in_proc = +6 + pnum = +3 + prow = +0 + pcol = +3 + nRow_in_proc = +12 + nCol_in_proc = +5 + pnum = +4 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +6 + pnum = +5 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +6 + pnum = +6 + prow = +1 + pcol = +2 + nRow_in_proc = +11 + nCol_in_proc = +6 + pnum = +7 + prow = +1 + pcol = +3 + nRow_in_proc = +11 + nCol_in_proc = +5 +receiver_size is +529 ; receiver_size of each process is: ++72 +72 +72 +60 +66 +66 +66 +55 +sender_size is +302 ; sender_size of each process is: ++72 +72 +72 +50 +0 +0 +0 +36 + + LCAO ALGORITHM --------------- ION=+2 ELEC=+1 -------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +302 + sender_size = +302 + last sender_buffer = +0.000505753 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000279413 + + Density error is +0.0119387896885 + + LCAO ALGORITHM --------------- ION=+2 ELEC=+2 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +302 + sender_size = +302 + last sender_buffer = +0.00049112904117 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.00025999978585 + + Density error is +0.00593599512564 + + LCAO ALGORITHM --------------- ION=+2 ELEC=+3 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +302 + sender_size = +302 + last sender_buffer = +0.000482669457098 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000250368527462 + + Density error is +0.00231707307531 + + LCAO ALGORITHM --------------- ION=+2 ELEC=+4 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +302 + sender_size = +302 + last sender_buffer = +0.000482133796456 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000249291012 + + Density error is +0.000644671621461 + + LCAO ALGORITHM --------------- ION=+2 ELEC=+5 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +302 + sender_size = +302 + last sender_buffer = +0.000483256470086 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000250628422739 + + Density error is +4.0788869485e-05 + + LCAO ALGORITHM --------------- ION=+2 ELEC=+6 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +302 + sender_size = +302 + last sender_buffer = +0.000483422790139 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000250737960387 + + Density error is +1.00285806757e-05 + + LCAO ALGORITHM --------------- ION=+2 ELEC=+7 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +302 + sender_size = +302 + last sender_buffer = +0.00048344369458 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000250754693923 + + Density error is +2.59393303922e-06 + + LCAO ALGORITHM --------------- ION=+2 ELEC=+8 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +302 + sender_size = +302 + last sender_buffer = +0.000483432646494 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000250748074125 + + Density error is +3.64271001892e-07 + + LCAO ALGORITHM --------------- ION=+2 ELEC=+9 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +302 + sender_size = +302 + last sender_buffer = +0.000483432996126 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000250748308342 + + Density error is +7.8274931146e-08 + + charge density convergence is achieved + final etot is -465.184893576 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 -0.2540227 -0.87770015 -0.74731415 + H2 -0.49786074 +3.8644669 +4.5705897 + O1 +0.75188344 -2.9867668 -3.8232755 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + -0.052862 +0.190314 +0.235641 + +0.190314 -1.590041 -1.856968 + +0.235641 -1.856968 -2.206370 + TOTAL-PRESSURE: -1.283091 KBAR + + + ------------------------------------------------------------------------------------------------ + Energy Potential Kinetic Temperature Pressure (KBAR) + -17.083917 -17.095223 +0.011305955 +1190.0447 -1.1830771 + ------------------------------------------------------------------------------------------------ + +output Pressure for check! +Virtual Pressure is -1.1830771 Kbar +Virial Term is -1.2830907 Kbar +Kenetic Term is +0.10001361 Kbar + + + ><><><><><><><><><><><><><><><><><><><><><>< + + MD STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + +-0.051983342 +0.17990822 +0.22451605 ++0.17990822 -1.4587099 -1.7104374 ++0.22451605 -1.7104374 -2.0385382 + + + + ------------------------------------------- + STEP OF MOLECULAR DYNAMICS : 2 + ------------------------------------------- + first order charge density extrapolation ! + searching radius is (Bohr)) = +12.01 + searching radius unit is (Bohr)) = +1.88973 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +6 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +6 + pnum = +2 + prow = +0 + pcol = +2 + nRow_in_proc = +12 + nCol_in_proc = +6 + pnum = +3 + prow = +0 + pcol = +3 + nRow_in_proc = +12 + nCol_in_proc = +5 + pnum = +4 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +6 + pnum = +5 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +6 + pnum = +6 + prow = +1 + pcol = +2 + nRow_in_proc = +11 + nCol_in_proc = +6 + pnum = +7 + prow = +1 + pcol = +3 + nRow_in_proc = +11 + nCol_in_proc = +5 +receiver_size is +529 ; receiver_size of each process is: ++72 +72 +72 +60 +66 +66 +66 +55 +sender_size is +302 ; sender_size of each process is: ++72 +72 +72 +50 +0 +0 +0 +36 + + LCAO ALGORITHM --------------- ION=+3 ELEC=+1 -------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +302 + sender_size = +302 + last sender_buffer = +0.000605504 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000428331 + + Density error is +0.0264280404041 + + LCAO ALGORITHM --------------- ION=+3 ELEC=+2 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +302 + sender_size = +302 + last sender_buffer = +0.000564200356588 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000386179820864 + + Density error is +0.0112903143226 + + LCAO ALGORITHM --------------- ION=+3 ELEC=+3 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +302 + sender_size = +302 + last sender_buffer = +0.00054518650655 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000368371742992 + + Density error is +0.00572100397965 + + LCAO ALGORITHM --------------- ION=+3 ELEC=+4 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +302 + sender_size = +302 + last sender_buffer = +0.000535430638756 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000359464908473 + + Density error is +0.0011982806926 + + LCAO ALGORITHM --------------- ION=+3 ELEC=+5 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +302 + sender_size = +302 + last sender_buffer = +0.000539055758382 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.00036324276321 + + Density error is +0.000108809257976 + + LCAO ALGORITHM --------------- ION=+3 ELEC=+6 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +302 + sender_size = +302 + last sender_buffer = +0.000539655650044 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.0003636908142 + + Density error is +2.01104536126e-05 + + LCAO ALGORITHM --------------- ION=+3 ELEC=+7 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +302 + sender_size = +302 + last sender_buffer = +0.000539610200082 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000363652481867 + + Density error is +4.46891487978e-06 + + LCAO ALGORITHM --------------- ION=+3 ELEC=+8 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +302 + sender_size = +302 + last sender_buffer = +0.00053959680912 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000363646195708 + + Density error is +1.03700398996e-06 + + LCAO ALGORITHM --------------- ION=+3 ELEC=+9 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +302 + sender_size = +302 + last sender_buffer = +0.000539596399287 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000363646064609 + + Density error is +8.52814656042e-08 + + charge density convergence is achieved + final etot is -465.974078493 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 -1.0452301 -1.628147 -0.95897066 + H2 -0.2074209 +2.9339429 +3.3400107 + O1 +1.252651 -1.3057959 -2.38104 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + -0.316211 -0.207284 +0.007046 + -0.207284 -1.346616 -1.287258 + +0.007046 -1.287258 -1.415184 + TOTAL-PRESSURE: -1.026004 KBAR + + + ------------------------------------------------------------------------------------------------ + Energy Potential Kinetic Temperature Pressure (KBAR) + -17.086316 -17.124225 +0.03790986 +3990.3241 -0.69064928 + ------------------------------------------------------------------------------------------------ + +output Pressure for check! +Virtual Pressure is -0.69064928 Kbar +Virial Term is -1.0260037 Kbar +Kenetic Term is +0.3353544 Kbar + + + ><><><><><><><><><><><><><><><><><><><><><>< + + MD STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + +-0.30607852 -0.2568077 -0.057965757 +-0.2568077 -0.92465385 -0.80152656 +-0.057965757 -0.80152656 -0.84121548 + + + + ------------------------------------------- + STEP OF MOLECULAR DYNAMICS : 3 + ------------------------------------------- + second order charge density extrapolation ! + searching radius is (Bohr)) = +12.01 + searching radius unit is (Bohr)) = +1.88973 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +6 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +6 + pnum = +2 + prow = +0 + pcol = +2 + nRow_in_proc = +12 + nCol_in_proc = +6 + pnum = +3 + prow = +0 + pcol = +3 + nRow_in_proc = +12 + nCol_in_proc = +5 + pnum = +4 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +6 + pnum = +5 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +6 + pnum = +6 + prow = +1 + pcol = +2 + nRow_in_proc = +11 + nCol_in_proc = +6 + pnum = +7 + prow = +1 + pcol = +3 + nRow_in_proc = +11 + nCol_in_proc = +5 +receiver_size is +529 ; receiver_size of each process is: ++72 +72 +72 +60 +66 +66 +66 +55 +sender_size is +324 ; sender_size of each process is: ++72 +72 +72 +72 +0 +0 +0 +36 + + LCAO ALGORITHM --------------- ION=+4 ELEC=+1 -------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +324 + sender_size = +324 + last sender_buffer = +0.000805509 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000647211 + + Density error is +0.0268936798505 + + LCAO ALGORITHM --------------- ION=+4 ELEC=+2 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +324 + sender_size = +324 + last sender_buffer = +0.000745427319782 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000589622773262 + + Density error is +0.0136307609483 + + LCAO ALGORITHM --------------- ION=+4 ELEC=+3 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +324 + sender_size = +324 + last sender_buffer = +0.000711418332619 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000553545423722 + + Density error is +0.00487998530233 + + LCAO ALGORITHM --------------- ION=+4 ELEC=+4 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +324 + sender_size = +324 + last sender_buffer = +0.00070554408152 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000546492143376 + + Density error is +0.000964784901582 + + LCAO ALGORITHM --------------- ION=+4 ELEC=+5 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +324 + sender_size = +324 + last sender_buffer = +0.000712253899577 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000552552990494 + + Density error is +0.000155879556688 + + LCAO ALGORITHM --------------- ION=+4 ELEC=+6 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +324 + sender_size = +324 + last sender_buffer = +0.000712471717247 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000552790642192 + + Density error is +2.20695710766e-05 + + LCAO ALGORITHM --------------- ION=+4 ELEC=+7 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +324 + sender_size = +324 + last sender_buffer = +0.000712368178388 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000552714230809 + + Density error is +3.82343324272e-06 + + LCAO ALGORITHM --------------- ION=+4 ELEC=+8 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +324 + sender_size = +324 + last sender_buffer = +0.000712366222427 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000552713477928 + + Density error is +1.07624072353e-06 + + LCAO ALGORITHM --------------- ION=+4 ELEC=+9 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +324 + sender_size = +324 + last sender_buffer = +0.000712369505027 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000552716587844 + + Density error is +1.087613316e-07 + + LCAO ALGORITHM --------------- ION=+4 ELEC=+10 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +324 + sender_size = +324 + last sender_buffer = +0.000712369632019 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000552716644997 + + Density error is +1.48948776073e-08 + + charge density convergence is achieved + final etot is -465.982928363 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 -1.5197172 -2.1348782 -1.1731997 + H2 +2.109118 -3.3948768 -5.28258 + O1 -0.58940077 +5.5297551 +6.4557797 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + -0.260135 -0.993003 -0.895526 + -0.993003 +0.262836 +1.051311 + -0.895526 +1.051311 +1.805220 + TOTAL-PRESSURE: +0.602641 KBAR + + + ------------------------------------------------------------------------------------------------ + Energy Potential Kinetic Temperature Pressure (KBAR) + -17.094185 -17.124551 +0.030365843 +3196.2544 +0.87125983 + ------------------------------------------------------------------------------------------------ + +output Pressure for check! +Virtual Pressure is +0.87125983 Kbar +Virial Term is +0.60264056 Kbar +Kenetic Term is +0.26861928 Kbar + + + ><><><><><><><><><><><><><><><><><><><><><>< + + MD STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + +-0.23421411 -0.97307726 -0.90488506 +-0.97307726 +0.64080615 +1.4243129 +-0.90488506 +1.4243129 +2.2071875 + + + + ------------------------------------------- + STEP OF MOLECULAR DYNAMICS : 4 + ------------------------------------------- + second order charge density extrapolation ! + searching radius is (Bohr)) = +12.01 + searching radius unit is (Bohr)) = +1.88973 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +6 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +6 + pnum = +2 + prow = +0 + pcol = +2 + nRow_in_proc = +12 + nCol_in_proc = +6 + pnum = +3 + prow = +0 + pcol = +3 + nRow_in_proc = +12 + nCol_in_proc = +5 + pnum = +4 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +6 + pnum = +5 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +6 + pnum = +6 + prow = +1 + pcol = +2 + nRow_in_proc = +11 + nCol_in_proc = +6 + pnum = +7 + prow = +1 + pcol = +3 + nRow_in_proc = +11 + nCol_in_proc = +5 +receiver_size is +529 ; receiver_size of each process is: ++72 +72 +72 +60 +66 +66 +66 +55 +sender_size is +360 ; sender_size of each process is: ++72 +72 +72 +72 +0 +0 +0 +72 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+1 -------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000678145 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000442502 + + Density error is +0.0728096018177 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+2 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000825971809597 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000585723319359 + + Density error is +0.0370134870519 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+3 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000915743853815 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000666595458794 + + Density error is +0.0113995201516 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+4 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000927002552412 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000679400961367 + + Density error is +0.00282752483127 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+5 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000917299148986 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000668656978578 + + Density error is +0.000624062957236 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+6 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000909844350146 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000665132681277 + + Density error is +0.000473288737237 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+7 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000920467780603 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000670282842984 + + Density error is +0.000600190844031 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+8 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000907099514072 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000664228826384 + + Density error is +0.000522796524407 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+9 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000922735558323 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000671672286646 + + Density error is +0.000852633138118 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+10 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000905923424592 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000663632992426 + + Density error is +0.00060843472121 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+11 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000923057668209 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000671743587963 + + Density error is +0.000781547786551 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+12 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000905805853858 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000663580375967 + + Density error is +0.000646494574386 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+13 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000923167123868 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000671800772781 + + Density error is +0.000704648716578 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+14 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.0009058595168 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000663645489892 + + Density error is +0.000631632880864 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+15 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000923134442993 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000671791964153 + + Density error is +0.000747852608571 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+16 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.00090582450452 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000663644042862 + + Density error is +0.000568973871703 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+17 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.00092310893318 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000671778619115 + + Density error is +0.000767527779634 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+18 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000905823094416 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000663645240844 + + Density error is +0.000568058396381 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+19 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000923113602368 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000671780974809 + + Density error is +0.000761902340355 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+20 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000905823877939 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000663645975082 + + Density error is +0.00056585985186 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+21 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000923113128966 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000671780273254 + + Density error is +0.000760403814282 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+22 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000905824491761 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000663646368775 + + Density error is +0.000565406686686 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+23 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000923113035985 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000671780150593 + + Density error is +0.00075999736254 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+24 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000905824734689 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000663646580373 + + Density error is +0.000565182355146 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+25 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000923112902761 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000671780114428 + + Density error is +0.000760085762765 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+26 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000905824708574 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000663646619722 + + Density error is +0.000565016542583 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+27 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000923112850175 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000671779830322 + + Density error is +0.000759582363974 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+28 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000905824849836 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000663646740645 + + Density error is +0.000564864100773 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+29 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000923112626404 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000671781792369 + + Density error is +0.000764055484302 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+30 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000905824045516 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000663644299845 + + Density error is +0.000569916864485 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+31 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000923114594272 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000671780264747 + + Density error is +0.00075804882341 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+32 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000905825650152 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000663634581979 + + Density error is +0.000592652178537 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+33 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000923120286234 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000671786091403 + + Density error is +0.000762590998502 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+34 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000905822303007 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000663648331953 + + Density error is +0.000559920580508 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+35 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000923112325781 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000671780119811 + + Density error is +0.000760918191063 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+36 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000905824681373 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000663646698804 + + Density error is +0.000564880173734 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+37 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000923112834477 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000671780272954 + + Density error is +0.000760505927869 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+38 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000905824656381 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000663646858604 + + Density error is +0.000564522148832 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+39 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000923112813096 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000671779475644 + + Density error is +0.000758823793303 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+40 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000905825194463 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000663644689725 + + Density error is +0.000569676608409 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+41 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000923114067421 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000671780375204 + + Density error is +0.00075899935577 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+42 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000905824772899 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000663645935139 + + Density error is +0.000566651746197 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+43 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000923113259622 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000671781221392 + + Density error is +0.0007619419722 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+44 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000905824598303 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000663641415931 + + Density error is +0.000576724443546 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+45 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.00092311627457 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.00067178210529 + + Density error is +0.000759637865256 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+46 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000905824051273 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000663646653409 + + Density error is +0.000564643181424 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+47 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000923112697148 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.0006717841833 + + Density error is +0.000769080985899 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+48 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000905822985592 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000663642972578 + + Density error is +0.000572379217844 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+49 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000923116024415 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000671777318848 + + Density error is +0.000749740909271 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+50 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000905826299565 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000663647889474 + + Density error is +0.000563051905881 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+51 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000923111718799 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000671779541842 + + Density error is +0.00076047217368 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+52 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000905824934431 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000663646874658 + + Density error is +0.000564646709987 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+53 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000923112708211 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000671779839775 + + Density error is +0.000759743913766 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+54 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000905824130081 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000663657668468 + + Density error is +0.000539960451953 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+55 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000923106508091 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000671769689434 + + Density error is +0.000746612085564 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+56 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000905829335635 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000663647216928 + + Density error is +0.000566212892759 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+57 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.0009231115236 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000671778439913 + + Density error is +0.000758346445745 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+58 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000905825486495 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000663646649111 + + Density error is +0.000565444782869 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+59 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000923102309645 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000671891475571 + + Density error is +0.00101419637878 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+60 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000905774014826 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.00066357649346 + + Density error is +0.000696367789454 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+61 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000923168650031 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000671818002807 + + Density error is +0.000763966475928 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+62 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000905810948342 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000663642621612 + + Density error is +0.000566497045906 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+63 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000923118651609 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000671783889219 + + Density error is +0.000760303226198 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+64 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000905823357328 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000663646205357 + + Density error is +0.000565273367331 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+65 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.00092311298795 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.00067178296518 + + Density error is +0.000766349192426 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+66 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.00090582326747 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000663637979471 + + Density error is +0.000582716627915 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+67 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000923118298204 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.00067178375658 + + Density error is +0.000760327221082 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+68 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000905823447548 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000663646226668 + + Density error is +0.000565287358468 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+69 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000923113441206 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000671780756473 + + Density error is +0.000760697529685 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+70 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.00090582456176 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000663645445355 + + Density error is +0.000567638520726 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+71 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000923113709035 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000671780463864 + + Density error is +0.000759686926575 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+72 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.00090582461619 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000663647489421 + + Density error is +0.000563115618899 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+73 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000923112394445 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000671779842522 + + Density error is +0.000760182747946 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+74 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000905824846834 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000663646852697 + + Density error is +0.000564654759355 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+75 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000923112635224 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000671781179413 + + Density error is +0.000762716020549 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+76 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000905823991806 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000663650043336 + + Density error is +0.000557037099308 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+77 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000923110880449 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000671779028281 + + Density error is +0.000760553933799 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+78 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.00090582528852 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000663644366172 + + Density error is +0.000570480620137 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+79 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000923114021877 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000671783330663 + + Density error is +0.000765387513959 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+80 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000905822922883 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000663652480207 + + Density error is +0.000551058911644 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+81 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000923109537471 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000671779088017 + + Density error is +0.000762551450408 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+82 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000905824993698 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.00066364704386 + + Density error is +0.000564358226268 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+83 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000923112814601 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.00067177761202 + + Density error is +0.000754799597738 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+84 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000905825967032 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000663646986728 + + Density error is +0.000564923272435 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+85 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000923112341169 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000671780384208 + + Density error is +0.000761404582036 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+86 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.0009058246236 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000663646288229 + + Density error is +0.000565815367678 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+87 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000923113176798 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000671780078756 + + Density error is +0.000759598320003 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+88 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000905824803471 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000663646732949 + + Density error is +0.000564896830715 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+89 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000923112809908 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000671780273458 + + Density error is +0.000760527967646 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+90 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000905824850838 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000663644177761 + + Density error is +0.000570665366993 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+91 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000923114733402 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000671777622126 + + Density error is +0.000752175909918 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+92 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000905826168702 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000663646166779 + + Density error is +0.000566869098307 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+93 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000923112874108 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000671780039491 + + Density error is +0.00075992800304 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+94 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000905825350385 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000663638493107 + + Density error is +0.000583687840219 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+95 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000923117600939 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000671786973821 + + Density error is +0.000768246832634 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+96 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000905822351594 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000663637669464 + + Density error is +0.000583910497859 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+97 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000923119173017 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000671784061171 + + Density error is +0.000759805838542 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+98 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000905823378686 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000663646104034 + + Density error is +0.000565535859993 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+99 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000923113638079 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000671779936141 + + Density error is +0.000758653234213 + + LCAO ALGORITHM --------------- ION=+5 ELEC=+100-------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.000905824915099 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000663646701694 + Energy (eV) & Occupations for spin=+1 K-point=+1 + +1 -25.3540 +2.00000 + +2 -13.6865 +2.00000 + +3 -8.56790 +2.00000 + +4 -6.72908 +2.00000 + +5 +1.14422 +0.00000 + +6 +4.87471 +0.00000 + +7 +11.0323 +0.00000 + +8 +11.1825 +0.00000 + + Density error is +0.000565023987483 + !! convergence has not been achieved @_@ + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 -0.065851644 -0.47382812 -0.44266566 + H2 +4.4826781 -9.3903234 -13.734304 + O1 -4.4168265 +9.8641515 +14.176970 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +0.504846 -0.963923 -1.396739 + -0.963923 +2.096159 +2.997442 + -1.396739 +2.997442 +4.270661 + TOTAL-PRESSURE: +2.290556 KBAR + + + ------------------------------------------------------------------------------------------------ + Energy Potential Kinetic Temperature Pressure (KBAR) + -17.074088 -17.093903 +0.019814497 +2085.6385 +2.4658367 + ------------------------------------------------------------------------------------------------ + +output Pressure for check! +Virtual Pressure is +2.4658367 Kbar +Virial Term is +2.2905557 Kbar +Kenetic Term is +0.17528102 Kbar + + + ><><><><><><><><><><><><><><><><><><><><><>< + + MD STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + ++0.59925171 -0.90430350 -1.4195661 +-0.90430350 +2.3343859 +3.1770528 +-1.4195661 +3.1770528 +4.4638724 + + + + ------------------------------------------- + STEP OF MOLECULAR DYNAMICS : 5 + ------------------------------------------- + second order charge density extrapolation ! + searching radius is (Bohr)) = +12.0100 + searching radius unit is (Bohr)) = +1.88973 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +6 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +6 + pnum = +2 + prow = +0 + pcol = +2 + nRow_in_proc = +12 + nCol_in_proc = +6 + pnum = +3 + prow = +0 + pcol = +3 + nRow_in_proc = +12 + nCol_in_proc = +5 + pnum = +4 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +6 + pnum = +5 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +6 + pnum = +6 + prow = +1 + pcol = +2 + nRow_in_proc = +11 + nCol_in_proc = +6 + pnum = +7 + prow = +1 + pcol = +3 + nRow_in_proc = +11 + nCol_in_proc = +5 +receiver_size is +529 ; receiver_size of each process is: ++72 +72 +72 +60 +66 +66 +66 +55 +sender_size is +338 ; sender_size of each process is: ++72 +72 +72 +50 +0 +0 +0 +72 + + LCAO ALGORITHM --------------- ION=+6 ELEC=+1 -------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000620425 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000301961 + + Density error is +0.0356036295465 + + LCAO ALGORITHM --------------- ION=+6 ELEC=+2 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000780045691608 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000435774540681 + + Density error is +0.0167683737225 + + LCAO ALGORITHM --------------- ION=+6 ELEC=+3 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000879931570098 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000520469784956 + + Density error is +0.00620028368997 + + LCAO ALGORITHM --------------- ION=+6 ELEC=+4 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000897661418270 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000534272295970 + + Density error is +0.00203341559831 + + LCAO ALGORITHM --------------- ION=+6 ELEC=+5 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000885354800300 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000523073989958 + + Density error is +0.000330198347912 + + LCAO ALGORITHM --------------- ION=+6 ELEC=+6 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000884979667854 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000522961027865 + + Density error is +6.11911457998e-05 + + LCAO ALGORITHM --------------- ION=+6 ELEC=+7 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000885119572453 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000523075885965 + + Density error is +1.43218260364e-05 + + LCAO ALGORITHM --------------- ION=+6 ELEC=+8 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000885150718448 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000523088722808 + + Density error is +2.18837817985e-06 + + LCAO ALGORITHM --------------- ION=+6 ELEC=+9 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000885140890232 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000523084100528 + + Density error is +2.41866010429e-07 + + LCAO ALGORITHM --------------- ION=+6 ELEC=+10 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000885140787820 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000523083916240 + + Density error is +1.22252587408e-07 + + LCAO ALGORITHM --------------- ION=+6 ELEC=+11 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000885140958785 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000523084004011 + + Density error is +5.00097552603e-09 + + charge density convergence is achieved + final etot is -465.855289261 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 +6.8550588 +5.4545413 +1.0167584 + H2 -0.96080994 +1.4868428 +2.3334545 + O1 -5.8942489 -6.9413841 -3.3502129 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +2.301989 +2.106077 +0.632201 + +2.106077 +1.094305 -0.313178 + +0.632201 -0.313178 -0.819242 + TOTAL-PRESSURE: +0.859017 KBAR + + + ------------------------------------------------------------------------------------------------ + Energy Potential Kinetic Temperature Pressure (KBAR) + -17.066307 -17.119860 +0.053553429 +5636.9382 +1.3327562 + ------------------------------------------------------------------------------------------------ + +output Pressure for check! +Virtual Pressure is +1.3327562 Kbar +Virial Term is +0.85901720 Kbar +Kenetic Term is +0.47373898 Kbar + + + ><><><><><><><><><><><><><><><><><><><><><>< + + MD STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + ++2.6146541 +1.8460009 +0.11909211 ++1.8460009 +1.3466002 +0.13622826 ++0.11909211 +0.13622826 +0.037014228 + + + + ------------------------------------------- + STEP OF MOLECULAR DYNAMICS : 6 + ------------------------------------------- + second order charge density extrapolation ! + searching radius is (Bohr)) = +12.0100 + searching radius unit is (Bohr)) = +1.88973 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +6 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +6 + pnum = +2 + prow = +0 + pcol = +2 + nRow_in_proc = +12 + nCol_in_proc = +6 + pnum = +3 + prow = +0 + pcol = +3 + nRow_in_proc = +12 + nCol_in_proc = +5 + pnum = +4 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +6 + pnum = +5 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +6 + pnum = +6 + prow = +1 + pcol = +2 + nRow_in_proc = +11 + nCol_in_proc = +6 + pnum = +7 + prow = +1 + pcol = +3 + nRow_in_proc = +11 + nCol_in_proc = +5 +receiver_size is +529 ; receiver_size of each process is: ++72 +72 +72 +60 +66 +66 +66 +55 +sender_size is +338 ; sender_size of each process is: ++72 +72 +72 +50 +0 +0 +0 +72 + + LCAO ALGORITHM --------------- ION=+7 ELEC=+1 -------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000803103 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000485518 + + Density error is +0.0572706716985 + + LCAO ALGORITHM --------------- ION=+7 ELEC=+2 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000770526780518 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000426616208879 + + Density error is +0.0296614013311 + + LCAO ALGORITHM --------------- ION=+7 ELEC=+3 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000790457841262 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000420661209701 + + Density error is +0.0145777130770 + + LCAO ALGORITHM --------------- ION=+7 ELEC=+4 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000791878051979 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000406055112289 + + Density error is +0.00286072890903 + + LCAO ALGORITHM --------------- ION=+7 ELEC=+5 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000789792237404 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000408718294265 + + Density error is +0.000606473517885 + + LCAO ALGORITHM --------------- ION=+7 ELEC=+6 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000789048367666 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000408350064909 + + Density error is +0.000133171484719 + + LCAO ALGORITHM --------------- ION=+7 ELEC=+7 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000789152076368 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000408338441528 + + Density error is +3.17318581541e-05 + + LCAO ALGORITHM --------------- ION=+7 ELEC=+8 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000789304045455 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000408446649269 + + Density error is +4.91246351719e-06 + + LCAO ALGORITHM --------------- ION=+7 ELEC=+9 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000789284701258 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000408432050517 + + Density error is +9.56798088488e-07 + + LCAO ALGORITHM --------------- ION=+7 ELEC=+10 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000789282094508 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000408430214471 + + Density error is +2.28168578197e-07 + + LCAO ALGORITHM --------------- ION=+7 ELEC=+11 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000789281963989 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000408430202407 + + Density error is +3.83614454547e-08 + + charge density convergence is achieved + final etot is -465.339575011 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 +1.3631292 +1.5013617 +0.69221926 + H2 -2.3706395 +2.2950607 +4.2474207 + O1 +1.0075103 -3.7964224 -4.9396399 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +0.224387 +1.128837 +1.081863 + +1.128837 -0.268818 -1.093794 + +1.081863 -1.093794 -2.004917 + TOTAL-PRESSURE: -0.683116 KBAR + + + ------------------------------------------------------------------------------------------------ + Energy Potential Kinetic Temperature Pressure (KBAR) + -17.069069 -17.100908 +0.031838673 +3351.2818 -0.40146815 + ------------------------------------------------------------------------------------------------ + +output Pressure for check! +Virtual Pressure is -0.40146815 Kbar +Virial Term is -0.68311623 Kbar +Kenetic Term is +0.28164808 Kbar + + + ><><><><><><><><><><><><><><><><><><><><><>< + + MD STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + ++0.74779690 +1.0971397 +0.69799315 ++1.0971397 -0.25938991 -1.0553947 ++0.69799315 -1.0553947 -1.6928115 + + + + ------------------------------------------- + STEP OF MOLECULAR DYNAMICS : 7 + ------------------------------------------- + second order charge density extrapolation ! + searching radius is (Bohr)) = +12.0100 + searching radius unit is (Bohr)) = +1.88973 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +6 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +6 + pnum = +2 + prow = +0 + pcol = +2 + nRow_in_proc = +12 + nCol_in_proc = +6 + pnum = +3 + prow = +0 + pcol = +3 + nRow_in_proc = +12 + nCol_in_proc = +5 + pnum = +4 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +6 + pnum = +5 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +6 + pnum = +6 + prow = +1 + pcol = +2 + nRow_in_proc = +11 + nCol_in_proc = +6 + pnum = +7 + prow = +1 + pcol = +3 + nRow_in_proc = +11 + nCol_in_proc = +5 +receiver_size is +529 ; receiver_size of each process is: ++72 +72 +72 +60 +66 +66 +66 +55 +sender_size is +338 ; sender_size of each process is: ++72 +72 +72 +50 +0 +0 +0 +72 + + LCAO ALGORITHM --------------- ION=+8 ELEC=+1 -------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000637114 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000347917 + + Density error is +0.0279868988565 + + LCAO ALGORITHM --------------- ION=+8 ELEC=+2 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000632619053268 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000353491250752 + + Density error is +0.0160497364349 + + LCAO ALGORITHM --------------- ION=+8 ELEC=+3 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000616617120484 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000347814270298 + + Density error is +0.00643948669625 + + LCAO ALGORITHM --------------- ION=+8 ELEC=+4 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000620608428406 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000346598827235 + + Density error is +0.00153379636683 + + LCAO ALGORITHM --------------- ION=+8 ELEC=+5 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000622933238137 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000345719520843 + + Density error is +0.000197008177640 + + LCAO ALGORITHM --------------- ION=+8 ELEC=+6 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000623617837761 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000346129323150 + + Density error is +4.39569848333e-05 + + LCAO ALGORITHM --------------- ION=+8 ELEC=+7 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000623541487986 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000346093745279 + + Density error is +1.00725568377e-05 + + LCAO ALGORITHM --------------- ION=+8 ELEC=+8 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000623494510056 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000346071048892 + + Density error is +1.68707594038e-06 + + LCAO ALGORITHM --------------- ION=+8 ELEC=+9 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000623498055090 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000346074877305 + + Density error is +2.52097872641e-07 + + LCAO ALGORITHM --------------- ION=+8 ELEC=+10 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000623497819078 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000346074780129 + + Density error is +6.91527960985e-08 + + charge density convergence is achieved + final etot is -464.648866818 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 -2.8962921 -0.84928988 +1.0950576 + H2 -2.8322207 +2.0199391 +4.2706853 + O1 +5.7285128 -1.1706492 -5.3657430 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + -1.914535 +0.160754 +1.525216 + +0.160754 -0.780432 -0.977244 + +1.525216 -0.977244 -2.191358 + TOTAL-PRESSURE: -1.628775 KBAR + + + ------------------------------------------------------------------------------------------------ + Energy Potential Kinetic Temperature Pressure (KBAR) + -17.065983 -17.075525 +0.0095416995 +1004.3422 -1.5443680 + ------------------------------------------------------------------------------------------------ + +output Pressure for check! +Virtual Pressure is -1.5443680 Kbar +Virial Term is -1.6287748 Kbar +Kenetic Term is +0.084406826 Kbar + + + ><><><><><><><><><><><><><><><><><><><><><>< + + MD STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + +-1.6997100 +0.22869475 +1.4712268 ++0.22869475 -0.75561377 -0.99449025 ++1.4712268 -0.99449025 -2.1777802 + + + + ------------------------------------------- + STEP OF MOLECULAR DYNAMICS : 8 + ------------------------------------------- + second order charge density extrapolation ! + searching radius is (Bohr)) = +12.0100 + searching radius unit is (Bohr)) = +1.88973 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +6 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +6 + pnum = +2 + prow = +0 + pcol = +2 + nRow_in_proc = +12 + nCol_in_proc = +6 + pnum = +3 + prow = +0 + pcol = +3 + nRow_in_proc = +12 + nCol_in_proc = +5 + pnum = +4 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +6 + pnum = +5 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +6 + pnum = +6 + prow = +1 + pcol = +2 + nRow_in_proc = +11 + nCol_in_proc = +6 + pnum = +7 + prow = +1 + pcol = +3 + nRow_in_proc = +11 + nCol_in_proc = +5 +receiver_size is +529 ; receiver_size of each process is: ++72 +72 +72 +60 +66 +66 +66 +55 +sender_size is +338 ; sender_size of each process is: ++72 +72 +72 +50 +0 +0 +0 +72 + + LCAO ALGORITHM --------------- ION=+9 ELEC=+1 -------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000556257 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000317525 + + Density error is +0.0168524255226 + + LCAO ALGORITHM --------------- ION=+9 ELEC=+2 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000591514916539 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000343152939293 + + Density error is +0.0101805709619 + + LCAO ALGORITHM --------------- ION=+9 ELEC=+3 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000605446557290 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000359571014259 + + Density error is +0.00384041566758 + + LCAO ALGORITHM --------------- ION=+9 ELEC=+4 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000608188590494 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000360979029745 + + Density error is +0.000706335200133 + + LCAO ALGORITHM --------------- ION=+9 ELEC=+5 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000603412013659 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000357844389110 + + Density error is +0.000108238367182 + + LCAO ALGORITHM --------------- ION=+9 ELEC=+6 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000603286658750 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000357803016371 + + Density error is +1.77732403071e-05 + + LCAO ALGORITHM --------------- ION=+9 ELEC=+7 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000603286158654 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000357787622278 + + Density error is +7.03484941842e-06 + + LCAO ALGORITHM --------------- ION=+9 ELEC=+8 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000603303104095 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000357789495275 + + Density error is +1.15683469036e-06 + + LCAO ALGORITHM --------------- ION=+9 ELEC=+9 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000603302334481 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000357788959158 + + Density error is +1.65276731036e-07 + + LCAO ALGORITHM --------------- ION=+9 ELEC=+10 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000603302463775 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000357788821951 + + Density error is +4.70942791828e-08 + + charge density convergence is achieved + final etot is -464.618020324 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 -3.8226842 -1.3526248 +1.1511761 + H2 -2.9840537 +1.7883652 +4.1250012 + O1 +6.8067378 -0.43574039 -5.2761774 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + -2.513126 -0.154419 +1.580371 + -0.154419 -0.825336 -0.815094 + +1.580371 -0.815094 -2.050107 + TOTAL-PRESSURE: -1.796189 KBAR + + + ------------------------------------------------------------------------------------------------ + Energy Potential Kinetic Temperature Pressure (KBAR) + -17.065137 -17.074391 +0.0092537393 +974.03207 -1.7143299 + ------------------------------------------------------------------------------------------------ + +output Pressure for check! +Virtual Pressure is -1.7143299 Kbar +Virial Term is -1.7961894 Kbar +Kenetic Term is +0.081859502 Kbar + + + ><><><><><><><><><><><><><><><><><><><><><>< + + MD STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + +-2.4882375 -0.19421902 +1.5264664 +-0.19421902 -0.75162905 -0.71145239 ++1.5264664 -0.71145239 -1.9031232 + + + + ------------------------------------------- + STEP OF MOLECULAR DYNAMICS : 9 + ------------------------------------------- + second order charge density extrapolation ! + searching radius is (Bohr)) = +12.0100 + searching radius unit is (Bohr)) = +1.88973 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +6 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +6 + pnum = +2 + prow = +0 + pcol = +2 + nRow_in_proc = +12 + nCol_in_proc = +6 + pnum = +3 + prow = +0 + pcol = +3 + nRow_in_proc = +12 + nCol_in_proc = +5 + pnum = +4 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +6 + pnum = +5 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +6 + pnum = +6 + prow = +1 + pcol = +2 + nRow_in_proc = +11 + nCol_in_proc = +6 + pnum = +7 + prow = +1 + pcol = +3 + nRow_in_proc = +11 + nCol_in_proc = +5 +receiver_size is +529 ; receiver_size of each process is: ++72 +72 +72 +60 +66 +66 +66 +55 +sender_size is +338 ; sender_size of each process is: ++72 +72 +72 +50 +0 +0 +0 +72 + + LCAO ALGORITHM --------------- ION=+10 ELEC=+1 -------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000767263 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000451427 + + Density error is +0.0146803417183 + + LCAO ALGORITHM --------------- ION=+10 ELEC=+2 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000764558418246 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000444812764521 + + Density error is +0.00862457369173 + + LCAO ALGORITHM --------------- ION=+10 ELEC=+3 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000762822989068 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000443268341033 + + Density error is +0.00155180165476 + + LCAO ALGORITHM --------------- ION=+10 ELEC=+4 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000762632500432 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000445302545447 + + Density error is +0.000251939591893 + + LCAO ALGORITHM --------------- ION=+10 ELEC=+5 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000762697331546 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000445433594061 + + Density error is +0.000100167592792 + + LCAO ALGORITHM --------------- ION=+10 ELEC=+6 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000762552750740 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000445326149352 + + Density error is +2.81604332644e-05 + + LCAO ALGORITHM --------------- ION=+10 ELEC=+7 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000762550271473 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000445317712265 + + Density error is +4.93152540068e-06 + + LCAO ALGORITHM --------------- ION=+10 ELEC=+8 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000762579353900 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000445332958332 + + Density error is +8.06533514515e-07 + + LCAO ALGORITHM --------------- ION=+10 ELEC=+9 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000762575553491 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000445329383593 + + Density error is +2.19885785751e-07 + + LCAO ALGORITHM --------------- ION=+10 ELEC=+10 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +338 + sender_size = +338 + last sender_buffer = +0.000762575680583 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000445329566572 + + Density error is +4.45979807950e-08 + + charge density convergence is achieved + final etot is -465.618546559 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 -3.2631797 -1.1783270 +0.93284405 + H2 -2.4852957 +1.1192417 +3.0256858 + O1 +5.7484754 +0.059085328 -3.9585299 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + -1.921731 -0.250129 +1.045306 + -0.250129 -0.550642 -0.443386 + +1.045306 -0.443386 -1.253788 + TOTAL-PRESSURE: -1.242054 KBAR + + + ------------------------------------------------------------------------------------------------ + Energy Potential Kinetic Temperature Pressure (KBAR) + -17.068010 -17.111160 +0.043150202 +4541.9132 -0.86034276 + ------------------------------------------------------------------------------------------------ + +output Pressure for check! +Virtual Pressure is -0.86034276 Kbar +Virial Term is -1.2420538 Kbar +Kenetic Term is +0.38171100 Kbar + + + ><><><><><><><><><><><><><><><><><><><><><>< + + MD STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + +-1.5337721 -0.42434142 +0.57122526 +-0.42434142 -0.41205425 -0.18181703 ++0.57122526 -0.18181703 -0.63520190 + + + + ------------------------------------------- + STEP OF MOLECULAR DYNAMICS : 10 + ------------------------------------------- + second order charge density extrapolation ! + searching radius is (Bohr)) = +12.0100 + searching radius unit is (Bohr)) = +1.88973 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +6 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +6 + pnum = +2 + prow = +0 + pcol = +2 + nRow_in_proc = +12 + nCol_in_proc = +6 + pnum = +3 + prow = +0 + pcol = +3 + nRow_in_proc = +12 + nCol_in_proc = +5 + pnum = +4 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +6 + pnum = +5 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +6 + pnum = +6 + prow = +1 + pcol = +2 + nRow_in_proc = +11 + nCol_in_proc = +6 + pnum = +7 + prow = +1 + pcol = +3 + nRow_in_proc = +11 + nCol_in_proc = +5 +receiver_size is +529 ; receiver_size of each process is: ++72 +72 +72 +60 +66 +66 +66 +55 +sender_size is +360 ; sender_size of each process is: ++72 +72 +72 +72 +0 +0 +0 +72 + + LCAO ALGORITHM --------------- ION=+11 ELEC=+1 -------------------------------- + +vlocal exchange index is built + buffer size(M): = 0 + buffer index size(M): = 0 + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.00129140 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000886049 + + Density error is +0.0423046345400 + + LCAO ALGORITHM --------------- ION=+11 ELEC=+2 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.00115332140046 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000762914006838 + + Density error is +0.0213523832394 + + LCAO ALGORITHM --------------- ION=+11 ELEC=+3 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.00106131173965 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000684736689882 + + Density error is +0.00671608506186 + + LCAO ALGORITHM --------------- ION=+11 ELEC=+4 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.00105199807923 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000676544008578 + + Density error is +0.00148517209710 + + LCAO ALGORITHM --------------- ION=+11 ELEC=+5 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.00106732760701 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000688941532829 + + Density error is +0.000158723174498 + + LCAO ALGORITHM --------------- ION=+11 ELEC=+6 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.00106750000594 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000688997886273 + + Density error is +2.84369273907e-05 + + LCAO ALGORITHM --------------- ION=+11 ELEC=+7 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.00106738459146 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000688911442981 + + Density error is +6.35714047631e-06 + + LCAO ALGORITHM --------------- ION=+11 ELEC=+8 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.00106738034647 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000688912778452 + + Density error is +1.13055677219e-06 + + LCAO ALGORITHM --------------- ION=+11 ELEC=+9 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.00106738369643 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000688915585093 + + Density error is +1.28438983532e-07 + + LCAO ALGORITHM --------------- ION=+11 ELEC=+10 -------------------------------- + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + cal_dk_gamma_from_2D, NSPIN = +1 + number of non-zero elements in sender_buffer = +360 + sender_size = +360 + last sender_buffer = +0.00106738402439 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000688915953349 + + Density error is +3.83813047794e-08 + + charge density convergence is achieved + final etot is -466.056600961 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 -0.65293569 +0.14467001 +0.62451703 + H2 +1.6137732 -3.9643303 -5.7287743 + O1 -0.96083753 +3.8196603 +5.1042573 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +0.125491 -0.470583 -0.646063 + -0.470583 +0.977543 +1.479382 + -0.646063 +1.479382 +2.154282 + TOTAL-PRESSURE: +1.085772 KBAR + + + ------------------------------------------------------------------------------------------------ + Energy Potential Kinetic Temperature Pressure (KBAR) + -17.080901 -17.127258 +0.046357165 +4879.4724 +1.4958518 + ------------------------------------------------------------------------------------------------ + +output Pressure for check! +Virtual Pressure is +1.4958518 Kbar +Virial Term is +1.0857717 Kbar +Kenetic Term is +0.41008011 Kbar + + + ><><><><><><><><><><><><><><><><><><><><><>< + + MD STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + ++0.79368934 -0.53832184 -1.2018942 +-0.53832184 +1.0412207 +1.5809550 +-1.2018942 +1.5809550 +2.6526455 + + + + + -------------------------------------------- + !FINAL_ETOT_IS -466.0566009612631 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total +120.88 9 +13. +1.0e+02 % + Driver driver_line +120.87 1 +1.2e+02 +1.e+02 % + PW_Basis setup_struc_factor +0.17977 11 +0.016 +0.15 % + ORB_control read_orb_first +0.10359 1 +0.10 +0.086 % + LCAO_Orbitals Read_Orbitals +0.10359 1 +0.10 +0.086 % + ORB_control set_orb_tables +1.2896 1 +1.3 +1.1 % + ORB_gen_tables gen_tables +1.2896 1 +1.3 +1.1 % + ORB_table_phi init_Table +0.52871 1 +0.53 +0.44 % + ORB_table_phi cal_ST_Phi12_R +0.51940 126 +0.0041 +0.43 % + ORB_table_beta init_Table_Beta +0.18014 1 +0.18 +0.15 % + ORB_table_beta VNL_PhiBeta_R +0.17860 56 +0.0032 +0.15 % + ORB_table_alpha init_Table_Alpha +0.24131 1 +0.24 +0.20 % + ORB_table_alpha S_PhiAlpha_R +0.23927 66 +0.0036 +0.20 % + ppcell_vl init_vloc +0.75564 1 +0.76 +0.63 % + Potential init_pot +3.0773 22 +0.14 +2.5 % + Potential set_local_pot +0.29905 22 +0.014 +0.25 % + PW_Basis recip2real +3.1667 267 +0.012 +2.6 % + PW_Basis gathers_scatterp +1.8973 267 +0.0071 +1.6 % + Charge atomic_rho +40.886 21 +1.9 +34. % + Potential v_of_rho +6.7022 224 +0.030 +5.5 % + XC_Functional v_xc +1.3653 235 +0.0058 +1.1 % + H_Hartree_pw v_hartree +5.0661 224 +0.023 +4.2 % + PW_Basis real2recip +5.5547 683 +0.0081 +4.6 % + PW_Basis gatherp_scatters +2.4305 683 +0.0036 +2.0 % + Potential set_vr_eff +0.18502 224 +0.00083 +0.15 % + Run_MD_LCAO opt_ions +116.42 1 +1.2e+02 +96. % + NVE setup +6.3194 1 +6.3 +5.2 % + MD_func force_stress +76.739 11 +7.0 +63. % + ESolver_KS_LCAO Run +36.091 11 +3.3 +30. % + ESolver_KS_LCAO beforescf +0.52594 11 +0.048 +0.44 % + ESolver_KS_LCAO beforesolver +0.47181 11 +0.043 +0.39 % + ESolver_KS_LCAO set_matrix_grid +0.46447 11 +0.042 +0.38 % + Grid_Technique init +0.46264 11 +0.042 +0.38 % + Grid_BigCell grid_expansion_index+0.34156 22 +0.016 +0.28 % + HSolverLCAO solve +18.102 202 +0.090 +15. % + HamiltLCAO updateHk +8.4775 202 +0.042 +7.0 % + Veff contributeHk +7.5710 202 +0.037 +6.3 % + Gint_interface cal_gint +11.485 415 +0.028 +9.5 % + Gint_Gamma distri_vl_index +0.13904 11 +0.013 +0.12 % + Gint_Gamma distri_vl_value +2.4488 202 +0.012 +2.0 % + Gint_Gamma distri_vl +33.282 101 +0.33 +28. % + DeePKS contributeHR +0.89954 202 +0.0045 +0.74 % + LCAO_Deepks cal_projected_DM +115.63 224 +0.52 +96. % + LCAO_gen_fixedH add_v_delta +33.133 101 +0.33 +27. % + LCAO_DESCRIPTOR add_v_delta +33.133 101 +0.33 +27. % + HSolverLCAO hamiltSolvePsiK +0.30865 202 +0.0015 +0.26 % + DiagoElpa elpa_solve +0.20916 202 +0.0010 +0.17 % + ElecStateLCAO psiToRho +9.3130 202 +0.046 +7.7 % + Charge_Mixing rhog_dot_product +0.13647 202 +0.00068 +0.11 % + Charge mix_rho +6.4874 192 +0.034 +5.4 % + Force_Stress_LCAO getForceStress +40.648 11 +3.7 +34. % + Forces cal_force_loc +0.29526 11 +0.027 +0.24 % + Forces cal_force_ew +0.13593 11 +0.012 +0.11 % + Stress_Func stress_loc +17.037 11 +1.5 +14. % + Stress_Func stress_har +0.14228 11 +0.013 +0.12 % + Stress_Func stress_ew +0.16520 11 +0.015 +0.14 % + Force_LCAO_gamma ftable_gamma +2.2675 11 +0.21 +1.9 % + Force_LCAO_gamma cal_fvl_dphi +1.5603 11 +0.14 +1.3 % + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + +1089. + ORB_table_phi Jl(x) +97.80 + Charge_Pulay Rrho +18.00 + Charge_Pulay dRrho +15.75 + Charge_Pulay drho +15.75 + PW_Basis struc_fac +4.040 + Grid_Meshcell index2normal +3.464 + Grid_Meshcell index2ucell +3.464 + ORB_table_phi Table_SR&TR +2.758 + Charge rho +2.250 + Charge rho_save +2.250 + Charge rho_core +2.250 + Potential vltot +2.250 + Potential vr +2.250 + Potential vr_eff +2.250 + Potential vr_eff1 +2.250 + Potential vnew +2.250 + Charge_Pulay rho_save2 +2.250 + Charge rhog +1.010 + Charge rhog_save +1.010 + Charge kin_r +1.010 + Charge kin_r_save +1.010 + Charge rhog_core +1.010 + ---------------------------------------------------------- + + Start Time : Fri Oct 28 10:37:22 2022 + Finish Time : Fri Oct 28 10:39:23 2022 + Total Time : 0 h 2 mins 1 secs diff --git a/tests/abacus.md.unconv/STRU b/tests/abacus.md.unconv/STRU new file mode 100644 index 000000000..583dc7f17 --- /dev/null +++ b/tests/abacus.md.unconv/STRU @@ -0,0 +1,30 @@ +ATOMIC_SPECIES +H 1.000 H_ONCV_PBE-1.0.upf +O 1.000 O_ONCV_PBE-1.0.upf + +LATTICE_CONSTANT +1.8897261254578281 + +LATTICE_VECTORS +14.524509151052237 0.0 0.0 +-0.014055052627607307 15.127720223675517 0.0 +-0.44236943482340674 0.4176481841581627 14.953520775917804 + +ATOMIC_POSITIONS +Cartesian # Cartesian(Unit is LATTICE_CONSTANT) +H +0.0 +2 +10.872796345702 0.993283528425 3.293903479780 1 1 1 +10.341931867309 14.686041612291 2.160229648213 1 1 1 +O +0.0 +1 +10.133374044864 0.350751910559 3.193008852349 1 1 1 + +NUMERICAL_ORBITAL +H_gga_6au_60Ry_2s1p.orb +O_gga_6au_60Ry_2s2p1d.orb + +NUMERICAL_DESCRIPTOR +jle.orb diff --git a/tests/abacus.md.unconv/water_coord b/tests/abacus.md.unconv/water_coord new file mode 100644 index 000000000..ecc44ff54 --- /dev/null +++ b/tests/abacus.md.unconv/water_coord @@ -0,0 +1,30 @@ +10.872796350496348 0.9932835288754391 3.2939034812246253 +10.341931871870555 14.68604161877169 2.160229649158359 +10.133374049330708 0.35075191072547013 3.1930088537671915 +10.875596903962581 0.9880230639791224 3.294283267373793 +10.340932445324116 14.707241021247025 2.180444768704261 +10.131572922410914 0.33481297314645064 3.1724139480731215 +10.875946512899734 0.9742940867070762 3.2874525737837845 +10.335129396686561 14.765726831702782 2.244759339615585 +10.137026362111317 0.2900561399627399 3.114930070750806 +10.866211192353447 0.9448558916181117 3.2713692272147012 +10.327325042169123 14.852520865071005 2.3413000888721016 +10.154566037175043 0.23270030168448053 3.0344726680643728 +10.816779119655678 0.8402109041170265 3.2122921680356837 +10.395667324863222 14.8699950440347 2.299927583015881 +10.135655827177713 0.31987111022087034 3.13492223309861 +10.85788660826978 0.8382308202051544 3.190428322236055 +10.44219368418471 14.847776586951918 2.235497832240507 +10.04802197924312 0.3440696512155273 3.2212158296736138 +10.912146283563677 0.8507366628636619 3.1752433716883677 +10.46584686779613 14.847702081658886 2.21204942839318 +9.970109120337806 0.33163831385005255 3.2598491840696275 +10.938461010776265 0.8550481103745606 3.170624112648334 +10.46217329738951 14.867117010669435 2.2298068413610004 +9.947467963531835 0.30791193732960354 3.246711030140842 +10.927892472067612 0.8463087228697117 3.1771120061231906 +10.429708008930213 14.903787026986583 2.2873644341533486 +9.990501790697786 0.27998130851630293 3.1826655438736364 +10.88583906063109 0.8262002169708562 3.1926004692970116 +10.373263281167354 14.951256075399488 2.3741154339075536 +10.088999929898165 0.25262076600225347 3.0804260809446107 \ No newline at end of file diff --git a/tests/abacus.md.unconv/water_force b/tests/abacus.md.unconv/water_force new file mode 100644 index 000000000..a3ef3858b --- /dev/null +++ b/tests/abacus.md.unconv/water_force @@ -0,0 +1,30 @@ +0.203673227663 -0.47618851334 -0.673198308232 +-0.497679578285 3.938931579746 4.649209009347 +0.294006350622 -3.462743066406 -3.976010701114 +-0.254022717293 -0.87770020844 -0.74731420223 +-0.497860772145 3.86446717052 4.570589962154 +0.751883489438 -2.98676696208 -3.823275759924 +-1.045230179415 -1.628147086821 -0.958970724628 +-0.207420915322 2.933943064626 3.340010877721 +1.252651094738 -1.305795977804 -2.381040153093 +-1.519717284879 -2.134878371745 -1.173199796326 +2.10911809397 -3.394877057008 -5.282580352734 +-0.589400809091 5.529755428753 6.45578014906 +6.855059278224 5.454541643043 1.016758449181 +-0.960810002863 1.486842944666 2.333454697801 +-5.894249275361 -6.941384587709 -3.350213146982 +1.36312925799 1.501361774798 0.692219305499 +-2.370639635238 2.295060837375 4.247420933792 +1.007510377248 -3.796422612173 -4.939640239291 +-2.896292249377 -0.849289935513 1.0950576947 +-2.832220895025 2.019939251673 4.270685618311 +5.728513144402 -1.17064931616 -5.365743313011 +-3.822684404614 -1.35262488924 1.15117622149 +-2.98405384748 1.788365306177 4.125001485576 +6.806738252094 -0.435740416937 -5.276177707066 +-3.263179899026 -1.178327094849 0.932844111407 +-2.485295875334 1.119241763062 3.025686004957 +5.74847577436 0.059085331787 -3.958530116363 +-0.652935734428 0.144670019023 0.624517068595 +1.613773327904 -3.96433056183 -5.728774672298 +-0.960837593476 3.819660542807 5.104257603703 \ No newline at end of file diff --git a/tests/abacus.md.unconv/water_virial b/tests/abacus.md.unconv/water_virial new file mode 100644 index 000000000..a227b7d69 --- /dev/null +++ b/tests/abacus.md.unconv/water_virial @@ -0,0 +1,30 @@ +0.24174151279974476 0.7147771971960454 0.5531447774724815 +0.7147771971960454 -3.198275400257512 -3.9986173546173713 +0.5531447774724815 -3.9986173546173713 -4.784204267393815 +-0.10840542517624387 0.39028170888624547 0.4832356927260805 +0.39028170888624547 -3.2607407742047494 -3.808136216020199 +0.4832356927260805 -3.808136216020199 -4.524663305527436 +-0.6484624525389577 -0.4250827028223907 0.014450445258066456 +-0.4250827028223907 -2.7615435750683743 -2.639816603886048 +0.014450445258066456 -2.639816603886048 -2.902156731044343 +-0.5334653285055465 -2.036378315527121 -1.8364798694439255 +-2.036378315527121 0.5390052757534562 2.15595314041675 +-1.8364798694439255 2.15595314041675 3.7020152287221335 +4.720752234241953 4.318991579821913 1.2964726739356265 +4.318991579821913 2.244120847659801 -0.6422435056740825 +1.2964726739356265 -0.6422435056740825 -1.6800417562513617 +0.4601569619910953 2.3149374828796883 2.2186059517481302 +2.3149374828796883 -0.5512735588090263 -2.243073402105155 +2.2186059517481302 -2.243073402105155 -4.111539708880487 +-3.926189929345843 0.32966207737438824 3.127803672721892 +0.32966207737438824 -1.6004533307700601 -2.004061504796424 +3.127803672721892 -2.004061504796424 -4.493878063171357 +-5.153737102685699 -0.31667179617794633 3.2409112685954504 +-0.31667179617794633 -1.6925385624499167 -1.671536502632919 +3.2409112685954504 -1.671536502632919 -4.2042109428574435 +-3.940946442117263 -0.5129457258274437 2.143637281434464 +-0.5129457258274437 -1.1292177271732293 -0.9092633792664692 +2.143637281434464 -0.9092633792664692 -2.5711782179590674 +0.2573469018622114 -0.9650383078890258 -1.3248995639092485 +-0.9650383078890258 2.004673847020464 3.0338088043725384 +-1.3248995639092485 3.0338088043725384 4.417845989981152 \ No newline at end of file diff --git a/tests/test_abacus_md.py b/tests/test_abacus_md.py index d039211b0..3621242db 100644 --- a/tests/test_abacus_md.py +++ b/tests/test_abacus_md.py @@ -11,27 +11,37 @@ class TestABACUSMD: def test_atom_names(self) : self.assertEqual(self.system_water.data['atom_names'], ['H', 'O']) self.assertEqual(self.system_Si.data['atom_names'], ['Si']) + self.assertEqual(self.system_water_unconv.data['atom_names'], ['H', 'O']) def test_atom_numbs(self) : self.assertEqual(self.system_water.data['atom_numbs'], [2, 1]) self.assertEqual(self.system_Si.data['atom_numbs'], [2]) + self.assertEqual(self.system_water_unconv.data['atom_numbs'], [2, 1]) def test_atom_types(self) : ref_type = [0, 0, 1] ref_type = np.array(ref_type) ref_type2 = np.array([0, 0]) + ref_type3 = np.array([0,0,1]) for ii in range(ref_type.shape[0]) : self.assertEqual(self.system_water.data['atom_types'][ii], ref_type[ii]) for ii in range(ref_type2.shape[0]) : self.assertEqual(self.system_Si.data['atom_types'][ii], ref_type2[ii]) + for ii in range(ref_type3.shape[0]) : + self.assertEqual(self.system_water_unconv.data['atom_types'][ii], ref_type3[ii]) def test_cell(self) : cell = bohr2ang * 28 * np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]]) cell2 = bohr2ang * 5.1 * np.array([[1, 1, 0], [1, 0, 1], [0, 1, 1]]) + cell3 = np.array([[1.45245092e+01, 0, 0], + [-1.40550526e-02, 1.51277202e+01, 0], + [-4.42369435e-01, 4.17648184e-01, 1.49535208e+01]]) for idx in range(np.shape(self.system_water.data['cells'])[0]): np.testing.assert_almost_equal(cell, self.system_water.data['cells'][idx], decimal = 5) for idx in range(np.shape(self.system_Si.data['cells'])[0]): np.testing.assert_almost_equal(self.system_Si.data['cells'][idx], cell2, decimal = 5) + for idx in range(np.shape(self.system_water_unconv.data['cells'])[0]): + np.testing.assert_almost_equal(self.system_water_unconv.data['cells'][idx], cell3, decimal = 5) def test_coord(self) : with open('abacus.md/water_coord') as fp: @@ -50,6 +60,14 @@ def test_coord(self) : coord = coord.reshape([4, 2, 3]) np.testing.assert_almost_equal(self.system_Si.data['coords'], coord, decimal = 5) + with open('abacus.md.unconv/water_coord') as fp3: + coord = [] + for ii in fp3 : + coord.append([float(jj) for jj in ii.split()]) + coord = np.array(coord) + coord = coord.reshape([10, 3, 3]) + np.testing.assert_almost_equal(self.system_water_unconv.data['coords'], coord, decimal = 5) + def test_force(self) : with open('abacus.md/water_force') as fp: force = [] @@ -59,7 +77,6 @@ def test_force(self) : force = force.reshape([5, 3, 3]) np.testing.assert_almost_equal(self.system_water.data['forces'], force, decimal=5) - with open('abacus.md.nostress/Si_force') as fp2: force = [] for ii in fp2 : @@ -68,6 +85,13 @@ def test_force(self) : force = force.reshape([4, 2, 3]) np.testing.assert_almost_equal(self.system_Si.data['forces'], force, decimal=5) + with open('abacus.md.unconv/water_force') as fp3: + force = [] + for ii in fp3 : + force.append([float(jj) for jj in ii.split()]) + force = np.array(force) + force = force.reshape([10, 3, 3]) + np.testing.assert_almost_equal(self.system_water_unconv.data['forces'], force, decimal=5) def test_virial(self) : with open('abacus.md/water_virial') as fp: @@ -78,12 +102,23 @@ def test_virial(self) : virial = virial.reshape([5, 3, 3]) np.testing.assert_almost_equal(self.system_water.data['virials'], virial, decimal=5) + with open('abacus.md.unconv/water_virial') as fp: + virial = [] + for ii in fp : + virial.append([float(jj) for jj in ii.split()]) + virial = np.array(virial) + virial = virial.reshape([10, 3, 3]) + np.testing.assert_almost_equal(self.system_water_unconv.data['virials'], virial, decimal=5) + def test_energy(self) : ref_energy = np.array([-466.69285117, -466.69929051, -466.69829826, -466.70364664, -466.6976083]) ref_energy2 = np.array([-211.77184603, -211.78111966, -211.79681663, -211.79875524]) + ref_energy3 = np.array([-464.87380991, -465.18489358, -465.97407849, -465.98292836, -465.85528926, + -465.33957501, -464.64886682, -464.61802032, -465.61854656, -466.05660096]) np.testing.assert_almost_equal(self.system_water.data['energies'], ref_energy) np.testing.assert_almost_equal(self.system_Si.data['energies'], ref_energy2) + np.testing.assert_almost_equal(self.system_water_unconv.data['energies'], ref_energy3) def test_to_system(self): pp_file=["H.upf","O.upf"] @@ -107,6 +142,7 @@ class TestABACUSMDLabeledOutput(unittest.TestCase, TestABACUSMD): def setUp(self): self.system_water = dpdata.LabeledSystem('abacus.md',fmt='abacus/md') # system with stress self.system_Si = dpdata.LabeledSystem('abacus.md.nostress',fmt='abacus/md') # system without stress + self.system_water_unconv = dpdata.LabeledSystem('abacus.md.unconv',fmt='abacus/md') #system with unconverged SCF def tearDown(self): if os.path.isfile('abacus.md/water_stru'): From 42e6877747992e7f970c52b8b5293da9f83e04aa Mon Sep 17 00:00:00 2001 From: Jinzhe Zeng Date: Mon, 31 Oct 2022 21:10:00 -0400 Subject: [PATCH 03/10] drop Python 3.6 support (#369) Just realized that #366 requires setuptools>=61 and setuptools 59 has dropped Python 3.6. --- pyproject.toml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 6cc28717b..87151506c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,5 +1,5 @@ [build-system] -requires = ["setuptools>=45", "setuptools_scm[toml]>=6.2"] +requires = ["setuptools>=61", "setuptools_scm[toml]>=6.2"] build-backend = "setuptools.build_meta" [project] @@ -23,7 +23,7 @@ dependencies = [ 'wcmatch', 'importlib_metadata>=1.4; python_version < "3.8"', ] -requires-python = ">=3.6" +requires-python = ">=3.7" readme = "README.md" keywords = ["lammps", "vasp", "deepmd-kit"] From f2bd6df9f2388d893c3917943642405247559c64 Mon Sep 17 00:00:00 2001 From: Jinzhe Zeng Date: Wed, 9 Nov 2022 20:39:32 -0500 Subject: [PATCH 04/10] remove duplicated rot_lower_triangular (#370) `LabeledSystem.rot_lower_triangular` is the same as `System.rot_lower_triangular`. It's not necessary to define twice. --- dpdata/system.py | 5 ----- 1 file changed, 5 deletions(-) diff --git a/dpdata/system.py b/dpdata/system.py index a2226d030..5451e22ae 100644 --- a/dpdata/system.py +++ b/dpdata/system.py @@ -1125,11 +1125,6 @@ def affine_map_fv(self, trans, f_idx) : if self.has_virial(): self.data['virials'][f_idx] = np.matmul(trans.T, np.matmul(self.data['virials'][f_idx], trans)) - @post_funcs.register("rot_lower_triangular") - def rot_lower_triangular(self) : - for ii in range(self.get_nframes()) : - self.rot_frame_lower_triangular(ii) - def rot_frame_lower_triangular(self, f_idx = 0) : trans = System.rot_frame_lower_triangular(self, f_idx = f_idx) self.affine_map_fv(trans, f_idx = f_idx) From 0bcd5b37874b9ab38874b9b6cc3ccc22d3ecb8b7 Mon Sep 17 00:00:00 2001 From: Jinzhe Zeng Date: Sun, 13 Nov 2022 18:41:58 -0500 Subject: [PATCH 05/10] support max_steps for ase minimizer (#372) Adds `max_steps` parameter to `ASEMinimizer`. --- dpdata/plugins/ase.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/dpdata/plugins/ase.py b/dpdata/plugins/ase.py index f61d46f6c..728df3298 100644 --- a/dpdata/plugins/ase.py +++ b/dpdata/plugins/ase.py @@ -221,6 +221,8 @@ class ASEMinimizer(Minimizer): ase optimizer class fmax : float, optional, default=5e-3 force convergence criterion + max_steps : int, optional + max steps to optimize optimizer_kwargs : dict, optional other parameters for optimizer """ @@ -228,6 +230,7 @@ def __init__(self, driver: Driver, optimizer: Type["Optimizer"] = None, fmax: float = 5e-3, + max_steps: int = None, optimizer_kwargs: dict = {}) -> None: self.calculator = driver.ase_calculator if optimizer is None: @@ -240,6 +243,7 @@ def __init__(self, **optimizer_kwargs.copy(), } self.fmax = fmax + self.max_steps = max_steps def minimize(self, data: dict) -> dict: """Minimize the geometry. @@ -261,7 +265,7 @@ def minimize(self, data: dict) -> dict: for atoms in structures: atoms.calc = self.calculator dyn = self.optimizer(atoms, **self.optimizer_kwargs) - dyn.run(fmax=self.fmax) + dyn.run(fmax=self.fmax, steps=self.max_steps) ls = dpdata.LabeledSystem(atoms, fmt="ase/structure", type_map=data['atom_names']) labeled_system.append(ls) - return labeled_system.data \ No newline at end of file + return labeled_system.data From afc02c4868f0fece2674dfbd61e3dcff7359999a Mon Sep 17 00:00:00 2001 From: Jinzhe Zeng Date: Tue, 15 Nov 2022 20:10:11 -0500 Subject: [PATCH 06/10] fix codecov (#373) Codecov python package is deprecated does not work any more. This patch migrates it to another version. --- .github/workflows/test.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index a480eb458..1f8caf806 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -22,8 +22,8 @@ jobs: - name: Install rdkit run: python -m pip install rdkit openbabel-wheel - name: Install dependencies - run: python -m pip install .[amber,ase,pymatgen] coverage codecov + run: python -m pip install .[amber,ase,pymatgen] coverage - name: Test run: cd tests && coverage run --source=../dpdata -m unittest && cd .. && coverage combine tests/.coverage && coverage report - name: Run codecov - run: codecov + uses: codecov/codecov-action@v3 From efbaae63afad5451dd5bb0c4f840042c9b5abc49 Mon Sep 17 00:00:00 2001 From: AngelJia <1165524245@qq.com> Date: Wed, 23 Nov 2022 13:41:55 +0800 Subject: [PATCH 07/10] fix bug in reading trajs with random tid (#377) fix #376 Co-authored-by: Sikai Yao --- dpdata/lammps/dump.py | 9 ++-- tests/lammps/traj_with_random_type_id.dump | 50 ++++++++++++++++++++++ tests/test_lammps_read_from_trajs.py | 44 +++++++++++++++++++ 3 files changed, 100 insertions(+), 3 deletions(-) create mode 100644 tests/lammps/traj_with_random_type_id.dump create mode 100644 tests/test_lammps_read_from_trajs.py diff --git a/dpdata/lammps/dump.py b/dpdata/lammps/dump.py index e40dc400b..9de719547 100644 --- a/dpdata/lammps/dump.py +++ b/dpdata/lammps/dump.py @@ -31,9 +31,11 @@ def get_atype(lines, type_idx_zero = False) : tidx = keys.index('type') - 2 atype = [] for ii in blk : - atype.append([int(ii.split()[id_idx]), int(ii.split()[tidx])]) + atype.append([int(ii.split()[tidx]), int(ii.split()[id_idx])]) + # sort with type id atype.sort() atype = np.array(atype, dtype = int) + atype = atype[:, ::-1] if type_idx_zero : return atype[:,1] - 1 else : @@ -76,6 +78,7 @@ def safe_get_posi(lines,cell,orig=np.zeros(3), unwrap=False) : assert coord_tp_and_sf is not None, 'Dump file does not contain atomic coordinates!' coordtype, sf, uw = coord_tp_and_sf id_idx = keys.index('id') - 2 + tidx = keys.index('type') - 2 xidx = keys.index(coordtype[0])-2 yidx = keys.index(coordtype[1])-2 zidx = keys.index(coordtype[2])-2 @@ -83,9 +86,9 @@ def safe_get_posi(lines,cell,orig=np.zeros(3), unwrap=False) : posis = [] for ii in blk : words = ii.split() - posis.append([float(words[id_idx]), float(words[xidx]), float(words[yidx]), float(words[zidx])]) + posis.append([float(words[tidx]), float(words[id_idx]), float(words[xidx]), float(words[yidx]), float(words[zidx])]) posis.sort() - posis = np.array(posis)[:,1:4] + posis = np.array(posis)[:,2:5] if not sf: posis = (posis - orig) @ np.linalg.inv(cell) # Convert to scaled coordinates for unscaled coordinates if uw and unwrap: diff --git a/tests/lammps/traj_with_random_type_id.dump b/tests/lammps/traj_with_random_type_id.dump new file mode 100644 index 000000000..471e97eb8 --- /dev/null +++ b/tests/lammps/traj_with_random_type_id.dump @@ -0,0 +1,50 @@ +ITEM: TIMESTEP +0 +ITEM: NUMBER OF ATOMS +16 +ITEM: BOX BOUNDS xy xz yz pp pp pp +0.0000000000000000e+00 6.8043376809999998e+00 2.5385198599999999e-02 +0.0000000000000000e+00 6.7821075796999999e+00 1.8630761460000000e-01 +0.0000000000000000e+00 6.6801861338000004e+00 6.5204177000000002e-02 +ITEM: ATOMS id type x y z +1 4 3.48873 0.0697213 6.67774 +2 4 3.38621 0.033338 3.34239 +3 4 1.79424 1.7281 5.01015 +4 4 3.48973 3.42896 6.67795 +5 4 3.40064 3.39148 3.34188 +6 2 6.69832 3.39136 3.34005 +7 3 1.80744 5.08708 5.01099 +8 3 5.10512 5.08007 5.01272 +9 3 1.70086 1.69544 1.66979 +10 4 5.09069 1.72876 5.00917 +11 4 0.119885 6.74841 3.33869 +12 4 4.99379 1.69262 1.67183 +13 4 0.199838 3.4185 6.67565 +14 4 1.7213 5.05235 1.66373 +15 4 0.21494 6.77616 6.67623 +16 6 5.00691 5.05 1.66532 +ITEM: TIMESTEP +10 +ITEM: NUMBER OF ATOMS +16 +ITEM: BOX BOUNDS xy xz yz pp pp pp +3.0951719137647604e-02 6.7713982144168243e+00 2.5146837349522749e-02 +3.1535098850918430e-02 6.7499602284333751e+00 1.8455822840494820e-01 +3.1362715442244227e-02 6.6488234183577575e+00 6.4591924584292706e-02 +ITEM: ATOMS id type x y z +1 6 3.52465 0.174767 6.64949 +2 4 3.44881 6.57204 3.4593 +3 3 1.85127 1.64364 4.94466 +4 4 3.4242 3.50712 6.53701 +5 4 3.46382 3.47183 3.41008 +6 4 6.63593 3.49936 3.46086 +7 4 1.85117 5.11268 4.96295 +8 3 5.18664 4.9445 5.05251 +9 3 1.70736 1.6591 1.6432 +10 4 5.23527 1.84126 5.03198 +11 4 6.59374 6.65872 3.38238 +12 4 5.00141 1.8369 1.76495 +13 4 6.64861 3.4664 6.51584 +14 4 1.60995 4.92415 1.66769 +15 4 6.62681 0.172193 6.54904 +16 2 4.88678 5.15478 1.589 \ No newline at end of file diff --git a/tests/test_lammps_read_from_trajs.py b/tests/test_lammps_read_from_trajs.py new file mode 100644 index 000000000..6f27ffd29 --- /dev/null +++ b/tests/test_lammps_read_from_trajs.py @@ -0,0 +1,44 @@ +import os +import numpy as np +import unittest +from context import dpdata + +class TestLmpReadFromTrajsWithRandomTypeId(unittest.TestCase): + + def setUp(self): + self.system = \ + dpdata.System(os.path.join('lammps', 'traj_with_random_type_id.dump'), fmt = 'lammps/dump', type_map = ["Ta","Nb","W","Mo","V","Al"]) + + def test_nframes (self) : + atype = self.system['atom_types'].tolist() + self.assertTrue(atype == [1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5]) + + coord = self.system['coords'].reshape([2, -1]) + + coord0_std = np.array([6.69832 , 3.39136 , 3.34005 , 1.80744 , 5.08708 , 5.01099 , + 5.10512 , 5.08007 , 5.01272 , 1.70086 , 1.69544 , 1.66979 , + 3.48873 , 0.0697213, 6.67774 , 3.38621 , 0.033338 , 3.34239 , + 1.79424 , 1.7281 , 5.01015 , 3.48973 , 3.42896 , 6.67795 , + 3.40064 , 3.39148 , 3.34188 , 5.09069 , 1.72876 , 5.00917 , + 0.119885 , 6.74841 , 3.33869 , 4.99379 , 1.69262 , 1.67183 , + 0.199838 , 3.4185 , 6.67565 , 1.7213 , 5.05235 , 1.66373 , + 0.21494 , 6.77616 , 6.67623 , 5.00691 , 5.05 , 1.66532 ]) + self.assertTrue(np.allclose(coord[0, ...], coord0_std)) + + coord1_std = np.array([4.85582828e+00, 5.12324490e+00, 1.55763728e+00, 1.82031828e+00, + 1.61210490e+00, 4.91329728e+00, 5.15568828e+00, 4.91296490e+00, + 5.02114728e+00, 1.67640828e+00, 1.62756490e+00, 1.61183728e+00, + 3.41785828e+00, 6.54050490e+00, 3.42793728e+00, 3.39324828e+00, + 3.47558490e+00, 6.50564728e+00, 3.43286828e+00, 3.44029490e+00, + 3.37871728e+00, 6.60497828e+00, 3.46782490e+00, 3.42949728e+00, + 1.82021828e+00, 5.08114490e+00, 4.93158728e+00, 5.20431828e+00, + 1.80972490e+00, 5.00061728e+00, 6.56278828e+00, 6.62718490e+00, + 3.35101728e+00, 4.97045828e+00, 1.80536490e+00, 1.73358728e+00, + 6.61765828e+00, 3.43486490e+00, 6.48447728e+00, 1.57899828e+00, + 4.89261490e+00, 1.63632728e+00, 6.59585828e+00, 1.40657901e-01, + 6.51767728e+00, 3.30914005e+00, 7.86399766e-02, 6.66581642e-04]) + self.assertTrue(np.allclose(coord[1, ...], coord1_std)) + +if __name__ == '__main__': + unittest.main() + From 7db1b4ce477714dfd76f9c2aeaf23cb72cb8280b Mon Sep 17 00:00:00 2001 From: Jinzhe Zeng Date: Mon, 28 Nov 2022 09:58:58 -0500 Subject: [PATCH 08/10] add Optional to type hints when default is None (#382) Signed-off-by: Jinzhe Zeng Signed-off-by: Jinzhe Zeng --- dpdata/cli.py | 7 ++++--- dpdata/deepmd/hdf5.py | 4 ++-- dpdata/gaussian/gjf.py | 6 +++--- dpdata/plugins/ase.py | 8 ++++---- dpdata/plugins/deepmd.py | 6 +++--- 5 files changed, 16 insertions(+), 15 deletions(-) diff --git a/dpdata/cli.py b/dpdata/cli.py index ef6eeab77..2b33f9590 100644 --- a/dpdata/cli.py +++ b/dpdata/cli.py @@ -1,5 +1,6 @@ """Command line interface for dpdata.""" import argparse +from typing import Optional from . import __version__ from .system import System, LabeledSystem, MultiSystems @@ -47,11 +48,11 @@ def dpdata_cli(): def convert(*, from_file: str, from_format: str = "auto", - to_file: str = None, - to_format: str = None, + to_file: Optional[str] = None, + to_format: Optional[str] = None, no_labeled: bool = False, multi: bool = False, - type_map: list = None, + type_map: Optional[list] = None, **kwargs): """Convert files from one format to another one. diff --git a/dpdata/deepmd/hdf5.py b/dpdata/deepmd/hdf5.py index 8bbd00484..0e807f058 100644 --- a/dpdata/deepmd/hdf5.py +++ b/dpdata/deepmd/hdf5.py @@ -1,5 +1,5 @@ """Utils for deepmd/hdf5 format.""" -from typing import Union +from typing import Optional, Union import h5py import numpy as np @@ -11,7 +11,7 @@ def to_system_data(f: Union[h5py.File, h5py.Group], folder: str, - type_map: list = None, + type_map: Optional[list] = None, labels: bool = True) : """Load a HDF5 file. diff --git a/dpdata/gaussian/gjf.py b/dpdata/gaussian/gjf.py index 588f1ed67..727732b86 100644 --- a/dpdata/gaussian/gjf.py +++ b/dpdata/gaussian/gjf.py @@ -3,7 +3,7 @@ # under LGPL 3.0 license """Generate Gaussian input file.""" -from typing import List, Tuple, Union +from typing import Optional, List, Tuple, Union import uuid import itertools import warnings @@ -107,8 +107,8 @@ def make_gaussian_input( multiplicity: Union[str ,int] = "auto", charge: int = 0, fragment_guesses: bool = False, - basis_set: str = None, - keywords_high_multiplicity: str = None, + basis_set: Optional[str] = None, + keywords_high_multiplicity: Optional[str] = None, nproc: int = 1, ) -> str: """Make gaussian input file. diff --git a/dpdata/plugins/ase.py b/dpdata/plugins/ase.py index 728df3298..fa2093e40 100644 --- a/dpdata/plugins/ase.py +++ b/dpdata/plugins/ase.py @@ -1,4 +1,4 @@ -from typing import TYPE_CHECKING, Type +from typing import Optional, TYPE_CHECKING, Type from dpdata.driver import Driver, Minimizer from dpdata.format import Format import numpy as np @@ -93,7 +93,7 @@ def from_labeled_system(self, atoms: "ase.Atoms", **kwargs) -> dict: info_dict['virials'] = virials return info_dict - def from_multi_systems(self, file_name: str, begin: int=None, end: int=None, step: int=None, ase_fmt: str=None, **kwargs) -> "ase.Atoms": + def from_multi_systems(self, file_name: str, begin: Optional[int] = None, end: Optional[int] = None, step: Optional[int] = None, ase_fmt: Optional[str] = None, **kwargs) -> "ase.Atoms": """Convert a ASE supported file to ASE Atoms. It will finally be converted to MultiSystems. @@ -228,9 +228,9 @@ class ASEMinimizer(Minimizer): """ def __init__(self, driver: Driver, - optimizer: Type["Optimizer"] = None, + optimizer: Optional[Type["Optimizer"]] = None, fmax: float = 5e-3, - max_steps: int = None, + max_steps: Optional[int] = None, optimizer_kwargs: dict = {}) -> None: self.calculator = driver.ase_calculator if optimizer is None: diff --git a/dpdata/plugins/deepmd.py b/dpdata/plugins/deepmd.py index aa69c44b8..c3b7f4ca5 100644 --- a/dpdata/plugins/deepmd.py +++ b/dpdata/plugins/deepmd.py @@ -1,4 +1,4 @@ -from typing import Union, List +from typing import Optional, Union, List import dpdata import dpdata.deepmd.raw @@ -108,7 +108,7 @@ def _from_system(self, file_name: Union[str, h5py.Group, h5py.File], type_map: L def from_system(self, file_name: Union[str, h5py.Group, h5py.File], - type_map: List[str]=None, + type_map: Optional[List[str]] = None, **kwargs) -> dict: """Convert HDF5 file to System data. @@ -134,7 +134,7 @@ def from_system(self, def from_labeled_system(self, file_name: Union[str, h5py.Group, h5py.File], - type_map: List[str]=None, + type_map: Optional[List[str]] = None, **kwargs) -> dict: """Convert HDF5 file to LabeledSystem data. From 7a1eea904984ca8beb92c687792fcfb916f069fd Mon Sep 17 00:00:00 2001 From: Jinzhe Zeng Date: Tue, 29 Nov 2022 22:11:14 -0500 Subject: [PATCH 09/10] add pass step to GitHub Actions (#384) Same as https://github.com/deepmodeling/deepmd-kit/pull/2141 --- .github/workflows/test.yml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 1f8caf806..e19f85d43 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -27,3 +27,8 @@ jobs: run: cd tests && coverage run --source=../dpdata -m unittest && cd .. && coverage combine tests/.coverage && coverage report - name: Run codecov uses: codecov/codecov-action@v3 + pass: + needs: [build] + runs-on: ubuntu-latest + steps: + - run: echo "All jobs passed" From 993600364a58228927095dec48c2227ed30263b5 Mon Sep 17 00:00:00 2001 From: Han Wang Date: Thu, 1 Dec 2022 08:53:11 +0800 Subject: [PATCH 10/10] fix issue #381. (#383) The returned system should be of the same type as the perturbed system Co-authored-by: Han Wang --- dpdata/system.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/dpdata/system.py b/dpdata/system.py index 5451e22ae..6089db46d 100644 --- a/dpdata/system.py +++ b/dpdata/system.py @@ -810,6 +810,11 @@ def perturb(self, perturbed_system : System The perturbed_system. It contains `pert_num` * frame_num of the input system frames. """ + if type(self) is not dpdata.System: + raise RuntimeError( + f'Using method perturb() of an instance of {type(self)}. ' + f'Must use method perturb() of the instance of class dpdata.System.' + ) perturbed_system = System() nframes = self.get_nframes() for ii in range(nframes):