diff --git a/.gitignore b/.gitignore index 2c2699eb..41ee080c 100644 --- a/.gitignore +++ b/.gitignore @@ -22,3 +22,6 @@ _version.py !tests/cp2k/aimd/cp2k.log !tests/cp2k/restart_aimd/ch4.log __pycache__ +docs/_build +docs/formats.csv +docs/api/ diff --git a/docs/conf.py b/docs/conf.py index bed869fd..dbe2c0bf 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -14,6 +14,7 @@ # import os import sys +import subprocess as sp from datetime import date sys.path.insert(0, os.path.abspath('..')) @@ -21,7 +22,7 @@ # -- Project information ----------------------------------------------------- project = 'dpdata' -copyright = '2019-%d, Deep Modeling ' % date.today().year +copyright = '2019-%d, DeepModeling ' % date.today().year author = 'Han Wang' # The short X.Y version @@ -40,6 +41,7 @@ # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ + 'deepmodeling_sphinx', 'sphinx_rtd_theme', 'sphinx.ext.mathjax', 'sphinx.ext.viewcode', @@ -170,8 +172,12 @@ def run_apidoc(_): module = os.path.join(cur_dir, "..", "dpdata") main(['-M', '--tocfile', 'api', '-H', 'API documentation', '-o', os.path.join(cur_dir, "api"), module, '--force']) +def run_formats(_): + sp.check_output([sys.executable, "make_format.py"]) + def setup(app): app.connect('builder-inited', run_apidoc) + app.connect('builder-inited', run_formats) intersphinx_mapping = { diff --git a/docs/formats.rst b/docs/formats.rst new file mode 100644 index 00000000..1920a848 --- /dev/null +++ b/docs/formats.rst @@ -0,0 +1,9 @@ +Supported Formats +================= + +dpdata supports the following formats: + +.. csv-table:: Supported Formats + :file: formats.csv + :header-rows: 1 + diff --git a/docs/index.rst b/docs/index.rst index 116e3f69..85e83716 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -10,6 +10,7 @@ Welcome to dpdata's documentation! :maxdepth: 2 :caption: Contents: + formats api/api .. mdinclude:: ../README.md diff --git a/docs/make_format.py b/docs/make_format.py new file mode 100644 index 00000000..61fc10a4 --- /dev/null +++ b/docs/make_format.py @@ -0,0 +1,90 @@ +import csv +from collections import defaultdict + +# ensure all plugins are loaded! +import dpdata.plugins +from dpdata.format import Format +from dpdata.system import get_cls_name + + +def get_formats() -> dict: + formats = defaultdict(list) + for kk, ff in Format.get_formats().items(): + formats[ff].append(kk) + return formats + +def detect_overridden(cls: Format, method: str) -> bool: + """Check whether a method is override + + Parameters + ---------- + cls : Format + a format + method : str + method name + + Returns + ------- + bool + whether a method is overridden + """ + return method in cls.__dict__ + +def get_cls_link(cls: object) -> str: + """Returns class link. + + Parameters + ---------- + cls : object + the class + + Returns + ------- + str + the link of a class + """ + return ':class:`%s <%s>`' % (cls.__name__, ".".join([cls.__module__, cls.__name__])) + +def check_supported(fmt: Format): + methods = set() + for mtd in [ + 'from_system', 'to_system', + 'from_labeled_system', 'to_labeled_system', + 'from_bond_order_system', 'to_bond_order_system', + 'from_multi_systems', 'to_multi_systems', + ]: + if detect_overridden(fmt, mtd): + methods.add(mtd) + if mtd == 'to_system': + methods.add('to_labeled_system') + if fmt.MultiMode != fmt.MultiModes.NotImplemented: + methods.add('from_multi_systems') + methods.add('to_multi_systems') + return methods + +method_links = { + "from_system": ":func:`System() `", + "to_system": ":func:`System.to() `", + "from_labeled_system": ":func:`LabeledSystem() `", + "to_labeled_system": ":func:`LabeledSystem.to() `", + "from_bond_order_system": ":func:`BondOrderSystem() `", + "to_bond_order_system": ":func:`BondOrderSystem.to() `", + "from_multi_systems": ":func:`MultiSystems.load_systems_from_file() `", + "to_multi_systems": ":func:`MultiSystems.to() `", +} + +if __name__ == "__main__": + formats = get_formats() + with open('formats.csv', 'w', newline='') as csvfile: + fieldnames = [ + 'Class', 'Alias', 'Supported Functions', + ] + writer = csv.DictWriter(csvfile, fieldnames=fieldnames) + + writer.writeheader() + for kk, vv in formats.items(): + writer.writerow({ + 'Class': get_cls_link(kk), + 'Alias': '\n'.join(('``%s``' % vvv for vvv in vv)), + 'Supported Functions': '\n'.join(method_links[mtd] for mtd in check_supported(kk)), + }) diff --git a/dpdata/abacus/md.py b/dpdata/abacus/md.py index 5b6a1730..8bd9c72c 100644 --- a/dpdata/abacus/md.py +++ b/dpdata/abacus/md.py @@ -1,6 +1,8 @@ +from ast import dump import os,sys import numpy as np -from .scf import ry2ev, kbar2evperang3, get_block, get_geometry_in, get_cell, get_coords +from .scf import ry2ev, bohr2ang, kbar2evperang3, get_block, get_geometry_in, get_cell, get_coords +import re # Read in geometries from an ABACUS MD trajectory. # The atomic coordinates are read in from generated files in OUT.XXXX. @@ -24,126 +26,49 @@ def get_path_out(fname, inlines): def get_coord_dump_freq(inlines): for line in inlines: - if len(line)>0 and "md_dumpmdfred" in line and "md_dumpmdfred" == line.split()[0]: + if len(line)>0 and "md_dumpfreq" in line and "md_dumpfreq" == line.split()[0]: return int(line.split()[1]) return 1 -# set up a cell according to cell info in cif file. -# maybe useful later -''' -def setup_cell(a, b, c, alpha, beta, gamma): - cell = np.zeros(3, 3) - cell[0, 0] = a - cell[1, 0] = b*np.cos(gamma/180*np.pi) - cell[1, 1] = b*np.sin(gamma/180*np.pi) - cell[2, 0] = c*np.cos(beta/180*np.pi) - cell[2, 1] = c*(b*np.cos(alpha/180*np.pi) - cell[1, 0]*np.cos(beta/180*np.pi))/cell[1, 1] - cell[2, 2] = np.sqrt(c**2 - cell[2, 0]**2 - cell[2, 1]**2) - return cell -''' - -def get_single_coord_from_cif(pos_file, atom_names, natoms, cell): - assert(len(atom_names) == len(natoms)) - nele = len(atom_names) +def get_coords_from_dump(dumplines, natoms): + nlines = len(dumplines) total_natoms = sum(natoms) - coord = np.zeros([total_natoms, 3]) - a = 0 - b = 0 - c = 0 - alpha = 0 - beta = 0 - gamma = 0 - with open(pos_file, "r") as fp: - lines = fp.read().split("\n") - for line in lines: - if "_cell_length_a" in line: - a = float(line.split()[1]) - if "_cell_length_b" in line: - b = float(line.split()[1]) - if "_cell_length_c" in line: - c = float(line.split()[1]) - if "_cell_angle_alpha" in line: - alpha = float(line.split()[1]) - if "_cell_angle_beta" in line: - beta = float(line.split()[1]) - if "_cell_angle_gamma" in line: - gamma = float(line.split()[1]) - assert(a > 0 and b > 0 and c > 0 and alpha > 0 and beta > 0 and gamma > 0) - #cell = setup_cell(a, b, c, alpha, beta, gamma) - coord_lines = get_block(lines=lines, keyword="_atom_site_fract_z", skip=0, nlines = total_natoms) - - ia_idx = 0 - for it in range(nele): - for ia in range(natoms[it]): - coord_line = coord_lines[ia_idx].split() - assert(coord_line[0] == atom_names[it]) - coord[ia_idx, 0] = float(coord_line[1]) - coord[ia_idx, 1] = float(coord_line[2]) - coord[ia_idx, 2] = float(coord_line[3]) - ia_idx+=1 - coord = np.matmul(coord, cell) - # important! Coordinates are converted to Cartesian coordinate. - return coord + nframes_dump = int(nlines/(total_natoms + 13)) - -def get_coords_from_cif(ndump, dump_freq, atom_names, natoms, types, path_out, cell): - total_natoms = sum(natoms) - #cell = np.zeros(ndump, 3, 3) - coords = np.zeros([ndump, total_natoms, 3]) - pos_file = os.path.join(path_out, "STRU_READIN_ADJUST.cif") - # frame 0 file is different from any other frames - coords[0] = get_single_coord_from_cif(pos_file, atom_names, natoms, cell) - for dump_idx in range(1, ndump): - pos_file = os.path.join(path_out, "md_pos_%d.cif" %(dump_idx*dump_freq)) - #print("dump_idx = %s" %dump_idx) - coords[dump_idx] = get_single_coord_from_cif(pos_file, atom_names, natoms, cell) - return coords + cells = np.zeros([nframes_dump, 3, 3]) + stresses = np.zeros([nframes_dump, 3, 3]) + forces = np.zeros([nframes_dump, total_natoms, 3]) + coords = np.zeros([nframes_dump, total_natoms, 3]) + iframe = 0 + for iline in range(nlines): + if "MDSTEP" in dumplines[iline]: + # read in LATTICE_CONSTANT + celldm = float(dumplines[iline+1].split(" ")[-1]) + # read in LATTICE_VECTORS + for ix in range(3): + cells[iframe, ix] = np.array([float(i) for i in re.split('\s+', dumplines[iline+3+ix])[-3:]]) * celldm + stresses[iframe, ix] = np.array([float(i) for i in re.split('\s+', dumplines[iline+7+ix])[-3:]]) + for iat in range(total_natoms): + coords[iframe, iat] = np.array([float(i) for i in re.split('\s+', dumplines[iline+11+iat])[-6:-3]])*celldm + forces[iframe, iat] = np.array([float(i) for i in re.split('\s+', dumplines[iline+11+iat])[-3:]]) + iframe += 1 + assert(iframe == nframes_dump) + cells *= bohr2ang + coords *= bohr2ang + stresses *= kbar2evperang3 + return coords, cells, forces, stresses -def get_energy_force_stress(outlines, inlines, dump_freq, ndump, natoms, atom_names): - stress = None - total_natoms = sum(natoms) - for line in inlines: - if len(line)>0 and "stress" in line and "stress" == line.split()[0] and "1" == line.split()[1]: - stress = np.zeros([ndump, 3, 3]) - break - if type(stress) != np.ndarray: - print("The ABACUS program has no stress output. Stress will not be read.") +def get_energy(outlines, ndump, dump_freq): + energy = [] nenergy = 0 - nforce = 0 - nstress = 0 - energy = np.zeros(ndump) - force = np.zeros([ndump, total_natoms, 3]) - for line_idx, line in enumerate(outlines): if "final etot is" in line: if nenergy%dump_freq == 0: - energy[int(nenergy/dump_freq)] = float(line.split()[-2]) + energy.append(float(line.split()[-2])) nenergy+=1 - if "TOTAL-FORCE (eV/Angstrom)" in line: - for iatom in range(0, total_natoms): - force_line = outlines[line_idx+5+iatom] - atom_force = [float(i) for i in force_line.split()[1:]] - assert(len(atom_force) == 3) - atom_force = np.array(atom_force) - if nforce%dump_freq == 0: - force[int(nforce/dump_freq), iatom] = atom_force - nforce+=1 - assert(nforce==nenergy) - if "TOTAL-STRESS (KBAR)" in line: - for idx in range(0, 3): - stress_line = outlines[line_idx+4+idx] - single_stress = [float(i) for i in stress_line.split()] - if len(single_stress) != 3: - print(single_stress) - assert(len(single_stress) == 3) - single_stress = np.array(single_stress) - if nstress%dump_freq == 0: - stress[int(nstress/dump_freq), idx] = single_stress - nstress+=1 - assert(nstress==nforce) - if type(stress) == np.ndarray: - stress *= kbar2evperang3 - return energy, force, stress + assert(ndump == len(energy)) + energy = np.array(energy) + return energy def get_frame (fname): @@ -164,23 +89,27 @@ def get_frame (fname): atom_names, natoms, types, coords = get_coords(celldm, cell, geometry_inlines, inlines) # This coords is not to be used. dump_freq = get_coord_dump_freq(inlines = inlines) - ndump = int(os.popen("ls -l %s | grep 'md_pos_' | wc -l" %path_out).readlines()[0]) + #ndump = int(os.popen("ls -l %s | grep 'md_pos_' | wc -l" %path_out).readlines()[0]) # number of dumped geometry files - coords = get_coords_from_cif(ndump, dump_freq, atom_names, natoms, types, path_out, cell) - - # TODO: Read in energies, forces and pressures. + #coords = get_coords_from_cif(ndump, dump_freq, atom_names, natoms, types, path_out, cell) + with open(os.path.join(path_out, "MD_dump"), 'r') as fp: + dumplines = fp.read().split('\n') + coords, cells, force, stress = get_coords_from_dump(dumplines, natoms) + ndump = np.shape(coords)[0] with open(os.path.join(path_out, "running_md.log"), 'r') as fp: outlines = fp.read().split('\n') - energy, force, stress = get_energy_force_stress(outlines, inlines, dump_freq, ndump, natoms, atom_names) - if type(stress) == np.ndarray: - stress *= np.linalg.det(cell) + energy = get_energy(outlines, ndump, dump_freq) + for iframe in range(ndump): + stress[iframe] *= np.linalg.det(cells[iframe, :, :].reshape([3, 3])) + if np.sum(np.abs(stress[0])) < 1e-10: + stress = None data = {} data['atom_names'] = atom_names data['atom_numbs'] = natoms data['atom_types'] = types - data['cells'] = np.zeros([ndump, 3, 3]) - for idx in range(ndump): - data['cells'][:, :, :] = cell + data['cells'] = cells + #for idx in range(ndump): + # data['cells'][:, :, :] = cell data['coords'] = coords data['energies'] = energy data['forces'] = force diff --git a/dpdata/abacus/scf.py b/dpdata/abacus/scf.py index 41dd40a7..f167c249 100644 --- a/dpdata/abacus/scf.py +++ b/dpdata/abacus/scf.py @@ -16,15 +16,18 @@ def get_block (lines, keyword, skip = 0, nlines = None): found = True blk_idx = idx + 1 + skip line_idx = 0 - while len(lines[blk_idx]) == 0: + while len(lines[blk_idx].split("\s+")) == 0: blk_idx += 1 - while len(lines[blk_idx]) != 0 and line_idx < nlines and blk_idx != len(lines): + while line_idx < nlines and blk_idx != len(lines): + if len(lines[blk_idx].split("\s+")) == 0 or lines[blk_idx] == "": + blk_idx+=1 + continue ret.append(lines[blk_idx]) blk_idx += 1 line_idx += 1 break if not found: - raise RuntimeError("The keyword %s is not found in the script." %keyword) + return None return ret def get_geometry_in(fname, inlines): @@ -111,9 +114,11 @@ def get_energy(outlines): raise RuntimeError("Final total energy cannot be found in output. Unknown problem.") return Etot -def get_force (outlines): +def get_force (outlines, natoms): force = [] - force_inlines = get_block (outlines, "TOTAL-FORCE (eV/Angstrom)", skip = 4) + force_inlines = get_block (outlines, "TOTAL-FORCE (eV/Angstrom)", skip = 4, nlines=np.sum(natoms)) + if force_inlines is None: + raise RuntimeError("TOTAL-FORCE (eV/Angstrom) is not found in running_scf.log. Please check.") for line in force_inlines: force.append([float(f) for f in line.split()[1:4]]) force = np.array(force) @@ -121,7 +126,9 @@ def get_force (outlines): def get_stress(outlines): stress = [] - stress_inlines = get_block(outlines, "TOTAL-STRESS (KBAR)", skip = 3) + stress_inlines = get_block(outlines, "TOTAL-STRESS (KBAR)", skip = 3, nlines=3) + if stress_inlines is None: + return None for line in stress_inlines: stress.append([float(f) for f in line.split()]) stress = np.array(stress) * kbar2evperang3 @@ -151,8 +158,10 @@ def get_frame (fname): atom_names, natoms, types, coords = get_coords(celldm, cell, geometry_inlines, inlines) energy = get_energy(outlines) - force = get_force (outlines) - stress = get_stress(outlines) * np.linalg.det(cell) + force = get_force (outlines, natoms) + stress = get_stress(outlines) + if stress is not None: + stress *= np.abs(np.linalg.det(cell)) data = {} data['atom_names'] = atom_names @@ -162,7 +171,8 @@ def get_frame (fname): data['coords'] = coords[np.newaxis, :, :] data['energies'] = np.array(energy)[np.newaxis] data['forces'] = force[np.newaxis, :, :] - data['virials'] = stress[np.newaxis, :, :] + if stress is not None: + data['virials'] = stress[np.newaxis, :, :] data['orig'] = np.zeros(3) # print("atom_names = ", data['atom_names']) # print("natoms = ", data['atom_numbs']) diff --git a/dpdata/amber/sqm.py b/dpdata/amber/sqm.py index f569ebe4..86a84e1d 100644 --- a/dpdata/amber/sqm.py +++ b/dpdata/amber/sqm.py @@ -65,7 +65,7 @@ def parse_sqm_out(fname): data['coords'] = np.array([coords]) energies = np.array(energies) - forces = np.array([forces], dtype=np.float32) * kcal2ev + forces = -np.array([forces], dtype=np.float64) * kcal2ev if len(forces) > 0: data['energies'] = energies data['forces'] = forces diff --git a/dpdata/cli.py b/dpdata/cli.py new file mode 100644 index 00000000..eaa7c76e --- /dev/null +++ b/dpdata/cli.py @@ -0,0 +1,75 @@ +"""Command line interface for dpdata.""" +import argparse + +from . import __version__ +from .system import System, LabeledSystem, MultiSystems + + +def dpdata_cli(): + """dpdata cli. + + Examples + -------- + .. code-block:: bash + + $ dpdata -iposcar POSCAR -odeepmd/npy -O data -n + """ + parser = argparse.ArgumentParser( + description="dpdata: Manipulating multiple atomic simulation data formats", + formatter_class=argparse.ArgumentDefaultsHelpFormatter, + ) + + parser.add_argument("from_file", type=str, help="read data from a file") + parser.add_argument("--to_file", "-O", type=str, help="dump data to a file") + parser.add_argument("--from_format", "-i", type=str, default="auto", help="the format of from_file") + parser.add_argument("--to_format", "-o", type=str, help="the format of to_file") + parser.add_argument("--no-labeled", "-n", action="store_true", help="labels aren't provided") + parser.add_argument("--multi", "-m", action="store_true", help="the system contains multiple directories") + parser.add_argument("--type-map", "-t", type=str, nargs="+", help="type map") + + parser.add_argument('--version', action='version', version='dpdata v%s' % __version__) + + parsed_args = parser.parse_args() + convert(**vars(parsed_args)) + + +def convert(*, + from_file: str, + from_format: str = "auto", + to_file: str = None, + to_format: str = None, + no_labeled: bool = False, + multi: bool = False, + type_map: list = None, + **kwargs): + """Convert files from one format to another one. + + Parameters + ---------- + from_file : str + read data from a file + from_format : str + the format of from_file + to_file : str + dump data to a file + to_format : str + the format of to_file + no_labeled : bool + labels aren't provided + multi : bool + the system contains multiple directories + type_map : list + type map + """ + if multi: + s = MultiSystems.from_file(from_file, fmt=from_format, type_map=type_map, labeled=not no_labeled) + elif not no_labeled: + s = LabeledSystem(from_file, fmt=from_format, type_map=type_map) + else: + s = System(from_file, fmt=from_format, type_map=type_map) + if to_format is not None: + out = s.to(to_format, to_file) + if isinstance(out, str): + print(out) + else: + print(s) diff --git a/dpdata/deepmd/hdf5.py b/dpdata/deepmd/hdf5.py index 5b623958..4b2486ba 100644 --- a/dpdata/deepmd/hdf5.py +++ b/dpdata/deepmd/hdf5.py @@ -77,6 +77,9 @@ def to_system_data(f: h5py.File, if len(all_data) > 0 : data[dt] = np.concatenate(all_data, axis = 0) + if 'cells' not in data: + nframes = data['coords'].shape[0] + data['cells'] = np.zeros((nframes, 3, 3)) return data def dump(f: h5py.File, diff --git a/dpdata/fhi_aims/output.py b/dpdata/fhi_aims/output.py index 99cb1203..4ee819c3 100755 --- a/dpdata/fhi_aims/output.py +++ b/dpdata/fhi_aims/output.py @@ -124,7 +124,7 @@ def analyze_block(lines, first_blk=False, md=True) : contents="\n".join(lines) try: natom=int(re.findall("Number of atoms.*([0-9]{1,})",lines)[0]) - except: + except Exception: natom=0 if first_blk: @@ -154,7 +154,7 @@ def analyze_block(lines, first_blk=False, md=True) : try: _eng_patt=re.compile(eng_patt) energy=float(_eng_patt.search(contents).group().split()[-2]) - except: + except Exception: energy=None if not energy: diff --git a/dpdata/plugins/abacus.py b/dpdata/plugins/abacus.py index 43403772..aec05a7d 100644 --- a/dpdata/plugins/abacus.py +++ b/dpdata/plugins/abacus.py @@ -5,6 +5,7 @@ @Format.register("abacus/scf") @Format.register("abacus/pw/scf") +@Format.register("abacus/lcao/scf") class AbacusSCFFormat(Format): #@Format.post("rot_lower_triangular") def from_labeled_system(self, file_name, **kwargs): diff --git a/dpdata/plugins/deepmd.py b/dpdata/plugins/deepmd.py index 6fd209a3..9379e9ec 100644 --- a/dpdata/plugins/deepmd.py +++ b/dpdata/plugins/deepmd.py @@ -29,7 +29,7 @@ class DeePMDCompFormat(Format): def from_system(self, file_name, type_map=None, **kwargs): return dpdata.deepmd.comp.to_system_data(file_name, type_map=type_map, labels=False) - def to_system(self, data, file_name, set_size=5000, prec=np.float32, **kwargs): + def to_system(self, data, file_name, set_size=5000, prec=np.float64, **kwargs): """ Dump the system in deepmd compressed format (numpy binary) to `folder`. @@ -58,7 +58,7 @@ def from_labeled_system(self, file_name, type_map=None, **kwargs): MultiMode = Format.MultiModes.Directory @Format.register("deepmd/hdf5") -class DeePMDCompFormat(Format): +class DeePMDHDF5Format(Format): """HDF5 format for DeePMD-kit. Examples @@ -83,7 +83,7 @@ def to_system(self, data : dict, file_name : str, set_size : int = 5000, - comp_prec : np.dtype = np.float32, + comp_prec : np.dtype = np.float64, **kwargs): s = file_name.split("#") name = s[1] if len(s) > 1 else "" diff --git a/dpdata/plugins/qe.py b/dpdata/plugins/qe.py index 0e8149d0..e6a1665a 100644 --- a/dpdata/plugins/qe.py +++ b/dpdata/plugins/qe.py @@ -27,7 +27,7 @@ def from_labeled_system(self, file_name, begin = 0, step = 1, **kwargs): return data @Format.register("qe/pw/scf") -class QECPTrajFormat(Format): +class QECPPWSCFFormat(Format): @Format.post("rot_lower_triangular") def from_labeled_system(self, file_name, **kwargs): data = {} diff --git a/dpdata/plugins/siesta.py b/dpdata/plugins/siesta.py index a601e132..6838dac3 100644 --- a/dpdata/plugins/siesta.py +++ b/dpdata/plugins/siesta.py @@ -34,7 +34,7 @@ def from_labeled_system(self, file_name, **kwargs): @Format.register("siesta/aimd_output") @Format.register_from("from_siesta_aiMD_output") -class SiestaOutputFormat(Format): +class SiestaAIMDOutputFormat(Format): def from_system(self, file_name, **kwargs): data = {} data['atom_names'], \ diff --git a/dpdata/plugins/vasp.py b/dpdata/plugins/vasp.py index 01aad202..d3504447 100644 --- a/dpdata/plugins/vasp.py +++ b/dpdata/plugins/vasp.py @@ -3,7 +3,7 @@ import dpdata.vasp.outcar import numpy as np from dpdata.format import Format - +from dpdata.utils import sort_atom_names, uniq_atom_names @Format.register("poscar") @Format.register("contcar") @@ -14,7 +14,9 @@ class VASPPoscarFormat(Format): def from_system(self, file_name, **kwargs): with open(file_name) as fp: lines = [line.rstrip('\n') for line in fp] - return dpdata.vasp.poscar.to_system_data(lines) + data = dpdata.vasp.poscar.to_system_data(lines) + data = uniq_atom_names(data) + return data def to_system(self, data, file_name, frame_idx=0, **kwargs): """ @@ -71,6 +73,7 @@ def from_labeled_system(self, file_name, begin=0, step=1, **kwargs): for ii in range(data['cells'].shape[0]): vol = np.linalg.det(np.reshape(data['cells'][ii], [3, 3])) data['virials'][ii] *= v_pref * vol + data = uniq_atom_names(data) return data @@ -102,4 +105,5 @@ def from_labeled_system(self, file_name, begin=0, step=1, **kwargs): for ii in range(data['cells'].shape[0]): vol = np.linalg.det(np.reshape(data['cells'][ii], [3, 3])) data['virials'][ii] *= v_pref * vol + data = uniq_atom_names(data) return data diff --git a/dpdata/qe/scf.py b/dpdata/qe/scf.py index 48f618a9..50312aee 100755 --- a/dpdata/qe/scf.py +++ b/dpdata/qe/scf.py @@ -70,7 +70,7 @@ def get_coords (lines, cell) : coord.append([float(jj) for jj in ii.split()[1:4]]) atom_symbol_list.append(ii.split()[0]) coord = np.array(coord) - coord = np.matmul(coord, cell.T) + coord = np.matmul(coord, cell) atom_symbol_list = np.array(atom_symbol_list) tmp_names, symbol_idx = np.unique(atom_symbol_list, return_index=True) atom_types = [] diff --git a/dpdata/rdkit/sanitize.py b/dpdata/rdkit/sanitize.py index 01f002e0..0e163740 100644 --- a/dpdata/rdkit/sanitize.py +++ b/dpdata/rdkit/sanitize.py @@ -22,7 +22,7 @@ def get_explicit_valence(atom, verbose=False): print( f"Explicit valence given by GetExplicitValence() and sum of bond order are inconsistent on {atom.GetSymbol()}{atom.GetIdx() + 1}, using sum of bond order.") return exp_val_calculated_from_bonds - except: + except Exception: return exp_val_calculated_from_bonds @@ -37,7 +37,7 @@ def regularize_formal_charges(mol, sanitize=True, verbose=False): try: Chem.SanitizeMol(mol) return mol - except: + except Exception: return None else: return mol diff --git a/dpdata/system.py b/dpdata/system.py index 3c3423c6..b003461c 100644 --- a/dpdata/system.py +++ b/dpdata/system.py @@ -16,6 +16,13 @@ from dpdata.plugin import Plugin from dpdata.format import Format +from dpdata.utils import ( + elements_index_map, + remove_pbc, + sort_atom_names, + add_atom_names, +) + def load_format(fmt): fmt = fmt.lower() formats = Format.get_formats() @@ -132,7 +139,19 @@ def from_fmt_obj(self, fmtobj, file_name, **kwargs): self.post_funcs.get_plugin(post_f)(self) return self - def to(self, fmt, *args, **kwargs): + def to(self, fmt: str, *args, **kwargs) -> 'System': + """Dump systems to the specific format. + + Parameters + ---------- + fmt : str + format + + Returns + ------- + System + self + """ return self.to_fmt_obj(load_format(fmt), *args, **kwargs) def to_fmt_obj(self, fmtobj, *args, **kwargs): @@ -155,7 +174,7 @@ def __str__(self): def __getitem__(self, key): """Returns proerty stored in System by key or by idx""" - if isinstance(key, (int, slice)): + if isinstance(key, (int, slice, list)): return self.sub_system(key) return self.data[key] @@ -341,27 +360,7 @@ def sort_atom_names(self, type_map=None): type_map : list type_map """ - if type_map is not None: - # assign atom_names index to the specify order - # atom_names must be a subset of type_map - assert (set(self.data['atom_names']).issubset(set(type_map))) - # for the condition that type_map is a proper superset of atom_names - # new_atoms = set(type_map) - set(self.data["atom_names"]) - new_atoms = [e for e in type_map if e not in self.data["atom_names"]] - if new_atoms: - self.add_atom_names(new_atoms) - # index that will sort an array by type_map - # a[as[a]] == b[as[b]] as == argsort - # as[as[b]] == as^{-1}[b] - # a[as[a][as[as[b]]]] = b[as[b][as^{-1}[b]]] = b[id] - idx = np.argsort(self.data['atom_names'])[np.argsort(np.argsort(type_map))] - else: - # index that will sort an array by alphabetical order - idx = np.argsort(self.data['atom_names']) - # sort atom_names, atom_numbs, atom_types by idx - self.data['atom_names'] = list(np.array(self.data['atom_names'])[idx]) - self.data['atom_numbs'] = list(np.array(self.data['atom_numbs'])[idx]) - self.data['atom_types'] = np.argsort(idx)[self.data['atom_types']] + self.data = sort_atom_names(self.data, type_map=type_map) def check_type_map(self, type_map): """ @@ -489,8 +488,7 @@ def add_atom_names(self, atom_names): """ Add atom_names that do not exist. """ - self.data['atom_names'].extend(atom_names) - self.data['atom_numbs'].extend([0 for _ in atom_names]) + self.data = add_atom_names(self.data, atom_names) def replicate(self, ncopy): """ @@ -1096,6 +1094,21 @@ def to_fmt_obj(self, fmtobj, directory, *args, **kwargs): for fn, ss in zip(fmtobj.to_multi_systems(self.systems.keys(), directory, **kwargs), self.systems.values()): ss.to_fmt_obj(fmtobj, fn, *args, **kwargs) return self + + def to(self, fmt: str, *args, **kwargs) -> "MultiSystems": + """Dump systems to the specific format. + + Parameters + ---------- + fmt : str + format + + Returns + ------- + MultiSystems + self + """ + return self.to_fmt_obj(load_format(fmt), *args, **kwargs) def __getitem__(self, key): """Returns proerty stored in System by key or by idx""" @@ -1229,6 +1242,20 @@ def pick_atom_idx(self, idx, nopbc=None): new_sys.append(ss.pick_atom_idx(idx, nopbc=nopbc)) return new_sys +def get_cls_name(cls: object) -> str: + """Returns the fully qualified name of a class, such as `np.ndarray`. + + Parameters + ---------- + cls : object + the class + + Returns + ------- + str + the fully qualified name of a class + """ + return ".".join([cls.__module__, cls.__name__]) def add_format_methods(): """Add format methods to System, LabeledSystem, and MultiSystems. @@ -1251,6 +1278,7 @@ def get_func(ff): # ff is not initized when defining from_format so cannot be polluted def from_format(self, file_name, **kwargs): return self.from_fmt_obj(ff(), file_name, **kwargs) + from_format.__doc__ = "Read data from :class:`%s` format." % (get_cls_name(ff)) return from_format setattr(System, method, get_func(formatcls)) @@ -1261,6 +1289,7 @@ def from_format(self, file_name, **kwargs): def get_func(ff): def to_format(self, *args, **kwargs): return self.to_fmt_obj(ff(), *args, **kwargs) + to_format.__doc__ = "Dump data to :class:`%s` format." % (get_cls_name(ff)) return to_format setattr(System, method, get_func(formatcls)) @@ -1298,26 +1327,3 @@ def check_LabeledSystem(data): assert( len(data['cells']) == len(data['coords']) == len(data['energies']) ) -def elements_index_map(elements,standard=False,inverse=False): - if standard: - elements.sort(key=lambda x: Element(x).Z) - if inverse: - return dict(zip(range(len(elements)),elements)) - else: - return dict(zip(elements,range(len(elements)))) -# %% - -def remove_pbc(system, protect_layer = 9): - nframes = len(system["coords"]) - natoms = len(system['coords'][0]) - for ff in range(nframes): - tmpcoord = system['coords'][ff] - cog = np.average(tmpcoord, axis = 0) - dist = tmpcoord - np.tile(cog, [natoms, 1]) - max_dist = np.max(np.linalg.norm(dist, axis = 1)) - h_cell_size = max_dist + protect_layer - cell_size = h_cell_size * 2 - shift = np.array([1,1,1]) * h_cell_size - cog - system['coords'][ff] = system['coords'][ff] + np.tile(shift, [natoms, 1]) - system['cells'][ff] = cell_size * np.eye(3) - return system diff --git a/dpdata/unit.py b/dpdata/unit.py index 7b5aeffc..299ac2bb 100644 --- a/dpdata/unit.py +++ b/dpdata/unit.py @@ -35,7 +35,7 @@ def check_unit(unit): raise RuntimeError(f"Invaild unit: {unit}") if lunit not in lconvs.keys(): raise RuntimeError(f"Invalid unit: {unit}") - except: + except Exception: raise RuntimeError(f"Invalid unit: {unit}") class Conversion(ABC): diff --git a/dpdata/utils.py b/dpdata/utils.py new file mode 100644 index 00000000..d0ccb26b --- /dev/null +++ b/dpdata/utils.py @@ -0,0 +1,91 @@ +import numpy as np +from dpdata.periodic_table import Element + +def elements_index_map(elements,standard=False,inverse=False): + if standard: + elements.sort(key=lambda x: Element(x).Z) + if inverse: + return dict(zip(range(len(elements)),elements)) + else: + return dict(zip(elements,range(len(elements)))) +# %% + +def remove_pbc(system, protect_layer = 9): + nframes = len(system["coords"]) + natoms = len(system['coords'][0]) + for ff in range(nframes): + tmpcoord = system['coords'][ff] + cog = np.average(tmpcoord, axis = 0) + dist = tmpcoord - np.tile(cog, [natoms, 1]) + max_dist = np.max(np.linalg.norm(dist, axis = 1)) + h_cell_size = max_dist + protect_layer + cell_size = h_cell_size * 2 + shift = np.array([1,1,1]) * h_cell_size - cog + system['coords'][ff] = system['coords'][ff] + np.tile(shift, [natoms, 1]) + system['cells'][ff] = cell_size * np.eye(3) + return system + +def add_atom_names(data, atom_names): + """ + Add atom_names that do not exist. + """ + data['atom_names'].extend(atom_names) + data['atom_numbs'].extend([0 for _ in atom_names]) + return data + +def sort_atom_names(data, type_map=None): + """ + Sort atom_names of the system and reorder atom_numbs and atom_types accoarding + to atom_names. If type_map is not given, atom_names will be sorted by + alphabetical order. If type_map is given, atom_names will be type_map. + + Parameters + ---------- + type_map : list + type_map + """ + if type_map is not None: + # assign atom_names index to the specify order + # atom_names must be a subset of type_map + assert (set(data['atom_names']).issubset(set(type_map))) + # for the condition that type_map is a proper superset of atom_names + # new_atoms = set(type_map) - set(data["atom_names"]) + new_atoms = [e for e in type_map if e not in data["atom_names"]] + if new_atoms: + data = add_atom_names(data, new_atoms) + # index that will sort an array by type_map + # a[as[a]] == b[as[b]] as == argsort + # as[as[b]] == as^{-1}[b] + # a[as[a][as[as[b]]]] = b[as[b][as^{-1}[b]]] = b[id] + idx = np.argsort(data['atom_names'])[np.argsort(np.argsort(type_map))] + else: + # index that will sort an array by alphabetical order + idx = np.argsort(data['atom_names']) + # sort atom_names, atom_numbs, atom_types by idx + data['atom_names'] = list(np.array(data['atom_names'])[idx]) + data['atom_numbs'] = list(np.array(data['atom_numbs'])[idx]) + data['atom_types'] = np.argsort(idx)[data['atom_types']] + return data + +def uniq_atom_names(data): + """ + Make the atom names uniq. For example + ['O', 'H', 'O', 'H', 'O'] -> ['O', 'H'] + + Parameters + ---------- + data : dict + data dict of `System`, `LabeledSystem` + + """ + unames = [] + uidxmap = [] + for idx,ii in enumerate(data['atom_names']): + if ii not in unames: + unames.append(ii) + uidxmap.append(unames.index(ii)) + data['atom_names'] = unames + tmp_type = list(data['atom_types']).copy() + data['atom_types'] = np.array([uidxmap[jj] for jj in tmp_type], dtype=int) + data['atom_numbs'] = [sum( ii == data['atom_types'] ) for ii in range(len(data['atom_names'])) ] + return data diff --git a/dpdata/vasp/outcar.py b/dpdata/vasp/outcar.py index 0e9e74d3..21256735 100644 --- a/dpdata/vasp/outcar.py +++ b/dpdata/vasp/outcar.py @@ -127,7 +127,9 @@ def analyze_block(lines, ntot, nelm) : virial[2][1] = tmp_v[4] virial[0][2] = tmp_v[5] virial[2][0] = tmp_v[5] - elif 'TOTAL-FORCE' in ii: + elif 'TOTAL-FORCE' in ii and ("ML" not in ii): + # use the lines with " POSITION TOTAL-FORCE (eV/Angst)" + # exclude the lines with " POSITION TOTAL-FORCE (eV/Angst) (ML)" for jj in range(idx+2, idx+2+ntot) : tmp_l = lines[jj] info = [float(ss) for ss in tmp_l.split()] diff --git a/setup.py b/setup.py index ec554be5..a0ee7c33 100644 --- a/setup.py +++ b/setup.py @@ -54,7 +54,8 @@ 'ase': ['ase'], 'amber': ['parmed'], 'pymatgen': ['pymatgen'], - 'docs': ['sphinx', 'recommonmark', 'sphinx_rtd_theme>=1.0.0rc1', 'numpydoc', 'm2r2'], - } + 'docs': ['sphinx', 'recommonmark', 'sphinx_rtd_theme>=1.0.0rc1', 'numpydoc', 'm2r2', 'deepmodeling-sphinx'], + }, + entry_points={"console_scripts": ["dpdata = dpdata.cli:dpdata_cli"]}, ) diff --git a/tests/abacus.md/INPUT b/tests/abacus.md/INPUT index d169ddf9..5986c0ba 100644 --- a/tests/abacus.md/INPUT +++ b/tests/abacus.md/INPUT @@ -1,30 +1,43 @@ INPUT_PARAMETERS -#Parameters (General) -suffix autotest -pseudo_dir ./ -ntype 1 -nbands 8 -calculation md -read_file_dir ./ +#Parameters (1.General) +suffix abacus +calculation md +ntype 2 +nbands 6 +symmetry 0 -#Parameters (Accuracy) -ecutwfc 20 -niter 20 +#Parameters (2.Iteration) +ecutwfc 50 +scf_thr 1e-2 +scf_nmax 50 -basis_type pw -nstep 21 # number of MD/relaxation steps +#Parameters (3.Basis) +basis_type lcao +gamma_only 1 -stress 1 -stress_thr 1e-6 -force 1 -force_thr_ev 1.0e-3 +#Parameters (4.Smearing) +smearing_method gaussian +smearing_sigma 0.02 -ks_solver cg -mixing_type pulay -mixing_beta 0.7 +#Parameters (5.Mixing) +mixing_type pulay +mixing_beta 0.4 -md_mdtype 1 # 0 for NVE; 1 for NVT with Nose Hoover; 2 for NVT with velocity rescaling -md_tfirst 10 # temperature, unit: K -md_dt 1 # unit: fs -md_rstmd 0 # 1 for restart -md_dumpmdfred 5 +#Parameters (6.Deepks) +#cal_force 1 +#test_force 1 +#deepks_out_labels 1 +#deepks_descriptor_lmax 2 +#deepks_scf 1 +#deepks_model model.ptg + +md_type 1 +md_dt 0.1 +md_tfirst 300 +md_tfreq 0.1 +md_restart 0 +md_dumpfreq 5 +md_nstep 20 +out_level m + +cal_stress 1 diff --git a/tests/abacus.md/OUT.abacus/MD_dump b/tests/abacus.md/OUT.abacus/MD_dump new file mode 100644 index 00000000..f3585236 --- /dev/null +++ b/tests/abacus.md/OUT.abacus/MD_dump @@ -0,0 +1,80 @@ +MDSTEP: 0 +LATTICE_CONSTANT: 1.000000000000 +LATTICE_VECTORS + 28.000000000000 0.000000000000 0.000000000000 + 0.000000000000 28.000000000000 0.000000000000 + 0.000000000000 0.000000000000 28.000000000000 +VIRIAL (KBAR) + 0.342473709368 -0.250611694353 -0.053956446640 + -0.250611694353 0.199085269192 -0.098626841062 + -0.053956446640 -0.098626841062 0.476228570252 +INDEX LABEL POSITIONS FORCE (eV/Angstrom) + 0 H 15.953212941138 18.765586146743 8.395247471322 0.863308639441 -0.443254999104 -0.756985212833 + 1 H 13.771131204099 20.615493002741 7.611989524536 -0.200930881908 0.468126173231 -1.160958093908 + 2 O 14.513210882571 19.684192208442 8.958321352729 -0.662377757533 -0.024871174127 1.917943306741 + + +MDSTEP: 5 +LATTICE_CONSTANT: 1.000000000000 +LATTICE_VECTORS + 28.000000000000 0.000000000000 0.000000000000 + 0.000000000000 28.000000000000 0.000000000000 + 0.000000000000 0.000000000000 28.000000000000 +VIRIAL (KBAR) + 0.154743825476 -0.125714918816 0.000149755944 + -0.125714918816 0.119479071004 -0.140313773379 + 0.000149755944 -0.140313773379 0.457169606881 +INDEX LABEL POSITIONS FORCE (eV/Angstrom) + 0 H 15.972712462196 18.750422243865 8.413062924828 0.308447002711 -0.100596917061 -0.518349474860 + 1 H 13.786987486168 20.622823511243 7.605308823456 -0.219930471300 0.466062785475 -1.095536719299 + 2 O 14.510983383443 19.684685730795 8.957619837020 -0.088516531411 -0.365465868414 1.613886194160 + + +MDSTEP: 10 +LATTICE_CONSTANT: 1.000000000000 +LATTICE_VECTORS + 28.000000000000 0.000000000000 0.000000000000 + 0.000000000000 28.000000000000 0.000000000000 + 0.000000000000 0.000000000000 28.000000000000 +VIRIAL (KBAR) + -0.091192063445 0.052076615726 0.020742614517 + 0.052076615726 -0.012621430602 -0.137196630015 + 0.020742614517 -0.137196630015 0.376312058179 +INDEX LABEL POSITIONS FORCE (eV/Angstrom) + 0 H 15.993574661987 18.734845521277 8.428473898762 -0.421531963990 0.478003484039 -0.602669270783 + 1 H 13.801966849306 20.632160064055 7.593719582169 0.265214977762 0.076407086378 -0.963824371968 + 2 O 14.508725280299 19.685078876234 8.957379058834 0.156316986228 -0.554410570417 1.566493642751 + + +MDSTEP: 15 +LATTICE_CONSTANT: 1.000000000000 +LATTICE_VECTORS + 28.000000000000 0.000000000000 0.000000000000 + 0.000000000000 28.000000000000 0.000000000000 + 0.000000000000 0.000000000000 28.000000000000 +VIRIAL (KBAR) + -0.247917742642 0.164910534300 0.034034337680 + 0.164910534300 -0.098300168752 -0.128317310754 + 0.034034337680 -0.128317310754 0.301502887031 +INDEX LABEL POSITIONS FORCE (eV/Angstrom) + 0 H 16.013474681966 18.720459436062 8.442030452618 -0.543198631066 0.457161183663 -0.206821526696 + 1 H 13.816825157151 20.642826422172 7.577781781099 0.022709639914 0.211549051866 -0.758980258266 + 2 O 14.506535423527 19.685313227829 8.957529083034 0.520488991152 -0.668710235529 0.965801784963 + + +MDSTEP: 20 +LATTICE_CONSTANT: 1.000000000000 +LATTICE_VECTORS + 28.000000000000 0.000000000000 0.000000000000 + 0.000000000000 28.000000000000 0.000000000000 + 0.000000000000 0.000000000000 28.000000000000 +VIRIAL (KBAR) + -0.404277528792 0.286670843238 0.018904177312 + 0.286670843238 -0.202681869786 -0.083866196906 + 0.018904177312 -0.083866196906 0.189108946079 +INDEX LABEL POSITIONS FORCE (eV/Angstrom) + 0 H 16.030788395118 18.708219053395 8.454627488439 -0.812329959008 0.587918500063 0.000941318509 + 1 H 13.831803451625 20.654370023278 7.558509583331 0.039826431878 0.100785737160 -0.450166047811 + 2 O 14.504500950754 19.685357126714 8.957949634007 0.772503527130 -0.688704237222 0.449224729302 + + diff --git a/tests/abacus.md/OUT.abacus/running_md.log b/tests/abacus.md/OUT.abacus/running_md.log new file mode 100644 index 00000000..c099ca4d --- /dev/null +++ b/tests/abacus.md/OUT.abacus/running_md.log @@ -0,0 +1,2284 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 4 + Start Time is Wed Apr 13 14:58:14 2022 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.abacus/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 4 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | 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 + lattice constant (Angstrom) = 0.529177 + + 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 Bohr ). + atom x y z mag vx vy vz + tauc_H1 15.9532129411 18.7655861467 8.39524747132 0 0 0 0 + tauc_H2 13.7711312041 20.6154930027 7.61198952454 0 0 0 0 + tauc_O1 14.5132108826 19.6841922084 8.95832135273 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: H_gga_8au_60Ry_2s1p.orb + orbital file: O_gga_7au_60Ry_2s2p1d.orb + + Volume (Bohr^3) = 21952 + Volume (A^3) = 3252.94689686 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +28 +0 +0 + +0 +28 +0 + +0 +0 +28 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.0357142857143 +0 +0 + +0 +0.0357142857143 +0 + +0 -0 +0.0357142857143 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | 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 + 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 + initial pseudo atomic orbital number = 0 + NLOCAL = 23 + + 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 = 6 + NBANDS = 6 + DONE : SETUP UNITCELL Time : 0.0345590766519 (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 + + 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 : 0.0349359968677 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves: | + | 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. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for wavefunc (unit:Ry) = 50 + [fft grid for wave functions] = 128, 128, 128 + [fft grid for charge/potential] = 128, 128, 128 + [fft grid division] = 2, 2, 2 + [big fft grid for charge/potential] = 64, 64, 64 + nbxx = 65536 + nrxx = 524288 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 1048171 + number of sticks = 12469 + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + number of plane waves = 1048171 + number of sticks = 12469 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 3117 262043 + 2 3118 262044 + 3 3117 262043 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(W) PW + 1 3117 262043 + 2 3118 262044 + 3 3117 262043 + 4 3117 262041 + --------------- sum ------------------- + 4 12469 1048171 + + SETUP COORDINATES OF PLANE WAVES + number of total plane waves = 1048171 + + SETUP COORDINATES OF PLANE WAVES + number of |g| = 3309 + max |g| = 5.06505102041 + min |g| = 0 + DONE : INIT PLANEWAVE Time : 1.2043611249 (SEC) + + DONE : INIT CHARGE Time : 1.25489114318 (SEC) + + DONE : INIT POTENTIAL Time : 1.26592466421 (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 0 801 0.01 8 1 1 + 2 0 1 801 0.01 8 1 1 + 3 1 0 801 0.01 8 1 1 + ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT + 1 0 0 701 0.01 7 1 1 + 2 0 1 701 0.01 7 1 1 + 3 1 0 701 0.01 7 1 1 + 4 1 1 701 0.01 7 1 1 + 5 2 0 701 0.01 7 1 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 = 144 + init_chg = atomic + nloc = 144 + searching radius is (Bohr)) = 16.01 + searching radius unit is (Bohr)) = 1 + enter setAlltoallvParameter, nblk = 1 +checkpoint 2 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 12 + nCol_in_proc = 12 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 12 + nCol_in_proc = 11 + pnum = 2 + prow = 1 + pcol = 0 + nRow_in_proc = 11 + nCol_in_proc = 12 + pnum = 3 + prow = 1 + pcol = 1 + nRow_in_proc = 11 + nCol_in_proc = 11 +receiver_size is 529 ; receiver_size of each process is: +144 132 132 121 +sender_size is 436 ; sender_size of each process is: +144 144 144 4 + gamma_only_local = 1 + + LCAO ALGORITHM ------------- MD = 1 ELEC = 1 -------------------------------- + +temp variables are deleted + +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 + start solver, ks_solver = genelpa + +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 = 436 + sender_size = 436 + last sender_buffer = 0.000987248 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000213871 + + Density error is 0.22907025181 + + LCAO ALGORITHM ------------- MD = 1 ELEC = 2 -------------------------------- + +temp variables are deleted + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + start solver, ks_solver = genelpa + +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 = 436 + sender_size = 436 + last sender_buffer = 0.00124178 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000232881 + + Density error is 0.0983063523487 + + LCAO ALGORITHM ------------- MD = 1 ELEC = 3 -------------------------------- + +temp variables are deleted + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + start solver, ks_solver = genelpa + +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 = 436 + sender_size = 436 + last sender_buffer = 0.00119187 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.00023854 + + Density error is 0.0630382071563 + + LCAO ALGORITHM ------------- MD = 1 ELEC = 4 -------------------------------- + +temp variables are deleted + vlocal data are put in sender_buffer, size(M): = 0 + vlocal data are exchanged, received size(M): = 0 + start solver, ks_solver = genelpa + +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 = 436 + sender_size = 436 + last sender_buffer = 0.00111123 + number of non-zero elements in receiver_buffer = 529 + receiver_size = 529 + last receiver_buffer = 0.000247594 + + Density error is 0.00212188907864 + + charge density convergence is achieved + final etot is -466.692851174 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 +0.86330858 -0.44325497 -0.75698516 + H2 -0.20093087 +0.46812614 -1.160958 + O1 -0.66237771 -0.024871173 +1.9179432 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +0.342474 -0.250612 -0.053956 + -0.250612 +0.199085 -0.098627 + -0.053956 -0.098627 +0.476229 + + ------------------------------------------- + STEP OF MOLECULAR DYNAMICS : 0 + ------------------------------------------- + +output Pressure for check! +Virtual Pressure is +0.364728 Kbar +Virial Term is +0.339263 Kbar +Kenetic Term is +0.025466 Kbar + + + ><><><><><><><><><><><><><><><><><><><><><>< + + MD STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +0.381046 -0.260771 -0.035926 + -0.260771 +0.213637 -0.116654 + -0.035926 -0.116654 +0.499502 + nloc = +144 + searching radius is (Bohr)) = +16.010000 + searching radius unit is (Bohr)) = +1.000000 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +12 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +11 + pnum = +2 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +12 + pnum = +3 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +11 +receiver_size is +529 ; receiver_size of each process is: ++144 +132 +132 +121 +sender_size is +436 ; sender_size of each process is: ++144 +144 +144 +4 + gamma_only_local = +1 + + LCAO ALGORITHM ------------- MD = 2 ELEC = 1 -------------------------------- + +temp variables are deleted + +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 + start solver, ks_solver = genelpa + +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 = +436 + sender_size = +436 + last sender_buffer = +0.001111 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000246 + + Density error is +0.000812965099 + + charge density convergence is achieved + final etot is -466.694119113669 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 +0.64655531 -0.33147708 -0.63237758 + H2 -0.27582922 +0.48531937 -1.07451897 + O1 -0.37072609 -0.15384229 +1.70689655 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +0.304825 -0.225915 -0.041597 + -0.225915 +0.184120 -0.109536 + -0.041597 -0.109536 +0.476180 + nloc = +144 + searching radius is (Bohr)) = +16.010000 + searching radius unit is (Bohr)) = +1.000000 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +12 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +11 + pnum = +2 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +12 + pnum = +3 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +11 +receiver_size is +529 ; receiver_size of each process is: ++144 +132 +132 +121 +sender_size is +436 ; sender_size of each process is: ++144 +144 +144 +4 + gamma_only_local = +1 + + LCAO ALGORITHM ------------- MD = 3 ELEC = 1 -------------------------------- + +temp variables are deleted + +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 + start solver, ks_solver = genelpa + +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 = +436 + sender_size = +436 + last sender_buffer = +0.001109 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000249 + + Density error is +0.000712200370 + + charge density convergence is achieved + final etot is -466.695421284274 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 +0.61896149 -0.29339215 -0.65503589 + H2 -0.21205075 +0.46474918 -1.12721978 + O1 -0.40691074 -0.17135703 +1.78225568 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +0.270131 -0.203129 -0.030432 + -0.203129 +0.169841 -0.118202 + -0.030432 -0.118202 +0.473338 + nloc = +144 + searching radius is (Bohr)) = +16.010000 + searching radius unit is (Bohr)) = +1.000000 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +12 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +11 + pnum = +2 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +12 + pnum = +3 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +11 +receiver_size is +529 ; receiver_size of each process is: ++144 +132 +132 +121 +sender_size is +436 ; sender_size of each process is: ++144 +144 +144 +4 + gamma_only_local = +1 + + LCAO ALGORITHM ------------- MD = 4 ELEC = 1 -------------------------------- + +temp variables are deleted + +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 + start solver, ks_solver = genelpa + +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 = +436 + sender_size = +436 + last sender_buffer = +0.001106 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000249 + + Density error is +0.000693457887 + + charge density convergence is achieved + final etot is -466.696750196281 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 +0.48644933 -0.21743108 -0.58788434 + H2 -0.24325232 +0.47926564 -1.10488732 + O1 -0.24319701 -0.26183455 +1.69277166 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +0.232348 -0.178143 -0.019038 + -0.178143 +0.154110 -0.127129 + -0.019038 -0.127129 +0.469916 + nloc = +144 + searching radius is (Bohr)) = +16.010000 + searching radius unit is (Bohr)) = +1.000000 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +12 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +11 + pnum = +2 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +12 + pnum = +3 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +11 +receiver_size is +529 ; receiver_size of each process is: ++144 +132 +132 +121 +sender_size is +436 ; sender_size of each process is: ++144 +144 +144 +4 + gamma_only_local = +1 + + LCAO ALGORITHM ------------- MD = 5 ELEC = 1 -------------------------------- + +temp variables are deleted + +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 + start solver, ks_solver = genelpa + +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 = +436 + sender_size = +436 + last sender_buffer = +0.001105 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000251 + + Density error is +0.000831214560 + + charge density convergence is achieved + final etot is -466.698028090263 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 +0.40250864 -0.15283133 -0.57921295 + H2 -0.19163250 +0.44793586 -1.10996658 + O1 -0.21087614 -0.29510452 +1.68917953 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +0.192212 -0.150822 -0.009745 + -0.150822 +0.135827 -0.133329 + -0.009745 -0.133329 +0.463055 + nloc = +144 + searching radius is (Bohr)) = +16.010000 + searching radius unit is (Bohr)) = +1.000000 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +12 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +11 + pnum = +2 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +12 + pnum = +3 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +11 +receiver_size is +529 ; receiver_size of each process is: ++144 +132 +132 +121 +sender_size is +436 ; sender_size of each process is: ++144 +144 +144 +4 + gamma_only_local = +1 + + LCAO ALGORITHM ------------- MD = 6 ELEC = 1 -------------------------------- + +temp variables are deleted + +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 + start solver, ks_solver = genelpa + +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 = +436 + sender_size = +436 + last sender_buffer = +0.001101 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000252 + + Density error is +0.000741826297 + + charge density convergence is achieved + final etot is -466.699290513689 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 +0.30844698 -0.10059691 -0.51834944 + H2 -0.21993046 +0.46606276 -1.09553665 + O1 -0.08851653 -0.36546584 +1.61388609 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +0.154744 -0.125715 +0.000150 + -0.125715 +0.119479 -0.140314 + +0.000150 -0.140314 +0.457170 + + ------------------------------------------- + STEP OF MOLECULAR DYNAMICS : 5 + ------------------------------------------- + +output Pressure for check! +Virtual Pressure is +0.270990 Kbar +Virial Term is +0.243798 Kbar +Kenetic Term is +0.027192 Kbar + + + ><><><><><><><><><><><><><><><><><><><><><>< + + MD STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +0.197322 -0.137704 +0.012493 + -0.137704 +0.137750 -0.159772 + +0.012493 -0.159772 +0.477896 + nloc = +144 + searching radius is (Bohr)) = +16.010000 + searching radius unit is (Bohr)) = +1.000000 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +12 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +11 + pnum = +2 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +12 + pnum = +3 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +11 +receiver_size is +529 ; receiver_size of each process is: ++144 +132 +132 +121 +sender_size is +436 ; sender_size of each process is: ++144 +144 +144 +4 + gamma_only_local = +1 + + LCAO ALGORITHM ------------- MD = 7 ELEC = 1 -------------------------------- + +temp variables are deleted + +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 + start solver, ks_solver = genelpa + +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 = +436 + sender_size = +436 + last sender_buffer = +0.001100 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000254 + + Density error is +0.001296852096 + + charge density convergence is achieved + final etot is -466.700352492361 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 +0.18090284 -0.00124347 -0.52452226 + H2 -0.13733836 +0.40367906 -1.08114493 + O1 -0.04356447 -0.40243559 +1.60566719 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +0.108237 -0.092885 +0.006743 + -0.092885 +0.096063 -0.142871 + +0.006743 -0.142871 +0.444942 + nloc = +144 + searching radius is (Bohr)) = +16.010000 + searching radius unit is (Bohr)) = +1.000000 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +12 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +11 + pnum = +2 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +12 + pnum = +3 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +11 +receiver_size is +529 ; receiver_size of each process is: ++144 +132 +132 +121 +sender_size is +436 ; sender_size of each process is: ++144 +144 +144 +4 + gamma_only_local = +1 + + LCAO ALGORITHM ------------- MD = 8 ELEC = 1 -------------------------------- + +temp variables are deleted + +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 + start solver, ks_solver = genelpa + +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 = +436 + sender_size = +436 + last sender_buffer = +0.001095 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000255 + + Density error is +0.001373100441 + + charge density convergence is achieved + final etot is -466.701391168881 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 +0.14255182 -0.00101230 -0.42624709 + H2 -0.21850033 +0.46069015 -1.06078607 + O1 +0.07594851 -0.45967785 +1.48703316 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +0.076272 -0.071788 +0.016002 + -0.071788 +0.082562 -0.149268 + +0.016002 -0.149268 +0.438978 + nloc = +144 + searching radius is (Bohr)) = +16.010000 + searching radius unit is (Bohr)) = +1.000000 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +12 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +11 + pnum = +2 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +12 + pnum = +3 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +11 +receiver_size is +529 ; receiver_size of each process is: ++144 +132 +132 +121 +sender_size is +436 ; sender_size of each process is: ++144 +144 +144 +4 + gamma_only_local = +1 + + LCAO ALGORITHM ------------- MD = 9 ELEC = 1 -------------------------------- + +temp variables are deleted + +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 + start solver, ks_solver = genelpa + +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 = +436 + sender_size = +436 + last sender_buffer = +0.001096 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000256 + + Density error is +0.002916062746 + + charge density convergence is achieved + final etot is -466.701752940586 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 -0.07047054 +0.18417814 -0.50830181 + H2 -0.02028818 +0.30684812 -1.03356989 + O1 +0.09075872 -0.49102625 +1.54187171 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +0.016733 -0.027790 +0.017836 + -0.027790 +0.048898 -0.145410 + +0.017836 -0.145410 +0.417656 + nloc = +144 + searching radius is (Bohr)) = +16.010000 + searching radius unit is (Bohr)) = +1.000000 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +12 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +11 + pnum = +2 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +12 + pnum = +3 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +11 +receiver_size is +529 ; receiver_size of each process is: ++144 +132 +132 +121 +sender_size is +436 ; sender_size of each process is: ++144 +144 +144 +4 + gamma_only_local = +1 + + LCAO ALGORITHM ------------- MD = 10 ELEC = 1 -------------------------------- + +temp variables are deleted + +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 + start solver, ks_solver = genelpa + +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 = +436 + sender_size = +436 + last sender_buffer = +0.001086 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000258 + + Density error is +0.004281856614 + + charge density convergence is achieved + final etot is -466.701784879168 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 +0.03821444 +0.03386400 -0.27622989 + H2 -0.29847686 +0.50989617 -1.00686614 + O1 +0.26026241 -0.54376017 +1.28309603 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +0.005309 -0.022976 +0.029731 + -0.022976 +0.048804 -0.155863 + +0.029731 -0.155863 +0.418836 + nloc = +144 + searching radius is (Bohr)) = +16.010000 + searching radius unit is (Bohr)) = +1.000000 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +12 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +11 + pnum = +2 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +12 + pnum = +3 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +11 +receiver_size is +529 ; receiver_size of each process is: ++144 +132 +132 +121 +sender_size is +436 ; sender_size of each process is: ++144 +144 +144 +4 + gamma_only_local = +1 + + LCAO ALGORITHM ------------- MD = 11 ELEC = 1 -------------------------------- + +temp variables are deleted + +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 + start solver, ks_solver = genelpa + +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 = +436 + sender_size = +436 + last sender_buffer = +0.001095 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000259 + + Density error is +0.008284286772 + + charge density convergence is achieved + final etot is -466.698298260896 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 -0.42153194 +0.47800345 -0.60266923 + H2 +0.26521496 +0.07640708 -0.96382431 + O1 +0.15631698 -0.55441053 +1.56649354 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + -0.091192 +0.052077 +0.020743 + +0.052077 -0.012621 -0.137197 + +0.020743 -0.137197 +0.376312 + + ------------------------------------------- + STEP OF MOLECULAR DYNAMICS : 10 + ------------------------------------------- + +output Pressure for check! +Virtual Pressure is +0.118981 Kbar +Virial Term is +0.090833 Kbar +Kenetic Term is +0.028148 Kbar + + + ><><><><><><><><><><><><><><><><><><><><><>< + + MD STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + -0.049247 +0.041841 +0.026216 + +0.041841 +0.006782 -0.157984 + +0.026216 -0.157984 +0.399408 + nloc = +144 + searching radius is (Bohr)) = +16.010000 + searching radius unit is (Bohr)) = +1.000000 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +12 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +11 + pnum = +2 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +12 + pnum = +3 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +11 +receiver_size is +529 ; receiver_size of each process is: ++144 +132 +132 +121 +sender_size is +436 ; sender_size of each process is: ++144 +144 +144 +4 + gamma_only_local = +1 + + LCAO ALGORITHM ------------- MD = 12 ELEC = 1 -------------------------------- + +temp variables are deleted + +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 + start solver, ks_solver = genelpa + +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 = +436 + sender_size = +436 + last sender_buffer = +0.001068 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000260 + + Density error is +0.013857092147 + + LCAO ALGORITHM ------------- MD = 12 ELEC = 2 -------------------------------- + +temp variables are deleted + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + start solver, ks_solver = genelpa + +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 = +436 + sender_size = +436 + last sender_buffer = +0.001085 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000261 + + Density error is +0.001589448966 + + charge density convergence is achieved + final etot is -466.703909676999 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 -0.28674705 +0.32257779 -0.39663257 + H2 +0.02955609 +0.25720918 -0.94465129 + O1 +0.25719096 -0.57978697 +1.34128386 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + -0.102767 +0.057764 +0.030039 + +0.057764 -0.014383 -0.144341 + +0.030039 -0.144341 +0.373965 + nloc = +144 + searching radius is (Bohr)) = +16.010000 + searching radius unit is (Bohr)) = +1.000000 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +12 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +11 + pnum = +2 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +12 + pnum = +3 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +11 +receiver_size is +529 ; receiver_size of each process is: ++144 +132 +132 +121 +sender_size is +436 ; sender_size of each process is: ++144 +144 +144 +4 + gamma_only_local = +1 + + LCAO ALGORITHM ------------- MD = 13 ELEC = 1 -------------------------------- + +temp variables are deleted + +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 + start solver, ks_solver = genelpa + +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 = +436 + sender_size = +436 + last sender_buffer = +0.001077 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000262 + + Density error is +0.002070240779 + + charge density convergence is achieved + final etot is -466.704036345606 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 -0.32428699 +0.29359387 -0.24641838 + H2 -0.12773856 +0.34751550 -0.88532823 + O1 +0.45202555 -0.64110937 +1.13174660 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + -0.129688 +0.076052 +0.035709 + +0.076052 -0.026981 -0.146605 + +0.035709 -0.146605 +0.363477 + nloc = +144 + searching radius is (Bohr)) = +16.010000 + searching radius unit is (Bohr)) = +1.000000 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +12 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +11 + pnum = +2 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +12 + pnum = +3 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +11 +receiver_size is +529 ; receiver_size of each process is: ++144 +132 +132 +121 +sender_size is +436 ; sender_size of each process is: ++144 +144 +144 +4 + gamma_only_local = +1 + + LCAO ALGORITHM ------------- MD = 14 ELEC = 1 -------------------------------- + +temp variables are deleted + +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 + start solver, ks_solver = genelpa + +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 = +436 + sender_size = +436 + last sender_buffer = +0.001080 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000264 + + Density error is +0.004359931704 + + charge density convergence is achieved + final etot is -466.702852817573 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 -0.55904989 +0.52796169 -0.41105586 + H2 +0.19505420 +0.09971169 -0.84000299 + O1 +0.36399569 -0.62767338 +1.25105885 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + -0.195852 +0.127521 +0.029560 + +0.127521 -0.069558 -0.132591 + +0.029560 -0.132591 +0.330830 + nloc = +144 + searching radius is (Bohr)) = +16.010000 + searching radius unit is (Bohr)) = +1.000000 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +12 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +11 + pnum = +2 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +12 + pnum = +3 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +11 +receiver_size is +529 ; receiver_size of each process is: ++144 +132 +132 +121 +sender_size is +436 ; sender_size of each process is: ++144 +144 +144 +4 + gamma_only_local = +1 + + LCAO ALGORITHM ------------- MD = 15 ELEC = 1 -------------------------------- + +temp variables are deleted + +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 + start solver, ks_solver = genelpa + +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 = +436 + sender_size = +436 + last sender_buffer = +0.001065 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000265 + + Density error is +0.006891676295 + + charge density convergence is achieved + final etot is -466.700543051512 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 -0.34568768 +0.25462803 -0.05926056 + H2 -0.26550846 +0.43144795 -0.80103265 + O1 +0.61119614 -0.68607598 +0.86029320 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + -0.187581 +0.117448 +0.041239 + +0.117448 -0.058254 -0.143489 + +0.041239 -0.143489 +0.334349 + nloc = +144 + searching radius is (Bohr)) = +16.010000 + searching radius unit is (Bohr)) = +1.000000 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +12 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +11 + pnum = +2 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +12 + pnum = +3 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +11 +receiver_size is +529 ; receiver_size of each process is: ++144 +132 +132 +121 +sender_size is +436 ; sender_size of each process is: ++144 +144 +144 +4 + gamma_only_local = +1 + + LCAO ALGORITHM ------------- MD = 16 ELEC = 1 -------------------------------- + +temp variables are deleted + +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 + start solver, ks_solver = genelpa + +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 = +436 + sender_size = +436 + last sender_buffer = +0.001081 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000268 + + Density error is +0.013146435036 + + LCAO ALGORITHM ------------- MD = 16 ELEC = 2 -------------------------------- + +temp variables are deleted + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + start solver, ks_solver = genelpa + +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 = +436 + sender_size = +436 + last sender_buffer = +0.001066 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000268 + + Density error is +0.001586984246 + + charge density convergence is achieved + final etot is -466.703646638347 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 -0.54319860 +0.45716115 -0.20682151 + H2 +0.02270964 +0.21154904 -0.75898021 + O1 +0.52048896 -0.66871019 +0.96580172 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + -0.247918 +0.164911 +0.034034 + +0.164911 -0.098300 -0.128317 + +0.034034 -0.128317 +0.301503 + + ------------------------------------------- + STEP OF MOLECULAR DYNAMICS : 15 + ------------------------------------------- + +output Pressure for check! +Virtual Pressure is +0.012883 Kbar +Virial Term is -0.014905 Kbar +Kenetic Term is +0.027788 Kbar + + + ><><><><><><><><><><><><><><><><><><><><><>< + + MD STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + -0.210636 +0.159462 +0.032546 + +0.159462 -0.080357 -0.150043 + +0.032546 -0.150043 +0.329644 + nloc = +144 + searching radius is (Bohr)) = +16.010000 + searching radius unit is (Bohr)) = +1.000000 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +12 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +11 + pnum = +2 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +12 + pnum = +3 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +11 +receiver_size is +529 ; receiver_size of each process is: ++144 +132 +132 +121 +sender_size is +436 ; sender_size of each process is: ++144 +144 +144 +4 + gamma_only_local = +1 + + LCAO ALGORITHM ------------- MD = 17 ELEC = 1 -------------------------------- + +temp variables are deleted + +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 + start solver, ks_solver = genelpa + +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 = +436 + sender_size = +436 + last sender_buffer = +0.001067 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000269 + + Density error is +0.003632561369 + + charge density convergence is achieved + final etot is -466.702235890628 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 -0.80094970 +0.67278361 -0.30718791 + H2 +0.24366564 +0.00932187 -0.67175682 + O1 +0.55728406 -0.68210548 +0.97894473 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + -0.307521 +0.211953 +0.026554 + +0.211953 -0.138106 -0.113019 + +0.026554 -0.113019 +0.268271 + nloc = +144 + searching radius is (Bohr)) = +16.010000 + searching radius unit is (Bohr)) = +1.000000 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +12 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +11 + pnum = +2 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +12 + pnum = +3 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +11 +receiver_size is +529 ; receiver_size of each process is: ++144 +132 +132 +121 +sender_size is +436 ; sender_size of each process is: ++144 +144 +144 +4 + gamma_only_local = +1 + + LCAO ALGORITHM ------------- MD = 18 ELEC = 1 -------------------------------- + +temp variables are deleted + +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 + start solver, ks_solver = genelpa + +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 = +436 + sender_size = +436 + last sender_buffer = +0.001054 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000271 + + Density error is +0.005595449442 + + charge density convergence is achieved + final etot is -466.700163595798 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 -0.59763214 +0.43904849 -0.03472448 + H2 -0.09248416 +0.25763720 -0.63673302 + O1 +0.69011630 -0.69668569 +0.67145750 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + -0.303840 +0.206886 +0.033204 + +0.206886 -0.132651 -0.117370 + +0.033204 -0.117370 +0.264195 + nloc = +144 + searching radius is (Bohr)) = +16.010000 + searching radius unit is (Bohr)) = +1.000000 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +12 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +11 + pnum = +2 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +12 + pnum = +3 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +11 +receiver_size is +529 ; receiver_size of each process is: ++144 +132 +132 +121 +sender_size is +436 ; sender_size of each process is: ++144 +144 +144 +4 + gamma_only_local = +1 + + LCAO ALGORITHM ------------- MD = 19 ELEC = 1 -------------------------------- + +temp variables are deleted + +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 + start solver, ks_solver = genelpa + +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 = +436 + sender_size = +436 + last sender_buffer = +0.001066 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000273 + + Density error is +0.010881139789 + + LCAO ALGORITHM ------------- MD = 19 ELEC = 2 -------------------------------- + +temp variables are deleted + vlocal data are put in sender_buffer, size(M): = +0 + vlocal data are exchanged, received size(M): = +0 + start solver, ks_solver = genelpa + +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 = +436 + sender_size = +436 + last sender_buffer = +0.001054 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000273 + + Density error is +0.001371997750 + + charge density convergence is achieved + final etot is -466.701537327762 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 -0.77301593 +0.61134487 -0.14930516 + H2 +0.13253222 +0.07664781 -0.58340174 + O1 +0.64048370 -0.68799268 +0.73270691 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + -0.355835 +0.248594 +0.024707 + +0.248594 -0.169021 -0.100853 + +0.024707 -0.100853 +0.231354 + nloc = +144 + searching radius is (Bohr)) = +16.010000 + searching radius unit is (Bohr)) = +1.000000 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +12 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +11 + pnum = +2 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +12 + pnum = +3 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +11 +receiver_size is +529 ; receiver_size of each process is: ++144 +132 +132 +121 +sender_size is +436 ; sender_size of each process is: ++144 +144 +144 +4 + gamma_only_local = +1 + + LCAO ALGORITHM ------------- MD = 20 ELEC = 1 -------------------------------- + +temp variables are deleted + +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 + start solver, ks_solver = genelpa + +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 = +436 + sender_size = +436 + last sender_buffer = +0.001054 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000275 + + Density error is +0.003244323553 + + charge density convergence is achieved + final etot is -466.699800890155 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 -0.98747030 +0.79286130 -0.23966801 + H2 +0.33571389 -0.11433771 -0.49025776 + O1 +0.65175640 -0.67852359 +0.72992577 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + -0.407715 +0.290577 +0.015274 + +0.290577 -0.205965 -0.083362 + +0.015274 -0.083362 +0.197294 + nloc = +144 + searching radius is (Bohr)) = +16.010000 + searching radius unit is (Bohr)) = +1.000000 + enter setAlltoallvParameter, nblk = +1 +checkpoint 2 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +12 + nCol_in_proc = +12 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +12 + nCol_in_proc = +11 + pnum = +2 + prow = +1 + pcol = +0 + nRow_in_proc = +11 + nCol_in_proc = +12 + pnum = +3 + prow = +1 + pcol = +1 + nRow_in_proc = +11 + nCol_in_proc = +11 +receiver_size is +529 ; receiver_size of each process is: ++144 +132 +132 +121 +sender_size is +436 ; sender_size of each process is: ++144 +144 +144 +4 + gamma_only_local = +1 + + LCAO ALGORITHM ------------- MD = 21 ELEC = 1 -------------------------------- + +temp variables are deleted + +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 + start solver, ks_solver = genelpa + +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 = +436 + sender_size = +436 + last sender_buffer = +0.001042 + number of non-zero elements in receiver_buffer = +529 + receiver_size = +529 + last receiver_buffer = +0.000277 + + Density error is +0.004953382147 + + charge density convergence is achieved + final etot is -466.697608297566 eV + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 -0.81232991 +0.58791846 +0.00094132 + H2 +0.03982643 +0.10078573 -0.45016602 + O1 +0.77250348 -0.68870419 +0.44922470 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + -0.404278 +0.286671 +0.018904 + +0.286671 -0.202682 -0.083866 + +0.018904 -0.083866 +0.189109 + + ------------------------------------------- + STEP OF MOLECULAR DYNAMICS : 20 + ------------------------------------------- + +output Pressure for check! +Virtual Pressure is -0.113167 Kbar +Virial Term is -0.139283 Kbar +Kenetic Term is +0.026116 Kbar + + + ><><><><><><><><><><><><><><><><><><><><><>< + + MD STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + -0.373570 +0.287440 +0.010819 + +0.287440 -0.188168 -0.105266 + +0.010819 -0.105266 +0.222236 + + + -------------------------------------------- + !FINAL_ETOT_IS -466.6976082975657505 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total +132.35550 11 +12.03 +100.00% + Run_lcao lcao_line +132.33977 1 +132.34 +99.99% + PW_Basis gen_pw +1.16916 1 +1.17 +0.88% + PW_complement get_total_pw +0.11398 10 +0.01 +0.09% + PW_complement setup_GVectors +0.25635 10 +0.03 +0.19% + mymath heapsort +0.20875 10 +0.02 +0.16% + PW_Basis setup_struc_factor +0.47204 21 +0.02 +0.36% + ORB_control read_orb_first +0.12504 1 +0.13 +0.09% + LCAO_Orbitals Read_Orbitals +0.12504 1 +0.13 +0.09% + ORB_control set_orb_tables +1.21148 1 +1.21 +0.92% + ORB_gen_tables gen_tables +1.21148 1 +1.21 +0.92% + ORB_table_phi init_Table +0.71243 1 +0.71 +0.54% + ORB_table_phi cal_ST_Phi12_R +0.70420 126 +0.01 +0.53% + ORB_table_beta init_Table_Beta +0.30461 1 +0.30 +0.23% + ORB_table_beta VNL_PhiBeta_R +0.30229 56 +0.01 +0.23% + Potential init_pot +24.59861 42 +0.59 +18.59% + Potential set_local_pot +1.80187 42 +0.04 +1.36% + FFT FFT3D +39.89220 1316 +0.03 +30.14% + Charge atomic_rho +3.11639 41 +0.08 +2.35% + Potential v_of_rho +36.45681 69 +0.53 +27.54% + XC_Functional v_xc +39.40750 90 +0.44 +29.77% + H_Hartree_pw v_hartree +5.69526 69 +0.08 +4.30% + Potential set_vr_eff +0.22940 69 +0.00 +0.17% + Run_MD_LCAO opt_ions +128.93060 1 +128.93 +97.41% + NVT_NHC setup +8.70219 1 +8.70 +6.57% + MD_func force_stress +63.15373 11 +5.74 +47.72% + LOOP_elec solve_elec_stru +30.69312 21 +1.46 +23.19% + LOOP_elec set_matrix_grid +1.76637 21 +0.08 +1.33% + Grid_Technique init +1.76335 21 +0.08 +1.33% + Grid_BigCellgrid_expansion_index +1.39932 42 +0.03 +1.06% + LOOP_elec solver +28.90742 21 +1.38 +21.84% + ELEC_scf scf +28.90729 21 +1.38 +21.84% + H_Ewald_pw compute_ewald +0.21927 21 +0.01 +0.17% + ELEC_cband_gamma cal_bands +5.01029 27 +0.19 +3.79% + LCAO_Hamilt cal_Hgamma +4.88214 27 +0.18 +3.69% + Gint_Gamma cal_vlocal +4.88196 27 +0.18 +3.69% + Gint_Gamma gamma_vlocal +3.34387 27 +0.12 +2.53% + Local_Orbital_Cha sum_bands +6.29288 27 +0.23 +4.75% + Gint_Gamma cal_rho +6.22736 27 +0.23 +4.71% + Gint_Gamma gamma_charge +6.22723 27 +0.23 +4.70% + Gint_Gamma reduce_charge +1.93070 27 +0.07 +1.46% + Charge mix_rho +2.62751 27 +0.10 +1.99% + Force_Stress_LCAO getForceStress +82.70782 21 +3.94 +62.49% + Forces cal_force_loc +1.64530 21 +0.08 +1.24% + Forces cal_force_ew +0.76779 21 +0.04 +0.58% + Stress_Func stress_loc +2.86125 21 +0.14 +2.16% + Stress_Func stress_har +2.01964 21 +0.10 +1.53% + Stress_Func stress_ew +1.07900 21 +0.05 +0.82% + Stress_Func stress_gga +4.78231 21 +0.23 +3.61% + Force_LCAO_gamma ftable_gamma +56.46509 21 +2.69 +42.66% + Force_LCAO_gamma cal_fvl_dphi +56.40976 21 +2.69 +42.62% + Gint_Gamma cal_force +44.33796 21 +2.11 +33.50% + Gint_Gamma gamma_force +26.79047 21 +1.28 +20.24% + Gint_Gamma gamma_force_wait +17.53623 21 +0.84 +13.25% + MD_func md_force_stress +60.66036 11 +5.51 +45.83% + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + +1374.8320 + ORB_table_phi Jl(x) +97.8037 + Charge_Pulay Rrho +32.0000 + Charge_Pulay dRrho +28.0000 + Charge_Pulay drho +28.0000 + Use_FFT porter +8.0000 + PW_Basis struc_fac +7.9969 + Grid_Meshcell index2normal +4.1684 + Grid_Meshcell index2ucell +4.1684 + Charge rho +4.0000 + Charge rho_save +4.0000 + Charge rho_core +4.0000 + Potential vltot +4.0000 + Potential vr +4.0000 + Potential vr_eff +4.0000 + Potential vr_eff1 +4.0000 + Potential vnew +4.0000 + Charge_Pulay rho_save2 +4.0000 + ORB_table_phi Table_SR&TR +3.2158 + Charge rhog +1.9992 + Charge rhog_save +1.9992 + Charge kin_r +1.9992 + Charge kin_r_save +1.9992 + Charge rhog_core +1.9992 + ORB_table_beta Table_NR +1.0437 + ---------------------------------------------------------- + + Start Time : Wed Apr 13 14:58:14 2022 + Finish Time : Wed Apr 13 15:00:27 2022 + Total Time : 0 h 2 mins 13 secs diff --git a/tests/abacus.md/OUT.autotest/STRU_READIN_ADJUST.cif b/tests/abacus.md/OUT.autotest/STRU_READIN_ADJUST.cif deleted file mode 100644 index 24779f6c..00000000 --- a/tests/abacus.md/OUT.autotest/STRU_READIN_ADJUST.cif +++ /dev/null @@ -1,21 +0,0 @@ -data_test - -_audit_creation_method generated by ABACUS - -_cell_length_a 3.81668 -_cell_length_b 3.81668 -_cell_length_c 3.81668 -_cell_angle_alpha 60 -_cell_angle_beta 60 -_cell_angle_gamma 60 - -_symmetry_space_group_name_H-M -_symmetry_Int_Tables_number - -loop_ -_atom_site_label -_atom_site_fract_x -_atom_site_fract_y -_atom_site_fract_z -Si 0 0 0 -Si 0.245 0.237 0.265 diff --git a/tests/abacus.md/OUT.autotest/md_pos_1.cif b/tests/abacus.md/OUT.autotest/md_pos_1.cif deleted file mode 100644 index 832aaef0..00000000 --- a/tests/abacus.md/OUT.autotest/md_pos_1.cif +++ /dev/null @@ -1,21 +0,0 @@ -data_test - -_audit_creation_method generated by ABACUS - -_cell_length_a 3.81668 -_cell_length_b 3.81668 -_cell_length_c 3.81668 -_cell_angle_alpha 60 -_cell_angle_beta 60 -_cell_angle_gamma 60 - -_symmetry_space_group_name_H-M -_symmetry_Int_Tables_number - -loop_ -_atom_site_label -_atom_site_fract_x -_atom_site_fract_y -_atom_site_fract_z -Si 0.00106888 0.99849 0.000247409 -Si 0.245535 0.237394 0.262886 diff --git a/tests/abacus.md/OUT.autotest/md_pos_10.cif b/tests/abacus.md/OUT.autotest/md_pos_10.cif deleted file mode 100644 index a7546cea..00000000 --- a/tests/abacus.md/OUT.autotest/md_pos_10.cif +++ /dev/null @@ -1,21 +0,0 @@ -data_test - -_audit_creation_method generated by ABACUS - -_cell_length_a 3.81668 -_cell_length_b 3.81668 -_cell_length_c 3.81668 -_cell_angle_alpha 60 -_cell_angle_beta 60 -_cell_angle_gamma 60 - -_symmetry_space_group_name_H-M -_symmetry_Int_Tables_number - -loop_ -_atom_site_label -_atom_site_fract_x -_atom_site_fract_y -_atom_site_fract_z -Si 0.00711478 0.993904 0.9916 -Si 0.253316 0.23197 0.255312 diff --git a/tests/abacus.md/OUT.autotest/md_pos_15.cif b/tests/abacus.md/OUT.autotest/md_pos_15.cif deleted file mode 100644 index 51f15b4e..00000000 --- a/tests/abacus.md/OUT.autotest/md_pos_15.cif +++ /dev/null @@ -1,21 +0,0 @@ -data_test - -_audit_creation_method generated by ABACUS - -_cell_length_a 3.81668 -_cell_length_b 3.81668 -_cell_length_c 3.81668 -_cell_angle_alpha 60 -_cell_angle_beta 60 -_cell_angle_gamma 60 - -_symmetry_space_group_name_H-M -_symmetry_Int_Tables_number - -loop_ -_atom_site_label -_atom_site_fract_x -_atom_site_fract_y -_atom_site_fract_z -Si 0.00722617 0.979891 0.000667301 -Si 0.260608 0.240666 0.237553 diff --git a/tests/abacus.md/OUT.autotest/md_pos_20.cif b/tests/abacus.md/OUT.autotest/md_pos_20.cif deleted file mode 100644 index 3d01862a..00000000 --- a/tests/abacus.md/OUT.autotest/md_pos_20.cif +++ /dev/null @@ -1,21 +0,0 @@ -data_test - -_audit_creation_method generated by ABACUS - -_cell_length_a 3.81668 -_cell_length_b 3.81668 -_cell_length_c 3.81668 -_cell_angle_alpha 60 -_cell_angle_beta 60 -_cell_angle_gamma 60 - -_symmetry_space_group_name_H-M -_symmetry_Int_Tables_number - -loop_ -_atom_site_label -_atom_site_fract_x -_atom_site_fract_y -_atom_site_fract_z -Si 0.0136053 0.987589 0.984304 -Si 0.261345 0.227707 0.245529 diff --git a/tests/abacus.md/OUT.autotest/md_pos_5.cif b/tests/abacus.md/OUT.autotest/md_pos_5.cif deleted file mode 100644 index b35b1102..00000000 --- a/tests/abacus.md/OUT.autotest/md_pos_5.cif +++ /dev/null @@ -1,21 +0,0 @@ -data_test - -_audit_creation_method generated by ABACUS - -_cell_length_a 3.81668 -_cell_length_b 3.81668 -_cell_length_c 3.81668 -_cell_angle_alpha 60 -_cell_angle_beta 60 -_cell_angle_gamma 60 - -_symmetry_space_group_name_H-M -_symmetry_Int_Tables_number - -loop_ -_atom_site_label -_atom_site_fract_x -_atom_site_fract_y -_atom_site_fract_z -Si 0.999048 0.984501 0.010401 -Si 0.2538 0.246892 0.24541 diff --git a/tests/abacus.md/OUT.autotest/running_md.log b/tests/abacus.md/OUT.autotest/running_md.log deleted file mode 100644 index 16f46050..00000000 --- a/tests/abacus.md/OUT.autotest/running_md.log +++ /dev/null @@ -1,2608 +0,0 @@ - - WELCOME TO ABACUS - - 'Atomic-orbital Based Ab-initio Computation at UStc' - - Website: http://abacus.ustc.edu.cn/ - - Version: Parallel, in development - Processor Number is 1 - Start Time is Fri Oct 15 14:37:16 2021 - - ------------------------------------------------------------------------------------ - - READING GENERAL INFORMATION - global_out_dir = OUT.autotest/ - global_in_card = INPUT - pseudo_dir = ./ - orbital_dir = ./ - pseudo_type = auto - DRANK = 1 - DSIZE = 1 - DCOLOR = 1 - GRANK = 1 - GSIZE = 1 - - - - - >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - | | - | 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 = 1 - atom label for species 1 = Si - lattice constant (Bohr) = 10.2 - lattice constant (Angstrom) = 5.39761 - - READING ATOM TYPE 1 - atom label = Si - L=0, number of zeta = 1 - L=1, number of zeta = 1 - L=2, number of zeta = 1 - number of atom for this type = 2 - start magnetization = FALSE - start magnetization = FALSE - - TOTAL ATOM NUMBER = 2 - - CARTESIAN COORDINATES ( UNIT = 10.2 Bohr ). - atom x y z mag vx vy vz - tauc_Si1 0 0 0 0 0 0 0 - tauc_Si2 0.241 0.255 0.250999999999 0 0 0 0 - - - Volume (Bohr^3) = 265.302 - Volume (A^3) = 39.3136533177 - - Lattice vectors: (Cartesian coordinate: in unit of a_0) - +0.5 +0.5 +0 - +0.5 +0 +0.5 - +0 +0.5 +0.5 - Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) - +1 +1 -1 - +1 -1 +1 - -1 +1 +1 - - - - - >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - | | - | 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 ./Si_ONCV_PBE-1.0.upf - pseudopotential type = NC - functional Ex = PBE - functional Ec = - functional GCEx = - functional GCEc = - nonlocal core correction = 0 - valence electrons = 4 - 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 - initial pseudo atomic orbital number = 0 - NLOCAL = 18 - - SETUP THE ELECTRONS NUMBER - electron number of element Si = 4 - total electron number of element Si = 8 - occupied bands = 4 - NBANDS = 8 - DONE : SETUP UNITCELL Time : 0.0648149461485 (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 = 8 - - KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT - 1 0 0 0 0.125 - 2 0.5 0 0 0.125 - 3 0 0.5 0 0.125 - 4 0.5 0.5 0 0.125 - 5 0 0 0.5 0.125 - 6 0.5 0 0.5 0.125 - 7 0 0.5 0.5 0.125 - 8 0.5 0.5 0.5 0.125 - - k-point number in this process = 8 - minimum distributed K point number = 8 - - KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT - 1 0 0 0 0.25 - 2 0.5 0.5 -0.5 0.25 - 3 0.5 -0.5 0.5 0.25 - 4 1 0 0 0.25 - 5 -0.5 0.5 0.5 0.25 - 6 0 1 0 0.25 - 7 0 0 1 0.25 - 8 0.5 0.5 0.5 0.25 - - KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT - 1 0 0 0 0.25 - 2 0.5 0 0 0.25 - 3 0 0.5 0 0.25 - 4 0.5 0.5 0 0.25 - 5 0 0 0.5 0.25 - 6 0.5 0 0.5 0.25 - 7 0 0.5 0.5 0.25 - 8 0.5 0.5 0.5 0.25 - DONE : INIT K-POINTS Time : 0.0652149026282 (SEC) - - - - - - >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - | | - | Setup plane waves: | - | 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. | - | | - <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< - - - - - - SETUP THE PLANE WAVE BASIS - energy cutoff for wavefunc (unit:Ry) = 20 - [fft grid for wave functions] = 24, 24, 24 - [fft grid for charge/potential] = 24, 24, 24 - [fft grid division] = 1, 1, 1 - [big fft grid for charge/potential] = 24, 24, 24 - nbxx = 13824 - nrxx = 13824 - - SETUP PLANE WAVES FOR CHARGE/POTENTIAL - number of plane waves = 3143 - number of sticks = 283 - - SETUP PLANE WAVES FOR WAVE FUNCTIONS - number of plane waves = 609 - number of sticks = 91 - - PARALLEL PW FOR CHARGE/POTENTIAL - PROC COLUMNS(POT) PW - 1 283 3143 - --------------- sum ------------------- - 1 283 3143 - - PARALLEL PW FOR WAVE FUNCTIONS - PROC COLUMNS(W) PW - 1 91 609 - --------------- sum ------------------- - 1 91 609 - - SETUP COORDINATES OF PLANE WAVES - number of total plane waves = 3143 - - SETUP COORDINATES OF PLANE WAVES - number of |g| = 72 - max |g| = 208 - min |g| = 0 - DONE : INIT PLANEWAVE Time : 0.0986429497134 (SEC) - - npwx = 411 - - SETUP NONLOCAL PSEUDOPOTENTIALS IN PLANE WAVE BASIS - Si non-local projectors: - projector 1 L=0 - projector 2 L=0 - projector 3 L=1 - projector 4 L=1 - TOTAL NUMBER OF NONLOCAL PROJECTORS = 16 - DONE : LOCAL POTENTIAL Time : 0.109992648242 (SEC) - - - Init Non-Local PseudoPotential table : - Init Non-Local-Pseudopotential done. - DONE : NON-LOCAL POTENTIAL Time : 0.122797146207 (SEC) - - start_pot = atomic - DONE : INIT POTENTIAL Time : 0.135785 (SEC) - - - Make real space PAO into reciprocal space. - max mesh points in Pseudopotential = 601 - dq(describe PAO in reciprocal space) = 0.01 - max q = 542 - - number of pseudo atomic orbitals for Si is 0 - DONE : INIT BASIS Time : 0.184089 (SEC) - - ...............Nose-Hoover Chain parameter initialization............... - Temperature = 3.16682e-05 - Temperature2 = 10.0004 - NHC frequency = 0.00120944 - NHC chain = 4 - Qmass = 1823.61 - ............................................................... - - PW ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- - K-point CG iter num Time(Sec) - 1 6.125000 0.314119 - 2 6.500000 0.327905 - 3 6.750000 0.334448 - 4 6.125000 0.309547 - 5 6.750000 0.112520 - 6 6.125000 0.024925 - 7 5.875000 0.024036 - 8 6.250000 0.025291 - - Density error is 0.108050841230 - - PW ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- - K-point CG iter num Time(Sec) - 1 2.500000 0.012342 - 2 2.250000 0.011339 - 3 2.625000 0.012621 - 4 3.250000 0.014770 - 5 2.500000 0.012183 - 6 3.125000 0.014333 - 7 2.125000 0.010831 - 8 2.625000 0.012575 - - Density error is 0.004334778560 - - PW ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- - K-point CG iter num Time(Sec) - 1 3.375000 0.015399 - 2 3.250000 0.014874 - 3 3.125000 0.014380 - 4 4.000000 0.017413 - 5 3.250000 0.014776 - 6 4.000000 0.017425 - 7 3.750000 0.016523 - 8 2.875000 0.013438 - - Density error is 0.000134739187 - - PW ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- - K-point CG iter num Time(Sec) - 1 3.750000 0.016717 - 2 3.250000 0.014854 - 3 3.375000 0.015229 - 4 4.000000 0.017399 - 5 3.500000 0.015669 - 6 4.000000 0.017380 - 7 4.500000 0.019148 - 8 3.375000 0.015188 - - Density error is 0.000014649703 - - PW ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- - K-point CG iter num Time(Sec) - 1 2.750000 0.013183 - 2 2.625000 0.012728 - 3 2.750000 0.013067 - 4 2.750000 0.013018 - 5 2.875000 0.013453 - 6 2.750000 0.013008 - 7 2.625000 0.012593 - 8 2.625000 0.012567 - - Density error is 0.000000599415 - - PW ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- - K-point CG iter num Time(Sec) - 1 3.125000 0.014489 - 2 3.625000 0.016131 - 3 3.250000 0.014781 - 4 4.375000 0.018739 - 5 3.375000 0.015250 - 6 4.000000 0.017425 - 7 4.250000 0.018253 - 8 3.375000 0.015213 - - Density error is 0.000000048534 - - PW ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- - K-point CG iter num Time(Sec) - 1 3.250000 0.015027 - 2 3.000000 0.013998 - 3 3.125000 0.014375 - 4 3.625000 0.016117 - 5 3.000000 0.013941 - 6 4.125000 0.017842 - 7 3.500000 0.015638 - 8 3.125000 0.014323 - - Density error is 0.000000002823 - - PW ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- - K-point CG iter num Time(Sec) - 1 3.500000 0.015909 - 2 3.125000 0.014437 - 3 3.000000 0.013954 - 4 3.500000 0.015692 - 5 3.250000 0.014873 - 6 3.250000 0.014791 - 7 3.375000 0.015237 - 8 3.125000 0.014335 - - Density error is 0.000000000061 - - charge density convergence is achieved - final etot is -211.771832657158 eV - - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - Si1 -0.885363 +0.500467 +0.150240 - Si2 +0.885363 -0.500467 -0.150240 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +123.045273 -3.807537 -13.541448 - -3.807537 +124.421298 +24.047975 - -13.541448 +24.047975 +125.016023 - -output Pressure for check! -Virtual Pressure is +124.231102 Kbar -Virial is +124.160865 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 1 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -15.564005 (Rydberg) - NVT Temperature : +10.000364 (K) - NVT Kinetic energy : +0.000190 (Rydberg) - NVT Potential energy : -15.564937 (Rydberg) - maxForce : +0.000400 - maxStep : +0.012800 - MD_STEP SystemE Conserved DeltaE Temperature - +1 -7.782469 -7.782003 +0.000000 +14.311776 - - PW ALGORITHM --------------- ION=+2 ELEC=+1 -------------------------------- - K-point CG iter num Time(Sec) - +1 +34.500000 +1.482434 - +2 +24.125000 +0.314735 - +3 +24.250000 +0.087904 - +4 +27.625000 +0.099392 - +5 +25.000000 +0.090634 - +6 +29.875000 +0.107431 - +7 +31.875000 +0.113921 - +8 +26.750000 +0.096067 - - Density error is +0.000008438536 - - PW ALGORITHM --------------- ION=+2 ELEC=+2 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.000000 +0.010623 - +2 +2.000000 +0.010501 - +3 +2.000000 +0.010437 - +4 +2.000000 +0.010430 - +5 +2.000000 +0.010417 - +6 +2.000000 +0.010392 - +7 +2.000000 +0.010413 - +8 +2.000000 +0.010431 - - Density error is +0.000000589537 - - PW ALGORITHM --------------- ION=+2 ELEC=+3 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.375000 +0.011909 - +2 +2.125000 +0.010960 - +3 +2.125000 +0.010853 - +4 +2.750000 +0.013046 - +5 +2.000000 +0.010421 - +6 +2.750000 +0.013030 - +7 +3.375000 +0.015237 - +8 +2.125000 +0.010850 - - Density error is +0.000000029687 - - PW ALGORITHM --------------- ION=+2 ELEC=+4 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.375000 +0.015446 - +2 +3.500000 +0.015794 - +3 +3.125000 +0.014440 - +4 +3.500000 +0.015678 - +5 +3.625000 +0.016125 - +6 +3.500000 +0.015643 - +7 +3.250000 +0.014765 - +8 +3.500000 +0.015638 - - Density error is +0.000000000296 - - charge density convergence is achieved - final etot is -211.778481425683 eV - - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - Si1 -0.815731 +0.355757 +0.109618 - Si2 +0.815731 -0.355757 -0.109618 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +122.843178 -2.800524 -9.609977 - -2.800524 +124.232437 +22.152784 - -9.609977 +22.152784 +124.529670 - -output Pressure for check! -Virtual Pressure is +123.968947 Kbar -Virial is +123.868428 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 2 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -15.564050 (Rydberg) - NVT Temperature : +33.255982 (K) - NVT Kinetic energy : +0.000632 (Rydberg) - NVT Potential energy : -15.565426 (Rydberg) - maxForce : +0.000304 - maxStep : +0.026509 - MD_STEP SystemE Conserved DeltaE Temperature - +2 -7.782713 -7.782025 +0.000000 +66.542608 - - PW ALGORITHM --------------- ION=+3 ELEC=+1 -------------------------------- - K-point CG iter num Time(Sec) - +1 +33.625000 +1.455297 - +2 +23.000000 +0.344287 - +3 +23.250000 +0.084591 - +4 +27.250000 +0.097961 - +5 +24.625000 +0.089419 - +6 +28.375000 +0.101985 - +7 +26.625000 +0.096635 - +8 +24.625000 +0.089249 - - Density error is +0.000021869323 - - PW ALGORITHM --------------- ION=+3 ELEC=+2 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.000000 +0.010696 - +2 +2.000000 +0.010427 - +3 +2.000000 +0.010429 - +4 +2.000000 +0.010408 - +5 +2.000000 +0.010427 - +6 +2.375000 +0.011750 - +7 +2.000000 +0.010404 - +8 +2.000000 +0.010397 - - Density error is +0.000001763699 - - PW ALGORITHM --------------- ION=+3 ELEC=+3 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.125000 +0.011012 - +2 +2.250000 +0.011394 - +3 +2.250000 +0.011290 - +4 +2.875000 +0.013481 - +5 +2.250000 +0.011358 - +6 +3.000000 +0.013927 - +7 +2.875000 +0.013486 - +8 +2.375000 +0.011717 - - Density error is +0.000000036065 - - PW ALGORITHM --------------- ION=+3 ELEC=+4 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.625000 +0.016348 - +2 +3.750000 +0.016579 - +3 +3.750000 +0.016547 - +4 +4.375000 +0.018704 - +5 +3.500000 +0.015695 - +6 +4.125000 +0.017849 - +7 +4.625000 +0.019620 - +8 +3.625000 +0.016087 - - Density error is +0.000000002244 - - PW ALGORITHM --------------- ION=+3 ELEC=+5 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.875000 +0.013691 - +2 +3.000000 +0.013966 - +3 +2.875000 +0.013492 - +4 +3.875000 +0.016984 - +5 +3.250000 +0.014831 - +6 +3.750000 +0.016559 - +7 +3.000000 +0.013909 - +8 +3.000000 +0.013880 - - Density error is +0.000000000184 - - charge density convergence is achieved - final etot is -211.794269556733 eV - - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - Si1 -0.462515 +0.083202 +0.018773 - Si2 +0.462515 -0.083202 -0.018773 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +122.815311 -0.492388 -2.246119 - -0.492388 +123.347654 +12.547878 - -2.246119 +12.547878 +123.364301 - -output Pressure for check! -Virtual Pressure is +123.643118 Kbar -Virial is +123.175755 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 3 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -15.564151 (Rydberg) - NVT Temperature : +88.343003 (K) - NVT Kinetic energy : +0.001679 (Rydberg) - NVT Potential energy : -15.566586 (Rydberg) - maxForce : +0.000084 - maxStep : +0.033756 - MD_STEP SystemE Conserved DeltaE Temperature - +3 -7.783293 -7.782076 +0.000000 +112.977290 - - PW ALGORITHM --------------- ION=+4 ELEC=+1 -------------------------------- - K-point CG iter num Time(Sec) - +1 +37.125000 +1.584397 - +2 +24.625000 +0.212187 - +3 +25.750000 +0.092986 - +4 +29.250000 +0.104765 - +5 +27.000000 +0.097458 - +6 +31.875000 +0.113833 - +7 +28.250000 +0.101426 - +8 +25.250000 +0.091166 - - Density error is +0.000033429323 - - PW ALGORITHM --------------- ION=+4 ELEC=+2 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.000000 +0.010606 - +2 +2.000000 +0.010470 - +3 +2.000000 +0.010394 - +4 +2.000000 +0.010391 - +5 +2.000000 +0.010403 - +6 +2.000000 +0.010374 - +7 +2.000000 +0.010374 - +8 +2.000000 +0.010432 - - Density error is +0.000002801781 - - PW ALGORITHM --------------- ION=+4 ELEC=+3 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.125000 +0.011027 - +2 +2.500000 +0.012197 - +3 +2.250000 +0.011338 - +4 +2.375000 +0.011707 - +5 +2.250000 +0.011301 - +6 +2.625000 +0.012578 - +7 +2.875000 +0.013474 - +8 +2.375000 +0.011758 - - Density error is +0.000000035628 - - PW ALGORITHM --------------- ION=+4 ELEC=+4 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.875000 +0.017185 - +2 +3.875000 +0.017012 - +3 +3.750000 +0.016533 - +4 +4.000000 +0.017359 - +5 +3.750000 +0.016991 - +6 +3.875000 +0.017340 - +7 +4.625000 +0.019603 - +8 +3.750000 +0.016469 - - Density error is +0.000000003655 - - PW ALGORITHM --------------- ION=+4 ELEC=+5 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.750000 +0.013239 - +2 +2.625000 +0.012645 - +3 +2.750000 +0.013035 - +4 +3.750000 +0.016496 - +5 +2.750000 +0.013016 - +6 +3.250000 +0.014762 - +7 +3.000000 +0.013915 - +8 +2.625000 +0.012541 - - Density error is +0.000000000196 - - charge density convergence is achieved - final etot is -211.798998994521 eV - - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - Si1 +0.045801 -0.211053 -0.052135 - Si2 -0.045801 +0.211053 +0.052135 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +123.007250 +1.421851 +5.725860 - +1.421851 +122.897686 -1.245212 - +5.725860 -1.245212 +123.005310 - -output Pressure for check! -Virtual Pressure is +123.763579 Kbar -Virial is +122.970082 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 4 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -15.564177 (Rydberg) - NVT Temperature : +103.974513 (K) - NVT Kinetic energy : +0.001976 (Rydberg) - NVT Potential energy : -15.566934 (Rydberg) - maxForce : +0.000019 - maxStep : +0.030839 - MD_STEP SystemE Conserved DeltaE Temperature - +4 -7.783467 -7.782089 +0.000000 +94.653093 - - PW ALGORITHM --------------- ION=+5 ELEC=+1 -------------------------------- - K-point CG iter num Time(Sec) - +1 +36.125000 +1.541803 - +2 +24.500000 +0.265063 - +3 +26.125000 +0.094359 - +4 +30.250000 +0.108286 - +5 +25.500000 +0.091682 - +6 +28.875000 +0.104719 - +7 +29.250000 +0.105021 - +8 +25.125000 +0.090821 - - Density error is +0.000028572302 - - PW ALGORITHM --------------- ION=+5 ELEC=+2 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.000000 +0.010595 - +2 +2.000000 +0.010418 - +3 +2.000000 +0.010451 - +4 +2.000000 +0.010412 - +5 +2.000000 +0.010426 - +6 +2.000000 +0.010384 - +7 +2.000000 +0.010373 - +8 +2.000000 +0.010418 - - Density error is +0.000002384066 - - PW ALGORITHM --------------- ION=+5 ELEC=+3 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.125000 +0.011011 - +2 +2.375000 +0.011743 - +3 +2.250000 +0.011317 - +4 +2.625000 +0.012578 - +5 +2.250000 +0.011279 - +6 +2.750000 +0.013007 - +7 +2.875000 +0.013443 - +8 +2.375000 +0.011684 - - Density error is +0.000000035575 - - PW ALGORITHM --------------- ION=+5 ELEC=+4 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.750000 +0.016778 - +2 +3.875000 +0.017042 - +3 +3.750000 +0.016539 - +4 +4.125000 +0.017849 - +5 +3.750000 +0.016577 - +6 +3.625000 +0.016055 - +7 +4.625000 +0.019602 - +8 +3.625000 +0.016048 - - Density error is +0.000000003086 - - PW ALGORITHM --------------- ION=+5 ELEC=+5 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.750000 +0.013198 - +2 +2.625000 +0.012687 - +3 +2.875000 +0.013502 - +4 +3.750000 +0.016536 - +5 +2.750000 +0.013120 - +6 +3.375000 +0.015253 - +7 +2.875000 +0.013430 - +8 +2.875000 +0.013424 - - Density error is +0.000000000189 - - charge density convergence is achieved - final etot is -211.787163106063 eV - - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - Si1 +0.531795 -0.423861 -0.074943 - Si2 -0.531795 +0.423861 +0.074943 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +123.156562 +2.191352 +11.539648 - +2.191352 +123.421604 -14.461358 - +11.539648 -14.461358 +123.871961 - -output Pressure for check! -Virtual Pressure is +124.148173 Kbar -Virial is +123.483375 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 5 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -15.564100 (Rydberg) - NVT Temperature : +61.015343 (K) - NVT Kinetic energy : +0.001159 (Rydberg) - NVT Potential energy : -15.566064 (Rydberg) - maxForce : +0.000177 - maxStep : +0.019294 - MD_STEP SystemE Conserved DeltaE Temperature - +5 -7.783032 -7.782050 +0.000000 +35.600513 - - PW ALGORITHM --------------- ION=+6 ELEC=+1 -------------------------------- - K-point CG iter num Time(Sec) - +1 +35.750000 +1.538779 - +2 +23.375000 +0.281560 - +3 +26.625000 +0.096030 - +4 +29.375000 +0.105067 - +5 +25.125000 +0.090691 - +6 +30.000000 +0.107285 - +7 +30.125000 +0.107224 - +8 +23.875000 +0.086308 - - Density error is +0.000013559050 - - PW ALGORITHM --------------- ION=+6 ELEC=+2 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.000000 +0.010587 - +2 +2.000000 +0.010411 - +3 +2.000000 +0.010387 - +4 +2.000000 +0.010385 - +5 +2.000000 +0.010401 - +6 +2.000000 +0.010372 - +7 +2.000000 +0.010373 - +8 +2.000000 +0.010387 - - Density error is +0.000001049378 - - PW ALGORITHM --------------- ION=+6 ELEC=+3 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.125000 +0.010993 - +2 +2.125000 +0.010884 - +3 +2.125000 +0.010912 - +4 +2.500000 +0.012157 - +5 +2.125000 +0.010852 - +6 +2.750000 +0.013010 - +7 +3.000000 +0.013908 - +8 +2.125000 +0.010824 - - Density error is +0.000000034124 - - PW ALGORITHM --------------- ION=+6 ELEC=+4 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.625000 +0.016280 - +2 +3.625000 +0.016107 - +3 +3.625000 +0.016126 - +4 +3.875000 +0.016930 - +5 +3.625000 +0.016102 - +6 +3.625000 +0.016047 - +7 +4.375000 +0.018675 - +8 +3.625000 +0.016036 - - Density error is +0.000000001047 - - PW ALGORITHM --------------- ION=+6 ELEC=+5 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.250000 +0.015029 - +2 +3.250000 +0.014818 - +3 +3.125000 +0.014333 - +4 +4.500000 +0.019099 - +5 +3.125000 +0.014369 - +6 +4.250000 +0.018282 - +7 +3.250000 +0.014734 - +8 +3.250000 +0.014725 - - Density error is +0.000000000093 - - charge density convergence is achieved - final etot is -211.773976096239 eV - - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - Si1 +0.830073 -0.488698 -0.076368 - Si2 -0.830073 +0.488698 +0.076368 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +123.079115 +2.349387 +13.341463 - +2.349387 +124.240376 -22.607891 - +13.341463 -22.607891 +124.847553 - -output Pressure for check! -Virtual Pressure is +124.305722 Kbar -Virial is +124.055681 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 6 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -15.564017 (Rydberg) - NVT Temperature : +13.869106 (K) - NVT Kinetic energy : +0.000264 (Rydberg) - NVT Potential energy : -15.565095 (Rydberg) - maxForce : +0.000353 - maxStep : +0.009591 - MD_STEP SystemE Conserved DeltaE Temperature - +6 -7.782547 -7.782009 +0.000000 +9.461554 - - PW ALGORITHM --------------- ION=+7 ELEC=+1 -------------------------------- - K-point CG iter num Time(Sec) - +1 +36.250000 +1.548029 - +2 +24.625000 +0.276619 - +3 +27.375000 +0.098665 - +4 +30.375000 +0.108527 - +5 +26.375000 +0.095093 - +6 +30.625000 +0.109686 - +7 +31.000000 +0.110332 - +8 +25.250000 +0.091074 - - Density error is +0.000006867857 - - PW ALGORITHM --------------- ION=+7 ELEC=+2 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.000000 +0.010576 - +2 +2.000000 +0.010440 - +3 +2.000000 +0.010510 - +4 +2.000000 +0.010413 - +5 +2.000000 +0.010403 - +6 +2.125000 +0.010838 - +7 +2.000000 +0.010376 - +8 +2.000000 +0.010387 - - Density error is +0.000000471169 - - PW ALGORITHM --------------- ION=+7 ELEC=+3 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.750000 +0.013211 - +2 +2.000000 +0.010520 - +3 +2.000000 +0.010489 - +4 +2.750000 +0.013013 - +5 +2.125000 +0.010843 - +6 +2.500000 +0.012183 - +7 +3.250000 +0.014821 - +8 +2.000000 +0.010417 - - Density error is +0.000000026949 - - PW ALGORITHM --------------- ION=+7 ELEC=+4 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.000000 +0.014095 - +2 +3.250000 +0.014863 - +3 +3.000000 +0.013942 - +4 +3.125000 +0.014354 - +5 +3.250000 +0.014813 - +6 +3.250000 +0.014752 - +7 +3.500000 +0.015640 - +8 +3.250000 +0.014764 - - Density error is +0.000000000178 - - charge density convergence is achieved - final etot is -211.775966500996 eV - - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - Si1 +0.841211 -0.388251 -0.083865 - Si2 -0.841211 +0.388251 +0.083865 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +122.888185 +2.498229 +10.607911 - +2.498229 +124.324706 -22.903208 - +10.607911 -22.903208 +124.699212 - -output Pressure for check! -Virtual Pressure is +124.037154 Kbar -Virial is +123.970701 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 7 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -15.564029 (Rydberg) - NVT Temperature : +20.830773 (K) - NVT Kinetic energy : +0.000396 (Rydberg) - NVT Potential energy : -15.565241 (Rydberg) - maxForce : +0.000327 - maxStep : +0.022260 - MD_STEP SystemE Conserved DeltaE Temperature - +7 -7.782620 -7.782015 +0.000000 +47.763680 - - PW ALGORITHM --------------- ION=+8 ELEC=+1 -------------------------------- - K-point CG iter num Time(Sec) - +1 +34.625000 +1.498024 - +2 +22.500000 +0.296778 - +3 +24.500000 +0.088638 - +4 +28.750000 +0.103008 - +5 +24.000000 +0.086877 - +6 +29.375000 +0.105138 - +7 +26.250000 +0.094433 - +8 +22.375000 +0.081172 - - Density error is +0.000016498376 - - PW ALGORITHM --------------- ION=+8 ELEC=+2 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.000000 +0.010574 - +2 +2.000000 +0.010443 - +3 +2.000000 +0.010379 - +4 +2.000000 +0.010399 - +5 +2.000000 +0.010420 - +6 +2.000000 +0.010425 - +7 +2.500000 +0.012164 - +8 +2.000000 +0.010416 - - Density error is +0.000001314992 - - PW ALGORITHM --------------- ION=+8 ELEC=+3 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.125000 +0.011051 - +2 +2.250000 +0.011345 - +3 +2.125000 +0.010869 - +4 +2.750000 +0.013016 - +5 +2.250000 +0.011286 - +6 +2.750000 +0.013011 - +7 +3.125000 +0.014347 - +8 +2.250000 +0.011259 - - Density error is +0.000000033932 - - PW ALGORITHM --------------- ION=+8 ELEC=+4 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.750000 +0.017140 - +2 +3.625000 +0.016310 - +3 +3.750000 +0.016631 - +4 +4.000000 +0.017495 - +5 +3.500000 +0.015705 - +6 +4.125000 +0.017878 - +7 +4.250000 +0.018300 - +8 +3.500000 +0.015635 - - Density error is +0.000000001483 - - PW ALGORITHM --------------- ION=+8 ELEC=+5 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.750000 +0.013210 - +2 +3.125000 +0.014428 - +3 +3.125000 +0.014340 - +4 +4.000000 +0.017385 - +5 +3.125000 +0.014518 - +6 +3.625000 +0.016115 - +7 +3.500000 +0.015627 - +8 +3.375000 +0.015173 - - Density error is +0.000000000115 - - charge density convergence is achieved - final etot is -211.790638622284 eV - - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - Si1 +0.562521 -0.158433 -0.082597 - Si2 -0.562521 +0.158433 +0.082597 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +122.818911 +2.300863 +4.331819 - +2.300863 +123.569280 -15.284717 - +4.331819 -15.284717 +123.616732 - -output Pressure for check! -Virtual Pressure is +123.670443 Kbar -Virial is +123.334974 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 8 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -15.564121 (Rydberg) - NVT Temperature : +72.197413 (K) - NVT Kinetic energy : +0.001372 (Rydberg) - NVT Potential energy : -15.566319 (Rydberg) - maxForce : +0.000132 - maxStep : +0.031989 - MD_STEP SystemE Conserved DeltaE Temperature - +8 -7.783160 -7.782060 +0.000000 +101.706395 - - PW ALGORITHM --------------- ION=+9 ELEC=+1 -------------------------------- - K-point CG iter num Time(Sec) - +1 +35.875000 +1.531937 - +2 +26.875000 +0.264962 - +3 +26.750000 +0.096733 - +4 +30.375000 +0.108739 - +5 +27.000000 +0.097620 - +6 +31.875000 +0.114026 - +7 +28.000000 +0.100499 - +8 +25.250000 +0.092090 - - Density error is +0.000030268617 - - PW ALGORITHM --------------- ION=+9 ELEC=+2 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.000000 +0.010942 - +2 +2.000000 +0.010442 - +3 +2.000000 +0.010413 - +4 +2.000000 +0.010444 - +5 +2.000000 +0.010413 - +6 +2.000000 +0.010372 - +7 +2.000000 +0.010379 - +8 +2.000000 +0.010382 - - Density error is +0.000002526424 - - PW ALGORITHM --------------- ION=+9 ELEC=+3 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.125000 +0.011021 - +2 +2.500000 +0.012194 - +3 +2.250000 +0.011346 - +4 +2.375000 +0.011731 - +5 +2.250000 +0.011785 - +6 +2.750000 +0.013400 - +7 +2.875000 +0.013483 - +8 +2.500000 +0.012132 - - Density error is +0.000000035287 - - PW ALGORITHM --------------- ION=+9 ELEC=+4 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.625000 +0.016272 - +2 +3.750000 +0.016595 - +3 +3.625000 +0.016152 - +4 +3.875000 +0.016950 - +5 +3.625000 +0.016113 - +6 +3.750000 +0.016497 - +7 +4.625000 +0.019580 - +8 +3.750000 +0.016488 - - Density error is +0.000000003280 - - PW ALGORITHM --------------- ION=+9 ELEC=+5 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.750000 +0.013195 - +2 +2.750000 +0.013069 - +3 +2.875000 +0.013452 - +4 +4.250000 +0.018388 - +5 +2.875000 +0.013480 - +6 +3.500000 +0.015655 - +7 +3.000000 +0.013869 - +8 +2.625000 +0.012553 - - Density error is +0.000000000193 - - charge density convergence is achieved - final etot is -211.799689533651 eV - - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - Si1 +0.088600 +0.125590 -0.036123 - Si2 -0.088600 -0.125590 +0.036123 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +122.942319 +0.972401 -3.404364 - +0.972401 +122.922036 -2.403271 - -3.404364 -2.403271 +122.959321 - -output Pressure for check! -Virtual Pressure is +123.655562 Kbar -Virial is +122.941225 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 9 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -15.564178 (Rydberg) - NVT Temperature : +102.774866 (K) - NVT Kinetic energy : +0.001953 (Rydberg) - NVT Potential energy : -15.566984 (Rydberg) - maxForce : +0.000009 - maxStep : +0.032288 - MD_STEP SystemE Conserved DeltaE Temperature - +9 -7.783492 -7.782089 +0.000000 +102.692994 - - PW ALGORITHM --------------- ION=+10 ELEC=+1 -------------------------------- - K-point CG iter num Time(Sec) - +1 +36.000000 +1.538429 - +2 +24.875000 +0.260502 - +3 +25.750000 +0.093167 - +4 +29.875000 +0.106972 - +5 +26.000000 +0.094130 - +6 +30.000000 +0.107537 - +7 +31.000000 +0.110836 - +8 +25.375000 +0.091698 - - Density error is +0.000030737201 - - PW ALGORITHM --------------- ION=+10 ELEC=+2 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.000000 +0.010666 - +2 +2.000000 +0.010444 - +3 +2.000000 +0.010477 - +4 +2.000000 +0.010404 - +5 +2.000000 +0.010414 - +6 +2.000000 +0.010377 - +7 +2.000000 +0.010374 - +8 +2.000000 +0.010388 - - Density error is +0.000002560646 - - PW ALGORITHM --------------- ION=+10 ELEC=+3 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.250000 +0.011451 - +2 +2.500000 +0.012257 - +3 +2.250000 +0.011301 - +4 +2.750000 +0.013040 - +5 +2.250000 +0.011288 - +6 +2.625000 +0.012593 - +7 +3.000000 +0.013923 - +8 +2.500000 +0.012151 - - Density error is +0.000000033975 - - PW ALGORITHM --------------- ION=+10 ELEC=+4 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.625000 +0.016339 - +2 +3.875000 +0.017015 - +3 +3.750000 +0.016527 - +4 +4.250000 +0.018269 - +5 +3.750000 +0.016535 - +6 +3.750000 +0.016493 - +7 +4.625000 +0.019590 - +8 +3.750000 +0.016482 - - Density error is +0.000000003387 - - PW ALGORITHM --------------- ION=+10 ELEC=+5 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.875000 +0.013682 - +2 +2.625000 +0.012626 - +3 +2.750000 +0.013042 - +4 +3.750000 +0.016591 - +5 +3.000000 +0.013926 - +6 +3.500000 +0.015660 - +7 +3.000000 +0.013942 - +8 +2.625000 +0.012582 - - Density error is +0.000000000211 - - charge density convergence is achieved - final etot is -211.791757080168 eV - - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - Si1 -0.416931 +0.372190 +0.054656 - Si2 +0.416931 -0.372190 -0.054656 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +123.112004 -1.386177 -10.090684 - -1.386177 +123.202765 +11.305489 - -10.090684 +11.305489 +123.552704 - -output Pressure for check! -Virtual Pressure is +124.010423 Kbar -Virial is +123.289157 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 10 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -15.564126 (Rydberg) - NVT Temperature : +73.190993 (K) - NVT Kinetic energy : +0.001391 (Rydberg) - NVT Potential energy : -15.566401 (Rydberg) - maxForce : +0.000119 - maxStep : +0.022835 - MD_STEP SystemE Conserved DeltaE Temperature - +10 -7.783201 -7.782063 +0.000000 +48.734190 - - PW ALGORITHM --------------- ION=+11 ELEC=+1 -------------------------------- - K-point CG iter num Time(Sec) - +1 +35.875000 +1.541778 - +2 +25.500000 +0.266144 - +3 +25.250000 +0.091185 - +4 +29.250000 +0.104785 - +5 +24.875000 +0.090153 - +6 +30.625000 +0.109517 - +7 +28.875000 +0.103393 - +8 +27.500000 +0.098937 - - Density error is +0.000016935127 - - PW ALGORITHM --------------- ION=+11 ELEC=+2 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.000000 +0.010679 - +2 +2.000000 +0.010521 - +3 +2.000000 +0.010402 - +4 +2.000000 +0.010379 - +5 +2.000000 +0.010446 - +6 +2.000000 +0.010416 - +7 +2.000000 +0.010382 - +8 +2.000000 +0.010370 - - Density error is +0.000001343508 - - PW ALGORITHM --------------- ION=+11 ELEC=+3 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.125000 +0.010997 - +2 +2.125000 +0.010874 - +3 +2.250000 +0.011252 - +4 +2.625000 +0.012581 - +5 +2.125000 +0.010886 - +6 +2.625000 +0.012585 - +7 +3.000000 +0.013888 - +8 +2.375000 +0.011709 - - Density error is +0.000000032255 - - PW ALGORITHM --------------- ION=+11 ELEC=+4 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.750000 +0.016894 - +2 +3.750000 +0.016617 - +3 +3.625000 +0.016129 - +4 +3.875000 +0.016962 - +5 +3.750000 +0.016549 - +6 +3.750000 +0.016487 - +7 +4.500000 +0.019118 - +8 +3.500000 +0.015592 - - Density error is +0.000000001579 - - PW ALGORITHM --------------- ION=+11 ELEC=+5 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.875000 +0.013663 - +2 +3.125000 +0.014367 - +3 +2.875000 +0.013494 - +4 +4.125000 +0.017819 - +5 +3.125000 +0.014308 - +6 +4.000000 +0.017389 - +7 +3.125000 +0.014286 - +8 +3.125000 +0.014297 - - Density error is +0.000000000113 - - charge density convergence is achieved - final etot is -211.777136772291 eV - - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - Si1 -0.774114 +0.493555 +0.132287 - Si2 +0.774114 -0.493555 -0.132287 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +123.125513 -3.354234 -13.360634 - -3.354234 +124.042603 +21.012997 - -13.360634 +21.012997 +124.630461 - -output Pressure for check! -Virtual Pressure is +124.275144 Kbar -Virial is +123.932859 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 11 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -15.564029 (Rydberg) - NVT Temperature : +20.916618 (K) - NVT Kinetic energy : +0.000397 (Rydberg) - NVT Potential energy : -15.565327 (Rydberg) - maxForce : +0.000325 - maxStep : +0.009427 - MD_STEP SystemE Conserved DeltaE Temperature - +11 -7.782663 -7.782015 +0.000000 +9.036895 - - PW ALGORITHM --------------- ION=+12 ELEC=+1 -------------------------------- - K-point CG iter num Time(Sec) - +1 +36.125000 +1.547415 - +2 +26.375000 +0.264168 - +3 +25.375000 +0.091673 - +4 +29.500000 +0.105644 - +5 +26.125000 +0.094314 - +6 +31.500000 +0.112479 - +7 +29.875000 +0.106803 - +8 +28.625000 +0.102367 - - Density error is +0.000006530970 - - PW ALGORITHM --------------- ION=+12 ELEC=+2 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.000000 +0.010577 - +2 +2.000000 +0.010466 - +3 +2.000000 +0.010402 - +4 +2.000000 +0.010371 - +5 +2.000000 +0.010404 - +6 +2.000000 +0.010385 - +7 +2.000000 +0.010377 - +8 +2.000000 +0.010356 - - Density error is +0.000000440898 - - PW ALGORITHM --------------- ION=+12 ELEC=+3 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.625000 +0.012786 - +2 +2.000000 +0.010477 - +3 +2.000000 +0.010393 - +4 +2.750000 +0.013027 - +5 +2.125000 +0.010923 - +6 +2.750000 +0.012995 - +7 +3.125000 +0.014337 - +8 +2.000000 +0.010365 - - Density error is +0.000000024207 - - PW ALGORITHM --------------- ION=+12 ELEC=+4 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.000000 +0.014107 - +2 +3.125000 +0.014392 - +3 +3.000000 +0.013912 - +4 +3.375000 +0.015251 - +5 +3.375000 +0.015234 - +6 +3.125000 +0.014438 - +7 +3.250000 +0.014784 - +8 +3.250000 +0.014731 - - Density error is +0.000000000170 - - charge density convergence is achieved - final etot is -211.774943325509 eV - - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - Si1 -0.854779 +0.436696 +0.135045 - Si2 +0.854779 -0.436696 -0.135045 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +122.950297 -3.436598 -11.810037 - -3.436598 +124.343261 +23.217684 - -11.810037 +23.217684 +124.792605 - -output Pressure for check! -Virtual Pressure is +124.092191 Kbar -Virial is +124.028721 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 12 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -15.564015 (Rydberg) - NVT Temperature : +13.061843 (K) - NVT Kinetic energy : +0.000248 (Rydberg) - NVT Potential energy : -15.565166 (Rydberg) - maxForce : +0.000355 - maxStep : +0.019395 - MD_STEP SystemE Conserved DeltaE Temperature - +12 -7.782583 -7.782007 +0.000000 +34.185920 - - PW ALGORITHM --------------- ION=+13 ELEC=+1 -------------------------------- - K-point CG iter num Time(Sec) - +1 +34.000000 +1.465002 - +2 +23.000000 +0.338683 - +3 +23.500000 +0.085138 - +4 +27.875000 +0.099984 - +5 +24.000000 +0.086926 - +6 +28.875000 +0.103425 - +7 +30.250000 +0.108009 - +8 +24.000000 +0.086816 - - Density error is +0.000013073792 - - PW ALGORITHM --------------- ION=+13 ELEC=+2 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.000000 +0.010625 - +2 +2.000000 +0.010427 - +3 +2.000000 +0.010396 - +4 +2.000000 +0.010386 - +5 +2.000000 +0.010431 - +6 +2.000000 +0.010378 - +7 +2.000000 +0.010379 - +8 +2.000000 +0.010393 - - Density error is +0.000001008013 - - PW ALGORITHM --------------- ION=+13 ELEC=+3 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.125000 +0.011016 - +2 +2.250000 +0.011351 - +3 +2.125000 +0.010831 - +4 +2.750000 +0.013017 - +5 +2.125000 +0.010830 - +6 +2.750000 +0.013067 - +7 +3.125000 +0.014333 - +8 +2.250000 +0.011270 - - Density error is +0.000000030793 - - PW ALGORITHM --------------- ION=+13 ELEC=+4 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.625000 +0.016352 - +2 +3.500000 +0.015679 - +3 +3.625000 +0.016117 - +4 +3.875000 +0.016947 - +5 +3.625000 +0.016079 - +6 +3.750000 +0.016476 - +7 +4.250000 +0.018229 - +8 +3.500000 +0.015618 - - Density error is +0.000000001065 - - PW ALGORITHM --------------- ION=+13 ELEC=+5 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.875000 +0.013652 - +2 +3.375000 +0.015279 - +3 +3.125000 +0.014327 - +4 +4.125000 +0.017830 - +5 +3.250000 +0.014748 - +6 +4.250000 +0.018231 - +7 +3.500000 +0.015621 - +8 +3.375000 +0.015172 - - Density error is +0.000000000097 - - charge density convergence is achieved - final etot is -211.787892336077 eV - - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - Si1 -0.634765 +0.219902 +0.063772 - Si2 +0.634765 -0.219902 -0.063772 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +122.810989 -1.646977 -5.949715 - -1.646977 +123.724465 +17.235456 - -5.949715 +17.235456 +123.839274 - -output Pressure for check! -Virtual Pressure is +123.698348 Kbar -Virial is +123.458243 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 13 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -15.564100 (Rydberg) - NVT Temperature : +58.268396 (K) - NVT Kinetic energy : +0.001107 (Rydberg) - NVT Potential energy : -15.566117 (Rydberg) - maxForce : +0.000172 - maxStep : +0.030214 - MD_STEP SystemE Conserved DeltaE Temperature - +13 -7.783059 -7.782050 +0.000000 +89.458675 - - PW ALGORITHM --------------- ION=+14 ELEC=+1 -------------------------------- - K-point CG iter num Time(Sec) - +1 +35.875000 +1.542133 - +2 +26.125000 +0.252769 - +3 +27.000000 +0.097434 - +4 +31.125000 +0.111257 - +5 +27.250000 +0.098368 - +6 +30.375000 +0.108770 - +7 +28.125000 +0.101032 - +8 +27.000000 +0.097412 - - Density error is +0.000027152014 - - PW ALGORITHM --------------- ION=+14 ELEC=+2 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.000000 +0.010571 - +2 +2.000000 +0.010418 - +3 +2.000000 +0.010469 - +4 +2.000000 +0.010378 - +5 +2.000000 +0.010391 - +6 +2.125000 +0.010816 - +7 +2.000000 +0.010413 - +8 +2.000000 +0.010387 - - Density error is +0.000002253887 - - PW ALGORITHM --------------- ION=+14 ELEC=+3 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.125000 +0.011042 - +2 +2.375000 +0.011756 - +3 +2.250000 +0.011280 - +4 +2.750000 +0.013020 - +5 +2.250000 +0.011259 - +6 +2.625000 +0.012556 - +7 +2.875000 +0.013452 - +8 +2.500000 +0.012282 - - Density error is +0.000000033052 - - PW ALGORITHM --------------- ION=+14 ELEC=+4 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.875000 +0.017209 - +2 +3.750000 +0.016568 - +3 +3.625000 +0.016133 - +4 +4.250000 +0.018248 - +5 +3.625000 +0.016119 - +6 +4.250000 +0.018240 - +7 +4.750000 +0.020036 - +8 +3.625000 +0.016022 - - Density error is +0.000000002963 - - PW ALGORITHM --------------- ION=+14 ELEC=+5 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.875000 +0.013700 - +2 +2.750000 +0.013049 - +3 +2.750000 +0.012990 - +4 +3.500000 +0.015607 - +5 +3.000000 +0.013859 - +6 +3.375000 +0.015179 - +7 +2.875000 +0.013422 - +8 +2.750000 +0.012955 - - Density error is +0.000000000187 - - charge density convergence is achieved - final etot is -211.799136169946 eV - - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - Si1 -0.198870 -0.070672 -0.020734 - Si2 +0.198870 +0.070672 +0.020734 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +122.902575 +0.551658 +1.913429 - +0.551658 +122.991496 +5.397063 - +1.913429 +5.397063 +123.003398 - -output Pressure for check! -Virtual Pressure is +123.594137 Kbar -Virial is +122.965823 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 14 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -15.564168 (Rydberg) - NVT Temperature : +96.770497 (K) - NVT Kinetic energy : +0.001839 (Rydberg) - NVT Potential energy : -15.566944 (Rydberg) - maxForce : +0.000017 - maxStep : +0.032116 - MD_STEP SystemE Conserved DeltaE Temperature - +14 -7.783472 -7.782084 +0.000000 +103.109630 - - PW ALGORITHM --------------- ION=+15 ELEC=+1 -------------------------------- - K-point CG iter num Time(Sec) - +1 +35.375000 +1.505918 - +2 +24.375000 +0.254664 - +3 +24.625000 +0.089084 - +4 +30.625000 +0.109605 - +5 +26.625000 +0.095625 - +6 +29.125000 +0.104515 - +7 +27.875000 +0.100128 - +8 +24.500000 +0.088547 - - Density error is +0.000030393373 - - PW ALGORITHM --------------- ION=+15 ELEC=+2 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.000000 +0.010563 - +2 +2.000000 +0.010432 - +3 +2.000000 +0.010404 - +4 +2.000000 +0.010375 - +5 +2.000000 +0.010381 - +6 +2.000000 +0.010377 - +7 +2.000000 +0.010377 - +8 +2.000000 +0.010354 - - Density error is +0.000002547296 - - PW ALGORITHM --------------- ION=+15 ELEC=+3 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.250000 +0.011476 - +2 +2.500000 +0.012193 - +3 +2.250000 +0.011277 - +4 +2.750000 +0.013015 - +5 +2.250000 +0.011319 - +6 +2.750000 +0.013017 - +7 +2.750000 +0.013009 - +8 +2.500000 +0.012125 - - Density error is +0.000000032257 - - PW ALGORITHM --------------- ION=+15 ELEC=+4 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.625000 +0.016335 - +2 +3.875000 +0.016993 - +3 +3.750000 +0.016491 - +4 +4.375000 +0.018723 - +5 +3.750000 +0.016532 - +6 +3.500000 +0.015608 - +7 +4.375000 +0.018691 - +8 +3.750000 +0.016462 - - Density error is +0.000000003366 - - PW ALGORITHM --------------- ION=+15 ELEC=+5 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.750000 +0.013287 - +2 +2.625000 +0.012630 - +3 +2.875000 +0.013438 - +4 +3.500000 +0.015728 - +5 +2.750000 +0.013063 - +6 +3.125000 +0.014314 - +7 +3.250000 +0.014752 - +8 +2.625000 +0.012547 - - Density error is +0.000000000185 - - charge density convergence is achieved - final etot is -211.794739884606 eV - - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - Si1 +0.297987 -0.327806 -0.066082 - Si2 -0.297987 +0.327806 +0.066082 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +123.100328 +1.856002 +8.909136 - +1.856002 +123.052207 -8.099784 - +8.909136 -8.099784 +123.317967 - -output Pressure for check! -Virtual Pressure is +123.881026 Kbar -Virial is +123.156834 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 15 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -15.564136 (Rydberg) - NVT Temperature : +79.642870 (K) - NVT Kinetic energy : +0.001513 (Rydberg) - NVT Potential energy : -15.566621 (Rydberg) - maxForce : +0.000076 - maxStep : +0.024468 - MD_STEP SystemE Conserved DeltaE Temperature - +15 -7.783310 -7.782068 +0.000000 +58.786721 - - PW ALGORITHM --------------- ION=+16 ELEC=+1 -------------------------------- - K-point CG iter num Time(Sec) - +1 +36.000000 +1.550421 - +2 +24.125000 +0.253604 - +3 +26.125000 +0.094431 - +4 +29.625000 +0.106054 - +5 +25.500000 +0.091700 - +6 +29.500000 +0.105684 - +7 +29.125000 +0.104354 - +8 +23.750000 +0.086118 - - Density error is +0.000019003017 - - PW ALGORITHM --------------- ION=+16 ELEC=+2 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.000000 +0.010587 - +2 +2.000000 +0.010446 - +3 +2.000000 +0.010445 - +4 +2.000000 +0.010404 - +5 +2.000000 +0.010390 - +6 +2.000000 +0.010379 - +7 +2.000000 +0.010378 - +8 +2.000000 +0.010370 - - Density error is +0.000001546864 - - PW ALGORITHM --------------- ION=+16 ELEC=+3 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.125000 +0.011046 - +2 +2.375000 +0.011756 - +3 +2.250000 +0.011289 - +4 +2.500000 +0.012140 - +5 +2.250000 +0.011313 - +6 +2.750000 +0.013017 - +7 +2.875000 +0.013462 - +8 +2.250000 +0.011249 - - Density error is +0.000000031769 - - PW ALGORITHM --------------- ION=+16 ELEC=+4 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.750000 +0.016761 - +2 +3.500000 +0.015694 - +3 +3.750000 +0.016521 - +4 +4.000000 +0.017360 - +5 +3.500000 +0.015655 - +6 +3.625000 +0.016032 - +7 +4.625000 +0.019569 - +8 +3.625000 +0.016039 - - Density error is +0.000000001918 - - PW ALGORITHM --------------- ION=+16 ELEC=+5 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.750000 +0.013196 - +2 +3.125000 +0.014455 - +3 +2.875000 +0.013481 - +4 +4.000000 +0.017394 - +5 +3.000000 +0.013924 - +6 +3.750000 +0.016493 - +7 +3.000000 +0.013924 - +8 +3.125000 +0.014310 - - Density error is +0.000000000142 - - charge density convergence is achieved - final etot is -211.780796729120 eV - - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - Si1 +0.685454 -0.466777 -0.074732 - Si2 -0.685454 +0.466777 +0.074732 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +123.145046 +2.237882 +12.724721 - +2.237882 +123.794533 -18.656690 - +12.724721 -18.656690 +124.345426 - -output Pressure for check! -Virtual Pressure is +124.174558 Kbar -Virial is +123.761668 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 16 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -15.564047 (Rydberg) - NVT Temperature : +29.284447 (K) - NVT Kinetic energy : +0.000556 (Rydberg) - NVT Potential energy : -15.565596 (Rydberg) - maxForce : +0.000262 - maxStep : +0.011494 - MD_STEP SystemE Conserved DeltaE Temperature - +16 -7.782798 -7.782023 +0.000000 +12.500370 - - PW ALGORITHM --------------- ION=+17 ELEC=+1 -------------------------------- - K-point CG iter num Time(Sec) - +1 +36.250000 +1.548769 - +2 +24.250000 +0.238733 - +3 +26.875000 +0.097094 - +4 +30.500000 +0.109091 - +5 +25.500000 +0.092283 - +6 +29.500000 +0.106987 - +7 +30.375000 +0.108359 - +8 +24.000000 +0.086977 - - Density error is +0.000007183223 - - PW ALGORITHM --------------- ION=+17 ELEC=+2 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.000000 +0.010577 - +2 +2.000000 +0.010427 - +3 +2.000000 +0.010496 - +4 +2.000000 +0.010394 - +5 +2.000000 +0.010418 - +6 +2.125000 +0.010931 - +7 +2.000000 +0.010379 - +8 +2.000000 +0.010422 - - Density error is +0.000000511477 - - PW ALGORITHM --------------- ION=+17 ELEC=+3 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.375000 +0.011921 - +2 +2.125000 +0.010910 - +3 +2.125000 +0.010844 - +4 +2.875000 +0.013531 - +5 +2.000000 +0.010405 - +6 +2.625000 +0.012594 - +7 +3.375000 +0.015197 - +8 +2.125000 +0.010844 - - Density error is +0.000000026283 - - PW ALGORITHM --------------- ION=+17 ELEC=+4 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.375000 +0.015456 - +2 +3.625000 +0.016132 - +3 +3.250000 +0.014828 - +4 +3.500000 +0.015635 - +5 +3.375000 +0.015239 - +6 +3.375000 +0.015161 - +7 +3.125000 +0.014336 - +8 +3.500000 +0.015643 - - Density error is +0.000000000237 - - charge density convergence is achieved - final etot is -211.774985509926 eV - - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - Si1 +0.833310 -0.445812 -0.078719 - Si2 -0.833310 +0.445812 +0.078719 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +122.994195 +2.379118 +12.171980 - +2.379118 +124.272817 -22.694125 - +12.171980 -22.694125 +124.774373 - -output Pressure for check! -Virtual Pressure is +124.101591 Kbar -Virial is +124.013795 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 17 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -15.564010 (Rydberg) - NVT Temperature : +8.524394 (K) - NVT Kinetic energy : +0.000162 (Rydberg) - NVT Potential energy : -15.565169 (Rydberg) - maxForce : +0.000340 - maxStep : +0.014988 - MD_STEP SystemE Conserved DeltaE Temperature - +17 -7.782584 -7.782005 +0.000000 +21.039416 - - PW ALGORITHM --------------- ION=+18 ELEC=+1 -------------------------------- - K-point CG iter num Time(Sec) - +1 +34.250000 +1.473409 - +2 +22.000000 +0.326542 - +3 +24.000000 +0.087028 - +4 +28.000000 +0.100599 - +5 +24.000000 +0.086910 - +6 +29.000000 +0.103884 - +7 +27.125000 +0.097431 - +8 +21.625000 +0.078627 - - Density error is +0.000009301236 - - PW ALGORITHM --------------- ION=+18 ELEC=+2 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.000000 +0.010625 - +2 +2.000000 +0.010448 - +3 +2.000000 +0.010394 - +4 +2.000000 +0.010369 - +5 +2.000000 +0.010395 - +6 +2.125000 +0.010809 - +7 +2.000000 +0.010374 - +8 +2.000000 +0.010352 - - Density error is +0.000000698839 - - PW ALGORITHM --------------- ION=+18 ELEC=+3 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.250000 +0.011468 - +2 +2.125000 +0.010873 - +3 +2.125000 +0.010841 - +4 +2.875000 +0.013464 - +5 +2.125000 +0.010821 - +6 +2.500000 +0.012141 - +7 +3.125000 +0.014320 - +8 +2.125000 +0.010803 - - Density error is +0.000000028756 - - PW ALGORITHM --------------- ION=+18 ELEC=+4 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.500000 +0.015856 - +2 +3.625000 +0.016113 - +3 +3.500000 +0.015631 - +4 +3.625000 +0.016042 - +5 +3.625000 +0.016071 - +6 +3.750000 +0.016468 - +7 +4.000000 +0.017389 - +8 +3.625000 +0.016045 - - Density error is +0.000000000545 - - charge density convergence is achieved - final etot is -211.784530531570 eV - - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - Si1 +0.693682 -0.275109 -0.084557 - Si2 -0.693682 +0.275109 +0.084557 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +122.844932 +2.424056 +7.513685 - +2.424056 +123.890142 -18.864028 - +7.513685 -18.864028 +124.067900 - -output Pressure for check! -Virtual Pressure is +123.748762 Kbar -Virial is +123.600991 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 18 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -15.564069 (Rydberg) - NVT Temperature : +42.047874 (K) - NVT Kinetic energy : +0.000799 (Rydberg) - NVT Potential energy : -15.565870 (Rydberg) - maxForce : +0.000213 - maxStep : +0.027051 - MD_STEP SystemE Conserved DeltaE Temperature - +18 -7.782935 -7.782034 +0.000000 +72.297418 - - PW ALGORITHM --------------- ION=+19 ELEC=+1 -------------------------------- - K-point CG iter num Time(Sec) - +1 +33.625000 +1.446761 - +2 +22.750000 +0.337746 - +3 +24.500000 +0.088664 - +4 +26.875000 +0.096374 - +5 +24.375000 +0.088118 - +6 +27.625000 +0.099005 - +7 +26.125000 +0.093894 - +8 +23.000000 +0.083275 - - Density error is +0.000022341414 - - PW ALGORITHM --------------- ION=+19 ELEC=+2 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.000000 +0.010590 - +2 +2.000000 +0.010429 - +3 +2.000000 +0.010400 - +4 +2.500000 +0.012143 - +5 +2.000000 +0.010418 - +6 +2.000000 +0.010354 - +7 +2.375000 +0.011685 - +8 +2.000000 +0.010357 - - Density error is +0.000001840522 - - PW ALGORITHM --------------- ION=+19 ELEC=+3 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.125000 +0.011068 - +2 +2.375000 +0.011775 - +3 +2.250000 +0.011276 - +4 +2.500000 +0.012134 - +5 +2.250000 +0.011291 - +6 +2.500000 +0.012133 - +7 +3.000000 +0.013910 - +8 +2.375000 +0.011695 - - Density error is +0.000000031328 - - PW ALGORITHM --------------- ION=+19 ELEC=+4 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.750000 +0.016750 - +2 +3.750000 +0.016541 - +3 +3.750000 +0.016522 - +4 +4.000000 +0.017360 - +5 +3.625000 +0.016071 - +6 +3.875000 +0.016922 - +7 +4.125000 +0.017815 - +8 +3.875000 +0.016914 - - Density error is +0.000000002386 - - PW ALGORITHM --------------- ION=+19 ELEC=+5 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.750000 +0.013224 - +2 +2.875000 +0.013511 - +3 +2.875000 +0.013467 - +4 +3.875000 +0.016967 - +5 +2.875000 +0.013449 - +6 +3.500000 +0.015602 - +7 +3.500000 +0.015614 - +8 +2.500000 +0.012112 - - Density error is +0.000000000165 - - charge density convergence is achieved - final etot is -211.797509996802 eV - - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - Si1 +0.315435 -0.012610 -0.062567 - Si2 -0.315435 +0.012610 +0.062567 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +122.869560 +1.699030 +0.355976 - +1.699030 +123.125358 -8.562365 - +0.355976 -8.562365 +123.115733 - -output Pressure for check! -Virtual Pressure is +123.544666 Kbar -Virial is +123.036884 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 19 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -15.564150 (Rydberg) - NVT Temperature : +86.724314 (K) - NVT Kinetic energy : +0.001648 (Rydberg) - NVT Potential energy : -15.566824 (Rydberg) - maxForce : +0.000039 - maxStep : +0.031849 - MD_STEP SystemE Conserved DeltaE Temperature - +19 -7.783412 -7.782075 +0.000000 +101.072847 - - PW ALGORITHM --------------- ION=+20 ELEC=+1 -------------------------------- - K-point CG iter num Time(Sec) - +1 +36.000000 +1.535621 - +2 +25.500000 +0.274161 - +3 +26.125000 +0.094184 - +4 +29.875000 +0.106798 - +5 +26.375000 +0.095103 - +6 +30.750000 +0.109985 - +7 +31.875000 +0.114172 - +8 +25.750000 +0.092841 - - Density error is +0.000029792721 - - PW ALGORITHM --------------- ION=+20 ELEC=+2 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.125000 +0.011051 - +2 +2.000000 +0.010426 - +3 +2.000000 +0.010378 - +4 +2.125000 +0.010793 - +5 +2.000000 +0.010367 - +6 +2.000000 +0.010355 - +7 +2.000000 +0.010362 - +8 +2.000000 +0.010354 - - Density error is +0.000002500903 - - PW ALGORITHM --------------- ION=+20 ELEC=+3 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.375000 +0.011932 - +2 +2.500000 +0.012164 - +3 +2.250000 +0.011253 - +4 +2.500000 +0.012117 - +5 +2.250000 +0.011252 - +6 +2.750000 +0.012983 - +7 +2.750000 +0.013005 - +8 +2.500000 +0.012105 - - Density error is +0.000000031164 - - PW ALGORITHM --------------- ION=+20 ELEC=+4 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.750000 +0.016752 - +2 +3.875000 +0.016963 - +3 +3.750000 +0.016481 - +4 +3.875000 +0.016934 - +5 +3.750000 +0.016474 - +6 +3.625000 +0.016019 - +7 +4.750000 +0.019994 - +8 +3.750000 +0.016447 - - Density error is +0.000000003269 - - PW ALGORITHM --------------- ION=+20 ELEC=+5 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.875000 +0.013655 - +2 +2.625000 +0.012594 - +3 +2.625000 +0.012553 - +4 +3.750000 +0.016475 - +5 +2.875000 +0.013402 - +6 +3.500000 +0.015683 - +7 +2.750000 +0.012961 - +8 +2.625000 +0.012526 - - Density error is +0.000000000179 - - charge density convergence is achieved - final etot is -211.797737534802 eV - - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - Si1 -0.171785 +0.257041 +0.008602 - Si2 +0.171785 -0.257041 -0.008602 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +123.033300 -0.204765 -6.972062 - -0.204765 +122.939153 +4.657249 - -6.972062 +4.657249 +123.108999 - -output Pressure for check! -Virtual Pressure is +123.737037 Kbar -Virial is +123.027151 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 20 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -15.564150 (Rydberg) - NVT Temperature : +85.566203 (K) - NVT Kinetic energy : +0.001626 (Rydberg) - NVT Potential energy : -15.566841 (Rydberg) - maxForce : +0.000036 - maxStep : +0.026933 - MD_STEP SystemE Conserved DeltaE Temperature - +20 -7.783421 -7.782075 +0.000000 +70.314105 - - PW ALGORITHM --------------- ION=+21 ELEC=+1 -------------------------------- - K-point CG iter num Time(Sec) - +1 +36.125000 +1.533770 - +2 +24.250000 +0.243025 - +3 +24.750000 +0.089487 - +4 +29.750000 +0.106362 - +5 +24.875000 +0.089914 - +6 +29.875000 +0.106912 - +7 +32.125000 +0.114500 - +8 +27.125000 +0.097630 - - Density error is +0.000022029241 - - PW ALGORITHM --------------- ION=+21 ELEC=+2 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.000000 +0.010617 - +2 +2.000000 +0.010405 - +3 +2.000000 +0.010373 - +4 +2.000000 +0.010365 - +5 +2.000000 +0.010388 - +6 +2.000000 +0.010360 - +7 +2.000000 +0.010347 - +8 +2.000000 +0.010369 - - Density error is +0.000001807441 - - PW ALGORITHM --------------- ION=+21 ELEC=+3 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.125000 +0.011063 - +2 +2.375000 +0.011747 - +3 +2.250000 +0.011261 - +4 +2.500000 +0.012112 - +5 +2.250000 +0.011278 - +6 +2.625000 +0.012552 - +7 +3.000000 +0.013891 - +8 +2.375000 +0.011680 - - Density error is +0.000000029382 - - PW ALGORITHM --------------- ION=+21 ELEC=+4 -------------------------------- - K-point CG iter num Time(Sec) - +1 +3.625000 +0.016299 - +2 +3.625000 +0.016094 - +3 +3.750000 +0.016491 - +4 +3.875000 +0.016919 - +5 +3.750000 +0.016502 - +6 +3.750000 +0.016462 - +7 +4.625000 +0.019557 - +8 +3.625000 +0.016026 - - Density error is +0.000000002371 - - PW ALGORITHM --------------- ION=+21 ELEC=+5 -------------------------------- - K-point CG iter num Time(Sec) - +1 +2.875000 +0.013673 - +2 +2.875000 +0.013455 - +3 +2.875000 +0.013422 - +4 +4.125000 +0.017806 - +5 +3.000000 +0.013879 - +6 +3.875000 +0.016927 - +7 +3.000000 +0.013878 - +8 +2.875000 +0.013406 - - Density error is +0.000000000178 - - charge density convergence is achieved - final etot is -211.785114277951 eV - - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - Si1 -0.597076 +0.443380 +0.097410 - Si2 +0.597076 -0.443380 -0.097410 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +123.145634 -2.476538 -12.011339 - -2.476538 +123.557627 +16.195950 - -12.011339 +16.195950 +124.041967 - -output Pressure for check! -Virtual Pressure is +124.075595 Kbar -Virial is +123.581743 Kbar - - -------------------------------------------------- - Molecular Dynamics (NVT) STEP 21 - -------------------------------------------------- --------------------------------------------------- - SUMMARY OF NVT CALCULATION - -------------------------------------------------- - NVT Conservation : -15.564066 (Rydberg) - NVT Temperature : +39.619227 (K) - NVT Kinetic energy : +0.000753 (Rydberg) - NVT Potential energy : -15.565913 (Rydberg) - maxForce : +0.000213 - maxStep : +0.014552 - MD_STEP SystemE Conserved DeltaE Temperature - +21 -7.782957 -7.782033 +0.000000 +19.004126 - - - -------------------------------------------- - !FINAL_ETOT_IS -211.7851142779510099 eV - -------------------------------------------- - - - - - - - |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- - total +35.575 15 +2.37 +100.00 % - Run_pw plane_wave_line +35.54 1 +35.54 +99.91 % - Run_MD_PW md_cells_pw +35.47 1 +35.47 +99.70 % - Potential init_pot +0.21 22 +0.01 +0.59 % - FFT FFT3D +21.26 126906 +0.00 +59.76 % - Potential v_of_rho +1.13 125 +0.01 +3.17 % - H_XC_pw v_xc +1.20 146 +0.01 +3.36 % - wavefunc wfcinit +0.97 22 +0.04 +2.73 % - pp_cell_vnl getvnl +0.46 1336 +0.00 +1.29 % - Hamilt_PW diagH_subspace +3.41 984 +0.00 +9.57 % - Hamilt_PW h_psi +24.29 52236 +0.00 +68.28 % - Hamilt_PW vloc +22.85 52236 +0.00 +64.24 % - Hamilt_PW vnl +1.29 52236 +0.00 +3.63 % - Hamilt_PW add_nonlocal_pp +0.75 52236 +0.00 +2.12 % - Run_MD_PW md_ions_pw +35.39 1 +35.39 +99.48 % - Electrons self_consistent +29.43 21 +1.40 +82.73 % - Electrons c_bands +25.56 103 +0.25 +71.86 % - Hamilt diagH_pw +25.14 824 +0.03 +70.67 % - Diago_CG diag +22.34 824 +0.03 +62.80 % - Charge sum_band +1.54 103 +0.01 +4.32 % - Charge mix_rho +0.20 103 +0.00 +0.57 % - Forces cal_force_nl +0.59 21 +0.03 +1.66 % - Stress_PW cal_stress +3.97 21 +0.19 +11.16 % - Stress_Func stress_ew +16.82 11 +1.53 +47.27 % - Force_Func stress_ew +16.82 11 +1.53 +47.27 % - Stress_Func stress_gga +0.11 21 +0.01 +0.31 % - Stress_Func stres_nl +3.76 21 +0.18 +10.57 % - ---------------------------------------------------------------------------------------- - - CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- - +5.1730 - ---------------------------------------------------------- - - Start Time : Fri Oct 15 14:37:16 2021 - Finish Time : Fri Oct 15 14:37:52 2021 - Total Time : 0 h 0 mins 36 secs diff --git a/tests/abacus.md/STRU b/tests/abacus.md/STRU index c3765e9b..1152c061 100644 --- a/tests/abacus.md/STRU +++ b/tests/abacus.md/STRU @@ -1,21 +1,32 @@ ATOMIC_SPECIES -Si 1.000 ./Si_ONCV_PBE-1.0.upf #Element, Mass, Pseudopotential +H 1.008 H_ONCV_PBE-1.0.upf +O 15.9994 O_ONCV_PBE-1.0.upf NUMERICAL_ORBITAL -./Si_gga_8au_60Ry_2s2p1d.orb +H_gga_8au_60Ry_2s1p.orb +O_gga_7au_60Ry_2s2p1d.orb + +NUMERICAL_DESCRIPTOR +jle.orb + LATTICE_CONSTANT -10.2 #Lattice constant +1 LATTICE_VECTORS -0.5 0.5 0.0 #Lattice vector 1 -0.5 0.0 0.5 #Lattice vector 2 -0.0 0.5 0.5 #Lattice vector 3 +28 0 0 +0 28 0 +0 0 28 ATOMIC_POSITIONS -Cartesian #Cartesian(Unit is LATTICE_CONSTANT) -Si #Name of element -0.0 #Magnetic for this element. -2 #Number of atoms -0.00 0.00 0.00 1 1 1 #x,y,z, move_x, move_y, move_z -0.241 0.255 0.251 1 1 1 +Cartesian + +H +0 +2 +-12.046787058887078 18.76558614676448 8.395247471328744 1 1 1 +-14.228868795885418 20.61549300274637 7.611989524516571 1 1 1 +O +0 +1 +-13.486789117423204 19.684192208418636 8.958321352749174 1 1 1 diff --git a/tests/abacus.md/Si_coord b/tests/abacus.md/Si_coord deleted file mode 100644 index fb8c5a8d..00000000 --- a/tests/abacus.md/Si_coord +++ /dev/null @@ -1,10 +0,0 @@ -0 0 0 -1.30082342 1.37638993 1.3547995 -5.35320953 2.72430477 2.68504527 -1.35126946 1.34726983 1.3286265 -2.70155326 2.69533522 5.35848569 -1.30969169 1.37268717 1.3150785 -2.66403555 0.02130293 2.64633444 -1.35284016 1.34443879 1.29061924 -2.70202696 2.69316139 5.32175227 -1.31985538 1.36795346 1.2771711 diff --git a/tests/abacus.md/Si_force b/tests/abacus.md/Si_force deleted file mode 100644 index b22dd3cc..00000000 --- a/tests/abacus.md/Si_force +++ /dev/null @@ -1,10 +0,0 @@ --0.885363 0.500467 0.15024 -0.885363 -0.500467 -0.15024 -0.830073 -0.488698 -0.076368 --0.830073 0.488698 0.076368 --0.774114 0.493555 0.132287 -0.774114 -0.493555 -0.132287 -0.685454 -0.466777 -0.074732 --0.685454 0.466777 0.074732 --0.597076 0.44338 0.09741 -0.597076 -0.44338 -0.09741 diff --git a/tests/abacus.md/Si_virial b/tests/abacus.md/Si_virial deleted file mode 100644 index 8ee02179..00000000 --- a/tests/abacus.md/Si_virial +++ /dev/null @@ -1,15 +0,0 @@ --3.01924575 0.09342813 0.33227574 -0.09342813 -3.05301021 -0.59008156 -0.33227574 -0.59008156 -3.06760338 --3.02007615 -0.05764851 -0.32736857 --0.05764851 -3.0485708 0.55474523 --0.32736857 0.55474523 -3.06346952 --3.02121465 0.08230513 0.32783898 -0.08230513 -3.04371791 -0.51561023 -0.32783898 -0.51561023 -3.05814259 --3.02169395 -0.05491244 -0.31223515 --0.05491244 -3.03763085 0.45779192 --0.31223515 0.45779192 -3.05114849 --3.02170837 0.0607685 0.29473041 -0.0607685 -3.03181773 -0.39741107 -0.29473041 -0.39741107 -3.04370231 diff --git a/tests/abacus.md/water_coord b/tests/abacus.md/water_coord new file mode 100644 index 00000000..86266ed1 --- /dev/null +++ b/tests/abacus.md/water_coord @@ -0,0 +1,15 @@ +8.44207673 9.93032054 4.44257364 +7.2873688 10.90924909 4.02809139 +7.68006046 10.41642593 4.74053951 +8.45239543 9.92229615 4.45200117 +7.29575958 10.91312823 4.02455611 +7.67888171 10.41668709 4.74016828 +8.46343523 9.9140533 4.46015631 +7.30368632 10.91806892 4.01842335 +7.67768678 10.41689514 4.74004087 +8.47396587 9.90644051 4.46733013 +7.311549 10.92371331 4.00998943 +7.67652796 10.41701915 4.74012026 +8.48312789 9.89996318 4.47399619 +7.31947517 10.92982192 3.99979102 +7.67545136 10.41704238 4.7403428 \ No newline at end of file diff --git a/tests/abacus.md/water_force b/tests/abacus.md/water_force new file mode 100644 index 00000000..b6ac9021 --- /dev/null +++ b/tests/abacus.md/water_force @@ -0,0 +1,15 @@ +8.63308639e-01 -4.43254999e-01 -7.56985213e-01 +-2.00930882e-01 4.68126173e-01 -1.16095809e+00 +-6.62377758e-01 -2.48711741e-02 1.91794331e+00 +3.08447003e-01 -1.00596917e-01 -5.18349475e-01 +-2.19930471e-01 4.66062785e-01 -1.09553672e+00 +-8.85165314e-02 -3.65465868e-01 1.61388619e+00 +-4.21531964e-01 4.78003484e-01 -6.02669271e-01 +2.65214978e-01 7.64070864e-02 -9.63824372e-01 +1.56316986e-01 -5.54410570e-01 1.56649364e+00 +-5.43198631e-01 4.57161184e-01 -2.06821527e-01 +2.27096399e-02 2.11549052e-01 -7.58980258e-01 +5.20488991e-01 -6.68710236e-01 9.65801785e-01 +-8.12329959e-01 5.87918500e-01 9.41318509e-04 +3.98264319e-02 1.00785737e-01 -4.50166048e-01 +7.72503527e-01 -6.88704237e-01 4.49224729e-01 \ No newline at end of file diff --git a/tests/abacus.md/water_virial b/tests/abacus.md/water_virial new file mode 100644 index 00000000..b707c9ae --- /dev/null +++ b/tests/abacus.md/water_virial @@ -0,0 +1,15 @@ +6.95335395e-01 -5.08824989e-01 -1.09549510e-01 +-5.08824989e-01 4.04209230e-01 -2.00245250e-01 +-1.09549510e-01 -2.00245250e-01 9.66902194e-01 +3.14181369e-01 -2.55243046e-01 3.04054313e-04 +-2.55243046e-01 2.42582203e-01 -2.84883570e-01 +3.04054313e-04 -2.84883570e-01 9.28206167e-01 +-1.85150181e-01 1.05732829e-01 4.21143979e-02 +1.05732829e-01 -2.56256968e-02 -2.78554734e-01 +4.21143979e-02 -2.78554734e-01 7.64038483e-01 +-5.03355372e-01 3.34823165e-01 6.91010112e-02 +3.34823165e-01 -1.99581996e-01 -2.60526766e-01 +6.91010112e-02 -2.60526766e-01 6.12151015e-01 +-8.20817678e-01 5.82037040e-01 3.83817596e-02 +5.82037040e-01 -4.11511524e-01 -1.70276239e-01 +3.83817596e-02 -1.70276239e-01 3.83953980e-01 \ No newline at end of file diff --git a/tests/ase/Al0He4O0/box.raw b/tests/ase_traj/Al0He4O0/box.raw similarity index 100% rename from tests/ase/Al0He4O0/box.raw rename to tests/ase_traj/Al0He4O0/box.raw diff --git a/tests/ase/Al0He4O0/coord.raw b/tests/ase_traj/Al0He4O0/coord.raw similarity index 100% rename from tests/ase/Al0He4O0/coord.raw rename to tests/ase_traj/Al0He4O0/coord.raw diff --git a/tests/ase/Al0He4O0/energy.raw b/tests/ase_traj/Al0He4O0/energy.raw similarity index 100% rename from tests/ase/Al0He4O0/energy.raw rename to tests/ase_traj/Al0He4O0/energy.raw diff --git a/tests/ase/Al0He4O0/force.raw b/tests/ase_traj/Al0He4O0/force.raw similarity index 100% rename from tests/ase/Al0He4O0/force.raw rename to tests/ase_traj/Al0He4O0/force.raw diff --git a/tests/ase/Al0He4O0/type.raw b/tests/ase_traj/Al0He4O0/type.raw similarity index 100% rename from tests/ase/Al0He4O0/type.raw rename to tests/ase_traj/Al0He4O0/type.raw diff --git a/tests/ase/Al0He4O0/type_map.raw 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rename to tests/ase_traj/Al8He4O12/force.raw diff --git a/tests/ase/Al8He4O12/type.raw b/tests/ase_traj/Al8He4O12/type.raw similarity index 100% rename from tests/ase/Al8He4O12/type.raw rename to tests/ase_traj/Al8He4O12/type.raw diff --git a/tests/ase/Al8He4O12/type_map.raw b/tests/ase_traj/Al8He4O12/type_map.raw similarity index 100% rename from tests/ase/Al8He4O12/type_map.raw rename to tests/ase_traj/Al8He4O12/type_map.raw diff --git a/tests/ase/Al8He4O12/virial.raw b/tests/ase_traj/Al8He4O12/virial.raw similarity index 100% rename from tests/ase/Al8He4O12/virial.raw rename to tests/ase_traj/Al8He4O12/virial.raw diff --git a/tests/ase/Al8He8O12/box.raw b/tests/ase_traj/Al8He8O12/box.raw similarity index 100% rename from tests/ase/Al8He8O12/box.raw rename to tests/ase_traj/Al8He8O12/box.raw diff --git a/tests/ase/Al8He8O12/coord.raw b/tests/ase_traj/Al8He8O12/coord.raw similarity index 100% rename from tests/ase/Al8He8O12/coord.raw rename to tests/ase_traj/Al8He8O12/coord.raw diff --git a/tests/ase/Al8He8O12/energy.raw b/tests/ase_traj/Al8He8O12/energy.raw similarity index 100% rename from tests/ase/Al8He8O12/energy.raw rename to tests/ase_traj/Al8He8O12/energy.raw diff --git a/tests/ase/Al8He8O12/force.raw b/tests/ase_traj/Al8He8O12/force.raw similarity index 100% rename from tests/ase/Al8He8O12/force.raw rename to tests/ase_traj/Al8He8O12/force.raw diff --git a/tests/ase/Al8He8O12/type.raw b/tests/ase_traj/Al8He8O12/type.raw similarity index 100% rename from tests/ase/Al8He8O12/type.raw rename to tests/ase_traj/Al8He8O12/type.raw diff --git a/tests/ase/Al8He8O12/type_map.raw b/tests/ase_traj/Al8He8O12/type_map.raw similarity index 100% rename from tests/ase/Al8He8O12/type_map.raw rename to tests/ase_traj/Al8He8O12/type_map.raw diff --git a/tests/ase/Al8He8O12/virial.raw b/tests/ase_traj/Al8He8O12/virial.raw similarity index 100% rename from tests/ase/Al8He8O12/virial.raw rename to tests/ase_traj/Al8He8O12/virial.raw diff --git a/tests/ase/HeAlO.traj b/tests/ase_traj/HeAlO.traj similarity index 100% rename from tests/ase/HeAlO.traj rename to tests/ase_traj/HeAlO.traj diff --git a/tests/poscars/6362_OUTCAR b/tests/poscars/6362_OUTCAR new file mode 100644 index 00000000..1a53e951 --- /dev/null +++ b/tests/poscars/6362_OUTCAR @@ -0,0 +1,3090 @@ + vasp.5.4.4.18Apr17-6-g9f103f2a35 (build Jun 05 2020 11:42:50) complex + + executed on LinuxIFC date 2022.02.03 14:31:21 + running on 16 total cores + distrk: each k-point on 16 cores, 1 groups + distr: one band on NCORES_PER_BAND= 4 cores, 4 groups + + +-------------------------------------------------------------------------------------------------------- + + + INCAR: + POTCAR: PAW_PBE B 06Sep2000 + POTCAR: PAW_PBE O 08Apr2002 + POTCAR: PAW_PBE B 06Sep2000 + POTCAR: PAW_PBE O 08Apr2002 + POTCAR: PAW_PBE B 06Sep2000 + POTCAR: PAW_PBE O 08Apr2002 + POTCAR: PAW_PBE B 06Sep2000 + POTCAR: PAW_PBE O 08Apr2002 + POTCAR: PAW_PBE B 06Sep2000 + POTCAR: PAW_PBE O 08Apr2002 + POTCAR: PAW_PBE B 06Sep2000 + VRHFIN =B: s2p1 + LEXCH = PE + EATOM = 71.1703 eV, 5.2309 Ry + + TITEL = PAW_PBE B 06Sep2000 + LULTRA = F use ultrasoft PP ? + IUNSCR = 1 unscreen: 0-lin 1-nonlin 2-no + RPACOR = 1.200 partial core radius + POMASS = 10.811; ZVAL = 3.000 mass and valenz + RCORE = 1.700 outmost cutoff radius + RWIGS = 1.710; RWIGS = 0.905 wigner-seitz radius (au A) + ENMAX = 318.614; ENMIN = 238.960 eV + ICORE = 2 local potential + LCOR = T correct aug charges + LPAW = T paw PP + EAUG = 535.514 + DEXC = 0.000 + RMAX = 1.732 core radius for proj-oper + RAUG = 1.300 factor for augmentation sphere + RDEP = 1.757 radius for radial grids + RDEPT = 1.436 core radius for aug-charge + + Atomic configuration + 4 entries + n l j E occ. + 1 0 0.50 -180.5896 2.0000 + 2 0 0.50 -9.4431 2.0000 + 2 1 0.50 -3.6068 1.0000 + 3 2 1.50 -4.0817 0.0000 + Description + l E TYP RCUT TYP RCUT + 0 -9.4430752 23 1.500 + 0 0.8675899 23 1.500 + 1 -3.6067955 23 1.700 + 1 6.1086146 23 1.700 + 2 -4.0817478 7 1.700 + local pseudopotential read in + partial core-charges read in + partial kinetic energy density read in + atomic valenz-charges read in + non local Contribution for L= 0 read in + real space projection operators read in + non local Contribution for L= 0 read in + real space projection operators read in + non local Contribution for L= 1 read in + real space projection operators read in + non local Contribution for L= 1 read in + real space projection operators read in + PAW grid and wavefunctions read in + + number of l-projection operators is LMAX = 4 + number of lm-projection operators is LMMAX = 8 + + POTCAR: PAW_PBE O 08Apr2002 + VRHFIN =O: s2p4 + LEXCH = PE + EATOM = 432.3788 eV, 31.7789 Ry + + TITEL = PAW_PBE O 08Apr2002 + LULTRA = F use ultrasoft PP ? + IUNSCR = 1 unscreen: 0-lin 1-nonlin 2-no + RPACOR = 1.200 partial core radius + POMASS = 16.000; ZVAL = 6.000 mass and valenz + RCORE = 1.520 outmost cutoff radius + RWIGS = 1.550; RWIGS = 0.820 wigner-seitz radius (au A) + ENMAX = 400.000; ENMIN = 300.000 eV + ICORE = 2 local potential + LCOR = T correct aug charges + LPAW = T paw PP + EAUG = 605.392 + DEXC = 0.000 + RMAX = 1.553 core radius for proj-oper + RAUG = 1.300 factor for augmentation sphere + RDEP = 1.550 radius for radial grids + RDEPT = 1.329 core radius for aug-charge + + Atomic configuration + 4 entries + n l j E occ. + 1 0 0.50 -514.6923 2.0000 + 2 0 0.50 -23.9615 2.0000 + 2 1 0.50 -9.0305 4.0000 + 3 2 1.50 -9.5241 0.0000 + Description + l E TYP RCUT TYP RCUT + 0 -23.9615318 23 1.200 + 0 -9.5240782 23 1.200 + 1 -9.0304911 23 1.520 + 1 8.1634956 23 1.520 + 2 -9.5240782 7 1.500 + local pseudopotential read in + partial core-charges read in + partial kinetic energy density read in + kinetic energy density of atom read in + atomic valenz-charges read in + non local Contribution for L= 0 read in + real space projection operators read in + non local Contribution for L= 0 read in + real space projection operators read in + non local Contribution for L= 1 read in + real space projection operators read in + non local Contribution for L= 1 read in + real space projection operators read in + PAW grid and wavefunctions read in + + number of l-projection operators is LMAX = 4 + number of lm-projection operators is LMMAX = 8 + + POTCAR: PAW_PBE B 06Sep2000 + VRHFIN =B: s2p1 + LEXCH = PE + EATOM = 71.1703 eV, 5.2309 Ry + + TITEL = PAW_PBE B 06Sep2000 + LULTRA = F use ultrasoft PP ? + IUNSCR = 1 unscreen: 0-lin 1-nonlin 2-no + RPACOR = 1.200 partial core radius + POMASS = 10.811; ZVAL = 3.000 mass and valenz + RCORE = 1.700 outmost cutoff radius + RWIGS = 1.710; RWIGS = 0.905 wigner-seitz radius (au A) + ENMAX = 318.614; ENMIN = 238.960 eV + ICORE = 2 local potential + LCOR = T correct aug charges + LPAW = T paw PP + EAUG = 535.514 + DEXC = 0.000 + RMAX = 1.732 core radius for proj-oper + RAUG = 1.300 factor for augmentation sphere + RDEP = 1.757 radius for radial grids + RDEPT = 1.436 core radius for aug-charge + + Atomic configuration + 4 entries + n l j E occ. + 1 0 0.50 -180.5896 2.0000 + 2 0 0.50 -9.4431 2.0000 + 2 1 0.50 -3.6068 1.0000 + 3 2 1.50 -4.0817 0.0000 + Description + l E TYP RCUT TYP RCUT + 0 -9.4430752 23 1.500 + 0 0.8675899 23 1.500 + 1 -3.6067955 23 1.700 + 1 6.1086146 23 1.700 + 2 -4.0817478 7 1.700 + local pseudopotential read in + partial core-charges read in + partial kinetic energy density read in + atomic valenz-charges read in + non local Contribution for L= 0 read in + real space projection operators read in + non local Contribution for L= 0 read in + real space projection operators read in + non local Contribution for L= 1 read in + real space projection operators read in + non local Contribution for L= 1 read in + real space projection operators read in + PAW grid and wavefunctions read in + + number of l-projection operators is LMAX = 4 + number of lm-projection operators is LMMAX = 8 + + POTCAR: PAW_PBE O 08Apr2002 + VRHFIN =O: s2p4 + LEXCH = PE + EATOM = 432.3788 eV, 31.7789 Ry + + TITEL = PAW_PBE O 08Apr2002 + LULTRA = F use ultrasoft PP ? + IUNSCR = 1 unscreen: 0-lin 1-nonlin 2-no + RPACOR = 1.200 partial core radius + POMASS = 16.000; ZVAL = 6.000 mass and valenz + RCORE = 1.520 outmost cutoff radius + RWIGS = 1.550; RWIGS = 0.820 wigner-seitz radius (au A) + ENMAX = 400.000; ENMIN = 300.000 eV + ICORE = 2 local potential + LCOR = T correct aug charges + LPAW = T paw PP + EAUG = 605.392 + DEXC = 0.000 + RMAX = 1.553 core radius for proj-oper + RAUG = 1.300 factor for augmentation sphere + RDEP = 1.550 radius for radial grids + RDEPT = 1.329 core radius for aug-charge + + Atomic configuration + 4 entries + n l j E occ. + 1 0 0.50 -514.6923 2.0000 + 2 0 0.50 -23.9615 2.0000 + 2 1 0.50 -9.0305 4.0000 + 3 2 1.50 -9.5241 0.0000 + Description + l E TYP RCUT TYP RCUT + 0 -23.9615318 23 1.200 + 0 -9.5240782 23 1.200 + 1 -9.0304911 23 1.520 + 1 8.1634956 23 1.520 + 2 -9.5240782 7 1.500 + local pseudopotential read in + partial core-charges read in + partial kinetic energy density read in + kinetic energy density of atom read in + atomic valenz-charges read in + non local Contribution for L= 0 read in + real space projection operators read in + non local Contribution for L= 0 read in + real space projection operators read in + non local Contribution for L= 1 read in + real space projection operators read in + non local Contribution for L= 1 read in + real space projection operators read in + PAW grid and wavefunctions read in + + number of l-projection operators is LMAX = 4 + number of lm-projection operators is LMMAX = 8 + + POTCAR: PAW_PBE B 06Sep2000 + VRHFIN =B: s2p1 + LEXCH = PE + EATOM = 71.1703 eV, 5.2309 Ry + + TITEL = PAW_PBE B 06Sep2000 + LULTRA = F use ultrasoft PP ? + IUNSCR = 1 unscreen: 0-lin 1-nonlin 2-no + RPACOR = 1.200 partial core radius + POMASS = 10.811; ZVAL = 3.000 mass and valenz + RCORE = 1.700 outmost cutoff radius + RWIGS = 1.710; RWIGS = 0.905 wigner-seitz radius (au A) + ENMAX = 318.614; ENMIN = 238.960 eV + ICORE = 2 local potential + LCOR = T correct aug charges + LPAW = T paw PP + EAUG = 535.514 + DEXC = 0.000 + RMAX = 1.732 core radius for proj-oper + RAUG = 1.300 factor for augmentation sphere + RDEP = 1.757 radius for radial grids + RDEPT = 1.436 core radius for aug-charge + + Atomic configuration + 4 entries + n l j E occ. + 1 0 0.50 -180.5896 2.0000 + 2 0 0.50 -9.4431 2.0000 + 2 1 0.50 -3.6068 1.0000 + 3 2 1.50 -4.0817 0.0000 + Description + l E TYP RCUT TYP RCUT + 0 -9.4430752 23 1.500 + 0 0.8675899 23 1.500 + 1 -3.6067955 23 1.700 + 1 6.1086146 23 1.700 + 2 -4.0817478 7 1.700 + local pseudopotential read in + partial core-charges read in + partial kinetic energy density read in + atomic valenz-charges read in + non local Contribution for L= 0 read in + real space projection operators read in + non local Contribution for L= 0 read in + real space projection operators read in + non local Contribution for L= 1 read in + real space projection operators read in + non local Contribution for L= 1 read in + real space projection operators read in + PAW grid and wavefunctions read in + + number of l-projection operators is LMAX = 4 + number of lm-projection operators is LMMAX = 8 + + POTCAR: PAW_PBE O 08Apr2002 + VRHFIN =O: s2p4 + LEXCH = PE + EATOM = 432.3788 eV, 31.7789 Ry + + TITEL = PAW_PBE O 08Apr2002 + LULTRA = F use ultrasoft PP ? + IUNSCR = 1 unscreen: 0-lin 1-nonlin 2-no + RPACOR = 1.200 partial core radius + POMASS = 16.000; ZVAL = 6.000 mass and valenz + RCORE = 1.520 outmost cutoff radius + RWIGS = 1.550; RWIGS = 0.820 wigner-seitz radius (au A) + ENMAX = 400.000; ENMIN = 300.000 eV + ICORE = 2 local potential + LCOR = T correct aug charges + LPAW = T paw PP + EAUG = 605.392 + DEXC = 0.000 + RMAX = 1.553 core radius for proj-oper + RAUG = 1.300 factor for augmentation sphere + RDEP = 1.550 radius for radial grids + RDEPT = 1.329 core radius for aug-charge + + Atomic configuration + 4 entries + n l j E occ. + 1 0 0.50 -514.6923 2.0000 + 2 0 0.50 -23.9615 2.0000 + 2 1 0.50 -9.0305 4.0000 + 3 2 1.50 -9.5241 0.0000 + Description + l E TYP RCUT TYP RCUT + 0 -23.9615318 23 1.200 + 0 -9.5240782 23 1.200 + 1 -9.0304911 23 1.520 + 1 8.1634956 23 1.520 + 2 -9.5240782 7 1.500 + local pseudopotential read in + partial core-charges read in + partial kinetic energy density read in + kinetic energy density of atom read in + atomic valenz-charges read in + non local Contribution for L= 0 read in + real space projection operators read in + non local Contribution for L= 0 read in + real space projection operators read in + non local Contribution for L= 1 read in + real space projection operators read in + non local Contribution for L= 1 read in + real space projection operators read in + PAW grid and wavefunctions read in + + number of l-projection operators is LMAX = 4 + number of lm-projection operators is LMMAX = 8 + + POTCAR: PAW_PBE B 06Sep2000 + VRHFIN =B: s2p1 + LEXCH = PE + EATOM = 71.1703 eV, 5.2309 Ry + + TITEL = PAW_PBE B 06Sep2000 + LULTRA = F use ultrasoft PP ? + IUNSCR = 1 unscreen: 0-lin 1-nonlin 2-no + RPACOR = 1.200 partial core radius + POMASS = 10.811; ZVAL = 3.000 mass and valenz + RCORE = 1.700 outmost cutoff radius + RWIGS = 1.710; RWIGS = 0.905 wigner-seitz radius (au A) + ENMAX = 318.614; ENMIN = 238.960 eV + ICORE = 2 local potential + LCOR = T correct aug charges + LPAW = T paw PP + EAUG = 535.514 + DEXC = 0.000 + RMAX = 1.732 core radius for proj-oper + RAUG = 1.300 factor for augmentation sphere + RDEP = 1.757 radius for radial grids + RDEPT = 1.436 core radius for aug-charge + + Atomic configuration + 4 entries + n l j E occ. + 1 0 0.50 -180.5896 2.0000 + 2 0 0.50 -9.4431 2.0000 + 2 1 0.50 -3.6068 1.0000 + 3 2 1.50 -4.0817 0.0000 + Description + l E TYP RCUT TYP RCUT + 0 -9.4430752 23 1.500 + 0 0.8675899 23 1.500 + 1 -3.6067955 23 1.700 + 1 6.1086146 23 1.700 + 2 -4.0817478 7 1.700 + local pseudopotential read in + partial core-charges read in + partial kinetic energy density read in + atomic valenz-charges read in + non local Contribution for L= 0 read in + real space projection operators read in + non local Contribution for L= 0 read in + real space projection operators read in + non local Contribution for L= 1 read in + real space projection operators read in + non local Contribution for L= 1 read in + real space projection operators read in + PAW grid and wavefunctions read in + + number of l-projection operators is LMAX = 4 + number of lm-projection operators is LMMAX = 8 + + POTCAR: PAW_PBE O 08Apr2002 + VRHFIN =O: s2p4 + LEXCH = PE + EATOM = 432.3788 eV, 31.7789 Ry + + TITEL = PAW_PBE O 08Apr2002 + LULTRA = F use ultrasoft PP ? + IUNSCR = 1 unscreen: 0-lin 1-nonlin 2-no + RPACOR = 1.200 partial core radius + POMASS = 16.000; ZVAL = 6.000 mass and valenz + RCORE = 1.520 outmost cutoff radius + RWIGS = 1.550; RWIGS = 0.820 wigner-seitz radius (au A) + ENMAX = 400.000; ENMIN = 300.000 eV + ICORE = 2 local potential + LCOR = T correct aug charges + LPAW = T paw PP + EAUG = 605.392 + DEXC = 0.000 + RMAX = 1.553 core radius for proj-oper + RAUG = 1.300 factor for augmentation sphere + RDEP = 1.550 radius for radial grids + RDEPT = 1.329 core radius for aug-charge + + Atomic configuration + 4 entries + n l j E occ. + 1 0 0.50 -514.6923 2.0000 + 2 0 0.50 -23.9615 2.0000 + 2 1 0.50 -9.0305 4.0000 + 3 2 1.50 -9.5241 0.0000 + Description + l E TYP RCUT TYP RCUT + 0 -23.9615318 23 1.200 + 0 -9.5240782 23 1.200 + 1 -9.0304911 23 1.520 + 1 8.1634956 23 1.520 + 2 -9.5240782 7 1.500 + local pseudopotential read in + partial core-charges read in + partial kinetic energy density read in + kinetic energy density of atom read in + atomic valenz-charges read in + non local Contribution for L= 0 read in + real space projection operators read in + non local Contribution for L= 0 read in + real space projection operators read in + non local Contribution for L= 1 read in + real space projection operators read in + non local Contribution for L= 1 read in + real space projection operators read in + PAW grid and wavefunctions read in + + number of l-projection operators is LMAX = 4 + number of lm-projection operators is LMMAX = 8 + + POTCAR: PAW_PBE B 06Sep2000 + VRHFIN =B: s2p1 + LEXCH = PE + EATOM = 71.1703 eV, 5.2309 Ry + + TITEL = PAW_PBE B 06Sep2000 + LULTRA = F use ultrasoft PP ? + IUNSCR = 1 unscreen: 0-lin 1-nonlin 2-no + RPACOR = 1.200 partial core radius + POMASS = 10.811; ZVAL = 3.000 mass and valenz + RCORE = 1.700 outmost cutoff radius + RWIGS = 1.710; RWIGS = 0.905 wigner-seitz radius (au A) + ENMAX = 318.614; ENMIN = 238.960 eV + ICORE = 2 local potential + LCOR = T correct aug charges + LPAW = T paw PP + EAUG = 535.514 + DEXC = 0.000 + RMAX = 1.732 core radius for proj-oper + RAUG = 1.300 factor for augmentation sphere + RDEP = 1.757 radius for radial grids + RDEPT = 1.436 core radius for aug-charge + + Atomic configuration + 4 entries + n l j E occ. + 1 0 0.50 -180.5896 2.0000 + 2 0 0.50 -9.4431 2.0000 + 2 1 0.50 -3.6068 1.0000 + 3 2 1.50 -4.0817 0.0000 + Description + l E TYP RCUT TYP RCUT + 0 -9.4430752 23 1.500 + 0 0.8675899 23 1.500 + 1 -3.6067955 23 1.700 + 1 6.1086146 23 1.700 + 2 -4.0817478 7 1.700 + local pseudopotential read in + partial core-charges read in + partial kinetic energy density read in + atomic valenz-charges read in + non local Contribution for L= 0 read in + real space projection operators read in + non local Contribution for L= 0 read in + real space projection operators read in + non local Contribution for L= 1 read in + real space projection operators read in + non local Contribution for L= 1 read in + real space projection operators read in + PAW grid and wavefunctions read in + + number of l-projection operators is LMAX = 4 + number of lm-projection operators is LMMAX = 8 + + POTCAR: PAW_PBE O 08Apr2002 + VRHFIN =O: s2p4 + LEXCH = PE + EATOM = 432.3788 eV, 31.7789 Ry + + TITEL = PAW_PBE O 08Apr2002 + LULTRA = F use ultrasoft PP ? + IUNSCR = 1 unscreen: 0-lin 1-nonlin 2-no + RPACOR = 1.200 partial core radius + POMASS = 16.000; ZVAL = 6.000 mass and valenz + RCORE = 1.520 outmost cutoff radius + RWIGS = 1.550; RWIGS = 0.820 wigner-seitz radius (au A) + ENMAX = 400.000; ENMIN = 300.000 eV + ICORE = 2 local potential + LCOR = T correct aug charges + LPAW = T paw PP + EAUG = 605.392 + DEXC = 0.000 + RMAX = 1.553 core radius for proj-oper + RAUG = 1.300 factor for augmentation sphere + RDEP = 1.550 radius for radial grids + RDEPT = 1.329 core radius for aug-charge + + Atomic configuration + 4 entries + n l j E occ. + 1 0 0.50 -514.6923 2.0000 + 2 0 0.50 -23.9615 2.0000 + 2 1 0.50 -9.0305 4.0000 + 3 2 1.50 -9.5241 0.0000 + Description + l E TYP RCUT TYP RCUT + 0 -23.9615318 23 1.200 + 0 -9.5240782 23 1.200 + 1 -9.0304911 23 1.520 + 1 8.1634956 23 1.520 + 2 -9.5240782 7 1.500 + local pseudopotential read in + partial core-charges read in + partial kinetic energy density read in + kinetic energy density of atom read in + atomic valenz-charges read in + non local Contribution for L= 0 read in + real space projection operators read in + non local Contribution for L= 0 read in + real space projection operators read in + non local Contribution for L= 1 read in + real space projection operators read in + non local Contribution for L= 1 read in + real space projection operators read in + PAW grid and wavefunctions read in + + number of l-projection operators is LMAX = 4 + number of lm-projection operators is LMMAX = 8 + + PAW_PBE B 06Sep2000 : + energy of atom 1 EATOM= -71.1703 + kinetic energy error for atom= 0.0020 (will be added to EATOM!!) + PAW_PBE O 08Apr2002 : + energy of atom 2 EATOM= -432.3788 + kinetic energy error for atom= 0.1156 (will be added to EATOM!!) + PAW_PBE B 06Sep2000 : + energy of atom 3 EATOM= -71.1703 + kinetic energy error for atom= 0.0020 (will be added to EATOM!!) + PAW_PBE O 08Apr2002 : + energy of atom 4 EATOM= -432.3788 + kinetic energy error for atom= 0.1156 (will be added to EATOM!!) + PAW_PBE B 06Sep2000 : + energy of atom 5 EATOM= -71.1703 + kinetic energy error for atom= 0.0020 (will be added to EATOM!!) + PAW_PBE O 08Apr2002 : + energy of atom 6 EATOM= -432.3788 + kinetic energy error for atom= 0.1156 (will be added to EATOM!!) + PAW_PBE B 06Sep2000 : + energy of atom 7 EATOM= -71.1703 + kinetic energy error for atom= 0.0020 (will be added to EATOM!!) + PAW_PBE O 08Apr2002 : + energy of atom 8 EATOM= -432.3788 + kinetic energy error for atom= 0.1156 (will be added to EATOM!!) + PAW_PBE B 06Sep2000 : + energy of atom 9 EATOM= -71.1703 + kinetic energy error for atom= 0.0020 (will be added to EATOM!!) + PAW_PBE O 08Apr2002 : + energy of atom 10 EATOM= -432.3788 + kinetic energy error for atom= 0.1156 (will be added to EATOM!!) + + + POSCAR: B8 O6 + positions in direct lattice + velocities in cartesian coordinates + exchange correlation table for LEXCH = 8 + RHO(1)= 0.500 N(1) = 2000 + RHO(2)= 100.500 N(2) = 4000 + + + +-------------------------------------------------------------------------------------------------------- + + + ion position nearest neighbor table + 1 1.000 0.904 0.839- 4 1.30 2 1.35 14 1.46 + 2 0.728 0.962 0.825- 1 1.35 12 1.38 + 3 0.168 0.556 0.506- 10 1.33 14 1.50 5 1.71 + 4 0.201 0.948 0.032- 1 1.30 11 1.40 + 5 0.336 0.372 0.591- 7 1.40 3 1.71 6 1.79 9 2.08 + 6 0.195 0.016 0.516- 14 1.47 9 1.77 5 1.79 11 1.88 + 7 0.640 0.401 0.537- 5 1.40 9 1.49 + 8 0.050 0.564 0.131- 13 1.37 10 1.38 11 1.64 + 9 0.590 0.108 0.465- 7 1.49 11 1.64 12 1.71 6 1.77 5 2.08 + 10 0.132 0.443 0.262- 3 1.33 8 1.38 + 11 0.296 0.877 0.207- 4 1.40 8 1.64 9 1.64 6 1.88 + 12 0.692 0.146 0.753- 13 1.37 2 1.38 9 1.71 + 13 0.763 0.412 0.941- 12 1.37 8 1.37 + 14 0.103 0.819 0.608- 1 1.46 6 1.47 3 1.50 + + LATTYP: Found a triclinic cell. + ALAT = 12.8260659206 + B/A-ratio = 0.6475198108 + C/A-ratio = 0.4858817341 + COS(alpha) = 0.0109955670 + COS(beta) = 0.3775664644 + COS(gamma) = 0.9085816773 + + Lattice vectors: + + A1 = ( 8.6500128306, -8.0520581611, -4.9849377528) + A2 = ( 6.1943171792, -5.5261467743, 0.2595194967) + A3 = ( -1.9627402695, -2.5535905087, -5.3351702227) + + +Analysis of symmetry for initial positions (statically): +===================================================================== + Subroutine PRICEL returns: + Original cell was already a primitive cell. + + + Routine SETGRP: Setting up the symmetry group for a + triclinic supercell. + + + Subroutine GETGRP returns: Found 1 space group operations + (whereof 1 operations were pure point group operations) + out of a pool of 2 trial point group operations. + + +The static configuration has the point symmetry C_1 . + + +Analysis of symmetry for dynamics (positions and initial velocities): +===================================================================== + Subroutine PRICEL returns: + Original cell was already a primitive cell. + + + Routine SETGRP: Setting up the symmetry group for a + triclinic supercell. + + + Subroutine GETGRP returns: Found 1 space group operations + (whereof 1 operations were pure point group operations) + out of a pool of 2 trial point group operations. + + +The dynamic configuration has the point symmetry C_1 . + + + Subroutine INISYM returns: Found 1 space group operations + (whereof 1 operations are pure point group operations), + and found 1 'primitive' translations + + + + KPOINTS: Automatic mesh + +Automatic generation of k-mesh. + generate k-points for: 7 6 6 +Space group operators: + irot det(A) alpha n_x n_y n_z tau_x tau_y tau_z + 1 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + + Subroutine IBZKPT returns following result: + =========================================== + + Found 128 irreducible k-points: + + Following reciprocal coordinates: + Coordinates Weight + 0.000000 0.000000 0.000000 1.000000 + 0.142857 0.000000 0.000000 2.000000 + 0.285714 0.000000 0.000000 2.000000 + 0.428571 0.000000 0.000000 2.000000 + 0.000000 0.166667 0.000000 2.000000 + 0.142857 0.166667 0.000000 2.000000 + 0.285714 0.166667 0.000000 2.000000 + 0.428571 0.166667 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maximal LDIM = 4 non local SUM 2l+1 LMDIM = 8 + total plane-waves NPLWV = 50400 + max r-space proj IRMAX = 1 max aug-charges IRDMAX= 6168 + dimension x,y,z NGX = 30 NGY = 40 NGZ = 42 + dimension x,y,z NGXF= 60 NGYF= 80 NGZF= 84 + support grid NGXF= 60 NGYF= 80 NGZF= 84 + ions per type = 1 1 1 1 2 1 2 1 2 2 + + NGX,Y,Z is equivalent to a cutoff of 11.29, 11.40, 11.19 a.u. + NGXF,Y,Z is equivalent to a cutoff of 22.57, 22.80, 22.38 a.u. + + SYSTEM = unknown system + POSCAR = B8 O6 + + Startparameter for this run: + NWRITE = 2 write-flag & timer + PREC = accura normal or accurate (medium, high low for compatibility) + ISTART = 0 job : 0-new 1-cont 2-samecut + ICHARG = 2 charge: 1-file 2-atom 10-const + ISPIN = 1 spin polarized calculation? + LNONCOLLINEAR = F non collinear calculations + LSORBIT = F spin-orbit coupling + INIWAV = 1 electr: 0-lowe 1-rand 2-diag + LASPH = F aspherical Exc in radial PAW + METAGGA= F non-selfconsistent MetaGGA calc. + + Electronic Relaxation 1 + ENCUT = 400.0 eV 29.40 Ry 5.42 a.u. 7.21 9.51 10.18*2*pi/ulx,y,z + ENINI = 400.0 initial cutoff + ENAUG = 605.4 eV augmentation charge cutoff + NELM = 60; NELMIN= 2; NELMDL= -5 # of ELM steps + EDIFF = 0.1E-03 stopping-criterion for ELM + LREAL = F real-space projection + NLSPLINE = F spline interpolate recip. space projectors + LCOMPAT= F compatible to vasp.4.4 + GGA_COMPAT = T GGA compatible to vasp.4.4-vasp.4.6 + LMAXPAW = -100 max onsite density + LMAXMIX = 2 max onsite mixed and CHGCAR + VOSKOWN= 0 Vosko Wilk Nusair interpolation + ROPT = 0.00000 0.00000 0.00000 0.00000 + ROPT = 0.00000 0.00000 0.00000 0.00000 + ROPT = 0.00000 0.00000 + Ionic relaxation + EDIFFG = 0.1E-02 stopping-criterion for IOM + NSW = 50 number of steps for IOM + NBLOCK = 1; KBLOCK = 50 inner block; outer block + IBRION = 2 ionic relax: 0-MD 1-quasi-New 2-CG + NFREE = 1 steps in history (QN), initial steepest desc. (CG) + ISIF = 3 stress and relaxation + IWAVPR = 11 prediction: 0-non 1-charg 2-wave 3-comb + ISYM = 2 0-nonsym 1-usesym 2-fastsym + LCORR = T Harris-Foulkes like correction to forces + + POTIM = 0.5000 time-step for ionic-motion + TEIN = 0.0 initial temperature + TEBEG = 0.0; TEEND = 0.0 temperature during run + SMASS = -3.00 Nose mass-parameter (am) + estimated Nose-frequenzy (Omega) = 0.10E-29 period in steps =****** mass= -0.446E-27a.u. + SCALEE = 1.0000 scale energy and forces + NPACO = 256; APACO = 16.0 distance and # of slots for P.C. + PSTRESS= 0.0 pullay stress + + Mass of Ions in am + POMASS = 10.81 16.00 10.81 16.00 10.81 16.00 10.81 16.00 + POMASS = 10.81 16.00 + Ionic Valenz + ZVAL = 3.00 6.00 3.00 6.00 3.00 6.00 3.00 6.00 + ZVAL = 3.00 6.00 + Atomic Wigner-Seitz radii + RWIGS = -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 + RWIGS = -1.00 -1.00 + virtual crystal weights + VCA = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 + VCA = 1.00 1.00 + NELECT = 60.0000 total number of electrons + NUPDOWN= -1.0000 fix difference up-down + + DOS related values: + EMIN = 10.00; EMAX =-10.00 energy-range for DOS + EFERMI = 0.00 + ISMEAR = 2; SIGMA = 0.10 broadening in eV -4-tet -1-fermi 0-gaus + + Electronic relaxation 2 (details) + IALGO = 68 algorithm + LDIAG = T sub-space diagonalisation (order eigenvalues) + LSUBROT= F optimize rotation matrix (better conditioning) + TURBO = 0 0=normal 1=particle mesh + IRESTART = 0 0=no restart 2=restart with 2 vectors + NREBOOT = 0 no. of reboots + NMIN = 0 reboot dimension + EREF = 0.00 reference energy to select bands + IMIX = 4 mixing-type and parameters + AMIX = 0.40; BMIX = 1.00 + AMIX_MAG = 1.60; BMIX_MAG = 1.00 + AMIN = 0.10 + WC = 100.; INIMIX= 1; MIXPRE= 1; MAXMIX= -45 + + Intra band minimization: + WEIMIN = 0.0010 energy-eigenvalue tresh-hold + EBREAK = 0.63E-06 absolut break condition + DEPER = 0.30 relativ break condition + + TIME = 0.40 timestep for ELM + + volume/ion in A,a.u. = 9.41 63.47 + Fermi-wavevector in a.u.,A,eV,Ry = 1.259758 2.380597 21.592304 1.586990 + Thomas-Fermi vector in A = 2.393301 + + Write flags + LWAVE = F write WAVECAR + LDOWNSAMPLE = F k-point downsampling of WAVECAR + LCHARG = F write CHGCAR + LVTOT = F write LOCPOT, total local potential + LVHAR = F write LOCPOT, Hartree potential only + LELF = F write electronic localiz. function (ELF) + LORBIT = 0 0 simple, 1 ext, 2 COOP (PROOUT), +10 PAW based schemes + + + Dipole corrections + LMONO = F monopole corrections only (constant potential shift) + LDIPOL = F correct potential (dipole corrections) + IDIPOL = 0 1-x, 2-y, 3-z, 4-all directions + EPSILON= 1.0000000 bulk dielectric constant + + Exchange correlation treatment: + GGA = -- GGA type + LEXCH = 8 internal setting for exchange type + VOSKOWN= 0 Vosko Wilk Nusair interpolation + LHFCALC = F Hartree Fock is set to + LHFONE = F Hartree Fock one center treatment + AEXX = 0.0000 exact exchange contribution + + Linear response parameters + LEPSILON= F determine dielectric tensor + LRPA = F only Hartree local field effects (RPA) + LNABLA = F use nabla operator in PAW spheres + LVEL = F velocity operator in full k-point grid + LINTERFAST= F fast interpolation + KINTER = 0 interpolate to denser k-point grid + CSHIFT =0.1000 complex shift for real part using Kramers Kronig + OMEGAMAX= -1.0 maximum frequency + DEG_THRESHOLD= 0.2000000E-02 threshold for treating states as degnerate + RTIME = -0.100 relaxation time in fs + (WPLASMAI= 0.000 imaginary part of plasma frequency in eV, 0.658/RTIME) + DFIELD = 0.0000000 0.0000000 0.0000000 field for delta impulse in time + + Orbital magnetization related: + ORBITALMAG= F switch on orbital magnetization + LCHIMAG = F perturbation theory with respect to B field + DQ = 0.001000 dq finite difference perturbation B field + LLRAUG = F two centre corrections for induced B field + + + +-------------------------------------------------------------------------------------------------------- + + + conjugate gradient relaxation 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0.1667 0.1667 plane waves: 2407 + k-point 32 : 0.2857 0.1667 0.1667 plane waves: 2399 + k-point 33 : 0.4286 0.1667 0.1667 plane waves: 2402 + k-point 34 : -0.4286 0.1667 0.1667 plane waves: 2395 + k-point 35 : -0.2857 0.1667 0.1667 plane waves: 2387 + k-point 36 : -0.1429 0.1667 0.1667 plane waves: 2377 + k-point 37 : 0.0000 0.3333 0.1667 plane waves: 2392 + k-point 38 : 0.1429 0.3333 0.1667 plane waves: 2390 + k-point 39 : 0.2857 0.3333 0.1667 plane waves: 2385 + k-point 40 : 0.4286 0.3333 0.1667 plane waves: 2391 + k-point 41 : -0.4286 0.3333 0.1667 plane waves: 2388 + k-point 42 : -0.2857 0.3333 0.1667 plane waves: 2394 + k-point 43 : -0.1429 0.3333 0.1667 plane waves: 2376 + k-point 44 : 0.0000 0.5000 0.1667 plane waves: 2383 + k-point 45 : 0.1429 0.5000 0.1667 plane waves: 2374 + k-point 46 : 0.2857 0.5000 0.1667 plane waves: 2389 + k-point 47 : 0.4286 0.5000 0.1667 plane waves: 2379 + k-point 48 : -0.4286 0.5000 0.1667 plane waves: 2393 + k-point 49 : -0.2857 0.5000 0.1667 plane waves: 2386 + k-point 50 : -0.1429 0.5000 0.1667 plane waves: 2375 + k-point 51 : 0.0000-0.3333 0.1667 plane waves: 2389 + k-point 52 : 0.1429-0.3333 0.1667 plane waves: 2393 + k-point 53 : 0.2857-0.3333 0.1667 plane waves: 2387 + k-point 54 : 0.4286-0.3333 0.1667 plane waves: 2394 + k-point 55 : -0.4286-0.3333 0.1667 plane waves: 2391 + k-point 56 : -0.2857-0.3333 0.1667 plane waves: 2404 + k-point 57 : -0.1429-0.3333 0.1667 plane waves: 2392 + k-point 58 : 0.0000-0.1667 0.1667 plane waves: 2396 + k-point 59 : 0.1429-0.1667 0.1667 plane waves: 2385 + k-point 60 : 0.2857-0.1667 0.1667 plane waves: 2389 + k-point 61 : 0.4286-0.1667 0.1667 plane waves: 2395 + k-point 62 : -0.4286-0.1667 0.1667 plane waves: 2403 + k-point 63 : -0.2857-0.1667 0.1667 plane waves: 2393 + k-point 64 : -0.1429-0.1667 0.1667 plane waves: 2390 + k-point 65 : 0.0000 0.0000 0.3333 plane waves: 2393 + k-point 66 : 0.1429 0.0000 0.3333 plane waves: 2403 + k-point 67 : 0.2857 0.0000 0.3333 plane waves: 2400 + k-point 68 : 0.4286 0.0000 0.3333 plane waves: 2400 + k-point 69 : -0.4286 0.0000 0.3333 plane waves: 2395 + k-point 70 : -0.2857 0.0000 0.3333 plane waves: 2397 + k-point 71 : -0.1429 0.0000 0.3333 plane waves: 2390 + k-point 72 : 0.0000 0.1667 0.3333 plane waves: 2396 + k-point 73 : 0.1429 0.1667 0.3333 plane waves: 2405 + k-point 74 : 0.2857 0.1667 0.3333 plane waves: 2395 + k-point 75 : 0.4286 0.1667 0.3333 plane waves: 2399 + k-point 76 : -0.4286 0.1667 0.3333 plane waves: 2396 + k-point 77 : -0.2857 0.1667 0.3333 plane waves: 2387 + k-point 78 : -0.1429 0.1667 0.3333 plane waves: 2385 + k-point 79 : 0.0000 0.3333 0.3333 plane waves: 2388 + k-point 80 : 0.1429 0.3333 0.3333 plane waves: 2393 + k-point 81 : 0.2857 0.3333 0.3333 plane waves: 2387 + k-point 82 : 0.4286 0.3333 0.3333 plane waves: 2387 + k-point 83 : -0.4286 0.3333 0.3333 plane waves: 2386 + k-point 84 : -0.2857 0.3333 0.3333 plane waves: 2387 + k-point 85 : -0.1429 0.3333 0.3333 plane waves: 2385 + k-point 86 : 0.0000 0.5000 0.3333 plane waves: 2388 + k-point 87 : 0.1429 0.5000 0.3333 plane waves: 2381 + k-point 88 : 0.2857 0.5000 0.3333 plane waves: 2382 + k-point 89 : 0.4286 0.5000 0.3333 plane waves: 2376 + k-point 90 : -0.4286 0.5000 0.3333 plane waves: 2387 + k-point 91 : -0.2857 0.5000 0.3333 plane waves: 2399 + k-point 92 : -0.1429 0.5000 0.3333 plane waves: 2398 + k-point 93 : 0.0000-0.3333 0.3333 plane waves: 2398 + k-point 94 : 0.1429-0.3333 0.3333 plane waves: 2395 + k-point 95 : 0.2857-0.3333 0.3333 plane waves: 2388 + k-point 96 : 0.4286-0.3333 0.3333 plane waves: 2391 + k-point 97 : -0.4286-0.3333 0.3333 plane waves: 2399 + k-point 98 : -0.2857-0.3333 0.3333 plane waves: 2398 + k-point 99 : -0.1429-0.3333 0.3333 plane waves: 2387 + k-point ** : 0.0000-0.1667 0.3333 plane waves: 2403 + k-point ** : 0.1429-0.1667 0.3333 plane waves: 2391 + k-point ** : 0.2857-0.1667 0.3333 plane waves: 2384 + k-point ** : 0.4286-0.1667 0.3333 plane waves: 2398 + k-point ** : -0.4286-0.1667 0.3333 plane waves: 2396 + k-point ** : -0.2857-0.1667 0.3333 plane waves: 2392 + k-point ** : -0.1429-0.1667 0.3333 plane waves: 2404 + k-point ** : 0.0000 0.0000 0.5000 plane waves: 2400 + k-point ** : 0.1429 0.0000 0.5000 plane waves: 2391 + k-point ** : 0.2857 0.0000 0.5000 plane waves: 2396 + k-point ** : 0.4286 0.0000 0.5000 plane waves: 2399 + k-point ** : 0.0000 0.1667 0.5000 plane waves: 2395 + k-point ** : 0.1429 0.1667 0.5000 plane waves: 2391 + k-point ** : 0.2857 0.1667 0.5000 plane waves: 2406 + k-point ** : 0.4286 0.1667 0.5000 plane waves: 2398 + k-point ** : -0.4286 0.1667 0.5000 plane waves: 2386 + k-point ** : -0.2857 0.1667 0.5000 plane waves: 2399 + k-point ** : -0.1429 0.1667 0.5000 plane waves: 2387 + k-point ** : 0.0000 0.3333 0.5000 plane waves: 2395 + k-point ** : 0.1429 0.3333 0.5000 plane waves: 2397 + k-point ** : 0.2857 0.3333 0.5000 plane waves: 2397 + k-point ** : 0.4286 0.3333 0.5000 plane waves: 2387 + k-point ** : -0.4286 0.3333 0.5000 plane waves: 2391 + k-point ** : -0.2857 0.3333 0.5000 plane waves: 2385 + k-point ** : -0.1429 0.3333 0.5000 plane waves: 2395 + k-point ** : 0.0000 0.5000 0.5000 plane waves: 2386 + k-point ** : 0.1429 0.5000 0.5000 plane waves: 2394 + k-point ** : 0.2857 0.5000 0.5000 plane waves: 2390 + k-point ** : 0.4286 0.5000 0.5000 plane waves: 2392 + + maximum and minimum number of plane-waves per node : 622 576 + + maximum number of plane-waves: 2411 + maximum index in each direction: + IXMAX= 7 IYMAX= 9 IZMAX= 10 + IXMIN= -7 IYMIN= -10 IZMIN= -10 + + + parallel 3D FFT for wavefunctions: + minimum data exchange during FFTs selected (reduces bandwidth) + parallel 3D FFT for charge: + minimum data exchange during FFTs selected (reduces bandwidth) + + + total amount of memory used by VASP MPI-rank0 99022. kBytes +======================================================================= + + base : 30000. kBytes + nonl-proj : 50600. kBytes + fftplans : 1305. kBytes + grid : 3834. kBytes + one-center: 12. kBytes + wavefun : 13271. kBytes + + INWAV: cpu time 0.0000: real time 0.0000 + Broyden mixing: mesh for mixing (old mesh) + NGX = 15 NGY = 19 NGZ = 21 + (NGX = 60 NGY = 80 NGZ = 84) + gives a total of 5985 points + + initial charge density was supplied: + charge density of overlapping atoms calculated + number of electron 60.0000000 magnetization + keeping initial charge density in first step + + +-------------------------------------------------------------------------------------------------------- + + + Maximum index for augmentation-charges 385 (set IRDMAX) + + +-------------------------------------------------------------------------------------------------------- + + + First call to EWALD: gamma= 0.348 + Maximum number of real-space cells 3x 3x 3 + Maximum number of reciprocal cells 2x 3x 3 + + FEWALD: cpu time 0.0024: real time 0.0026 + + +--------------------------------------- Iteration 1( 1) --------------------------------------- + + + POTLOK: cpu time 0.0486: real time 0.0507 + SETDIJ: cpu time 0.0037: real time 0.0037 + EDDAV: cpu time 3.9920: real time 4.0057 + DOS: cpu time 0.0072: real time 0.0072 + -------------------------------------------- + LOOP: cpu time 4.0515: real time 4.0673 + + eigenvalue-minimisations : 10240 + total energy-change (2. order) : 0.2630383E+03 (-0.2764715E+04) + number of electron 60.0000000 magnetization + augmentation part 60.0000000 magnetization + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 146.90699857 + Ewald energy TEWEN = -2087.53862760 + -Hartree energ DENC = -1056.60076398 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 224.05028418 + PAW double counting = 2427.29578539 -2431.24524980 + entropy T*S EENTRO = -0.00017706 + eigenvalues EBANDS = -122.75551221 + atomic energy EATOM = 3162.92556708 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = 263.03830454 eV + + energy without entropy = 263.03848160 energy(sigma->0) = 263.03834881 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 2) --------------------------------------- + + + EDDAV: cpu time 4.6638: real time 4.7403 + DOS: cpu time 0.0071: real time 0.0072 + -------------------------------------------- + LOOP: cpu time 4.6709: real time 4.7475 + + eigenvalue-minimisations : 12824 + total energy-change (2. order) :-0.3499719E+03 (-0.3375392E+03) + number of electron 60.0000000 magnetization + augmentation part 60.0000000 magnetization + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 146.90699857 + Ewald energy TEWEN = -2087.53862760 + -Hartree energ DENC = -1056.60076398 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 224.05028418 + PAW double counting = 2427.29578539 -2431.24524980 + entropy T*S EENTRO = 0.00003039 + eigenvalues EBANDS = -472.72765627 + atomic energy EATOM = 3162.92556708 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -86.93363207 eV + + energy without entropy = -86.93366246 energy(sigma->0) = -86.93363967 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 3) --------------------------------------- + + + EDDAV: cpu time 4.5573: real time 4.6069 + DOS: cpu time 0.0073: real time 0.0075 + -------------------------------------------- + LOOP: cpu time 4.5646: real time 4.6144 + + eigenvalue-minimisations : 12336 + total energy-change (2. order) :-0.1977494E+02 (-0.1961238E+02) + number of electron 60.0000000 magnetization + augmentation part 60.0000000 magnetization + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 146.90699857 + Ewald energy TEWEN = -2087.53862760 + -Hartree energ DENC = -1056.60076398 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 224.05028418 + PAW double counting = 2427.29578539 -2431.24524980 + entropy T*S EENTRO = 0.00217790 + eigenvalues EBANDS = -492.50474751 + atomic energy EATOM = 3162.92556708 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -106.70857579 eV + + energy without entropy = -106.71075369 energy(sigma->0) = -106.70912027 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 4) --------------------------------------- + + + EDDAV: cpu time 4.7553: real time 4.8543 + DOS: cpu time 0.0074: real time 0.0075 + -------------------------------------------- + LOOP: cpu time 4.7627: real time 4.8618 + + eigenvalue-minimisations : 12792 + total energy-change (2. order) :-0.2779531E+00 (-0.2776537E+00) + number of electron 60.0000000 magnetization + augmentation part 60.0000000 magnetization + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 146.90699857 + Ewald energy TEWEN = -2087.53862760 + -Hartree energ DENC = -1056.60076398 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 224.05028418 + PAW double counting = 2427.29578539 -2431.24524980 + entropy T*S EENTRO = 0.00218491 + eigenvalues EBANDS = -492.78270758 + atomic energy EATOM = 3162.92556708 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -106.98652886 eV + + energy without entropy = -106.98871377 energy(sigma->0) = -106.98707509 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 5) --------------------------------------- + + + EDDAV: cpu time 4.6964: real time 4.7626 + DOS: cpu time 0.0071: real time 0.0073 + CHARGE: cpu time 0.3545: real time 0.3561 + MIXING: cpu time 0.0017: real time 0.0017 + -------------------------------------------- + LOOP: cpu time 5.0598: real time 5.1277 + + eigenvalue-minimisations : 12672 + total energy-change (2. order) :-0.4251493E-02 (-0.4250900E-02) + number of electron 60.0000006 magnetization + augmentation part 4.4686737 magnetization + + Broyden mixing: + rms(total) = 0.18298E+01 rms(broyden)= 0.18283E+01 + rms(prec ) = 0.32945E+01 + weight for this iteration 100.00 + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 146.90699857 + Ewald energy TEWEN = -2087.53862760 + -Hartree energ DENC = -1056.60076398 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 224.05028418 + PAW double counting = 2427.29578539 -2431.24524980 + entropy T*S EENTRO = 0.00218825 + eigenvalues EBANDS = -492.78696242 + atomic energy EATOM = 3162.92556708 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -106.99078035 eV + + energy without entropy = -106.99296860 energy(sigma->0) = -106.99132742 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 6) --------------------------------------- + + + POTLOK: cpu time 0.0448: real time 0.0465 + SETDIJ: cpu time 0.0036: real time 0.0040 + EDDIAG: cpu time 0.7940: real time 0.7958 + RMM-DIIS: cpu time 3.2860: real time 3.2960 + ORTHCH: cpu time 0.0547: real time 0.0548 + DOS: cpu time 0.0077: real time 0.0077 + CHARGE: cpu time 0.3559: real time 0.3566 + MIXING: cpu time 0.0017: real time 0.0017 + -------------------------------------------- + LOOP: cpu time 4.5484: real time 4.5631 + + eigenvalue-minimisations : 10240 + total energy-change (2. order) : 0.7601924E+01 (-0.2216313E+01) + number of electron 60.0000006 magnetization + augmentation part 3.9282890 magnetization + + Broyden mixing: + rms(total) = 0.78536E+00 rms(broyden)= 0.78495E+00 + rms(prec ) = 0.12502E+01 + weight for this iteration 100.00 + + eigenvalues of (default mixing * dielectric matrix) + average eigenvalue GAMMA= 1.1199 + 1.1199 + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 146.90699857 + Ewald energy TEWEN = -2087.53862760 + -Hartree energ DENC = -1145.69573028 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 229.73383638 + PAW double counting = 3513.13519406 -3519.04458897 + entropy T*S EENTRO = 0.00062476 + eigenvalues EBANDS = -399.81213054 + atomic energy EATOM = 3162.92556708 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -99.38885655 eV + + energy without entropy = -99.38948131 energy(sigma->0) = -99.38901274 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 7) --------------------------------------- + + + POTLOK: cpu time 0.0428: real time 0.0448 + SETDIJ: cpu time 0.0036: real time 0.0036 + EDDIAG: cpu time 0.7944: real time 0.7961 + RMM-DIIS: cpu time 3.2961: real time 3.3066 + ORTHCH: cpu time 0.0579: real time 0.0584 + DOS: cpu time 0.0077: real time 0.0078 + CHARGE: cpu time 0.3560: real time 0.3568 + MIXING: cpu time 0.0017: real time 0.0017 + -------------------------------------------- + LOOP: cpu time 4.5603: real time 4.5758 + + eigenvalue-minimisations : 10240 + total energy-change (2. order) : 0.8097187E+00 (-0.1586561E+00) + number of electron 60.0000006 magnetization + augmentation part 3.9045046 magnetization + + Broyden mixing: + rms(total) = 0.42025E+00 rms(broyden)= 0.42020E+00 + rms(prec ) = 0.61185E+00 + weight for this iteration 100.00 + + eigenvalues of (default mixing * dielectric matrix) + average eigenvalue GAMMA= 1.6338 + 1.0269 2.2408 + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 146.90699857 + Ewald energy TEWEN = -2087.53862760 + -Hartree energ DENC = -1163.06495530 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 230.84918340 + PAW double counting = 4409.87806289 -4416.11302928 + entropy T*S EENTRO = 0.00150037 + eigenvalues EBANDS = -382.42383793 + atomic energy EATOM = 3162.92556708 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -98.57913781 eV + + energy without entropy = -98.58063818 energy(sigma->0) = -98.57951290 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 8) --------------------------------------- + + + POTLOK: cpu time 0.0441: real time 0.0457 + SETDIJ: cpu time 0.0036: real time 0.0039 + EDDIAG: cpu time 0.7935: real time 0.7957 + RMM-DIIS: cpu time 3.2970: real time 3.3076 + ORTHCH: cpu time 0.0537: real time 0.0539 + DOS: cpu time 0.0075: real time 0.0075 + CHARGE: cpu time 0.3573: real time 0.3579 + MIXING: cpu time 0.0016: real time 0.0016 + -------------------------------------------- + LOOP: cpu time 4.5584: real time 4.5738 + + eigenvalue-minimisations : 10240 + total energy-change (2. order) : 0.1326031E+00 (-0.6034512E-01) + number of electron 60.0000006 magnetization + augmentation part 3.9033224 magnetization + + Broyden mixing: + rms(total) = 0.10296E+00 rms(broyden)= 0.10294E+00 + rms(prec ) = 0.14871E+00 + weight for this iteration 100.00 + + eigenvalues of (default mixing * dielectric matrix) + average eigenvalue GAMMA= 1.5474 + 2.4067 1.0644 1.1710 + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 146.90699857 + Ewald energy TEWEN = -2087.53862760 + -Hartree energ DENC = -1177.13823050 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 231.78206515 + PAW double counting = 5412.41695662 -5418.85397147 + entropy T*S EENTRO = 0.00165194 + eigenvalues EBANDS = -368.94894447 + atomic energy EATOM = 3162.92556708 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -98.44653468 eV + + energy without entropy = -98.44818662 energy(sigma->0) = -98.44694766 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 9) --------------------------------------- + + + POTLOK: cpu time 0.0429: real time 0.0446 + SETDIJ: cpu time 0.0035: real time 0.0036 + EDDIAG: cpu time 0.7913: real time 0.7932 + RMM-DIIS: cpu time 3.3094: real time 3.3224 + ORTHCH: cpu time 0.0537: real time 0.0539 + DOS: cpu time 0.0079: real time 0.0079 + CHARGE: cpu time 0.3592: real time 0.3597 + MIXING: cpu time 0.0017: real time 0.0017 + -------------------------------------------- + LOOP: cpu time 4.5695: real time 4.5869 + + eigenvalue-minimisations : 10243 + total energy-change (2. order) :-0.4460786E-02 (-0.3635682E-02) + number of electron 60.0000006 magnetization + augmentation part 3.8932577 magnetization + + Broyden mixing: + rms(total) = 0.34533E-01 rms(broyden)= 0.34518E-01 + rms(prec ) = 0.52857E-01 + weight for this iteration 100.00 + + eigenvalues of (default mixing * dielectric matrix) + average eigenvalue GAMMA= 1.5774 + 1.0036 1.0036 2.4386 1.8639 + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 146.90699857 + Ewald energy TEWEN = -2087.53862760 + -Hartree energ DENC = -1180.68672003 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 232.02681441 + PAW double counting = 5666.65476593 -5673.10833363 + entropy T*S EENTRO = 0.00170854 + eigenvalues EBANDS = -365.63316873 + atomic energy EATOM = 3162.92556708 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -98.45099546 eV + + energy without entropy = -98.45270400 energy(sigma->0) = -98.45142260 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 10) --------------------------------------- + + + POTLOK: cpu time 0.0426: real time 0.0444 + SETDIJ: cpu time 0.0036: real time 0.0036 + EDDIAG: cpu time 0.7985: real time 0.8004 + RMM-DIIS: cpu time 3.2811: real time 3.3203 + ORTHCH: cpu time 0.0538: real time 0.0539 + DOS: cpu time 0.0075: real time 0.0075 + CHARGE: cpu time 0.3587: real time 0.3612 + MIXING: cpu time 0.0017: real time 0.0018 + -------------------------------------------- + LOOP: cpu time 4.5474: real time 4.5931 + + eigenvalue-minimisations : 10240 + total energy-change (2. order) :-0.1381779E-02 (-0.5191530E-03) + number of electron 60.0000006 magnetization + augmentation part 3.8936367 magnetization + + Broyden mixing: + rms(total) = 0.92284E-02 rms(broyden)= 0.92258E-02 + rms(prec ) = 0.15739E-01 + weight for this iteration 100.00 + + eigenvalues of (default mixing * dielectric matrix) + average eigenvalue GAMMA= 1.5674 + 2.4958 1.9541 1.0167 1.0167 1.3538 + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 146.90699857 + Ewald energy TEWEN = -2087.53862760 + -Hartree energ DENC = -1180.47955418 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 232.02390403 + PAW double counting = 5726.19905861 -5732.61878043 + entropy T*S EENTRO = 0.00170012 + eigenvalues EBANDS = -365.87264344 + atomic energy EATOM = 3162.92556708 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -98.45237724 eV + + energy without entropy = -98.45407736 energy(sigma->0) = -98.45280227 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 11) --------------------------------------- + + + POTLOK: cpu time 0.0422: real time 0.0445 + SETDIJ: cpu time 0.0035: real time 0.0036 + EDDIAG: cpu time 0.7855: real time 0.8004 + RMM-DIIS: cpu time 3.0134: real time 3.0798 + ORTHCH: cpu time 0.0534: real time 0.0546 + DOS: cpu time 0.0075: real time 0.0077 + CHARGE: cpu time 0.3563: real time 0.3639 + MIXING: cpu time 0.0018: real time 0.0020 + -------------------------------------------- + LOOP: cpu time 4.2636: real time 4.3564 + + eigenvalue-minimisations : 9287 + total energy-change (2. order) :-0.3580742E-03 (-0.7392879E-04) + number of electron 60.0000006 magnetization + augmentation part 3.8950608 magnetization + + Broyden mixing: + rms(total) = 0.33056E-02 rms(broyden)= 0.33044E-02 + rms(prec ) = 0.56741E-02 + weight for this iteration 100.00 + + eigenvalues of (default mixing * dielectric matrix) + average eigenvalue GAMMA= 1.5707 + 2.4625 2.2805 1.5796 1.0599 1.0599 0.9814 + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 146.90699857 + Ewald energy TEWEN = -2087.53862760 + -Hartree energ DENC = -1180.34501552 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 232.01929388 + PAW double counting = 5734.97478683 -5741.38339865 + entropy T*S EENTRO = 0.00169579 + eigenvalues EBANDS = -366.01403568 + atomic energy EATOM = 3162.92556708 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -98.45273532 eV + + energy without entropy = -98.45443110 energy(sigma->0) = -98.45315926 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 1( 12) --------------------------------------- + + + POTLOK: cpu time 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59.9999997 magnetization + augmentation part 3.8316504 magnetization + + Broyden mixing: + rms(total) = 0.65852E-01 rms(broyden)= 0.65805E-01 + rms(prec ) = 0.10507E+00 + weight for this iteration 100.00 + + eigenvalues of (default mixing * dielectric matrix) + average eigenvalue GAMMA= 1.4130 + 1.0966 1.7293 + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 140.29769129 + Ewald energy TEWEN = -2059.93155867 + -Hartree energ DENC = -1188.42830713 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 230.41879260 + PAW double counting = 5535.20857559 -5541.57292902 + entropy T*S EENTRO = 0.00162106 + eigenvalues EBANDS = -377.42874495 + atomic energy EATOM = 3162.92556708 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -98.50929215 eV + + energy without entropy = -98.51091321 energy(sigma->0) = -98.50969741 + + 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STRESS: cpu time 8.9242: real time 9.0802 + FORCOR: cpu time 0.0547: real time 0.0566 + FORHAR: cpu time 0.0235: real time 0.0238 + MIXING: cpu time 0.0016: real time 0.0017 + OFIELD: cpu time 0.0000: real time 0.0000 + + FORCE on cell =-STRESS in cart. coord. units (eV): + Direction XX YY ZZ XY YZ ZX + -------------------------------------------------------------------------------------- + Alpha Z 140.29769 140.29769 140.29769 + Ewald -962.26912 -558.16190 -539.50559 -206.78766 -59.29309 200.01510 + Hartree 259.44808 450.71081 478.55243 -64.64985 24.20725 101.47116 + E(xc) -258.92299 -258.09289 -258.23502 -0.72716 -0.44261 0.41147 + Local -124.98283 -715.57203 -759.06929 253.39970 22.98229 -293.58752 + n-local -153.23632 -154.62445 -155.28041 -0.01121 -0.04459 0.12335 + augment 41.93814 41.36973 41.53710 0.84868 0.50599 -0.24295 + Kinetic 1055.15300 1049.09832 1046.21223 19.87543 13.31325 -9.10796 + Fock 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + ------------------------------------------------------------------------------------- + Total -2.57435 -4.97472 -5.49085 1.94793 1.22848 -0.91735 + in kB -29.91376 -57.80594 -63.80334 22.63485 14.27492 -10.65957 + external pressure = -50.51 kB Pullay stress = 0.00 kB + + + VOLUME and BASIS-vectors are now : + ----------------------------------------------------------------------------- + energy-cutoff : 400.00 + volume of cell : 137.88 + direct lattice vectors reciprocal lattice vectors + 4.420319418 0.031982402 0.104451101 0.224111130 0.072337249 0.067435387 + -1.771979189 5.670050444 -0.193304893 -0.003642930 0.178618132 0.099475048 + -0.668647815 -3.107733066 5.555781533 -0.004340137 0.004854772 0.182185946 + + length of vectors + 4.421668991 5.943630967 6.400922055 0.244961237 0.204482256 0.182302289 + + + FORCES acting on ions + electron-ion (+dipol) ewald-force non-local-force convergence-correction + ----------------------------------------------------------------------------------------------- + -.149E+01 0.176E+02 -.801E+01 0.126E+01 -.181E+02 0.100E+02 0.129E+01 0.279E+00 -.133E+01 -.382E-02 0.314E-02 -.174E-02 + 0.749E+02 0.633E+02 -.390E+02 -.101E+03 -.809E+02 0.484E+02 0.251E+02 0.185E+02 -.969E+01 0.352E-01 0.398E-02 -.799E-02 + -.189E+02 0.623E+02 -.562E+02 0.230E+02 -.673E+02 0.583E+02 -.427E+01 0.536E+01 -.319E+01 0.221E-02 0.252E-02 -.325E-02 + -.467E+02 0.108E+02 -.862E+02 0.586E+02 -.587E+00 0.975E+02 -.122E+02 -.106E+02 -.116E+02 0.789E-03 0.111E-01 -.734E-02 + 0.983E+02 0.303E+02 -.459E+02 -.103E+03 -.291E+02 0.459E+02 0.451E+01 -.115E+01 -.315E+00 0.216E-02 0.471E-02 -.368E-02 + 0.498E+02 -.532E+02 0.359E+02 -.490E+02 0.592E+02 -.362E+02 -.656E+00 -.611E+01 0.793E+00 0.321E-02 -.436E-02 0.142E-02 + -.457E+02 -.428E+02 0.343E+02 0.658E+02 0.718E+02 -.367E+02 -.200E+02 -.295E+02 0.240E+01 -.263E-01 0.141E-02 -.808E-05 + -.273E+02 -.721E+02 -.571E+01 0.293E+02 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0.690E+01 0.280E-01 0.242E-01 0.158E-02 + + + POSITION TOTAL-FORCE (eV/Angst) + ----------------------------------------------------------------------------------- + 2.24709 2.54721 4.59756 1.064268 -0.240069 0.709699 + 0.96484 2.90665 4.47246 -0.572670 0.894982 -0.260024 + -0.59023 1.57999 2.71803 -0.129602 0.311032 -1.092448 + -0.80749 5.28564 0.01536 -0.251615 -0.362281 -0.331039 + 0.43394 0.28479 3.23879 -0.409538 0.124439 -0.376329 + 0.49993 -1.50902 2.89420 0.190856 -0.082359 0.419314 + 1.74502 0.62659 2.96491 0.186340 -0.558161 -0.081466 + -0.86390 2.77900 0.62088 0.262914 -0.080273 0.328385 + 2.10268 -0.80889 2.62312 -0.231363 0.005539 0.164683 + -0.38853 1.70187 1.37949 -0.628758 0.269964 0.733729 + -0.37776 4.33087 1.00648 -0.163825 0.164810 -0.263355 + 2.29460 -1.50019 4.23487 -0.055162 0.410388 0.635515 + 2.02166 -0.54550 5.24099 0.564815 -0.779514 -0.833044 + -1.39574 2.76870 3.23754 0.173341 -0.078498 0.246379 + ----------------------------------------------------------------------------------- + total drift: -0.002427 -0.005668 0.002356 + + +-------------------------------------------------------------------------------------------------------- + + + + FREE ENERGIE OF THE ION-ELECTRON SYSTEM (eV) + --------------------------------------------------- + free energy TOTEN = -98.49812024 eV + + energy without entropy= -98.49972750 energy(sigma->0) = -98.49852205 + + d Force = 0.1456122E-01[-0.175E-01, 0.466E-01] d Energy = 0.4530980E-01-0.307E-01 + d Force =-0.3274266E+01[-0.344E+01,-0.311E+01] d Ewald =-0.2760707E+02 0.243E+02 + + +-------------------------------------------------------------------------------------------------------- + + + POTLOK: cpu time 0.0460: real time 0.0469 + + +-------------------------------------------------------------------------------------------------------- + + + Steepest descent step on ions: + trial-energy change: -0.045310 1 .order -0.048945 -0.367204 0.269313 + (g-gl).g = 0.367E+00 g.g = 0.367E+00 gl.gl = 0.000E+00 + g(Force) = 0.460E-01 g(Stress)= 0.321E+00 ortho = 0.000E+00 + gamma = 0.00000 + trial = 1.00000 + opt step = 0.56849 (harmonic = 0.57690) maximal distance =0.01023556 + next E = -98.556518 (d E = -0.10371) + + +-------------------------------------------------------------------------------------------------------- + + + WAVPRE: cpu time 0.0481: real time 0.0500 + FEWALD: cpu time 0.0006: real time 0.0006 + GENKIN: cpu time 0.0407: real time 0.0413 + ORTHCH: cpu time 0.2534: real time 0.2594 + LOOP+: cpu time 43.0269: real time 43.7668 + + +--------------------------------------- Iteration 3( 1) --------------------------------------- + + + POTLOK: cpu time 0.0426: real time 0.0452 + SETDIJ: cpu time 0.0035: real time 0.0035 + EDDAV: cpu time 4.3258: real time 4.3883 + DOS: cpu time 0.0077: real time 0.0078 + CHARGE: cpu time 0.3553: real time 0.3624 + MIXING: cpu time 0.0015: real time 0.0015 + -------------------------------------------- + LOOP: cpu time 4.7364: real time 4.8087 + + eigenvalue-minimisations : 11784 + total energy-change (2. order) :-0.1704091E+00 (-0.4864128E+00) + number of electron 60.0000000 magnetization + augmentation part 3.7953909 magnetization + + Broyden mixing: + rms(total) = 0.24371E+00 rms(broyden)= 0.24357E+00 + rms(prec ) = 0.39611E+00 + weight for this iteration 100.00 + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 143.09345939 + Ewald energy TEWEN = -2071.83328434 + -Hartree energ DENC = -1197.40864083 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 231.89369250 + PAW double counting = 5450.12539634 -5456.24725297 + entropy T*S EENTRO = 0.00163668 + eigenvalues EBANDS = -361.21910969 + atomic energy EATOM = 3162.92556708 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -98.66853584 eV + + energy without entropy = -98.67017252 energy(sigma->0) = -98.66894501 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 3( 2) --------------------------------------- + + + POTLOK: cpu time 0.0419: real time 0.0447 + SETDIJ: cpu time 0.0035: real time 0.0035 + EDDIAG: cpu time 0.7901: real time 0.8029 + RMM-DIIS: cpu time 3.3160: real time 3.3505 + ORTHCH: cpu time 0.0537: real time 0.0542 + DOS: cpu time 0.0077: real time 0.0078 + CHARGE: cpu time 0.3618: real time 0.3649 + MIXING: cpu time 0.0015: real time 0.0015 + -------------------------------------------- + LOOP: cpu time 4.5763: real time 4.6302 + + eigenvalue-minimisations : 10240 + total energy-change (2. order) : 0.1042838E+00 (-0.3623114E-01) + number of electron 60.0000000 magnetization + augmentation part 3.8610000 magnetization + + Broyden mixing: + rms(total) = 0.65185E-01 rms(broyden)= 0.65101E-01 + rms(prec ) = 0.10079E+00 + weight for this iteration 100.00 + + eigenvalues of (default mixing * dielectric matrix) + average eigenvalue GAMMA= 1.1914 + 1.1914 + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 143.09345939 + Ewald energy TEWEN = -2071.83328434 + -Hartree energ DENC = -1186.48680916 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 231.21121294 + PAW double counting = 5494.62030129 -5500.68491859 + entropy T*S EENTRO = 0.00167467 + eigenvalues EBANDS = -371.41145528 + atomic energy EATOM = 3162.92556708 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -98.56425202 eV + + energy without entropy = -98.56592669 energy(sigma->0) = -98.56467068 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 3( 3) --------------------------------------- + + + POTLOK: cpu time 0.0423: real time 0.0445 + SETDIJ: cpu time 0.0035: real time 0.0035 + EDDIAG: cpu time 0.8048: real time 0.8077 + RMM-DIIS: cpu time 3.3346: real time 3.3697 + ORTHCH: cpu time 0.0543: real time 0.0548 + DOS: cpu time 0.0078: real time 0.0078 + CHARGE: cpu time 0.3596: real time 0.3620 + MIXING: cpu time 0.0016: real time 0.0016 + -------------------------------------------- + LOOP: cpu time 4.6084: real time 4.6516 + + eigenvalue-minimisations : 10240 + total energy-change (2. order) : 0.6706531E-02 (-0.1784655E-02) + number of electron 60.0000000 magnetization + augmentation part 3.8673352 magnetization + + Broyden mixing: + rms(total) = 0.29845E-01 rms(broyden)= 0.29830E-01 + rms(prec ) = 0.47235E-01 + weight for this iteration 100.00 + + eigenvalues of (default mixing * dielectric matrix) + average eigenvalue GAMMA= 1.4461 + 1.0814 1.8109 + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 143.09345939 + Ewald energy TEWEN = -2071.83328434 + -Hartree energ DENC = -1185.27411615 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 231.13214582 + PAW double counting = 5528.97386257 -5535.12089719 + entropy T*S EENTRO = 0.00166441 + eigenvalues EBANDS = -372.45594706 + atomic energy EATOM = 3162.92556708 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -98.55754548 eV + + energy without entropy = -98.55920989 energy(sigma->0) = -98.55796159 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 3( 4) --------------------------------------- + + + POTLOK: cpu time 0.0423: real time 0.0463 + SETDIJ: cpu time 0.0037: real time 0.0037 + EDDIAG: cpu time 0.7926: real time 0.8034 + RMM-DIIS: cpu time 3.3085: real time 3.3625 + ORTHCH: cpu time 0.0533: real time 0.0544 + DOS: cpu time 0.0069: real time 0.0070 + CHARGE: cpu time 0.3544: real time 0.3624 + MIXING: cpu time 0.0016: real time 0.0016 + -------------------------------------------- + LOOP: cpu time 4.5632: real time 4.6412 + + eigenvalue-minimisations : 10240 + total energy-change (2. order) : 0.2032134E-02 (-0.2747340E-03) + number of electron 60.0000000 magnetization + augmentation part 3.8635854 magnetization + + Broyden mixing: + rms(total) = 0.98421E-02 rms(broyden)= 0.98394E-02 + rms(prec ) = 0.14905E-01 + weight for this iteration 100.00 + + eigenvalues of (default mixing * dielectric matrix) + average eigenvalue GAMMA= 1.4396 + 2.2591 1.0299 1.0299 + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 143.09345939 + Ewald energy TEWEN = -2071.83328434 + -Hartree energ DENC = -1185.36396110 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 231.13482864 + PAW double counting = 5555.27082692 -5561.49777342 + entropy T*S EENTRO = 0.00167183 + eigenvalues EBANDS = -372.28684834 + atomic energy EATOM = 3162.92556708 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -98.55551335 eV + + energy without entropy = -98.55718518 energy(sigma->0) = -98.55593131 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 3( 5) --------------------------------------- + + + POTLOK: cpu time 0.0424: real time 0.0447 + SETDIJ: cpu time 0.0036: real time 0.0036 + EDDIAG: cpu time 0.7958: real time 0.8041 + RMM-DIIS: cpu time 2.6408: real time 2.6585 + ORTHCH: cpu time 0.0531: real time 0.0541 + DOS: cpu time 0.0077: real time 0.0079 + CHARGE: cpu time 0.3608: real time 0.3638 + MIXING: cpu time 0.0017: real time 0.0017 + -------------------------------------------- + LOOP: cpu time 3.9060: real time 3.9385 + + eigenvalue-minimisations : 7579 + total energy-change (2. order) : 0.1425420E-03 (-0.4012904E-04) + number of electron 60.0000000 magnetization + augmentation part 3.8637920 magnetization + + Broyden mixing: + rms(total) = 0.20458E-02 rms(broyden)= 0.20426E-02 + rms(prec ) = 0.34108E-02 + weight for this iteration 100.00 + + eigenvalues of (default mixing * dielectric matrix) + average eigenvalue GAMMA= 1.4365 + 2.2510 1.0427 1.0427 1.4097 + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 143.09345939 + Ewald energy TEWEN = -2071.83328434 + -Hartree energ DENC = -1185.11077540 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 231.11841020 + PAW double counting = 5564.07232556 -5570.32203541 + entropy T*S EENTRO = 0.00166759 + eigenvalues EBANDS = -372.50070547 + atomic energy EATOM = 3162.92556708 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -98.55537081 eV + + energy without entropy = -98.55703840 energy(sigma->0) = -98.55578771 + + +-------------------------------------------------------------------------------------------------------- + + + + +--------------------------------------- Iteration 3( 6) --------------------------------------- + + + POTLOK: cpu time 0.0421: real time 0.0451 + SETDIJ: cpu time 0.0035: real time 0.0035 + EDDIAG: cpu time 0.8039: real time 0.8075 + RMM-DIIS: cpu time 2.2802: real time 2.3100 + ORTHCH: cpu time 0.0572: real time 0.0575 + DOS: cpu time 0.0076: real time 0.0077 + -------------------------------------------- + LOOP: cpu time 3.1946: real time 3.2314 + + eigenvalue-minimisations : 6084 + total energy-change (2. order) :-0.4982669E-05 (-0.3814231E-05) + number of electron 60.0000000 magnetization + augmentation part 3.8637920 magnetization + + Free energy of the ion-electron system (eV) + --------------------------------------------------- + alpha Z PSCENC = 143.09345939 + Ewald energy TEWEN = -2071.83328434 + -Hartree energ DENC = -1185.09605586 + -exchange EXHF = 0.00000000 + -V(xc)+E(xc) XCENC = 231.11745553 + PAW double counting = 5564.18592911 -5570.43530033 + entropy T*S EENTRO = 0.00166873 + eigenvalues EBANDS = -372.51481509 + atomic energy EATOM = 3162.92556708 + Solvation Ediel_sol = 0.00000000 + --------------------------------------------------- + free energy TOTEN = -98.55537579 eV + + energy without entropy = -98.55704452 energy(sigma->0) = -98.55579297 + + +-------------------------------------------------------------------------------------------------------- + + + + + average (electrostatic) potential at core + the test charge radii are 0.7672 0.7215 0.7672 0.7215 0.7672 0.7215 0.7672 0.7215 0.7672 0.7215) + (the norm of the test charge is 1.0000) + 1 -31.7220 2 -73.8574 3 -31.0325 4 -73.5489 5 -30.1491 + 6 -30.7060 7 -73.4225 8 -30.0144 9 -29.0800 10 -73.7729 + 11 -28.6275 12 -30.7476 13 -73.5419 14 -75.6514 + + + + E-fermi : 2.8432 XC(G=0): -9.8327 alpha+bet : -9.8916 + + diff --git a/tests/poscars/POSCAR.oh.d.dup b/tests/poscars/POSCAR.oh.d.dup new file mode 100644 index 00000000..81743a6d --- /dev/null +++ b/tests/poscars/POSCAR.oh.d.dup @@ -0,0 +1,11 @@ +Cubic BN + 3.57 + 0.00 0.50 0.50 + 0.45 0.00 0.50 + 0.55 0.51 0.00 + O H O + 1 1 1 +Direct + 0.00 0.00 0.00 +0.24727453 0.25272547 0.24777007 + 1.00 0.00 0.00 diff --git a/tests/pymatgen/FA-001.vasp b/tests/pymatgen_data/FA-001.vasp similarity index 100% rename from tests/pymatgen/FA-001.vasp rename to tests/pymatgen_data/FA-001.vasp diff --git a/tests/pymatgen/FA-001.xyz b/tests/pymatgen_data/FA-001.xyz similarity index 100% rename from tests/pymatgen/FA-001.xyz rename to tests/pymatgen_data/FA-001.xyz diff --git a/tests/pymatgen/mol2-new.vasp b/tests/pymatgen_data/mol2-new.vasp similarity index 100% rename from tests/pymatgen/mol2-new.vasp rename to tests/pymatgen_data/mol2-new.vasp diff --git a/tests/pymatgen/mol2.vasp b/tests/pymatgen_data/mol2.vasp similarity index 100% rename from tests/pymatgen/mol2.vasp rename to tests/pymatgen_data/mol2.vasp diff --git a/tests/test_abacus_md.py b/tests/test_abacus_md.py index 1ce7cf8d..2ed61a99 100644 --- a/tests/test_abacus_md.py +++ b/tests/test_abacus_md.py @@ -9,54 +9,52 @@ class TestABACUSMD: def test_atom_names(self) : - self.assertEqual(self.system_Si.data['atom_names'], ['Si']) - #self.assertEqual(self.system_h2o.data['atom_names'], ['O','H']) + self.assertEqual(self.system_water.data['atom_names'], ['H', 'O']) def test_atom_numbs(self) : - self.assertEqual(self.system_Si.data['atom_numbs'], [2]) - #self.assertEqual(self.system_h2o.data['atom_numbs'], [64,128]) + self.assertEqual(self.system_water.data['atom_numbs'], [2, 1]) def test_atom_types(self) : - ref_type = [0, 0] + ref_type = [0, 0, 1] ref_type = np.array(ref_type) for ii in range(ref_type.shape[0]) : - self.assertEqual(self.system_Si.data['atom_types'][ii], ref_type[ii]) + self.assertEqual(self.system_water.data['atom_types'][ii], ref_type[ii]) def test_cell(self) : - cell = bohr2ang * 10.2 * np.array([[0.5, 0.5, 0], [0.5, 0, 0.5], [0, 0.5, 0.5]]) - for idx in range(np.shape(self.system_Si.data['cells'])[0]): + cell = bohr2ang * 28 * np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]]) + for idx in range(np.shape(self.system_water.data['cells'])[0]): for ii in range(cell.shape[0]) : for jj in range(cell.shape[1]) : - self.assertAlmostEqual(self.system_Si.data['cells'][idx][ii][jj], cell[ii][jj]) + self.assertAlmostEqual(self.system_water.data['cells'][idx][ii][jj], cell[ii][jj]) def test_coord(self) : - fp = open('abacus.md/Si_coord') + fp = open('abacus.md/water_coord') coord = [] for ii in fp : coord.append([float(jj) for jj in ii.split()]) coord = np.array(coord) - coord = coord.reshape([5, 2, 3]) + coord = coord.reshape([5, 3, 3]) for ii in range(coord.shape[0]) : for jj in range(coord.shape[1]) : for kk in range(coord.shape[2]): - self.assertAlmostEqual(self.system_Si.data['coords'][ii][jj][kk], coord[ii][jj][kk]) + self.assertAlmostEqual(self.system_water.data['coords'][ii][jj][kk], coord[ii][jj][kk]) fp.close() def test_force(self) : - fp = open('abacus.md/Si_force') + fp = open('abacus.md/water_force') force = [] for ii in fp : force.append([float(jj) for jj in ii.split()]) force = np.array(force) - force = force.reshape([5, 2, 3]) + force = force.reshape([5, 3, 3]) for ii in range(force.shape[0]) : for jj in range(force.shape[1]) : for kk in range(force.shape[2]): - self.assertAlmostEqual(self.system_Si.data['forces'][ii][jj][kk], force[ii][jj][kk]) + self.assertAlmostEqual(self.system_water.data['forces'][ii][jj][kk], force[ii][jj][kk]) fp.close() def test_virial(self) : - fp = open('abacus.md/Si_virial') + fp = open('abacus.md/water_virial') virial = [] for ii in fp : virial.append([float(jj) for jj in ii.split()]) @@ -65,21 +63,20 @@ def test_virial(self) : for ii in range(virial.shape[0]) : for jj in range(virial.shape[1]) : for kk in range(virial.shape[2]) : - self.assertAlmostEqual(self.system_Si.data['virials'][ii][jj][kk], virial[ii][jj][kk]) + self.assertAlmostEqual(self.system_water.data['virials'][ii][jj][kk], virial[ii][jj][kk]) fp.close() def test_energy(self) : - ref_energy = np.array([-211.77183266, -211.7739761 , -211.77713677, -211.78079673, - -211.78511428]) + ref_energy = np.array([-466.69285117, -466.69929051, -466.69829826, -466.70364664, + -466.6976083]) for ii in range(5): - self.assertAlmostEqual(self.system_Si.data['energies'][ii], ref_energy[ii]) + self.assertAlmostEqual(self.system_water.data['energies'][ii], ref_energy[ii]) class TestABACUSMDLabeledOutput(unittest.TestCase, TestABACUSMD): def setUp(self): - self.system_Si = dpdata.LabeledSystem('abacus.md',fmt='abacus/md') - # self.system_h2o = dpdata.LabeledSystem('qe.scf/02.out',fmt='qe/pw/scf') + self.system_water = dpdata.LabeledSystem('abacus.md',fmt='abacus/md') if __name__ == '__main__': diff --git a/tests/test_amber_md.py b/tests/test_amber_md.py index 758c6d00..d3189a0d 100644 --- a/tests/test_amber_md.py +++ b/tests/test_amber_md.py @@ -3,7 +3,12 @@ import shutil from context import dpdata from comp_sys import CompLabeledSys, IsPBC - +try: + import parmed +except ModuleNotFoundError: + skip_parmed_related_test=True +else: + skip_parmed_related_test=False class TestAmberMD(unittest.TestCase, CompLabeledSys, IsPBC): def setUp (self) : @@ -19,6 +24,7 @@ def tearDown(self) : if os.path.exists('tmp.deepmd.npy'): shutil.rmtree('tmp.deepmd.npy') +@unittest.skipIf(skip_parmed_related_test,"skip parmed related test. install parmed to fix") class TestAmberMDTarget(unittest.TestCase, CompLabeledSys, IsPBC): def setUp(self): ll="amber/corr/low_level" @@ -35,4 +41,4 @@ def setUp(self): self.v_places = 6 if __name__ == '__main__': - unittest.main() \ No newline at end of file + unittest.main() diff --git a/tests/test_ase_traj.py b/tests/test_ase_traj.py index 43ecaa02..6c37a31c 100644 --- a/tests/test_ase_traj.py +++ b/tests/test_ase_traj.py @@ -3,23 +3,31 @@ import unittest from context import dpdata from comp_sys import CompLabeledSys, IsPBC +try: + import ase +except ModuleNotFoundError: + skip_ase = True +else: + skip_ase = False +@unittest.skipIf(skip_ase,"skip ase related test. install ase to fix") class TestASEtraj1(unittest.TestCase, CompLabeledSys, IsPBC): def setUp (self) : - self.multi_systems = dpdata.MultiSystems.from_file('ase/HeAlO.traj', fmt='ase/structure') + self.multi_systems = dpdata.MultiSystems.from_file('ase_traj/HeAlO.traj', fmt='ase_traj/structure') self.system_1 = self.multi_systems.systems['Al0He4O0'] - self.system_2 = dpdata.LabeledSystem('ase/Al0He4O0', fmt='deepmd') + self.system_2 = dpdata.LabeledSystem('ase_traj/Al0He4O0', fmt='deepmd') self.places = 6 self.e_places = 6 self.f_places = 6 self.v_places = 4 +@unittest.skipIf(skip_ase,"skip ase related test. install ase to fix") class TestASEtraj1(unittest.TestCase, CompLabeledSys, IsPBC): def setUp (self) : - self.system_temp0 = dpdata.MultiSystems.from_file(file_name='ase/HeAlO.traj', fmt='ase/structure') + self.system_temp0 = dpdata.MultiSystems.from_file(file_name='ase_traj/HeAlO.traj', fmt='ase/structure') self.system_1 = self.system_temp0.systems['Al2He1O3'] # .sort_atom_types() - self.system_temp1 = dpdata.LabeledSystem('ase/Al2He1O3', fmt='deepmd') - self.system_temp2 = dpdata.LabeledSystem('ase/Al4He4O6', fmt='deepmd') + self.system_temp1 = dpdata.LabeledSystem('ase_traj/Al2He1O3', fmt='deepmd') + self.system_temp2 = dpdata.LabeledSystem('ase_traj/Al4He4O6', fmt='deepmd') self.system_temp3 = dpdata.MultiSystems(self.system_temp2, self.system_temp1) self.system_2 = self.system_temp3.systems['Al2He1O3'] self.places = 6 diff --git a/tests/test_cli.py b/tests/test_cli.py new file mode 100644 index 00000000..3d6d29e4 --- /dev/null +++ b/tests/test_cli.py @@ -0,0 +1,17 @@ +import unittest +from context import dpdata +from poscars.poscar_ref_oh import TestPOSCARoh +import subprocess as sp + + +class TestCli(unittest.TestCase, TestPOSCARoh): + + @classmethod + def setUpClass(cls) -> None: + sp.check_output(["dpdata", "poscars/conf.lmp", "--type-map", "O", "H", "-olammps/lmp", "-O", "tmp.lmp", "--no-labeled"]) + cls.system = dpdata.System('tmp.lmp', fmt='lammps/lmp', + type_map = ['O', 'H']) + + @classmethod + def tearDownClass(cls) -> None: + cls.system = None diff --git a/tests/test_pick_atom_idx.py b/tests/test_pick_atom_idx.py index 7e13cca9..bb6af61f 100644 --- a/tests/test_pick_atom_idx.py +++ b/tests/test_pick_atom_idx.py @@ -5,7 +5,7 @@ try: import parmed exist_module=True -except: +except Exception: exist_module=False class TestPickAtomIdx(unittest.TestCase, CompSys, IsNoPBC): diff --git a/tests/test_pymatgen_molecule.py b/tests/test_pymatgen_molecule.py index 4a1eb029..d80acc92 100644 --- a/tests/test_pymatgen_molecule.py +++ b/tests/test_pymatgen_molecule.py @@ -2,17 +2,24 @@ import numpy as np import unittest from context import dpdata +try: + import pymatgen +except ModuleNotFoundError: + skip_pymatgen=True +else: + skip_pymatgen=False +@unittest.skipIf(skip_pymatgen,"skip pymatgen related test. install pymatgen to fix") class TestPOSCARCart(unittest.TestCase): def setUp(self): self.system = dpdata.System() - self.system.from_pymatgen_molecule(os.path.join('pymatgen', 'FA-001.xyz')) + self.system.from_pymatgen_molecule(os.path.join('pymatgen_data', 'FA-001.xyz')) self.assertEqual(list(self.system["atom_types"]), [0, 1, 2, 1, 1, 2, 1, 1]) def test_poscar_to_molecule(self): tmp_system = dpdata.System() - tmp_system.from_vasp_poscar(os.path.join('pymatgen', 'mol2.vasp')) + tmp_system.from_vasp_poscar(os.path.join('pymatgen_data', 'mol2.vasp')) natoms = len(tmp_system['coords'][0]) tmpcoord = tmp_system['coords'][0] cog = np.average(tmpcoord, axis = 0) diff --git a/tests/test_to_ase.py b/tests/test_to_ase.py index 1cd7200a..4ea870c7 100644 --- a/tests/test_to_ase.py +++ b/tests/test_to_ase.py @@ -7,7 +7,7 @@ from ase import Atoms from ase.io import write exist_module=True -except: +except Exception: exist_module=False @unittest.skipIf(not exist_module,"skip test_ase") diff --git a/tests/test_to_pymatgen.py b/tests/test_to_pymatgen.py index 5922828b..0077a049 100644 --- a/tests/test_to_pymatgen.py +++ b/tests/test_to_pymatgen.py @@ -6,7 +6,7 @@ try: from pymatgen import Structure exist_module=True -except: +except Exception: exist_module=False @unittest.skipIf(not exist_module,"skip pymatgen") diff --git a/tests/test_to_pymatgen_entry.py b/tests/test_to_pymatgen_entry.py index ef7cb942..e0a952be 100644 --- a/tests/test_to_pymatgen_entry.py +++ b/tests/test_to_pymatgen_entry.py @@ -7,7 +7,7 @@ try: from pymatgen.entries.computed_entries import ComputedStructureEntry exist_module=True -except: +except Exception: exist_module=False @unittest.skipIf(not exist_module,"skip pymatgen") diff --git a/tests/test_vasp_outcar.py b/tests/test_vasp_outcar.py index ff591af4..6306c1ef 100644 --- a/tests/test_vasp_outcar.py +++ b/tests/test_vasp_outcar.py @@ -3,6 +3,7 @@ import unittest from context import dpdata from comp_sys import CompLabeledSys, IsPBC +from dpdata.utils import uniq_atom_names class TestVaspOUTCAR(unittest.TestCase, CompLabeledSys, IsPBC): def setUp (self) : @@ -53,5 +54,36 @@ def setUp (self) : self.v_places = 6 +class TestDuplicatedAtomNames(unittest.TestCase): + def test(self): + system = dpdata.LabeledSystem('poscars/6362_OUTCAR', fmt = 'vasp/outcar') + expected_types = [0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 1] + self.assertEqual(list(system['atom_types']), expected_types) + self.assertEqual(system['atom_names'], ['B', 'O']) + self.assertEqual(system['atom_numbs'], [8, 6]) + + def test_type_map(self): + system = dpdata.LabeledSystem('poscars/6362_OUTCAR', fmt = 'vasp/outcar', type_map = ['O', 'B']) + expected_types = [1, 0, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 0] + self.assertEqual(list(system['atom_types']), expected_types) + self.assertEqual(system['atom_names'], ['O', 'B']) + self.assertEqual(system['atom_numbs'], [6, 8]) + + +class TestUniqAtomNames(unittest.TestCase): + def test(self): + data = {} + data['atom_names'] = ['O', 'H', 'O', 'H'] + data['atom_types'] = np.array([0, 1, 2, 3, 3, 2, 1], dtype=int) + + data = uniq_atom_names(data) + self.assertEqual(list(data['atom_types']), + [0, 1, 0, 1, 1, 0, 1]) + self.assertEqual(list(data['atom_names']), + ['O', 'H']) + self.assertEqual(list(data['atom_numbs']), + [3, 4]) + + if __name__ == '__main__': unittest.main() diff --git a/tests/test_vasp_poscar_to_system.py b/tests/test_vasp_poscar_to_system.py index f1248175..760da63a 100644 --- a/tests/test_vasp_poscar_to_system.py +++ b/tests/test_vasp_poscar_to_system.py @@ -17,6 +17,19 @@ def setUp(self): self.system = dpdata.System() self.system.from_vasp_poscar(os.path.join('poscars', 'POSCAR.oh.d')) +class TestPOSCARDirectDuplicated(unittest.TestCase): + def test(self): + ss = dpdata.System(os.path.join('poscars', 'POSCAR.oh.d.dup'), fmt='vasp/poscar') + self.assertEqual(ss['atom_names'], ['O', 'H']) + self.assertEqual(ss['atom_numbs'], [2, 1]) + self.assertEqual(list(ss['atom_types']), [0, 1, 0]) + + def test_type_map(self): + ss = dpdata.System(os.path.join('poscars', 'POSCAR.oh.d.dup'), fmt='vasp/poscar', type_map=['H', 'O']) + self.assertEqual(ss['atom_names'], ['H', 'O']) + self.assertEqual(ss['atom_numbs'], [1, 2]) + self.assertEqual(list(ss['atom_types']), [1, 0, 1]) + class TestVaspPOSCARTypeMap(unittest.TestCase, CompSys, IsPBC): def setUp(self): sys0 = dpdata.System('poscars/POSCAR.oh.d', fmt = 'vasp/poscar') diff --git a/tests/test_water_ions.py b/tests/test_water_ions.py index 3a9436b6..f2fab203 100644 --- a/tests/test_water_ions.py +++ b/tests/test_water_ions.py @@ -6,7 +6,7 @@ import ase import ase.neighborlist exist_ase=True -except: +except Exception: exist_ase=False class TestIons(unittest.TestCase):