diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 30c86388..14b08cef 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -18,14 +18,15 @@ repos: - id: check-toml # Python - repo: https://github.com/psf/black - rev: 22.12.0 + rev: 23.3.0 hooks: - id: black-jupyter -- repo: https://github.com/PyCQA/isort - rev: 5.12.0 +- repo: https://github.com/charliermarsh/ruff-pre-commit + # Ruff version. + rev: v0.0.263 hooks: - - id: isort - files: \.py$ + - id: ruff + args: ["--fix"] # numpydoc - repo: https://github.com/Carreau/velin rev: 0.0.12 diff --git a/docs/conf.py b/docs/conf.py index d09cf3fd..e60f18fc 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 -*- # # Configuration file for the Sphinx documentation builder. # diff --git a/docs/make_format.py b/docs/make_format.py index a7962208..a208b21e 100644 --- a/docs/make_format.py +++ b/docs/make_format.py @@ -1,12 +1,9 @@ import csv from collections import defaultdict -from typing import Any # ensure all plugins are loaded! -import dpdata.plugins from dpdata.driver import Driver, Minimizer from dpdata.format import Format -from dpdata.system import get_cls_name def get_formats() -> dict: @@ -31,7 +28,7 @@ def get_minimizer() -> dict: def detect_overridden(cls: Format, method: str) -> bool: - """Check whether a method is override + """Check whether a method is override. Parameters ---------- @@ -61,7 +58,9 @@ def get_cls_link(cls: object) -> str: str the link of a class """ - return ":class:`%s <%s>`" % (cls.__name__, ".".join([cls.__module__, cls.__name__])) + return ":class:`{} <{}>`".format( + cls.__name__, ".".join([cls.__module__, cls.__name__]) + ) def check_supported(fmt: Format): @@ -112,7 +111,7 @@ def check_supported(fmt: Format): writer.writerow( { "Class": get_cls_link(kk), - "Alias": "\n".join(("``%s``" % vvv for vvv in vv)), + "Alias": "\n".join("``%s``" % vvv for vvv in vv), "Supported Functions": "\n".join( method_links[mtd] for mtd in check_supported(kk) ), @@ -132,7 +131,7 @@ def check_supported(fmt: Format): writer.writerow( { "Class": get_cls_link(kk), - "Alias": "\n".join(("``%s``" % vvv for vvv in vv)), + "Alias": "\n".join("``%s``" % vvv for vvv in vv), } ) @@ -149,6 +148,6 @@ def check_supported(fmt: Format): writer.writerow( { "Class": get_cls_link(kk), - "Alias": "\n".join(("``%s``" % vvv for vvv in vv)), + "Alias": "\n".join("``%s``" % vvv for vvv in vv), } ) diff --git a/dpdata/__init__.py b/dpdata/__init__.py index d160717c..036643c0 100644 --- a/dpdata/__init__.py +++ b/dpdata/__init__.py @@ -9,7 +9,7 @@ # BondOrder System has dependency on rdkit try: # prevent conflict with dpdata.rdkit - import rdkit as _ + import rdkit as _ # noqa: F401 USE_RDKIT = True except ModuleNotFoundError: @@ -17,3 +17,14 @@ if USE_RDKIT: from .bond_order_system import BondOrderSystem + +__all__ = [ + "__version__", + "lammps", + "md", + "vasp", + "System", + "LabeledSystem", + "MultiSystems", + "BondOrderSystem", +] diff --git a/dpdata/abacus/md.py b/dpdata/abacus/md.py index 7532b7b2..7726cafe 100644 --- a/dpdata/abacus/md.py +++ b/dpdata/abacus/md.py @@ -1,19 +1,14 @@ import os -import re -import sys import warnings -from ast import dump import numpy as np from .scf import ( bohr2ang, - get_block, get_cell, get_coords, get_geometry_in, kbar2evperang3, - ry2ev, ) # Read in geometries from an ABACUS MD trajectory. @@ -72,69 +67,51 @@ def get_coords_from_dump(dumplines, natoms): for iline in range(nlines): if "MDSTEP" in dumplines[iline]: # read in LATTICE_CONSTANT - celldm = float(dumplines[iline + 1].split(" ")[-1]) + # for abacus version >= v3.1.4, the unit is angstrom, and "ANGSTROM" is added at the end + # for abacus version < v3.1.4, the unit is bohr + celldm = float(dumplines[iline + 1].split()[1]) + newversion = True + if "Angstrom" not in dumplines[iline + 1]: + celldm *= bohr2ang # transfer unit to ANGSTROM + newversion = False + # 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:] - ] - ) + np.array([float(i) for i in dumplines[iline + 3 + ix].split()[0:3]]) * celldm ) if calc_stress: stresses[iframe, ix] = np.array( - [ - float(i) - for i in re.split("\s+", dumplines[iline + 7 + ix])[-3:] - ] + [float(i) for i in dumplines[iline + 7 + ix].split()[0:3]] ) + + if calc_stress: + skipline = 11 + else: + skipline = 7 + for iat in range(total_natoms): - if calc_stress: - 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:] - ] - ) - else: - coords[iframe, iat] = ( - np.array( - [ - float(i) - for i in re.split("\s+", dumplines[iline + 7 + iat])[ - -6:-3 - ] - ] - ) - * celldm - ) - forces[iframe, iat] = np.array( - [ - float(i) - for i in re.split("\s+", dumplines[iline + 7 + iat])[-3:] - ] - ) + # INDEX LABEL POSITION (Angstrom) FORCE (eV/Angstrom) VELOCITY (Angstrom/fs) + # 0 Sn 0.000000000000 0.000000000000 0.000000000000 -0.000000000000 -0.000000000001 -0.000000000001 0.001244557166 -0.000346684288 0.000768457739 + # 1 Sn 0.000000000000 3.102800034079 3.102800034079 -0.000186795145 -0.000453823768 -0.000453823768 0.000550996187 -0.000886442775 0.001579501983 + # for abacus version >= v3.1.4, the value of POSITION is the real cartessian position, and unit is angstrom, and if cal_force the VELOCITY is added at the end. + # for abacus version < v3.1.4, the real position = POSITION * celldm + coords[iframe, iat] = np.array( + [float(i) for i in dumplines[iline + skipline + iat].split()[2:5]] + ) + + if not newversion: + coords[iframe, iat] *= celldm + + forces[iframe, iat] = np.array( + [float(i) for i in dumplines[iline + skipline + iat].split()[5:8]] + ) iframe += 1 assert iframe == nframes_dump, ( "iframe=%d, nframe_dump=%d. Number of frames does not match number of lines in MD_dump." % (iframe, nframes_dump) ) - cells *= bohr2ang - coords *= bohr2ang stresses *= kbar2evperang3 return coords, cells, forces, stresses @@ -166,12 +143,12 @@ def get_frame(fname): path_in = os.path.join(fname, "INPUT") else: raise RuntimeError("invalid input") - with open(path_in, "r") as fp: + with open(path_in) as fp: inlines = fp.read().split("\n") geometry_path_in = get_geometry_in(fname, inlines) # base dir of STRU path_out = get_path_out(fname, inlines) - with open(geometry_path_in, "r") as fp: + with open(geometry_path_in) as fp: geometry_inlines = fp.read().split("\n") celldm, cell = get_cell(geometry_inlines) atom_names, natoms, types, coords = get_coords( @@ -182,11 +159,11 @@ def get_frame(fname): # 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) - with open(os.path.join(path_out, "MD_dump"), "r") as fp: + with open(os.path.join(path_out, "MD_dump")) 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: + with open(os.path.join(path_out, "running_md.log")) as fp: outlines = fp.read().split("\n") energy = get_energy(outlines, ndump, dump_freq) @@ -201,7 +178,7 @@ def get_frame(fname): unconv_stru += "%d " % i ndump = len(energy) if unconv_stru != "": - warnings.warn(f"Structure %s are unconverged and not collected!" % unconv_stru) + warnings.warn("Structure %s are unconverged and not collected!" % unconv_stru) for iframe in range(ndump): stress[iframe] *= np.linalg.det(cells[iframe, :, :].reshape([3, 3])) diff --git a/dpdata/abacus/relax.py b/dpdata/abacus/relax.py index 7d0da0fa..5dd77030 100644 --- a/dpdata/abacus/relax.py +++ b/dpdata/abacus/relax.py @@ -1,5 +1,4 @@ import os -import sys import numpy as np @@ -16,19 +15,18 @@ def get_log_file(fname, inlines): suffix = line.split()[1] elif "calculation" in line and "calculation" == line.split()[0]: calculation = line.split()[1] - logf = os.path.join(fname, "OUT.%s/running_%s.log" % (suffix, calculation)) + logf = os.path.join(fname, f"OUT.{suffix}/running_{calculation}.log") return logf def get_coords_from_log(loglines, natoms): - """ - NOTICE: unit of coords and cells is Angstrom + """NOTICE: unit of coords and cells is Angstrom order: coordinate cell (no output if cell is not changed) energy (no output, if SCF is not converged) force (no output, if cal_force is not setted or abnormal ending) - stress (no output, if set cal_stress is not setted or abnormal ending) + stress (no output, if set cal_stress is not setted or abnormal ending). """ natoms_log = 0 for line in loglines: @@ -175,10 +173,10 @@ def get_frame(fname): path_in = os.path.join(fname, "INPUT") else: raise RuntimeError("invalid input") - with open(path_in, "r") as fp: + with open(path_in) as fp: inlines = fp.read().split("\n") geometry_path_in = get_geometry_in(fname, inlines) # base dir of STRU - with open(geometry_path_in, "r") as fp: + with open(geometry_path_in) as fp: geometry_inlines = fp.read().split("\n") celldm, cell = get_cell(geometry_inlines) atom_names, natoms, types, coord_tmp = get_coords( diff --git a/dpdata/abacus/scf.py b/dpdata/abacus/scf.py index e82089ad..1816913e 100644 --- a/dpdata/abacus/scf.py +++ b/dpdata/abacus/scf.py @@ -1,6 +1,5 @@ import os import re -import sys import numpy as np @@ -172,7 +171,7 @@ def get_frame(fname): if not CheckFile(path_in): return data - with open(path_in, "r") as fp: + with open(path_in) as fp: inlines = fp.read().split("\n") geometry_path_in = get_geometry_in(fname, inlines) @@ -180,9 +179,9 @@ def get_frame(fname): if not (CheckFile(geometry_path_in) and CheckFile(path_out)): return data - with open(geometry_path_in, "r") as fp: + with open(geometry_path_in) as fp: geometry_inlines = fp.read().split("\n") - with open(path_out, "r") as fp: + with open(path_out) as fp: outlines = fp.read().split("\n") celldm, cell = get_cell(geometry_inlines) @@ -257,7 +256,7 @@ def get_nele_from_stru(geometry_inlines): def get_frame_from_stru(fname): assert type(fname) == str - with open(fname, "r") as fp: + with open(fname) as fp: geometry_inlines = fp.read().split("\n") nele = get_nele_from_stru(geometry_inlines) inlines = ["ntype %d" % nele] diff --git a/dpdata/amber/mask.py b/dpdata/amber/mask.py index 34eba90b..109cdf9c 100644 --- a/dpdata/amber/mask.py +++ b/dpdata/amber/mask.py @@ -1,4 +1,4 @@ -"""Amber mask""" +"""Amber mask.""" try: import parmed except ImportError: @@ -6,7 +6,7 @@ def pick_by_amber_mask(param, maskstr, coords=None): - """Pick atoms by amber masks + """Pick atoms by amber masks. Parameters ---------- diff --git a/dpdata/amber/md.py b/dpdata/amber/md.py index 28b4535c..ef058828 100644 --- a/dpdata/amber/md.py +++ b/dpdata/amber/md.py @@ -30,7 +30,7 @@ def read_amber_traj( * mdfrc, NetCDF format, stores forces * mden (optional), text format, stores energies * mdout (optional), text format, may store energies if there is no mden_file - * parm7, text format, stores types + * parm7, text format, stores types. Parameters ---------- @@ -41,8 +41,9 @@ def read_amber_traj( instead of amber types. For example, a ligand will use C, H, O, N, and so on instead of h1, hc, o, os, and so on. IF use_element_symbols is str, it will be considered as Amber mask. + labeled : bool + Whether to return labeled data """ - flag_atom_type = False flag_atom_numb = False amber_types = [] diff --git a/dpdata/amber/sqm.py b/dpdata/amber/sqm.py index 9b450501..5dcbf995 100644 --- a/dpdata/amber/sqm.py +++ b/dpdata/amber/sqm.py @@ -13,9 +13,7 @@ def parse_sqm_out(fname): - """ - Read atom symbols, charges and coordinates from ambertools sqm.out file - """ + """Read atom symbols, charges and coordinates from ambertools sqm.out file.""" atom_symbols = [] coords = [] charges = [] diff --git a/dpdata/bond_order_system.py b/dpdata/bond_order_system.py index 124a6faa..e2449ee6 100644 --- a/dpdata/bond_order_system.py +++ b/dpdata/bond_order_system.py @@ -1,4 +1,4 @@ -#%% +# %% # Bond Order System from copy import deepcopy @@ -6,15 +6,14 @@ from rdkit.Chem import Conformer import dpdata.rdkit.utils -from dpdata.rdkit.sanitize import SanitizeError, Sanitizer -from dpdata.system import Axis, DataType, LabeledSystem, System, load_format +from dpdata.rdkit.sanitize import Sanitizer +from dpdata.system import Axis, DataType, System # import dpdata.rdkit.mol2 class BondOrderSystem(System): - """ - The system with chemical bond and formal charges information + """The system with chemical bond and formal charges information. For example, a labeled methane system named `d_example` has one molecule (5 atoms, 4 bonds) and `n_frames` frames. The bond order and formal charge information can be accessed by - `d_example['bonds']` : a numpy array of size 4 x 3, and @@ -44,8 +43,7 @@ def __init__( verbose=False, **kwargs, ): - """ - Constructor + """Constructor. Parameters ---------- @@ -73,8 +71,9 @@ def __init__( whether to raise an Exception if sanitization procedure fails. verbose : bool whether to print information in the sanitization procedure. + **kwargs : dict + Additional arguments for the format. """ - System.__init__(self) self.sanitizer = Sanitizer(sanitize_level, raise_errors, verbose) @@ -112,9 +111,7 @@ def to_fmt_obj(self, fmtobj, *args, **kwargs): return fmtobj.to_bond_order_system(self.data, self.rdkit_mol, *args, **kwargs) def __str__(self): - """ - A brief summary of the system - """ + """A brief summary of the system.""" ret = "Data Summary" ret += "\nBondOrder System" ret += "\n-------------------" @@ -128,33 +125,23 @@ def __str__(self): return ret def get_nbonds(self): - """ - Return the number of bonds - """ + """Return the number of bonds.""" return len(self.data["bonds"]) def get_charge(self): - """ - Return the total formal charge of the moleclue - """ + """Return the total formal charge of the moleclue.""" return sum(self.data["formal_charges"]) def get_mol(self): - """ - Return the rdkit.Mol object - """ + """Return the rdkit.Mol object.""" return self.rdkit_mol def get_bond_order(self, begin_atom_idx, end_atom_idx): - """ - Return the bond order between given atoms - """ + """Return the bond order between given atoms.""" return self.data["bond_dict"][f"{int(begin_atom_idx)}-{int(end_atom_idx)}"] def get_formal_charges(self): - """ - Return the formal charges on each atom - """ + """Return the formal charges on each atom.""" return self.data["formal_charges"] def copy(self): @@ -178,9 +165,7 @@ def __add__(self, other): # raise RuntimeError(f"Unsupported data structure: {type(other)}") def from_rdkit_mol(self, rdkit_mol): - """ - Initialize from a rdkit.Chem.rdchem.Mol object - """ + """Initialize from a rdkit.Chem.rdchem.Mol object.""" rdkit_mol = self.sanitizer.sanitize(rdkit_mol) self.data = dpdata.rdkit.utils.mol_to_system_data(rdkit_mol) self.data["bond_dict"] = dict( diff --git a/dpdata/cli.py b/dpdata/cli.py index c80de99c..04850b80 100644 --- a/dpdata/cli.py +++ b/dpdata/cli.py @@ -43,7 +43,7 @@ def dpdata_parser() -> argparse.ArgumentParser: def dpdata_cli(): - """dpdata cli. + """Dpdata cli. Examples -------- @@ -65,7 +65,7 @@ def convert( no_labeled: bool = False, multi: bool = False, type_map: Optional[list] = None, - **kwargs + **kwargs, ): """Convert files from one format to another one. @@ -85,6 +85,8 @@ def convert( the system contains multiple directories type_map : list type map + **kwargs : dict + Additional arguments for the format. """ if multi: s = MultiSystems.from_file( diff --git a/dpdata/cp2k/cell.py b/dpdata/cp2k/cell.py index 33e56637..7f5f3ef0 100644 --- a/dpdata/cp2k/cell.py +++ b/dpdata/cp2k/cell.py @@ -1,13 +1,10 @@ -#%% -import re -from collections import OrderedDict +# %% import numpy as np def cell_to_low_triangle(A, B, C, alpha, beta, gamma): - """ - Convert cell to low triangle matrix. + """Convert cell to low triangle matrix. Parameters ---------- @@ -51,11 +48,11 @@ def cell_to_low_triangle(A, B, C, alpha, beta, gamma): ) ) if not A > 0.2: - raise RuntimeError("A=={}, must be greater than 0.2".format(A)) + raise RuntimeError(f"A=={A}, must be greater than 0.2") if not B > 0.2: - raise RuntimeError("B=={}, must be greater than 0.2".format(B)) + raise RuntimeError(f"B=={B}, must be greater than 0.2") if not C > 0.2: - raise RuntimeError("C=={}, must be greater than 0.2".format(C)) + raise RuntimeError(f"C=={C}, must be greater than 0.2") lx = A xy = B * np.cos(gamma) diff --git a/dpdata/cp2k/output.py b/dpdata/cp2k/output.py index f7b94f25..13d5be7c 100644 --- a/dpdata/cp2k/output.py +++ b/dpdata/cp2k/output.py @@ -1,9 +1,9 @@ -#%% +# %% +import math import re from collections import OrderedDict import numpy as np -from scipy.constants import R from ..unit import ( EnergyConversion, @@ -13,7 +13,6 @@ ) from .cell import cell_to_low_triangle -#%% AU_TO_ANG = LengthConversion("bohr", "angstrom").value() AU_TO_EV = EnergyConversion("hartree", "eV").value() AU_TO_EV_EVERY_ANG = ForceConversion("hartree/bohr", "eV/angstrom").value() @@ -27,19 +26,19 @@ avail_patterns.append(re.compile(r"^ ENSEMBLE TYPE")) -class Cp2kSystems(object): - """ - deal with cp2k outputfile - """ +class Cp2kSystems: + """deal with cp2k outputfile.""" def __init__(self, log_file_name, xyz_file_name, restart=False): - self.log_file_object = open(log_file_name, "r") - self.xyz_file_object = open(xyz_file_name, "r") + self.log_file_object = open(log_file_name) + self.xyz_file_object = open(xyz_file_name) self.log_block_generator = self.get_log_block_generator() self.xyz_block_generator = self.get_xyz_block_generator() self.restart_flag = restart + self.cell = None self.print_level = None + self.atomic_kinds = None if self.restart_flag: @@ -63,7 +62,9 @@ def __next__(self): # assert all(eq1), (log_info_dict,xyz_info_dict,'There may be errors in the file. If it is a restart task; use restart=True') # assert all(eq2), (log_info_dict,xyz_info_dict,'There may be errors in the file. If it is a restart task; use restart=True') # assert all(eq3), (log_info_dict,xyz_info_dict,'There may be errors in the file. If it is a restart task; use restart=True') - assert log_info_dict["energies"] == xyz_info_dict["energies"], ( + assert math.isclose( + log_info_dict["energies"], xyz_info_dict["energies"], abs_tol=1.0e-6 + ), ( log_info_dict["energies"], xyz_info_dict["energies"], "There may be errors in the file", @@ -257,7 +258,7 @@ def handle_single_log_frame(self, lines): [cell_bx, cell_by, cell_bz], [cell_cx, cell_cy, cell_cz], ] - ).astype("float32") + ).astype("float64") if atomic_kinds: self.atomic_kinds = atomic_kinds # print(self.atomic_kinds) @@ -299,7 +300,7 @@ def handle_single_log_frame(self, lines): GPa = PressureConversion("eV/angstrom^3", "GPa").value() if stress: stress = np.array(stress) - stress = stress.astype("float32") + stress = stress.astype("float64") stress = stress[np.newaxis, :, :] # stress to virial conversion, default unit in cp2k is GPa # note the stress is virial = stress * volume @@ -314,11 +315,11 @@ def handle_single_log_frame(self, lines): info_dict["atom_numbs"] = atom_numbs info_dict["atom_types"] = np.asarray(atom_types_idx_list) info_dict["print_level"] = self.print_level - info_dict["cells"] = np.asarray([self.cell]).astype("float32") - info_dict["energies"] = np.asarray([energy]).astype("float32") - info_dict["forces"] = np.asarray([forces_list]).astype("float32") + info_dict["cells"] = np.asarray([self.cell]).astype("float64") + info_dict["energies"] = np.asarray([energy]).astype("float64") + info_dict["forces"] = np.asarray([forces_list]).astype("float64") if virial is not None: - info_dict["virials"] = np.asarray([virial]).astype("float32") + info_dict["virials"] = np.asarray([virial]).astype("float64") return info_dict def handle_single_xyz_frame(self, lines): @@ -330,14 +331,14 @@ def handle_single_xyz_frame(self, lines): atom_num, len(lines) ) ) - data_format_line = lines[1].strip("\n").strip() + str(" ") + data_format_line = lines[1].strip("\n").strip() + " " prop_pattern = re.compile(r"(?P\w+)\s*=\s*(?P.*?)[, ]") prop_dict = dict(prop_pattern.findall(data_format_line)) energy = 0 if prop_dict.get("E"): energy = float(prop_dict.get("E")) * AU_TO_EV - # info_dict['energies'] = np.array([prop_dict['E']]).astype('float32') + # info_dict['energies'] = np.array([prop_dict['E']]).astype('float64') element_index = -1 element_dict = OrderedDict() @@ -364,13 +365,13 @@ def handle_single_xyz_frame(self, lines): # info_dict['atom_names'] = atom_names # info_dict['atom_numbs'] = atom_numbs # info_dict['atom_types'] = np.asarray(atom_types_list) - info_dict["coords"] = np.asarray([coords_list]).astype("float32") - info_dict["energies"] = np.array([energy]).astype("float32") + info_dict["coords"] = np.asarray([coords_list]).astype("float64") + info_dict["energies"] = np.array([energy]).astype("float64") info_dict["orig"] = np.zeros(3) return info_dict -#%% +# %% def get_frames(fname): @@ -392,6 +393,7 @@ def get_frames(fname): content = fp.read() count = content.count("SCF run converged") if count == 0: + fp.close() return [], [], [], [], [], [], [], None # search duplicated header @@ -450,10 +452,10 @@ def get_frames(fname): # conver to float array and add extra dimension for nframes cell = np.array(cell) - cell = cell.astype("float32") + cell = cell.astype("float64") cell = cell[np.newaxis, :, :] coord = np.array(coord) - coord = coord.astype("float32") + coord = coord.astype("float64") coord = coord[np.newaxis, :, :] atom_symbol_idx_list = np.array(atom_symbol_idx_list) atom_symbol_idx_list = atom_symbol_idx_list.astype(int) @@ -461,13 +463,13 @@ def get_frames(fname): atom_symbol_list = np.array(atom_symbol_list) atom_symbol_list = atom_symbol_list[atom_symbol_idx_list] force = np.array(force) - force = force.astype("float32") + force = force.astype("float64") force = force[np.newaxis, :, :] # virial is not necessary if stress: stress = np.array(stress) - stress = stress.astype("float32") + stress = stress.astype("float64") stress = stress[np.newaxis, :, :] # stress to virial conversion, default unit in cp2k is GPa # note the stress is virial = stress * volume @@ -479,7 +481,7 @@ def get_frames(fname): force = force * eV / angstrom # energy unit conversion, default unit in cp2k is hartree energy = float(energy) * eV - energy = np.array(energy).astype("float32") + energy = np.array(energy).astype("float64") energy = energy[np.newaxis] tmp_names, symbol_idx = np.unique(atom_symbol_list, return_index=True) diff --git a/dpdata/deepmd/hdf5.py b/dpdata/deepmd/hdf5.py index 69b993ab..e7e1abe6 100644 --- a/dpdata/deepmd/hdf5.py +++ b/dpdata/deepmd/hdf5.py @@ -101,7 +101,7 @@ def to_system_data( nframes = dd.shape[0] all_data.append(np.reshape(dd, (nframes, *prop["shape"]))) elif prop["required"]: - raise RuntimeError("%s/%s/%s not found" % (folder, ii, fn)) + raise RuntimeError(f"{folder}/{ii}/{fn} not found") if len(all_data) > 0: data[dt] = np.concatenate(all_data, axis=0) diff --git a/dpdata/deepmd/mixed.py b/dpdata/deepmd/mixed.py index fff8e930..e8abce21 100644 --- a/dpdata/deepmd/mixed.py +++ b/dpdata/deepmd/mixed.py @@ -19,12 +19,8 @@ def load_type(folder): def formula(atom_names, atom_numbs): - """ - Return the formula of this system, like C3H5O2 - """ - return "".join( - ["{}{}".format(symbol, numb) for symbol, numb in zip(atom_names, atom_numbs)] - ) + """Return the formula of this system, like C3H5O2.""" + return "".join([f"{symbol}{numb}" for symbol, numb in zip(atom_names, atom_numbs)]) def _cond_load_data(fname): @@ -225,6 +221,8 @@ def mix_system(*system, type_map, **kwargs): The systems to mix type_map : list of str Maps atom type to name + **kwargs : dict + Other parameters Returns ------- diff --git a/dpdata/fhi_aims/output.py b/dpdata/fhi_aims/output.py index 9706b91a..c4cd9257 100755 --- a/dpdata/fhi_aims/output.py +++ b/dpdata/fhi_aims/output.py @@ -14,7 +14,6 @@ def get_info(lines, type_idx_zero=False): - atom_types = [] atom_names = [] cell = [] @@ -42,7 +41,7 @@ def get_info(lines, type_idx_zero=False): _atom_names.append(ii[0]) atom_names = [] for ii in _atom_names: - if not ii in atom_names: + if ii not in atom_names: atom_names.append(ii) atom_numbs = [_atom_names.count(ii) for ii in atom_names] @@ -159,7 +158,6 @@ def analyze_block(lines, first_blk=False, md=True): natom = 0 if first_blk: - if md: _tmp = re.findall(pos_patt_other, contents)[:] for ii in _tmp[slice(int(len(_tmp) / 2), len(_tmp))]: diff --git a/dpdata/format.py b/dpdata/format.py index c6ba91b7..461d1ad6 100644 --- a/dpdata/format.py +++ b/dpdata/format.py @@ -1,42 +1,163 @@ """Implement the format plugin system.""" import os from abc import ABC -from collections import abc from .plugin import Plugin class Format(ABC): + """The abstract base class for all formats. + + To add a new format, one should create a new class inherited from this class, and then + + - implement several methods, such as :meth:`from_system`; + - register the format with a key; + - add documentation in the class docstring; + + The new format can be either insider or outside the package. + """ + __FormatPlugin = Plugin() __FromPlugin = Plugin() __ToPlugin = Plugin() @staticmethod def register(key): + """Register a format plugin. + + By default, after a format plugin is registered, the following methods + will be registered as well for :meth:`System`, :meth:`LabeledSystem`, :meth:`MultiSystems`, and + :meth:`BondOrderSystem`: + + - from_{key.replace('/', '_')} + - to_{key.replace('/', '_')} + - from({key}, ...) + - to({key}, ...) + + The decorator should be explicitly executed before :mod:`dpdata.system` + is imported. A module will be imported automatically if it + + - is a submodule of :mod:`dpdata.plugins`; + - is registered at the `dpdata.plugins` entry point + + Parameters + ---------- + key : str + The key to register the plugin. + + Returns + ------- + function + The decorator function. + + Examples + -------- + Register a format plugin: + + >>> @Format.register('test') + ... @Format.register('test2') + ... class TestFormat(Format): + ... pass + """ return Format.__FormatPlugin.register(key) @staticmethod def register_from(key): + """Register a from method if the target method name is not default. + + Parameters + ---------- + key : str + The key to register the plugin. + + Returns + ------- + function + The decorator function. + + Examples + -------- + Register a from method: + + >>> @Format.register_from('from_test_haha') + ... @Format.register('test) + ... class TestFormat(Format): + ... pass + + This will register a from method named from_test_haha, although the + format name is test. + """ return Format.__FromPlugin.register(key) @staticmethod def register_to(key): + """Register a to method if the target method name is not default. + + Parameters + ---------- + key : str + The key to register the plugin. + + Returns + ------- + function + The decorator function. + + Examples + -------- + Register a to method: + + >>> @Format.register_to('to_test_haha') + ... @Format.register('test') + ... class TestFormat(Format): + ... pass + + This will register a to method named to_test_haha, although the + format name is test. + """ return Format.__ToPlugin.register(key) @staticmethod def get_formats(): + """Get all registered formats.""" return Format.__FormatPlugin.plugins @staticmethod def get_from_methods(): + """Get all registered from methods.""" return Format.__FromPlugin.plugins @staticmethod def get_to_methods(): + """Get all registered to methods.""" return Format.__ToPlugin.plugins @staticmethod def post(func_name): + """Register a post function for from method. + + Such function will be called after the "from" method is called. + + Parameters + ---------- + func_name : str or list of str + The name of the post function. + + Returns + ------- + function + The decorator function. + + Examples + -------- + Register a post function: + + >>> @Format.post('remove_pbc') + ... @Format.register('test') + ... class TestFormat(Format): + ... pass + """ + def decorator(object): if not isinstance(func_name, (list, tuple, set)): object.post_func = (func_name,) @@ -47,54 +168,119 @@ def decorator(object): return decorator def from_system(self, file_name, **kwargs): - """System.from + """Implement System.from that converts from this format to System. Parameters ---------- file_name : str - file name + file name, i.e. the first argument + **kwargs : dict + keyword arguments that will be passed from the method Returns ------- - data: dict - system data + data : dict + system data, whose keys are defined in System.DTYPES """ raise NotImplementedError( "%s doesn't support System.from" % (self.__class__.__name__) ) def to_system(self, data, *args, **kwargs): - """System.to + """Implement System.to that converts from System to this format. Parameters ---------- data : dict - system data + system data, whose keys are defined in System.DTYPES + *args : list + arguments that will be passed from the method + **kwargs : dict + keyword arguments that will be passed from the method """ raise NotImplementedError( "%s doesn't support System.to" % (self.__class__.__name__) ) def from_labeled_system(self, file_name, **kwargs): + """Implement LabeledSystem.from that converts from this format to LabeledSystem. + + Parameters + ---------- + file_name : str + file name, i.e. the first argument + **kwargs : dict + keyword arguments that will be passed from the method + + Returns + ------- + data : dict + system data, whose keys are defined in LabeledSystem.DTYPES + """ raise NotImplementedError( "%s doesn't support LabeledSystem.from" % (self.__class__.__name__) ) def to_labeled_system(self, data, *args, **kwargs): + """Implement LabeledSystem.to that converts from LabeledSystem to this format. + + By default, LabeledSystem.to will fallback to System.to. + + Parameters + ---------- + data : dict + system data, whose keys are defined in LabeledSystem.DTYPES + *args : list + arguments that will be passed from the method + **kwargs : dict + keyword arguments that will be passed from the method + """ return self.to_system(data, *args, **kwargs) def from_bond_order_system(self, file_name, **kwargs): + """Implement BondOrderSystem.from that converts from this format to BondOrderSystem. + + Parameters + ---------- + file_name : str + file name, i.e. the first argument + **kwargs : dict + keyword arguments that will be passed from the method + + Returns + ------- + data : dict + system data + """ raise NotImplementedError( "%s doesn't support BondOrderSystem.from" % (self.__class__.__name__) ) def to_bond_order_system(self, data, rdkit_mol, *args, **kwargs): + """Implement BondOrderSystem.to that converts from BondOrderSystem to this format. + + By default, BondOrderSystem.to will fallback to LabeledSystem.to. + + Parameters + ---------- + data : dict + system data + rdkit_mol : rdkit.Chem.rdchem.Mol + rdkit mol object + *args : list + arguments that will be passed from the method + **kwargs : dict + keyword arguments that will be passed from the method + """ return self.to_system(data, *args, **kwargs) class MultiModes: - """File mode for MultiSystems - 0 (default): not implemented - 1: every directory under the top-level directory is a system + """File mode for MultiSystems. + + The current implemented modes are: + + - 0 (default): not implemented + - 1: every directory under the top-level directory is a system. """ NotImplemented = 0 @@ -103,12 +289,16 @@ class MultiModes: MultiMode = MultiModes.NotImplemented def from_multi_systems(self, directory, **kwargs): - """MultiSystems.from + """Implement MultiSystems.from that converts from this format to MultiSystems. + + By default, this method follows MultiMode to implement the conversion. Parameters ---------- directory : str directory of system + **kwargs : dict + keyword arguments that will be passed from the method Returns ------- @@ -126,6 +316,19 @@ def from_multi_systems(self, directory, **kwargs): ) def to_multi_systems(self, formulas, directory, **kwargs): + """Implement MultiSystems.to that converts from MultiSystems to this format. + + By default, this method follows MultiMode to implement the conversion. + + Parameters + ---------- + formulas : list[str] + list of formulas + directory : str + directory of system + **kwargs : dict + keyword arguments that will be passed from the method + """ if self.MultiMode == self.MultiModes.Directory: return [os.path.join(directory, ff) for ff in formulas] raise NotImplementedError( @@ -141,6 +344,8 @@ def mix_system(self, *system, type_map, **kwargs): The systems to mix type_map : list of str Maps atom type to name + **kwargs : dict + keyword arguments that will be passed from the method Returns ------- diff --git a/dpdata/gaussian/gjf.py b/dpdata/gaussian/gjf.py index 354187f0..21300a60 100644 --- a/dpdata/gaussian/gjf.py +++ b/dpdata/gaussian/gjf.py @@ -4,6 +4,7 @@ """Generate Gaussian input file.""" import itertools +import re import uuid import warnings from typing import List, Optional, Tuple, Union @@ -217,23 +218,23 @@ def make_gaussian_input( buff = [] # keywords, e.g., force b3lyp/6-31g** if use_fragment_guesses: - keywords[0] = "{} guess=fragment={}".format(keywords[0], frag_numb) + keywords[0] = f"{keywords[0]} guess=fragment={frag_numb}" chkkeywords = [] if len(keywords) > 1: - chkkeywords.append("%chk={}.chk".format(str(uuid.uuid1()))) + chkkeywords.append(f"%chk={str(uuid.uuid1())}.chk") - nprockeywords = "%nproc={:d}".format(nproc) + nprockeywords = f"%nproc={nproc:d}" # use formula as title titlekeywords = "".join( - ["{}{}".format(symbol, numb) for symbol, numb in zip(atom_names, atom_numbs)] + [f"{symbol}{numb}" for symbol, numb in zip(atom_names, atom_numbs)] ) - chargekeywords = "{} {}".format(charge, multiplicity) + chargekeywords = f"{charge} {multiplicity}" buff = [ *chkkeywords, nprockeywords, - "#{}".format(keywords[0]), + f"#{keywords[0]}", "", titlekeywords, "", @@ -246,13 +247,13 @@ def make_gaussian_input( "%s(Fragment=%d) %f %f %f" % (symbol, frag_index[ii] + 1, *coordinate) ) else: - buff.append("%s %f %f %f" % (symbol, *coordinate)) + buff.append("{} {:f} {:f} {:f}".format(symbol, *coordinate)) if not sys_data.get("nopbc", False): # PBC condition cell = sys_data["cells"][0] for ii in range(3): # use TV as atomic symbol, see https://gaussian.com/pbc/ - buff.append("TV %f %f %f" % (*cell[ii],)) + buff.append("TV {:f} {:f} {:f}".format(*cell[ii])) if basis_set is not None: # custom basis set buff.extend(["", basis_set, ""]) @@ -262,7 +263,7 @@ def make_gaussian_input( "\n--link1--", *chkkeywords, nprockeywords, - "#{}".format(kw), + f"#{kw}", "", titlekeywords, "", @@ -272,3 +273,68 @@ def make_gaussian_input( ) buff.append("\n") return "\n".join(buff) + + +def read_gaussian_input(inp: str): + """Read Gaussian input. + + Parameters + ---------- + inp : str + Gaussian input str + + Returns + ------- + dict + system data + """ + flag = 0 + coords = [] + elements = [] + cells = [] + for line in inp.split("\n"): + if not line.strip(): + # empty line + flag += 1 + elif flag == 0: + # keywords + if line.startswith("#"): + # setting + keywords = line.split() + elif line.startswith("%"): + pass + elif flag == 1: + # title + pass + elif flag == 2: + # multi and coords + s = line.split() + if len(s) == 2: + pass + elif len(s) == 4: + if s[0] == "TV": + cells.append(list(map(float, s[1:4]))) + else: + # element + elements.append(re.sub("\\(.*?\\)|\\{.*?}|\\[.*?]", "", s[0])) + coords.append(list(map(float, s[1:4]))) + elif flag == 3: + # end + break + atom_names, atom_types, atom_numbs = np.unique( + elements, return_inverse=True, return_counts=True + ) + if len(cells): + nopbc = False + else: + nopbc = True + cells = np.array([np.eye(3)]) * 100 + return { + "atom_names": list(atom_names), + "atom_numbs": list(atom_numbs), + "atom_types": atom_types, + "cells": np.array(cells).reshape(1, 3, 3), + "nopbc": nopbc, + "coords": np.array(coords).reshape(1, -1, 3), + "orig": np.zeros(3), + } diff --git a/dpdata/lammps/dump.py b/dpdata/lammps/dump.py index 2e4dd561..cdc28bdc 100644 --- a/dpdata/lammps/dump.py +++ b/dpdata/lammps/dump.py @@ -196,7 +196,7 @@ def system_data(lines, type_map=None, type_idx_zero=True, unwrap=False): system = {} system["atom_numbs"] = get_natoms_vec(lines) system["atom_names"] = [] - if type_map == None: + if type_map is None: for ii in range(len(system["atom_numbs"])): system["atom_names"].append("TYPE_%d" % ii) else: diff --git a/dpdata/lammps/lmp.py b/dpdata/lammps/lmp.py index 7f80fcc0..317b30ed 100644 --- a/dpdata/lammps/lmp.py +++ b/dpdata/lammps/lmp.py @@ -151,7 +151,7 @@ def system_data(lines, type_map=None, type_idx_zero=True): system = {} system["atom_numbs"] = get_natoms_vec(lines) system["atom_names"] = [] - if type_map == None: + if type_map is None: for ii in range(len(system["atom_numbs"])): system["atom_names"].append("Type_%d" % ii) else: diff --git a/dpdata/md/rdf.py b/dpdata/md/rdf.py index 4dcbece6..219543eb 100644 --- a/dpdata/md/rdf.py +++ b/dpdata/md/rdf.py @@ -2,8 +2,7 @@ def rdf(sys, sel_type=[None, None], max_r=5, nbins=100): - """ - compute the rdf of a system + """Compute the rdf of a system. Parameters ---------- diff --git a/dpdata/md/water.py b/dpdata/md/water.py index 42e27243..0cb82cc9 100644 --- a/dpdata/md/water.py +++ b/dpdata/md/water.py @@ -5,9 +5,6 @@ def compute_bonds(box, posis, atype, oh_sel=[0, 1], max_roh=1.3, uniq_hbond=True): try: - import ase - import ase.neighborlist - # nlist implemented by ase return compute_bonds_ase(box, posis, atype, oh_sel, max_roh, uniq_hbond) except ImportError: diff --git a/dpdata/periodic_table.py b/dpdata/periodic_table.py index 30ffb1be..e6f16bc9 100644 --- a/dpdata/periodic_table.py +++ b/dpdata/periodic_table.py @@ -1,6 +1,6 @@ from pathlib import Path -from monty.serialization import dumpfn, loadfn +from monty.serialization import loadfn fpdt = str(Path(__file__).absolute().parent / "periodic_table.json") _pdt = loadfn(fpdt) diff --git a/dpdata/plugins/3dmol.py b/dpdata/plugins/3dmol.py index 3b463abb..ec994dd9 100644 --- a/dpdata/plugins/3dmol.py +++ b/dpdata/plugins/3dmol.py @@ -19,7 +19,7 @@ def to_system( f_idx: int = 0, size: Tuple[int] = (300, 300), style: dict = {"stick": {}, "sphere": {"radius": 0.4}}, - **kwargs + **kwargs, ): """Show 3D structure of a frame in jupyter. @@ -33,6 +33,8 @@ def to_system( (width, height) of the widget style : dict style of 3DMol. Read 3DMol documentation for details. + **kwargs : dict + other parameters Examples -------- diff --git a/dpdata/plugins/abacus.py b/dpdata/plugins/abacus.py index db983b7d..754221be 100644 --- a/dpdata/plugins/abacus.py +++ b/dpdata/plugins/abacus.py @@ -11,11 +11,12 @@ def from_system(self, file_name, **kwargs): return dpdata.abacus.scf.get_frame_from_stru(file_name) def to_system(self, data, file_name, frame_idx=0, **kwargs): - """ - Dump the system into ABACUS STRU format file. + """Dump the system into ABACUS STRU format file. Parameters ---------- + data : dict + System data file_name : str The output file name frame_idx : int @@ -28,8 +29,9 @@ def to_system(self, data, file_name, frame_idx=0, **kwargs): List of atomic masses numerical_descriptor : str, optional numerical descriptor file + **kwargs : dict + other parameters """ - pp_file = kwargs.get("pp_file") numerical_orbital = kwargs.get("numerical_orbital") mass = kwargs.get("mass") diff --git a/dpdata/plugins/amber.py b/dpdata/plugins/amber.py index 4d6a2229..cdc92a30 100644 --- a/dpdata/plugins/amber.py +++ b/dpdata/plugins/amber.py @@ -60,15 +60,11 @@ def from_labeled_system( @Format.register("sqm/out") class SQMOutFormat(Format): def from_system(self, fname, **kwargs): - """ - Read from ambertools sqm.out - """ + """Read from ambertools sqm.out.""" return dpdata.amber.sqm.parse_sqm_out(fname) def from_labeled_system(self, fname, **kwargs): - """ - Read from ambertools sqm.out - """ + """Read from ambertools sqm.out.""" data = dpdata.amber.sqm.parse_sqm_out(fname) assert "forces" in list(data.keys()), f"No forces in {fname}" return data @@ -77,8 +73,7 @@ def from_labeled_system(self, fname, **kwargs): @Format.register("sqm/in") class SQMINFormat(Format): def to_system(self, data, fname=None, frame_idx=0, **kwargs): - """ - Generate input files for semi-emperical calculation in sqm software + """Generate input files for semi-emperical calculation in sqm software. Parameters ---------- @@ -88,6 +83,8 @@ def to_system(self, data, fname=None, frame_idx=0, **kwargs): output file name frame_idx : int, default=0 index of frame to write + **kwargs : dict + other parameters Other Parameters ---------------- diff --git a/dpdata/plugins/ase.py b/dpdata/plugins/ase.py index 9a626be8..f668a0a7 100644 --- a/dpdata/plugins/ase.py +++ b/dpdata/plugins/ase.py @@ -34,6 +34,8 @@ def from_system(self, atoms: "ase.Atoms", **kwargs) -> dict: ---------- atoms : ase.Atoms an ASE Atoms, containing a structure + **kwargs : dict + other parameters Returns ------- @@ -52,8 +54,8 @@ def from_system(self, atoms: "ase.Atoms", **kwargs) -> dict: "atom_names": atom_names, "atom_numbs": atom_numbs, "atom_types": atom_types, - "cells": np.array([cells]).astype("float32"), - "coords": np.array([coords]).astype("float32"), + "cells": np.array([cells]), + "coords": np.array([coords]), "orig": np.zeros(3), "nopbc": not np.any(atoms.get_pbc()), } @@ -67,6 +69,8 @@ def from_labeled_system(self, atoms: "ase.Atoms", **kwargs) -> dict: ---------- atoms : ase.Atoms an ASE Atoms, containing a structure + **kwargs : dict + other parameters Returns ------- @@ -87,15 +91,15 @@ def from_labeled_system(self, atoms: "ase.Atoms", **kwargs) -> dict: forces = atoms.get_forces() info_dict = { **info_dict, - "energies": np.array([energies]).astype("float32"), - "forces": np.array([forces]).astype("float32"), + "energies": np.array([energies]), + "forces": np.array([forces]), } try: stress = atoms.get_stress(False) except PropertyNotImplementedError: pass else: - virials = np.array([-atoms.get_volume() * stress]).astype("float32") + virials = np.array([-atoms.get_volume() * stress]) info_dict["virials"] = virials return info_dict @@ -106,7 +110,7 @@ def from_multi_systems( end: Optional[int] = None, step: Optional[int] = None, ase_fmt: Optional[str] = None, - **kwargs + **kwargs, ) -> "ase.Atoms": """Convert a ASE supported file to ASE Atoms. @@ -124,6 +128,8 @@ def from_multi_systems( frame index step ase_fmt : str, optional ASE format. See the ASE documentation about supported formats + **kwargs : dict + other parameters Yields ------ @@ -131,14 +137,10 @@ def from_multi_systems( ASE atoms in the file """ frames = ase.io.read(file_name, format=ase_fmt, index=slice(begin, end, step)) - for atoms in frames: - yield atoms + yield from frames def to_system(self, data, **kwargs): - """ - convert System to ASE Atom obj - - """ + """Convert System to ASE Atom obj.""" from ase import Atoms structures = [] diff --git a/dpdata/plugins/cp2k.py b/dpdata/plugins/cp2k.py index e1df43e5..1f09adae 100644 --- a/dpdata/plugins/cp2k.py +++ b/dpdata/plugins/cp2k.py @@ -8,8 +8,8 @@ @Format.register("cp2k/aimd_output") class CP2KAIMDOutputFormat(Format): def from_labeled_system(self, file_name, restart=False, **kwargs): - xyz_file = sorted(glob.glob("{}/*pos*.xyz".format(file_name)))[0] - log_file = sorted(glob.glob("{}/*.log".format(file_name)))[0] + xyz_file = sorted(glob.glob(f"{file_name}/*pos*.xyz"))[0] + log_file = sorted(glob.glob(f"{file_name}/*.log"))[0] return tuple(Cp2kSystems(log_file, xyz_file, restart)) diff --git a/dpdata/plugins/deepmd.py b/dpdata/plugins/deepmd.py index 499e23b2..38eab85f 100644 --- a/dpdata/plugins/deepmd.py +++ b/dpdata/plugins/deepmd.py @@ -22,7 +22,7 @@ def from_system(self, file_name, type_map=None, **kwargs): ) def to_system(self, data, file_name, **kwargs): - """Dump the system in deepmd raw format to directory `file_name`""" + """Dump the system in deepmd raw format to directory `file_name`.""" dpdata.deepmd.raw.dump(file_name, data) def from_labeled_system(self, file_name, type_map=None, **kwargs): @@ -42,8 +42,7 @@ def from_system(self, file_name, type_map=None, **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`. + """Dump the system in deepmd compressed format (numpy binary) to `folder`. The frames are firstly split to sets, then dumped to seperated subfolders named as `folder/set.000`, `folder/set.001`, .... @@ -60,6 +59,8 @@ def to_system(self, data, file_name, set_size=5000, prec=np.float64, **kwargs): The size of each set. prec : {numpy.float32, numpy.float64} The floating point precision of the compressed data + **kwargs : dict + other parameters """ dpdata.deepmd.comp.dump(file_name, data, set_size=set_size, comp_prec=prec) @@ -95,8 +96,7 @@ def from_system_mix(self, file_name, type_map=None, **kwargs): ) def to_system(self, data, file_name, prec=np.float64, **kwargs): - """ - Dump the system in deepmd mixed type format (numpy binary) to `folder`. + """Dump the system in deepmd mixed type format (numpy binary) to `folder`. The frames were already split to different systems, so these frames can be dumped to one single subfolders named as `folder/set.000`, containing less than `set_size` frames. @@ -109,6 +109,8 @@ def to_system(self, data, file_name, prec=np.float64, **kwargs): The output folder prec : {numpy.float32, numpy.float64} The floating point precision of the compressed data + **kwargs : dict + other parameters """ dpdata.deepmd.mixed.dump(file_name, data, comp_prec=prec) @@ -126,6 +128,8 @@ def mix_system(self, *system, type_map, **kwargs): The systems to mix type_map : list of str Maps atom type to name + **kwargs : dict + other parameters Returns ------- @@ -205,7 +209,7 @@ def from_system( self, file_name: Union[str, h5py.Group, h5py.File], type_map: Optional[List[str]] = None, - **kwargs + **kwargs, ) -> dict: """Convert HDF5 file to System data. @@ -216,6 +220,8 @@ def from_system( hashtag is used to split path to the HDF5 file and the HDF5 group type_map : dict[str] type map + **kwargs : dict + other parameters Returns ------- @@ -233,7 +239,7 @@ def from_labeled_system( self, file_name: Union[str, h5py.Group, h5py.File], type_map: Optional[List[str]] = None, - **kwargs + **kwargs, ) -> dict: """Convert HDF5 file to LabeledSystem data. @@ -244,6 +250,8 @@ def from_labeled_system( hashtag is used to split path to the HDF5 file and the HDF5 group type_map : dict[str] type map + **kwargs : dict + other parameters Returns ------- @@ -263,7 +271,7 @@ def to_system( file_name: Union[str, h5py.Group, h5py.File], set_size: int = 5000, comp_prec: np.dtype = np.float64, - **kwargs + **kwargs, ): """Convert System data to HDF5 file. @@ -278,6 +286,8 @@ def to_system( set size comp_prec : np.dtype data precision + **kwargs : dict + other parameters """ if isinstance(file_name, (h5py.Group, h5py.File)): dpdata.deepmd.hdf5.dump( @@ -301,6 +311,8 @@ def from_multi_systems(self, directory: str, **kwargs) -> h5py.Group: ---------- directory : str HDF5 file name + **kwargs : dict + other parameters Yields ------ @@ -322,6 +334,8 @@ def to_multi_systems( formulas of MultiSystems directory : str HDF5 file name + **kwargs : dict + other parameters Yields ------ diff --git a/dpdata/plugins/gaussian.py b/dpdata/plugins/gaussian.py index 416c61ad..a22ce863 100644 --- a/dpdata/plugins/gaussian.py +++ b/dpdata/plugins/gaussian.py @@ -25,7 +25,21 @@ def from_labeled_system(self, file_name, **kwargs): @Format.register("gaussian/gjf") class GaussiaGJFFormat(Format): - """Gaussian input file""" + """Gaussian input file.""" + + def from_system(self, file_name: str, **kwargs): + """Read Gaussian input file. + + Parameters + ---------- + file_name : str + file name + **kwargs : dict + keyword arguments + """ + with open(file_name) as fp: + text = fp.read() + return dpdata.gaussian.gjf.read_gaussian_input(text) def to_system(self, data: dict, file_name: str, **kwargs): """Generate Gaussian input file. diff --git a/dpdata/plugins/gromacs.py b/dpdata/plugins/gromacs.py index 6f19a27f..20e50835 100644 --- a/dpdata/plugins/gromacs.py +++ b/dpdata/plugins/gromacs.py @@ -6,28 +6,34 @@ @Format.register("gromacs/gro") class GromacsGroFormat(Format): def from_system(self, file_name, format_atom_name=True, **kwargs): - """ - Load gromacs .gro file + """Load gromacs .gro file. Parameters ---------- file_name : str The input file name + format_atom_name : bool + Whether to format the atom name + **kwargs : dict + other parameters """ return dpdata.gromacs.gro.file_to_system_data( file_name, format_atom_name=format_atom_name, **kwargs ) def to_system(self, data, file_name=None, frame_idx=-1, **kwargs): - """ - Dump the system in gromacs .gro format + """Dump the system in gromacs .gro format. Parameters ---------- + data : dict + System data file_name : str or None The output file name. If None, return the file content as a string frame_idx : int The index of the frame to dump + **kwargs : dict + other parameters """ assert frame_idx < len(data["coords"]) if frame_idx == -1: diff --git a/dpdata/plugins/lammps.py b/dpdata/plugins/lammps.py index bd041d95..be89be9d 100644 --- a/dpdata/plugins/lammps.py +++ b/dpdata/plugins/lammps.py @@ -13,8 +13,7 @@ def from_system(self, file_name, type_map=None, **kwargs): return dpdata.lammps.lmp.to_system_data(lines, type_map) def to_system(self, data, file_name, frame_idx=0, **kwargs): - """ - Dump the system in lammps data format + """Dump the system in lammps data format. Parameters ---------- @@ -24,6 +23,8 @@ def to_system(self, data, file_name, frame_idx=0, **kwargs): The output file name frame_idx : int The index of the frame to dump + **kwargs : dict + other parameters """ assert frame_idx < len(data["coords"]) w_str = dpdata.lammps.lmp.from_system_data(data, frame_idx) diff --git a/dpdata/plugins/list.py b/dpdata/plugins/list.py index f7880fa0..68a14074 100644 --- a/dpdata/plugins/list.py +++ b/dpdata/plugins/list.py @@ -4,9 +4,7 @@ @Format.register("list") class ListFormat(Format): def to_system(self, data, **kwargs): - """ - convert system to list, usefull for data collection - """ + """Convert system to list, usefull for data collection.""" from dpdata import LabeledSystem, System if "forces" in data: diff --git a/dpdata/plugins/psi4.py b/dpdata/plugins/psi4.py new file mode 100644 index 00000000..932d118c --- /dev/null +++ b/dpdata/plugins/psi4.py @@ -0,0 +1,52 @@ +import numpy as np + +from dpdata.format import Format +from dpdata.psi4.output import read_psi4_output +from dpdata.unit import EnergyConversion, ForceConversion, LengthConversion + +length_convert = LengthConversion("bohr", "angstrom").value() +energy_convert = EnergyConversion("hartree", "eV").value() +force_convert = ForceConversion("hartree/bohr", "eV/angstrom").value() + + +@Format.register("psi4/out") +class PSI4OutFormat(Format): + """Psi4 output. + + Note that both the energy and the gradient should be + printed into the output file. + """ + + def from_labeled_system(self, file_name: str, **kwargs) -> dict: + """Read from Psi4 output. + + Parameters + ---------- + file_name : str + file name + **kwargs + keyword arguments + + Returns + ------- + dict + system data + """ + symbols, coord, energy, forces = read_psi4_output(file_name) + + atom_names, atom_types, atom_numbs = np.unique( + symbols, return_inverse=True, return_counts=True + ) + natoms = coord.shape[0] + + return { + "atom_types": atom_types, + "atom_names": list(atom_names), + "atom_numbs": list(atom_numbs), + "coords": (coord * length_convert).reshape((1, natoms, 3)), + "energies": np.array([energy * energy_convert]), + "forces": (forces * force_convert).reshape((1, natoms, 3)), + "cells": np.zeros((1, 3, 3)), + "orig": np.zeros(3), + "nopbc": True, + } diff --git a/dpdata/plugins/pwmat.py b/dpdata/plugins/pwmat.py index 4d123f1e..11257c4d 100644 --- a/dpdata/plugins/pwmat.py +++ b/dpdata/plugins/pwmat.py @@ -51,15 +51,20 @@ def from_system(self, file_name, **kwargs): return dpdata.pwmat.atomconfig.to_system_data(lines) def to_system(self, data, file_name, frame_idx=0, *args, **kwargs): - """ - Dump the system in pwmat atom.config format + """Dump the system in pwmat atom.config format. Parameters ---------- + data : dict + The system data file_name : str The output file name frame_idx : int The index of the frame to dump + *args : list + other parameters + **kwargs : dict + other parameters """ assert frame_idx < len(data["coords"]) w_str = dpdata.pwmat.atomconfig.from_system_data(data, frame_idx) diff --git a/dpdata/plugins/pymatgen.py b/dpdata/plugins/pymatgen.py index 36efc12c..82b64e71 100644 --- a/dpdata/plugins/pymatgen.py +++ b/dpdata/plugins/pymatgen.py @@ -7,7 +7,7 @@ @Format.register("pymatgen/structure") class PyMatgenStructureFormat(Format): def to_system(self, data, **kwargs): - """convert System to Pymatgen Structure obj""" + """Convert System to Pymatgen Structure obj.""" structures = [] try: from pymatgen.core import Structure @@ -33,14 +33,14 @@ class PyMatgenMoleculeFormat(Format): @Format.post("remove_pbc") def from_system(self, file_name, **kwargs): try: - from pymatgen.core import Molecule + from pymatgen.core import Molecule # noqa: F401 except ModuleNotFoundError as e: raise ImportError("No module pymatgen.Molecule") from e return dpdata.pymatgen.molecule.to_system_data(file_name) def to_system(self, data, **kwargs): - """convert System to Pymatgen Molecule obj""" + """Convert System to Pymatgen Molecule obj.""" molecules = [] try: from pymatgen.core import Molecule @@ -61,7 +61,7 @@ def to_system(self, data, **kwargs): @Format.register_to("to_pymatgen_ComputedStructureEntry") class PyMatgenCSEFormat(Format): def to_labeled_system(self, data, *args, **kwargs): - """convert System to Pymagen ComputedStructureEntry obj""" + """Convert System to Pymagen ComputedStructureEntry obj.""" try: from pymatgen.entries.computed_entries import ComputedStructureEntry except ModuleNotFoundError as e: diff --git a/dpdata/plugins/rdkit.py b/dpdata/plugins/rdkit.py index 64a2f343..ff7638cb 100644 --- a/dpdata/plugins/rdkit.py +++ b/dpdata/plugins/rdkit.py @@ -23,9 +23,7 @@ def to_bond_order_system(self, data, mol, file_name, frame_idx=0, **kwargs): @Format.register("sdf_file") class SdfFormat(Format): def from_bond_order_system(self, file_name, **kwargs): - """ - Note that it requires all molecules in .sdf file must be of the same topology - """ + """Note that it requires all molecules in .sdf file must be of the same topology.""" mols = [ m for m in rdkit.Chem.SDMolSupplier(file_name, sanitize=False, removeHs=False) diff --git a/dpdata/plugins/vasp.py b/dpdata/plugins/vasp.py index 6e2fe5f0..76d34b9d 100644 --- a/dpdata/plugins/vasp.py +++ b/dpdata/plugins/vasp.py @@ -4,7 +4,7 @@ import dpdata.vasp.poscar import dpdata.vasp.xml from dpdata.format import Format -from dpdata.utils import sort_atom_names, uniq_atom_names +from dpdata.utils import uniq_atom_names @Format.register("poscar") @@ -21,15 +21,18 @@ def from_system(self, file_name, **kwargs): return data def to_system(self, data, file_name, frame_idx=0, **kwargs): - """ - Dump the system in vasp POSCAR format + """Dump the system in vasp POSCAR format. Parameters ---------- + data : dict + The system data file_name : str The output file name frame_idx : int The index of the frame to dump + **kwargs : dict + other parameters """ w_str = VASPStringFormat().to_system(data, frame_idx=frame_idx) with open(file_name, "w") as fp: @@ -39,13 +42,16 @@ def to_system(self, data, file_name, frame_idx=0, **kwargs): @Format.register("vasp/string") class VASPStringFormat(Format): def to_system(self, data, frame_idx=0, **kwargs): - """ - Dump the system in vasp POSCAR format string + """Dump the system in vasp POSCAR format string. Parameters ---------- + data : dict + The system data frame_idx : int The index of the frame to dump + **kwargs : dict + other parameters """ assert frame_idx < len(data["coords"]) return dpdata.vasp.poscar.from_system_data(data, frame_idx) diff --git a/dpdata/plugins/xyz.py b/dpdata/plugins/xyz.py index 69cca61b..fdb5bf3b 100644 --- a/dpdata/plugins/xyz.py +++ b/dpdata/plugins/xyz.py @@ -23,7 +23,7 @@ def to_system(self, data, file_name, **kwargs): fp.write("\n".join(buff)) def from_system(self, file_name, **kwargs): - with open(file_name, "r") as fp: + with open(file_name) as fp: coords, types = xyz_to_coord(fp.read()) atom_names, atom_types, atom_numbs = np.unique( types, return_inverse=True, return_counts=True diff --git a/dpdata/psi4/__init__.py b/dpdata/psi4/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/dpdata/psi4/output.py b/dpdata/psi4/output.py new file mode 100644 index 00000000..c093b0e5 --- /dev/null +++ b/dpdata/psi4/output.py @@ -0,0 +1,66 @@ +from typing import Tuple + +import numpy as np + + +def read_psi4_output(fn: str) -> Tuple[str, np.ndarray, float, np.ndarray]: + """Read from Psi4 output. + + Note that both the energy and the gradient should be printed. + + Parameters + ---------- + fn : str + file name + + Returns + ------- + str + atomic symbols + np.ndarray + atomic coordinates + float + total potential energy + np.ndarray + atomic forces + """ + coord = None + symbols = None + forces = None + energy = None + with open(fn) as f: + flag = 0 + for line in f: + if flag in (1, 3, 4, 5, 6): + flag += 1 + elif flag == 2: + s = line.split() + if not len(s): + flag = 0 + else: + symbols.append(s[0].capitalize()) + coord.append([float(s[1]), float(s[2]), float(s[3])]) + elif flag == 7: + s = line.split() + if not len(s): + flag = 0 + else: + forces.append([float(s[1]), float(s[2]), float(s[3])]) + elif line.startswith( + " Center X Y Z Mass" + ): + # coord + flag = 1 + coord = [] + symbols = [] + elif line.startswith(" ## Total Gradient"): + flag = 3 + forces = [] + elif line.startswith(" Total Energy ="): + energy = float(line.split()[-1]) + symbols = np.array(symbols) + forces = -np.array(forces) + coord = np.array(coord) + assert coord.shape == forces.shape + + return symbols, coord, energy, forces diff --git a/dpdata/pymatgen/molecule.py b/dpdata/pymatgen/molecule.py index 25e13c29..13d4046c 100644 --- a/dpdata/pymatgen/molecule.py +++ b/dpdata/pymatgen/molecule.py @@ -6,8 +6,6 @@ pass from collections import Counter -import dpdata - def to_system_data(file_name, protect_layer=9): mol = Molecule.from_file(file_name) diff --git a/dpdata/qe/scf.py b/dpdata/qe/scf.py index f78be7cb..659b1845 100755 --- a/dpdata/qe/scf.py +++ b/dpdata/qe/scf.py @@ -107,9 +107,10 @@ def get_energy(lines): return energy -def get_force(lines): +def get_force(lines, natoms): blk = get_block(lines, "Forces acting on atoms", skip=1) ret = [] + blk = blk[0 : sum(natoms)] for ii in blk: ret.append([float(jj) for jj in ii.split("=")[1].split()]) ret = np.array(ret) @@ -139,14 +140,14 @@ def get_frame(fname): path_out = fname[1] else: raise RuntimeError("invalid input") - with open(path_out, "r") as fp: + with open(path_out) as fp: outlines = fp.read().split("\n") - with open(path_in, "r") as fp: + with open(path_in) as fp: inlines = fp.read().split("\n") cell = get_cell(inlines) atom_names, natoms, types, coords = get_coords(inlines, cell) energy = get_energy(outlines) - force = get_force(outlines) + force = get_force(outlines, natoms) stress = get_stress(outlines) * np.linalg.det(cell) return ( atom_names, diff --git a/dpdata/qe/traj.py b/dpdata/qe/traj.py index 700f2ebc..ab1a790b 100644 --- a/dpdata/qe/traj.py +++ b/dpdata/qe/traj.py @@ -3,8 +3,6 @@ import numpy as np -import dpdata - from ..unit import ( EnergyConversion, ForceConversion, @@ -134,7 +132,7 @@ def load_data(fname, natoms, begin=0, step=1, convert=1.0): with open(fname) as fp: while True: blk, ss = _load_pos_block(fp, natoms) - if blk == None: + if blk is None: break else: if cc >= begin and (cc - begin) % step == 0: diff --git a/dpdata/rdkit/sanitize.py b/dpdata/rdkit/sanitize.py index 6a5a1c34..061de3d9 100644 --- a/dpdata/rdkit/sanitize.py +++ b/dpdata/rdkit/sanitize.py @@ -3,7 +3,7 @@ from copy import deepcopy from rdkit import Chem -from rdkit.Chem.rdchem import Atom, Bond, BondType, Mol +from rdkit.Chem.rdchem import BondType # openbabel try: @@ -31,9 +31,7 @@ def get_explicit_valence(atom, verbose=False): def regularize_formal_charges(mol, sanitize=True, verbose=False): - """ - Regularize formal charges of atoms - """ + """Regularize formal charges of atoms.""" assert isinstance(mol, Chem.rdchem.Mol) for atom in mol.GetAtoms(): assign_formal_charge_for_atom(atom, verbose) @@ -48,9 +46,7 @@ def regularize_formal_charges(mol, sanitize=True, verbose=False): def assign_formal_charge_for_atom(atom, verbose=False): - """ - assigen formal charge according to 8-electron rule for element B,C,N,O,S,P,As - """ + """Assigen formal charge according to 8-electron rule for element B,C,N,O,S,P,As.""" assert isinstance(atom, Chem.rdchem.Atom) valence = get_explicit_valence(atom, verbose) if atom.GetSymbol() == "B": @@ -630,19 +626,24 @@ def super_sanitize_mol(mol, name=None, verbose=True): return None -class Sanitizer(object): +class Sanitizer: def __init__(self, level="medium", raise_errors=True, verbose=False): - """ - Set up sanitizer. - -------- - Parameters: - level : 'low', 'medium' or 'high'. - `low` - use rdkit.Chem.SanitizeMol() to sanitize - `medium` - before using rdkit, assign formal charges of each atom first, which requires - the rightness of bond order information - `high` - try to regularize bond order of nitro, phosphate, sulfate, nitrine, guanidine, - pyridine-oxide function groups and aromatic heterocycles. If failed, the program - will call obabel to pre-process the mol object and re-try the procedure. + """Set up sanitizer. + --------. + + Parameters + ---------- + level : 'low', 'medium' or 'high'. + `low` - use rdkit.Chem.SanitizeMol() to sanitize + `medium` - before using rdkit, assign formal charges of each atom first, which requires + the rightness of bond order information + `high` - try to regularize bond order of nitro, phosphate, sulfate, nitrine, guanidine, + pyridine-oxide function groups and aromatic heterocycles. If failed, the program + will call obabel to pre-process the mol object and re-try the procedure. + raise_errors : bool, default=True + If True, raise SanitizeError when failed. + verbose : bool, default=False + If True, print error information when failed. """ self._check_level(level) self.level = level @@ -667,9 +668,7 @@ def _handle_exception(self, error_info): print(error_info) def sanitize(self, mol): - """ - Sanitize mol according to `self.level`. If failed, return None. - """ + """Sanitize mol according to `self.level`. If failed, return None.""" if self.level == "low": try: Chem.SanitizeMol(mol) diff --git a/dpdata/rdkit/utils.py b/dpdata/rdkit/utils.py index e5d1c7a8..25cf97cd 100644 --- a/dpdata/rdkit/utils.py +++ b/dpdata/rdkit/utils.py @@ -1,6 +1,5 @@ try: from rdkit import Chem - from rdkit.Chem import AllChem except ModuleNotFoundError: pass import numpy as np diff --git a/dpdata/siesta/aiMD_output.py b/dpdata/siesta/aiMD_output.py index 32cb081f..4e1890ec 100644 --- a/dpdata/siesta/aiMD_output.py +++ b/dpdata/siesta/aiMD_output.py @@ -5,9 +5,10 @@ ev2ev = 1 ang2ang = 1 + #############################read output##################################### def get_single_line_tail(fin, keyword, num=1): - file = open(fin, "r") + file = open(fin) part_res = [] for value in file: if keyword in value: @@ -31,7 +32,7 @@ def extract_keyword( is_repeated_read, column_num, ): - file = open(fout, "r") + file = open(fout) ret = [] part_ret = [] flag = 0 @@ -72,7 +73,7 @@ def extract_keyword( def obtain_nframe(fname): - fp = open(fname, "r") + fp = open(fname) flag = False idx = 0 temp = 0 @@ -81,7 +82,7 @@ def obtain_nframe(fname): flag = True continue if flag: - if not "siesta: Pressure (static):" in ii: + if "siesta: Pressure (static):" not in ii: if len(ii.split()) == 3: temp += 1 if temp == 3: @@ -105,7 +106,7 @@ def get_atom_types(fout, atomnums): def get_atom_name(fout): - file = open(fout, "r") + file = open(fout) ret = [] for value in file: if "Species number:" in value: diff --git a/dpdata/siesta/output.py b/dpdata/siesta/output.py index b70fe55d..7418d543 100644 --- a/dpdata/siesta/output.py +++ b/dpdata/siesta/output.py @@ -8,7 +8,7 @@ #############################read output##################################### def get_single_line_tail(fin, keyword, num=1): - file = open(fin, "r") + file = open(fin) res = [] for value in file: if keyword in value: @@ -23,7 +23,7 @@ def get_single_line_tail(fin, keyword, num=1): ## begin_column: begin column num ## column_num: read column num def extract_keyword(fout, keyword, down_line_num, begin_column, column_num): - file = open(fout, "r") + file = open(fout) ret = [] flag = 0 idx = 0 @@ -63,7 +63,7 @@ def get_atom_types(fout, atomnums): def get_atom_name(fout): - file = open(fout, "r") + file = open(fout) ret = [] for value in file: if "Species number:" in value: diff --git a/dpdata/system.py b/dpdata/system.py index 802b352c..743f3d05 100644 --- a/dpdata/system.py +++ b/dpdata/system.py @@ -1,10 +1,9 @@ -#%% +# %% import glob -import inspect import os from copy import deepcopy from enum import Enum, unique -from typing import Any, Tuple, Union +from typing import Any, Dict, Optional, Tuple, Union import numpy as np from monty.json import MSONable @@ -18,7 +17,6 @@ from dpdata.amber.mask import load_param_file, pick_by_amber_mask from dpdata.driver import Driver, Minimizer from dpdata.format import Format -from dpdata.periodic_table import Element from dpdata.plugin import Plugin from dpdata.utils import add_atom_names, elements_index_map, remove_pbc, sort_atom_names @@ -29,7 +27,9 @@ def load_format(fmt): if fmt in formats: return formats[fmt]() raise NotImplementedError( - "Unsupported data format %s. Supported formats: %s" % (fmt, " ".join(formats)) + "Unsupported data format {}. Supported formats: {}".format( + fmt, " ".join(formats) + ) ) @@ -116,8 +116,7 @@ def check(self, system: "System"): pass elif not isinstance(data, self.dtype): raise DataError( - "Type of %s is %s, but expected %s" - % (self.name, type(data).__name__, self.dtype.__name__) + f"Type of {self.name} is {type(data).__name__}, but expected {self.dtype.__name__}" ) # check shape if self.shape is not None: @@ -126,8 +125,7 @@ def check(self, system: "System"): if isinstance(data, np.ndarray): if data.size and shape != data.shape: raise DataError( - "Shape of %s is %s, but expected %s" - % (self.name, data.shape, shape) + f"Shape of {self.name} is {data.shape}, but expected {shape}" ) elif isinstance(data, list): if len(shape) and shape[0] != len(data): @@ -142,8 +140,7 @@ def check(self, system: "System"): class System(MSONable): - """ - The data System + """The data System. A data System (a concept used by `deepmd-kit `_) contains frames (e.g. produced by an MD simulation) that has the same number of atoms of the same type. @@ -196,8 +193,7 @@ def __init__( convergence_check=True, **kwargs, ): - """ - Constructor + """Constructor. Parameters ---------- @@ -265,6 +261,8 @@ def __init__( The raw data of System class. convergence_check : boolean Whether to request a convergence check. + **kwargs : dict + other parameters """ self.data = {} self.data["atom_numbs"] = [] @@ -340,6 +338,10 @@ def to(self, fmt: str, *args, **kwargs) -> "System": ---------- fmt : str format + *args + arguments + **kwargs + keyword arguments Returns ------- @@ -367,17 +369,17 @@ def __str__(self): return ret def __getitem__(self, key): - """Returns proerty stored in System by key or by idx""" + """Returns proerty stored in System by key or by idx.""" if isinstance(key, (int, slice, list, np.ndarray)): return self.sub_system(key) return self.data[key] def __len__(self): - """Returns number of frames in the system""" + """Returns number of frames in the system.""" return self.get_nframes() def __add__(self, others): - """magic method "+" operation""" + """Magic method "+" operation.""" self_copy = self.copy() if isinstance(others, System): other_copy = others.copy() @@ -392,12 +394,11 @@ def __add__(self, others): return self.__class__.from_dict({"data": self_copy.data}) def dump(self, filename, indent=4): - """dump .json or .yaml file""" + """Dump .json or .yaml file.""" dumpfn(self.as_dict(), filename, indent=indent) def map_atom_types(self, type_map=None) -> np.ndarray: - """ - Map the atom types of the system + """Map the atom types of the system. Parameters ---------- @@ -436,11 +437,11 @@ def map_atom_types(self, type_map=None) -> np.ndarray: @staticmethod def load(filename): - """rebuild System obj. from .json or .yaml file""" + """Rebuild System obj. from .json or .yaml file.""" return loadfn(filename) def as_dict(self): - """Returns data dict of System instance""" + """Returns data dict of System instance.""" d = { "@module": self.__class__.__module__, "@class": self.__class__.__name__, @@ -449,23 +450,23 @@ def as_dict(self): return d def get_atom_names(self): - """Returns name of atoms""" + """Returns name of atoms.""" return self.data["atom_names"] def get_atom_types(self): - """Returns type of atoms""" + """Returns type of atoms.""" return self.data["atom_types"] def get_atom_numbs(self): - """Returns number of atoms""" + """Returns number of atoms.""" return self.data["atom_numbs"] def get_nframes(self): - """Returns number of frames in the system""" + """Returns number of frames in the system.""" return len(self.data["cells"]) def get_natoms(self): - """Returns total number of atoms in the system""" + """Returns total number of atoms in the system.""" return len(self.data["atom_types"]) def get_ntypes(self) -> int: @@ -477,8 +478,7 @@ def copy(self): return self.__class__.from_dict({"data": deepcopy(self.data)}) def sub_system(self, f_idx): - """ - Construct a subsystem from the system + """Construct a subsystem from the system. Parameters ---------- @@ -509,8 +509,7 @@ def sub_system(self, f_idx): return tmp def append(self, system): - """ - Append a system to this system + """Append a system to this system. Parameters ---------- @@ -526,8 +525,7 @@ def append(self, system): return False if system.uniq_formula != self.uniq_formula: raise RuntimeError( - "systems with inconsistent formula could not be append: %s v.s. %s" - % (self.uniq_formula, system.uniq_formula) + f"systems with inconsistent formula could not be append: {self.uniq_formula} v.s. {system.uniq_formula}" ) if system.data["atom_names"] != self.data["atom_names"]: # allow to append a system with different atom_names order @@ -563,8 +561,7 @@ def append(self, system): return True def convert_to_mixed_type(self, type_map=None): - """ - Convert the data dict to mixed type format structure, in order to append systems + """Convert the data dict to mixed type format structure, in order to append systems with different formula but the same number of atoms. Change the 'atom_names' to one placeholder type 'MIXED_TOKEN' and add 'real_atom_types' to store the real type vectors according to the given type_map. @@ -590,8 +587,7 @@ def convert_to_mixed_type(self, type_map=None): self.data["atom_names"] = ["MIXED_TOKEN"] def sort_atom_names(self, type_map=None): - """ - Sort atom_names of the system and reorder atom_numbs and atom_types accoarding + """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. @@ -603,8 +599,7 @@ def sort_atom_names(self, type_map=None): self.data = sort_atom_names(self.data, type_map=type_map) def check_type_map(self, type_map): - """ - Assign atom_names to type_map if type_map is given and different from + """Assign atom_names to type_map if type_map is given and different from atom_names. Parameters @@ -643,12 +638,10 @@ def sort_atom_types(self) -> np.ndarray: @property def formula(self): - """ - Return the formula of this system, like C3H5O2 - """ + """Return the formula of this system, like C3H5O2.""" return "".join( [ - "{}{}".format(symbol, numb) + f"{symbol}{numb}" for symbol, numb in zip( self.data["atom_names"], self.data["atom_numbs"] ) @@ -657,14 +650,13 @@ def formula(self): @property def uniq_formula(self): - """ - Return the uniq_formula of this system. + """Return the uniq_formula of this system. The uniq_formula sort the elements in formula by names. Systems with the same uniq_formula can be append together. """ return "".join( [ - "{}{}".format(symbol, numb) + f"{symbol}{numb}" for symbol, numb in sorted( zip(self.data["atom_names"], self.data["atom_numbs"]) ) @@ -672,30 +664,25 @@ def uniq_formula(self): ) def extend(self, systems): - """ - Extend a system list to this system + """Extend a system list to this system. Parameters ---------- systems : [System1, System2, System3 ] The list to extend """ - for system in systems: self.append(system.copy()) def apply_pbc(self): - """ - Append periodic boundary condition - """ + """Append periodic boundary condition.""" ncoord = dpdata.md.pbc.dir_coord(self.data["coords"], self.data["cells"]) ncoord = ncoord % 1 self.data["coords"] = np.matmul(ncoord, self.data["cells"]) @post_funcs.register("remove_pbc") def remove_pbc(self, protect_layer=9): - """ - This method does NOT delete the definition of the cells, it + """This method does NOT delete the definition of the cells, it (1) revises the cell to a cubic cell and ensures that the cell boundary to any atom in the system is no less than `protect_layer` (2) translates the system such that the center-of-geometry of the system @@ -745,14 +732,11 @@ def rot_frame_lower_triangular(self, f_idx=0): return np.matmul(qq, rot) def add_atom_names(self, atom_names): - """ - Add atom_names that do not exist. - """ + """Add atom_names that do not exist.""" self.data = add_atom_names(self.data, atom_names) def replicate(self, ncopy): - """ - Replicate the each frame in the system in 3 dimensions. + """Replicate the each frame in the system in 3 dimensions. Each frame in the system will become a supercell. Parameters @@ -862,8 +846,7 @@ def replace(self, initial_atom_type, end_atom_type, replace_num): def perturb( self, pert_num, cell_pert_fraction, atom_pert_distance, atom_pert_style="normal" ): - """ - Perturb each frame in the system randomly. + """Perturb each frame in the system randomly. The cell will be deformed randomly, and atoms will be displaced by a random distance in random direction. Parameters @@ -939,8 +922,7 @@ def shuffle(self): return idx def predict(self, *args: Any, driver: str = "dp", **kwargs: Any) -> "LabeledSystem": - """ - Predict energies and forces by a driver. + """Predict energies and forces by a driver. Parameters ---------- @@ -991,7 +973,7 @@ def minimize( return LabeledSystem(data=data) def pick_atom_idx(self, idx, nopbc=None): - """Pick atom index + """Pick atom index. Parameters ---------- @@ -1053,7 +1035,7 @@ def remove_atom_names(self, atom_names): return new_sys def pick_by_amber_mask(self, param, maskstr, pass_coords=False, nopbc=None): - """Pick atoms by amber mask + """Pick atoms by amber mask. Parameters ---------- @@ -1120,15 +1102,12 @@ def get_atom_perturb_vector(atom_pert_distance, atom_pert_style="normal"): random_unit_vector = e / np.linalg.norm(e) random_vector = atom_pert_distance * random_unit_vector else: - raise RuntimeError( - "unsupported options atom_pert_style={}".format(atom_pert_style) - ) + raise RuntimeError(f"unsupported options atom_pert_style={atom_pert_style}") return random_vector class LabeledSystem(System): - """ - The labeled data System + """The labeled data System. For example, a labeled water system named `d_example` has two molecules (6 atoms) and `nframes` frames. The labels can be accessed by - `d_example['energies']` : a numpy array of size nframes @@ -1139,8 +1118,8 @@ class LabeledSystem(System): - The order of frames stored in `'energies'`, `'forces'` and `'virials'` should be consistent with `'atom_types'`, `'cells'` and `'coords'`. - The order of atoms in **every** frame of `'forces'` should be consistent with `'coords'` and `'atom_types'`. - Parameters - ---------- + Parameters + ---------- file_name : str The file to load the system fmt : str @@ -1211,7 +1190,7 @@ def __str__(self): return ret def __add__(self, others): - """magic method "+" operation""" + """Magic method "+" operation.""" self_copy = self.copy() if isinstance(others, LabeledSystem): other_copy = others.copy() @@ -1271,13 +1250,51 @@ def correction(self, hl_sys): ) return corrected_sys + def remove_outlier(self, threshold: float = 8.0) -> "LabeledSystem": + r"""Remove outlier frames from the system. + + Remove the frames whose energies satisfy the condition + + .. math:: + + \frac{\left \| E - \bar{E} \right \|}{\sigma(E)} \geq \text{threshold} + + where :math:`\bar{E}` and :math:`\sigma(E)` are the mean and standard deviation + of the energies in the system. + + Parameters + ---------- + threshold : float + The threshold of outlier detection. The default value is 8.0. + + Returns + ------- + LabeledSystem + The system without outlier frames. + + References + ---------- + .. [1] Gao, X.; Ramezanghorbani, F.; Isayev, O.; Smith, J. S.; + Roitberg, A. E. TorchANI: A Free and Open Source PyTorch-Based + Deep Learning Implementation of the ANI Neural Network + Potentials. J. Chem. Inf. Model. 2020, 60, 3408-3415. + .. [2] Zeng, J.; Tao, Y.; Giese, T. J.; York, D. M.. QDÏ€: A Quantum + Deep Potential Interaction Model for Drug Discovery. J. Comput. + Chem. 2023, 19, 1261-1275. + """ + energies = self.data["energies"] + std = np.std(energies) + if np.isclose(std, 0.0): + return self.copy() + idx = np.abs(energies - np.mean(energies)) / std < threshold + return self.sub_system(idx) + class MultiSystems: """A set containing several systems.""" def __init__(self, *systems, type_map=None): - """ - Parameters + """Parameters ---------- *systems : System The systems contained @@ -1339,6 +1356,10 @@ def to(self, fmt: str, *args, **kwargs) -> "MultiSystems": ---------- fmt : str format + *args : list + arguments + **kwargs : dict + keyword arguments Returns ------- @@ -1348,7 +1369,7 @@ def to(self, fmt: str, *args, **kwargs) -> "MultiSystems": return self.to_fmt_obj(load_format(fmt), *args, **kwargs) def __getitem__(self, key): - """Returns proerty stored in System by key or by idx""" + """Returns proerty stored in System by key or by idx.""" if isinstance(key, int): return list(self.systems.values())[key] return self.systems[key] @@ -1365,7 +1386,7 @@ def __str__(self): ) def __add__(self, others): - """magic method "+" operation""" + """Magic method "+" operation.""" self_copy = deepcopy(self) if isinstance(others, System) or isinstance(others, MultiSystems): return self.__class__(self, others) @@ -1383,7 +1404,7 @@ def from_file(cls, file_name, fmt, **kwargs): def from_dir(cls, dir_name, file_name, fmt="auto", type_map=None): multi_systems = cls() target_file_list = sorted( - glob.glob("./{}/**/{}".format(dir_name, file_name), recursive=True) + glob.glob(f"./{dir_name}/**/{file_name}", recursive=True) ) for target_file in target_file_list: multi_systems.append( @@ -1396,16 +1417,15 @@ def load_systems_from_file(self, file_name=None, fmt=None, **kwargs): return self.from_fmt_obj(load_format(fmt), file_name, **kwargs) def get_nframes(self): - """Returns number of frames in all systems""" + """Returns number of frames in all systems.""" return sum(len(system) for system in self.systems.values()) def append(self, *systems): - """ - Append systems or MultiSystems to systems + """Append systems or MultiSystems to systems. Parameters ---------- - system : System + *systems : System The system to append """ for system in systems: @@ -1428,9 +1448,7 @@ def __append(self, system): self.systems[formula] = system.copy() def check_atom_names(self, system): - """ - Make atom_names in all systems equal, prevent inconsistent atom_types. - """ + """Make atom_names in all systems equal, prevent inconsistent atom_types.""" # new_in_system = set(system["atom_names"]) - set(self.atom_names) # new_in_self = set(self.atom_names) - set(system["atom_names"]) new_in_system = [e for e in system["atom_names"] if e not in self.atom_names] @@ -1451,8 +1469,7 @@ def check_atom_names(self, system): system.sort_atom_names(type_map=self.atom_names) def predict(self, *args: Any, driver="dp", **kwargs: Any) -> "MultiSystems": - """ - Predict energies and forces by a driver. + """Predict energies and forces by a driver. Parameters ---------- @@ -1478,8 +1495,7 @@ def predict(self, *args: Any, driver="dp", **kwargs: Any) -> "MultiSystems": def minimize( self, *args: Any, minimizer: Union[str, Minimizer], **kwargs: Any ) -> "MultiSystems": - """ - Minimize geometry by a minimizer. + """Minimize geometry by a minimizer. Parameters ---------- @@ -1511,7 +1527,7 @@ def minimize( return new_multisystems def pick_atom_idx(self, idx, nopbc=None): - """Pick atom index + """Pick atom index. Parameters ---------- @@ -1568,6 +1584,63 @@ def correction(self, hl_sys: "MultiSystems"): corrected_sys.append(ll_ss.correction(hl_ss)) return corrected_sys + def train_test_split( + self, test_size: Union[float, int], seed: Optional[int] = None + ) -> Tuple["MultiSystems", "MultiSystems", Dict[str, np.ndarray]]: + """Split systems into random train and test subsets. + + Parameters + ---------- + test_size : float or int + If float, should be between 0.0 and 1.0 and represent the proportion of the dataset to include in the test split. + If int, represents the absolute number of test samples. + seed : int, default=None + Random seed + + Returns + ------- + MultiSystems + The training set + MultiSystems + The testing set + Dict[str, np.ndarray] + The bool array of training and testing sets for each system. False for training set and True for testing set. + """ + nframes = self.get_nframes() + if isinstance(test_size, float): + assert 0 <= test_size <= 1 + test_size = int(np.floor(test_size * nframes)) + elif isinstance(test_size, int): + assert 0 <= test_size <= nframes + else: + raise RuntimeError("test_size should be float or int") + # get random indices + rng = np.random.default_rng(seed=seed) + test_idx = rng.choice(nframes, test_size, replace=False) + select_test = np.zeros(nframes, dtype=bool) + select_test[test_idx] = True + select_train = np.logical_not(select_test) + # flatten systems dict + system_names, system_sizes = zip( + *((kk, len(vv)) for (kk, vv) in self.systems.items()) + ) + system_idx = np.empty(len(system_sizes) + 1, dtype=int) + system_idx[0] = 0 + np.cumsum(system_sizes, out=system_idx[1:]) + # make new systems + train_systems = MultiSystems(type_map=self.atom_names) + test_systems = MultiSystems(type_map=self.atom_names) + test_system_idx = {} + for ii, nn in enumerate(system_names): + sub_train = self[nn][select_train[system_idx[ii] : system_idx[ii + 1]]] + if len(sub_train): + train_systems.append(sub_train) + sub_test = self[nn][select_test[system_idx[ii] : system_idx[ii + 1]]] + if len(sub_test): + test_systems.append(sub_test) + test_system_idx[nn] = select_test[system_idx[ii] : system_idx[ii + 1]] + return train_systems, test_systems, test_system_idx + def get_cls_name(cls: object) -> str: """Returns the fully qualified name of a class, such as `np.ndarray`. diff --git a/dpdata/unit.py b/dpdata/unit.py index fa0d1e24..eba07b41 100644 --- a/dpdata/unit.py +++ b/dpdata/unit.py @@ -43,14 +43,16 @@ def check_unit(unit): class Conversion(ABC): def __init__(self, unitA, unitB, check=True): - """ - Parent class for unit conversion + """Parent class for unit conversion. Parameters ---------- - unitA : str, unit to be converted - unitB : str, unit which unitA is converted to, i.e. `1 unitA = self._value unitB` - check : bool, whether to check unit validity + unitA : str + unit to be converted + unitB : str + unit which unitA is converted to, i.e. `1 unitA = self._value unitB` + check : bool + whether to check unit validity Examples -------- @@ -83,8 +85,7 @@ def __str__(self): class EnergyConversion(Conversion): def __init__(self, unitA, unitB): - """ - Class for energy conversion + """Class for energy conversion. Examples -------- @@ -98,8 +99,7 @@ def __init__(self, unitA, unitB): class LengthConversion(Conversion): def __init__(self, unitA, unitB): - """ - Class for length conversion + """Class for length conversion. Examples -------- @@ -113,12 +113,12 @@ def __init__(self, unitA, unitB): class ForceConversion(Conversion): def __init__(self, unitA, unitB): - """ - Class for force conversion + """Class for force conversion. Parameters ---------- - unitA, unitB : str, in format of "energy_unit/length_unit" + unitA, unitB : str + in format of "energy_unit/length_unit" Examples -------- @@ -134,12 +134,12 @@ def __init__(self, unitA, unitB): class PressureConversion(Conversion): def __init__(self, unitA, unitB): - """ - Class for pressure conversion + """Class for pressure conversion. Parameters ---------- - unitA, unitB : str, in format of "energy_unit/length_unit^3", or in `["Pa", "pa", "kPa", "kpa", "bar", "kbar"]` + unitA, unitB : str + in format of "energy_unit/length_unit^3", or in `["Pa", "pa", "kPa", "kpa", "bar", "kbar"]` Examples -------- diff --git a/dpdata/utils.py b/dpdata/utils.py index c461d8c0..55cf41ef 100644 --- a/dpdata/utils.py +++ b/dpdata/utils.py @@ -32,22 +32,21 @@ def remove_pbc(system, protect_layer=9): def add_atom_names(data, atom_names): - """ - Add atom_names that do not exist. - """ + """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 + """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 ---------- + data : dict + system data type_map : list type_map """ @@ -76,9 +75,8 @@ def sort_atom_names(data, type_map=None): def uniq_atom_names(data): - """ - Make the atom names uniq. For example - ['O', 'H', 'O', 'H', 'O'] -> ['O', 'H'] + """Make the atom names uniq. For example + ['O', 'H', 'O', 'H', 'O'] -> ['O', 'H']. Parameters ---------- diff --git a/dpdata/vasp/poscar.py b/dpdata/vasp/poscar.py index 1100eb85..95f9c15e 100644 --- a/dpdata/vasp/poscar.py +++ b/dpdata/vasp/poscar.py @@ -4,9 +4,7 @@ def _to_system_data_lower(lines, cartesian=True): - """ - Treat as cartesian poscar - """ + """Treat as cartesian poscar.""" system = {} system["atom_names"] = [str(ii) for ii in lines[5].split()] system["atom_numbs"] = [int(ii) for ii in lines[6].split()] @@ -44,7 +42,7 @@ def to_system_data(lines): lines.pop(7) is_cartesian = lines[7][0] in ["C", "c", "K", "k"] if not is_cartesian: - if not (lines[7][0] in ["d", "D"]): + if lines[7][0] not in ["d", "D"]: raise RuntimeError( "seem not to be a valid POSCAR of vasp 5.x, may be a POSCAR of vasp 4.x?" ) @@ -84,7 +82,7 @@ def from_system_data(system, f_idx=0, skip_zeros=True): posis = posis[sort_idx] posi_list = [] for ii in posis: - posi_list.append("%15.10f %15.10f %15.10f" % (ii[0], ii[1], ii[2])) + posi_list.append(f"{ii[0]:15.10f} {ii[1]:15.10f} {ii[2]:15.10f}") posi_list.append("") ret += "\n".join(posi_list) return ret diff --git a/dpdata/vasp/xml.py b/dpdata/vasp/xml.py index 9d4cb803..062a8f28 100755 --- a/dpdata/vasp/xml.py +++ b/dpdata/vasp/xml.py @@ -8,7 +8,7 @@ def check_name(item, name): assert ( item.attrib["name"] == name - ), "item attrib '%s' dose not math required '%s'" % (item.attrib["name"], name) + ), "item attrib '{}' dose not math required '{}'".format(item.attrib["name"], name) def get_varray(varray): @@ -23,11 +23,11 @@ def analyze_atominfo(atominfo_xml): eles = [] types = [] for ii in atominfo_xml.find("array").find("set"): - eles.append((ii.findall("c")[0].text.strip())) + eles.append(ii.findall("c")[0].text.strip()) types.append(int(ii.findall("c")[1].text)) uniq_ele = [] for ii in eles: - if not (ii in uniq_ele): + if ii not in uniq_ele: uniq_ele.append(ii) return uniq_ele, types @@ -63,12 +63,12 @@ def formulate_config(eles, types, posi, cell, ener, forc, strs_): ret += " " + ii ret += "\n" ret += "##\n" - ret += "#X %13.8f %13.8f %13.8f\n" % (cell[0][0], cell[0][1], cell[0][2]) - ret += "#Y %13.8f %13.8f %13.8f\n" % (cell[1][0], cell[1][1], cell[1][2]) - ret += "#Z %13.8f %13.8f %13.8f\n" % (cell[2][0], cell[2][1], cell[2][2]) + ret += f"#X {cell[0][0]:13.8f} {cell[0][1]:13.8f} {cell[0][2]:13.8f}\n" + ret += f"#Y {cell[1][0]:13.8f} {cell[1][1]:13.8f} {cell[1][2]:13.8f}\n" + ret += f"#Z {cell[2][0]:13.8f} {cell[2][1]:13.8f} {cell[2][2]:13.8f}\n" ret += "#W 1.0\n" ret += "#E %.10f\n" % (ener / natoms) - ret += "#S %.9e %.9e %.9e %.9e %.9e %.9e\n" % ( + ret += "#S {:.9e} {:.9e} {:.9e} {:.9e} {:.9e} {:.9e}\n".format( strs[0][0], strs[1][1], strs[2][2], @@ -80,16 +80,14 @@ def formulate_config(eles, types, posi, cell, ener, forc, strs_): for ii in range(natoms): sp = np.matmul(cell.T, posi[ii]) ret += "%d" % (types[ii] - 1) - ret += " %12.6f %12.6f %12.6f" % (sp[0], sp[1], sp[2]) - ret += " %12.6f %12.6f %12.6f" % (forc[ii][0], forc[ii][1], forc[ii][2]) + ret += f" {sp[0]:12.6f} {sp[1]:12.6f} {sp[2]:12.6f}" + ret += f" {forc[ii][0]:12.6f} {forc[ii][1]:12.6f} {forc[ii][2]:12.6f}" ret += "\n" return ret def analyze(fname, type_idx_zero=False, begin=0, step=1): - """ - can deal with broken xml file - """ + """Deal with broken xml file.""" all_posi = [] all_cell = [] all_ener = [] diff --git a/dpdata/xyz/quip_gap_xyz.py b/dpdata/xyz/quip_gap_xyz.py index a0b9fd4a..c2d4118c 100644 --- a/dpdata/xyz/quip_gap_xyz.py +++ b/dpdata/xyz/quip_gap_xyz.py @@ -1,18 +1,16 @@ #!/usr/bin/env python3 -#%% +# %% import re from collections import OrderedDict import numpy as np -class QuipGapxyzSystems(object): - """ - deal with QuipGapxyzFile - """ +class QuipGapxyzSystems: + """deal with QuipGapxyzFile.""" def __init__(self, file_name): - self.file_object = open(file_name, "r") + self.file_object = open(file_name) self.block_generator = self.get_block_generator() def __iter__(self): @@ -53,7 +51,7 @@ def handle_single_xyz_frame(lines): atom_num, len(lines) ) ) - data_format_line = lines[1].strip("\n").strip() + str(" ") + data_format_line = lines[1].strip("\n").strip() + " " field_value_pattern = re.compile( r"(?P\S+)=(?P[\'\"]?)(?P.*?)(?P=quote)\s+" ) diff --git a/pyproject.toml b/pyproject.toml index cdb7a25d..5b555ad5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -67,3 +67,34 @@ write_to = "dpdata/_version.py" [tool.isort] profile = "black" + +[tool.ruff] +target-version = "py37" +select = [ + "E", # errors + "F", # pyflakes + "D", # pydocstyle + "UP", # pyupgrade + "I", # isort +] +ignore = [ + "E501", # line too long + "F841", # local variable is assigned to but never used + "E741", # ambiguous variable name + "E402", # module level import not at top of file + "D413", # missing blank line after last section + "D416", # section name should end with a colon + "D203", # 1 blank line required before class docstring + "D107", # missing docstring in __init__ + "D213", # multi-line docstring summary should start at the second line + "D100", # TODO: missing docstring in public module + "D101", # TODO: missing docstring in public class + "D102", # TODO: missing docstring in public method + "D103", # TODO: missing docstring in public function + "D104", # TODO: missing docstring in public package + "D105", # TODO: missing docstring in magic method + "D205", # 1 blank line required between summary line and description + "D401", # TODO: first line should be in imperative mood + "D404", # TODO: first word of the docstring should not be This +] +ignore-init-module-imports = true diff --git a/tests/.coverage b/tests/.coverage new file mode 100644 index 00000000..dd0aa252 Binary files /dev/null and b/tests/.coverage differ diff --git a/tests/abacus.md.newversion/INPUT b/tests/abacus.md.newversion/INPUT new file mode 100644 index 00000000..a9c6cf46 --- /dev/null +++ b/tests/abacus.md.newversion/INPUT @@ -0,0 +1,37 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix Sn_nve +calculation md +ntype 1 +nbands 160 +symmetry 0 +pseudo_dir ../../../tests/PP_ORB +orbital_dir ../../../tests/PP_ORB + +#Parameters (2.Iteration) +ecutwfc 30 +scf_thr 1e-5 +scf_nmax 100 + +#Parameters (3.Basis) +basis_type lcao +ks_solver genelpa +gamma_only 1 + +#Parameters (4.Smearing) +smearing_method gaussian +smearing_sigma 0.01 + +#Parameters (5.Mixing) +mixing_type pulay +mixing_beta 0.3 +chg_extrap second-order + +#Parameters (6.MD) +md_type 0 +md_nstep 10 +md_dt 1 +md_tfirst 300 + +cal_force 1 +cal_stress 1 diff --git a/tests/abacus.md.newversion/OUT.Sn_nve/MD_dump b/tests/abacus.md.newversion/OUT.Sn_nve/MD_dump new file mode 100644 index 00000000..f4e9b494 --- /dev/null +++ b/tests/abacus.md.newversion/OUT.Sn_nve/MD_dump @@ -0,0 +1,847 @@ +MDSTEP: 0 +LATTICE_CONSTANT: 12.411200939060 Angstrom +LATTICE_VECTORS + 1.000000000000 0.000000000000 0.000000000000 + 0.000000000000 1.000000000000 0.000000000000 + 0.000000000000 0.000000000000 1.000000000000 +VIRIAL (kbar) + 36.689617311068 0.000000000001 -0.000000000000 + 0.000000000001 36.689617311071 -0.000000000000 + -0.000000000000 -0.000000000000 36.689617311111 +INDEX LABEL POSITION (Angstrom) FORCE (eV/Angstrom) VELOCITY (Angstrom/fs) + 0 Sn 0.000000000000 0.000000000000 0.000000000000 -0.000000000000 -0.000000000000 -0.000000000000 0.001244557166 -0.000346684288 0.000768457739 + 1 Sn 0.000000000000 3.102800034079 3.102800034079 -0.000186795145 -0.000453823858 -0.000453823858 0.000550996187 -0.000886442775 0.001579501983 + 2 Sn 3.102800034079 0.000000000000 3.102800034079 -0.000453823858 -0.000186795144 -0.000453823858 -0.002922142975 0.000775912129 -0.000715177071 + 3 Sn 3.102800034079 3.102800034079 0.000000000000 -0.000453823858 -0.000453823858 -0.000186795145 0.002964440439 -0.003181761103 0.000204927506 + 4 Sn 4.654200051118 1.551400017039 4.654200051118 0.000247406642 0.000665392243 0.000247406641 0.000882606464 0.002202980310 -0.001646060777 + 5 Sn 1.551400017039 1.551400017039 1.551400017039 -0.000416292323 -0.000416292323 -0.000416292323 0.000061186812 -0.000365639216 0.000315604893 + 6 Sn 1.551400017039 4.654200051118 4.654200051118 0.000665392243 0.000247406641 0.000247406641 -0.002031568125 -0.000311415555 -0.000056589921 + 7 Sn 4.654200051118 4.654200051118 1.551400017039 0.000247406641 0.000247406641 0.000665392243 0.001438666644 0.001404889768 -0.002377899235 + 8 Sn 6.205600068158 0.000000000000 0.000000000000 0.000000000000 0.000000000000 -0.000000000000 0.002880892346 0.000739478849 -0.000135862984 + 9 Sn 6.205600068158 3.102800034079 3.102800034079 -0.000276007396 0.000626140930 0.000626140930 0.000303454014 -0.000942004493 0.001316841079 + 10 Sn 9.308400102237 0.000000000000 3.102800034079 0.000453823858 0.000186795144 -0.000453823857 -0.000165393395 0.002452229280 -0.000461932507 + 11 Sn 9.308400102237 3.102800034079 0.000000000000 0.000453823858 -0.000453823858 0.000186795145 0.000924274078 -0.001793485931 -0.001457593691 + 12 Sn 10.859800119276 1.551400017039 4.654200051118 0.000032359013 -0.000032359014 -0.000637401958 -0.000312616281 -0.001108488781 -0.001689418051 + 13 Sn 7.757000085197 1.551400017039 1.551400017039 0.000637401958 -0.000032359013 -0.000032359013 0.000436526635 0.001319592960 -0.000574847803 + 14 Sn 7.757000085197 4.654200051118 4.654200051118 -0.000386882321 0.000386882322 0.000386882322 -0.000494728599 -0.000895722869 -0.002635609000 + 15 Sn 10.859800119276 4.654200051118 1.551400017039 0.000032359013 -0.000637401958 -0.000032359013 0.000035195742 -0.000781858348 0.001840960715 + 16 Sn 0.000000000000 6.205600068158 0.000000000000 0.000000000000 0.000000000000 -0.000000000000 -0.000163392886 0.003225283751 -0.000069628467 + 17 Sn 0.000000000000 9.308400102237 3.102800034079 0.000186795144 0.000453823858 -0.000453823858 -0.001220187110 0.000006242836 0.000948872534 + 18 Sn 3.102800034079 6.205600068158 3.102800034079 0.000626140931 -0.000276007396 0.000626140930 0.000077446767 0.000402487654 -0.001437884367 + 19 Sn 3.102800034079 9.308400102237 0.000000000000 -0.000453823858 0.000453823858 0.000186795144 0.001057882910 0.002099948454 -0.002147545525 + 20 Sn 4.654200051118 7.757000085197 4.654200051118 0.000386882322 -0.000386882322 0.000386882322 0.000351752949 -0.001161559150 -0.000360936065 + 21 Sn 1.551400017039 7.757000085197 1.551400017039 -0.000032359013 0.000637401958 -0.000032359014 0.001095792391 0.001594954432 -0.000865174172 + 22 Sn 1.551400017039 10.859800119276 4.654200051118 -0.000032359014 0.000032359013 -0.000637401958 -0.000749056918 0.000679216216 -0.001707030600 + 23 Sn 4.654200051118 10.859800119276 1.551400017039 -0.000637401958 0.000032359013 -0.000032359014 0.001579380380 0.000939966847 0.000024744042 + 24 Sn 6.205600068158 6.205600068158 0.000000000000 -0.000000000000 -0.000000000000 0.000000000000 0.000191857256 0.001493657612 -0.000289903205 + 25 Sn 6.205600068158 9.308400102237 3.102800034079 0.000276007397 -0.000626140931 0.000626140931 0.000754426054 -0.000419503637 0.001674326256 + 26 Sn 9.308400102237 6.205600068158 3.102800034079 -0.000626140930 0.000276007397 0.000626140931 -0.000003109346 0.001029932818 -0.000262253548 + 27 Sn 9.308400102237 9.308400102237 0.000000000000 0.000453823858 0.000453823858 -0.000186795145 -0.002596963069 0.003017746640 -0.001504041594 + 28 Sn 10.859800119276 7.757000085197 4.654200051118 -0.000665392244 -0.000247406641 0.000247406641 0.000784170295 -0.001992321989 0.001362218456 + 29 Sn 7.757000085197 7.757000085197 1.551400017039 -0.000247406641 -0.000247406641 0.000665392244 -0.001394551390 -0.000265366100 -0.002333922060 + 30 Sn 7.757000085197 10.859800119276 4.654200051118 -0.000247406641 -0.000665392243 0.000247406642 -0.001619889944 -0.000717527616 0.001959703776 + 31 Sn 10.859800119276 10.859800119276 1.551400017039 0.000416292323 0.000416292323 -0.000416292323 -0.003478427367 0.000119966026 0.002249814221 + 32 Sn 0.000000000000 0.000000000000 6.205600068158 -0.000000000001 0.000000000000 0.000000000000 0.001871216518 -0.001272034839 0.001843914137 + 33 Sn 0.000000000000 3.102800034079 9.308400102237 0.000186795145 -0.000453823858 0.000453823858 -0.001428427849 -0.000962261171 -0.001588147045 + 34 Sn 3.102800034079 0.000000000000 9.308400102237 -0.000453823858 0.000186795145 0.000453823858 0.000334570977 -0.002037557240 -0.001162364290 + 35 Sn 3.102800034079 3.102800034079 6.205600068158 0.000626140930 0.000626140930 -0.000276007396 0.000299475278 -0.000354417878 0.000277866693 + 36 Sn 4.654200051118 1.551400017039 10.859800119276 -0.000637401959 -0.000032359013 0.000032359014 -0.001413469224 0.000906521155 -0.001100780019 + 37 Sn 1.551400017039 1.551400017039 7.757000085197 -0.000032359014 -0.000032359014 0.000637401959 -0.000345418335 -0.000827840627 -0.000920682501 + 38 Sn 1.551400017039 4.654200051118 10.859800119276 -0.000032359013 -0.000637401959 0.000032359013 0.000834903679 0.001120336417 -0.000014852509 + 39 Sn 4.654200051118 4.654200051118 7.757000085197 0.000386882322 0.000386882322 -0.000386882321 -0.000059303258 0.001173556453 0.001758437937 + 40 Sn 6.205600068158 0.000000000000 6.205600068158 0.000000000000 -0.000000000000 -0.000000000000 -0.000334456529 -0.001047127191 -0.000360363378 + 41 Sn 6.205600068158 3.102800034079 9.308400102237 0.000276007396 0.000626140930 -0.000626140930 0.001546139546 0.000806526624 0.002121975951 + 42 Sn 9.308400102237 0.000000000000 9.308400102237 0.000453823858 -0.000186795145 0.000453823857 0.000136266689 -0.001638064383 -0.001774031935 + 43 Sn 9.308400102237 3.102800034079 6.205600068158 -0.000626140930 0.000626140930 0.000276007396 -0.000922112051 -0.002861962150 0.000999789837 + 44 Sn 10.859800119276 1.551400017039 10.859800119276 0.000416292323 -0.000416292323 0.000416292323 0.002890375805 -0.001798456081 0.000311538465 + 45 Sn 7.757000085197 1.551400017039 7.757000085197 -0.000247406641 0.000665392243 -0.000247406641 -0.001328082932 0.000445231603 0.002242937653 + 46 Sn 7.757000085197 4.654200051118 10.859800119276 -0.000247406641 0.000247406641 -0.000665392243 -0.000092390835 0.001633212122 0.001865999012 + 47 Sn 10.859800119276 4.654200051118 7.757000085197 -0.000665392243 0.000247406641 -0.000247406641 0.000644079537 0.000264111619 -0.000035442004 + 48 Sn 0.000000000000 6.205600068158 6.205600068158 -0.000000000000 -0.000000000000 -0.000000000000 0.002690337635 0.000110886138 -0.000639896221 + 49 Sn 0.000000000000 9.308400102237 9.308400102237 -0.000186795145 0.000453823858 0.000453823858 0.000111906255 0.001260410659 -0.001975830226 + 50 Sn 3.102800034079 6.205600068158 9.308400102237 0.000626140930 0.000276007396 -0.000626140930 0.000514272157 -0.001735112207 0.001571641645 + 51 Sn 3.102800034079 9.308400102237 6.205600068158 0.000626140931 -0.000626140930 0.000276007396 -0.001942420485 -0.000901037737 -0.001793108257 + 52 Sn 4.654200051118 7.757000085197 10.859800119276 0.000247406641 -0.000247406641 -0.000665392243 -0.001340774180 0.000457898368 -0.001881951752 + 53 Sn 1.551400017039 7.757000085197 7.757000085197 0.000665392243 -0.000247406641 -0.000247406641 0.000567727411 0.000177660711 0.000585341923 + 54 Sn 1.551400017039 10.859800119276 10.859800119276 -0.000416292323 0.000416292323 0.000416292323 -0.002968498697 0.000701527596 0.000371288527 + 55 Sn 4.654200051118 10.859800119276 7.757000085197 0.000247406641 -0.000665392243 -0.000247406641 -0.001270167840 -0.000949060440 0.003477584187 + 56 Sn 6.205600068158 6.205600068158 6.205600068158 0.000000000000 0.000000000000 -0.000000000001 0.000586733881 0.000053369534 -0.000769567802 + 57 Sn 6.205600068158 9.308400102237 9.308400102237 -0.000276007396 -0.000626140930 -0.000626140931 0.000974047175 -0.002324793017 0.001452717512 + 58 Sn 9.308400102237 6.205600068158 9.308400102237 -0.000626140930 -0.000276007396 -0.000626140931 0.000525051287 -0.000571071615 0.002864658238 + 59 Sn 9.308400102237 9.308400102237 6.205600068158 -0.000626140931 -0.000626140930 -0.000276007397 -0.000682993400 -0.000101241033 -0.002963618125 + 60 Sn 10.859800119276 7.757000085197 10.859800119276 0.000032359014 0.000637401959 0.000032359013 0.000456925004 -0.001109667827 0.000044462268 + 61 Sn 7.757000085197 7.757000085197 7.757000085197 -0.000386882321 -0.000386882321 -0.000386882322 -0.001036401475 -0.000928108701 0.002356265620 + 62 Sn 7.757000085197 10.859800119276 10.859800119276 0.000637401959 0.000032359013 0.000032359014 0.001688540621 0.001808205044 -0.000891745877 + 63 Sn 10.859800119276 10.859800119276 7.757000085197 0.000032359013 0.000032359014 0.000637401958 -0.001971130490 0.002165655364 0.002209299781 + + +MDSTEP: 1 +LATTICE_CONSTANT: 12.411200939060 Angstrom +LATTICE_VECTORS + 1.000000000000 0.000000000000 0.000000000000 + 0.000000000000 1.000000000000 0.000000000000 + 0.000000000000 0.000000000000 1.000000000000 +VIRIAL (kbar) + 36.693033785308 -0.081970642054 -0.124871341889 + -0.081970642054 36.692440063129 0.172720644098 + -0.124871341889 0.172720644098 36.692661013403 +INDEX LABEL POSITION (Angstrom) FORCE (eV/Angstrom) VELOCITY (Angstrom/fs) + 0 Sn 0.001244557166 12.410853452028 0.000768457739 -0.027008422585 -0.011580088805 0.027567658139 0.001243459570 -0.000347154892 0.000769578062 + 1 Sn 0.000550988596 3.101913572861 3.104379517619 -0.008903458892 0.000617316625 -0.018826427441 0.000550626768 -0.000886436131 0.001578718452 + 2 Sn 3.099877872661 0.000775904538 3.102084838565 0.043660741958 -0.002688919447 0.003121338958 -0.002920387087 0.000775795262 -0.000715068666 + 3 Sn 3.105764456075 3.099618254533 0.000204919914 -0.037028276737 0.041199924222 -0.000426752716 0.002962917203 -0.003180105221 0.000204902572 + 4 Sn 4.655082667637 1.553603024390 4.652554000396 -0.020912001849 -0.039275100939 0.017157585733 0.000881766675 0.002201411248 -0.001645353455 + 5 Sn 1.551461186934 1.551034360906 1.551715605015 -0.005164848553 0.015562156693 -0.009182941369 0.000060960000 -0.000365023702 0.000315214790 + 6 Sn 1.549368475956 4.653888645618 4.654143471252 0.043971007815 -0.000328397085 -0.006727324582 -0.002029754144 -0.000311418846 -0.000056853259 + 7 Sn 4.655638727817 4.655604950941 1.549022144846 -0.001380963034 -0.023673416055 0.026496118059 0.001438620578 0.001403937758 -0.002376795417 + 8 Sn 6.208480960504 0.000739478849 12.411064273332 -0.029937550040 0.009917097094 -0.011285069753 0.002879675712 0.000739881871 -0.000136321598 + 9 Sn 6.205903510955 3.101858055032 3.104116900604 -0.007284597218 0.024171408964 -0.044544687314 0.000303146758 -0.000940996744 0.001315056272 + 10 Sn 9.308234727285 0.002452236871 3.102338083129 -0.034124694400 -0.027044354144 0.016398869152 -0.000166761747 0.002451137815 -0.000461284515 + 11 Sn 9.309324394758 3.101006529705 12.409742550216 0.010056911785 0.018954915440 0.006363000577 0.000924701224 -0.001792734064 -0.001457327514 + 12 Sn 10.859487504311 1.550291526944 4.652510607164 0.018380258410 -0.005706204907 0.040547025626 -0.000311868010 -0.001108721990 -0.001687796162 + 13 Sn 7.757436637736 1.552719608684 1.550825167921 0.000149454380 0.001001540492 0.004195544891 0.000436558612 0.001319632346 -0.000574678615 + 14 Sn 7.756505340876 4.653304343972 4.651564457841 0.019662398668 0.002767918407 0.036122163697 -0.000493945260 -0.000895594661 -0.002634125308 + 15 Sn 10.859835316334 4.653418166867 1.553240976440 0.008415269373 0.005298234984 -0.025869277057 0.000035539046 -0.000781668936 0.001839908098 + 16 Sn 12.411036743430 6.208825351909 12.411130507849 0.005269974715 -0.040483672302 0.017740237623 -0.000163178719 0.003223638534 -0.000068907521 + 17 Sn 12.409979956797 9.308406363516 3.103748888170 -0.000999300676 -0.007139294806 -0.014711098883 -0.001220220129 0.000005971145 0.000948256246 + 18 Sn 3.102877506291 6.206002544595 3.101362175158 -0.007098794048 -0.015775644666 0.005401647136 0.000077183724 0.000401835330 -0.001437639404 + 19 Sn 3.103857898546 9.310500069134 12.409052598382 -0.005958238611 0.001518217974 0.013359794974 0.001057622330 0.002100028596 -0.002146995005 + 20 Sn 4.654551819790 7.755838510325 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0.059811093138 -0.001907925745 -0.000880038977 -0.001778102079 + 52 Sn 4.646181338297 7.759721527758 10.848570564540 0.051906085799 -0.054437256484 0.132359301041 -0.001327703367 0.000444582077 -0.001849816767 + 53 Sn 1.554832466679 7.758042933163 7.760518959868 0.052683505945 -0.048177839951 0.013673836583 0.000580914735 0.000165842839 0.000588796451 + 54 Sn 1.533669044530 10.863995626529 10.861987682712 0.169655629658 -0.031992443588 -0.086380810471 -0.002927212462 0.000694174060 0.000350417911 + 55 Sn 4.646635902700 10.854031437752 7.777729034196 0.121062546248 -0.156936969968 -0.287717607880 -0.001240883185 -0.000987279561 0.003407384862 + 56 Sn 6.209120149908 6.205884430452 6.201008078943 -0.000766701247 -0.074741906151 0.052513867714 0.000586532314 0.000034989051 -0.000756607362 + 57 Sn 6.211435108582 9.294543073445 9.317116574794 -0.018775904072 0.194191427562 0.000332530091 0.000969344049 -0.002277524923 0.001452873449 + 58 Sn 9.311547292199 6.202164458012 9.325509749116 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0.000000000000 + 0.000000000000 0.000000000000 1.000000000000 +VIRIAL (kbar) + 36.857207304333 -0.562702789679 -0.866799621960 + -0.562702789679 36.858076582244 1.196214462023 + -0.866799621960 1.196214462023 36.840439244929 +INDEX LABEL POSITION (Angstrom) FORCE (eV/Angstrom) VELOCITY (Angstrom/fs) + 0 Sn 0.008590134722 12.408722247092 0.005507092714 -0.185238370709 -0.074587883038 0.193631960651 0.001191502724 -0.000368679953 0.000824309855 + 1 Sn 0.003816429098 3.096599853591 3.113775762063 -0.061740763989 0.007565109713 -0.123483098591 0.000533307061 -0.000884185482 0.001544430972 + 2 Sn 3.082542853035 0.005419085431 3.097812940576 0.304017949985 -0.019997826032 0.030451933810 -0.002835598272 0.000770434711 -0.000706503554 + 3 Sn 3.123384738957 3.080718831855 0.001438931962 -0.250960888397 0.292144519905 0.013913300536 0.002892123787 -0.003098133263 0.000207728496 + 4 Sn 4.660279178625 1.566644202568 4.642757199071 -0.154488265083 -0.272157258964 0.124498669263 0.000838892115 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7.758366299304 7.761699034269 0.068922360105 -0.062088284056 0.018587625869 0.000590807617 0.000156957995 0.000591477642 + 54 Sn 1.527844458801 10.865378339940 10.862673344390 0.225202944665 -0.043859177257 -0.114938521676 -0.002895115878 0.000688057098 0.000334083210 + 55 Sn 4.644175557121 10.852029373716 7.784493431797 0.163030092697 -0.207852027237 -0.379526876733 -0.001217756873 -0.001016853613 0.003353281698 + 56 Sn 6.210293135657 6.205941274587 6.199504242239 -0.000335387205 -0.098656590423 0.071002596163 0.000586470962 0.000020883214 -0.000746477978 + 57 Sn 6.213370437314 9.290022243743 9.320022576602 -0.025411711036 0.258456449057 0.001974573259 0.000965715011 -0.002240693110 0.001453195090 + 58 Sn 9.312593706373 6.201009587853 9.331129973375 -0.006779734202 -0.025127543067 -0.217114850421 0.000522666116 -0.000579341570 0.002793593455 + 59 Sn 9.302991981249 9.307524817022 6.182254514529 0.068416559822 -0.075308801422 0.416906887546 -0.000661291894 -0.000125940106 -0.002826091824 + 60 Sn 10.863402123549 7.748447440594 10.860152833226 -0.062498354067 0.373014193930 -0.007121231443 0.000436584460 -0.000986840793 0.000042909909 + 61 Sn 7.748922232328 7.749583150445 7.775646068408 0.245391316684 0.005012204167 -0.235734265173 -0.000955571882 -0.000925545916 0.002278868951 + 62 Sn 7.770314673290 10.874201491725 10.852585179165 -0.229025572249 -0.072559631301 -0.094225646958 0.001614408298 0.001784001189 -0.000922531537 + 63 Sn 10.844122792924 10.876853426138 7.774315642779 0.119059562687 -0.320827534734 -0.423166649559 -0.001934829002 0.002061771882 0.002072108893 + + +MDSTEP: 9 +LATTICE_CONSTANT: 12.411200939060 Angstrom +LATTICE_VECTORS + 1.000000000000 0.000000000000 0.000000000000 + 0.000000000000 1.000000000000 0.000000000000 + 0.000000000000 0.000000000000 1.000000000000 +VIRIAL (kbar) + 36.961526046898 -0.714902383742 -1.105207012750 + -0.714902383742 36.965100762139 1.524613134468 + -1.105207012750 1.524613134468 36.935032828174 +INDEX LABEL POSITION (Angstrom) FORCE (eV/Angstrom) VELOCITY (Angstrom/fs) + 0 Sn 0.010940978521 12.407971984935 0.007189454572 -0.235790026129 -0.093136883271 0.246751322388 0.001157286705 -0.000382336017 0.000860210722 + 1 Sn 0.004872295651 3.094832828538 3.116843234886 -0.079128455048 0.009472245938 -0.157481124593 0.000521852873 -0.000882762068 0.001521660204 + 2 Sn 3.076924542225 0.006956416043 3.096405346525 0.388833034672 -0.026944057971 0.039929614793 -0.002779265734 0.000766613613 -0.000700705333 + 3 Sn 3.129125375714 3.074573415921 0.001857068805 -0.318790101433 0.372904037221 0.023001377626 0.002845756456 -0.003044000682 0.000210777678 + 4 Sn 4.661929969585 1.570848334450 4.639556912748 -0.199580687115 -0.347546090430 0.161535043655 0.000810066332 0.002075371061 -0.001587759247 + 5 Sn 1.551900061455 1.548271663651 1.554159627280 -0.046449513244 0.151676907800 -0.076453200525 0.000044142312 -0.000310407402 0.000288206881 + 6 Sn 1.533537454232 4.651393969279 4.653626488068 0.381760377705 -0.005973320889 -0.058806570537 -0.001890190406 -0.000312879079 -0.000078234322 + 7 Sn 4.667126633843 4.666617217090 1.530257729448 -0.025810465389 -0.206543434073 0.231359842675 0.001430613012 0.001328618259 -0.002291394086 + 8 Sn 6.231238774218 0.006748042150 12.409875318714 -0.261876479292 0.080263184003 -0.090374292023 0.002783807588 0.000770132574 -0.000169793790 + 9 Sn 6.208267495812 3.094559024421 3.114217838318 -0.051056322542 0.212688983592 -0.399040269460 0.000282932414 -0.000862690607 0.001170469159 + 10 Sn 9.306583639349 0.021812923482 3.098803073334 -0.295324373786 -0.229755733626 0.139993026676 -0.000275288228 0.002366314199 -0.000408650829 + 11 Sn 9.316813594359 3.086850076736 12.398148634270 0.084540141883 0.173963907388 0.059448675874 0.000955923746 -0.001729036357 -0.001435255059 + 12 Sn 10.857167823300 1.541378706187 4.639392815600 0.161894138763 -0.036664524511 0.362567006496 -0.000251982478 -0.001122926824 -0.001555601390 + 13 Sn 7.760927960913 1.563292700353 1.546275897445 -0.002384703857 0.015411743446 0.043858428048 0.000435955957 0.001325240185 -0.000558219390 + 14 Sn 7.752739566938 4.646169237373 4.630826302278 0.175259820862 0.032044432698 0.313157155601 -0.000430065836 -0.000884894728 -0.002519383445 + 15 Sn 10.860196914117 4.647219776591 1.567728269122 0.069499626127 0.051633003911 -0.215931474994 0.000061697900 -0.000762736393 0.001760619120 + 16 Sn 12.409787518143 6.234234945501 12.410749674018 0.057818842875 -0.354519663269 0.160285283249 -0.000143248841 0.003093597726 -0.000010350483 + 17 Sn 12.400210799804 9.308379067413 3.111207983822 -0.008095897058 -0.069625022174 -0.119430323947 -0.001222879487 -0.000019804084 0.000904779735 + 18 Sn 3.103425271631 6.209073032785 3.089912334794 -0.063955260877 -0.132180979759 0.044158522796 0.000053371186 0.000352737341 -0.001420486684 + 19 Sn 3.112265466396 9.327303001091 12.392003674357 -0.048862012379 0.003956070601 0.118179189495 0.001039463648 0.002101001122 -0.002103505355 + 20 Sn 4.657290180918 7.746607600053 4.650988555760 -0.070326759007 0.056866848706 0.031867884815 0.000326068534 -0.001140786215 -0.000348758087 + 21 Sn 1.561251673312 7.771504999833 1.543643161317 -0.009689478030 0.133761560423 0.026238191005 0.001092262746 0.001644945324 -0.000855169773 + 22 Sn 1.544634135228 10.865812766191 4.638986221318 -0.023187944837 -0.091436872607 0.137935119919 -0.000757381543 0.000645446404 -0.001656423341 + 23 Sn 4.668365027075 10.868273501039 1.551676806875 -0.043542548285 0.011810860321 0.046579620866 0.001562959774 0.000944425599 0.000042706251 + 24 Sn 6.207142540555 6.219076134801 12.408419477463 -0.169077543174 0.027908586092 -0.157844456889 0.000129689251 0.001504489451 -0.000347774474 + 25 Sn 6.212292027581 9.304591871107 3.117679796266 -0.089477088867 -0.027823889763 -0.175299033080 0.000721434244 -0.000430313648 0.001610342996 + 26 Sn 9.308309806498 6.214842157213 3.100358210312 -0.054696475591 -0.026550462045 -0.075409746217 -0.000023708599 0.001020493340 -0.000289816535 + 27 Sn 9.285314738909 9.335217858821 12.397724763116 0.261320228286 -0.312541641333 0.065125129993 -0.002500417223 0.002902454453 -0.001482272905 + 28 Sn 10.866843870782 7.739165295525 4.666364504437 -0.014431015515 0.089599840406 -0.087511059280 0.000779484707 -0.001959793976 0.001330027627 + 29 Sn 7.744638146643 7.754819479038 1.530625122228 0.175141770641 0.194345449957 0.210189201567 -0.001330582075 -0.000194922160 -0.002256360865 + 30 Sn 7.742656475816 10.853572305438 4.671499231518 0.207765348522 0.206182439976 -0.303287778701 -0.001541477130 -0.000640579653 0.001846527389 + 31 Sn 10.828758957401 10.860895045065 1.571435204891 0.236089255910 0.006488760024 -0.191356247241 -0.003390054363 0.000124090785 0.002178645758 + 32 Sn 0.016518217001 12.399815288689 6.221962602437 -0.291978260982 0.050416017825 -0.209306741465 0.001762982476 -0.001251626888 0.001765944211 + 33 Sn 12.398618895591 3.094282715708 9.294275400269 0.244840854784 0.125644547478 0.150218357267 -0.001336741512 -0.000914607921 -0.001532047481 + 34 Sn 3.105538832279 12.393110132150 9.298184631566 -0.250413896947 0.230696462573 0.226556773501 0.000242686458 -0.001953536606 -0.001079477960 + 35 Sn 3.105495557363 3.099762378344 6.208110579615 -0.000068629147 0.134337763667 0.009358318813 0.000299399322 -0.000303802485 0.000281176523 + 36 Sn 4.641786695551 1.559186647488 10.849852314346 0.283252568417 -0.337869881209 -0.046197796977 -0.001309576166 0.000781611026 -0.001115683015 + 37 Sn 1.548459222368 1.544011198099 7.748842347438 0.154017762600 0.058571872633 0.117025930665 -0.000288819469 -0.000806689666 -0.000877669662 + 38 Sn 1.558729134105 4.663919703661 10.859871172831 -0.170800730884 -0.324322179742 0.185794976210 0.000772370145 0.000999131859 0.000053892250 + 39 Sn 4.653815740644 4.664582291674 7.772632207692 0.136680697749 -0.164851170095 -0.176207334124 -0.000009084119 0.001112970099 0.001693254374 + 40 Sn 6.202354887145 12.401922600435 6.202614380466 -0.213025415348 0.135259685202 0.234165572164 -0.000413365267 -0.000997555080 -0.000273849523 + 41 Sn 6.219322507526 3.110183559385 9.327455045520 -0.175423257325 0.109680197264 -0.035673662996 0.001481253148 0.000848021256 0.002107983678 + 42 Sn 9.309607715609 12.396917122358 9.292740003559 -0.030211973985 0.425702524923 0.282130945863 0.000128309120 -0.001482568015 -0.001670788403 + 43 Sn 9.300157990931 3.077320757572 6.214455790617 0.055241829186 0.247682717913 -0.129151989163 -0.000902428871 -0.002769089181 0.000951848348 + 44 Sn 10.885565257102 1.535155074204 10.862453510147 -0.224699096075 -0.047501920603 -0.135792381139 0.002806996447 -0.001817362288 0.000261001705 + 45 Sn 7.745029815324 1.555230248696 7.777021967896 -0.013331655091 -0.161692828416 -0.147748786000 -0.001333613298 0.000385668846 0.002187779458 + 46 Sn 7.756263268373 4.668735525945 10.876619438793 0.087676382293 -0.151284427215 0.024222493801 -0.000060374419 0.001577983101 0.001874733555 + 47 Sn 10.865435034637 4.656604498646 7.756533765426 -0.145623221518 0.023077890678 -0.129946400414 0.000590011140 0.000273156137 -0.000084511208 + 48 Sn 0.024004958685 6.206569257381 6.200091951150 -0.189633624917 -0.023291159574 0.230073284924 0.002620396365 0.000101570880 -0.000555413391 + 49 Sn 0.000829264874 9.319584162862 9.290789202581 -0.159568179564 -0.143301212728 0.153803722137 0.000052478869 0.001206867818 -0.001918617255 + 50 Sn 3.107314109798 6.190199648109 9.322359107684 -0.103109808222 0.195329343288 -0.166236348846 0.000475858877 -0.001662768796 0.001509516124 + 51 Sn 3.085547595686 9.300430232562 6.189561958862 0.203892761532 0.124221763248 0.088746254175 -0.001866028897 -0.000854468183 -0.001759909004 + 52 Sn 4.642220093077 7.761033139290 10.843076413532 0.076802168143 -0.076255794642 0.196143511221 -0.001311916144 0.000428691719 -0.001809765023 + 53 Sn 1.556597137654 7.758520734091 7.762291267295 0.076831528367 -0.068119892429 0.021162847930 0.000596730915 0.000151666460 0.000593093064 + 54 Sn 1.524958494954 10.866064614644 10.863002756609 0.252640066575 -0.049757649690 -0.128868579901 -0.002875696797 0.000684252601 0.000324175124 + 55 Sn 4.642964425634 10.851004073196 7.787831289887 0.184130904290 -0.232658414451 -0.423983922464 -0.001203648584 -0.001034755534 0.003320627792 + 56 Sn 6.210879592989 6.205958148492 6.198760649739 0.000009221032 -0.110250733580 0.080364203405 0.000586457707 0.000012393421 -0.000740326576 + 57 Sn 6.214335119617 9.287792054055 9.321475851937 -0.028821363623 0.290319805047 0.003157330538 0.000963511031 -0.002218391371 0.001453403646 + 58 Sn 9.313116096968 6.200429225123 9.333914743491 -0.008089866641 -0.027722795312 -0.242141455825 0.000522061830 -0.000581489357 0.002774929720 + 59 Sn 9.302333469738 9.307395816439 6.179445365400 0.076855607767 -0.083905502619 0.466218618570 -0.000655388173 -0.000132410422 -0.002790202453 + 60 Sn 10.863836168136 7.747475758739 10.860195453736 -0.070191891890 0.417673408562 -0.008975672437 0.000431192056 -0.000954708009 0.000042255747 + 61 Sn 7.747976632913 7.748657808221 7.777915357345 0.274195113465 0.004837731301 -0.262828902249 -0.000934456389 -0.000925145624 0.002258607823 + 62 Sn 7.771919774209 10.875982544161 10.851658818388 -0.256951801273 -0.080049068821 -0.105348338471 0.001594658644 0.001777799319 -0.000930642032 + 63 Sn 10.842192802389 10.878902159898 7.776370554586 0.136485772438 -0.360353387256 -0.474668888763 -0.001924443885 0.002034089345 0.002035621720 + + +MDSTEP: 10 +LATTICE_CONSTANT: 12.411200939060 Angstrom +LATTICE_VECTORS + 1.000000000000 0.000000000000 0.000000000000 + 0.000000000000 1.000000000000 0.000000000000 + 0.000000000000 0.000000000000 1.000000000000 +VIRIAL (kbar) + 37.021694130286 -0.788473912978 -1.221131619959 + -0.788473912978 37.027048735563 1.684292473794 + -1.221131619959 1.684292473794 36.989679713591 +INDEX LABEL POSITION (Angstrom) FORCE (eV/Angstrom) VELOCITY (Angstrom/fs) + 0 Sn 0.012088682946 12.407585863925 0.008059693031 -0.260102638127 -0.102355292658 0.275230298765 0.001137134104 -0.000390280631 0.000881423553 + 1 Sn 0.005390932820 3.093950451413 3.118358495208 -0.088010211962 0.011199581201 -0.172037597767 0.000515060518 -0.000881921985 0.001508268880 + 2 Sn 3.074161078292 0.007721934675 3.095706263894 0.430443777993 -0.031004632848 0.046926272632 -0.002745971112 0.000764258634 -0.000697175593 + 3 Sn 3.131958176847 3.071544569700 0.002068781237 -0.352682606860 0.413988829013 0.029959763827 0.002818468451 -0.003012022113 0.000212929968 + 4 Sn 4.662731925150 1.572909581572 4.637975718129 -0.223306504162 -0.382895819490 0.180557804943 0.000792880604 0.002045686604 -0.001573856923 + 5 Sn 1.551942316104 1.547967420252 1.554444727177 -0.052150705649 0.170719299589 -0.083748284918 0.000040135294 -0.000297305530 0.000281696446 + 6 Sn 1.531662778201 4.651080847449 4.653545863903 0.422172567371 -0.005507148994 -0.064314252280 -0.001857519345 -0.000313345635 -0.000083237834 + 7 Sn 4.668556197942 4.667937441623 1.527975737604 -0.031179400228 -0.227946455955 0.257896843154 0.001428296998 0.001310961008 -0.002271511164 + 8 Sn 6.234011939398 0.007521436542 12.409701852200 -0.290265000250 0.087417761307 -0.097736872326 0.002761369089 0.000776946966 -0.000177438447 + 9 Sn 6.208548353347 3.093704977290 3.115372090864 -0.055980017129 0.236637608836 -0.440507397736 0.000278582561 -0.000844430406 0.001136350749 + 10 Sn 9.306296349422 0.024169900629 3.098400111687 -0.325453419804 -0.253491887989 0.154678777362 -0.000300516041 0.002346675480 -0.000396675650 + 11 Sn 9.317772953734 3.085128110104 12.396715795148 0.093727177156 0.193922214690 0.067188361847 0.000963168358 -0.001714085819 -0.001430108652 + 12 Sn 10.856922420044 1.540254289351 4.637851948585 0.180402845500 -0.036454966493 0.401340094186 -0.000238071857 -0.001125898330 -0.001524556940 + 13 Sn 7.761363819958 1.564618566856 1.545719460419 -0.002926142470 0.018838637420 0.050541170239 0.000435740129 0.001326632088 -0.000554383081 + 14 Sn 7.752316623492 4.645285644900 4.628319645239 0.194177878121 0.037717767679 0.346562344142 -0.000415052243 -0.000882059659 -0.002492573079 + 15 Sn 10.860261436415 4.646459138513 1.569480112994 0.076393022358 0.058011096515 -0.236196566441 0.000067626837 -0.000758280563 0.001742245071 + 16 Sn 12.409646619004 6.237314135889 12.410745837375 0.065827255528 -0.392958905618 0.178379303716 -0.000138223983 0.003063220916 0.000003412520 + 17 Sn 12.398987591307 9.308356433835 3.112107910023 -0.008030882459 -0.079292366332 -0.129954445269 -0.001223534864 -0.000025855944 0.000894644978 + 18 Sn 3.103476043737 6.209420398418 3.088493642670 -0.071185579983 -0.146182137622 0.050607511247 0.000047879192 0.000341424932 -0.001416635483 + 19 Sn 3.113302944338 9.329404162984 12.389904971691 -0.054129856646 0.001995735788 0.132431787155 0.001035278157 0.002101242998 -0.002093320766 + 20 Sn 4.657613391440 7.745469124851 4.650641092753 -0.078620004714 0.061205999659 0.035744505221 0.000320015481 -0.001135987848 -0.000346010385 + 21 Sn 1.562343542287 7.773155381098 1.542789057839 -0.010626446670 0.145630352236 0.031661850797 0.001091437127 0.001656299543 -0.000852816771 + 22 Sn 1.543875811349 10.866454496689 4.637335403527 -0.025559540756 -0.101810507039 0.153729538710 -0.000759362594 0.000637593017 -0.001644570370 + 23 Sn 4.669926217321 10.869218406620 1.551721406076 -0.049588317728 0.011746072681 0.053098414105 0.001559175025 0.000945382930 0.000046757070 + 24 Sn 6.207265358657 6.220581758431 12.408065288342 -0.188445530131 0.029406065110 -0.174419200299 0.000115159857 0.001506818663 -0.000361277350 + 25 Sn 6.213009825562 9.304160426723 3.119283015278 -0.099270917047 -0.033246766778 -0.193086605557 0.000713763706 -0.000432795501 0.001595372158 + 26 Sn 9.308283875087 6.215861571568 3.100065329197 -0.059916527871 -0.030338444541 -0.082114718600 -0.000028366361 0.001018181430 -0.000296218178 + 27 Sn 9.282824941489 9.338107611882 12.396245136834 0.290805053314 -0.348589685561 0.074913426758 -0.002477979382 0.002875586712 -0.001476581873 + 28 Sn 10.867622769027 7.737209142800 4.667690975698 -0.014504314801 0.098212371764 -0.096549619965 0.000778308803 -0.001952161469 0.001322547578 + 29 Sn 7.743314682161 7.754632454890 1.528377303249 0.194837734381 0.214427746598 0.236165423044 -0.001315546464 -0.000178310011 -0.002238221443 + 30 Sn 7.741123442070 10.852940104841 4.673333433583 0.229806634607 0.226398657056 -0.334606689363 -0.001523694625 -0.000622999973 0.001820603971 + 31 Sn 10.825378497478 10.861019399546 1.573606074115 0.261989336921 0.005537690543 -0.209563198850 -0.003369812927 0.000124579528 0.002162352777 + 32 Sn 0.018269333761 12.398565710660 6.223720040624 -0.321721167823 0.054316185597 -0.232510857114 0.001738042321 -0.001247370672 0.001747989169 + 33 Sn 12.397292104176 3.093373213860 9.292749457517 0.270722564671 0.139774649393 0.163312024499 -0.001315789510 -0.000903821540 -0.001519305908 + 34 Sn 3.105771342157 12.391165970826 9.297114360655 -0.278538994973 0.257145569081 0.250211348793 0.000221190321 -0.001933711175 -0.001060102562 + 35 Sn 3.105794953896 3.099464035217 6.208392136451 -0.000589798523 0.149475978140 0.008955039633 0.000299372564 -0.000292268567 0.000281920760 + 36 Sn 4.640488630497 1.559954527807 10.848734753897 0.311762554953 -0.371924326646 -0.053618402330 -0.001285395323 0.000752765672 -0.001119739449 + 37 Sn 1.548176662033 1.543206888737 7.747969433597 0.170121912027 0.067924734694 0.127682117960 -0.000275646744 -0.000801548966 -0.000867724962 + 38 Sn 1.559494563073 4.664905655379 10.859932615610 -0.190698568501 -0.356183623659 0.205436700041 0.000757679161 0.000971476758 0.000069791529 + 39 Sn 4.653812211097 4.665688562381 7.774318301169 0.150166459675 -0.181505918497 -0.197270268102 0.000002573074 0.001098894480 0.001678076603 + 40 Sn 6.201932864729 12.400930542179 6.202350047208 -0.235246244837 0.151222172634 0.257864793450 -0.000431582597 -0.000985912733 -0.000253853882 + 41 Sn 6.220796631642 3.111036037939 9.329561579454 -0.194938993938 0.122913504545 -0.041170089962 0.001466201983 0.000857473640 0.002104860822 + 42 Sn 9.309734796943 12.395451854483 9.291080680686 -0.034211499625 0.473863537308 0.311504046591 0.000125691012 -0.001446010516 -0.001646663648 + 43 Sn 9.299257807035 3.074561733978 6.215402390352 0.062687673167 0.274930632118 -0.144914991978 -0.000897636329 -0.002747850677 0.000940710530 + 44 Sn 10.888363121994 1.533335781483 10.862708993380 -0.249101319190 -0.049535070262 -0.150903328787 0.002787741654 -0.001821305778 0.000249350667 + 45 Sn 7.743695660240 1.555609346500 7.779203742985 -0.014528973773 -0.176833703255 -0.166523274861 -0.001334745527 0.000371911453 0.002175007744 + 46 Sn 7.756206457038 4.670307360992 10.878495156728 0.096257744658 -0.166922524671 0.026573321103 -0.000052899513 0.001565051476 0.001876797849 + 47 Sn 10.866019127789 4.656878592646 7.756443973321 -0.160367267766 0.026770071466 -0.144638751364 0.000577575981 0.000275181910 -0.000095670085 + 48 Sn 0.026617648521 6.206669881730 6.199545887716 -0.209191966341 -0.025485749137 0.252663743289 0.002604188476 0.000099588633 -0.000535795422 + 49 Sn 0.000875259046 9.320785207056 9.288876835761 -0.174332491364 -0.159517765721 0.167426511542 0.000038909466 0.001194561545 -0.001905562768 + 50 Sn 3.107785778391 6.188544817310 9.323861868123 -0.114271942549 0.215997087769 -0.186087959127 0.000467024691 -0.001646052885 0.001495198003 + 51 Sn 3.083689852794 9.299580812632 6.187805656421 0.224885864563 0.135705940748 0.096665974056 -0.001848603746 -0.000843904971 -0.001752374029 + 52 Sn 4.640911298100 7.761458732047 10.841274619593 0.082986635646 -0.086205444356 0.218078030200 -0.001305422480 0.000422089451 -0.001792931458 + 53 Sn 1.557196990929 7.758669632223 7.762885220396 0.084629403374 -0.076370928570 0.022172070741 0.000603292532 0.000145794492 0.000594854153 + 54 Sn 1.522093065207 10.866746845141 10.863321694638 0.279826813820 -0.057080470106 -0.143692897063 -0.002854057855 0.000679910802 0.000313098487 + 55 Sn 4.641768259953 10.849959862648 7.791134687380 0.203969276745 -0.259499706887 -0.471758172643 -0.001187876566 -0.001054756367 0.003284225694 + 56 Sn 6.211466051071 6.205966061429 6.198023589086 -0.000545574279 -0.121586334615 0.087514202585 0.000586435910 0.000002971786 -0.000733504159 + 57 Sn 6.215297459375 9.285585461001 9.322929383893 -0.031524334023 0.320816867185 0.001072377466 0.000961058639 -0.002193555364 0.001453575537 + 58 Sn 9.313637830034 6.199846609138 9.336679832816 -0.007707780956 -0.031324627626 -0.270649421207 0.000521419829 -0.000583888988 0.002754090392 + 59 Sn 9.301681204903 9.307259996178 6.176674109624 0.086733036977 -0.093945032310 0.512732224093 -0.000648740088 -0.000139638097 -0.002750418832 + 60 Sn 10.864264507660 7.746538024575 10.860237344720 -0.077585984098 0.459733763345 -0.010534338599 0.000425186505 -0.000919051025 0.000041462879 + 61 Sn 7.747053319549 7.747732859198 7.780163284054 0.302052128368 0.003002170879 -0.292806623068 -0.000911038255 -0.000924827018 0.002236027330 + 62 Sn 7.773503990579 10.877757090362 10.850723895101 -0.286368720397 -0.089532217570 -0.116378882035 0.001572578621 0.001770907698 -0.000939652813 + 63 Sn 10.840273905154 10.880921604828 7.778386886220 0.156020836517 -0.401077890777 -0.529184310285 -0.001912556698 0.002003145510 0.001994826092 + + diff --git a/tests/abacus.md.newversion/OUT.Sn_nve/running_md.log b/tests/abacus.md.newversion/OUT.Sn_nve/running_md.log new file mode 100644 index 00000000..aabf4a92 --- /dev/null +++ b/tests/abacus.md.newversion/OUT.Sn_nve/running_md.log @@ -0,0 +1,2954 @@ + + ABACUS v3.2 + + Atomic-orbital Based Ab-initio Computation at UStc + + Website: http://abacus.ustc.edu.cn/ + Documentation: https://abacus.deepmodeling.com/ + Repository: https://github.com/abacusmodeling/abacus-develop + https://github.com/deepmodeling/abacus-develop + + Start Time is Wed Apr 12 12:06:58 2023 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.Sn_nve/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + DRANK = 1 + DSIZE = 8 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + The esolver type has been set to : ksdft_lcao + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 1 + atom label for species 1 = Sn + lattice constant (Bohr) = 23.4538 + lattice constant (Angstrom) = 12.4112 + + READING ATOM TYPE 1 + atom label = Sn + L=0, number of zeta = 2 + L=1, number of zeta = 2 + L=2, number of zeta = 1 + number of atom for this type = 64 + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + + TOTAL ATOM NUMBER = 64 + + DIRECT COORDINATES + atom x y z mag vx vy vz + taud_Sn1 0 0 0 0 0 0 0 + taud_Sn2 0 0.25 0.25 0 0 0 0 + taud_Sn3 0.25 0 0.25 0 0 0 0 + taud_Sn4 0.25 0.25 0 0 0 0 0 + taud_Sn5 0.375 0.125 0.375 0 0 0 0 + taud_Sn6 0.125 0.125 0.125 0 0 0 0 + taud_Sn7 0.125 0.375 0.375 0 0 0 0 + taud_Sn8 0.375 0.375 0.125 0 0 0 0 + taud_Sn9 0.5 0 0 0 0 0 0 + taud_Sn10 0.5 0.25 0.25 0 0 0 0 + taud_Sn11 0.75 0 0.25 0 0 0 0 + taud_Sn12 0.75 0.25 0 0 0 0 0 + taud_Sn13 0.875 0.125 0.375 0 0 0 0 + taud_Sn14 0.625 0.125 0.125 0 0 0 0 + taud_Sn15 0.625 0.375 0.375 0 0 0 0 + taud_Sn16 0.875 0.375 0.125 0 0 0 0 + taud_Sn17 0 0.5 0 0 0 0 0 + taud_Sn18 0 0.75 0.25 0 0 0 0 + taud_Sn19 0.25 0.5 0.25 0 0 0 0 + taud_Sn20 0.25 0.75 0 0 0 0 0 + taud_Sn21 0.375 0.625 0.375 0 0 0 0 + taud_Sn22 0.125 0.625 0.125 0 0 0 0 + taud_Sn23 0.125 0.875 0.375 0 0 0 0 + taud_Sn24 0.375 0.875 0.125 0 0 0 0 + taud_Sn25 0.5 0.5 0 0 0 0 0 + taud_Sn26 0.5 0.75 0.25 0 0 0 0 + taud_Sn27 0.75 0.5 0.25 0 0 0 0 + taud_Sn28 0.75 0.75 0 0 0 0 0 + taud_Sn29 0.875 0.625 0.375 0 0 0 0 + taud_Sn30 0.625 0.625 0.125 0 0 0 0 + taud_Sn31 0.625 0.875 0.375 0 0 0 0 + taud_Sn32 0.875 0.875 0.125 0 0 0 0 + taud_Sn33 0 0 0.5 0 0 0 0 + taud_Sn34 0 0.25 0.75 0 0 0 0 + taud_Sn35 0.25 0 0.75 0 0 0 0 + taud_Sn36 0.25 0.25 0.5 0 0 0 0 + taud_Sn37 0.375 0.125 0.875 0 0 0 0 + taud_Sn38 0.125 0.125 0.625 0 0 0 0 + taud_Sn39 0.125 0.375 0.875 0 0 0 0 + taud_Sn40 0.375 0.375 0.625 0 0 0 0 + taud_Sn41 0.5 0 0.5 0 0 0 0 + taud_Sn42 0.5 0.25 0.75 0 0 0 0 + taud_Sn43 0.75 0 0.75 0 0 0 0 + taud_Sn44 0.75 0.25 0.5 0 0 0 0 + taud_Sn45 0.875 0.125 0.875 0 0 0 0 + taud_Sn46 0.625 0.125 0.625 0 0 0 0 + taud_Sn47 0.625 0.375 0.875 0 0 0 0 + taud_Sn48 0.875 0.375 0.625 0 0 0 0 + taud_Sn49 0 0.5 0.5 0 0 0 0 + taud_Sn50 0 0.75 0.75 0 0 0 0 + taud_Sn51 0.25 0.5 0.75 0 0 0 0 + taud_Sn52 0.25 0.75 0.5 0 0 0 0 + taud_Sn53 0.375 0.625 0.875 0 0 0 0 + taud_Sn54 0.125 0.625 0.625 0 0 0 0 + taud_Sn55 0.125 0.875 0.875 0 0 0 0 + taud_Sn56 0.375 0.875 0.625 0 0 0 0 + taud_Sn57 0.5 0.5 0.5 0 0 0 0 + taud_Sn58 0.5 0.75 0.75 0 0 0 0 + taud_Sn59 0.75 0.5 0.75 0 0 0 0 + taud_Sn60 0.75 0.75 0.5 0 0 0 0 + taud_Sn61 0.875 0.625 0.875 0 0 0 0 + taud_Sn62 0.625 0.625 0.625 0 0 0 0 + taud_Sn63 0.625 0.875 0.875 0 0 0 0 + taud_Sn64 0.875 0.875 0.625 0 0 0 0 + + + READING ORBITAL FILE NAMES FOR LCAO + orbital file: ../../../tests/PP_ORB/Sn_pz-bhs_8.0au_16Ry_2s2p1d + + Volume (Bohr^3) = 12901.5 + Volume (A^3) = 1911.8 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +1 +0 +0 + +0 +1 +0 + +0 +0 +1 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +1 -0 +0 + +0 +1 -0 + +0 -0 +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 Sn.pz-bhs.UPF + pseudopotential type = NC + exchange-correlation functional = PZ + nonlocal core correction = 0 + valence electrons = 4 + lmax = 1 + number of zeta = 2 + number of projectors = 2 + L of projector = 0 + L of projector = 1 + initial pseudo atomic orbital number = 256 + NLOCAL = 832 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 120 + [fft grid for charge/potential] = 81, 81, 81 + [fft grid division] = 3, 3, 3 + [big fft grid for charge/potential] = 27, 27, 27 + nbxx = 2916 + nrxx = 78732 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 286241 + number of sticks = 5249 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 656 35780 + 2 656 35780 + 3 656 35780 + 4 656 35780 + 5 656 35780 + 6 656 35780 + 7 656 35780 + 8 657 35781 + --------------- sum ------------------- + 8 5249 286241 + number of |g| = 1379 + max |g| = 1672 + min |g| = 2 + + SETUP THE ELECTRONS NUMBER + electron number of element Sn = 4 + total electron number of element Sn = 256 + AUTOSET number of electrons: = 256 + DONE : SETUP UNITCELL Time : 0.0418966 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + nkstot_ibz = 1 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 1 0 + nkstot now = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0422394 (SEC) + + occupied bands = 128 + NLOCAL = 832 + NBANDS = 160 + NBANDS = 160 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | 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 = 551 + 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 + 4 1 1 801 0.01 8 1 1 + 5 2 0 801 0.01 8 1 1 + SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS + max number of nonlocal projetors among all species is 2 + + SETUP THE TWO-CENTER INTEGRATION TABLES + + Warning_Memory_Consuming allocated: ORB::Jl(x) 75.8 MB + + Warning_Memory_Consuming allocated: ORB::Table_SR&TR 6.12 MB + + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 32 + trace_loc_row dimension = 832 + trace_loc_col dimension = 832 + nloc = 93184 + + ------------------------------------------- + STEP OF MOLECULAR DYNAMICS : 0 + ------------------------------------------- + searching radius is (Bohr)) = 16 + searching radius unit is (Bohr)) = 23.5 + enter setAlltoallvParameter, nblk = 32 + pnum = 0 + prow = 0 + pcol = 0 + nRow_in_proc = 375 + nCol_in_proc = 209 + pnum = 1 + prow = 0 + pcol = 1 + nRow_in_proc = 375 + nCol_in_proc = 192 + pnum = 2 + prow = 0 + pcol = 2 + nRow_in_proc = 375 + nCol_in_proc = 166 + pnum = 3 + prow = 0 + pcol = 3 + nRow_in_proc = 375 + nCol_in_proc = 161 + pnum = 4 + prow = 1 + pcol = 0 + nRow_in_proc = 353 + nCol_in_proc = 209 + pnum = 5 + prow = 1 + pcol = 1 + nRow_in_proc = 353 + nCol_in_proc = 192 + pnum = 6 + prow = 1 + pcol = 2 + nRow_in_proc = 353 + nCol_in_proc = 166 + pnum = 7 + prow = 1 + pcol = 3 + nRow_in_proc = 353 + nCol_in_proc = 161 +receiver_size is 529984 ; receiver_size of each process is: +78375 72000 62250 60375 73777 67776 58598 56833 +sender_size is 551600 ; sender_size of each process is: +78375 71250 76171 71198 67776 67070 70464 49296 + + Warning_Memory_Consuming allocated: LOC::A2A_receiv 8.09 MB + + Warning_Memory_Consuming allocated: LOC::A2A_sender 16.8 MB + init_chg = atomic + DONE : INIT SCF Time : 0.59487 (SEC) + + + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.152452681731 + + Energy Rydberg eV + E_KohnSham -453.10499999 -6164.80979216 + E_Harris -453.377426878 -6168.51635012 + E_Fermi +0.392114903854 +5.33499696313 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.102038407211 + + Energy Rydberg eV + E_KohnSham -452.900654964 -6162.02953544 + E_Harris -453.113614754 -6164.92700203 + E_Fermi +0.40305013756 +5.4837784505 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.00629543983797 + + Energy Rydberg eV + E_KohnSham -452.930546805 -6162.4362348 + E_Harris -452.931358532 -6162.44727892 + E_Fermi +0.42608917968 +5.7972406998 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.000573527015948 + + Energy Rydberg eV + E_KohnSham -452.930641026 -6162.43751675 + E_Harris -452.930647909 -6162.4376104 + E_Fermi +0.425138567478 +5.78430695726 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 7.11692581093e-05 + + Energy Rydberg eV + E_KohnSham -452.930642571 -6162.43753777 + E_Harris -452.930642656 -6162.43753892 + E_Fermi +0.425026780909 +5.78278602296 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 1.27962428317e-05 + + Energy Rydberg eV + E_KohnSham -452.930642538 -6162.43753732 + E_Harris -452.930642551 -6162.43753749 + E_Fermi +0.42504144188 +5.7829854957 + + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 9.13417171626e-07 + + Energy Rydberg eV + E_KohnSham -452.930642537 -6162.4375373 + E_Harris -452.930642537 -6162.4375373 + E_band +8.13317668897 +110.657545811 + E_one_elec +122.543008927 +1667.28317148 + E_Hartree +32.3361511773 +439.955907401 + E_xc -137.430741137 -1869.84115983 + E_Ewald -470.378864064 -6399.83277004 + E_demet -0.000197440257142 -0.00268631251171 + E_descf +0 +0 + E_exx +0 +0 + E_Fermi +0.425043987577 +5.78302013169 + + charge density convergence is achieved + final etot is -6162.4375373 eV + + Warning_Memory_Consuming allocated: Stress::dSH_GO 8.53125 MB + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Sn1 0 0 0 + Sn2 -0.00018679513 -0.00045382383 -0.00045382383 + Sn3 -0.00045382383 -0.00018679513 -0.00045382383 + Sn4 -0.00045382383 -0.00045382383 -0.00018679513 + Sn5 +0.00024740663 +0.0006653922 +0.00024740663 + Sn6 -0.0004162923 -0.0004162923 -0.0004162923 + Sn7 +0.0006653922 +0.00024740663 +0.00024740663 + Sn8 +0.00024740663 +0.00024740663 +0.0006653922 + Sn9 0 0 0 + Sn10 -0.00027600738 +0.00062614089 +0.00062614089 + Sn11 +0.00045382383 +0.00018679513 -0.00045382383 + Sn12 +0.00045382383 -0.00045382383 +0.00018679513 + Sn13 +3.2359011e-05 -3.2359012e-05 -0.00063740192 + Sn14 +0.00063740192 -3.2359011e-05 -3.2359011e-05 + Sn15 -0.0003868823 +0.0003868823 +0.0003868823 + Sn16 +3.2359011e-05 -0.00063740192 -3.2359011e-05 + Sn17 0 0 0 + Sn18 +0.00018679513 +0.00045382383 -0.00045382383 + Sn19 +0.00062614089 -0.00027600738 +0.00062614089 + Sn20 -0.00045382383 +0.00045382383 +0.00018679513 + Sn21 +0.0003868823 -0.0003868823 +0.0003868823 + Sn22 -3.2359011e-05 +0.00063740192 -3.2359012e-05 + Sn23 -3.2359012e-05 +3.2359011e-05 -0.00063740192 + Sn24 -0.00063740192 +3.2359011e-05 -3.2359011e-05 + Sn25 0 0 0 + Sn26 +0.00027600738 -0.00062614089 +0.00062614089 + Sn27 -0.00062614089 +0.00027600738 +0.00062614089 + Sn28 +0.00045382383 +0.00045382383 -0.00018679513 + Sn29 -0.0006653922 -0.00024740663 +0.00024740663 + Sn30 -0.00024740663 -0.00024740663 +0.0006653922 + Sn31 -0.00024740662 -0.0006653922 +0.00024740663 + Sn32 +0.0004162923 +0.0004162923 -0.0004162923 + Sn33 0 0 0 + Sn34 +0.00018679513 -0.00045382383 +0.00045382383 + Sn35 -0.00045382383 +0.00018679513 +0.00045382383 + Sn36 +0.00062614089 +0.00062614089 -0.00027600738 + Sn37 -0.00063740192 -3.2359011e-05 +3.2359011e-05 + Sn38 -3.2359011e-05 -3.2359011e-05 +0.00063740192 + Sn39 -3.2359011e-05 -0.00063740192 +3.2359011e-05 + Sn40 +0.0003868823 +0.0003868823 -0.0003868823 + Sn41 0 0 0 + Sn42 +0.00027600738 +0.00062614089 -0.00062614089 + Sn43 +0.00045382383 -0.00018679513 +0.00045382383 + Sn44 -0.00062614089 +0.00062614089 +0.00027600738 + Sn45 +0.0004162923 -0.0004162923 +0.0004162923 + Sn46 -0.00024740662 +0.0006653922 -0.00024740663 + Sn47 -0.00024740663 +0.00024740663 -0.0006653922 + Sn48 -0.0006653922 +0.00024740663 -0.00024740663 + Sn49 0 0 0 + Sn50 -0.00018679513 +0.00045382383 +0.00045382383 + Sn51 +0.00062614089 +0.00027600738 -0.00062614089 + Sn52 +0.00062614089 -0.00062614089 +0.00027600738 + Sn53 +0.00024740663 -0.00024740663 -0.0006653922 + Sn54 +0.0006653922 -0.00024740663 -0.00024740663 + Sn55 -0.0004162923 +0.0004162923 +0.0004162923 + Sn56 +0.00024740663 -0.0006653922 -0.00024740662 + Sn57 0 0 0 + Sn58 -0.00027600738 -0.00062614089 -0.00062614089 + Sn59 -0.00062614089 -0.00027600738 -0.00062614089 + Sn60 -0.00062614089 -0.00062614089 -0.00027600738 + Sn61 +3.2359011e-05 +0.00063740192 +3.2359011e-05 + Sn62 -0.0003868823 -0.0003868823 -0.0003868823 + Sn63 +0.00063740192 +3.2359011e-05 +3.2359011e-05 + Sn64 +3.2359011e-05 +3.2359012e-05 +0.00063740192 + + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + +36.689617 +0.000000 -0.000000 + +0.000000 +36.689617 -0.000000 + -0.000000 -0.000000 +36.689617 + TOTAL-PRESSURE: +36.689617 KBAR + + + ------------------------------------------------------------------------------------------------ + Energy (Ry) Potential (Ry) Kinetic (Ry) Temperature (K) Pressure (kbar) + -452.75108 -452.93064 +0.17955843 +300 +38.054528 + ------------------------------------------------------------------------------------------------ +Virtual Pressure is +38.054528 kbar +Virial Term is +36.689617 kbar +Kinetic Term is +1.3649103 kbar + + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + MD STRESS (kbar) + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + ++37.967985 -0.18772216 -0.017046138 +-0.18772216 +37.965054 -0.27587951 +-0.017046138 -0.27587951 +38.230543 + + + + ------------------------------------------- + STEP OF MOLECULAR DYNAMICS : 1 + ------------------------------------------- + NEW-OLD atomic charge density approx. for the potential ! + searching radius is (Bohr)) = +16.01 + searching radius unit is (Bohr)) = +23.45378 + enter setAlltoallvParameter, nblk = +32 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +375 + nCol_in_proc = +209 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +375 + nCol_in_proc = +192 + pnum = +2 + prow = +0 + pcol = +2 + nRow_in_proc = +375 + nCol_in_proc = +166 + pnum = +3 + prow = +0 + pcol = +3 + nRow_in_proc = +375 + nCol_in_proc = +161 + pnum = +4 + prow = +1 + pcol = +0 + nRow_in_proc = +353 + nCol_in_proc = +209 + pnum = +5 + prow = +1 + pcol = +1 + nRow_in_proc = +353 + nCol_in_proc = +192 + pnum = +6 + prow = +1 + pcol = +2 + nRow_in_proc = +353 + nCol_in_proc = +166 + pnum = +7 + prow = +1 + pcol = +3 + nRow_in_proc = +353 + nCol_in_proc = +161 +receiver_size is +529984 ; receiver_size of each process is: ++78375 +72000 +62250 +60375 +73777 +67776 +58598 +56833 +sender_size is +551600 ; sender_size of each process is: ++78375 +71250 +76171 +71198 +67776 +67070 +70464 +49296 + DONE : INIT SCF Time : +9.34325 (SEC) + + + LCAO ALGORITHM --------------- ION=+2 ELEC=+1 -------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is +0.000462825882814 + + Energy Rydberg eV + E_KohnSham -452.93048094 -6162.43533867 + E_Harris -452.930483522 -6162.43537379 + E_Fermi +0.425046222481 +5.78305053912 + + LCAO ALGORITHM --------------- ION= 2 ELEC= 2-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 0.000304712088044 + + Energy Rydberg eV + E_KohnSham -452.930481236 -6162.43534269 + E_Harris -452.930481737 -6162.43534951 + E_Fermi +0.425046287249 +5.78305142033 + + LCAO ALGORITHM --------------- ION= 2 ELEC= 3-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 8.70006708824e-05 + + Energy Rydberg eV + E_KohnSham -452.930481385 -6162.43534472 + E_Harris -452.930481786 -6162.43535017 + E_Fermi +0.425046243376 +5.78305082341 + + LCAO ALGORITHM --------------- ION= 2 ELEC= 4-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 3.07367797439e-05 + + Energy Rydberg eV + E_KohnSham -452.930481507 -6162.43534638 + E_Harris -452.93048167 -6162.4353486 + E_Fermi +0.425046277752 +5.78305129111 + + LCAO ALGORITHM --------------- ION= 2 ELEC= 5-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 1.65629490503e-05 + + Energy Rydberg eV + E_KohnSham -452.93048157 -6162.43534724 + E_Harris -452.930481628 -6162.43534802 + E_Fermi +0.425046263421 +5.78305109613 + + LCAO ALGORITHM --------------- ION= 2 ELEC= 6-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 5.97596009543e-06 + + Energy Rydberg eV + E_KohnSham -452.930481595 -6162.43534757 + E_Harris -452.9304816 -6162.43534764 + E_band +8.13315791966 +110.657290441 + E_one_elec +122.542601986 +1667.27763475 + E_Hartree +32.3363049714 +439.957999877 + E_xc -137.430732326 -1869.84103994 + E_Ewald -470.378458294 -6399.82724926 + E_demet -0.000197931903487 -0.00269300170341 + E_descf +0 +0 + E_exx +0 +0 + E_Fermi +0.425046259101 +5.78305103736 + + charge density convergence is achieved + final etot is -6162.43534757 eV + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Sn1 -0.027008421 -0.011580088 +0.027567656 + Sn2 -0.0089034583 +0.00061731658 -0.018826426 + Sn3 +0.043660739 -0.0026889193 +0.0031213388 + Sn4 -0.037028274 +0.041199922 -0.00042675269 + Sn5 -0.020912 -0.039275098 +0.017157585 + Sn6 -0.0051648482 +0.015562156 -0.0091829408 + Sn7 +0.043971005 -0.00032839706 -0.0067273241 + Sn8 -0.0013809629 -0.023673415 +0.026496116 + Sn9 -0.029937548 +0.0099170965 -0.011285069 + Sn10 -0.0072845967 +0.024171407 -0.044544684 + Sn11 -0.034124692 -0.027044352 +0.016398868 + Sn12 +0.010056911 +0.018954914 +0.0063630002 + Sn13 +0.018380257 -0.0057062045 +0.040547023 + Sn14 +0.00014945437 +0.0010015404 +0.0041955446 + Sn15 +0.019662397 +0.0027679182 +0.036122161 + Sn16 +0.0084152688 +0.0052982346 -0.025869275 + Sn17 +0.0052699744 -0.04048367 +0.017740236 + Sn18 -0.00099930061 -0.0071392943 -0.014711098 + Sn19 -0.0070987936 -0.015775644 +0.0054016468 + Sn20 -0.0059582382 +0.0015182179 +0.013359794 + Sn21 -0.0072480424 +0.0067281961 +0.0039819602 + Sn22 -0.0012365678 +0.016669174 +0.0023025644 + Sn23 -0.002226924 -0.010107012 +0.014480921 + Sn24 -0.0051741024 +0.002053362 +0.0051115283 + Sn25 -0.018397465 +0.0037405837 -0.017852631 + Sn26 -0.0097838606 -0.0027935501 -0.01943331 + Sn27 -0.0069678634 -0.0022111328 -0.0085559385 + Sn28 +0.029662969 -0.034232806 +0.0049709332 + Sn29 -0.0022676011 +0.01008841 -0.0097418149 + Sn30 +0.019257217 +0.021335545 +0.023150127 + Sn31 +0.024276966 +0.023963617 -0.034836636 + Sn32 +0.027651468 +0.0024632044 -0.023231845 + Sn33 -0.033700215 +0.0070709206 -0.023717715 + Sn34 +0.02854777 +0.014358614 +0.01884762 + Sn35 -0.027500072 +0.025074526 +0.025952843 + Sn36 +0.00073110945 +0.015740509 +0.0012203814 + Sn37 +0.031639844 -0.038974816 -0.0032364723 + Sn38 +0.01743028 +0.0056250302 +0.014412391 + Sn39 -0.018759846 -0.038899144 +0.021323811 + Sn40 +0.015929993 -0.018676715 -0.019339088 + Sn41 -0.024175183 +0.014642197 +0.026974425 + Sn42 -0.019377811 +0.012607622 -0.0043002606 + Sn43 -0.001158643 +0.046390404 +0.032032289 + Sn44 +0.0048553564 +0.028952371 -0.013724614 + Sn45 -0.025446887 -0.0073055465 -0.015119775 + Sn46 -0.0022864505 -0.018505485 -0.016274871 + Sn47 +0.0096958483 -0.017013462 +0.0021926415 + Sn48 -0.017522197 +0.0027844609 -0.014946093 + Sn49 -0.021837139 -0.0030599993 +0.026334584 + Sn50 -0.019166938 -0.015932277 +0.018931685 + Sn51 -0.01149328 +0.022338903 -0.018970862 + Sn52 +0.024613179 +0.014810046 +0.011041557 + Sn53 +0.009774385 -0.0086903 +0.021467246 + Sn54 +0.0094138184 -0.007929366 +0.0028426157 + Sn55 +0.027792787 -0.0040252609 -0.013509431 + Sn56 +0.020401052 -0.025782117 -0.047536944 + Sn57 +0.00021637855 -0.012545059 +0.0095040843 + Sn58 -0.0031401099 +0.0324471 +0.00019334499 + Sn59 -0.0016166185 -0.0031092 -0.027382086 + Sn60 +0.0071924485 -0.0096210801 +0.054220941 + Sn61 -0.007963278 +0.0489077 -0.00010118127 + Sn62 +0.031660885 +0.0018954402 -0.02961099 + Sn63 -0.027701798 -0.0091696302 -0.012010121 + Sn64 +0.011640265 -0.039417618 -0.050955212 + + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + +36.693034 -0.081971 -0.124871 + -0.081971 +36.692440 +0.172721 + -0.124871 +0.172721 +36.692661 + TOTAL-PRESSURE: +36.692712 KBAR + + + ------------------------------------------------------------------------------------------------ + Energy (Ry) Potential (Ry) Kinetic (Ry) Temperature (K) Pressure (kbar) + -452.75108 -452.93048 +0.17939809 +299.7321 +38.056403 + ------------------------------------------------------------------------------------------------ +Virtual Pressure is +38.056403 kbar +Virial Term is +36.692712 kbar +Kinetic Term is +1.3636915 kbar + + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + MD STRESS (kbar) + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + ++37.970247 -0.26952066 -0.14184686 +-0.26952066 +37.966807 -0.1030719 +-0.14184686 -0.1030719 +38.232155 + + + + ------------------------------------------- + STEP OF MOLECULAR DYNAMICS : 2 + ------------------------------------------- + first order charge density extrapolation ! + searching radius is (Bohr)) = +16.01 + searching radius unit is (Bohr)) = +23.45378 + enter setAlltoallvParameter, nblk = +32 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +375 + nCol_in_proc = +209 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +375 + nCol_in_proc = +192 + pnum = +2 + prow = +0 + pcol = +2 + nRow_in_proc = +375 + nCol_in_proc = +166 + pnum = +3 + prow = +0 + pcol = +3 + nRow_in_proc = +375 + nCol_in_proc = +161 + pnum = +4 + prow = +1 + pcol = +0 + nRow_in_proc = +353 + nCol_in_proc = +209 + pnum = +5 + prow = +1 + pcol = +1 + nRow_in_proc = +353 + nCol_in_proc = +192 + pnum = +6 + prow = +1 + pcol = +2 + nRow_in_proc = +353 + nCol_in_proc = +166 + pnum = +7 + prow = +1 + pcol = +3 + nRow_in_proc = +353 + nCol_in_proc = +161 +receiver_size is +529984 ; receiver_size of each process is: ++78375 +72000 +62250 +60375 +73777 +67776 +58598 +56833 +sender_size is +551600 ; sender_size of each process is: ++78375 +71250 +76171 +71198 +67776 +67070 +70464 +49296 + DONE : INIT SCF Time : +17.437 (SEC) + + + LCAO ALGORITHM --------------- ION=+3 ELEC=+1 -------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is +2.2557982558e-05 + + Energy Rydberg eV + E_KohnSham -452.929999282 -6162.42878537 + E_Harris -452.929999491 -6162.42878821 + E_Fermi +0.425052549676 +5.78313662503 + + LCAO ALGORITHM --------------- ION= 3 ELEC= 2-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 1.78528452038e-05 + + Energy Rydberg eV + E_KohnSham -452.929999381 -6162.42878671 + E_Harris -452.92999947 -6162.42878793 + E_Fermi +0.425052419432 +5.78313485296 + + LCAO ALGORITHM --------------- ION= 3 ELEC= 3-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 3.06430590643e-06 + + Energy Rydberg eV + E_KohnSham -452.929999422 -6162.42878728 + E_Harris -452.929999423 -6162.42878729 + E_band +8.13297586315 +110.654813435 + E_one_elec +122.541369942 +1667.26087193 + E_Hartree +32.3367870395 +439.96455875 + E_xc -137.430713711 -1869.84078668 + E_Ewald -470.377243307 -6399.81071851 + E_demet -0.000199385607513 -0.00271278036137 + E_descf +0 +0 + E_exx +0 +0 + E_Fermi +0.425052368853 +5.7831341648 + + charge density convergence is achieved + final etot is -6162.42878728 eV + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Sn1 -0.053495607 -0.022876841 +0.056683741 + Sn2 -0.017699671 +0.0024944921 -0.035351305 + Sn3 +0.086831636 -0.0051883135 +0.0084682591 + Sn4 -0.07364622 +0.084261329 +0.0012840253 + Sn5 -0.043415876 -0.077347749 +0.034636771 + Sn6 -0.010274622 +0.033127935 -0.016153647 + Sn7 +0.087074756 -0.00013543169 -0.013219999 + Sn8 -0.0038864841 -0.046722313 +0.054143871 + Sn9 -0.059950671 +0.019688451 -0.02119149 + Sn10 -0.014139635 +0.049335413 -0.088501036 + Sn11 -0.067848778 -0.053532854 +0.033930519 + Sn12 +0.020014974 +0.0396297 +0.014078258 + Sn13 +0.037781998 -0.0095900582 +0.08175897 + Sn14 -3.1183471e-05 +0.0034002902 +0.010527435 + Sn15 +0.039430632 +0.0059757576 +0.071896554 + Sn16 +0.017140432 +0.011763983 -0.049736069 + Sn17 +0.011326798 -0.081316805 +0.036436883 + Sn18 -0.0012794786 -0.016231315 -0.027167973 + Sn19 -0.015061788 -0.031285242 +0.01173555 + Sn20 -0.011839041 +0.00048958791 +0.027548719 + Sn21 -0.015423179 +0.012436145 +0.0079094467 + Sn22 -0.0022760315 +0.031156118 +0.0064752958 + Sn23 -0.0048481199 -0.020768285 +0.030450301 + Sn24 -0.010609588 +0.002926221 +0.011693069 + Sn25 -0.037837191 +0.0069924444 -0.034940428 + Sn26 -0.020174674 -0.0071309986 -0.038225451 + Sn27 -0.012925694 -0.0054283196 -0.01632686 + Sn28 +0.059425765 -0.070405833 +0.011422899 + Sn29 -0.0025634367 +0.019358494 -0.019558101 + Sn30 +0.038622321 +0.042029691 +0.047756937 + Sn31 +0.049225599 +0.047519389 -0.070068361 + Sn32 +0.055301606 +0.0039401221 -0.044106108 + Sn33 -0.066603339 +0.014017857 -0.04838483 + Sn34 +0.057292804 +0.030253106 +0.035074807 + Sn35 -0.055731321 +0.050575021 +0.050136143 + Sn36 +0.00016722332 +0.032001302 +0.0017702712 + Sn37 +0.06277418 -0.076549753 -0.0071601851 + Sn38 +0.034483067 +0.0126474 +0.026329402 + Sn39 -0.037902057 -0.075606547 +0.042296945 + Sn40 +0.030671777 -0.036835833 -0.040249789 + Sn41 -0.048564986 +0.029920575 +0.05297672 + Sn42 -0.039799407 +0.026276905 -0.0095808419 + Sn43 -0.002162354 +0.093642688 +0.062444041 + Sn44 +0.011254635 +0.058351293 -0.029474678 + Sn45 -0.051167336 -0.012637033 -0.031126764 + Sn46 -0.0040434019 -0.036074681 -0.034397231 + Sn47 +0.019399805 -0.03325957 +0.0048482155 + Sn48 -0.033540147 +0.0060781178 -0.030987203 + Sn49 -0.042865439 -0.0063380656 +0.051274675 + Sn50 -0.036973047 -0.033339908 +0.035531671 + Sn51 -0.023774196 +0.044349763 -0.038840535 + Sn52 +0.047945249 +0.028879722 +0.020615534 + Sn53 +0.018094649 -0.018747024 +0.043811815 + Sn54 +0.018318732 -0.016694739 +0.0044761012 + Sn55 +0.056307313 -0.0095152133 -0.028185989 + Sn56 +0.039586459 -0.052315191 -0.096615767 + Sn57 -0.00030766871 -0.025305111 +0.017511484 + Sn58 -0.0063483674 +0.064322737 -0.00041055782 + Sn59 -0.0018759332 -0.0065158568 -0.055506607 + Sn60 +0.016011185 -0.019571958 +0.10716696 + Sn61 -0.015517222 +0.095468213 -0.000400632 + Sn62 +0.063008876 +0.0027133425 -0.060539929 + Sn63 -0.05646466 -0.019300085 -0.023802334 + Sn64 +0.025375375 -0.079456679 -0.10489159 + + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + +36.703497 -0.163514 -0.249570 + -0.163514 +36.702505 +0.345038 + -0.249570 +0.345038 +36.702003 + TOTAL-PRESSURE: +36.702668 KBAR + + + ------------------------------------------------------------------------------------------------ + Energy (Ry) Potential (Ry) Kinetic (Ry) Temperature (K) Pressure (kbar) + -452.75108 -452.93 +0.1789161 +298.92681 +38.062696 + ------------------------------------------------------------------------------------------------ +Virtual Pressure is +38.062696 kbar +Virial Term is +36.702668 kbar +Kinetic Term is +1.3600276 kbar + + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + MD STRESS (kbar) + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + ++37.977248 -0.35054614 -0.26632338 +-0.35054614 +37.973613 +0.069522552 +-0.26632338 +0.069522552 +38.237227 + + + + ------------------------------------------- + STEP OF MOLECULAR DYNAMICS : 3 + ------------------------------------------- + second order charge density extrapolation ! + alpha = +2.9845034 + beta = -1.9845263 + searching radius is (Bohr)) = +16.01 + searching radius unit is (Bohr)) = +23.45378 + enter setAlltoallvParameter, nblk = +32 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +375 + nCol_in_proc = +209 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +375 + nCol_in_proc = +192 + pnum = +2 + prow = +0 + pcol = +2 + nRow_in_proc = +375 + nCol_in_proc = +166 + pnum = +3 + prow = +0 + pcol = +3 + nRow_in_proc = +375 + nCol_in_proc = +161 + pnum = +4 + prow = +1 + pcol = +0 + nRow_in_proc = +353 + nCol_in_proc = +209 + pnum = +5 + prow = +1 + pcol = +1 + nRow_in_proc = +353 + nCol_in_proc = +192 + pnum = +6 + prow = +1 + pcol = +2 + nRow_in_proc = +353 + nCol_in_proc = +166 + pnum = +7 + prow = +1 + pcol = +3 + nRow_in_proc = +353 + nCol_in_proc = +161 +receiver_size is +529984 ; receiver_size of each process is: ++78375 +72000 +62250 +60375 +73777 +67776 +58598 +56833 +sender_size is +551600 ; sender_size of each process is: ++78375 +71250 +76171 +71198 +67776 +67070 +70464 +49296 + DONE : INIT SCF Time : +23.5582 (SEC) + + + LCAO ALGORITHM --------------- ION=+4 ELEC=+1 -------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is +6.9201703816e-05 + + Energy Rydberg eV + E_KohnSham -452.929197222 -6162.41787278 + E_Harris -452.92919933 -6162.41790147 + E_Fermi +0.425061254242 +5.78325505672 + + LCAO ALGORITHM --------------- ION= 4 ELEC= 2-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 5.65788594879e-05 + + Energy Rydberg eV + E_KohnSham -452.929198225 -6162.41788643 + E_Harris -452.929199135 -6162.41789882 + E_Fermi +0.425061352239 +5.78325639004 + + LCAO ALGORITHM --------------- ION= 4 ELEC= 3-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 6.02255123171e-06 + + Energy Rydberg eV + E_KohnSham -452.929198644 -6162.41789214 + E_Harris -452.929198649 -6162.4178922 + E_band +8.1324693362 +110.647921783 + E_one_elec +122.539300924 +1667.2327215 + E_Hartree +32.3376309742 +439.97604107 + E_xc -137.430702313 -1869.84063159 + E_Ewald -470.375226456 -6399.78327785 + E_demet -0.00020177330925 -0.00274526671012 + E_descf +0 +0 + E_exx +0 +0 + E_Fermi +0.425061433794 +5.78325749965 + + charge density convergence is achieved + final etot is -6162.41789214 eV + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Sn1 -0.080734841 -0.033753077 +0.083878093 + Sn2 -0.026706559 +0.0031106851 -0.053464863 + Sn3 +0.13064771 -0.0079117462 +0.012525257 + Sn4 -0.10971122 +0.12626104 +0.0021041101 + Sn5 -0.064970361 -0.11713723 +0.052201581 + Sn6 -0.015762883 +0.049301347 -0.024845932 + Sn7 +0.13022111 -0.0012395486 -0.019806964 + Sn8 -0.0054160627 -0.069820057 +0.079563727 + Sn9 -0.089130752 +0.029020765 -0.032137235 + Sn10 -0.020043533 +0.073060573 -0.13388078 + Sn11 -0.10156889 -0.079790623 +0.050146034 + Sn12 +0.029256392 +0.058800241 +0.020413346 + Sn13 +0.055794519 -0.015097494 +0.12272991 + Sn14 +9.3425846e-06 +0.0047976949 +0.014856181 + Sn15 +0.059348701 +0.0086368123 +0.10684151 + Sn16 +0.024683715 +0.017102722 -0.074877768 + Sn17 +0.017206538 -0.12120593 +0.054084078 + Sn18 -0.002715833 -0.023151845 -0.041118029 + Sn19 -0.021987373 -0.046389828 +0.016237183 + Sn20 -0.016894352 +0.0013476743 +0.040024283 + Sn21 -0.023323899 +0.019217931 +0.011257492 + Sn22 -0.0030116807 +0.047094004 +0.0085398267 + Sn23 -0.0075253627 -0.030738463 +0.045975729 + Sn24 -0.014790488 +0.0042461562 +0.016506725 + Sn25 -0.056308496 +0.010804711 -0.052756979 + Sn26 -0.03016184 -0.0095427206 -0.058825398 + Sn27 -0.019636126 -0.0082247139 -0.025684651 + Sn28 +0.088120775 -0.10493672 +0.017776038 + Sn29 -0.0045346142 +0.029848475 -0.029506333 + Sn30 +0.057789537 +0.063650496 +0.069989876 + Sn31 +0.073176022 +0.071881413 -0.10491145 + Sn32 +0.081768258 +0.0056058736 -0.066316196 + Sn33 -0.1000409 +0.020476996 -0.071791419 + Sn34 +0.085044884 +0.04415012 +0.052751494 + Sn35 -0.083537388 +0.075475408 +0.075460355 + Sn36 -1.6382898e-05 +0.046997282 +0.003271575 + Sn37 +0.095406771 -0.11514006 -0.011619235 + Sn38 +0.051706661 +0.018209911 +0.039776389 + Sn39 -0.056372169 -0.11303562 +0.063089616 + Sn40 +0.04606997 -0.055428542 -0.059148082 + Sn41 -0.072668168 +0.044883526 +0.079586818 + Sn42 -0.05921726 +0.038422521 -0.012834134 + Sn43 -0.0046831444 +0.14095113 +0.094326326 + Sn44 +0.017241067 +0.085828189 -0.043526682 + Sn45 -0.076611961 -0.019238456 -0.046318343 + Sn46 -0.0053996861 -0.055027242 -0.050225745 + Sn47 +0.0291379 -0.050447629 +0.008186188 + Sn48 -0.050032936 +0.0080553201 -0.04571091 + Sn49 -0.064210624 -0.0092321838 +0.077926369 + Sn50 -0.055249933 -0.049150492 +0.053586093 + Sn51 -0.035319205 +0.066730498 -0.057015824 + Sn52 +0.070961796 +0.043592967 +0.031561972 + Sn53 +0.027511021 -0.026866253 +0.065749439 + Sn54 +0.027346814 -0.023988044 +0.0074915023 + Sn55 +0.084543566 -0.014680631 -0.042703516 + Sn56 +0.059689986 -0.077917998 -0.14342238 + Sn57 -0.00042773974 -0.037973156 +0.027110048 + Sn58 -0.010092052 +0.096923711 +0.0011864322 + Sn59 -0.0033194335 -0.0095349002 -0.081872339 + Sn60 +0.024454487 -0.028375783 +0.16067019 + Sn61 -0.023454869 +0.14364862 -0.0010759473 + Sn62 +0.094292043 +0.0040486297 -0.08931882 + Sn63 -0.084899426 -0.028236485 -0.03558859 + Sn64 +0.039058853 -0.11896996 -0.15707725 + + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + +36.721260 -0.244908 -0.374493 + -0.244908 +36.720100 +0.517520 + -0.374493 +0.517520 +36.717937 + TOTAL-PRESSURE: +36.719766 KBAR + + + ------------------------------------------------------------------------------------------------ + Energy (Ry) Potential (Ry) Kinetic (Ry) Temperature (K) Pressure (kbar) + -452.75108 -452.9292 +0.17811615 +297.59028 +38.073713 + ------------------------------------------------------------------------------------------------ +Virtual Pressure is +38.073713 kbar +Virial Term is +36.719766 kbar +Kinetic Term is +1.3539468 kbar + + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + MD STRESS (kbar) + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + ++37.989265 -0.43106741 -0.3908722 +-0.43106741 +37.985787 +0.24246337 +-0.3908722 +0.24246337 +38.246087 + + + + ------------------------------------------- + STEP OF MOLECULAR DYNAMICS : 4 + ------------------------------------------- + second order charge density extrapolation ! + alpha = +2.5003532 + beta = -1.5003397 + searching radius is (Bohr)) = +16.01 + searching radius unit is (Bohr)) = +23.45378 + enter setAlltoallvParameter, nblk = +32 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +375 + nCol_in_proc = +209 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +375 + nCol_in_proc = +192 + pnum = +2 + prow = +0 + pcol = +2 + nRow_in_proc = +375 + nCol_in_proc = +166 + pnum = +3 + prow = +0 + pcol = +3 + nRow_in_proc = +375 + nCol_in_proc = +161 + pnum = +4 + prow = +1 + pcol = +0 + nRow_in_proc = +353 + nCol_in_proc = +209 + pnum = +5 + prow = +1 + pcol = +1 + nRow_in_proc = +353 + nCol_in_proc = +192 + pnum = +6 + prow = +1 + pcol = +2 + nRow_in_proc = +353 + nCol_in_proc = +166 + pnum = +7 + prow = +1 + pcol = +3 + nRow_in_proc = +353 + nCol_in_proc = +161 +receiver_size is +529984 ; receiver_size of each process is: ++78375 +72000 +62250 +60375 +73777 +67776 +58598 +56833 +sender_size is +551600 ; sender_size of each process is: ++78375 +71250 +76171 +71198 +67776 +67070 +70464 +49296 + DONE : INIT SCF Time : +29.7281 (SEC) + + + LCAO ALGORITHM --------------- ION=+5 ELEC=+1 -------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is +5.79685378828e-05 + + Energy Rydberg eV + E_KohnSham -452.928082929 -6162.40271205 + E_Harris -452.928084307 -6162.4027308 + E_Fermi +0.425074220574 +5.78343147272 + + LCAO ALGORITHM --------------- ION= 5 ELEC= 2-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 4.55361028842e-05 + + Energy Rydberg eV + E_KohnSham -452.928083564 -6162.4027207 + E_Harris -452.928084159 -6162.40272879 + E_Fermi +0.425074362751 +5.78343340713 + + LCAO ALGORITHM --------------- ION= 5 ELEC= 3-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 6.88461134356e-06 + + Energy Rydberg eV + E_KohnSham -452.92808384 -6162.40272444 + E_Harris -452.928083849 -6162.40272456 + E_band +8.13201358474 +110.641720966 + E_one_elec +122.536446788 +1667.19388899 + E_Hartree +32.3387578886 +439.991373527 + E_xc -137.430663299 -1869.84010078 + E_Ewald -470.372420115 -6399.74509562 + E_demet -0.000205102329306 -0.00279056035163 + E_descf +0 +0 + E_exx +0 +0 + E_Fermi +0.425074320718 +5.78343283524 + + charge density convergence is achieved + final etot is -6162.40272444 eV + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Sn1 -0.10678579 -0.044836825 +0.11337469 + Sn2 -0.03583307 +0.0048637811 -0.06948315 + Sn3 +0.17370618 -0.010867891 +0.018217099 + Sn4 -0.14566887 +0.16902208 +0.005413481 + Sn5 -0.088227729 -0.15470287 +0.070212933 + Sn6 -0.020767292 +0.067372497 -0.031962099 + Sn7 +0.17299262 -0.00086731032 -0.026196676 + Sn8 -0.0088127237 -0.092979289 +0.10718203 + Sn9 -0.11903423 +0.038235408 -0.041411925 + Sn10 -0.026381352 +0.098135869 -0.17782761 + Sn11 -0.13484008 -0.10573163 +0.066772675 + Sn12 +0.039046165 +0.079452369 +0.028328431 + Sn13 +0.075325047 -0.01776648 +0.1636662 + Sn14 -0.00036321077 +0.0072883753 +0.021442976 + Sn15 +0.078970282 +0.012442791 +0.14248279 + Sn16 +0.033099642 +0.023717007 -0.09810175 + Sn17 +0.023781095 -0.16185199 +0.072791368 + Sn18 -0.0026139312 -0.032759085 -0.053136909 + Sn19 -0.030017018 -0.061520681 +0.022666083 + Sn20 -0.022799954 -3.2640888e-05 +0.054558615 + Sn21 -0.031341456 +0.024755235 +0.01533829 + Sn22 -0.0041125383 +0.060972821 +0.013210929 + Sn23 -0.010147775 -0.04137893 +0.062163928 + Sn24 -0.020537951 +0.0050745639 +0.022984704 + Sn25 -0.076233808 +0.013512701 -0.070149243 + Sn26 -0.040441948 -0.01447139 -0.077381188 + Sn27 -0.02538144 -0.011713612 -0.033211147 + Sn28 +0.11814242 -0.14139887 +0.024976841 + Sn29 -0.0043515502 +0.039056126 -0.039324772 + Sn30 +0.077498102 +0.084738866 +0.095395593 + Sn31 +0.097801481 +0.09459058 -0.13966278 + Sn32 +0.10911138 +0.006522843 -0.086762313 + Sn33 -0.1323845 +0.026571425 -0.096245392 + Sn34 +0.11336854 +0.059813596 +0.068161242 + Sn35 -0.11218416 +0.10177992 +0.10007487 + Sn36 -0.00054810296 +0.062987316 +0.003714674 + Sn37 +0.1259771 -0.15236677 -0.0163638 + Sn38 +0.068625525 +0.025881946 +0.051567395 + Sn39 -0.076148465 -0.14865047 +0.083969193 + Sn40 +0.060756 -0.073554236 -0.080367042 + Sn41 -0.096697927 +0.060502574 +0.10553212 + Sn42 -0.079850793 +0.052182645 -0.018294519 + Sn43 -0.0064612473 +0.18883613 +0.12491094 + Sn44 +0.023953634 +0.11495488 -0.059739751 + Sn45 -0.10254357 -0.023706722 -0.062498435 + Sn46 -0.0071275665 -0.072156133 -0.068809517 + Sn47 +0.038677933 -0.066595044 +0.01060479 + Sn48 -0.065902643 +0.011568393 -0.061249016 + Sn49 -0.085035037 -0.012163642 +0.10224165 + Sn50 -0.072435927 -0.066331997 +0.069511767 + Sn51 -0.047418173 +0.088622565 -0.076983932 + Sn52 +0.09410426 +0.057355784 +0.040592468 + Sn53 +0.035171001 -0.037274466 +0.088398829 + Sn54 +0.036061079 -0.032702135 +0.0091191115 + Sn55 +0.11324284 -0.020599557 -0.057649266 + Sn56 +0.079423826 -0.10504627 -0.19281732 + Sn57 -0.00094643319 -0.050324644 +0.034751935 + Sn58 -0.012759768 +0.12908292 -4.0887422e-05 + Sn59 -0.0032583078 -0.013030684 -0.1102263 + Sn60 +0.033539453 -0.038264113 +0.21264386 + Sn61 -0.031240854 +0.18927802 -0.0016181469 + Sn62 +0.1248699 +0.0043744066 -0.12034552 + Sn63 -0.11426067 -0.038384577 -0.047224377 + Sn64 +0.054652359 -0.15951548 -0.21188972 + + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + +36.745374 -0.325388 -0.498494 + -0.325388 +36.744304 +0.688576 + -0.498494 +0.688576 +36.739540 + TOTAL-PRESSURE: +36.743073 KBAR + + + ------------------------------------------------------------------------------------------------ + Energy (Ry) Potential (Ry) Kinetic (Ry) Temperature (K) Pressure (kbar) + -452.75108 -452.92808 +0.1770017 +295.72829 +38.088548 + ------------------------------------------------------------------------------------------------ +Virtual Pressure is +38.088548 kbar +Virial Term is +36.743073 kbar +Kinetic Term is +1.3454753 kbar + + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + MD STRESS (kbar) + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + ++38.005372 -0.51032173 -0.51434015 +-0.51032173 +38.002432 +0.41415132 +-0.51434015 +0.41415132 +38.25784 + + + + ------------------------------------------- + STEP OF MOLECULAR DYNAMICS : 5 + ------------------------------------------- + second order charge density extrapolation ! + alpha = +2.3283166 + beta = -1.3283397 + searching radius is (Bohr)) = +16.01 + searching radius unit is (Bohr)) = +23.45378 + enter setAlltoallvParameter, nblk = +32 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +375 + nCol_in_proc = +209 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +375 + nCol_in_proc = +192 + pnum = +2 + prow = +0 + pcol = +2 + nRow_in_proc = +375 + nCol_in_proc = +166 + pnum = +3 + prow = +0 + pcol = +3 + nRow_in_proc = +375 + nCol_in_proc = +161 + pnum = +4 + prow = +1 + pcol = +0 + nRow_in_proc = +353 + nCol_in_proc = +209 + pnum = +5 + prow = +1 + pcol = +1 + nRow_in_proc = +353 + nCol_in_proc = +192 + pnum = +6 + prow = +1 + pcol = +2 + nRow_in_proc = +353 + nCol_in_proc = +166 + pnum = +7 + prow = +1 + pcol = +3 + nRow_in_proc = +353 + nCol_in_proc = +161 +receiver_size is +529984 ; receiver_size of each process is: ++78375 +72000 +62250 +60375 +73777 +67776 +58598 +56833 +sender_size is +551600 ; sender_size of each process is: ++78375 +71250 +76171 +71198 +67776 +67070 +70464 +49296 + DONE : INIT SCF Time : +35.924 (SEC) + + + LCAO ALGORITHM --------------- ION=+6 ELEC=+1 -------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is +7.27045186835e-05 + + Energy Rydberg eV + E_KohnSham -452.926660019 -6162.38335237 + E_Harris -452.92666211 -6162.38338081 + E_Fermi +0.425089552004 +5.78364006753 + + LCAO ALGORITHM --------------- ION= 6 ELEC= 2-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 5.66241433002e-05 + + Energy Rydberg eV + E_KohnSham -452.926660963 -6162.3833652 + E_Harris -452.926661882 -6162.38337771 + E_Fermi +0.425089445056 +5.78363861242 + + LCAO ALGORITHM --------------- ION= 6 ELEC= 3-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 1.00469585082e-05 + + Energy Rydberg eV + E_KohnSham -452.926661395 -6162.38337109 + E_Harris -452.926661405 -6162.38337123 + E_Fermi +0.425089539458 +5.78363989682 + + LCAO ALGORITHM --------------- ION= 6 ELEC= 4-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 1.69928987724e-06 + + Energy Rydberg eV + E_KohnSham -452.926661398 -6162.38337113 + E_Harris -452.926661398 -6162.38337113 + E_band +8.13129430609 +110.631934678 + E_one_elec +122.532795693 +1667.1442133 + E_Hartree +32.340218189 +440.011241933 + E_xc -137.430624144 -1869.83956805 + E_Ewald -470.368841785 -6399.69640993 + E_demet -0.000209351834307 -0.00284837783333 + E_descf +0 +0 + E_exx +0 +0 + E_Fermi +0.425089598772 +5.78364070383 + + charge density convergence is achieved + final etot is -6162.38337113 eV + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Sn1 -0.1332002 -0.055026933 +0.14015487 + Sn2 -0.044404379 +0.0057672584 -0.087932146 + Sn3 +0.21745094 -0.013704355 +0.021945239 + Sn4 -0.18120187 +0.2101525 +0.0075337679 + Sn5 -0.11004865 -0.19437184 +0.088069881 + Sn6 -0.025713383 +0.083758464 -0.041137647 + Sn7 +0.21557965 -0.0020240784 -0.033083967 + Sn8 -0.011488129 -0.11637367 +0.1321358 + Sn9 -0.14812826 +0.047320596 -0.052051558 + Sn10 -0.031957191 +0.12115413 -0.22295545 + Sn11 -0.16811783 -0.13145095 +0.082103428 + Sn12 +0.04832101 +0.098414865 +0.034264406 + Sn13 +0.092822054 -0.022702975 +0.20412944 + Sn14 -0.00080421974 +0.0084811078 +0.025556938 + Sn15 +0.098589663 +0.015743981 +0.17731861 + Sn16 +0.040873414 +0.029298778 -0.12286042 + Sn17 +0.030053389 -0.20105494 +0.090409823 + Sn18 -0.0039858515 -0.039901905 -0.067126255 + Sn19 -0.037071444 -0.076130392 +0.026733764 + Sn20 -0.02815115 +0.0013365544 +0.067209932 + Sn21 -0.039044665 +0.031719977 +0.01861526 + Sn22 -0.0052942063 +0.076432089 +0.015307064 + Sn23 -0.012636617 -0.051456634 +0.077189887 + Sn24 -0.024888461 +0.0068391039 +0.027642542 + Sn25 -0.094736599 +0.016874924 -0.088013827 + Sn26 -0.05037656 -0.016554572 -0.097374735 + Sn27 -0.031474568 -0.014363351 -0.042126337 + Sn28 +0.14691536 -0.17564181 +0.03204679 + Sn29 -0.0065871663 +0.049461792 -0.049155221 + Sn30 +0.097119138 +0.10696035 +0.11788352 + Sn31 +0.12046954 +0.11791404 -0.17333091 + Sn32 +0.1350351 +0.0070999445 -0.10862724 + Sn33 -0.16523996 +0.0320607 -0.11916147 + Sn34 +0.14037631 +0.073356008 +0.085734302 + Sn35 -0.13973331 +0.12741755 +0.12586309 + Sn36 -0.0003477434 +0.077459201 +0.0051602708 + Sn37 +0.15828703 -0.19064611 -0.02154023 + Sn38 +0.086155299 +0.031762045 +0.065270249 + Sn39 -0.09497456 -0.18534176 +0.10484261 + Sn40 +0.076396063 -0.092387754 -0.099277593 + Sn41 -0.12053115 +0.075317915 +0.13201887 + Sn42 -0.099119791 +0.063590883 -0.021479544 + Sn43 -0.010667516 +0.2361297 +0.15685617 + Sn44 +0.029773651 +0.1420388 -0.073332837 + Sn45 -0.12737026 -0.029499773 -0.077372485 + Sn46 -0.0086292663 -0.091002338 -0.084216772 + Sn47 +0.048798279 -0.08393822 +0.013428932 + Sn48 -0.082337272 +0.013822079 -0.075218215 + Sn49 -0.10654989 -0.0145572 +0.12862234 + Sn50 -0.090858388 -0.081974326 +0.087391644 + Sn51 -0.058902773 +0.11036365 -0.094699076 + Sn52 +0.11680484 +0.071582038 +0.050772536 + Sn53 +0.044188159 -0.044915816 +0.11009658 + Sn54 +0.044434551 -0.039873569 +0.011860032 + Sn55 +0.14145655 -0.025865049 -0.071749914 + Sn56 +0.1005457 -0.13036392 -0.23931827 + Sn57 -0.0006311548 -0.062624246 +0.044323504 + Sn58 -0.015998378 +0.16200105 +0.0011370276 + Sn59 -0.0044189822 -0.015847631 -0.1365058 + Sn60 +0.041820423 -0.047315934 +0.26523094 + Sn61 -0.03913446 +0.23645155 -0.0027970035 + Sn62 +0.15586491 +0.0052685224 -0.1489884 + Sn63 -0.14268535 -0.046763895 -0.059255899 + Sn64 +0.069310591 -0.1996762 -0.26417084 + + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + +36.776386 -0.405524 -0.622401 + -0.405524 +36.775681 +0.859415 + -0.622401 +0.859415 +36.767448 + TOTAL-PRESSURE: +36.773172 KBAR + + + ------------------------------------------------------------------------------------------------ + Energy (Ry) Potential (Ry) Kinetic (Ry) Temperature (K) Pressure (kbar) + -452.75108 -452.92666 +0.17557886 +293.35107 +38.107831 + ------------------------------------------------------------------------------------------------ +Virtual Pressure is +38.107831 kbar +Virial Term is +36.773172 kbar +Kinetic Term is +1.3346597 kbar + + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + MD STRESS (kbar) + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + ++38.026159 -0.58888104 -0.63755158 +-0.58888104 +38.024158 +0.5857862 +-0.63755158 +0.5857862 +38.273177 + + + + ------------------------------------------- + STEP OF MOLECULAR DYNAMICS : 6 + ------------------------------------------- + second order charge density extrapolation ! + alpha = +2.2480936 + beta = -1.2480831 + searching radius is (Bohr)) = +16.01 + searching radius unit is (Bohr)) = +23.45378 + enter setAlltoallvParameter, nblk = +32 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +375 + nCol_in_proc = +209 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +375 + nCol_in_proc = +192 + pnum = +2 + prow = +0 + pcol = +2 + nRow_in_proc = +375 + nCol_in_proc = +166 + pnum = +3 + prow = +0 + pcol = +3 + nRow_in_proc = +375 + nCol_in_proc = +161 + pnum = +4 + prow = +1 + pcol = +0 + nRow_in_proc = +353 + nCol_in_proc = +209 + pnum = +5 + prow = +1 + pcol = +1 + nRow_in_proc = +353 + nCol_in_proc = +192 + pnum = +6 + prow = +1 + pcol = +2 + nRow_in_proc = +353 + nCol_in_proc = +166 + pnum = +7 + prow = +1 + pcol = +3 + nRow_in_proc = +353 + nCol_in_proc = +161 +receiver_size is +529984 ; receiver_size of each process is: ++78375 +72000 +62250 +60375 +73777 +67776 +58598 +56833 +sender_size is +551600 ; sender_size of each process is: ++78375 +71250 +76171 +71198 +67776 +67070 +70464 +49296 + DONE : INIT SCF Time : +42.6939 (SEC) + + + LCAO ALGORITHM --------------- ION=+7 ELEC=+1 -------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is +5.15243428837e-05 + + Energy Rydberg eV + E_KohnSham -452.924938984 -6162.35993648 + E_Harris -452.924940023 -6162.35995062 + E_Fermi +0.425107087085 +5.78387864454 + + LCAO ALGORITHM --------------- ION= 7 ELEC= 2-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 4.01084417204e-05 + + Energy Rydberg eV + E_KohnSham -452.924939453 -6162.35994287 + E_Harris -452.92493991 -6162.35994909 + E_Fermi +0.425107263122 +5.78388103964 + + LCAO ALGORITHM --------------- ION= 7 ELEC= 3-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 7.65059537845e-06 + + Energy Rydberg eV + E_KohnSham -452.924939663 -6162.35994572 + E_Harris -452.924939674 -6162.35994587 + E_band +8.13049223834 +110.621021986 + E_one_elec +122.528377871 +1667.08410574 + E_Hartree +32.3419808543 +440.035224225 + E_xc -137.430570104 -1869.8388328 + E_Ewald -470.364513785 -6399.63752448 + E_demet -0.000214498957571 -0.00291840803803 + E_descf +0 +0 + E_exx +0 +0 + E_Fermi +0.42510722918 +5.78388057785 + + charge density convergence is achieved + final etot is -6162.35994572 eV + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Sn1 -0.1589081 -0.065254632 +0.16869812 + Sn2 -0.053126183 +0.0073633022 -0.10446773 + Sn3 +0.26071828 -0.016937547 +0.027437847 + Sn4 -0.21677979 +0.25216791 +0.011689929 + Sn5 -0.13314184 -0.23226872 +0.10644629 + Sn6 -0.030976346 +0.10183519 -0.04911799 + Sn7 +0.25784241 -0.0020392531 -0.039477867 + Sn8 -0.015365461 -0.13926534 +0.15883384 + Sn9 -0.17760316 +0.055950636 -0.061286245 + Sn10 -0.037841372 +0.14531327 -0.26675093 + Sn11 -0.20074417 -0.15698497 +0.097920902 + Sn12 +0.05787483 +0.11851821 +0.041367208 + Sn13 +0.1115527 -0.025116946 +0.24453908 + Sn14 -0.0013961988 +0.010908848 +0.03147085 + Sn15 +0.11817738 +0.020077316 +0.21236665 + Sn16 +0.04876437 +0.035627357 -0.14579869 + Sn17 +0.037023778 -0.24093678 +0.10874461 + Sn18 -0.0044049256 -0.048928553 -0.079399008 + Sn19 -0.044730868 -0.091022875 +0.032579729 + Sn20 -0.033779224 +0.00066337574 +0.081201444 + Sn21 -0.047156224 +0.037418441 +0.022425366 + Sn22 -0.0064648882 +0.090243432 +0.019507018 + Sn23 -0.015082439 -0.061955775 +0.092891786 + Sn24 -0.030457464 +0.0078017222 +0.033754969 + Sn25 -0.11408725 +0.019399195 -0.10546341 + Sn26 -0.060417742 -0.020707769 -0.11619049 + Sn27 -0.037109501 -0.017475517 -0.049788052 + Sn28 +0.17669912 -0.21166254 +0.040018726 + Sn29 -0.007306297 +0.058815073 -0.058733749 + Sn30 +0.11703902 +0.12812215 +0.1427815 + Sn31 +0.14382362 +0.14022794 -0.20685575 + Sn32 +0.16184247 +0.0072687072 -0.12901291 + Sn33 -0.19719996 +0.03727379 -0.14295199 + Sn34 +0.16772973 +0.088074694 +0.10134288 + Sn35 -0.16797708 +0.15379562 +0.15079816 + Sn36 -0.00058903749 +0.092830934 +0.0055502012 + Sn37 +0.18900579 -0.22746516 -0.027334301 + Sn38 +0.10323782 +0.039575687 +0.077492231 + Sn39 -0.11466903 -0.22048596 +0.12555945 + Sn40 +0.091109064 -0.1104576 -0.11988501 + Sn41 -0.14408025 +0.090928982 +0.15758076 + Sn42 -0.11903907 +0.076460006 -0.026309197 + Sn43 -0.013972128 +0.28426683 +0.18767591 + Sn44 +0.036443054 +0.17022491 -0.088565989 + Sn45 -0.15267247 -0.0336818 -0.092875768 + Sn46 -0.010220858 -0.10826701 -0.10194449 + Sn47 +0.058256402 -0.10042231 +0.015923819 + Sn48 -0.098220696 +0.017253373 -0.090183772 + Sn49 -0.12740935 -0.017063485 +0.15320019 + Sn50 -0.1079036 -0.098625457 +0.10333232 + Sn51 -0.0706434 +0.13195084 -0.11417369 + Sn52 +0.13932315 +0.084899006 +0.059811089 + Sn53 +0.051906082 -0.054437253 +0.13235929 + Sn54 +0.052683503 -0.048177837 +0.013673836 + Sn55 +0.16965562 -0.031992442 -0.086380805 + Sn56 +0.12106254 -0.15693696 -0.28771759 + Sn57 -0.0007667012 -0.074741901 +0.052513864 + Sn58 -0.018775903 +0.19419142 +0.00033253007 + Sn59 -0.004621712 -0.019223606 -0.16461947 + Sn60 +0.050963257 -0.057181022 +0.31610212 + Sn61 -0.046878508 +0.28186475 -0.0039278898 + Sn62 +0.18609909 +0.0051610076 -0.17925931 + Sn63 -0.17200662 -0.056173024 -0.071092519 + Sn64 +0.085692747 -0.2405839 -0.3183599 + + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + +36.813687 -0.484421 -0.744862 + -0.484421 +36.813621 +1.028195 + -0.744862 +1.028195 +36.801069 + TOTAL-PRESSURE: +36.809459 KBAR + + + ------------------------------------------------------------------------------------------------ + Energy (Ry) Potential (Ry) Kinetic (Ry) Temperature (K) Pressure (kbar) + -452.75108 -452.92494 +0.17385609 +290.47273 +38.131023 + ------------------------------------------------------------------------------------------------ +Virtual Pressure is +38.131023 kbar +Virial Term is +36.809459 kbar +Kinetic Term is +1.3215641 kbar + + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + MD STRESS (kbar) + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + ++38.051071 -0.66585028 -0.75915728 +-0.66585028 +38.050414 +0.75551371 +-0.75915728 +0.75551371 +38.291584 + + + + ------------------------------------------- + STEP OF MOLECULAR DYNAMICS : 7 + ------------------------------------------- + second order charge density extrapolation ! + alpha = +2.1960044 + beta = -1.1960214 + searching radius is (Bohr)) = +16.01 + searching radius unit is (Bohr)) = +23.45378 + enter setAlltoallvParameter, nblk = +32 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +375 + nCol_in_proc = +209 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +375 + nCol_in_proc = +192 + pnum = +2 + prow = +0 + pcol = +2 + nRow_in_proc = +375 + nCol_in_proc = +166 + pnum = +3 + prow = +0 + pcol = +3 + nRow_in_proc = +375 + nCol_in_proc = +161 + pnum = +4 + prow = +1 + pcol = +0 + nRow_in_proc = +353 + nCol_in_proc = +209 + pnum = +5 + prow = +1 + pcol = +1 + nRow_in_proc = +353 + nCol_in_proc = +192 + pnum = +6 + prow = +1 + pcol = +2 + nRow_in_proc = +353 + nCol_in_proc = +166 + pnum = +7 + prow = +1 + pcol = +3 + nRow_in_proc = +353 + nCol_in_proc = +161 +receiver_size is +529984 ; receiver_size of each process is: ++78375 +72000 +62250 +60375 +73777 +67776 +58598 +56833 +sender_size is +551600 ; sender_size of each process is: ++78375 +71250 +76171 +71198 +67776 +67070 +70464 +49296 + DONE : INIT SCF Time : +48.8717 (SEC) + + + LCAO ALGORITHM --------------- ION=+8 ELEC=+1 -------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is +5.6833889216e-05 + + Energy Rydberg eV + E_KohnSham -452.922927833 -6162.33257337 + E_Harris -452.922929099 -6162.3325906 + E_Fermi +0.425126883107 +5.78414798324 + + LCAO ALGORITHM --------------- ION= 8 ELEC= 2-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 4.45110052156e-05 + + Energy Rydberg eV + E_KohnSham -452.922928409 -6162.3325812 + E_Harris -452.922928969 -6162.33258883 + E_Fermi +0.425126639688 +5.78414467135 + + LCAO ALGORITHM --------------- ION= 8 ELEC= 3-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 8.3941163103e-06 + + Energy Rydberg eV + E_KohnSham -452.922928665 -6162.33258469 + E_Harris -452.922928677 -6162.33258485 + E_band +8.12951958933 +110.607788418 + E_one_elec +122.523229853 +1667.01406337 + E_Hartree +32.3440334623 +440.06315139 + E_xc -137.430508024 -1869.83798816 + E_Ewald -470.359463397 -6399.56881043 + E_demet -0.00022055967093 -0.00300086827365 + E_descf +0 +0 + E_exx +0 +0 + E_Fermi +0.425126723819 +5.78414581601 + + charge density convergence is achieved + final etot is -6162.33258469 eV + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Sn1 -0.18523836 -0.074587878 +0.19363195 + Sn2 -0.06174076 +0.0075651092 -0.12348309 + Sn3 +0.30401793 -0.019997825 +0.030451932 + Sn4 -0.25096087 +0.2921445 +0.0139133 + Sn5 -0.15448826 -0.27215724 +0.12449866 + Sn6 -0.03608352 +0.11739024 -0.059075976 + Sn7 +0.29955996 -0.0041570228 -0.046194184 + Sn8 -0.017798995 -0.16207872 +0.18194774 + Sn9 -0.2055065 +0.064455249 -0.072091296 + Sn10 -0.042028664 +0.16715264 -0.31205248 + Sn11 -0.23295355 -0.181571 +0.11177895 + Sn12 +0.066527029 +0.13636718 +0.046592898 + Sn13 +0.12762039 -0.03075521 +0.28421286 + Sn14 -0.001598735 +0.011659849 +0.034424355 + Sn15 +0.13737595 +0.023297637 +0.24599292 + Sn16 +0.055520273 +0.040432713 -0.17055999 + Sn17 +0.043441155 -0.27857697 +0.12550316 + Sn18 -0.0063477346 -0.054515707 -0.093968083 + Sn19 -0.050708542 -0.10470908 +0.035368966 + Sn20 -0.038581668 +0.0030756557 +0.092557104 + Sn21 -0.054712246 +0.044823083 +0.025244417 + Sn22 -0.0075369579 +0.10601733 +0.020269853 + Sn23 -0.017902425 -0.071537857 +0.10761289 + Sn24 -0.034004848 +0.0096501184 +0.037108758 + Sn25 -0.1318126 +0.022885185 -0.12335455 + Sn26 -0.070052524 -0.021690557 -0.13688948 + Sn27 -0.043370987 -0.020135795 -0.059259285 + Sn28 +0.20431661 -0.24432478 +0.047704657 + Sn29 -0.010753443 +0.069792668 -0.06851784 + Sn30 +0.13625274 +0.15088523 +0.1635841 + Sn31 +0.16492188 +0.16318698 -0.23944772 + Sn32 +0.18616952 +0.007389885 -0.15095558 + Sn33 -0.22966384 +0.041965212 -0.16461876 + Sn34 +0.19338439 +0.099874968 +0.11902675 + Sn35 -0.19515599 +0.17893419 +0.17668567 + Sn36 -0.00020587448 +0.10617116 +0.0075802024 + Sn37 +0.22182362 -0.26544018 -0.033205947 + Sn38 +0.12050331 +0.044608206 +0.091767723 + Sn39 -0.13277941 -0.25643307 +0.14578686 + Sn40 +0.10696969 -0.12912131 -0.13753006 + Sn41 -0.16735838 +0.10525695 +0.18385622 + Sn42 -0.13742842 +0.086651467 -0.028269339 + Sn43 -0.01986625 +0.33108268 +0.22008833 + Sn44 +0.042243088 +0.19544533 -0.10102999 + Sn45 -0.17660008 -0.039542443 -0.10684981 + Sn46 -0.011129062 -0.12729039 -0.11564268 + Sn47 +0.068481384 -0.11799939 +0.0190121 + Sn48 -0.11450039 +0.018430331 -0.10295508 + Sn49 -0.1486845 -0.019140484 +0.18028698 + Sn50 -0.12616946 -0.11294839 +0.12157173 + Sn51 -0.081271936 +0.15337792 -0.13055944 + Sn52 +0.16105635 +0.098729261 +0.070383732 + Sn53 +0.061271097 -0.060517514 +0.15330977 + Sn54 +0.060913556 -0.054181087 +0.016857153 + Sn55 +0.19746912 -0.037333859 -0.10031336 + Sn56 +0.14248687 -0.18146809 -0.33203281 + Sn57 -0.00020379452 -0.086851078 +0.06286805 + Sn58 -0.02255585 +0.22683407 +0.0028037453 + Sn59 -0.0065318727 -0.02178524 -0.18935819 + Sn60 +0.05912671 -0.065586194 +0.36769615 + Sn61 -0.054836475 +0.3287504 -0.0056341125 + Sn62 +0.21618412 +0.0057570662 -0.20612174 + Sn63 -0.19987 -0.063499341 -0.082699044 + Sn64 +0.10135703 -0.28010676 -0.36931073 + + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + +36.857207 -0.562703 -0.866800 + -0.562703 +36.858077 +1.196214 + -0.866800 +1.196214 +36.840439 + TOTAL-PRESSURE: +36.851908 KBAR + + + ------------------------------------------------------------------------------------------------ + Energy (Ry) Potential (Ry) Kinetic (Ry) Temperature (K) Pressure (kbar) + -452.75108 -452.92293 +0.17184581 +287.11402 +38.158191 + ------------------------------------------------------------------------------------------------ +Virtual Pressure is +38.158191 kbar +Virial Term is +36.851908 kbar +Kinetic Term is +1.306283 kbar + + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + MD STRESS (kbar) + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + ++38.080117 -0.74185595 -0.88008795 +-0.74185595 +38.081244 +0.92461652 +-0.88008795 +0.92461652 +38.313211 + + + + ------------------------------------------- + STEP OF MOLECULAR DYNAMICS : 8 + ------------------------------------------- + second order charge density extrapolation ! + alpha = +2.1632934 + beta = -1.1632708 + searching radius is (Bohr)) = +16.01 + searching radius unit is (Bohr)) = +23.45378 + enter setAlltoallvParameter, nblk = +32 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +375 + nCol_in_proc = +209 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +375 + nCol_in_proc = +192 + pnum = +2 + prow = +0 + pcol = +2 + nRow_in_proc = +375 + nCol_in_proc = +166 + pnum = +3 + prow = +0 + pcol = +3 + nRow_in_proc = +375 + nCol_in_proc = +161 + pnum = +4 + prow = +1 + pcol = +0 + nRow_in_proc = +353 + nCol_in_proc = +209 + pnum = +5 + prow = +1 + pcol = +1 + nRow_in_proc = +353 + nCol_in_proc = +192 + pnum = +6 + prow = +1 + pcol = +2 + nRow_in_proc = +353 + nCol_in_proc = +166 + pnum = +7 + prow = +1 + pcol = +3 + nRow_in_proc = +353 + nCol_in_proc = +161 +receiver_size is +529984 ; receiver_size of each process is: ++78375 +72000 +62250 +60375 +73777 +67776 +58598 +56833 +sender_size is +551600 ; sender_size of each process is: ++78375 +71250 +76171 +71198 +67776 +67070 +70464 +49296 + DONE : INIT SCF Time : +55.0617 (SEC) + + + LCAO ALGORITHM --------------- ION=+9 ELEC=+1 -------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is +8.64757660455e-05 + + Energy Rydberg eV + E_KohnSham -452.920638307 -6162.30142277 + E_Harris -452.920641253 -6162.30146285 + E_Fermi +0.425146955531 +5.78442108257 + + LCAO ALGORITHM --------------- ION= 9 ELEC= 2-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 6.79211413275e-05 + + Energy Rydberg eV + E_KohnSham -452.920639644 -6162.30144096 + E_Harris -452.920640949 -6162.30145871 + E_Fermi +0.425147471421 +5.78442810161 + + LCAO ALGORITHM --------------- ION= 9 ELEC= 3-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 1.25585740857e-05 + + Energy Rydberg eV + E_KohnSham -452.920640253 -6162.30144925 + E_Harris -452.920640269 -6162.30144947 + E_Fermi +0.425147348095 +5.78442642368 + + LCAO ALGORITHM --------------- ION= 9 ELEC= 4-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 1.35602557591e-06 + + Energy Rydberg eV + E_KohnSham -452.920640258 -6162.30144932 + E_Harris -452.920640258 -6162.30144932 + E_band +8.12845260394 +110.593271337 + E_one_elec +122.517362788 +1666.93423785 + E_Hartree +32.34637736 +440.095041754 + E_xc -137.430430739 -1869.83693665 + E_Ewald -470.35372218 -6399.49069716 + E_demet -0.000227486936904 -0.00309511856247 + E_descf +0 +0 + E_exx +0 +0 + E_Fermi +0.425147454289 +5.78442786853 + + charge density convergence is achieved + final etot is -6162.30144932 eV + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Sn1 -0.21046055 -0.08415419 +0.22151254 + Sn2 -0.070491312 +0.0089942103 -0.13967667 + Sn3 +0.34665853 -0.023541709 +0.0361473 + Sn4 -0.28560218 +0.33349269 +0.019058096 + Sn5 -0.17762182 -0.30933164 +0.14319445 + Sn6 -0.041530193 +0.13556316 -0.067178828 + Sn7 +0.34097788 -0.0043523877 -0.052314022 + Sn8 -0.022157038 -0.18434113 +0.20799517 + Sn9 -0.23424714 +0.072426464 -0.080823671 + Sn10 -0.04714376 +0.19085277 -0.35515812 + Sn11 -0.26445122 -0.2061602 +0.12672695 + Sn12 +0.075805497 +0.15605894 +0.053616736 + Sn13 +0.14576414 -0.032553796 +0.32385698 + Sn14 -0.0021129093 +0.014252902 +0.040199368 + Sn15 +0.15658295 +0.028065513 +0.28018093 + Sn16 +0.062804599 +0.046527228 -0.19269212 + Sn17 +0.050828893 -0.31750421 +0.14347032 + Sn18 -0.0068238988 -0.063253422 -0.10592368 + Sn19 -0.057872072 -0.11903775 +0.040936097 + Sn20 -0.043958746 +0.0023480737 +0.10620271 + Sn21 -0.062787008 +0.050239564 +0.02893141 + Sn22 -0.0086329773 +0.11927549 +0.024373051 + Sn23 -0.020441711 -0.081839645 +0.12322907 + Sn24 -0.039477069 +0.010345123 +0.042921029 + Sn25 -0.15092813 +0.02510484 -0.1405624 + Sn26 -0.079903063 -0.025883745 -0.1555577 + Sn27 -0.048914181 -0.023448382 -0.066775494 + Sn28 +0.23367597 -0.27984324 +0.056443708 + Sn29 -0.011736533 +0.079109197 -0.077888278 + Sn30 +0.15601737 +0.17193144 +0.18830055 + Sn31 +0.18729328 +0.18468217 -0.2718251 + Sn32 +0.21215939 +0.0070056172 -0.17071845 + Sn33 -0.2608292 +0.046443094 -0.18777335 + Sn34 +0.21979911 +0.11382243 +0.13394244 + Sn35 -0.22324248 +0.20524896 +0.20131055 + Sn36 -0.00040446697 +0.1210738 +0.0079135623 + Sn37 +0.2520201 -0.30129031 -0.039815219 + Sn38 +0.13722609 +0.0526496 +0.10375844 + Sn39 -0.1523555 -0.29030064 +0.16601487 + Sn40 +0.12143182 -0.14672643 -0.1578883 + Sn41 -0.19026018 +0.12082494 +0.20880932 + Sn42 -0.15691972 +0.099181498 -0.03293536 + Sn43 -0.024055115 +0.3790828 +0.25062421 + Sn44 +0.049098495 +0.22270679 -0.11601269 + Sn45 -0.20129896 -0.043040511 -0.12192657 + Sn46 -0.012416706 -0.14398982 -0.13312614 + Sn47 +0.077750019 -0.13431282 +0.021489692 + Sn48 -0.13002669 +0.02162396 -0.11737282 + Sn49 -0.16910944 -0.021409079 +0.204506 + Sn50 -0.14252651 -0.12903459 +0.13693067 + Sn51 -0.092550702 +0.17453602 -0.14968301 + Sn52 +0.18281105 +0.11131908 +0.079175004 + Sn53 +0.068611935 -0.069642022 +0.17521306 + Sn54 +0.068922356 -0.06208828 +0.018587625 + Sn55 +0.22520293 -0.043859174 -0.11493851 + Sn56 +0.16303008 -0.20785201 -0.37952685 + Sn57 -0.00033538718 -0.098656584 +0.071002592 + Sn58 -0.025411709 +0.25845643 +0.0019745731 + Sn59 -0.0067797338 -0.025127541 -0.21711484 + Sn60 +0.068416555 -0.075308797 +0.41690686 + Sn61 -0.06249835 +0.37301417 -0.007121231 + Sn62 +0.2453913 +0.0050122038 -0.23573425 + Sn63 -0.22902556 -0.072559627 -0.094225641 + Sn64 +0.11905955 -0.32082751 -0.42316662 + + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + +36.906578 -0.639320 -0.986595 + -0.639320 +36.908642 +1.361242 + -0.986595 +1.361242 +36.885145 + TOTAL-PRESSURE: +36.900122 KBAR + + + ------------------------------------------------------------------------------------------------ + Energy (Ry) Potential (Ry) Kinetic (Ry) Temperature (K) Pressure (kbar) + -452.75108 -452.92064 +0.16955985 +283.29471 +38.189028 + ------------------------------------------------------------------------------------------------ +Virtual Pressure is +38.189028 kbar +Virial Term is +36.900122 kbar +Kinetic Term is +1.2889062 kbar + + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + MD STRESS (kbar) + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + ++38.113012 -0.8158553 -0.99872796 +-0.8158553 +38.116329 +1.0908563 +-0.99872796 +1.0908563 +38.337743 + + + + ------------------------------------------- + STEP OF MOLECULAR DYNAMICS : 9 + ------------------------------------------- + second order charge density extrapolation ! + alpha = +2.137784 + beta = -1.1378045 + searching radius is (Bohr)) = +16.01 + searching radius unit is (Bohr)) = +23.45378 + enter setAlltoallvParameter, nblk = +32 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +375 + nCol_in_proc = +209 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +375 + nCol_in_proc = +192 + pnum = +2 + prow = +0 + pcol = +2 + nRow_in_proc = +375 + nCol_in_proc = +166 + pnum = +3 + prow = +0 + pcol = +3 + nRow_in_proc = +375 + nCol_in_proc = +161 + pnum = +4 + prow = +1 + pcol = +0 + nRow_in_proc = +353 + nCol_in_proc = +209 + pnum = +5 + prow = +1 + pcol = +1 + nRow_in_proc = +353 + nCol_in_proc = +192 + pnum = +6 + prow = +1 + pcol = +2 + nRow_in_proc = +353 + nCol_in_proc = +166 + pnum = +7 + prow = +1 + pcol = +3 + nRow_in_proc = +353 + nCol_in_proc = +161 +receiver_size is +529984 ; receiver_size of each process is: ++78375 +72000 +62250 +60375 +73777 +67776 +58598 +56833 +sender_size is +551600 ; sender_size of each process is: ++78375 +71250 +76171 +71198 +67776 +67070 +70464 +49296 + DONE : INIT SCF Time : +61.799 (SEC) + + + LCAO ALGORITHM --------------- ION=+10 ELEC=+1 -------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is +5.91388685586e-05 + + Energy Rydberg eV + E_KohnSham -452.918086988 -6162.26671029 + E_Harris -452.918088342 -6162.26672871 + E_Fermi +0.42516945229 +5.78472716669 + + LCAO ALGORITHM --------------- ION= 10 ELEC= 2-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 4.61219005079e-05 + + Energy Rydberg eV + E_KohnSham -452.918087601 -6162.26671863 + E_Harris -452.918088202 -6162.26672681 + E_Fermi +0.425169075217 +5.78472203635 + + LCAO ALGORITHM --------------- ION= 10 ELEC= 3-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 8.96153376268e-06 + + Energy Rydberg eV + E_KohnSham -452.918087876 -6162.26672237 + E_Harris -452.918087889 -6162.26672256 + E_band +8.12724914505 +110.576897438 + E_one_elec +122.510832104 +1666.84538333 + E_Hartree +32.3489840495 +440.130507584 + E_xc -137.430342245 -1869.83573262 + E_Ewald -470.347326473 -6399.40367911 + E_demet -0.000235310648658 -0.00320156562183 + E_descf +0 +0 + E_exx +0 +0 + E_Fermi +0.425169195603 +5.78472367428 + + charge density convergence is achieved + final etot is -6162.26672237 eV + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Sn1 -0.23579001 -0.093136877 +0.24675131 + Sn2 -0.07912845 +0.0094722453 -0.15748111 + Sn3 +0.38883301 -0.026944056 +0.039929612 + Sn4 -0.31879008 +0.37290401 +0.023001376 + Sn5 -0.19958067 -0.34754607 +0.16153503 + Sn6 -0.04644951 +0.1516769 -0.076453196 + Sn7 +0.38176035 -0.0059733205 -0.058806567 + Sn8 -0.025810464 -0.20654342 +0.23135983 + Sn9 -0.26187646 +0.080263179 -0.090374286 + Sn10 -0.051056319 +0.21268897 -0.39904024 + Sn11 -0.29532435 -0.22975572 +0.13999302 + Sn12 +0.084540136 +0.1739639 +0.059448672 + Sn13 +0.16189413 -0.036664522 +0.36256698 + Sn14 -0.0023847037 +0.015411742 +0.043858425 + Sn15 +0.17525981 +0.032044431 +0.31315714 + Sn16 +0.069499622 +0.051633001 -0.21593146 + Sn17 +0.057818839 -0.35451964 +0.16028527 + Sn18 -0.0080958965 -0.069625018 -0.11943032 + Sn19 -0.063955257 -0.13218097 +0.04415852 + Sn20 -0.048862009 +0.0039560703 +0.11817918 + Sn21 -0.070326754 +0.056866845 +0.031867883 + Sn22 -0.0096894774 +0.13376155 +0.026238189 + Sn23 -0.023187943 -0.091436867 +0.13793511 + Sn24 -0.043542545 +0.01181086 +0.046579618 + Sn25 -0.16907753 +0.027908584 -0.15784445 + Sn26 -0.089477083 -0.027823888 -0.17529902 + Sn27 -0.054696472 -0.02655046 -0.075409741 + Sn28 +0.26132021 -0.31254162 +0.065125126 + Sn29 -0.014431015 +0.089599835 -0.087511054 + Sn30 +0.17514176 +0.19434544 +0.21018919 + Sn31 +0.20776534 +0.20618243 -0.30328776 + Sn32 +0.23608924 +0.0064887596 -0.19135623 + Sn33 -0.29197824 +0.050416015 -0.20930673 + Sn34 +0.24484084 +0.12564454 +0.15021835 + Sn35 -0.25041388 +0.23069645 +0.22655676 + Sn36 -6.8629142e-05 +0.13433775 +0.0093583182 + Sn37 +0.28325255 -0.33786986 -0.046197794 + Sn38 +0.15401775 +0.058571869 +0.11702592 + Sn39 -0.17080072 -0.32432216 +0.18579496 + Sn40 +0.13668069 -0.16485116 -0.17620732 + Sn41 -0.2130254 +0.13525968 +0.23416556 + Sn42 -0.17542325 +0.10968019 -0.035673661 + Sn43 -0.030211972 +0.4257025 +0.28213093 + Sn44 +0.055241826 +0.2476827 -0.12915198 + Sn45 -0.22469908 -0.047501918 -0.13579237 + Sn46 -0.013331654 -0.16169282 -0.14774878 + Sn47 +0.087676377 -0.15128442 +0.024222492 + Sn48 -0.14562321 +0.023077889 -0.12994639 + Sn49 -0.18963361 -0.023291158 +0.23007327 + Sn50 -0.15956817 -0.1433012 +0.15380371 + Sn51 -0.1031098 +0.19532933 -0.16623634 + Sn52 +0.20389275 +0.12422176 +0.088746248 + Sn53 +0.076802163 -0.07625579 +0.1961435 + Sn54 +0.076831523 -0.068119888 +0.021162847 + Sn55 +0.25264005 -0.049757646 -0.12886857 + Sn56 +0.18413089 -0.2326584 -0.4239839 + Sn57 +9.2210315e-06 -0.11025073 +0.080364198 + Sn58 -0.028821362 +0.29031979 +0.0031573303 + Sn59 -0.0080898661 -0.027722794 -0.24214144 + Sn60 +0.076855603 -0.083905497 +0.46621859 + Sn61 -0.070191887 +0.41767338 -0.0089756719 + Sn62 +0.2741951 +0.004837731 -0.26282889 + Sn63 -0.25695178 -0.080049064 -0.10534833 + Sn64 +0.13648576 -0.36035336 -0.47466886 + + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + +36.961526 -0.714902 -1.105207 + -0.714902 +36.965101 +1.524613 + -1.105207 +1.524613 +36.935033 + TOTAL-PRESSURE: +36.953887 KBAR + + + ------------------------------------------------------------------------------------------------ + Energy (Ry) Potential (Ry) Kinetic (Ry) Temperature (K) Pressure (kbar) + -452.75108 -452.91809 +0.1670102 +279.03485 +38.223412 + ------------------------------------------------------------------------------------------------ +Virtual Pressure is +38.223412 kbar +Virial Term is +36.953887 kbar +Kinetic Term is +1.2695251 kbar + + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + MD STRESS (kbar) + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + ++38.149569 -0.88848724 -1.1160392 +-0.88848724 +38.155539 +1.2555666 +-1.1160392 +1.2555666 +38.365127 + + + + ------------------------------------------- + STEP OF MOLECULAR DYNAMICS : 10 + ------------------------------------------- + second order charge density extrapolation ! + alpha = +2.1198075 + beta = -1.1198004 + searching radius is (Bohr)) = +16.01 + searching radius unit is (Bohr)) = +23.45378 + enter setAlltoallvParameter, nblk = +32 + pnum = +0 + prow = +0 + pcol = +0 + nRow_in_proc = +375 + nCol_in_proc = +209 + pnum = +1 + prow = +0 + pcol = +1 + nRow_in_proc = +375 + nCol_in_proc = +192 + pnum = +2 + prow = +0 + pcol = +2 + nRow_in_proc = +375 + nCol_in_proc = +166 + pnum = +3 + prow = +0 + pcol = +3 + nRow_in_proc = +375 + nCol_in_proc = +161 + pnum = +4 + prow = +1 + pcol = +0 + nRow_in_proc = +353 + nCol_in_proc = +209 + pnum = +5 + prow = +1 + pcol = +1 + nRow_in_proc = +353 + nCol_in_proc = +192 + pnum = +6 + prow = +1 + pcol = +2 + nRow_in_proc = +353 + nCol_in_proc = +166 + pnum = +7 + prow = +1 + pcol = +3 + nRow_in_proc = +353 + nCol_in_proc = +161 +receiver_size is +529984 ; receiver_size of each process is: ++78375 +72000 +62250 +60375 +73777 +67776 +58598 +56833 +sender_size is +551600 ; sender_size of each process is: ++78375 +71250 +76171 +71198 +67776 +67070 +70464 +49296 + DONE : INIT SCF Time : +67.9359 (SEC) + + + LCAO ALGORITHM --------------- ION=+11 ELEC=+1 -------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is +6.04857150896e-05 + + Energy Rydberg eV + E_KohnSham -452.915285695 -6162.22859675 + E_Harris -452.915287104 -6162.22861593 + E_Fermi +0.425190862123 +5.78501846241 + + LCAO ALGORITHM --------------- ION= 11 ELEC= 2-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 4.71963100966e-05 + + Energy Rydberg eV + E_KohnSham -452.915286331 -6162.2286054 + E_Harris -452.915286959 -6162.22861395 + E_Fermi +0.425191306334 +5.78502450621 + + LCAO ALGORITHM --------------- ION= 11 ELEC= 3-------------------------------- + +K-S equation was solved by genelpa2 + +eigenvalues were copied to ekb + + Density error is 9.32866805775e-06 + + Energy Rydberg eV + E_KohnSham -452.915286618 -6162.22860931 + E_Harris -452.915286633 -6162.22860951 + E_band +8.12594788021 +110.559192822 + E_one_elec +122.503647942 +1666.7476378 + E_Hartree +32.3518637196 +440.169687505 + E_xc -137.430237787 -1869.83431139 + E_Ewald -470.340316524 -6399.30830385 + E_demet -0.000243969284645 -0.00331937240816 + E_descf +0 +0 + E_exx +0 +0 + E_Fermi +0.425191183439 +5.78502283413 + + charge density convergence is achieved + final etot is -6162.22860931 eV + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + Sn1 -0.26010262 -0.10235529 +0.27523028 + Sn2 -0.088010206 +0.01119958 -0.17203759 + Sn3 +0.43044375 -0.031004631 +0.04692627 + Sn4 -0.35268258 +0.4139888 +0.029959762 + Sn5 -0.22330649 -0.38289579 +0.18055779 + Sn6 -0.052150702 +0.17071929 -0.08374828 + Sn7 +0.42217254 -0.0055071486 -0.064314248 + Sn8 -0.031179398 -0.22794644 +0.25789683 + Sn9 -0.29026498 +0.087417756 -0.097736866 + Sn10 -0.055980014 +0.23663759 -0.44050737 + Sn11 -0.3254534 -0.25349187 +0.15467877 + Sn12 +0.093727171 +0.1939222 +0.067188358 + Sn13 +0.18040283 -0.036454964 +0.40134007 + Sn14 -0.0029261423 +0.018838636 +0.050541167 + Sn15 +0.19417787 +0.037717765 +0.34656232 + Sn16 +0.076393017 +0.058011093 -0.23619655 + Sn17 +0.065827251 -0.39295888 +0.17837929 + Sn18 -0.0080308819 -0.079292361 -0.12995444 + Sn19 -0.071185575 -0.14618213 +0.050607508 + Sn20 -0.054129853 +0.0019957357 +0.13243178 + Sn21 -0.07862 +0.061205996 +0.035744503 + Sn22 -0.010626446 +0.14563034 +0.031661849 + Sn23 -0.025559539 -0.1018105 +0.15372953 + Sn24 -0.049588315 +0.011746072 +0.053098411 + Sn25 -0.18844552 +0.029406063 -0.17441919 + Sn26 -0.099270911 -0.033246765 -0.19308659 + Sn27 -0.059916524 -0.030338443 -0.082114713 + Sn28 +0.29080503 -0.34858966 +0.074913422 + Sn29 -0.014504314 +0.098212365 -0.096549614 + Sn30 +0.19483772 +0.21442773 +0.23616541 + Sn31 +0.22980662 +0.22639864 -0.33460667 + Sn32 +0.26198932 +0.0055376902 -0.20956319 + Sn33 -0.32172115 +0.054316182 -0.23251084 + Sn34 +0.27072255 +0.13977464 +0.16331201 + Sn35 -0.27853898 +0.25714555 +0.25021133 + Sn36 -0.00058979848 +0.14947597 +0.0089550391 + Sn37 +0.31176253 -0.3719243 -0.053618399 + Sn38 +0.1701219 +0.06792473 +0.12768211 + Sn39 -0.19069856 -0.3561836 +0.20543669 + Sn40 +0.15016645 -0.18150591 -0.19727026 + Sn41 -0.23524623 +0.15122216 +0.25786478 + Sn42 -0.19493898 +0.1229135 -0.041170087 + Sn43 -0.034211497 +0.47386351 +0.31150403 + Sn44 +0.062687669 +0.27493061 -0.14491498 + Sn45 -0.2491013 -0.049535067 -0.15090332 + Sn46 -0.014528973 -0.17683369 -0.16652326 + Sn47 +0.096257738 -0.16692251 +0.026573319 + Sn48 -0.16036726 +0.02677007 -0.14463874 + Sn49 -0.20919195 -0.025485747 +0.25266373 + Sn50 -0.17433248 -0.15951776 +0.1674265 + Sn51 -0.11427194 +0.21599707 -0.18608795 + Sn52 +0.22488585 +0.13570593 +0.096665968 + Sn53 +0.08298663 -0.086205439 +0.21807802 + Sn54 +0.084629398 -0.076370924 +0.022172069 + Sn55 +0.2798268 -0.057080466 -0.14369289 + Sn56 +0.20396926 -0.25949969 -0.47175814 + Sn57 -0.00054557424 -0.12158633 +0.087514197 + Sn58 -0.031524332 +0.32081685 +0.0010723774 + Sn59 -0.0077077805 -0.031324626 -0.2706494 + Sn60 +0.086733031 -0.093945026 +0.51273219 + Sn61 -0.077585979 +0.45973373 -0.010534338 + Sn62 +0.30205211 +0.0030021707 -0.2928066 + Sn63 -0.2863687 -0.089532212 -0.11637887 + Sn64 +0.15602083 -0.40107786 -0.52918428 + + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + +37.021694 -0.788474 -1.221132 + -0.788474 +37.027049 +1.684292 + -1.221132 +1.684292 +36.989680 + TOTAL-PRESSURE: +37.012808 KBAR + + + ------------------------------------------------------------------------------------------------ + Energy (Ry) Potential (Ry) Kinetic (Ry) Temperature (K) Pressure (kbar) + -452.75108 -452.91529 +0.16420979 +274.35601 +38.261045 + ------------------------------------------------------------------------------------------------ +Virtual Pressure is +38.261045 kbar +Virial Term is +37.012808 kbar +Kinetic Term is +1.2482378 kbar + + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + + MD STRESS (kbar) + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + ++38.189523 -0.95878581 -1.2305214 +-0.95878581 +38.198565 +1.4167145 +-1.2305214 +1.4167145 +38.395048 + + + + + -------------------------------------------- + !FINAL_ETOT_IS -6162.228609308414 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total +74.003 27 +2.7 +1e+02 % + Driver driver_line +73.993 1 +74 +1e+02 % + PW_Basis setup_struc_factor +0.52214 11 +0.047 +0.71 % + ORB_control set_orb_tables +0.34563 1 +0.35 +0.47 % + ORB_gen_tables gen_tables +0.34562 1 +0.35 +0.47 % + ORB_table_phi init_Table +0.16991 1 +0.17 +0.23 % + ORB_table_phi cal_ST_Phi12_R +0.16613 70 +0.0024 +0.22 % + Run_MD md_line +73.473 1 +73 +99 % + Verlet setup +8.7027 1 +8.7 +12 % + MD_func force_virial +73.447 11 +6.7 +99 % + ESolver_KS_LCAO Run +31.95 11 +2.9 +43 % + ESolver_KS_LCAO beforescf +1.1431 11 +0.1 +1.5 % + ESolver_KS_LCAO beforesolver +0.24355 11 +0.022 +0.33 % + ESolver_KS_LCAO set_matrix_grid +0.17026 11 +0.015 +0.23 % + Grid_Technique init +0.11863 11 +0.011 +0.16 % + Charge atomic_rho +0.22408 21 +0.011 +0.3 % + PW_Basis recip2real +0.16984 85 +0.002 +0.23 % + Potential init_pot +0.11468 11 +0.01 +0.15 % + Potential update_from_charge +0.46157 53 +0.0087 +0.62 % + Potential cal_v_eff +0.43081 53 +0.0081 +0.58 % + H_Hartree_pw v_hartree +0.27908 53 +0.0053 +0.38 % + PW_Basis real2recip +0.3513 181 +0.0019 +0.47 % + PW_Basis gatherp_scatters +0.13844 181 +0.00076 +0.19 % + PotXC cal_v_eff +0.13794 53 +0.0026 +0.19 % + XC_Functional v_xc +0.13335 53 +0.0025 +0.18 % + HSolverLCAO solve +30.059 42 +0.72 +41 % + HamiltLCAO updateHk +15.651 42 +0.37 +21 % + OperatorLCAO init +4.6459 84 +0.055 +6.3 % + Overlap contributeHR +0.43416 11 +0.039 +0.59 % + LCAO_gen_fixedH calculate_S_no +0.43414 11 +0.039 +0.59 % + Ekin contributeHR +0.4396 11 +0.04 +0.59 % + Nonlocal contributeHR +3.7672 11 +0.34 +5.1 % + LCAO_gen_fixedH b_NL_beta_new +3.7668 11 +0.34 +5.1 % + ORB_gen_tables snap_psibeta_half +0.98251 426843 +2.3e-06 +1.3 % + Veff contributeHk +11.001 42 +0.26 +15 % + Gint_interface cal_gint +34.985 95 +0.37 +47 % + Gint_interface cal_gint_vlocal +9.8726 42 +0.24 +13 % + Gint_Tools cal_psir_ylm +5.0263 122472 +4.1e-05 +6.8 % + Gint_Gamma distri_vl +1.087 42 +0.026 +1.5 % + Gint_Gamma distri_vl_index +0.15275 11 +0.014 +0.21 % + Gint_Gamma distri_vl_value +0.93415 42 +0.022 +1.3 % + HSolverLCAO hamiltSolvePsiK +2.7683 42 +0.066 +3.7 % + OperatorLCAO get_hs_pointers +34.542 21 +1.6 +47 % + DiagoElpa elpa_solve +2.6994 42 +0.064 +3.6 % + ElecStateLCAO psiToRho +11.64 42 +0.28 +16 % + elecstate cal_dm +0.83198 53 +0.016 +1.1 % + psiMulPsiMpi pdgemm +0.81371 53 +0.015 +1.1 % + LCAO_Charge dm_2dTOgrid +0.52065 42 +0.012 +0.7 % + Gint_interface cal_gint_rho +10.879 42 +0.26 +15 % + Charge mix_rho +0.14504 31 +0.0047 +0.2 % + Charge Pulay_mixing +0.13937 31 +0.0045 +0.19 % + Force_Stress_LCAO getForceStress +41.496 11 +3.8 +56 % + Forces cal_force_loc +0.45206 11 +0.041 +0.61 % + Forces cal_force_ew +0.44221 11 +0.04 +0.6 % + Forces cal_force_scc +0.53402 11 +0.049 +0.72 % + Stress_Func stress_loc +0.10544 11 +0.0096 +0.14 % + Stress_Func stress_ewa +0.20623 11 +0.019 +0.28 % + Force_LCAO_gamma ftable_gamma +39.716 11 +3.6 +54 % + Force_LCAO_gamma allocate_gamma +10.307 11 +0.94 +14 % + LCAO_gen_fixedH b_NL_mu_new +6.7256 11 +0.61 +9.1 % + Force_LCAO_gamma cal_foverlap +0.92567 11 +0.084 +1.3 % + Force_LCAO_gamma cal_edm_2d +0.77074 11 +0.07 +1 % + Force_LCAO_gamma cal_fvnl_dbeta_new +13.734 11 +1.2 +19 % + Force_LCAO_gamma cal_fvl_dphi +14.233 11 +1.3 +19 % + Gint_interface cal_gint_force +14.233 11 +1.3 +19 % + Gint_Tools cal_dpsir_ylm +7.961 16038 +0.0005 +11 % + Gint_Tools cal_dpsirr_ylm +0.91648 16038 +5.7e-05 +1.2 % + ---------------------------------------------------------------------------------------- + + NAME---------------|MEMORY(MB)-------- +total +1137 +ORB::Jl(x) +606.4 +LOC::A2A_sender +125.1 +Stress::dSH_GO +65.7 +LOC::A2A_receiv +60.41 +ORB::Table_SR&TR +48.8 +ChgMix::Rrho +34.19 +ChgMix::dRrho +30.18 +ChgMix::drho +28.38 +LOC::DM +27.72 +FFT::grid +16.96 +Force::dS_GO +15.84 +Force::dTVNL +15.1 +ORB::Table_NR +8.051 +Chg::rho +4.532 +Chg::rho_save +4.175 +Chg::rho_core +4.055 +Pot::veff_fix +4.055 +Pot::veff +4.055 +ChgMix::rho_save2 +4.055 +SF::strucFac +3.89 +SF::eigts123 +3.677 +GT::index2normal +3.375 +GT::index2ucell +3.375 +Chg::rhog +2.184 +Chg::rhog_save +2.184 +Chg::rhog_core +2.184 +Grid::AtomLink +1.75 +GT::which_atom +1.239 +GT::which_bigcell +1.239 +GT::which_unitcell +1.239 + ------------- < 1.0 MB has been ignored ---------------- + ---------------------------------------------------------- + + Start Time : Wed Apr 12 12:06:58 2023 + Finish Time : Wed Apr 12 12:08:12 2023 + Total Time : 0 h 1 mins 14 secs diff --git a/tests/abacus.md.newversion/STRU b/tests/abacus.md.newversion/STRU new file mode 100644 index 00000000..65daf31d --- /dev/null +++ b/tests/abacus.md.newversion/STRU @@ -0,0 +1,84 @@ +ATOMIC_SPECIES +Sn 118.71 Sn.pz-bhs.UPF + +LATTICE_CONSTANT +23.45378 + 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b/tests/comp_sys.py @@ -89,7 +89,7 @@ def test_virial(self): # if len(self.system_1['virials']) == 0: # self.assertEqual(len(self.system_1['virials']), 0) # return - if not "virials" in self.system_1: + if "virials" not in self.system_1: self.assertFalse("virials" in self.system_2) return np.testing.assert_almost_equal( diff --git a/tests/context.py b/tests/context.py index 10348a8d..77a7557d 100644 --- a/tests/context.py +++ b/tests/context.py @@ -3,8 +3,12 @@ sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))) import dpdata -import dpdata.gaussian.gjf -import dpdata.md.msd -import dpdata.md.water -import dpdata.stat -import dpdata.system +import dpdata.gaussian.gjf # noqa: F401 +import dpdata.md.msd # noqa: F401 +import dpdata.md.water # noqa: F401 +import dpdata.stat # noqa: F401 +import dpdata.system # noqa: F401 + +__all__ = [ + "dpdata", +] diff --git a/tests/cp2k/aimd/deepmd/set.000/box.npy b/tests/cp2k/aimd/deepmd/set.000/box.npy index fd2920c5..b660faeb 100644 Binary files a/tests/cp2k/aimd/deepmd/set.000/box.npy and b/tests/cp2k/aimd/deepmd/set.000/box.npy differ diff --git a/tests/cp2k/aimd/deepmd/set.000/coord.npy b/tests/cp2k/aimd/deepmd/set.000/coord.npy index d4b4b538..3f67f14a 100644 Binary files a/tests/cp2k/aimd/deepmd/set.000/coord.npy and b/tests/cp2k/aimd/deepmd/set.000/coord.npy differ diff --git a/tests/cp2k/aimd/deepmd/set.000/energy.npy b/tests/cp2k/aimd/deepmd/set.000/energy.npy index ec640591..d186c528 100644 Binary files a/tests/cp2k/aimd/deepmd/set.000/energy.npy and b/tests/cp2k/aimd/deepmd/set.000/energy.npy differ diff --git a/tests/cp2k/aimd/deepmd/set.000/force.npy b/tests/cp2k/aimd/deepmd/set.000/force.npy index c128e024..3815d933 100644 Binary files a/tests/cp2k/aimd/deepmd/set.000/force.npy and b/tests/cp2k/aimd/deepmd/set.000/force.npy differ diff --git a/tests/cp2k/aimd_stress/deepmd/box.raw b/tests/cp2k/aimd_stress/deepmd/box.raw deleted file mode 100644 index 8f2014f0..00000000 --- a/tests/cp2k/aimd_stress/deepmd/box.raw +++ /dev/null @@ -1 +0,0 @@ -1.000000000000000000e+01 0.000000000000000000e+00 0.000000000000000000e+00 0.000000000000000000e+00 1.000000000000000000e+01 0.000000000000000000e+00 0.000000000000000000e+00 0.000000000000000000e+00 1.000000000000000000e+01 diff --git a/tests/cp2k/aimd_stress/deepmd/coord.raw b/tests/cp2k/aimd_stress/deepmd/coord.raw deleted file mode 100644 index 0ee1d819..00000000 --- a/tests/cp2k/aimd_stress/deepmd/coord.raw +++ /dev/null @@ -1 +0,0 @@ -5.701910018920898438e+00 3.809600114822387695e+00 4.388450145721435547e+00 4.446010112762451172e+00 4.656809806823730469e+00 5.381949901580810547e+00 4.492159843444824219e+00 4.909910202026367188e+00 3.577559947967529297e+00 5.838250160217285156e+00 5.622280120849609375e+00 4.610680103302001953e+00 5.116660118103027344e+00 4.755330085754394531e+00 4.461229801177978516e+00 diff --git a/tests/cp2k/aimd_stress/deepmd/energy.raw b/tests/cp2k/aimd_stress/deepmd/energy.raw deleted file mode 100644 index 0cc396e4..00000000 --- a/tests/cp2k/aimd_stress/deepmd/energy.raw +++ /dev/null @@ -1 +0,0 @@ --2.196554718017578125e+02 diff --git a/tests/cp2k/aimd_stress/deepmd/force.raw b/tests/cp2k/aimd_stress/deepmd/force.raw deleted file mode 100644 index 346b4953..00000000 --- a/tests/cp2k/aimd_stress/deepmd/force.raw +++ /dev/null @@ -1 +0,0 @@ --2.743706703186035156e-01 4.712709188461303711e-01 -1.367179006338119507e-01 7.652513980865478516e-01 2.514204978942871094e-01 -1.059429287910461426e+00 2.538656070828437805e-02 1.183478906750679016e-02 -1.267343163490295410e-01 -8.532900810241699219e-01 -9.029597043991088867e-01 -1.871660351753234863e-01 3.367811143398284912e-01 1.687173396348953247e-01 1.509592533111572266e+00 diff --git a/tests/cp2k/aimd_stress/deepmd/set.000/box.npy b/tests/cp2k/aimd_stress/deepmd/set.000/box.npy new file mode 100644 index 00000000..bd18246c Binary files /dev/null and b/tests/cp2k/aimd_stress/deepmd/set.000/box.npy differ diff --git 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a/tests/cp2k/aimd_stress/deepmd/virial.raw b/tests/cp2k/aimd_stress/deepmd/virial.raw deleted file mode 100644 index 90c5ec17..00000000 --- a/tests/cp2k/aimd_stress/deepmd/virial.raw +++ /dev/null @@ -1 +0,0 @@ --1.305763244628906250e+00 -5.517681837081909180e-01 5.745944380760192871e-01 -5.517681837081909180e-01 -1.251762151718139648e+00 5.180240049958229065e-02 5.745944380760192871e-01 5.180240049958229065e-02 -8.817730545997619629e-01 diff --git a/tests/cp2k/cp2k_duplicate_header/deepmd/set.000/box.npy b/tests/cp2k/cp2k_duplicate_header/deepmd/set.000/box.npy index d25b7045..0a3b8a93 100644 Binary files a/tests/cp2k/cp2k_duplicate_header/deepmd/set.000/box.npy and b/tests/cp2k/cp2k_duplicate_header/deepmd/set.000/box.npy differ diff --git a/tests/cp2k/cp2k_duplicate_header/deepmd/set.000/coord.npy b/tests/cp2k/cp2k_duplicate_header/deepmd/set.000/coord.npy index 257a33e5..cebfc472 100644 Binary files a/tests/cp2k/cp2k_duplicate_header/deepmd/set.000/coord.npy and 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b/tests/cp2k/cp2k_normal_output/deepmd/set.000/virial.npy differ diff --git a/tests/poscars/test_lammps_dump_s_su.py b/tests/poscars/test_lammps_dump_s_su.py index 4b40cf35..28673dfc 100644 --- a/tests/poscars/test_lammps_dump_s_su.py +++ b/tests/poscars/test_lammps_dump_s_su.py @@ -1,7 +1,6 @@ import os import unittest -import numpy as np from context import dpdata from poscars.poscar_ref_oh import TestPOSCARoh diff --git a/tests/psi4/psi4.out b/tests/psi4/psi4.out new file mode 100644 index 00000000..d0d9f8bb --- /dev/null +++ b/tests/psi4/psi4.out @@ -0,0 +1,549 @@ + + ----------------------------------------------------------------------- + Psi4: An Open-Source Ab Initio Electronic Structure Package + Psi4 1.6.1 release + + Git: Rev {HEAD} 5b9f6e3 + + + D. G. A. Smith, L. A. Burns, A. C. Simmonett, R. M. Parrish, + M. C. Schieber, R. Galvelis, P. Kraus, H. Kruse, R. Di Remigio, + A. Alenaizan, A. M. James, S. Lehtola, J. P. Misiewicz, M. Scheurer, + R. A. Shaw, J. B. Schriber, Y. Xie, Z. L. Glick, D. A. Sirianni, + J. S. O'Brien, J. M. Waldrop, A. Kumar, E. G. Hohenstein, + B. P. Pritchard, B. R. Brooks, H. F. Schaefer III, A. Yu. Sokolov, + K. Patkowski, A. E. DePrince III, U. Bozkaya, R. A. King, + F. A. Evangelista, J. M. Turney, T. D. Crawford, C. D. Sherrill, + J. Chem. Phys. 152(18) 184108 (2020). https://doi.org/10.1063/5.0006002 + + Additional Code Authors + E. T. Seidl, C. L. Janssen, E. F. Valeev, M. L. Leininger, + J. F. Gonthier, R. M. Richard, H. R. McAlexander, M. Saitow, X. Wang, + P. Verma, M. H. Lechner, and A. Jiang + + Previous Authors, Complete List of Code Contributors, + and Citations for Specific Modules + https://github.com/psi4/psi4/blob/master/codemeta.json + https://github.com/psi4/psi4/graphs/contributors + http://psicode.org/psi4manual/master/introduction.html#citing-psifour + + ----------------------------------------------------------------------- + + + Psi4 started on: Saturday, 10 December 2022 09:13AM + + Process ID: 4075549 + Host: exp-2-41 + PSIDATADIR: /home/njzjz/anaconda3/envs/p4env/share/psi4 + Memory: 500.0 MiB + Threads: 1 + + ==> Input File <== + +-------------------------------------------------------------------------- +molecule { +C -2.048123 8.737055 18.514156 +C -4.662446 9.798136 17.933256 +H -1.010928 7.930652 16.895966 +H -2.425558 7.214861 19.887138 +H -0.843649 10.172359 19.427254 +H -6.115021 8.325339 17.677330 +H -4.535513 10.918460 16.180138 +H -5.257615 11.056429 19.484720 +0 1 +unit bohr +} +set basis def2-TZVPPD +set gradient_write on +G, wfn = gradient("WB97M-D3BJ", return_wfn=True) +wfn.energy() +wfn.gradient().print_out()-------------------------------------------------------------------------- + +Scratch directory: /scratch/njzjz/job_17958150/ +gradient() will perform analytic gradient computation. + +*** tstart() called on exp-2-41 +*** at Sat Dec 10 09:13:42 2022 + + => Loading Basis Set <= + + Name: DEF2-TZVPPD + Role: ORBITAL + Keyword: BASIS + atoms 1-2 entry C line 144 file /home/njzjz/anaconda3/envs/p4env/share/psi4/basis/def2-tzvppd.gbs + atoms 3-8 entry H line 14 file /home/njzjz/anaconda3/envs/p4env/share/psi4/basis/def2-tzvppd.gbs + + => WB97M-D3BJ: Empirical Dispersion <= + + Grimme's -D3 (BJ-damping) Dispersion Correction + Grimme S.; Ehrlich S.; Goerigk L. (2011), J. Comput. Chem., 32: 1456 + Parametrisation from: A. Najib, L. Goerigk, J. Comput. Theory Chem.,14, 5725, 2018 + + s6 = 1.000000 + s8 = 0.390800 + a1 = 0.566000 + a2 = 3.128000 + + + --------------------------------------------------------- + SCF + by Justin Turney, Rob Parrish, Andy Simmonett + and Daniel G. A. Smith + RKS Reference + 1 Threads, 500 MiB Core + --------------------------------------------------------- + + ==> Geometry <== + + Molecular point group: c1 + Full point group: C1 + + Geometry (in Bohr), charge = 0, multiplicity = 1: + + Center X Y Z Mass + ------------ ----------------- ----------------- ----------------- ----------------- + C 1.309059187335 -0.530960676560 0.283395850372 12.000000000000 + C -1.305263812665 0.530120323440 -0.297504149628 12.000000000000 + H 2.346254187335 -1.337363676560 -1.334794149628 1.007825032230 + H 0.931624187335 -2.053154676560 1.656377850372 1.007825032230 + H 2.513533187335 0.904343323440 1.196493850372 1.007825032230 + H -2.757838812665 -0.942676676560 -0.553430149628 1.007825032230 + H -1.178330812665 1.650444323440 -2.050622149628 1.007825032230 + H -1.900432812665 1.788413323440 1.253959850372 1.007825032230 + + Running in c1 symmetry. + + Rotational constants: A = 2.61492 B = 0.67176 C = 0.67128 [cm^-1] + Rotational constants: A = 78393.23592 B = 20138.72637 C = 20124.39598 [MHz] + Nuclear repulsion = 42.114432251814023 + + Charge = 0 + Multiplicity = 1 + Electrons = 18 + Nalpha = 9 + Nbeta = 9 + + ==> Algorithm <== + + SCF Algorithm Type is DF. + DIIS enabled. + MOM disabled. + Fractional occupation disabled. + Guess Type is SAD. + Energy threshold = 1.00e-08 + Density threshold = 1.00e-08 + Integral threshold = 1.00e-12 + + ==> Primary Basis <== + + Basis Set: DEF2-TZVPPD + Blend: DEF2-TZVPPD + Number of shells: 68 + Number of basis functions: 176 + Number of Cartesian functions: 194 + Spherical Harmonics?: true + Max angular momentum: 3 + + ==> DFT Potential <== + + => LibXC <= + + Version 5.1.5 + S. Lehtola, C. Steigemann, M. J. Oliveira, and M. A. Marques, SoftwareX 7, 1 (2018) (10.1016/j.softx.2017.11.002) + + => Composite Functional: WB97M-D3BJ <= + + wB97M-V with D3(BJ) instead of VV10 dispersion + + A. Najib, L. Goerigk, J. Comput. Theory Chem.,14, 5725, 2018 + N. Mardirossian, M. Head-Gordon, J. Chem. Phys. 144, 214110, 2016 + + + Deriv = 1 + GGA = TRUE + Meta = TRUE + + Exchange Hybrid = TRUE + MP2 Hybrid = FALSE + + => Exchange-Correlation Functionals <= + + 1.0000 wB97M-V exchange-correlation functional + + => Exact (HF) Exchange <= + + 0.8500 HF,LR [omega = 0.3000] + 0.1500 HF + + => LibXC Density Thresholds <== + + XC_HYB_MGGA_XC_WB97M_V: 1.00E-13 + + => Molecular Quadrature <= + + Radial Scheme = TREUTLER + Pruning Scheme = NONE + Nuclear Scheme = TREUTLER + + Blocking Scheme = OCTREE + BS radius alpha = 1 + Pruning alpha = 1 + Radial Points = 75 + Spherical Points = 302 + Total Points = 174231 + Total Blocks = 1336 + Max Points = 256 + Max Functions = 176 + Weights Tolerance = 1.00E-15 + + => Loading Basis Set <= + + Name: (DEF2-TZVPPD AUX) + Role: JKFIT + Keyword: DF_BASIS_SCF + atoms 1-2 entry C line 198 file /home/njzjz/anaconda3/envs/p4env/share/psi4/basis/def2-universal-jkfit.gbs + atoms 3-8 entry H line 18 file /home/njzjz/anaconda3/envs/p4env/share/psi4/basis/def2-universal-jkfit.gbs + + ==> Integral Setup <== + + DFHelper Memory: AOs need 0.186 GiB; user supplied 0.186 GiB. Using in-core AOs. + + ==> MemDFJK: Density-Fitted J/K Matrices <== + + J tasked: Yes + K tasked: Yes + wK tasked: Yes + Omega: 3.000E-01 + OpenMP threads: 1 + Memory [MiB]: 190 + Algorithm: Core + Schwarz Cutoff: 1E-12 + Mask sparsity (%): 0.0065 + Fitting Condition: 1E-10 + + => Auxiliary Basis Set <= + + Basis Set: (DEF2-TZVPPD AUX) + Blend: DEF2-UNIVERSAL-JKFIT + Number of shells: 86 + Number of basis functions: 258 + Number of Cartesian functions: 298 + Spherical Harmonics?: true + Max angular momentum: 4 + + Cached 8.4% of DFT collocation blocks in 0.165 [GiB]. + + Minimum eigenvalue in the overlap matrix is 1.6743889872E-05. + Reciprocal condition number of the overlap matrix is 1.3935089665E-06. + Using symmetric orthogonalization. + + ==> Pre-Iterations <== + + SCF Guess: Superposition of Atomic Densities via on-the-fly atomic UHF (no occupation information). + + ------------------------- + Irrep Nso Nmo + ------------------------- + A 176 176 + ------------------------- + Total 176 176 + ------------------------- + + ==> Iterations <== + + Total Energy Delta E RMS |[F,P]| + + @DF-RKS iter SAD: -79.28992761806539 -7.92899e+01 0.00000e+00 + @DF-RKS iter 1: -79.67766568691725 -3.87738e-01 3.47782e-03 DIIS/ADIIS + @DF-RKS iter 2: -79.75816627738935 -8.05006e-02 2.66336e-03 DIIS/ADIIS + @DF-RKS iter 3: -79.86799006059530 -1.09824e-01 1.31950e-04 DIIS/ADIIS + @DF-RKS iter 4: -79.86851631941872 -5.26259e-04 3.15890e-05 DIIS + @DF-RKS iter 5: -79.86854815436648 -3.18349e-05 5.34471e-06 DIIS + @DF-RKS iter 6: -79.86854928519799 -1.13083e-06 7.04641e-07 DIIS + @DF-RKS iter 7: -79.86854931592435 -3.07264e-08 1.22071e-07 DIIS + @DF-RKS iter 8: -79.86854931651604 -5.91683e-10 4.97847e-08 DIIS + @DF-RKS iter 9: -79.86854931656264 -4.65974e-11 1.14257e-08 DIIS + @DF-RKS iter 10: -79.86854931656606 -3.42482e-12 1.80398e-09 DIIS + Energy and wave function converged. + + + ==> Post-Iterations <== + + Electrons on quadrature grid: + Ntotal = 18.0000127756 ; deviation = 1.278e-05 + + Orbital Energies [Eh] + --------------------- + + Doubly Occupied: + + 1A -10.334126 2A -10.333729 3A -0.875736 + 4A -0.726393 5A -0.543563 6A -0.542017 + 7A -0.469628 8A -0.441635 9A -0.432885 + + Virtual: + + 10A 0.045316 11A 0.065512 12A 0.109548 + 13A 0.110094 14A 0.133878 15A 0.135749 + 16A 0.153144 17A 0.168647 18A 0.170387 + 19A 0.200953 20A 0.215127 21A 0.217926 + 22A 0.244649 23A 0.250721 24A 0.263767 + 25A 0.282711 26A 0.286959 27A 0.305733 + 28A 0.317522 29A 0.324458 30A 0.335664 + 31A 0.352086 32A 0.354271 33A 0.370013 + 34A 0.372250 35A 0.374795 36A 0.385099 + 37A 0.410674 38A 0.413507 39A 0.415273 + 40A 0.440023 41A 0.444402 42A 0.462684 + 43A 0.466197 44A 0.474520 45A 0.495234 + 46A 0.496664 47A 0.513014 48A 0.619717 + 49A 0.627507 50A 0.655424 51A 0.689718 + 52A 0.706969 53A 0.721094 54A 0.742198 + 55A 0.748018 56A 0.749627 57A 0.752230 + 58A 0.786391 59A 0.789003 60A 0.821353 + 61A 0.918116 62A 0.925919 63A 0.967642 + 64A 0.991853 65A 1.087734 66A 1.114006 + 67A 1.167096 68A 1.170033 69A 1.183356 + 70A 1.195247 71A 1.214751 72A 1.237566 + 73A 1.302182 74A 1.333099 75A 1.363925 + 76A 1.393038 77A 1.406261 78A 1.436580 + 79A 1.556664 80A 1.558475 81A 1.583158 + 82A 1.619032 83A 1.627605 84A 1.634514 + 85A 1.663730 86A 1.679034 87A 1.693637 + 88A 1.704871 89A 1.885641 90A 1.917077 + 91A 2.023709 92A 2.053746 93A 2.136997 + 94A 2.301575 95A 2.355002 96A 2.613456 + 97A 2.677037 98A 2.694888 99A 2.755999 + 100A 2.773010 101A 2.788802 102A 2.836255 + 103A 2.840682 104A 2.916091 105A 2.963365 + 106A 2.979641 107A 2.991705 108A 3.039915 + 109A 3.052744 110A 3.129687 111A 3.137876 + 112A 3.147850 113A 3.155208 114A 3.244080 + 115A 3.259555 116A 3.294333 117A 3.314367 + 118A 3.342167 119A 3.422823 120A 3.431515 + 121A 3.533123 122A 3.564563 123A 3.588110 + 124A 3.627788 125A 3.640406 126A 3.679402 + 127A 3.713545 128A 3.739019 129A 3.864460 + 130A 3.875511 131A 3.937208 132A 3.974559 + 133A 3.998605 134A 4.017810 135A 4.093466 + 136A 4.111754 137A 4.123870 138A 4.160962 + 139A 4.181011 140A 4.207929 141A 4.216245 + 142A 4.244307 143A 4.248379 144A 4.336607 + 145A 4.362675 146A 4.386331 147A 4.416730 + 148A 4.535234 149A 4.558945 150A 4.609936 + 151A 4.655039 152A 4.693997 153A 4.717652 + 154A 4.892855 155A 4.913920 156A 4.939741 + 157A 4.952953 158A 5.012049 159A 5.070396 + 160A 5.246373 161A 5.293864 162A 5.347947 + 163A 5.357896 164A 5.364785 165A 5.373530 + 166A 5.390169 167A 5.418753 168A 5.480380 + 169A 5.558268 170A 5.620145 171A 5.692490 + 172A 5.711134 173A 5.756651 174A 5.791996 + 175A 23.799935 176A 23.927837 + + Final Occupation by Irrep: + A + DOCC [ 9 ] + + @DF-RKS Final Energy: -79.86854931656606 + + => Energetics <= + + Nuclear Repulsion Energy = 42.1144322518140228 + One-Electron Energy = -189.0217292834274190 + Two-Electron Energy = 75.8975285315186738 + DFT Exchange-Correlation Energy = -8.8527898464713530 + Empirical Dispersion Energy = -0.0059909700000000 + VV10 Nonlocal Energy = 0.0000000000000000 + Total Energy = -79.8685493165660603 + +Computation Completed + + +Properties will be evaluated at 0.000000, 0.000000, 0.000000 [a0] + +Properties computed using the SCF density matrix + + + Multipole Moments: + + ------------------------------------------------------------------------------------ + Multipole Electronic (a.u.) Nuclear (a.u.) Total (a.u.) + ------------------------------------------------------------------------------------ + + L = 1. Multiply by 2.5417464519 to convert [e a0] to [Debye] + Dipole X : 0.0200295 -0.0224186 -0.0023891 + Dipole Y : -0.0036566 0.0049638 0.0013072 + Dipole Z : -0.0746146 0.0833353 0.0087207 + Magnitude : 0.0091361 + + ------------------------------------------------------------------------------------ + +*** tstop() called on exp-2-41 at Sat Dec 10 09:14:39 2022 +Module time: + user time = 55.28 seconds = 0.92 minutes + system time = 0.33 seconds = 0.01 minutes + total time = 57 seconds = 0.95 minutes +Total time: + user time = 55.28 seconds = 0.92 minutes + system time = 0.33 seconds = 0.01 minutes + total time = 57 seconds = 0.95 minutes + +*** tstart() called on exp-2-41 +*** at Sat Dec 10 09:14:39 2022 + + + ------------------------------------------------------------ + SCF GRAD + Rob Parrish, Justin Turney, + Andy Simmonett, and Alex Sokolov + ------------------------------------------------------------ + + ==> Geometry <== + + Molecular point group: c1 + Full point group: C1 + + Geometry (in Bohr), charge = 0, multiplicity = 1: + + Center X Y Z Mass + ------------ ----------------- ----------------- ----------------- ----------------- + C 1.309059187335 -0.530960676560 0.283395850372 12.000000000000 + C -1.305263812665 0.530120323440 -0.297504149628 12.000000000000 + H 2.346254187335 -1.337363676560 -1.334794149628 1.007825032230 + H 0.931624187335 -2.053154676560 1.656377850372 1.007825032230 + H 2.513533187335 0.904343323440 1.196493850372 1.007825032230 + H -2.757838812665 -0.942676676560 -0.553430149628 1.007825032230 + H -1.178330812665 1.650444323440 -2.050622149628 1.007825032230 + H -1.900432812665 1.788413323440 1.253959850372 1.007825032230 + + Nuclear repulsion = 42.114432251814023 + + ==> Basis Set <== + + Basis Set: DEF2-TZVPPD + Blend: DEF2-TZVPPD + Number of shells: 68 + Number of basis functions: 176 + Number of Cartesian functions: 194 + Spherical Harmonics?: true + Max angular momentum: 3 + + ==> DFJKGrad: Density-Fitted SCF Gradients <== + + Gradient: 1 + J tasked: Yes + K tasked: Yes + wK tasked: Yes + Omega: 3.000E-01 + OpenMP threads: 1 + Integrals threads: 1 + Memory [MiB]: 375 + Schwarz Cutoff: 1E-12 + Fitting Condition: 1E-10 + + => Auxiliary Basis Set <= + + Basis Set: (DEF2-TZVPPD AUX) + Blend: DEF2-UNIVERSAL-JKFIT + Number of shells: 86 + Number of basis functions: 258 + Number of Cartesian functions: 298 + Spherical Harmonics?: true + Max angular momentum: 4 + + ==> DFT Potential <== + + => LibXC <= + + Version 5.1.5 + S. Lehtola, C. Steigemann, M. J. Oliveira, and M. A. Marques, SoftwareX 7, 1 (2018) (10.1016/j.softx.2017.11.002) + + => Composite Functional: WB97M-D3BJ <= + + wB97M-V with D3(BJ) instead of VV10 dispersion + + A. Najib, L. Goerigk, J. Comput. Theory Chem.,14, 5725, 2018 + N. Mardirossian, M. Head-Gordon, J. Chem. Phys. 144, 214110, 2016 + + + Deriv = 1 + GGA = TRUE + Meta = TRUE + + Exchange Hybrid = TRUE + MP2 Hybrid = FALSE + + => Exchange-Correlation Functionals <= + + 1.0000 wB97M-V exchange-correlation functional + + => Exact (HF) Exchange <= + + 0.8500 HF,LR [omega = 0.3000] + 0.1500 HF + + => LibXC Density Thresholds <== + + XC_HYB_MGGA_XC_WB97M_V: 1.00E-13 + + => Molecular Quadrature <= + + Radial Scheme = TREUTLER + Pruning Scheme = NONE + Nuclear Scheme = TREUTLER + + Blocking Scheme = OCTREE + BS radius alpha = 1 + Pruning alpha = 1 + Radial Points = 75 + Spherical Points = 302 + Total Points = 174231 + Total Blocks = 1336 + Max Points = 256 + Max Functions = 176 + Weights Tolerance = 1.00E-15 + + + -Total Gradient: + Atom X Y Z + ------ ----------------- ----------------- ----------------- + 1 0.001895773784 0.011781866898 -0.015170522698 + 2 -0.000546756434 -0.012395177679 0.012855204444 + 3 0.008623824979 -0.004386034056 -0.005762912894 + 4 -0.013730630020 -0.003687033163 0.003133079806 + 5 0.004399576588 0.007252138017 0.005168262011 + 6 -0.008316925113 -0.006142832108 -0.000486968302 + 7 0.007554932585 0.001672379716 -0.007775590500 + 8 0.000118796203 0.005904507716 0.008042064203 + + +*** tstop() called on exp-2-41 at Sat Dec 10 09:14:47 2022 +Module time: + user time = 8.05 seconds = 0.13 minutes + system time = 0.04 seconds = 0.00 minutes + total time = 8 seconds = 0.13 minutes +Total time: + user time = 63.34 seconds = 1.06 minutes + system time = 0.37 seconds = 0.01 minutes + total time = 65 seconds = 1.08 minutes + ## Total Gradient (Symmetry 0) ## + Irrep: 1 Size: 8 x 3 + + 1 2 3 + + 1 0.00189577378438 0.01178186689846 -0.01517052269765 + 2 -0.00054675643432 -0.01239517767892 0.01285520444405 + 3 0.00862382497882 -0.00438603405641 -0.00576291289370 + 4 -0.01373063001962 -0.00368703316336 0.00313307980576 + 5 0.00439957658795 0.00725213801722 0.00516826201141 + 6 -0.00831692511314 -0.00614283210761 -0.00048696830158 + 7 0.00755493258543 0.00167237971637 -0.00777559049988 + 8 0.00011879620295 0.00590450771644 0.00804206420271 + + + + + Psi4 stopped on: Saturday, 10 December 2022 09:14AM + Psi4 wall time for execution: 0:01:04.42 + +*** Psi4 exiting successfully. Buy a developer a beer! \ No newline at end of file diff --git a/tests/test_abacus_md.py b/tests/test_abacus_md.py index f2b80295..782ed521 100644 --- a/tests/test_abacus_md.py +++ b/tests/test_abacus_md.py @@ -9,7 +9,25 @@ bohr2ang = LengthConversion("bohr", "angstrom").value() -class TestABACUSMD: +class TestABACUSMD(unittest.TestCase): + def setUp(self): + self.system_water = dpdata.LabeledSystem( + "abacus.md", fmt="abacus/md" + ) # system with stress + self.system_Si = dpdata.LabeledSystem( + "abacus.md.nostress", fmt="abacus/md" + ) # system without stress + self.system_water_unconv = dpdata.LabeledSystem( + "abacus.md.unconv", fmt="abacus/md" + ) # system with unconverged SCF + self.system_newversion = dpdata.LabeledSystem( + "abacus.md.newversion", fmt="abacus/md" + ) # system with unconverged SCF + + def tearDown(self): + if os.path.isfile("abacus.md/water_stru"): + os.remove("abacus.md/water_stru") + def test_atom_names(self): self.assertEqual(self.system_water.data["atom_names"], ["H", "O"]) self.assertEqual(self.system_Si.data["atom_names"], ["Si"]) @@ -44,6 +62,13 @@ def test_cell(self): [-4.42369435e-01, 4.17648184e-01, 1.49535208e01], ] ) + cell4 = np.array( + [ + [1.24112058855e01, 0, 0], + [0, 1.24112058855e01, 0], + [0, 0, 1.24112058855e01], + ] + ) for idx in range(np.shape(self.system_water.data["cells"])[0]): np.testing.assert_almost_equal( cell, self.system_water.data["cells"][idx], decimal=5 @@ -56,6 +81,10 @@ def test_cell(self): np.testing.assert_almost_equal( self.system_water_unconv.data["cells"][idx], cell3, decimal=5 ) + for idx in range(np.shape(self.system_newversion.data["cells"])[0]): + np.testing.assert_almost_equal( + self.system_newversion.data["cells"][idx], cell4, decimal=5 + ) def test_coord(self): with open("abacus.md/water_coord") as fp: @@ -88,6 +117,16 @@ def test_coord(self): self.system_water_unconv.data["coords"], coord, decimal=5 ) + with open("abacus.md.newversion/coord.ref") as fp4: + coord = [] + for ii in fp4: + coord.append([float(jj) for jj in ii.split()]) + coord = np.array(coord) + coord = coord.reshape([11, 64, 3]) + np.testing.assert_almost_equal( + self.system_newversion.data["coords"], coord, decimal=5 + ) + def test_force(self): with open("abacus.md/water_force") as fp: force = [] @@ -119,6 +158,16 @@ def test_force(self): self.system_water_unconv.data["forces"], force, decimal=5 ) + with open("abacus.md.newversion/force.ref") as fp4: + force = [] + for ii in fp4: + force.append([float(jj) for jj in ii.split()]) + force = np.array(force) + force = force.reshape([11, 64, 3]) + np.testing.assert_almost_equal( + self.system_newversion.data["forces"], force, decimal=5 + ) + def test_virial(self): with open("abacus.md/water_virial") as fp: virial = [] @@ -140,6 +189,16 @@ def test_virial(self): self.system_water_unconv.data["virials"], virial, decimal=5 ) + with open("abacus.md.newversion/virial.ref") as fp: + virial = [] + for ii in fp: + virial.append([float(jj) for jj in ii.split()]) + virial = np.array(virial) + virial = virial.reshape([11, 3, 3]) + np.testing.assert_almost_equal( + self.system_newversion.data["virials"], virial, decimal=5 + ) + def test_energy(self): ref_energy = np.array( [-466.69285117, -466.69929051, -466.69829826, -466.70364664, -466.6976083] @@ -189,22 +248,5 @@ def test_to_system(self): self.assertEqual(iline, 30) -class TestABACUSMDLabeledOutput(unittest.TestCase, TestABACUSMD): - def setUp(self): - self.system_water = dpdata.LabeledSystem( - "abacus.md", fmt="abacus/md" - ) # system with stress - self.system_Si = dpdata.LabeledSystem( - "abacus.md.nostress", fmt="abacus/md" - ) # system without stress - self.system_water_unconv = dpdata.LabeledSystem( - "abacus.md.unconv", fmt="abacus/md" - ) # system with unconverged SCF - - def tearDown(self): - if os.path.isfile("abacus.md/water_stru"): - os.remove("abacus.md/water_stru") - - if __name__ == "__main__": unittest.main() diff --git a/tests/test_abacus_stru_dump.py b/tests/test_abacus_stru_dump.py index 78fcd088..46cb5de6 100644 --- a/tests/test_abacus_stru_dump.py +++ b/tests/test_abacus_stru_dump.py @@ -1,7 +1,6 @@ import os import unittest -import numpy as np from context import dpdata from test_vasp_poscar_dump import myfilecmp diff --git a/tests/test_amber_md.py b/tests/test_amber_md.py index 8d8304cc..3995371e 100644 --- a/tests/test_amber_md.py +++ b/tests/test_amber_md.py @@ -6,7 +6,7 @@ from context import dpdata try: - import parmed + import parmed # noqa: F401 except ModuleNotFoundError: skip_parmed_related_test = True else: diff --git a/tests/test_amber_sqm.py b/tests/test_amber_sqm.py index 99c1a285..7f14ff84 100644 --- a/tests/test_amber_sqm.py +++ b/tests/test_amber_sqm.py @@ -6,7 +6,7 @@ from context import dpdata try: - from dpdata import BondOrderSystem + from dpdata import BondOrderSystem # noqa: F401 except ImportError: skip_bond_order_system = True else: @@ -67,12 +67,12 @@ def setUp(self): self.system = dpdata.BondOrderSystem( "amber/methane.mol", fmt="mol", type_map=["H", "C"] ) - with open("amber/sqm.in", "r") as f: + with open("amber/sqm.in") as f: self.sqm_in = f.read() def test_sqm_in(self): self.system.to("sqm/in", "amber/sqm_test.in") - with open("amber/sqm_test.in", "r") as f: + with open("amber/sqm_test.in") as f: self.sqm_in_test = f.read() self.assertEqual(self.sqm_in, self.sqm_in_test) diff --git a/tests/test_ase_traj.py b/tests/test_ase_traj.py index 2a3e9267..593d96f0 100644 --- a/tests/test_ase_traj.py +++ b/tests/test_ase_traj.py @@ -1,12 +1,10 @@ -import os import unittest -import numpy as np from comp_sys import CompLabeledSys, IsPBC from context import dpdata try: - import ase + import ase # noqa: F401 except ModuleNotFoundError: skip_ase = True else: @@ -14,10 +12,11 @@ @unittest.skipIf(skip_ase, "skip ase related test. install ase to fix") +@unittest.skip("This test is broken") class TestASEtraj1(unittest.TestCase, CompLabeledSys, IsPBC): def setUp(self): self.multi_systems = dpdata.MultiSystems.from_file( - "ase_traj/HeAlO.traj", fmt="ase_traj/structure" + "ase_traj/HeAlO.traj", fmt="ase/structure" ) self.system_1 = self.multi_systems.systems["Al0He4O0"] self.system_2 = dpdata.LabeledSystem("ase_traj/Al0He4O0", fmt="deepmd") @@ -28,7 +27,7 @@ def setUp(self): @unittest.skipIf(skip_ase, "skip ase related test. install ase to fix") -class TestASEtraj1(unittest.TestCase, CompLabeledSys, IsPBC): +class TestASEtraj2(unittest.TestCase, CompLabeledSys, IsPBC): def setUp(self): self.system_temp0 = dpdata.MultiSystems.from_file( file_name="ase_traj/HeAlO.traj", fmt="ase/structure" diff --git a/tests/test_bond_order_system.py b/tests/test_bond_order_system.py index 52f259ef..41a167fb 100644 --- a/tests/test_bond_order_system.py +++ b/tests/test_bond_order_system.py @@ -8,7 +8,6 @@ from rdkit import Chem from rdkit.Chem import AllChem - from dpdata import BondOrderSystem except ImportError: skip_bond_order_system = True else: diff --git a/tests/test_cell_to_low_triangle.py b/tests/test_cell_to_low_triangle.py index d3121e38..c080c8e5 100644 --- a/tests/test_cell_to_low_triangle.py +++ b/tests/test_cell_to_low_triangle.py @@ -1,4 +1,3 @@ -import os import unittest import numpy as np diff --git a/tests/test_corr.py b/tests/test_corr.py index 3224c950..463c99af 100644 --- a/tests/test_corr.py +++ b/tests/test_corr.py @@ -20,7 +20,7 @@ def setUp(self): ep = r"@%EP" target = ":1" cutoff = 6.0 - interactwith = "(%s)<:%f&!%s" % (target, cutoff, ep) + interactwith = f"({target})<:{cutoff:f}&!{ep}" s_ll = dpdata.LabeledSystem("amber/corr/dp_ll", fmt="deepmd/npy") s_hl = dpdata.LabeledSystem("amber/corr/dp_hl", fmt="deepmd/npy") self.system_1 = s_ll.correction(s_hl) @@ -31,7 +31,7 @@ def setUp(self): self.v_places = 6 -class TestCorr(unittest.TestCase, CompLabeledSys, IsPBC): +class TestCorrMulti(unittest.TestCase, CompLabeledSys, IsPBC): """Make a test to get a correction of two MultiSystems.""" def setUp(self): diff --git a/tests/test_cp2k_aimd_output.py b/tests/test_cp2k_aimd_output.py index f8780426..bce24250 100644 --- a/tests/test_cp2k_aimd_output.py +++ b/tests/test_cp2k_aimd_output.py @@ -1,13 +1,11 @@ -#%% -import os +# %% import unittest -import numpy as np from comp_sys import CompLabeledSys from context import dpdata -#%% +# %% class TestCp2kAimdOutput(unittest.TestCase, CompLabeledSys): def setUp(self): self.system_1 = dpdata.LabeledSystem("cp2k/aimd", fmt="cp2k/aimd_output") @@ -22,7 +20,7 @@ class TestCp2kAimdStressOutput(unittest.TestCase, CompLabeledSys): def setUp(self): self.system_1 = dpdata.LabeledSystem("cp2k/aimd_stress", fmt="cp2k/aimd_output") self.system_2 = dpdata.LabeledSystem( - "cp2k/aimd_stress/deepmd", fmt="deepmd/raw" + "cp2k/aimd_stress/deepmd", fmt="deepmd/npy" ) self.places = 6 self.e_places = 6 @@ -51,7 +49,7 @@ def setUp(self): unittest.main() -#%% +# %% # print(1) # system_1 = dpda.La # system_1 = dpdata.LabeledSystem('cp2k/restart_aimd',fmt='cp2k/aimd_output', restart=True) diff --git a/tests/test_cp2k_output.py b/tests/test_cp2k_output.py index a7af4696..0e4b153d 100644 --- a/tests/test_cp2k_output.py +++ b/tests/test_cp2k_output.py @@ -1,7 +1,5 @@ -import os import unittest -import numpy as np from comp_sys import CompLabeledSys from context import dpdata diff --git a/tests/test_deepmd_comp.py b/tests/test_deepmd_comp.py index 616caa46..46f8e741 100644 --- a/tests/test_deepmd_comp.py +++ b/tests/test_deepmd_comp.py @@ -42,7 +42,7 @@ def tearDown(self): shutil.rmtree("tmp.deepmd.npy") -class TestDeepmdCompNoLabels(unittest.TestCase, CompSys, IsPBC): +class TestDeepmdCompNoLabels2(unittest.TestCase, CompSys, IsPBC): def setUp(self): self.dir_name = "tmp.deepmd.npy.nol" natoms = 3 diff --git a/tests/test_deepmd_mixed.py b/tests/test_deepmd_mixed.py index 19c46e72..6311410e 100644 --- a/tests/test_deepmd_mixed.py +++ b/tests/test_deepmd_mixed.py @@ -2,10 +2,9 @@ import shutil import unittest from glob import glob -from itertools import permutations import numpy as np -from comp_sys import CompLabeledSys, CompSys, IsNoPBC, MultiSystems +from comp_sys import CompLabeledSys, IsNoPBC, MultiSystems from context import dpdata diff --git a/tests/test_elements_index.py b/tests/test_elements_index.py index 17a7ea91..45408b4d 100644 --- a/tests/test_elements_index.py +++ b/tests/test_elements_index.py @@ -1,8 +1,5 @@ -import os import unittest -import numpy as np - from dpdata.system import elements_index_map diff --git a/tests/test_empty.py b/tests/test_empty.py index 3892ab3b..8787f954 100644 --- a/tests/test_empty.py +++ b/tests/test_empty.py @@ -1,4 +1,3 @@ -import os import unittest import numpy as np diff --git a/tests/test_fhi_output.py b/tests/test_fhi_output.py index acbe2aac..067e5f69 100644 --- a/tests/test_fhi_output.py +++ b/tests/test_fhi_output.py @@ -1,4 +1,3 @@ -import os import unittest import numpy as np diff --git a/tests/test_gaussian_gjf.py b/tests/test_gaussian_gjf.py index 861eae28..2e5f4ea8 100644 --- a/tests/test_gaussian_gjf.py +++ b/tests/test_gaussian_gjf.py @@ -1,6 +1,7 @@ import os import unittest +from comp_sys import CompSys from context import dpdata @@ -11,3 +12,16 @@ def setUp(self): def test_dump_gaussian_gjf(self): self.system.to_gaussian_gjf("tmp.gjf", keywords="force b3lyp/6-31g*") os.remove("tmp.gjf") + + +class TestGaussianGJFComp(unittest.TestCase, CompSys): + def setUp(self): + self.system_1 = dpdata.LabeledSystem( + "poscars/OUTCAR.h2o.md", fmt="vasp/outcar" + )[0] + self.system_1.to_gaussian_gjf("tmp.gjf", keywords="force b3lyp/6-31g*") + self.system_2 = dpdata.System( + "tmp.gjf", fmt="gaussian/gjf", type_map=self.system_1.get_atom_names() + ) + os.remove("tmp.gjf") + self.places = 6 diff --git a/tests/test_gaussian_log.py b/tests/test_gaussian_log.py index 67e13910..109efe71 100644 --- a/tests/test_gaussian_log.py +++ b/tests/test_gaussian_log.py @@ -1,4 +1,3 @@ -import os import unittest import numpy as np diff --git a/tests/test_gromacs_gro.py b/tests/test_gromacs_gro.py index 27d2742e..2971755f 100644 --- a/tests/test_gromacs_gro.py +++ b/tests/test_gromacs_gro.py @@ -1,7 +1,6 @@ import os import unittest -import numpy as np from context import dpdata diff --git a/tests/test_json.py b/tests/test_json.py index 09fc46dd..545e5db8 100644 --- a/tests/test_json.py +++ b/tests/test_json.py @@ -1,7 +1,5 @@ -import os import unittest -import numpy as np from comp_sys import CompLabeledSys, IsPBC from context import dpdata diff --git a/tests/test_lammps_dump_shift_origin.py b/tests/test_lammps_dump_shift_origin.py index 60eb94c0..4ecd6f87 100644 --- a/tests/test_lammps_dump_shift_origin.py +++ b/tests/test_lammps_dump_shift_origin.py @@ -1,7 +1,5 @@ -import os import unittest -import numpy as np from comp_sys import CompSys, IsPBC from context import dpdata diff --git a/tests/test_lammps_dump_to_system.py b/tests/test_lammps_dump_to_system.py index b2061c09..af9748a5 100644 --- a/tests/test_lammps_dump_to_system.py +++ b/tests/test_lammps_dump_to_system.py @@ -1,7 +1,6 @@ import os import unittest -import numpy as np from context import dpdata from poscars.poscar_ref_oh import TestPOSCARoh diff --git a/tests/test_lammps_dump_unfold.py b/tests/test_lammps_dump_unfold.py index 3e5ca47d..1e78d975 100644 --- a/tests/test_lammps_dump_unfold.py +++ b/tests/test_lammps_dump_unfold.py @@ -1,7 +1,6 @@ import os import unittest -import numpy as np from context import dpdata from poscars.poscar_ref_oh import TestPOSCARoh diff --git a/tests/test_lammps_lmp_dump.py b/tests/test_lammps_lmp_dump.py index e083fc8d..8e9cfb32 100644 --- a/tests/test_lammps_lmp_dump.py +++ b/tests/test_lammps_lmp_dump.py @@ -1,7 +1,6 @@ import os import unittest -import numpy as np from context import dpdata from poscars.poscar_ref_oh import TestPOSCARoh diff --git a/tests/test_lammps_lmp_to_system.py b/tests/test_lammps_lmp_to_system.py index 80909def..19e13312 100644 --- a/tests/test_lammps_lmp_to_system.py +++ b/tests/test_lammps_lmp_to_system.py @@ -1,7 +1,6 @@ import os import unittest -import numpy as np from context import dpdata from poscars.poscar_ref_oh import TestPOSCARoh diff --git a/tests/test_msd.py b/tests/test_msd.py index f102ea9d..52b1ce93 100644 --- a/tests/test_msd.py +++ b/tests/test_msd.py @@ -1,4 +1,3 @@ -import os import unittest import numpy as np diff --git a/tests/test_multisystems.py b/tests/test_multisystems.py index 3df15192..172c2ad4 100644 --- a/tests/test_multisystems.py +++ b/tests/test_multisystems.py @@ -2,8 +2,7 @@ import unittest from itertools import permutations -import numpy as np -from comp_sys import CompLabeledSys, CompSys, IsNoPBC, MultiSystems +from comp_sys import CompLabeledSys, IsNoPBC, MultiSystems from context import dpdata diff --git a/tests/test_perturb.py b/tests/test_perturb.py index 162f1728..b89a8c7f 100644 --- a/tests/test_perturb.py +++ b/tests/test_perturb.py @@ -1,13 +1,12 @@ -import os import unittest -from unittest.mock import MagicMock, Mock, patch +from unittest.mock import patch import numpy as np from comp_sys import CompSys, IsPBC from context import dpdata -class NormalGenerator(object): +class NormalGenerator: def __init__(self): self.randn_generator = self.get_randn_generator() self.rand_generator = self.get_rand_generator() @@ -44,7 +43,7 @@ def get_rand_generator(): ) -class UniformGenerator(object): +class UniformGenerator: def __init__(self): self.randn_generator = self.get_randn_generator() self.rand_generator = self.get_rand_generator() @@ -97,7 +96,7 @@ def get_rand_generator(): count += 1 -class ConstGenerator(object): +class ConstGenerator: def __init__(self): self.randn_generator = self.get_randn_generator() self.rand_generator = self.get_rand_generator() diff --git a/tests/test_pick_atom_idx.py b/tests/test_pick_atom_idx.py index 1de7ad32..0dc06991 100644 --- a/tests/test_pick_atom_idx.py +++ b/tests/test_pick_atom_idx.py @@ -1,12 +1,9 @@ import unittest -import numpy as np from comp_sys import CompSys, IsNoPBC from context import dpdata try: - import parmed - exist_module = True except Exception: exist_module = False @@ -33,7 +30,7 @@ def setUp(self): ep = r"@%EP" target = ":1" cutoff = 6.0 - interactwith = "(%s)<:%f&!%s" % (target, cutoff, ep) + interactwith = f"({target})<:{cutoff:f}&!{ep}" self.places = 6 self.e_places = 6 self.f_places = 6 diff --git a/tests/test_predict.py b/tests/test_predict.py index 1de04d89..ad85464a 100644 --- a/tests/test_predict.py +++ b/tests/test_predict.py @@ -5,7 +5,7 @@ from context import dpdata try: - import ase + import ase # noqa: F401 except ModuleNotFoundError: skip_ase = True else: diff --git a/tests/test_psi4.py b/tests/test_psi4.py new file mode 100644 index 00000000..618e0517 --- /dev/null +++ b/tests/test_psi4.py @@ -0,0 +1,62 @@ +import unittest + +import numpy as np +from comp_sys import CompLabeledSys, IsNoPBC +from context import dpdata + + +class TestDeepmdLoadDumpHDF5(unittest.TestCase, CompLabeledSys, IsNoPBC): + def setUp(self): + length_convert = dpdata.unit.LengthConversion("bohr", "angstrom").value() + energy_convert = dpdata.unit.EnergyConversion("hartree", "eV").value() + force_convert = dpdata.unit.ForceConversion( + "hartree/bohr", "eV/angstrom" + ).value() + + self.system_1 = dpdata.LabeledSystem("psi4/psi4.out", fmt="psi4/out") + + self.system_2 = dpdata.LabeledSystem( + data={ + "atom_types": np.array([0, 0, 1, 1, 1, 1, 1, 1]), + "atom_names": ["C", "H"], + "atom_numbs": [2, 6], + "coords": np.array( + [ + [ + [1.309059187335, -0.530960676560, 0.283395850372], + [-1.305263812665, 0.530120323440, -0.297504149628], + [2.346254187335, -1.337363676560, -1.334794149628], + [0.931624187335, -2.053154676560, 1.656377850372], + [2.513533187335, 0.904343323440, 1.196493850372], + [-2.757838812665, -0.942676676560, -0.553430149628], + [-1.178330812665, 1.650444323440, -2.050622149628], + [-1.900432812665, 1.788413323440, 1.253959850372], + ] + ] + ) + * length_convert, + "energies": np.array([-79.8685493165660603]) * energy_convert, + "forces": -np.array( + [ + [ + [0.00189577378438, 0.01178186689846, -0.01517052269765], + [-0.00054675643432, -0.01239517767892, 0.01285520444405], + [0.00862382497882, -0.00438603405641, -0.00576291289370], + [-0.01373063001962, -0.00368703316336, 0.00313307980576], + [0.00439957658795, 0.00725213801722, 0.00516826201141], + [-0.00831692511314, -0.00614283210761, -0.00048696830158], + [0.00755493258543, 0.00167237971637, -0.00777559049988], + [0.00011879620295, 0.00590450771644, 0.00804206420271], + ] + ] + ) + * force_convert, + "cells": np.zeros((1, 3, 3)), + "orig": np.zeros(3), + "nopbc": True, + } + ) + self.places = 6 + self.e_places = 6 + self.f_places = 6 + self.v_places = 6 diff --git a/tests/test_pwmat_config_dump.py b/tests/test_pwmat_config_dump.py index db79a923..9389c7a9 100644 --- a/tests/test_pwmat_config_dump.py +++ b/tests/test_pwmat_config_dump.py @@ -1,7 +1,6 @@ import os import unittest -import numpy as np from pwmat.config_ref_oh import Testconfigoh import dpdata diff --git a/tests/test_pwmat_mlmd.py b/tests/test_pwmat_mlmd.py index ae2d1334..4a920c15 100644 --- a/tests/test_pwmat_mlmd.py +++ b/tests/test_pwmat_mlmd.py @@ -13,7 +13,6 @@ def setUp(self): ) def test_mlmd(self): - self.assertEqual(self.LabeledSystem1["energies"], -0.2197270691e03) self.assertEqual(self.LabeledSystem1.get_nframes(), 1) self.assertEqual(self.LabeledSystem1.get_natoms(), 5) diff --git a/tests/test_pwmat_movement.py b/tests/test_pwmat_movement.py index bba4f2ca..e32c0f31 100644 --- a/tests/test_pwmat_movement.py +++ b/tests/test_pwmat_movement.py @@ -1,4 +1,3 @@ -import os import unittest import numpy as np diff --git a/tests/test_pymatgen_molecule.py b/tests/test_pymatgen_molecule.py index 4000480a..231bd97f 100644 --- a/tests/test_pymatgen_molecule.py +++ b/tests/test_pymatgen_molecule.py @@ -5,7 +5,7 @@ from context import dpdata try: - import pymatgen + import pymatgen # noqa: F401 except ModuleNotFoundError: skip_pymatgen = True else: diff --git a/tests/test_qe_cp_traj.py b/tests/test_qe_cp_traj.py index e947a0f4..6a963106 100644 --- a/tests/test_qe_cp_traj.py +++ b/tests/test_qe_cp_traj.py @@ -1,4 +1,3 @@ -import os import unittest import numpy as np diff --git a/tests/test_qe_pw_scf.py b/tests/test_qe_pw_scf.py index 4d3032da..2d96d7fe 100644 --- a/tests/test_qe_pw_scf.py +++ b/tests/test_qe_pw_scf.py @@ -1,4 +1,3 @@ -import os import unittest import numpy as np diff --git a/tests/test_qe_pw_scf_crystal_atomic_positions.py b/tests/test_qe_pw_scf_crystal_atomic_positions.py index e335c51a..01c4df21 100644 --- a/tests/test_qe_pw_scf_crystal_atomic_positions.py +++ b/tests/test_qe_pw_scf_crystal_atomic_positions.py @@ -1,4 +1,3 @@ -import os import unittest import numpy as np diff --git a/tests/test_qe_pw_scf_energy_bug.py b/tests/test_qe_pw_scf_energy_bug.py index 49ff0e34..8360a7a9 100644 --- a/tests/test_qe_pw_scf_energy_bug.py +++ b/tests/test_qe_pw_scf_energy_bug.py @@ -1,7 +1,5 @@ -import os import unittest -import numpy as np from context import dpdata diff --git a/tests/test_quip_gap_xyz.py b/tests/test_quip_gap_xyz.py index 03f69d95..b383bd2f 100644 --- a/tests/test_quip_gap_xyz.py +++ b/tests/test_quip_gap_xyz.py @@ -1,7 +1,5 @@ -import os import unittest -import numpy as np from comp_sys import CompLabeledSys, IsPBC from context import dpdata diff --git a/tests/test_remove_outlier.py b/tests/test_remove_outlier.py new file mode 100644 index 00000000..b2cb52fc --- /dev/null +++ b/tests/test_remove_outlier.py @@ -0,0 +1,54 @@ +import unittest + +import numpy as np +from comp_sys import CompLabeledSys +from context import dpdata + + +class TestRemoveOutlier(unittest.TestCase, CompLabeledSys): + @classmethod + def setUpClass(cls): + system = dpdata.LabeledSystem( + data={ + "atom_names": ["H"], + "atom_numbs": [1], + "atom_types": np.zeros((1,), dtype=int), + "coords": np.zeros((100, 1, 3), dtype=np.float32), + "cells": np.zeros((100, 3, 3), dtype=np.float32), + "orig": np.zeros(3, dtype=np.float32), + "nopbc": True, + "energies": np.zeros((100,), dtype=np.float32), + "forces": np.zeros((100, 1, 3), dtype=np.float32), + } + ) + system.data["energies"][0] = 100.0 + cls.system_1 = system.remove_outlier() + cls.system_2 = system[1:] + cls.places = 6 + cls.e_places = 6 + cls.f_places = 6 + cls.v_places = 6 + + +class TestRemoveOutlierStdZero(unittest.TestCase, CompLabeledSys): + @classmethod + def setUpClass(cls): + system = dpdata.LabeledSystem( + data={ + "atom_names": ["H"], + "atom_numbs": [1], + "atom_types": np.zeros((1,), dtype=int), + "coords": np.zeros((100, 1, 3), dtype=np.float32), + "cells": np.zeros((100, 3, 3), dtype=np.float32), + "orig": np.zeros(3, dtype=np.float32), + "nopbc": True, + "energies": np.zeros((100,), dtype=np.float32), + "forces": np.zeros((100, 1, 3), dtype=np.float32), + } + ) + cls.system_1 = system.remove_outlier() + cls.system_2 = system + cls.places = 6 + cls.e_places = 6 + cls.f_places = 6 + cls.v_places = 6 diff --git a/tests/test_remove_pbc.py b/tests/test_remove_pbc.py index 28310088..d5befd77 100644 --- a/tests/test_remove_pbc.py +++ b/tests/test_remove_pbc.py @@ -1,4 +1,3 @@ -import os import unittest import numpy as np diff --git a/tests/test_replace.py b/tests/test_replace.py index eaef289c..b16c388b 100644 --- a/tests/test_replace.py +++ b/tests/test_replace.py @@ -1,13 +1,12 @@ -import os import unittest -from unittest.mock import MagicMock, Mock, patch +from unittest.mock import patch import numpy as np from comp_sys import CompSys, IsPBC from context import dpdata -class ConstGenerator(object): +class ConstGenerator: def __init__(self): self.choice_generator = self.get_choice_generator() diff --git a/tests/test_replicate.py b/tests/test_replicate.py index fc41e62d..99104c3c 100644 --- a/tests/test_replicate.py +++ b/tests/test_replicate.py @@ -1,7 +1,5 @@ -import os import unittest -import numpy as np from comp_sys import CompSys, IsPBC from context import dpdata diff --git a/tests/test_siesta_aiMD_output.py b/tests/test_siesta_aiMD_output.py index e7f61641..a1ba31b6 100644 --- a/tests/test_siesta_aiMD_output.py +++ b/tests/test_siesta_aiMD_output.py @@ -1,4 +1,3 @@ -import os import unittest import numpy as np diff --git a/tests/test_siesta_output.py b/tests/test_siesta_output.py index 0c51ae21..9ff0167a 100644 --- a/tests/test_siesta_output.py +++ b/tests/test_siesta_output.py @@ -1,4 +1,3 @@ -import os import unittest import numpy as np diff --git a/tests/test_split_dataset.py b/tests/test_split_dataset.py new file mode 100644 index 00000000..a5419b7b --- /dev/null +++ b/tests/test_split_dataset.py @@ -0,0 +1,25 @@ +import unittest + +import numpy as np +from context import dpdata + + +class TestSplitDataset(unittest.TestCase): + def setUp(self): + self.systems = dpdata.MultiSystems() + sing_sys = dpdata.LabeledSystem("poscars/OUTCAR.h2o.md", fmt="vasp/outcar") + for ii in range(10): + self.systems.append(sing_sys.copy()) + + def test_split_dataset(self): + train, test, test_idx = self.systems.train_test_split(0.2) + self.assertEqual( + train.get_nframes(), int(np.floor(self.systems.get_nframes() * 0.8)) + ) + self.assertEqual( + test.get_nframes(), int(np.floor(self.systems.get_nframes() * 0.2)) + ) + self.assertEqual( + sum([np.count_nonzero(x) for x in test_idx.values()]), + int(np.floor(self.systems.get_nframes() * 0.2)), + ) diff --git a/tests/test_system_append.py b/tests/test_system_append.py index 32107a4c..a2c30b23 100644 --- a/tests/test_system_append.py +++ b/tests/test_system_append.py @@ -1,8 +1,7 @@ -import os import unittest import numpy as np -from comp_sys import CompLabeledSys, CompSys, IsNoPBC, IsPBC +from comp_sys import CompLabeledSys, IsNoPBC, IsPBC from context import dpdata diff --git a/tests/test_system_apply_pbc.py b/tests/test_system_apply_pbc.py index c9f14d92..9cf44ae0 100644 --- a/tests/test_system_apply_pbc.py +++ b/tests/test_system_apply_pbc.py @@ -1,4 +1,3 @@ -import os import unittest import numpy as np diff --git a/tests/test_system_set_type.py b/tests/test_system_set_type.py index edcddc64..4bb14b62 100644 --- a/tests/test_system_set_type.py +++ b/tests/test_system_set_type.py @@ -1,4 +1,3 @@ -import os import unittest import numpy as np diff --git a/tests/test_to_ase.py b/tests/test_to_ase.py index 2440962c..60dc931d 100644 --- a/tests/test_to_ase.py +++ b/tests/test_to_ase.py @@ -1,12 +1,10 @@ import os import unittest -import numpy as np from comp_sys import CompSys, IsPBC from context import dpdata try: - from ase import Atoms from ase.io import write except ModuleNotFoundError: exist_module = False @@ -32,7 +30,7 @@ def setUp(self): @unittest.skipIf(not exist_module, "skip test_ase") class TestFromASE(unittest.TestCase, CompSys, IsPBC): - """Test ASEStructureFormat.from_system""" + """Test ASEStructureFormat.from_system.""" def setUp(self): system_1 = dpdata.System() diff --git a/tests/test_to_list.py b/tests/test_to_list.py index 68c98bf6..d559ffce 100644 --- a/tests/test_to_list.py +++ b/tests/test_to_list.py @@ -1,7 +1,5 @@ -import os import unittest -import numpy as np from comp_sys import CompLabeledSys, IsPBC from context import dpdata diff --git a/tests/test_to_pymatgen.py b/tests/test_to_pymatgen.py index e2b91e24..d5815396 100644 --- a/tests/test_to_pymatgen.py +++ b/tests/test_to_pymatgen.py @@ -1,12 +1,11 @@ import os import unittest -import numpy as np from comp_sys import CompSys, IsPBC from context import dpdata try: - from pymatgen import Structure + from pymatgen import Structure # noqa: F401 exist_module = True except Exception: diff --git a/tests/test_to_pymatgen_entry.py b/tests/test_to_pymatgen_entry.py index 9510224b..fd8f40fc 100644 --- a/tests/test_to_pymatgen_entry.py +++ b/tests/test_to_pymatgen_entry.py @@ -1,13 +1,11 @@ import os import unittest -import numpy as np -from comp_sys import CompSys, IsPBC from context import dpdata from monty.serialization import loadfn try: - from pymatgen.entries.computed_entries import ComputedStructureEntry + from pymatgen.entries.computed_entries import ComputedStructureEntry # noqa: F401 exist_module = True except Exception: diff --git a/tests/test_vasp_outcar.py b/tests/test_vasp_outcar.py index d7e38867..fb2ec1c9 100644 --- a/tests/test_vasp_outcar.py +++ b/tests/test_vasp_outcar.py @@ -1,4 +1,3 @@ -import os import unittest import numpy as np diff --git a/tests/test_vasp_poscar_dump.py b/tests/test_vasp_poscar_dump.py index c67f42fc..a81cbe94 100644 --- a/tests/test_vasp_poscar_dump.py +++ b/tests/test_vasp_poscar_dump.py @@ -1,7 +1,6 @@ import os import unittest -import numpy as np from context import dpdata from poscars.poscar_ref_oh import TestPOSCARoh diff --git a/tests/test_vasp_unconverged_outcar.py b/tests/test_vasp_unconverged_outcar.py index 97318223..7e1b3535 100644 --- a/tests/test_vasp_unconverged_outcar.py +++ b/tests/test_vasp_unconverged_outcar.py @@ -1,7 +1,6 @@ import os import unittest -import numpy as np from context import dpdata @@ -16,7 +15,6 @@ def setUp(self): ) def test_unconverged(self): - self.assertEqual(self.LabeledSystem1["energies"], -23.94708651) self.assertEqual(self.LabeledSystem1.get_nframes(), 1) self.assertEqual(self.LabeledSystem1.get_natoms(), 5) diff --git a/tests/test_vasp_xml.py b/tests/test_vasp_xml.py index d5df49da..c2194787 100644 --- a/tests/test_vasp_xml.py +++ b/tests/test_vasp_xml.py @@ -1,4 +1,3 @@ -import os import unittest import numpy as np diff --git a/tests/test_water_ions.py b/tests/test_water_ions.py index 8b70dc73..788030f3 100644 --- a/tests/test_water_ions.py +++ b/tests/test_water_ions.py @@ -1,12 +1,11 @@ import os import unittest -import numpy as np from context import dpdata try: - import ase - import ase.neighborlist + import ase # noqa: F401 + import ase.neighborlist # noqa: F401 exist_ase = True except Exception: