diff --git a/dpdata/gaussian/fchk.py b/dpdata/gaussian/fchk.py new file mode 100644 index 000000000..816a999ce --- /dev/null +++ b/dpdata/gaussian/fchk.py @@ -0,0 +1,175 @@ +from __future__ import annotations + +from typing import TYPE_CHECKING + +import numpy as np + +from dpdata.utils import open_file + +if TYPE_CHECKING: + from dpdata.utils import FileType + +from ..periodic_table import ELEMENTS +from ..unit import ( + EnergyConversion, + ForceConversion, + HessianConversion, + LengthConversion, +) + +length_convert = LengthConversion("bohr", "angstrom").value() +energy_convert = EnergyConversion("hartree", "eV").value() +force_convert = ForceConversion("hartree/bohr", "eV/angstrom").value() +hessian_convert = HessianConversion("hartree/bohr^2", "eV/angstrom^2").value() + + +def create_full_hessian(hessian_raw: list | np.ndarray, natoms: int) -> np.ndarray: + """ + Reconstructs the full, symmetric Hessian matrix from a 1D array + containing its lower triangular elements. + + Args: + hessian_raw (list | np.ndarray): A 1D list or NumPy array containing the + lower triangular elements (including the + diagonal) of the Hessian matrix. + natoms (int): The number of atoms in the system. + + Returns + ------- + np.ndarray: A full, symmetric (3*natoms, 3*natoms) Hessian matrix. + + Raises + ------ + ValueError: If the number of elements in `hessian_raw` does not match + the expected number for the lower triangle of a + (3*natoms, 3*natoms) matrix. + """ + # Convert input to a NumPy array in case it's a list + hessian_block = np.array(hessian_raw) + + # Calculate the dimension of the final matrix + dim = 3 * natoms + + # Validate that the input data has the correct length + # A lower triangle of an n x n matrix has n*(n+1)/2 elements + expected_length = dim * (dim + 1) // 2 + if hessian_block.size != expected_length: + raise ValueError( + f"Input length {hessian_block.size} != expected {expected_length}" + ) + + # Create a zero matrix, then fill the lower triangle + hessian_full = np.zeros((dim, dim), dtype=hessian_block.dtype) + lower_triangle_indices = np.tril_indices(dim) + hessian_full[lower_triangle_indices] = hessian_block + + # This is done by copying the lower triangle to the upper triangle + # M_full = M_lower + M_lower.T - diag(M_lower) + hessian_full = hessian_full + hessian_full.T - np.diag(np.diag(hessian_full)) + + return hessian_full + + +def to_system_data(file_name: FileType, has_forces=True, has_hessian=True): + """Read Gaussian fchk file. + + Parameters + ---------- + file_name : str + file name + has_forces : bool, default True + whether to read force + Note: Cartesian Gradient in fchk file is converted to forces by taking negative sign + has_hessian : bool, default True + whether to read hessian + + Returns + ------- + data : dict + system data, including hessian if has_hessian is True + """ + data = {} + natoms = 0 + atom_numbers = [] + coords_t = [] + energy_t = [] + forces_t = [] + hessian_t = [] + # Read fchk file + with open_file(file_name) as fp: + for line in fp: + if isinstance(line, bytes): + line = line.decode(errors="ignore") + if "Number of atoms" in line: + natoms = int(line.split()[-1]) + elif "Atomic numbers" in line and "I" in line: + n = int(line.split()[-1]) + atom_numbers = [] + while len(atom_numbers) < n: + next_line = next(fp) + if isinstance(next_line, bytes): + next_line = next_line.decode(errors="ignore") + atom_numbers += [int(x) for x in next_line.split()] + elif "Current cartesian coordinates" in line and "R" in line: + n = int(line.split()[-1]) + coords_raw = [] + while len(coords_raw) < n: + next_line = next(fp) + if isinstance(next_line, bytes): + next_line = next_line.decode(errors="ignore") + coords_raw += [float(x) for x in next_line.split()] + coords = np.array(coords_raw).reshape(-1, 3) * length_convert + coords_t.append(coords) + elif "Total Energy" in line: + energy = float(line.split()[-1]) * energy_convert + energy_t.append(energy) + elif "Cartesian Gradient" in line: + n = int(line.split()[-1]) + forces_raw = [] + while len(forces_raw) < n: + next_line = next(fp) + if isinstance(next_line, bytes): + next_line = next_line.decode(errors="ignore") + forces_raw += [float(x) for x in next_line.split()] + # Cartesian Gradient is the negative of forces: F = -∇E + forces = -np.array(forces_raw).reshape(-1, 3) * force_convert + forces_t.append(forces) + elif "Cartesian Force Constants" in line and "R" in line: + n = int(line.split()[-1]) + hessian_raw = [] + while len(hessian_raw) < n: + next_line = next(fp) + if isinstance(next_line, bytes): + next_line = next_line.decode(errors="ignore") + hessian_raw += [float(x) for x in next_line.split()] + hessian_full = ( + create_full_hessian(hessian_raw, natoms) * hessian_convert + ) + # store as (natoms, 3, natoms, 3) to align with registered shape + hessian_t.append(hessian_full.reshape(natoms, 3, natoms, 3)) + # Assert key data + assert coords_t, "cannot find coords" + assert energy_t, "cannot find energy" + if has_forces: + assert forces_t, "cannot find forces" + if has_hessian: + assert hessian_t, "cannot find hessian" + # Assemble data + atom_symbols = [ELEMENTS[z - 1] for z in atom_numbers] + atom_names, atom_types, atom_numbs = np.unique( + atom_symbols, return_inverse=True, return_counts=True + ) + data["atom_names"] = list(atom_names) + data["atom_numbs"] = list(atom_numbs) + data["atom_types"] = atom_types + data["coords"] = np.array(coords_t).reshape(-1, natoms, 3) + data["orig"] = np.zeros(3) + data["cells"] = np.array([np.eye(3) * 100]) + data["nopbc"] = True + if energy_t: + data["energies"] = np.array(energy_t) + if has_forces and forces_t: + data["forces"] = np.array(forces_t) + if has_hessian and hessian_t: + data["hessian"] = np.array(hessian_t) + return data diff --git a/dpdata/plugins/gaussian.py b/dpdata/plugins/gaussian.py index 9cba45989..d2c0f7237 100644 --- a/dpdata/plugins/gaussian.py +++ b/dpdata/plugins/gaussian.py @@ -5,8 +5,12 @@ import tempfile from typing import TYPE_CHECKING +import numpy as np + +import dpdata.gaussian.fchk import dpdata.gaussian.gjf import dpdata.gaussian.log +from dpdata.data_type import Axis, DataType from dpdata.driver import Driver from dpdata.format import Format from dpdata.utils import open_file @@ -15,6 +19,18 @@ from dpdata.utils import FileType +def register_hessian_data(data): + if "hessian" in data: + dt = DataType( + "hessian", + np.ndarray, + (Axis.NFRAMES, Axis.NATOMS, 3, Axis.NATOMS, 3), + required=False, + deepmd_name="hessian", + ) + dpdata.LabeledSystem.register_data_type(dt) + + @Format.register("gaussian/log") class GaussianLogFormat(Format): def from_labeled_system(self, file_name: FileType, md=False, **kwargs): @@ -24,6 +40,21 @@ def from_labeled_system(self, file_name: FileType, md=False, **kwargs): return {"energies": [], "forces": [], "nopbc": True} +@Format.register("gaussian/fchk") +class GaussianFChkFormat(Format): + def from_labeled_system( + self, file_name: FileType, has_forces=True, has_hessian=True, **kwargs + ): + try: + data = dpdata.gaussian.fchk.to_system_data( + file_name, has_forces=has_forces, has_hessian=has_hessian + ) + register_hessian_data(data) + return data + except AssertionError: + return {"energies": [], "forces": [], "hessian": [], "nopbc": True} + + @Format.register("gaussian/md") class GaussianMDFormat(Format): def from_labeled_system(self, file_name: FileType, **kwargs): diff --git a/dpdata/unit.py b/dpdata/unit.py index 9c96827cd..aabfd05c8 100644 --- a/dpdata/unit.py +++ b/dpdata/unit.py @@ -152,6 +152,34 @@ def __init__(self, unitA, unitB): self.set_value(econv / lconv) +class HessianConversion(Conversion): + def __init__(self, unitA, unitB): + """Class for Hessian (second derivative) unit conversion. + + Parameters + ---------- + unitA, unitB : str + in format of "energy_unit/length_unit^2" + + Examples + -------- + >>> conv = HessianConversion("hartree/bohr^2", "eV/angstrom^2") + >>> conv.value() + 97.1736242922823 + """ + super().__init__(unitA, unitB, check=False) + eunitA, lunitA = self._split_unit(unitA) + eunitB, lunitB = self._split_unit(unitB) + econv = EnergyConversion(eunitA, eunitB).value() + lconv = LengthConversion(lunitA, lunitB).value() + self.set_value(econv / lconv**2) + + def _split_unit(self, unit): + eunit = unit.split("/")[0] + lunit = unit.split("/")[1][:-2] + return eunit, lunit + + class PressureConversion(Conversion): def __init__(self, unitA, unitB): """Class for pressure conversion. diff --git a/tests/gaussian/waterfreq.gaussianfchk b/tests/gaussian/waterfreq.gaussianfchk new file mode 100644 index 000000000..932818985 --- /dev/null +++ b/tests/gaussian/waterfreq.gaussianfchk @@ -0,0 +1,1292 @@ +Title Card Required +Freq RB3LYP 6-31G(d) +Number of atoms I 3 +Info1-9 I N= 9 + 12 10 0 0 0 101 + 6 18 -502 +Full Title C N= 2 +Title Card Required +Route C N= 3 +#P b3lyp 6-31g* freq nosymm +Charge I 0 +Multiplicity I 1 +Number of electrons I 10 +Number of alpha electrons I 5 +Number of beta electrons I 5 +Number of basis functions I 19 +Number of independent functions I 19 +Number of point charges in /Mol/ I 0 +Number of translation vectors I 0 +Atomic numbers I N= 3 + 8 1 1 +Nuclear charges R N= 3 + 8.00000000E+00 1.00000000E+00 1.00000000E+00 +Current cartesian coordinates R N= 9 + 4.90413352E-01 1.96165345E-01 0.00000000E+00 2.30455043E+00 1.96165345E-01 + 0.00000000E+00 -1.15158058E-01 1.90624622E+00 0.00000000E+00 +Number of symbols in /Mol/ I 0 +Force Field I 0 +Atom Types C N= 3 + +Int Atom Types I N= 3 + 0 0 0 +MM charges R N= 3 + 0.00000000E+00 0.00000000E+00 0.00000000E+00 +Integer atomic weights I N= 3 + 16 1 1 +Real atomic weights R N= 3 + 1.59949146E+01 1.00782504E+00 1.00782504E+00 +Atom fragment info I N= 3 + 0 0 0 +Atom residue num I N= 3 + 0 0 0 +Nuclear spins I N= 3 + 0 1 1 +Nuclear ZEff R N= 3 + -5.60000000E+00 -1.00000000E+00 -1.00000000E+00 +Nuclear ZNuc R N= 3 + 8.00000000E+00 1.00000000E+00 1.00000000E+00 +Nuclear QMom R N= 3 + 0.00000000E+00 0.00000000E+00 0.00000000E+00 +Nuclear GFac R N= 3 + 0.00000000E+00 2.79284600E+00 2.79284600E+00 +MicOpt I N= 3 + -1 -1 -1 +Number of residues I 0 +Number of secondary structures I 0 +Number of contracted shells I 8 +Number of primitive shells I 19 +Pure/Cartesian d shells I 1 +Pure/Cartesian f shells I 0 +Highest angular momentum I 2 +Largest degree of contraction I 6 +Shell types I N= 8 + 0 -1 -1 2 0 0 + 0 0 +Number of primitives per shell I N= 8 + 6 3 1 1 3 1 + 3 1 +Shell to atom map I N= 8 + 1 1 1 1 2 2 + 3 3 +Primitive exponents R N= 19 + 5.48467166E+03 8.25234946E+02 1.88046958E+02 5.29645000E+01 1.68975704E+01 + 5.79963534E+00 1.55396162E+01 3.59993359E+00 1.01376175E+00 2.70005823E-01 + 8.00000000E-01 1.87311370E+01 2.82539436E+00 6.40121692E-01 1.61277759E-01 + 1.87311370E+01 2.82539436E+00 6.40121692E-01 1.61277759E-01 +Contraction coefficients R N= 19 + 1.83107443E-03 1.39501722E-02 6.84450781E-02 2.32714336E-01 4.70192898E-01 + 3.58520853E-01 -1.10777550E-01 -1.48026263E-01 1.13076702E+00 1.00000000E+00 + 1.00000000E+00 3.34946043E-02 2.34726953E-01 8.13757326E-01 1.00000000E+00 + 3.34946043E-02 2.34726953E-01 8.13757326E-01 1.00000000E+00 +P(S=P) Contraction coefficients R N= 19 + 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 + 0.00000000E+00 7.08742682E-02 3.39752839E-01 7.27158577E-01 1.00000000E+00 + 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 + 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 +Coordinates of each shell R N= 24 + 4.90413352E-01 1.96165345E-01 0.00000000E+00 4.90413352E-01 1.96165345E-01 + 0.00000000E+00 4.90413352E-01 1.96165345E-01 0.00000000E+00 4.90413352E-01 + 1.96165345E-01 0.00000000E+00 2.30455043E+00 1.96165345E-01 0.00000000E+00 + 2.30455043E+00 1.96165345E-01 0.00000000E+00 -1.15158058E-01 1.90624622E+00 + 0.00000000E+00 -1.15158058E-01 1.90624622E+00 0.00000000E+00 +Num ILSW I 100 +ILSW I N= 100 + 0 1 0 0 2 0 + 0 0 0 0 402 -1 + 5 0 0 0 2 0 + 0 0 0 0 1 0 + 1 1 0 0 0 0 + 0 0 100000 0 -1 0 + 0 0 0 0 0 0 + 0 0 0 1 0 0 + 0 -2000000000 1 0 0 0 + 0 0 4 52 0 0 + 0 0 5 0 0 0 + 0 0 0 3 0 1 + 0 0 0 0 0 0 + 0 0 0 0 0 0 + 0 0 0 0 0 0 + 0 0 0 0 0 0 + 0 0 0 0 +Num RLSW I 52 +RLSW R N= 52 + 8.00000000E-01 7.20000000E-01 1.00000000E+00 8.10000000E-01 2.00000000E-01 + 0.00000000E+00 0.00000000E+00 1.00000000E+00 0.00000000E+00 0.00000000E+00 + 0.00000000E+00 0.00000000E+00 1.00000000E+00 0.00000000E+00 0.00000000E+00 + 0.00000000E+00 0.00000000E+00 1.00000000E+00 0.00000000E+00 0.00000000E+00 + 0.00000000E+00 0.00000000E+00 1.00000000E+00 0.00000000E+00 0.00000000E+00 + 0.00000000E+00 0.00000000E+00 1.00000000E+00 0.00000000E+00 0.00000000E+00 + 0.00000000E+00 0.00000000E+00 1.00000000E+00 0.00000000E+00 0.00000000E+00 + 0.00000000E+00 0.00000000E+00 0.00000000E+00 1.00000000E+00 1.00000000E+00 + 0.00000000E+00 1.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 + 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 + 0.00000000E+00 0.00000000E+00 +MxBond I 2 +NBond I N= 3 + 2 1 1 +IBond I N= 6 + 2 3 1 0 1 0 +RBond R N= 6 + 1.00000000E+00 1.00000000E+00 1.00000000E+00 0.00000000E+00 1.00000000E+00 + 0.00000000E+00 +Virial Ratio R 2.007529071266385E+00 +SCF Energy R -7.640801970624457E+01 +Total Energy R -7.640801970624457E+01 +RMS Force R 8.584249608062611E-03 +RMS Density R 8.716129495562998E-10 +NImag I 0 +Job Status I 1 +Nuclear derivative order I 2 +External E-field R N= 35 + 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 + 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 + 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 + 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 + 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 + 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 + 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 +IOpCl I 0 +IROHF I 0 +Alpha Orbital Energies R N= 19 + -1.91334781E+01 -9.96513214E-01 -5.30064370E-01 -3.60838519E-01 -2.89782822E-01 + 6.55013132E-02 1.52683602E-01 8.00477181E-01 8.48793376E-01 8.92189100E-01 + 8.92403099E-01 1.07366796E+00 1.17570714E+00 1.73998106E+00 1.74507831E+00 + 1.78547353E+00 2.29893442E+00 2.59363559E+00 3.56651601E+00 +Alpha MO coefficients R N= 361 + 9.92842486E-01 2.62183925E-02 6.26994246E-04 8.87176583E-04 -6.25098404E-17 + 1.02899449E-02 2.70340093E-06 3.82525205E-06 -8.66449577E-18 -7.80127195E-03 + -7.79311974E-03 -7.76664561E-03 1.32911417E-05 3.37699398E-17 4.52006635E-17 + 3.78792807E-04 -1.08998190E-03 3.78792745E-04 -1.08998190E-03 -2.10153832E-01 + 4.70402739E-01 7.07379334E-02 1.00091876E-01 -3.66431452E-17 4.39156052E-01 + 3.30573258E-02 4.67750345E-02 3.10807251E-17 1.87476570E-02 1.60404963E-02 + -1.06573649E-02 -4.41371895E-03 2.91841099E-16 2.85593035E-16 1.39486592E-01 + 6.44222085E-03 1.39486596E-01 6.44221920E-03 -7.06895573E-11 -1.89671322E-10 + 4.21288804E-01 -2.97737487E-01 -1.99986965E-16 -5.68901000E-09 2.14868277E-01 + -1.51853882E-01 2.38120135E-16 3.22317310E-02 -3.22317255E-02 2.56405620E-09 + 1.31795842E-02 -3.16214581E-17 -6.00262264E-17 2.41021551E-01 1.34039117E-01 + -2.41021551E-01 -1.34039105E-01 8.40456503E-02 -1.68458938E-01 3.23494283E-01 + 4.57733828E-01 -2.07336388E-16 -3.96392691E-01 2.22713727E-01 3.15132642E-01 + -3.51599025E-17 1.60691308E-02 3.35050199E-02 -1.45683025E-04 2.84272466E-02 + -6.27567571E-17 2.61234200E-17 1.37614128E-01 1.09871048E-01 1.37614133E-01 + 1.09871039E-01 2.02975593E-17 -1.66113035E-16 4.41977303E-18 4.90439231E-16 + 6.43683692E-01 3.94700705E-16 4.59435118E-16 -5.03797979E-16 5.07062835E-01 + -2.48643191E-16 6.77196190E-17 -1.05706992E-16 -1.51873339E-16 1.98074483E-02 + 2.80268901E-02 -5.10351850E-17 -1.06503246E-16 5.97027592E-16 -4.54478231E-16 + -1.03694849E-01 1.23211743E-01 1.53676471E-01 2.17447139E-01 -1.61071057E-16 + 1.29271528E+00 2.62463670E-01 3.71377398E-01 1.53572360E-16 -4.09959858E-02 + -3.57423800E-02 -5.86073483E-02 8.56541704E-03 -2.46879989E-16 1.12381927E-17 + -1.00532202E-01 -9.82785033E-01 -1.00532210E-01 -9.82784828E-01 -8.57590507E-09 + 1.40045081E-08 -3.33665688E-01 2.35811617E-01 -1.39833622E-16 9.16143626E-08 + -6.34530553E-01 4.48441898E-01 1.89160939E-16 -1.61209042E-02 1.61208939E-02 + -7.25129572E-09 -6.59185005E-03 6.71641498E-17 -2.54833329E-17 9.58791184E-02 + 1.28932318E+00 -9.58791591E-02 -1.28932330E+00 3.65811046E-09 -2.10196444E-08 + -1.67194652E-01 1.18161492E-01 8.33535030E-15 4.57596841E-09 -3.77092282E-01 + 2.66502439E-01 -8.78679292E-15 1.68619548E-01 -1.68619548E-01 -1.06224599E-08 + 6.89486813E-02 -6.03232428E-17 -5.95442364E-16 8.47790479E-01 -6.04877779E-01 + -8.47790386E-01 6.04877748E-01 4.46174837E-02 -2.49126859E-01 -2.89600197E-01 + -4.09774812E-01 -9.09185710E-15 2.52051508E-01 5.87299882E-02 8.31009961E-02 + 9.59550583E-15 8.76665637E-02 1.58337195E-02 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0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 + 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 + 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 + 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 + 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 + 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 + 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 + 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 + 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 + 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 + 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 + 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 + 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 + 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 + 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 +Gaussian Version C N= 2 +ES64L-G16RevB.01 diff --git a/tests/gaussian/waterfreq.gaussianlog b/tests/gaussian/waterfreq.gaussianlog new file mode 100644 index 000000000..a721433fb --- /dev/null +++ b/tests/gaussian/waterfreq.gaussianlog @@ -0,0 +1,738 @@ + Entering Gaussian System, Link 0=g16 + Input=water_freq.gjf + Output=water_freq.log + Initial command: + /home/bwli/soft//g16/l1.exe "/home/bwli/soft//g16/scratch/Gau-1906092.inp" -scrdir="/home/bwli/soft//g16/scratch/" + Default is to use a total of 48 processors: + 48 via shared-memory + 1 via Linda + Entering Link 1 = /home/bwli/soft//g16/l1.exe PID= 1906103. + + Copyright (c) 1988-2017, Gaussian, Inc. All Rights Reserved. + + This is part of the Gaussian(R) 16 program. It is based on + the Gaussian(R) 09 system (copyright 2009, Gaussian, Inc.), + the Gaussian(R) 03 system (copyright 2003, Gaussian, Inc.), + the Gaussian(R) 98 system (copyright 1998, Gaussian, Inc.), + the Gaussian(R) 94 system (copyright 1995, Gaussian, Inc.), + the Gaussian 92(TM) system (copyright 1992, Gaussian, Inc.), + the Gaussian 90(TM) system (copyright 1990, Gaussian, Inc.), + the Gaussian 88(TM) system (copyright 1988, Gaussian, Inc.), + the Gaussian 86(TM) system (copyright 1986, Carnegie Mellon + University), and the Gaussian 82(TM) system (copyright 1983, + Carnegie Mellon University). Gaussian is a federally registered + trademark of Gaussian, Inc. + + This software contains proprietary and confidential information, + including trade secrets, belonging to Gaussian, Inc. + + This software is provided under written license and may be + used, copied, transmitted, or stored only in accord with that + written license. + + The following legend is applicable only to US Government + contracts under FAR: + + RESTRICTED RIGHTS LEGEND + + Use, reproduction and disclosure by the US Government is + subject to restrictions as set forth in subparagraphs (a) + and (c) of the Commercial Computer Software - Restricted + Rights clause in FAR 52.227-19. + + Gaussian, Inc. + 340 Quinnipiac St., Bldg. 40, Wallingford CT 06492 + + + --------------------------------------------------------------- + Warning -- This program may not be used in any manner that + competes with the business of Gaussian, Inc. or will provide + assistance to any competitor of Gaussian, Inc. The licensee + of this program is prohibited from giving any competitor of + Gaussian, Inc. access to this program. By using this program, + the user acknowledges that Gaussian, Inc. is engaged in the + business of creating and licensing software in the field of + computational chemistry and represents and warrants to the + licensee that it is not a competitor of Gaussian, Inc. and that + it will not use this program in any manner prohibited above. + --------------------------------------------------------------- + + + Cite this work as: + Gaussian 16, Revision B.01, + M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, + M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, + G. A. Petersson, H. Nakatsuji, X. Li, M. Caricato, A. V. Marenich, + J. Bloino, B. G. Janesko, R. Gomperts, B. Mennucci, H. P. Hratchian, + J. V. Ortiz, A. F. Izmaylov, J. L. Sonnenberg, D. Williams-Young, + F. Ding, F. Lipparini, F. Egidi, J. Goings, B. Peng, A. Petrone, + T. Henderson, D. Ranasinghe, V. G. Zakrzewski, J. Gao, N. Rega, + G. Zheng, W. Liang, M. Hada, M. Ehara, K. Toyota, R. Fukuda, + J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, + T. Vreven, K. Throssell, J. A. Montgomery, Jr., J. E. Peralta, + F. Ogliaro, M. J. Bearpark, J. J. Heyd, E. N. Brothers, K. N. Kudin, + V. N. Staroverov, T. A. Keith, R. Kobayashi, J. Normand, + K. Raghavachari, A. P. Rendell, J. C. Burant, S. S. Iyengar, + J. Tomasi, M. Cossi, J. M. Millam, M. Klene, C. Adamo, R. Cammi, + J. W. Ochterski, R. L. Martin, K. Morokuma, O. Farkas, + J. B. Foresman, and D. J. Fox, Gaussian, Inc., Wallingford CT, 2016. + + ****************************************** + Gaussian 16: ES64L-G16RevB.01 20-Dec-2017 + 31-Jul-2025 + ****************************************** + %chk=water_freq.chk + Default route: IOp(8/117=-99) IOp(7/127=-99) + --------------------------- + #P b3lyp 6-31g* freq nosymm + --------------------------- + 1/10=4,30=1,38=1/1,3; + 2/12=2,15=1,17=6,18=5,40=1/2; + 3/5=1,6=6,7=1,11=2,25=1,30=1,71=2,74=-5,140=1/1,2,3; + 4//1; + 5/5=2,38=5,98=1/2; + 8/6=4,10=90,11=11,117=-99/1; + 11/6=1,8=1,9=11,15=111,16=1,31=1/1,2,10; + 10/6=1,31=1/2; + 6/7=2,8=2,9=2,10=2,28=1/1; + 7/8=1,10=1,25=1,30=1,127=-99/1,2,3,16; + 1/10=4,30=1/3; + 99//99; + Leave Link 1 at Thu Jul 31 11:46:22 2025, MaxMem= 0 cpu: 4.8 elap: 0.1 + (Enter /home/bwli/soft//g16/l101.exe) + ------------------- + Title Card Required + ------------------- + Symbolic Z-matrix: + Charge = 0 Multiplicity = 1 + O 0.25952 0.10381 0. + H 1.21952 0.10381 0. + H -0.06094 1.00874 0. + + ITRead= 0 0 0 + MicOpt= -1 -1 -1 + NAtoms= 3 NQM= 3 NQMF= 0 NMMI= 0 NMMIF= 0 + NMic= 0 NMicF= 0. + Isotopes and Nuclear Properties: + (Nuclear quadrupole moments (NQMom) in fm**2, nuclear magnetic moments (NMagM) + in nuclear magnetons) + + Atom 1 2 3 + IAtWgt= 16 1 1 + AtmWgt= 15.9949146 1.0078250 1.0078250 + NucSpn= 0 1 1 + AtZEff= -0.0000000 -0.0000000 -0.0000000 + NQMom= 0.0000000 0.0000000 0.0000000 + NMagM= 0.0000000 2.7928460 2.7928460 + AtZNuc= 8.0000000 1.0000000 1.0000000 + Leave Link 101 at Thu Jul 31 11:46:23 2025, MaxMem= 6442450944 cpu: 10.9 elap: 0.3 + (Enter /home/bwli/soft//g16/l103.exe) + + GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad + Berny optimization. + Initialization pass. + Trust Radius=3.00D-01 FncErr=1.00D-07 GrdErr=1.00D-07 EigMax=2.50D+02 EigMin=1.00D-04 + Number of steps in this run= 2 maximum allowed number of steps= 2. + GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad + + Leave Link 103 at Thu Jul 31 11:46:24 2025, MaxMem= 6442450944 cpu: 1.0 elap: 0.1 + (Enter /home/bwli/soft//g16/l202.exe) + Input orientation: + --------------------------------------------------------------------- + Center Atomic Atomic Coordinates (Angstroms) + Number Number Type X Y Z + --------------------------------------------------------------------- + 1 8 0 0.259516 0.103806 0.000000 + 2 1 0 1.219516 0.103806 0.000000 + 3 1 0 -0.060939 1.008742 0.000000 + --------------------------------------------------------------------- + Distance matrix (angstroms): + 1 2 3 + 1 O 0.000000 + 2 H 0.960000 0.000000 + 3 H 0.960000 1.567952 0.000000 + Symmetry turned off by external request. + Stoichiometry H2O + Framework group C2V[C2(O),SGV(H2)] + Deg. of freedom 2 + Full point group C2V NOp 4 + Rotational constants (GHZ): 919.6759726 407.9403292 282.5913771 + Leave Link 202 at Thu Jul 31 11:46:25 2025, MaxMem= 6442450944 cpu: 1.4 elap: 0.1 + (Enter /home/bwli/soft//g16/l301.exe) + Standard basis: 6-31G(d) (6D, 7F) + Ernie: Thresh= 0.10000D-02 Tol= 0.10000D-05 Strict=F. + 19 basis functions, 36 primitive gaussians, 19 cartesian basis functions + 5 alpha electrons 5 beta electrons + nuclear repulsion energy 9.1571160234 Hartrees. + IExCor= 402 DFT=T Ex+Corr=B3LYP ExCW=0 ScaHFX= 0.200000 + ScaDFX= 0.800000 0.720000 1.000000 0.810000 ScalE2= 1.000000 1.000000 + IRadAn= 5 IRanWt= -1 IRanGd= 0 ICorTp=0 IEmpDi= 4 + NAtoms= 3 NActive= 3 NUniq= 3 SFac= 1.00D+00 NAtFMM= 60 NAOKFM=F Big=F + Integral buffers will be 131072 words long. + Raffenetti 2 integral format. + Two-electron integral symmetry is turned off. + Leave Link 301 at Thu Jul 31 11:46:26 2025, MaxMem= 6442450944 cpu: 6.0 elap: 0.2 + (Enter /home/bwli/soft//g16/l302.exe) + NPDir=0 NMtPBC= 1 NCelOv= 1 NCel= 1 NClECP= 1 NCelD= 1 + NCelK= 1 NCelE2= 1 NClLst= 1 CellRange= 0.0. + One-electron integrals computed using PRISM. + NBasis= 19 RedAO= T EigKep= 2.24D-02 NBF= 19 + NBsUse= 19 1.00D-06 EigRej= -1.00D+00 NBFU= 19 + Precomputing XC quadrature grid using + IXCGrd= 4 IRadAn= 5 IRanWt= -1 IRanGd= 0 AccXCQ= 0.00D+00. + Generated NRdTot= 0 NPtTot= 0 NUsed= 0 NTot= 32 + NSgBfM= 19 19 19 19 19 MxSgAt= 3 MxSgA2= 3. + Leave Link 302 at Thu Jul 31 11:46:27 2025, MaxMem= 6442450944 cpu: 11.8 elap: 0.3 + (Enter /home/bwli/soft//g16/l303.exe) + DipDrv: MaxL=1. + Leave Link 303 at Thu Jul 31 11:46:29 2025, MaxMem= 6442450944 cpu: 5.3 elap: 0.3 + (Enter /home/bwli/soft//g16/l401.exe) + ExpMin= 1.61D-01 ExpMax= 5.48D+03 ExpMxC= 8.25D+02 IAcc=3 IRadAn= 5 AccDes= 0.00D+00 + Harris functional with IExCor= 402 and IRadAn= 5 diagonalized for initial guess. + HarFok: IExCor= 402 AccDes= 0.00D+00 IRadAn= 5 IDoV= 1 UseB2=F ITyADJ=14 + ICtDFT= 3500011 ScaDFX= 1.000000 1.000000 1.000000 1.000000 + FoFCou: FMM=F IPFlag= 0 FMFlag= 100000 FMFlg1= 0 + NFxFlg= 0 DoJE=T BraDBF=F KetDBF=T FulRan=T + wScrn= 0.000000 ICntrl= 500 IOpCl= 0 I1Cent= 200000004 NGrid= 0 + NMat0= 1 NMatS0= 1 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0 + Symmetry not used in FoFCou. + Harris En= -76.4478373738359 + JPrj=0 DoOrth=F DoCkMO=F. + Leave Link 401 at Thu Jul 31 11:46:31 2025, MaxMem= 6442450944 cpu: 21.7 elap: 0.5 + (Enter /home/bwli/soft//g16/l502.exe) + Keep R1 ints in memory in canonical form, NReq=41439931. + FoFCou: FMM=F IPFlag= 0 FMFlag= 0 FMFlg1= 0 + NFxFlg= 0 DoJE=F BraDBF=F KetDBF=F FulRan=T + wScrn= 0.000000 ICntrl= 600 IOpCl= 0 I1Cent= 0 NGrid= 0 + NMat0= 1 NMatS0= 190 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0 + Symmetry not used in FoFCou. + Two-electron integral symmetry not used. + Closed shell SCF: + Using DIIS extrapolation, IDIIS= 1040. + NGot= 6442450944 LenX= 6442430559 LenY= 6442429677 + Requested convergence on RMS density matrix=1.00D-08 within 128 cycles. + Requested convergence on MAX density matrix=1.00D-06. + Requested convergence on energy=1.00D-06. + No special actions if energy rises. + Integral accuracy reduced to 1.0D-05 until final iterations. + + Cycle 1 Pass 0 IDiag 1: + E= -76.3286056992138 + DIIS: error= 7.82D-02 at cycle 1 NSaved= 1. + NSaved= 1 IEnMin= 1 EnMin= -76.3286056992138 IErMin= 1 ErrMin= 7.82D-02 + ErrMax= 7.82D-02 0.00D+00 EMaxC= 1.00D-01 BMatC= 1.07D-01 BMatP= 1.07D-01 + IDIUse=3 WtCom= 2.18D-01 WtEn= 7.82D-01 + Coeff-Com: 0.100D+01 + Coeff-En: 0.100D+01 + Coeff: 0.100D+01 + Gap= 0.210 Goal= None Shift= 0.000 + GapD= 0.210 DampG=1.000 DampE=0.500 DampFc=0.5000 IDamp=-1. + Damping current iteration by 5.00D-01 + RMSDP=2.97D-02 MaxDP=2.22D-01 OVMax= 1.98D-01 + + Cycle 2 Pass 0 IDiag 1: + E= -76.3563072933733 Delta-E= -0.027701594160 Rises=F Damp=T + DIIS: error= 1.88D-02 at cycle 2 NSaved= 2. + NSaved= 2 IEnMin= 2 EnMin= -76.3563072933733 IErMin= 2 ErrMin= 1.88D-02 + ErrMax= 1.88D-02 0.00D+00 EMaxC= 1.00D-01 BMatC= 6.21D-03 BMatP= 1.07D-01 + IDIUse=3 WtCom= 8.12D-01 WtEn= 1.88D-01 + Coeff-Com: 0.178D+00 0.822D+00 + Coeff-En: 0.292D+00 0.708D+00 + Coeff: 0.200D+00 0.800D+00 + Gap= 0.341 Goal= None Shift= 0.000 + RMSDP=3.57D-03 MaxDP=3.75D-02 DE=-2.77D-02 OVMax= 1.12D-01 + + Cycle 3 Pass 0 IDiag 1: + E= -76.4078884603956 Delta-E= -0.051581167022 Rises=F Damp=F + DIIS: error= 3.13D-03 at cycle 3 NSaved= 3. + NSaved= 3 IEnMin= 3 EnMin= -76.4078884603956 IErMin= 3 ErrMin= 3.13D-03 + ErrMax= 3.13D-03 0.00D+00 EMaxC= 1.00D-01 BMatC= 1.92D-04 BMatP= 6.21D-03 + IDIUse=3 WtCom= 9.69D-01 WtEn= 3.13D-02 + Coeff-Com: 0.382D-01-0.112D-02 0.963D+00 + Coeff-En: 0.000D+00 0.000D+00 0.100D+01 + Coeff: 0.370D-01-0.108D-02 0.964D+00 + Gap= 0.355 Goal= None Shift= 0.000 + RMSDP=4.61D-04 MaxDP=3.84D-03 DE=-5.16D-02 OVMax= 3.14D-03 + + Cycle 4 Pass 0 IDiag 1: + E= -76.4080180172644 Delta-E= -0.000129556869 Rises=F Damp=F + DIIS: error= 2.85D-04 at cycle 4 NSaved= 4. + NSaved= 4 IEnMin= 4 EnMin= -76.4080180172644 IErMin= 4 ErrMin= 2.85D-04 + ErrMax= 2.85D-04 0.00D+00 EMaxC= 1.00D-01 BMatC= 2.23D-06 BMatP= 1.92D-04 + IDIUse=3 WtCom= 9.97D-01 WtEn= 2.85D-03 + Coeff-Com: 0.578D-02-0.167D-01 0.206D+00 0.805D+00 + Coeff-En: 0.000D+00 0.000D+00 0.000D+00 0.100D+01 + Coeff: 0.577D-02-0.166D-01 0.206D+00 0.805D+00 + Gap= 0.355 Goal= None Shift= 0.000 + RMSDP=3.83D-05 MaxDP=1.86D-04 DE=-1.30D-04 OVMax= 2.73D-04 + + Cycle 5 Pass 0 IDiag 1: + E= -76.4080196000863 Delta-E= -0.000001582822 Rises=F Damp=F + DIIS: error= 5.13D-05 at cycle 5 NSaved= 5. + NSaved= 5 IEnMin= 5 EnMin= -76.4080196000863 IErMin= 5 ErrMin= 5.13D-05 + ErrMax= 5.13D-05 0.00D+00 EMaxC= 1.00D-01 BMatC= 3.65D-08 BMatP= 2.23D-06 + IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 + Coeff-Com: 0.475D-03-0.274D-03-0.974D-03-0.900D-02 0.101D+01 + Coeff: 0.475D-03-0.274D-03-0.974D-03-0.900D-02 0.101D+01 + Gap= 0.355 Goal= None Shift= 0.000 + RMSDP=7.49D-06 MaxDP=6.60D-05 DE=-1.58D-06 OVMax= 4.20D-05 + + Initial convergence to 1.0D-05 achieved. Increase integral accuracy. + Cycle 6 Pass 1 IDiag 1: + E= -76.4080197062382 Delta-E= -0.000000106152 Rises=F Damp=F + DIIS: error= 6.23D-07 at cycle 1 NSaved= 1. + NSaved= 1 IEnMin= 1 EnMin= -76.4080197062382 IErMin= 1 ErrMin= 6.23D-07 + ErrMax= 6.23D-07 0.00D+00 EMaxC= 1.00D-01 BMatC= 3.70D-12 BMatP= 3.70D-12 + IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 + Coeff-Com: 0.100D+01 + Coeff: 0.100D+01 + Gap= 0.355 Goal= None Shift= 0.000 + RMSDP=7.49D-06 MaxDP=6.60D-05 DE=-1.06D-07 OVMax= 1.21D-06 + + Cycle 7 Pass 1 IDiag 1: + E= -76.4080197062441 Delta-E= -0.000000000006 Rises=F Damp=F + DIIS: error= 1.67D-07 at cycle 2 NSaved= 2. + NSaved= 2 IEnMin= 2 EnMin= -76.4080197062441 IErMin= 2 ErrMin= 1.67D-07 + ErrMax= 1.67D-07 0.00D+00 EMaxC= 1.00D-01 BMatC= 5.91D-13 BMatP= 3.70D-12 + IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 + Coeff-Com: 0.194D+00 0.806D+00 + Coeff: 0.194D+00 0.806D+00 + Gap= 0.355 Goal= None Shift= 0.000 + RMSDP=5.48D-08 MaxDP=3.62D-07 DE=-5.88D-12 OVMax= 4.29D-07 + + Cycle 8 Pass 1 IDiag 1: + E= -76.4080197062442 Delta-E= -0.000000000000 Rises=F Damp=F + DIIS: error= 1.89D-07 at cycle 3 NSaved= 3. + NSaved= 3 IEnMin= 3 EnMin= -76.4080197062442 IErMin= 2 ErrMin= 1.67D-07 + ErrMax= 1.89D-07 0.00D+00 EMaxC= 1.00D-01 BMatC= 5.19D-13 BMatP= 5.91D-13 + IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 + Coeff-Com: -0.579D-01 0.482D+00 0.576D+00 + Coeff: -0.579D-01 0.482D+00 0.576D+00 + Gap= 0.355 Goal= None Shift= 0.000 + RMSDP=2.32D-08 MaxDP=1.87D-07 DE=-1.42D-13 OVMax= 1.59D-07 + + Cycle 9 Pass 1 IDiag 1: + E= -76.4080197062446 Delta-E= -0.000000000000 Rises=F Damp=F + DIIS: error= 3.86D-09 at cycle 4 NSaved= 4. + NSaved= 4 IEnMin= 4 EnMin= -76.4080197062446 IErMin= 4 ErrMin= 3.86D-09 + ErrMax= 3.86D-09 0.00D+00 EMaxC= 1.00D-01 BMatC= 3.14D-16 BMatP= 5.19D-13 + IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 + Coeff-Com: -0.218D-02 0.917D-02 0.343D-01 0.959D+00 + Coeff: -0.218D-02 0.917D-02 0.343D-01 0.959D+00 + Gap= 0.355 Goal= None Shift= 0.000 + RMSDP=8.72D-10 MaxDP=6.90D-09 DE=-3.69D-13 OVMax= 7.62D-09 + + SCF Done: E(RB3LYP) = -76.4080197062 A.U. after 9 cycles + NFock= 9 Conv=0.87D-09 -V/T= 2.0075 + KE= 7.583703724817D+01 PE=-1.989174591291D+02 EE= 3.751528615130D+01 + Leave Link 502 at Thu Jul 31 11:46:32 2025, MaxMem= 6442450944 cpu: 15.2 elap: 0.4 + (Enter /home/bwli/soft//g16/l801.exe) + DoSCS=F DFT=T ScalE2(SS,OS)= 1.000000 1.000000 + Range of M.O.s used for correlation: 1 19 + NBasis= 19 NAE= 5 NBE= 5 NFC= 0 NFV= 0 + NROrb= 19 NOA= 5 NOB= 5 NVA= 14 NVB= 14 + Leave Link 801 at Thu Jul 31 11:46:34 2025, MaxMem= 6442450944 cpu: 1.9 elap: 0.4 + (Enter /home/bwli/soft//g16/l1101.exe) + Using compressed storage, NAtomX= 3. + Will process 4 centers per pass. + Leave Link 1101 at Thu Jul 31 11:46:37 2025, MaxMem= 6442450944 cpu: 7.7 elap: 0.3 + (Enter /home/bwli/soft//g16/l1102.exe) + Symmetrizing basis deriv contribution to polar: + IMax=3 JMax=2 DiffMx= 0.00D+00 + Leave Link 1102 at Thu Jul 31 11:46:38 2025, MaxMem= 6442450944 cpu: 4.5 elap: 0.2 + (Enter /home/bwli/soft//g16/l1110.exe) + Forming Gx(P) for the SCF density, NAtomX= 3. + Integral derivatives from FoFJK, PRISM(SPDF). + Do as many integral derivatives as possible in FoFJK. + G2DrvN: MDV= 6442450580. + G2DrvN: will do 4 centers at a time, making 1 passes. + Calling FoFCou, ICntrl= 3107 FMM=F I1Cent= 0 AccDes= 0.00D+00. + FoFJK: IHMeth= 1 ICntrl= 3107 DoSepK=F KAlg= 0 I1Cent= 0 FoldK=F + IRaf= 0 NMat= 1 IRICut= 1 DoRegI=T DoRafI=F ISym2E= 0 IDoP0=0 IntGTp=1. + FoFCou: FMM=F IPFlag= 0 FMFlag= 100000 FMFlg1= 0 + NFxFlg= 0 DoJE=F BraDBF=F KetDBF=F FulRan=T + wScrn= 0.000000 ICntrl= 3107 IOpCl= 0 I1Cent= 0 NGrid= 0 + NMat0= 1 NMatS0= 1 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0 + Symmetry not used in FoFCou. + End of G2Drv F.D. properties file 721 does not exist. + End of G2Drv F.D. properties file 722 does not exist. + End of G2Drv F.D. properties file 788 does not exist. + Leave Link 1110 at Thu Jul 31 11:46:39 2025, MaxMem= 6442450944 cpu: 18.9 elap: 0.6 + (Enter /home/bwli/soft//g16/l1002.exe) + Minotr: Closed shell wavefunction. + IDoAtm=111 + Direct CPHF calculation. + Differentiating once with respect to electric field. + with respect to dipole field. + Differentiating once with respect to nuclear coordinates. + Requested convergence is 1.0D-08 RMS, and 1.0D-07 maximum. + Secondary convergence is 1.0D-12 RMS, and 1.0D-12 maximum. + NewPWx=T KeepS1=F KeepF1=F KeepIn=T MapXYZ=F SortEE=F KeepMc=T. + 874 words used for storage of precomputed grid. + Keep R1 ints in memory in canonical form, NReq=41274230. + FoFCou: FMM=F IPFlag= 0 FMFlag= 0 FMFlg1= 0 + NFxFlg= 0 DoJE=F BraDBF=F KetDBF=F FulRan=T + wScrn= 0.000000 ICntrl= 600 IOpCl= 0 I1Cent= 0 NGrid= 0 + NMat0= 1 NMatS0= 190 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0 + Symmetry not used in FoFCou. + Two-electron integral symmetry not used. + MDV= 6442450944 using IRadAn= 1. + Solving linear equations simultaneously, MaxMat= 0. + There are 12 degrees of freedom in the 1st order CPHF. IDoFFX=6 NUNeed= 3. + 9 vectors produced by pass 0 Test12= 5.83D-16 8.33D-09 XBig12= 2.92D+00 1.07D+00. + AX will form 9 AO Fock derivatives at one time. + 9 vectors produced by pass 1 Test12= 5.83D-16 8.33D-09 XBig12= 1.15D-01 1.44D-01. + 9 vectors produced by pass 2 Test12= 5.83D-16 8.33D-09 XBig12= 7.78D-04 1.42D-02. + 9 vectors produced by pass 3 Test12= 5.83D-16 8.33D-09 XBig12= 7.10D-07 4.30D-04. + 8 vectors produced by pass 4 Test12= 5.83D-16 8.33D-09 XBig12= 2.73D-10 8.53D-06. + 3 vectors produced by pass 5 Test12= 5.83D-16 8.33D-09 XBig12= 6.27D-14 1.12D-07. + InvSVY: IOpt=1 It= 1 EMax= 4.44D-16 + Solved reduced A of dimension 47 with 9 vectors. + FullF1: Do perturbations 1 to 3. + Isotropic polarizability for W= 0.000000 5.08 Bohr**3. + End of Minotr F.D. properties file 721 does not exist. + End of Minotr F.D. properties file 722 does not exist. + End of Minotr F.D. properties file 788 does not exist. + Leave Link 1002 at Thu Jul 31 11:46:40 2025, MaxMem= 6442450944 cpu: 19.1 elap: 0.5 + (Enter /home/bwli/soft//g16/l601.exe) + Copying SCF densities to generalized density rwf, IOpCl= 0 IROHF=0. + + ********************************************************************** + + Population analysis using the SCF Density. + + ********************************************************************** + + Alpha occ. eigenvalues -- -19.13348 -0.99651 -0.53006 -0.36084 -0.28978 + Alpha virt. eigenvalues -- 0.06550 0.15268 0.80048 0.84879 0.89219 + Alpha virt. eigenvalues -- 0.89240 1.07367 1.17571 1.73998 1.74508 + Alpha virt. eigenvalues -- 1.78547 2.29893 2.59364 3.56652 + Condensed to atoms (all electrons): + 1 2 3 + 1 O 8.292274 0.247237 0.247237 + 2 H 0.247237 0.380379 -0.020990 + 3 H 0.247237 -0.020990 0.380379 + Mulliken charges: + 1 + 1 O -0.786748 + 2 H 0.393374 + 3 H 0.393374 + Sum of Mulliken charges = -0.00000 + Mulliken charges with hydrogens summed into heavy atoms: + 1 + 1 O -0.000000 + APT charges: + 1 + 1 O -0.524140 + 2 H 0.262070 + 3 H 0.262070 + Sum of APT charges = 0.00000 + APT charges with hydrogens summed into heavy atoms: + 1 + 1 O 0.000000 + Electronic spatial extent (au): = 23.1056 + Charge= -0.0000 electrons + Dipole moment (field-independent basis, Debye): + X= 1.1542 Y= 1.6331 Z= 0.0000 Tot= 1.9998 + Quadrupole moment (field-independent basis, Debye-Ang): + XX= -3.9900 YY= -4.8004 ZZ= -7.1850 + XY= -0.2335 XZ= -0.0000 YZ= 0.0000 + Traceless Quadrupole moment (field-independent basis, Debye-Ang): + XX= 1.3351 YY= 0.5247 ZZ= -1.8599 + XY= -0.2335 XZ= -0.0000 YZ= 0.0000 + Octapole moment (field-independent basis, Debye-Ang**2): + XXX= -2.6134 YYY= -1.3752 ZZZ= 0.0000 XYY= -2.1589 + XXY= -0.9339 XXZ= -0.0000 XZZ= -2.1422 YZZ= -1.1386 + YYZ= 0.0000 XYZ= 0.0000 + Hexadecapole moment (field-independent basis, Debye-Ang**3): + XXXX= -6.3033 YYYY= -5.6244 ZZZZ= -5.1928 XXXY= -0.4233 + XXXZ= -0.0000 YYYX= -0.8950 YYYZ= 0.0000 ZZZX= -0.0000 + ZZZY= 0.0000 XXYY= -3.0225 XXZZ= -2.6811 YYZZ= -2.1563 + XXYZ= 0.0000 YYXZ= -0.0000 ZZXY= -0.2455 + N-N= 9.157116023409D+00 E-N=-1.989174590256D+02 KE= 7.583703724817D+01 + Exact polarizability: 6.596 -1.116 5.805 0.000 -0.000 2.843 + Approx polarizability: 8.015 -1.365 7.048 0.000 -0.000 3.101 + No NMR shielding tensors so no spin-rotation constants. + Leave Link 601 at Thu Jul 31 11:46:41 2025, MaxMem= 6442450944 cpu: 6.1 elap: 0.2 + (Enter /home/bwli/soft//g16/l701.exe) + ... and contract with generalized density number 0. + Compute integral second derivatives. + Leave Link 701 at Thu Jul 31 11:46:42 2025, MaxMem= 6442450944 cpu: 9.4 elap: 0.3 + (Enter /home/bwli/soft//g16/l702.exe) + L702 exits ... SP integral derivatives will be done elsewhere. + Leave Link 702 at Thu Jul 31 11:46:43 2025, MaxMem= 6442450944 cpu: 1.7 elap: 0.1 + (Enter /home/bwli/soft//g16/l703.exe) + Integral derivatives from FoFJK, PRISM(SPDF). + Compute integral second derivatives, UseDBF=F ICtDFT= 0. + Calling FoFJK, ICntrl= 100127 FMM=F ISym2X=0 I1Cent= 0 IOpClX= 0 NMat=1 NMatS=1 NMatT=0. + FoFJK: IHMeth= 1 ICntrl= 100127 DoSepK=F KAlg= 0 I1Cent= 0 FoldK=F + IRaf= 0 NMat= 1 IRICut= 1 DoRegI=T DoRafI=F ISym2E= 0 IDoP0=0 IntGTp=1. + FoFCou: FMM=F IPFlag= 0 FMFlag= 100000 FMFlg1= 800 + NFxFlg= 0 DoJE=F BraDBF=F KetDBF=F FulRan=T + wScrn= 0.000000 ICntrl= 100127 IOpCl= 0 I1Cent= 0 NGrid= 0 + NMat0= 1 NMatS0= 1 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0 + Symmetry not used in FoFCou. + Leave Link 703 at Thu Jul 31 11:46:44 2025, MaxMem= 6442450944 cpu: 35.2 elap: 0.8 + (Enter /home/bwli/soft//g16/l716.exe) + Dipole = 4.54087017D-01 6.42518309D-01 2.32554128D-16 + Polarizability= 6.59560434D+00-1.11642875D+00 5.80490429D+00 + 1.92621132D-15-1.37779844D-15 2.84325849D+00 + Full mass-weighted force constant matrix: + Low frequencies --- -544.2957 -290.4692 0.0009 0.0012 0.0018 107.1369 + Low frequencies --- 1621.3301 3821.6419 3986.3183 + Diagonal vibrational polarizability: + 0.3453056 0.6303768 0.0000000 + Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering + activities (A**4/AMU), depolarization ratios for plane and unpolarized + incident light, reduced masses (AMU), force constants (mDyne/A), + and normal coordinates: + 1 2 3 + A A A + Frequencies -- 1621.3301 3821.6419 3986.1600 + Red. masses -- 1.0863 1.0418 1.0868 + Frc consts -- 1.6824 8.9651 10.1741 + IR Inten -- 88.8292 2.9677 35.9184 + Atom AN X Y Z X Y Z X Y Z + 1 8 -0.04 -0.06 -0.00 -0.03 -0.04 0.00 -0.06 0.04 -0.00 + 2 1 -0.00 0.71 -0.00 0.71 -0.04 0.00 0.71 -0.00 -0.00 + 3 1 0.67 0.23 -0.00 -0.27 0.65 0.00 0.24 -0.66 -0.00 + + ------------------- + - Thermochemistry - + ------------------- + Temperature 298.150 Kelvin. Pressure 1.00000 Atm. + Atom 1 has atomic number 8 and mass 15.99491 + Atom 2 has atomic number 1 and mass 1.00783 + Atom 3 has atomic number 1 and mass 1.00783 + Molecular mass: 18.01056 amu. + Principal axes and moments of inertia in atomic units: + 1 2 3 + Eigenvalues -- 1.96237 4.42403 6.38640 + X 0.81664 0.57715 0.00000 + Y -0.57715 0.81664 0.00000 + Z -0.00000 0.00000 1.00000 + This molecule is an asymmetric top. + Rotational symmetry number 2. + Rotational temperatures (Kelvin) 44.13749 19.57805 13.56225 + Rotational constants (GHZ): 919.67597 407.94033 282.59138 + Zero-point vibrational energy 56398.7 (Joules/Mol) + 13.47962 (Kcal/Mol) + Vibrational temperatures: 2332.73 5498.49 5735.20 + (Kelvin) + + Zero-point correction= 0.021481 (Hartree/Particle) + Thermal correction to Energy= 0.024317 + Thermal correction to Enthalpy= 0.025261 + Thermal correction to Gibbs Free Energy= 0.003865 + Sum of electronic and zero-point Energies= -76.386539 + Sum of electronic and thermal Energies= -76.383703 + Sum of electronic and thermal Enthalpies= -76.382759 + Sum of electronic and thermal Free Energies= -76.404154 + + E (Thermal) CV S + KCal/Mol Cal/Mol-Kelvin Cal/Mol-Kelvin + Total 15.259 6.010 45.030 + Electronic 0.000 0.000 0.000 + Translational 0.889 2.981 34.608 + Rotational 0.889 2.981 10.415 + Vibrational 13.481 0.049 0.007 + Q Log10(Q) Ln(Q) + Total Bot 0.166736D-01 -1.777970 -4.093927 + Total V=0 0.126666D+09 8.102661 18.657067 + Vib (Bot) 0.131687D-09 -9.880457 -22.750594 + Vib (V=0) 0.100040D+01 0.000174 0.000400 + Electronic 0.100000D+01 0.000000 0.000000 + Translational 0.300431D+07 6.477745 14.915559 + Rotational 0.421447D+02 1.624743 3.741109 + + Title Card Required + IR Spectrum + + 3 3 1 + 9 8 6 + 8 2 2 + 6 2 1 + + X X X + X X + X X + X X + X X + X X + X X + X X + X + X + X + X + X + X + X + X + X + X + X + X + + ------------------------------------------------------------------- + Center Atomic Forces (Hartrees/Bohr) + Number Number X Y Z + ------------------------------------------------------------------- + 1 8 -0.012127815 -0.017160737 -0.000000000 + 2 1 0.005534152 0.008954943 -0.000000000 + 3 1 0.006593663 0.008205794 0.000000000 + ------------------------------------------------------------------- + Cartesian Forces: Max 0.017160737 RMS 0.008584250 + Z-matrix is all fixed cartesians, so copy forces. + Force constants in Cartesian coordinates: + 1 2 3 4 5 + 1 0.633669D+00 + 2 -0.143437D+00 0.532081D+00 + 3 0.000000D+00 0.000000D+00 -0.200692D-01 + 4 -0.536549D+00 0.276686D-01 0.000000D+00 0.547924D+00 + 5 -0.398358D-01 -0.463346D-01 0.000000D+00 -0.112639D-01 0.454248D-01 + 6 0.000000D+00 0.000000D+00 0.100320D-01 0.000000D+00 0.000000D+00 + 7 -0.971200D-01 0.115768D+00 0.000000D+00 -0.113758D-01 0.510998D-01 + 8 0.183273D+00 -0.485746D+00 0.000000D+00 -0.164047D-01 0.909873D-03 + 9 0.000000D+00 0.000000D+00 0.100373D-01 0.000000D+00 0.000000D+00 + 6 7 8 9 + 6 -0.479578D-02 + 7 0.000000D+00 0.108496D+00 + 8 0.000000D+00 -0.166868D+00 0.484837D+00 + 9 -0.523620D-02 0.000000D+00 0.000000D+00 -0.480107D-02 + Leave Link 716 at Thu Jul 31 11:46:47 2025, MaxMem= 6442450944 cpu: 5.0 elap: 0.2 + (Enter /home/bwli/soft//g16/l103.exe) + + GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad + Berny optimization. + Search for a local minimum. + Step number 1 out of a maximum of 2 + All quantities printed in internal units (Hartrees-Bohrs-Radians) + Second derivative matrix not updated -- analytic derivatives used. + The second derivative matrix: + X1 Y1 Z1 X2 Y2 + X1 0.63367 + Y1 -0.14344 0.53208 + Z1 0.00000 -0.00000 -0.02007 + X2 -0.53655 0.02767 0.00000 0.54792 + Y2 -0.03984 -0.04633 0.00000 -0.01126 0.04542 + Z2 0.00000 0.00000 0.01003 -0.00000 -0.00000 + X3 -0.09712 0.11577 -0.00000 -0.01138 0.05110 + Y3 0.18327 -0.48575 0.00000 -0.01640 0.00091 + Z3 -0.00000 0.00000 0.01004 -0.00000 -0.00000 + Z2 X3 Y3 Z3 + Z2 -0.00480 + X3 0.00000 0.10850 + Y3 0.00000 -0.16687 0.48484 + Z3 -0.00524 0.00000 -0.00000 -0.00480 + ITU= 0 + Eigenvalues --- 0.15097 0.76589 1.03419 + Angle between quadratic step and forces= 43.70 degrees. + Linear search not attempted -- first point. + B after Tr= -0.013183 -0.018654 0.000000 + Rot= 1.000000 0.000000 -0.000000 0.000000 Ang= 0.00 deg. + Variable Old X -DE/DX Delta X Delta X Delta X New X + (Linear) (Quad) (Total) + X1 0.49041 -0.01213 0.00000 -0.02163 -0.03481 0.45560 + Y1 0.19617 -0.01716 0.00000 -0.03061 -0.04926 0.14691 + Z1 0.00000 -0.00000 0.00000 0.00000 0.00000 0.00000 + X2 2.30455 0.00553 0.00000 -0.00619 -0.01938 2.28517 + Y2 0.19617 0.00895 0.00000 0.06928 0.05063 0.24679 + Z2 0.00000 -0.00000 0.00000 0.00000 -0.00000 -0.00000 + X3 -0.11516 0.00659 0.00000 0.06737 0.05419 -0.06097 + Y3 1.90625 0.00821 0.00000 0.01729 -0.00137 1.90488 + Z3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + Item Value Threshold Converged? + Maximum Force 0.017161 0.000450 NO + RMS Force 0.008584 0.000300 NO + Maximum Displacement 0.054191 0.001800 NO + RMS Displacement 0.032516 0.001200 NO + Predicted change in Energy=-9.798810D-04 + GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad + + Leave Link 103 at Thu Jul 31 11:46:47 2025, MaxMem= 6442450944 cpu: 7.1 elap: 0.2 + (Enter /home/bwli/soft//g16/l9999.exe) + + ---------------------------------------------------------------------- + + Electric dipole moment (input orientation): + (Debye = 10**-18 statcoulomb cm , SI units = C m) + (au) (Debye) (10**-30 SI) + Tot 0.786781D+00 0.199980D+01 0.667061D+01 + x 0.454087D+00 0.115417D+01 0.384991D+01 + y 0.642518D+00 0.163312D+01 0.544750D+01 + z 0.000000D+00 0.000000D+00 0.000000D+00 + + Dipole polarizability, Alpha (input orientation). + (esu units = cm**3 , SI units = C**2 m**2 J**-1) + Alpha(0;0): + (au) (10**-24 esu) (10**-40 SI) + iso 0.508126D+01 0.752964D+00 0.837786D+00 + aniso 0.393415D+01 0.582981D+00 0.648654D+00 + xx 0.659560D+01 0.977368D+00 0.108747D+01 + yx -0.111643D+01 -0.165438D+00 -0.184074D+00 + yy 0.580490D+01 0.860198D+00 0.957099D+00 + zx 0.000000D+00 0.000000D+00 0.000000D+00 + zy 0.000000D+00 0.000000D+00 0.000000D+00 + zz 0.284326D+01 0.421327D+00 0.468790D+00 + + ---------------------------------------------------------------------- + + Dipole orientation: + 8 0.23460157 -0.16579998 0.44323647 + 1 1.44445586 -1.02084041 1.49025692 + 1 -0.97525268 0.68924041 1.49025700 + + Electric dipole moment (dipole orientation): + (Debye = 10**-18 statcoulomb cm , SI units = C m) + (au) (Debye) (10**-30 SI) + Tot 0.786781D+00 0.199980D+01 0.667061D+01 + x 0.000000D+00 0.000000D+00 0.000000D+00 + y 0.000000D+00 0.000000D+00 0.000000D+00 + z 0.786781D+00 0.199980D+01 0.667061D+01 + + Dipole polarizability, Alpha (dipole orientation). + (esu units = cm**3 , SI units = C**2 m**2 J**-1) + Alpha(0;0): + (au) (10**-24 esu) (10**-40 SI) + iso 0.508126D+01 0.752964D+00 0.837786D+00 + aniso 0.393415D+01 0.582981D+00 0.648654D+00 + xx 0.587191D+01 0.870127D+00 0.968147D+00 + yx -0.214044D+01 -0.317180D+00 -0.352910D+00 + yy 0.435597D+01 0.645488D+00 0.718202D+00 + zx 0.000000D+00 0.000000D+00 0.000000D+00 + zy 0.000000D+00 0.000000D+00 0.000000D+00 + zz 0.501589D+01 0.743278D+00 0.827009D+00 + + ---------------------------------------------------------------------- + + Test job not archived. + 1\1\GINC-MASTER\Freq\RB3LYP\6-31G(d)\H2O1\BWLI\31-Jul-2025\0\\#P b3lyp + 6-31g* freq nosymm\\Title Card Required\\0,1\O,0.25951557,0.10380623, + 0.\H,1.21951557,0.10380623,0.\H,-0.06093902,1.00874206,0.\\Version=ES6 + 4L-G16RevB.01\HF=-76.4080197\RMSD=8.716e-10\RMSF=8.584e-03\ZeroPoint=0 + .0214811\Thermal=0.0243167\Dipole=0.454087,0.6425183,0.\DipoleDeriv=-0 + .4218905,0.0321989,0.,0.0321987,-0.3990856,0.,0.,0.,-0.7514445,0.11880 + 82,-0.0380562,0.,-0.0593969,0.2916792,0.,0.,0.,0.3757222,0.3030823,0.0 + 058573,0.,0.0271982,0.1074064,0.,0.,0.,0.3757223\Polar=6.5956043,-1.11 + 64287,5.8049043,0.,0.,2.8432585\Quadrupole=0.9926505,0.390137,-1.38278 + 75,-0.1736145,0.,0.\PG=C02V [C2(O1),SGV(H2)]\NImag=0\\0.63366863,-0.14 + 343674,0.53208110,0.,0.,-0.02006924,-0.53654867,0.02766860,0.,0.547924 + 48,-0.03983584,-0.04633463,0.,-0.01126391,0.04542476,0.,0.,0.01003198, + 0.,0.,-0.00479578,-0.09711996,0.11576814,0.,-0.01137581,0.05109975,0., + 0.10849577,0.18327258,-0.48574647,0.,-0.01640469,0.00090987,0.,-0.1668 + 6789,0.48483660,0.,0.,0.01003727,0.,0.,-0.00523620,0.,0.,-0.00480107\\ + 0.01212782,0.01716074,0.,-0.00553415,-0.00895494,0.,-0.00659366,-0.008 + 20579,0.\\\@ + + + ALL PAPERS THAT YOU SAVE WILL NEVER BE NEEDED UNTIL + SUCH TIME AS THEY ARE DISPOSED OF, WHEN THEY BECOME + ESSENTIAL. + + -- JOHN CORCORAN IN + PAUL DICKSON'S "THE OFFICIAL RULES" + Job cpu time: 0 days 0 hours 3 minutes 19.4 seconds. + Elapsed time: 0 days 0 hours 0 minutes 6.3 seconds. + File lengths (MBytes): RWF= 17 Int= 0 D2E= 0 Chk= 2 Scr= 2 + Normal termination of Gaussian 16 at Thu Jul 31 11:46:48 2025. diff --git a/tests/test_gaussian_fchk.py b/tests/test_gaussian_fchk.py new file mode 100644 index 000000000..0da31a90f --- /dev/null +++ b/tests/test_gaussian_fchk.py @@ -0,0 +1,181 @@ +from __future__ import annotations + +import unittest + +import numpy as np +from context import dpdata + + +class TestGaussianLoadFchk(unittest.TestCase): + def setUp(self): + self.system = dpdata.LabeledSystem( + "gaussian/waterfreq.gaussianfchk", fmt="gaussian/fchk" + ) + self.atom_names = ["H", "O"] + self.atom_numbs = [2, 1] + self.nframes = 1 + self.atom_types = [1, 0, 0] + + def test_atom_names(self): + """Test that atom names are correctly read.""" + self.assertEqual(self.system.data["atom_names"], self.atom_names) + + def test_atom_numbs(self): + """Test that atom numbers are correctly read.""" + self.assertEqual(self.system.data["atom_numbs"], self.atom_numbs) + + def test_nframes(self): + """Test that number of frames is correct.""" + self.assertEqual(len(self.system), self.nframes) + + def test_atom_types(self): + """Test that atom types are correctly assigned.""" + for ii in range(len(self.atom_types)): + self.assertEqual(self.system.data["atom_types"][ii], self.atom_types[ii]) + + def test_nopbc(self): + """Test that nopbc is set to True for fchk files.""" + self.assertEqual(self.system.nopbc, True) + + def test_energies_exist(self): + """Test that energies are present and have correct shape.""" + self.assertIn("energies", self.system.data) + self.assertEqual(len(self.system.data["energies"]), 1) + self.assertIsInstance(self.system.data["energies"], np.ndarray) + + def test_forces_exist(self): + """Test that forces are present and have correct shape.""" + self.assertIn("forces", self.system.data) + self.assertEqual(self.system.data["forces"].shape, (1, 3, 3)) + self.assertIsInstance(self.system.data["forces"], np.ndarray) + + def test_hessian_exist(self): + """Test that hessian matrix is present and has correct shape.""" + self.assertIn("hessian", self.system.data) + self.assertEqual(self.system.data["hessian"].shape, (1, 3, 3, 3, 3)) + self.assertIsInstance(self.system.data["hessian"], np.ndarray) + + def test_coords_exist(self): + """Test that coordinates are present and have correct shape.""" + self.assertIn("coords", self.system.data) + self.assertEqual(self.system.data["coords"].shape, (1, 3, 3)) + self.assertIsInstance(self.system.data["coords"], np.ndarray) + + def test_cells_exist(self): + """Test that cells are present and have correct shape.""" + self.assertIn("cells", self.system.data) + self.assertEqual(self.system.data["cells"].shape, (1, 3, 3)) + self.assertIsInstance(self.system.data["cells"], np.ndarray) + + def test_orig_exist(self): + """Test that origin is present and has correct shape.""" + self.assertIn("orig", self.system.data) + self.assertEqual(self.system.data["orig"].shape, (3,)) + self.assertIsInstance(self.system.data["orig"], np.ndarray) + + +class TestGaussianFchkVsLog(unittest.TestCase): + """Test to compare results from fchk and log files.""" + + def setUp(self): + # Load both fchk and log files + self.system_fchk = dpdata.LabeledSystem( + "gaussian/waterfreq.gaussianfchk", fmt="gaussian/fchk" + ) + self.system_log = dpdata.LabeledSystem( + "gaussian/waterfreq.gaussianlog", fmt="gaussian/log" + ) + + # Get conversion factors from dpdata + from dpdata.unit import EnergyConversion, ForceConversion, LengthConversion + + self.energy_convert = EnergyConversion("hartree", "eV").value() + self.force_convert = ForceConversion("hartree/bohr", "eV/angstrom").value() + self.length_convert = LengthConversion("bohr", "angstrom").value() + + def test_energies_consistency(self): + """Test that energies from fchk and log files are consistent.""" + # Check that both files have energies + self.assertIn("energies", self.system_fchk.data) + self.assertIn("energies", self.system_log.data) + + # Check that energies have the same length + self.assertEqual( + len(self.system_fchk.data["energies"]), + len(self.system_log.data["energies"]), + ) + + # Check that energies are equal (allowing for small numerical differences) + fchk_energy = self.system_fchk.data["energies"][0] + log_energy = self.system_log.data["energies"][0] + self.assertAlmostEqual(fchk_energy, log_energy, places=6) + + def test_forces_consistency(self): + """Test that forces from fchk and log files are consistent.""" + # Check that both files have forces + self.assertIn("forces", self.system_fchk.data) + self.assertIn("forces", self.system_log.data) + + # Check that forces have the same shape + self.assertEqual( + self.system_fchk.data["forces"].shape, self.system_log.data["forces"].shape + ) + + # Check that forces are equal (allowing for small numerical differences) + fchk_forces = self.system_fchk.data["forces"][0] + log_forces = self.system_log.data["forces"][0] + np.testing.assert_array_almost_equal(fchk_forces, log_forces, decimal=6) + + def test_coordinates_consistency(self): + """Test that coordinates from fchk and log files are consistent.""" + # Check that both files have coordinates + self.assertIn("coords", self.system_fchk.data) + self.assertIn("coords", self.system_log.data) + + # Check that coordinates have the same shape + self.assertEqual( + self.system_fchk.data["coords"].shape, self.system_log.data["coords"].shape + ) + + # Check that coordinates are equal (allowing for small numerical differences) + fchk_coords = self.system_fchk.data["coords"][0] + log_coords = self.system_log.data["coords"][0] + np.testing.assert_array_almost_equal(fchk_coords, log_coords, decimal=6) + + def test_atom_info_consistency(self): + """Test that atom information is consistent between fchk and log files.""" + # Check atom names + self.assertEqual( + self.system_fchk.data["atom_names"], self.system_log.data["atom_names"] + ) + + # Check atom numbers + self.assertEqual( + self.system_fchk.data["atom_numbs"], self.system_log.data["atom_numbs"] + ) + + # Check atom types + np.testing.assert_array_equal( + self.system_fchk.data["atom_types"], self.system_log.data["atom_types"] + ) + + def test_system_properties_consistency(self): + """Test that system properties are consistent between fchk and log files.""" + # Check number of frames + self.assertEqual(len(self.system_fchk), len(self.system_log)) + + # Check nopbc property + self.assertEqual(self.system_fchk.nopbc, self.system_log.nopbc) + + # Check that both have the same data keys + fchk_keys = set(self.system_fchk.data.keys()) + log_keys = set(self.system_log.data.keys()) + + # fchk has hessian, log doesn't, so we exclude it from comparison + fchk_keys.discard("hessian") + + self.assertEqual(fchk_keys, log_keys) + + +if __name__ == "__main__": + unittest.main()