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# fmt: off
"""Tests for the gaussian-out format."""
from io import StringIO
import numpy as np
import pytest
from ase import units
from ase.io import read
from ase.io.formats import match_magic
BUF_H2O = r"""
Entering Gaussian System, Link 0=g16
...
******************************************
Gaussian 16: ES64L-G16RevA.03 25-Dec-2016
6-Apr-2021
******************************************
...
Input orientation:
---------------------------------------------------------------------
Center Atomic Atomic Coordinates (Angstroms)
Number Number Type X Y Z
---------------------------------------------------------------------
1 8 0 0.000000 0.000000 0.119262
2 1 0 0.000000 0.763239 -0.477047
3 1 0 0.000000 -0.763239 -0.477047
---------------------------------------------------------------------
...
SCF Done: E(RHF) = -75.9834173665 A.U. after 10 cycles
"""
BUF_H2O_MULLIKEN = r"""
(Enter /opt/bwhpc/common/chem/gaussian/g16.C.01/x86_64-Intel-avx2-source/g16/l601.exe)
...
Mulliken charges:
1
1 O -0.792441
2 H 0.396221
3 H 0.396221
Sum of Mulliken charges = -0.00000
""" # noqa: E501
BUF_H2O_LOWDIN = r"""
Lowdin Atomic Charges:
1
1 O -0.584488
2 H 0.292244
3 H 0.292244
Sum of Lowdin charges = -0.00000
"""
BUF_H2O_L601_DIPOLE = r"""
Dipole moment (field-independent basis, Debye):
X= 0.0000 Y= -0.0000 Z= -2.6431 Tot= 2.6431
""" # noqa: E501
BUF_H2O_HIRSHFELD = r"""
Hirshfeld charges, spin densities, dipoles, and CM5 charges using IRadAn= 5:
Q-H S-H Dx Dy Dz Q-CM5
1 O -0.338600 0.000000 0.000000 -0.000000 -0.367327 -0.665793
2 H 0.169300 0.000000 -0.000000 0.161888 -0.145504 0.332897
3 H 0.169300 0.000000 -0.000000 -0.161888 -0.145504 0.332897
Tot -0.000000 0.000000 -0.000000 -0.000000 -0.658335 -0.000000
""" # noqa: E501
BUF_H2O_L716 = r"""
(Enter /opt/bwhpc/common/chem/gaussian/g16.C.01/x86_64-Intel-avx2-source/g16/l716.exe)
Dipole = 3.27065103D-16-1.33226763D-15-1.03989005D+00
-------------------------------------------------------------------
Center Atomic Forces (Hartrees/Bohr)
Number Number X Y Z
-------------------------------------------------------------------
1 8 -0.000000000 -0.000000000 -0.036558637
2 1 -0.000000000 -0.003968101 0.018279318
3 1 0.000000000 0.003968101 0.018279318
-------------------------------------------------------------------
""" # noqa: E501
BUF_O2 = r"""
Input orientation:
---------------------------------------------------------------------
Center Atomic Atomic Coordinates (Angstroms)
Number Number Type X Y Z
---------------------------------------------------------------------
1 8 0 0.000000 0.000000 0.622978
2 8 0 0.000000 0.000000 -0.622978
---------------------------------------------------------------------
...
SCF Done: E(UHF) = -149.541919412 A.U. after 10 cycles
"""
BUF_O2_MULLIKEN = r"""
(Enter /opt/bwhpc/common/chem/gaussian/g16.C.01/x86_64-Intel-avx2-source/g16/l601.exe)
...
Mulliken charges and spin densities:
1 2
1 O 0.000000 1.000000
2 O -0.000000 1.000000
Sum of Mulliken charges = -0.00000 2.00000
""" # noqa: E501
BUF_F2_RHF = r"""
Entering Gaussian System, Link 0=g16
...
Input orientation:
---------------------------------------------------------------------
Center Atomic Atomic Coordinates (Angstroms)
Number Number Type X Y Z
---------------------------------------------------------------------
1 9 0 0.000000 0.000000 0.700000
2 9 0 0.000000 0.000000 -0.700000
---------------------------------------------------------------------
...
SCF Done: E(RHF) = -198.700044583 A.U. after 8 cycles
"""
BUF_F2_MP2 = BUF_F2_RHF + r"""
...
E2 = -0.4264521750D+00 EUMP2 = -0.19912649675787D+03
"""
BUF_F2_CCSD = BUF_F2_MP2 + r"""
...
Wavefunction amplitudes converged. E(Corr)= -199.13391098
"""
BUF_F2_CCSD_T = BUF_F2_CCSD + r"""
...
CCSD(T)= -0.19914648303D+03
"""
BUF_H2O_OPT = r""" Entering Gaussian System, Link 0=g16
Initial command:
...
(Enter /soft/gaussian/16-c.02/g16/l202.exe)
Input orientation:
---------------------------------------------------------------------
Center Atomic Atomic Coordinates (Angstroms)
Number Number Type X Y Z
---------------------------------------------------------------------
1 8 0 0.000000 0.000000 0.117782
2 1 0 0.000000 0.756577 -0.476307
3 1 0 -0.000000 -0.756577 -0.476307
---------------------------------------------------------------------
Distance matrix (angstroms):
1 2 3
1 O 0.000000
2 H 0.961952 0.000000
3 H 0.961952 1.513154 0.000000
Stoichiometry H2O
Framework group C2V[C2(O),SGV(H2)]
Deg. of freedom 2
Full point group C2V NOp 4
RotChk: IX=0 Diff= 3.20D-16
Largest Abelian subgroup C2V NOp 4
Largest concise Abelian subgroup C2 NOp 2
Standard orientation:
---------------------------------------------------------------------
Center Atomic Atomic Coordinates (Angstroms)
Number Number Type X Y Z
---------------------------------------------------------------------
1 8 0 0.000000 0.000000 0.118818
2 1 0 -0.000000 0.756577 -0.475272
3 1 0 -0.000000 -0.756577 -0.475272
---------------------------------------------------------------------
...
SCF Done: E(RB3LYP) = -76.4259945508 A.U. after 9 cycles
***** Axes restored to original set *****
-------------------------------------------------------------------
Center Atomic Forces (Hartrees/Bohr)
Number Number X Y Z
-------------------------------------------------------------------
1 8 -0.000000000 0.000000000 -0.006569831
2 1 -0.000000000 -0.005632960 0.003284915
3 1 0.000000000 0.005632960 0.003284915
-------------------------------------------------------------------
...
(Enter /soft/gaussian/16-c.02/g16/l202.exe)
Input orientation:
---------------------------------------------------------------------
Center Atomic Atomic Coordinates (Angstroms)
Number Number Type X Y Z
---------------------------------------------------------------------
1 8 0 -0.000000 -0.000000 0.117858
2 1 0 0.000000 0.756683 -0.476345
3 1 0 -0.000000 -0.756683 -0.476345
---------------------------------------------------------------------
Distance matrix (angstroms):
1 2 3
1 O 0.000000
2 H 0.962105 0.000000
3 H 0.962105 1.513366 0.000000
Stoichiometry H2O
Framework group C2V[C2(O),SGV(H2)]
Deg. of freedom 2
Full point group C2V NOp 4
RotChk: IX=0 Diff= 4.65D-16
Largest Abelian subgroup C2V NOp 4
Largest concise Abelian subgroup C2 NOp 2
Standard orientation:
---------------------------------------------------------------------
Center Atomic Atomic Coordinates (Angstroms)
Number Number Type X Y Z
---------------------------------------------------------------------
1 8 0 -0.000000 0.000000 0.118841
2 1 0 0.000000 0.756683 -0.475362
3 1 0 -0.000000 -0.756683 -0.475362
---------------------------------------------------------------------
...
SCF Done: E(RB3LYP) = -76.4260779687 A.U. after 7 cycles
...
***** Axes restored to original set *****
-------------------------------------------------------------------
Center Atomic Forces (Hartrees/Bohr)
Number Number X Y Z
-------------------------------------------------------------------
1 8 -0.000000000 -0.000000000 0.000176354
2 1 0.000000000 0.000122881 -0.000088177
3 1 0.000000000 -0.000122881 -0.000088177
-------------------------------------------------------------------
Cartesian Forces: Max 0.000176354 RMS 0.000092406
"""
def test_match_magic():
"""Test if the file type can be guessed correctly."""
bytebuf = BUF_H2O.encode('ascii')
assert match_magic(bytebuf).name == 'gaussian-out'
def test_gaussian_out_l601():
"""Test if positions and energy are parsed correctly.
Test also if dipole moment is parsed correctly from `l601.exe`.
This corresponds to the options without `Forces` and `Pop=None`.
"""
buf = BUF_H2O + BUF_H2O_MULLIKEN + BUF_H2O_L601_DIPOLE
atoms = read(StringIO(buf), format='gaussian-out')
assert str(atoms.symbols) == 'OH2'
assert atoms.positions == pytest.approx(np.array([
[+0.000000, +0.000000, +0.119262],
[+0.000000, +0.763239, -0.477047],
[+0.000000, -0.763239, -0.477047],
]))
assert not any(atoms.pbc)
assert atoms.cell.rank == 0
energy = atoms.get_potential_energy()
assert energy / units.Ha == pytest.approx(-75.9834173665)
charges_ref = pytest.approx(np.array([-0.792441, +0.396221, +0.396221]))
assert atoms.get_charges() == charges_ref
dipole_moment_ref = pytest.approx(np.array([+0.0000, -0.0000, -2.6431]))
assert atoms.get_dipole_moment() / units.Debye == dipole_moment_ref
def test_gaussian_out_l716():
"""Test if forces and dipole moment are parsed correctly from `l716.exe`.
This corresponds to the options with `Forces` and `Pop=None`.
"""
atoms = read(StringIO(BUF_H2O + BUF_H2O_L716), format='gaussian-out')
forces = atoms.get_forces()
assert forces / (units.Ha / units.Bohr) == pytest.approx(np.array([
[-0.000000000, -0.000000000, -0.036558637],
[-0.000000000, -0.003968101, +0.018279318],
[+0.000000000, +0.003968101, +0.018279318],
]))
assert atoms.get_dipole_moment() / units.Bohr == pytest.approx(np.array(
[+3.27065103e-16, -1.33226763e-15, -1.03989005e+00],
))
def test_gaussian_out_lowdin():
"""Test if Löwdin charges are parsed correctly from `l601.exe`.
This corresponds to the options with `IOp(6/80=1)`.
"""
buf = BUF_H2O + BUF_H2O_MULLIKEN + BUF_H2O_LOWDIN
atoms = read(StringIO(buf), format='gaussian-out')
charges_ref = pytest.approx(np.array([-0.584488, +0.292244, +0.292244]))
assert atoms.get_charges() == charges_ref
def test_gaussian_out_hirshfeld():
"""Test if Hirshfeld charges are parsed correctly from `l601.exe`.
This corresponds to the options with `Pop=Hirshfeld`.
"""
buf = BUF_H2O + BUF_H2O_MULLIKEN + BUF_H2O_HIRSHFELD
atoms = read(StringIO(buf), format='gaussian-out')
charges_ref = pytest.approx(np.array([-0.338600, +0.169300, +0.169300]))
assert atoms.get_charges() == charges_ref
assert atoms.get_magnetic_moments() == pytest.approx(np.zeros(3))
def test_spin_polarized():
"""Test if spin polarized calculations are parsed correctly."""
buf = BUF_O2 + BUF_O2_MULLIKEN
atoms = read(StringIO(buf), format='gaussian-out')
assert atoms.get_charges() == pytest.approx(np.zeros(2))
assert atoms.get_magnetic_moments() == pytest.approx(np.ones(2))
def test_mp2():
"""Test if the MP2 energy is parsed correctly."""
atoms = read(StringIO(BUF_F2_MP2), format="gaussian-out")
energy = atoms.get_potential_energy()
assert energy / units.Ha == pytest.approx(-0.19912649675787e+03)
def test_ccsd():
"""Test if the CCSD energy is parsed correctly."""
atoms = read(StringIO(BUF_F2_CCSD), format="gaussian-out")
energy = atoms.get_potential_energy()
assert energy / units.Ha == pytest.approx(-199.13391098)
def test_ccsd_t():
"""Test if the CCSD(T) energy is parsed correctly."""
atoms = read(StringIO(BUF_F2_CCSD_T), format="gaussian-out")
energy = atoms.get_potential_energy()
assert energy / units.Ha == pytest.approx(-0.19914648303e+03)
def test_gaussian_opt():
"""Test if we determine the correct number of geometries in the output
produced during optimization"""
atoms = read(StringIO(BUF_H2O_OPT), format="gaussian-out", index=':')
assert len(atoms) == 2
# Ensure the energy and forces were parsed and differ
assert atoms[0].get_potential_energy() != atoms[1].get_potential_energy()
assert not np.isclose(atoms[0].get_forces(), atoms[1].get_forces()).all()
|
