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# fmt: off
import io
import numpy as np
import pytest
from ase.atoms import Atoms
from ase.calculators.calculator import compare_atoms
from ase.io import read
from ase.io.orca import (
read_dipole,
read_energy,
read_geom_orcainp,
read_orca_outputs,
write_orca,
)
from ase.units import Bohr, Hartree
def test_orca_inputfile():
sample_inputfile = """ ! engrad B3LYP def2-TZVPP
%pal nprocs 4 end
*xyz 0 1
O 0.0 0.0 0.0
H 1.0 0.0 0.0
H 0.0 1.0 0.0
*
"""
sample_inputfile_lines = sample_inputfile.splitlines()
atoms = Atoms('OHH', positions=[(0, 0, 0), (1, 0, 0), (0, 1, 0)])
kw = dict(charge=0, mult=1,
orcasimpleinput='engrad B3LYP def2-TZVPP',
orcablocks='%pal nprocs 4 end')
write_orca('orca.inp', atoms, kw)
with open('orca.inp') as fd:
lines = fd.readlines()
assert len(lines) == len(sample_inputfile_lines)
for line, expected_line in zip(lines, sample_inputfile_lines):
assert line.strip() == expected_line.strip()
def test_read_geom_orcainp():
atoms = Atoms('OHH', positions=[(0, 0, 0), (1, 0, 0), (0, 1, 0)])
kw = dict(charge=0, mult=1,
orcasimpleinput='B3LYP def2-TZVPP',
orcablocks='%pal nprocs 4 end')
fname = 'orcamolecule_test.inp'
write_orca(fname, atoms, kw)
with open(fname) as test:
atoms2 = read_geom_orcainp(test)
assert not compare_atoms(atoms, atoms2, tol=1e-7)
def test_read_orca_outputs():
sample_outputfile = """\
--------------------------------------------
MULLIKEN ATOMIC CHARGES AND SPIN POPULATIONS
--------------------------------------------
0 F : -0.223492 0.725756
1 Si: 0.515710 -0.002768
2 C : -0.452154 0.089331
3 C : -0.696844 0.022858
4 C : -0.694442 0.017446
5 C : -0.698397 0.000030
6 H : 0.207679 -0.001384
7 H : 0.184093 -0.000681
8 H : 0.184873 -0.000435
9 H : 0.184661 -0.000913
10 H : 0.212080 -0.002038
11 H : 0.185083 -0.000575
12 H : 0.182349 0.000294
13 H : 0.181951 0.000082
14 H : 0.209136 -0.000591
15 C : 0.381353 0.032364
16 C : -0.006580 0.031356
17 C : -0.123313 0.027413
18 C : -0.141712 -0.010118
19 C : -0.117620 0.060307
20 C : -0.141521 -0.009931
21 C : -0.123495 0.027134
22 H : 0.162169 -0.001285
23 H : 0.155246 0.000176
24 H : 0.156288 -0.002719
25 H : 0.155160 0.000168
26 H : 0.161737 -0.001275
Sum of atomic charges : -0.0000000
Sum of atomic spin populations: 1.0000000
Number of atoms ... 3
---------------------------------
CARTESIAN COORDINATES (ANGSTROEM)
---------------------------------
O 0.0000000 0.0000000 0.0000000
H 1.8897261 0.0000000 0.0000000
H 0.0000000 1.8897261 0.0000000
-------
TIMINGS
-------
Total SCF time: 0 days 0 hours 0 min 3 sec
Total time .... 3.805 sec
Sum of individual times .... 3.040 sec ( 79.9%)
Fock matrix formation .... 2.425 sec ( 63.7%)
XC integration .... 0.095 sec ( 3.9% of F)
Basis function eval. .... 0.020 sec ( 21.5% of XC)
Density eval. .... 0.013 sec ( 13.9% of XC)
XC-Functional eval. .... 0.012 sec ( 12.7% of XC)
XC-Potential eval. .... 0.022 sec ( 23.1% of XC)
Diagonalization .... 0.004 sec ( 0.1%)
Density matrix formation .... 0.047 sec ( 1.2%)
Population analysis .... 0.002 sec ( 0.1%)
Initial guess .... 0.470 sec ( 12.3%)
Orbital Transformation .... 0.000 sec ( 0.0%)
Orbital Orthonormalization .... 0.000 sec ( 0.0%)
DIIS solution .... 0.001 sec ( 0.0%)
SOSCF solution .... 0.010 sec ( 0.3%)
Grid generation .... 0.081 sec ( 2.1%)
------------------------- --------------------
FINAL SINGLE POINT ENERGY -76.422436201230
------------------------- --------------------
ORCA TERMINATED NORMALLY
""" # noqa: E501, W291
sample_engradfile = """\
#
# Number of atoms
#
3
#
# The current total energy in Eh
#
-76.422436201230
#
# The current gradient in Eh/bohr
#
-0.047131484960
-0.047131484716
0.000000000053
0.025621056182
0.021510428527
0.000000000034
0.021510428778
0.025621056189
-0.000000000087
#
# The atomic numbers and current coordinates in Bohr
#
8 0.0000000 0.0000000 0.0000000
1 1.8897261 0.0000000 0.0000000
1 0.0000000 1.8897261 0.0000000
"""
with open('orcamolecule_test.out', 'w') as fd:
fd.write(sample_outputfile)
with open('orcamolecule_test.engrad', 'w') as engrad:
engrad.write(sample_engradfile)
results_sample = {
'energy': -2079.560412394247,
'forces': np.array([
[2.42359838e+00, 2.42359837e+00, -2.72536956e-09],
[-1.31748767e+00, -1.10611070e+00, -1.74835028e-09],
[-1.10611071e+00, -1.31748767e+00, 4.47371984e-09]])}
results_sample['free_energy'] = results_sample['energy']
with pytest.warns(DeprecationWarning):
results = read_orca_outputs('.', 'orcamolecule_test.out')
keys = set(results)
assert keys == set(results_sample)
for key in keys:
# each result can be either float or ndarray.
assert results[key] == pytest.approx(results_sample[key])
def test_read_dipole():
"""Test if the dipole moment is parsed correctly."""
text = """\
-------------
DIPOLE MOMENT
-------------
X Y Z
Electronic contribution: 1.84602 -0.21505 -0.30526
Nuclear contribution : 1.30721 0.21236 0.34181
-----------------------------------------
Total Dipole Moment : 3.15323 -0.00269 0.03656
-----------------------------------------
Magnitude (a.u.) : 3.15344
Magnitude (Debye) : 8.01540
"""
dipole = read_dipole(io.StringIO(text))
dipole_ref = np.array((+3.15323, -0.00269, +0.03656)) * Bohr
np.testing.assert_allclose(dipole, dipole_ref)
def test_read_energy():
"""Test if the energy is parse correctly."""
text = """\
------------------------- --------------------
FINAL SINGLE POINT ENERGY -815.959737266080
------------------------- --------------------
"""
energy = read_energy(io.StringIO(text))
energy_ref = -815.959737266080 * Hartree
assert energy == energy_ref
def test_read_orca_output_file():
sample_outputfile = """\
*****************
* O R C A *
*****************
*******************************
* Energy+Gradient Calculation *
*******************************
---------------------------------
CARTESIAN COORDINATES (ANGSTROEM)
---------------------------------
O 0.0000000 0.0000000 0.0000000
H 1.8897261 0.0000000 0.0000000
H 0.0000000 1.8897261 0.0000000
----------------------
SHARK INTEGRAL PACKAGE
----------------------
Number of atoms ... 3
------------------
CARTESIAN GRADIENT
------------------
1 O : -0.047131485 -0.047131485 0.0000000001
2 H : 0.025621056 0.021510429 0.0000000000
3 H : 0.021510429 0.025621056 -0.0000000001
------------------------- --------------------
FINAL SINGLE POINT ENERGY -76.422436201230
------------------------- --------------------
ORCA TERMINATED NORMALLY
""" # noqa: W293
with open('orca_test.out', 'w') as fd:
fd.write(sample_outputfile)
results_sample = {
'energy': -2079.560412394247,
'forces': np.array([
[2.42359838e+00, 2.42359837e+00, -5.14220671e-09],
[-1.31748766e+00, -1.10611070e+00, -0.0000000e-00],
[-1.10611071e+00, -1.31748767e+00, 5.14220671e-09]]),
'positions': np.array([
[0.0000000, 0.0000000, 0.0000000],
[1.8897261, 0.0000000, 0.0000000],
[0.0000000, 1.8897261, 0.0000000]])}
results_sample['free_energy'] = results_sample['energy']
atoms = read('orca_test.out')
assert results_sample['energy'] == pytest.approx(atoms.get_total_energy())
assert results_sample['forces'] == pytest.approx(atoms.get_forces())
assert results_sample['positions'] == pytest.approx(atoms.get_positions())
|
