1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
|
# Copyright (c) 2024, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Test Born-Oppenheimer molecular dynamics (BOMD) logfiles in cclib."""
class GenericBOMDTest:
"""Generic Born-Oppenheimer molecular dynamics unittest"""
# To calculate the initial set of forces/velocities, programs
# first converge the energy at the input geometry, so there is
# always one more geometry/energy than MD step.
nsteps = 35
nenergies = 36
def testdimscfenergies(self, data) -> None:
"""Are the number of parsed energies consistent with the number of MD
steps?
"""
assert data.scfenergies.shape == (self.nenergies,)
def testdimatomcoords(self, data) -> None:
"""Are the number of parsed geometries consistent with the number of
MD steps?
"""
assert data.atomcoords.shape == (self.nenergies, 20, 3)
def testdimtime(self, data) -> None:
"""Are the number of time points consistent with the number of MD
steps?
"""
assert data.time.shape == (self.nsteps,)
class GaussianBOMDTest(GenericBOMDTest):
"""Customized Born-Oppenheimer molecular dynamics unittest"""
# This may have something to do with our corrections for
# extrapolation step rejection.
nenergies = 35
|
