HideyoshiNakazone/CrystalPol
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Fixes Tests Implementations

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This commit is contained in:
Vitor Hideyoshi
2023-02-10 09:07:50 -03:00
parent 3716017cb0
commit 0f7484756b
6 changed files with 72 additions and 37 deletions
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2
.gitignore vendored
View File

@@ -1,3 +1,5 @@
*.pyc
.idea/
simfiles

4
config.example.yml
View File

@@ -1,8 +1,8 @@
crystal_pol:
mem: 42
mem: 28
n_procs: 20
level: "b3lyp/aug-cc-pVDZ"
pop: "chelpg"
mult: [0, 1]
n_atoms: 18
comment: "DC-MBI UAEnvolvida"
comment: "Crystal"

4
crystal.example.gjf
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@@ -1,5 +1,5 @@
%mem=42GB
%Nprocs=20
%mem=30GB
%Nprocs=24
#p ${LEVEL} POP=${POP} density=current NoSymm (CHARGE - A partir do segundo)
${COMMENTARY} passo 1

53
crystalpol/gaussian.py
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@@ -3,7 +3,7 @@ from crystalpol.shared.system.crystal import Crystal
from crystalpol.shared.config import Config
from pathlib import Path, PosixPath
from typing import TextIO
from typing import TextIO, Union
import subprocess
import textwrap
import shutil
@@ -25,8 +25,14 @@ class Gaussian:
def run(self, cycle: int, crystal: Crystal) -> None:
file = Path("simfiles", f"crystal-{str(cycle).zfill(2)}.gjf")
self.create_simulation_dir()
file = Path(
"simfiles",
f"crystal-{str(cycle).zfill(2)}",
f"crystal-{str(cycle).zfill(2)}.gjf"
)
self.create_step_dir(cycle)
self.make_gaussian_input(cycle, file, crystal)
if shutil.which("bash") is not None:
@@ -35,7 +41,7 @@ class Gaussian:
"bash",
"-c",
"exec -a {}-step{} {} {}".format(
self.qmprog, cycle, self.qmprog, file.name
self.qmprog, cycle, self.qmprog, str(file)
),
]
)
@@ -47,6 +53,19 @@ class Gaussian:
return self.read_charges_from_gaussian_output()
def create_step_dir(self, cycle):
step_dir = Path(
"simfiles",
f"crystal-{str(cycle).zfill(2)}"
)
if not os.path.exists(step_dir):
os.makedirs(step_dir)
else:
raise RuntimeError(
f"Step directory '{str(step_dir)}' already exists. "
f"Please remove it before proceeding."
)
def create_simulation_dir(self):
if not os.path.exists(self.config.simulation_dir):
os.makedirs(self.config.simulation_dir)
@@ -56,17 +75,17 @@ class Gaussian:
f"Please remove it before proceeding."
)
def make_gaussian_input(self, cycle: int, file: PosixPath, crystal: Crystal) -> str:
def make_gaussian_input(self, cycle: int, file: Union[PosixPath, Path], crystal: Crystal) -> str:
with open(file, 'w+') as fh:
fh.write(f"%Mem={self.config.mem}MB\n")
fh.write(f"%Mem={self.config.mem}Gb\n")
fh.write(f"%Nprocs={self.config.n_procs}\n")
kwords_line = f"#P {self.config.level} " \
f"Pop = {self.config.pop} " \
f"Density = Current " \
f"Pop={self.config.pop} " \
f"Density=Current " \
f"NoSymm "
if cycle > 1:
@@ -77,17 +96,19 @@ class Gaussian:
fh.write(f"\n{self.config.comment} - Cycle number {cycle}\n")
fh.write("\n")
fh.write(f"{self.config.mult[0]}, {self.config.mult[1]}\n")
fh.write(f"{self.config.mult[0]} {self.config.mult[1]}\n")
for atom in crystal[0][0]:
symbol = atom_symbol[atom.na]
fh.write(
f"{symbol:<2s} "
f"{atom.rx:>10.5f} "
f"{atom.ry:>10.5f} "
f"{atom.rz:>10.5f}\n"
f"{float(atom.rx):>10.5f} "
f"{float(atom.ry):>10.5f} "
f"{float(atom.rz):>10.5f}\n"
)
fh.write("\n")
if cycle > 1:
self.make_gaussian_charges(fh, crystal)
@@ -96,8 +117,6 @@ class Gaussian:
def make_gaussian_charges(self, fh: TextIO, crystal: Crystal) -> None:
fh.write("\n")
for index_cell, cell in enumerate(crystal):
for index_mol, molecule in enumerate(cell):
if (index_cell == 0 and index_mol != 0) or (index_cell != 0):
@@ -105,10 +124,12 @@ class Gaussian:
symbol = atom_symbol[atom.na]
fh.write(
f"{symbol:<2s} "
f"{atom.rx:>10.5f} "
f"{atom.ry:>10.5f} "
f"{atom.rz:>10.5f}\n"
f"{float(atom.rx):>10.5f} "
f"{float(atom.ry):>10.5f} "
f"{float(atom.rz):>10.5f}\n"
)
fh.write("\n")
def read_charges_from_gaussian_output(self) -> None:
pass

36
tests/shared/test_gaussian.py
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@@ -4,6 +4,7 @@ from crystalpol.shared.system.atom import Atom
from crystalpol.shared.config import Config
from crystalpol.gaussian import Gaussian
from pathlib import Path
from io import StringIO
from unittest import mock, TestCase
@@ -38,6 +39,7 @@ class TestGaussian(TestCase):
@mock.patch('crystalpol.gaussian.os')
def test_create_simulation_dir(self, os_mock):
os_mock.path.exists.return_value = False
os_mock.makedirs = mock.MagicMock()
gaussian = Gaussian(
Config(
@@ -53,6 +55,7 @@ class TestGaussian(TestCase):
@mock.patch('crystalpol.gaussian.os')
def test_create_simulation_dir_raises_exception(self, os_mock):
os_mock.path.exists.return_value = True
os_mock.makedirs = mock.MagicMock()
gaussian = Gaussian(
Config(
mem=1,
@@ -64,6 +67,7 @@ class TestGaussian(TestCase):
with self.assertRaises(RuntimeError):
gaussian.create_simulation_dir()
# @mock.patch('crystalpol.gaussian.os')
@mock.patch('crystalpol.gaussian.open')
def test_make_gaussian_input_cycle_1(self, open_mock):
@@ -78,16 +82,17 @@ class TestGaussian(TestCase):
n_atoms=10
)
)
gaussian_input = gaussian.make_gaussian_input(1, crystal)
gaussian_input = gaussian.make_gaussian_input(1, Path(), crystal)
expected_output = """\
%Mem=1MB
%Mem=1Gb
%Nprocs=1
#P b3lyp/aug-cc-pVDZ Pop = chelpg Density = Current NoSymm
#P b3lyp/aug-cc-pVDZ Pop=chelpg Density=Current NoSymm
crystalpol - Cycle number 1
0, 1
H 0.00000 0.00000 0.00000
0 1
H 0.00000 0.00000 0.00000
"""
self.assertEqual(gaussian_input, expected_output)
@@ -107,16 +112,17 @@ H 0.00000 0.00000 0.00000
)
gaussian_input = gaussian.make_gaussian_input(2, "test", crystal)
expected_output = """\
%Mem=1MB
%Mem=1Gb
%Nprocs=1
#P b3lyp/aug-cc-pVDZ Pop = chelpg Density = Current NoSymm charge
#P b3lyp/aug-cc-pVDZ Pop=chelpg Density=Current NoSymm charge
crystalpol - Cycle number 2
0, 1
H 0.00000 0.00000 0.00000
0 1
H 0.00000 0.00000 0.00000
H 0.00000 0.00000 0.00000
H 0.00000 0.00000 0.00000
"""
self.assertEqual(gaussian_input, expected_output)
@@ -136,13 +142,15 @@ H 0.00000 0.00000 0.00000
file.seek(0)
charges_string = file.read()
expected_charges = '\nH 0.00000 0.00000 0.00000\n'
expected_charges = 'H 0.00000 0.00000 0.00000\n\n'
self.assertEqual(charges_string, expected_charges)
@mock.patch('crystalpol.gaussian.os')
@mock.patch('crystalpol.gaussian.subprocess.call', autospec=True, return_value=0)
@mock.patch('crystalpol.gaussian.Gaussian.make_gaussian_input')
def test_run(self, subprocess_call_mock, make_gaussian_input_mock):
def test_run(self, make_gaussian_input_mock, subprocess_call_mock, os_mock):
os_mock.path.exists.return_value = False
gaussian = Gaussian(
Config(
@@ -155,9 +163,11 @@ H 0.00000 0.00000 0.00000
self.assertTrue(subprocess_call_mock.called)
@mock.patch('crystalpol.gaussian.os')
@mock.patch('crystalpol.gaussian.subprocess.call', autospec=True, return_value=1)
@mock.patch('crystalpol.gaussian.Gaussian.make_gaussian_input')
def test_run_raises_exception(self, subprocess_call_mock, make_gaussian_input_mock):
def test_run_raises_exception(self, subprocess_call_mock, make_gaussian_input_mock, os_mock):
os_mock.path.exists.return_value = False
gaussian = Gaussian(
Config(

8
tests/test_polarization.py
View File

@@ -6,7 +6,6 @@ from crystalpol.shared.system.molecule import Molecule
from unittest import TestCase, mock
import unittest
GEOM_DATA = """\
Cl 0.529511 -1.626652 1.247344
N 3.703161 2.470259 1.679277
@@ -85,9 +84,12 @@ class TestPolarization(TestCase):
self.assertEqual(len(pol.crystal), 2)
self.assertEqual(len(pol.crystal[0]), 1)
@mock.patch('builtins.open', mock.mock_open(read_data=GEOM_DATA))
def test_run(self):
@mock.patch('crystalpol.gaussian.subprocess.call', autospec=True, return_value=0)
@mock.patch('crystalpol.gaussian.os')
def test_run(self, os_mock, subprocess_call_mock):
os_mock.path.exists.return_value = False
pol = Polarization("geom_file", "outfile", self.config)
pol.run()