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Merge pull request #15 from HideyoshiNakazone/updates-version-pipeline

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Updates Version Pipeline
This commit is contained in:
Vitor Hideyoshi
2024-07-24 00:59:10 -03:00
committed by GitHub
parent c1257266a2 f428aedd93
commit 4242bde158
12 changed files with 484 additions and 521 deletions
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35
.github/workflows/python-pypi-test-upload.yml vendored
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@@ -1,35 +0,0 @@
# This workflow will install Python dependencies, run tests and lint with a single version of Python
# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
name: Upload CrystalPol to PyPI Test
on:
push:
branches: [ develop ]
permissions:
contents: read
jobs:
pypi-upload-test:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- name: Set up Python 3.8
uses: actions/setup-python@v3
with:
python-version: "3.8"
- name: Install dependencies
run: |
python -m pip install --upgrade pip poetry
python -m poetry install
- name: Test with unittest
run: |
python -m poetry run python -m unittest -v
- name: Upload Pip Package
run: |
python -m poetry config repositories.testpypi https://test.pypi.org/legacy/
python -m poetry publish --build --username __token__ --password ${{secrets.PYPI_TEST_TOKEN}} --repository testpypi

74
.github/workflows/python-pypi-upload.yml vendored
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@@ -4,32 +4,62 @@
name: Upload CrystalPol to PyPI
on:
push:
branches: [ main ]
push
permissions:
contents: read
contents: read
jobs:
pypi-upload:
test:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
with:
fetch-depth: 0
- name: Install poetry
run: pipx install poetry
runs-on: ubuntu-latest
- name: Set up Python 3.10
uses: actions/setup-python@v3
with:
python-version: "3.10"
- name: Install dependencies
run: |
poetry self add "poetry-dynamic-versioning[plugin]"
if [ -f pyproject.toml ]; then poetry install; fi
- name: Run unittest
run: |
poetry run python -m unittest
steps:
- uses: actions/checkout@v3
- name: Set up Python 3.8
uses: actions/setup-python@v3
with:
python-version: "3.8"
- name: Install dependencies
run: |
python -m pip install --upgrade pip poetry
python -m poetry install
- name: Test with unittest
run: |
python -m poetry run python -m unittest -v
- name: Upload Pip Package
run: |
python -m poetry config repositories.pypi https://upload.pypi.org/legacy/
python -m poetry publish --build --username __token__ --password ${{secrets.PYPI_TOKEN}} --repository pypi
pypi-upload:
needs: [test]
if: startsWith(github.ref, 'refs/tags/v')
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
with:
fetch-depth: 0
- name: Install poetry
run: pipx install poetry
- name: Set up Python 3.10
uses: actions/setup-python@v3
with:
python-version: "3.10"
- name: Install dependencies
run: |
poetry self add "poetry-dynamic-versioning[plugin]"
if [ -f pyproject.toml ]; then poetry install; fi
- name: Build Python Package
run: |
poetry build -f sdist
poetry install
echo "Built CrystalPol - $(poetry version)"
- name: Configure PyPI
run: |
poetry config repositories.pypi https://upload.pypi.org/legacy/
poetry config pypi-token.pypi ${{secrets.PYPI_TOKEN}}
- name: Upload Python Package
run: |
poetry publish --repository pypi

30
.github/workflows/python-tests.yml vendored
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@@ -1,30 +0,0 @@
# This workflow will install Python dependencies, run tests and lint with a single version of Python
# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
name: Python application
on:
push
permissions:
contents: read
jobs:
run-unitest:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- name: Set up Python 3.8
uses: actions/setup-python@v3
with:
python-version: "3.8"
- name: Install dependencies
run: |
python -m pip install --upgrade pip poetry
python -m poetry install
- name: Test with unittest
run: |
poetry run python -m unittest -v

4
.pre-commit-config.yaml
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@@ -1,12 +1,12 @@
repos:
- repo: https://github.com/psf/black
rev: 23.3.0
rev: 24.4.2
hooks:
- id: black
args: [--config=pyproject.toml]
- repo: https://github.com/pycqa/isort
rev: 5.12.0
rev: 5.13.2
hooks:
- id: isort
files: "\\.(py)$"

5
config.example.yml
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@@ -1,8 +1,9 @@
crystal_pol:
mem: 24
n_procs: 20
n_procs: 24
level: "b3lyp/aug-cc-pVDZ"
pop: "chelpg"
mult: [0, 1]
n_atoms: 18
comment: "Crystal"
comment: "Crystal"
charge_tolerance: 0.0001

3
crystalpol/__init__.py
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@@ -0,0 +1,3 @@
from importlib import metadata
VERSION = metadata.version("crystalpol")

41
crystalpol/__main__.py
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@@ -1,19 +1,19 @@
from crystalpol import VERSION
from crystalpol.polarization import Polarization
from crystalpol.shared.config import Config
from crystalpol.shared.utils.log import Log
from yaml.loader import SafeLoader
from pathlib import Path
import setproctitle
import yaml
from yaml.loader import SafeLoader
import argparse
import logging
import yaml
import os
from pathlib import Path
__VERSION = "v0.0.1"
os.nice(+19)
setproctitle.setproctitle("crystalpol-{}".format(__VERSION))
setproctitle.setproctitle("crystalpol-{}".format(VERSION))
def main():
@@ -24,28 +24,31 @@ def main():
parser = argparse.ArgumentParser(prog="CrystalPol")
parser.add_argument(
"-v", "--version", action="version", version=f"crystalpol-{__VERSION}"
"-v", "--version", action="version", version=f"crystalpol-{VERSION}"
)
parser.add_argument(
"-c", "--config",
"-c",
"--config",
dest="config",
default="config.yml",
metavar="INFILE",
help="Config file of crystalpol [default = config.yml]"
help="Config file of crystalpol [default = config.yml]",
)
parser.add_argument(
"-i", "--input",
"-i",
"--input",
dest="infile",
default="crystal.xyz",
metavar="INFILE",
help="Input file of crystalpol [default = crystal.xyz]"
help="Input file of crystalpol [default = crystal.xyz]",
)
parser.add_argument(
"-o", "--output",
"-o",
"--output",
dest="outfile",
default="run.log",
metavar="OUTFILE",
help="Output file of crystalpol [default = run.log]"
help="Output file of crystalpol [default = run.log]",
)
args = parser.parse_args()
@@ -53,20 +56,16 @@ def main():
if log_file.exists():
log_file.rename(log_file.with_suffix(".log.backup"))
logging.basicConfig(
filename=args.outfile,
format='%(message)s',
level=logging.INFO
)
logging.basicConfig(filename=args.outfile, format="%(message)s", level=logging.INFO)
try:
with open(args.config) as file:
data = yaml.load(file, Loader=SafeLoader)
config = Config(**data.get('crystal_pol'))
config = Config(**data.get("crystal_pol"))
except IOError:
raise RuntimeError('Invalid or Missing Config File.')
raise RuntimeError("Invalid or Missing Config File.")
Log.make_header(__VERSION, config.to_dict())
Log.make_header(VERSION, config.to_dict())
pol = Polarization(args.infile, args.outfile, config)
pol.run()

38
crystalpol/polarization.py
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@@ -1,18 +1,16 @@
from crystalpol.shared.system.molecule import Molecule
from crystalpol.shared.system.crystal import Crystal
from crystalpol.shared.system.atom import Atom
from crystalpol.shared.config import Config
from crystalpol.gaussian import Gaussian
from typing import List, Tuple
from crystalpol.shared.config import Config
from crystalpol.shared.system.atom import Atom
from crystalpol.shared.system.crystal import Crystal
from crystalpol.shared.system.molecule import Molecule
from crystalpol.shared.utils.log import Log
import sys
from crystalpol.shared.utils.log import Log
from typing import List, Tuple
class Polarization:
__slots__ = ('geom_file', 'outfile', 'config', 'gaussian', 'crystal')
__slots__ = ("geom_file", "outfile", "config", "gaussian", "crystal")
def __init__(self, geom_file: str, outfile: str, config: Config) -> None:
self.crystal = None
@@ -33,21 +31,22 @@ class Polarization:
max_charge_diff = sys.float_info.max
while max_charge_diff >= self.config.charge_tolerance:
max_charge_diff, charge_diff = self.update_crystal_charges(
max_charge_diff, min_charge_diff, charge_diff = self.update_crystal_charges(
self.gaussian.run(cycle, self.crystal),
)
Log.make_run(
cycle,
max_charge_diff if cycle != 1 else 0,
min_charge_diff if cycle != 1 else 0,
charge_diff,
self.crystal
self.crystal,
)
cycle += 1
def read_crystal(self) -> None:
with open(self.geom_file, 'r') as geom_file:
with open(self.geom_file, "r") as geom_file:
lines = geom_file.readlines()
molecules = self._get_molecules_from_lines(lines)
@@ -57,7 +56,7 @@ class Polarization:
for molecule in molecules:
self.crystal.add_cell([molecule])
def update_crystal_charges(self, charges: List[float]) -> Tuple[float, list]:
def update_crystal_charges(self, charges: List[float]) -> Tuple[float, float, list]:
charge_diff = []
@@ -68,9 +67,12 @@ class Polarization:
charge_diff.append(abs(atom.chg - charges[index]))
atom.chg = charges[index]
max_charge_diff = abs(max(charge_diff, key=abs)) if charge_diff else sys.float_info.max
max_charge_diff = (
abs(max(charge_diff, key=abs)) if charge_diff else sys.float_info.max
)
min_charge_diff = abs(min(charge_diff, key=abs)) if charge_diff else 0
return max_charge_diff, charge_diff
return max_charge_diff, min_charge_diff, charge_diff
def _get_molecules_from_lines(self, lines: List[str]) -> List[Molecule]:
if (len(lines) % self.config.n_atoms) == 0:
@@ -82,7 +84,9 @@ class Polarization:
symbol, rx, ry, rz = tuple(atom_line.split())
mol.add_atom(
Atom(
rx, ry, rz,
rx,
ry,
rz,
symbol=symbol.ljust(2),
)
)
@@ -105,4 +109,4 @@ class Polarization:
@staticmethod
def split(array: List, partitions: int):
for i in range(0, len(array), partitions):
yield array[i: i + partitions]
yield array[i : i + partitions]

52
crystalpol/shared/utils/log.py
View File

@@ -19,31 +19,55 @@ class Log:
logger.info(f"Your python version is {sys.version}\n")
logger.info(f"Program started on {weekday_date_time()}\n")
logger.info("------------------------------------------------------------------------------------------")
logger.info(" CRYSTALPOL variables being used in this run: ")
logger.info("------------------------------------------------------------------------------------------\n")
logger.info(
"------------------------------------------------------------------------------------------"
)
logger.info(
" CRYSTALPOL variables being used in this run: "
)
logger.info(
"------------------------------------------------------------------------------------------\n"
)
for key, value in config_dict.items():
logger.info(f"\t{key} = {(value if value else 'Not set')}")
logger.info("------------------------------------------------------------------------------------------")
logger.info(f" RUN Results: ")
logger.info("------------------------------------------------------------------------------------------\n")
logger.info(
"------------------------------------------------------------------------------------------"
)
logger.info(
f" RUN Results: "
)
logger.info(
"------------------------------------------------------------------------------------------\n"
)
@staticmethod
def make_run(cycle, max_charge_diff, charge_diff, crystal, logger=None):
def make_run(
cycle, max_charge_diff, min_charge_diff, charge_diff, crystal, logger=None
):
if logger is None:
logger = logging.getLogger()
logger.info(f"cycle: {cycle}")
logger.info(f"\nMax charge diff: {max_charge_diff:.5f}")
logger.info(f"cycle: {cycle}\n")
logger.info(f"Max charge diff: {max_charge_diff:.5f}")
logger.info(f"Min charge diff: {min_charge_diff:.5f}")
logger.info(f"Charge Diff: {charge_diff}\n")
logger.info(f"------------------------------------------------------------------------------------------")
logger.info(f" S rx ry rz chg ")
logger.info(f"------------------------------------------------------------------------------------------")
logger.info(
f"------------------------------------------------------------------------------------------"
)
logger.info(
f" S rx ry rz chg "
)
logger.info(
f"------------------------------------------------------------------------------------------"
)
for atom in crystal[0][0]:
logger.info(
f" {atom.symbol.rjust(2)} {float(atom.rx):.6f} {float(atom.ry):.6f} {float(atom.rz):.6f} {float(atom.chg):.6f} ")
f" {atom.symbol.rjust(2)} {float(atom.rx):.6f} {float(atom.ry):.6f} {float(atom.rz):.6f} {float(atom.chg):.6f} "
)
logger.info("\n------------------------------------------------------------------------------------------\n")
logger.info(
"\n------------------------------------------------------------------------------------------\n"
)

584
poetry.lock generated
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@@ -1,38 +1,34 @@
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name = "black"
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version = "23.12.1"
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python-versions = ">=3.8"
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[package.extras]
test = ["pytest"]
[[package]]
name = "setuptools"
version = "67.7.2"
description = "Easily download, build, install, upgrade, and uninstall Python packages"
category = "dev"
optional = false
python-versions = ">=3.7"
files = [
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testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8 (<5)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pip (>=19.1)", "pip-run (>=8.8)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-timeout", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
testing-integration = ["build[virtualenv]", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"]
[[package]]
name = "tomli"
version = "2.0.1"
description = "A lil' TOML parser"
category = "dev"
optional = false
python-versions = ">=3.7"
files = [
@@ -497,36 +481,34 @@ files = [
[[package]]
name = "typing-extensions"
version = "4.5.0"
description = "Backported and Experimental Type Hints for Python 3.7+"
category = "dev"
version = "4.12.2"
description = "Backported and Experimental Type Hints for Python 3.8+"
optional = false
python-versions = ">=3.7"
python-versions = ">=3.8"
files = [
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]
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name = "virtualenv"
version = "20.23.0"
version = "20.26.3"
description = "Virtual Python Environment builder"
category = "dev"
optional = false
python-versions = ">=3.7"
files = [
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distlib = ">=0.3.6,<1"
filelock = ">=3.11,<4"
platformdirs = ">=3.2,<4"
distlib = ">=0.3.7,<1"
filelock = ">=3.12.2,<4"
platformdirs = ">=3.9.1,<5"
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docs = ["furo (>=2023.3.27)", "proselint (>=0.13)", "sphinx (>=6.1.3)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=22.12)"]
test = ["covdefaults (>=2.3)", "coverage (>=7.2.3)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.3.1)", "pytest-env (>=0.8.1)", "pytest-freezegun (>=0.4.2)", "pytest-mock (>=3.10)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=67.7.1)", "time-machine (>=2.9)"]
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test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10)"]
[metadata]
lock-version = "2.0"

24
pyproject.toml
View File

@@ -1,6 +1,6 @@
[tool.poetry]
name = "crystalpol"
version = "0.0.1-5"
version = "0.0.0"
description = "Crystal Optimization Automation using Gaussian16"
authors = ["Vitor Hideyoshi <vitor.h.n.batista@gmail.com>"]
license = "GPL-2.0-only"
@@ -21,26 +21,16 @@ poethepoet = "^0.20.0"
[tool.poetry.scripts]
crystalpol = "crystalpol.__main__:main"
[tool.poetry-dynamic-versioning]
enable = true
vcs = "git"
[build-system]
requires = ["poetry-core"]
build-backend = "poetry.core.masonry.api"
build-backend = "poetry_dynamic_versioning.backend"
[tool.poe.tasks]
hooks = "pre-commit install"
[tool.coverage.run]
omit = [
"mega_conversao/src/utilidades/trata.py",
"mega_conversao/src/modulos/*",
"tests/*",
]
data_file = "coverage/.coverage"
[tool.coverage.html]
directory = "coverage/html"
[tool.coverage.lcov]
output = "coverage/lcov.info"
hooks = "pre-commit install --config .pre-commit-config.yaml"
[tool.isort]
profile = "black"

115
tests/shared/utils/test_log.py
View File

@@ -1,12 +1,11 @@
from crystalpol.shared.system.molecule import Molecule
from crystalpol.shared.system.crystal import Crystal
from crystalpol.shared.system.atom import Atom
from crystalpol.shared.config import Config
from crystalpol.shared.system.atom import Atom
from crystalpol.shared.system.crystal import Crystal
from crystalpol.shared.system.molecule import Molecule
from crystalpol.shared.utils.log import Log
from io import StringIO
import logging
from io import StringIO
from unittest import TestCase, mock
@@ -16,53 +15,50 @@ class TestLog(TestCase):
self.log_stream = StringIO()
logging.basicConfig(
stream=self.log_stream,
format='%(message)s',
level=logging.INFO
stream=self.log_stream, format="%(message)s", level=logging.INFO
)
self.logger = logging.getLogger()
def tearDown(self):
logging.getLogger().removeHandler(
logging.getLogger().handlers[0]
)
logging.getLogger().removeHandler(logging.getLogger().handlers[0])
del self.logger
del self.log_stream
@mock.patch('crystalpol.shared.utils.log.sys')
@mock.patch('crystalpol.shared.utils.log.weekday_date_time')
@mock.patch("crystalpol.shared.utils.log.sys")
@mock.patch("crystalpol.shared.utils.log.weekday_date_time")
def test_make_header(self, weekday_date_time_mock, sys_mock):
weekday_date_time_mock.return_value = 'Test Day'
sys_mock.version = 'Test Version'
weekday_date_time_mock.return_value = "Test Day"
sys_mock.version = "Test Version"
config = Config(
mem=1,
level="b3lyp/aug-cc-pVDZ",
n_atoms=10
)
Log.make_header('test', config.to_dict(), logger=self.logger)
config = Config(mem=1, level="b3lyp/aug-cc-pVDZ", n_atoms=10)
Log.make_header("test", config.to_dict(), logger=self.logger)
expected_log_stream = [
'##########################################################################################\n',
'############## Welcome to CRYSTALPOL version test ##############\n',
'##########################################################################################\n', '\n',
'Your python version is Test Version\n', '\n',
'Program started on Test Day\n', '\n',
'------------------------------------------------------------------------------------------\n',
' CRYSTALPOL variables being used in this run: \n',
'------------------------------------------------------------------------------------------\n', '\n',
'\tmem = 1\n',
'\tlevel = b3lyp/aug-cc-pVDZ\n',
'\tn_atoms = 10\n',
'\tn_procs = 1\n',
'\tpop = chelpg\n',
'\tcomment = crystalpol\n',
'\tcharge_tolerance = 0.02\n',
'\tsimulation_dir = simfiles\n',
'\tmult = [0, 1]\n',
'------------------------------------------------------------------------------------------\n',
' RUN Results: \n',
'------------------------------------------------------------------------------------------\n', '\n'
"##########################################################################################\n",
"############## Welcome to CRYSTALPOL version test ##############\n",
"##########################################################################################\n",
"\n",
"Your python version is Test Version\n",
"\n",
"Program started on Test Day\n",
"\n",
"------------------------------------------------------------------------------------------\n",
" CRYSTALPOL variables being used in this run: \n",
"------------------------------------------------------------------------------------------\n",
"\n",
"\tmem = 1\n",
"\tlevel = b3lyp/aug-cc-pVDZ\n",
"\tn_atoms = 10\n",
"\tn_procs = 1\n",
"\tpop = chelpg\n",
"\tcomment = crystalpol\n",
"\tcharge_tolerance = 0.02\n",
"\tsimulation_dir = simfiles\n",
"\tmult = [0, 1]\n",
"------------------------------------------------------------------------------------------\n",
" RUN Results: \n",
"------------------------------------------------------------------------------------------\n",
"\n",
]
self.log_stream.seek(0)
@@ -71,17 +67,24 @@ class TestLog(TestCase):
def test_make_run(self):
Log.make_run(1, 0.000000, [], self.create_crystal(), logger=self.logger)
Log.make_run(
1, 0.00001, 0.000001, [], self.create_crystal(), logger=self.logger
)
expected_log_stream = [
'cycle: 1\n', '\n',
'Max charge diff: 0.00000\n',
'Charge Diff: []\n', '\n',
'------------------------------------------------------------------------------------------\n',
' S rx ry rz chg \n',
'------------------------------------------------------------------------------------------\n',
' H 0.000000 0.000000 0.000000 0.000000 \n', '\n',
'------------------------------------------------------------------------------------------\n', '\n'
"cycle: 1\n",
"\n",
"Max charge diff: 0.00001\n",
"Min charge diff: 0.00000\n",
"Charge Diff: []\n",
"\n",
"------------------------------------------------------------------------------------------\n",
" S rx ry rz chg \n",
"------------------------------------------------------------------------------------------\n",
" H 0.000000 0.000000 0.000000 0.000000 \n",
"\n",
"------------------------------------------------------------------------------------------\n",
"\n",
]
self.log_stream.seek(0)
@@ -90,21 +93,13 @@ class TestLog(TestCase):
@staticmethod
def create_crystal():
crystal_structure = [
['H ']
]
crystal_structure = [["H "]]
crystal = Crystal(crystal_structure)
molecule = Molecule("TESTE")
molecule.add_atom(
Atom(
na=1,
rx=0.000000,
ry=0.000000,
rz=0.000000,
chg=0.000000
)
Atom(na=1, rx=0.000000, ry=0.000000, rz=0.000000, chg=0.000000)
)
crystal.add_cell([molecule])