HideyoshiNakazone/CrystalPol
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Implements Better Tests and Logging

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This commit is contained in:
Vitor Hideyoshi
2023-03-01 02:49:28 -03:00
parent 32ca95086a
commit aea34bf214
17 changed files with 1147 additions and 72 deletions
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31
.github/workflows/python-tests.yml vendored Normal file
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@@ -0,0 +1,31 @@
# 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:
branches: [ "main", "develop" ]
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 pipenv
if [ -f Pipfile ]; then pipenv install; fi
- name: Test with unittest
run: |
pipenv run python -m unittest

2
.gitignore vendored
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@@ -1,6 +1,8 @@
*.log *.log
*.log.backup *.log.backup
!gaussian_output_example.log
*.pyc *.pyc
.idea/ .idea/

0
crystal.xyz → crystal.example.xyz
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2
crystalpol/__main__.py
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@@ -69,7 +69,7 @@ def main():
except IOError: except IOError:
raise RuntimeError('Invalid or Missing Config File.') raise RuntimeError('Invalid or Missing Config File.')
Log.make_header(__VERSION, data.get('crystal_pol')) Log.make_header(__VERSION, config.to_dict())
pol = Polarization(args.infile, args.outfile, config) pol = Polarization(args.infile, args.outfile, config)
pol.run() pol.run()

11
crystalpol/gaussian.py
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@@ -81,9 +81,6 @@ class Gaussian:
with open(file, 'w+') as fh: with open(file, 'w+') as fh:
chk_path = file.with_suffix('.chk')
fh.write(f"%Chk={chk_path}\n")
fh.write(f"%Mem={self.config.mem}Gb\n") fh.write(f"%Mem={self.config.mem}Gb\n")
fh.write(f"%Nprocs={self.config.n_procs}\n") fh.write(f"%Nprocs={self.config.n_procs}\n")
@@ -120,13 +117,13 @@ class Gaussian:
fh.seek(0) fh.seek(0)
return fh.read() return fh.read()
def make_gaussian_charges(self, fh: TextIO, crystal: Crystal) -> None: @staticmethod
def make_gaussian_charges(fh: TextIO, crystal: Crystal) -> None:
for index_cell, cell in enumerate(crystal): for index_cell, cell in enumerate(crystal):
for index_mol, molecule in enumerate(cell): for index_mol, molecule in enumerate(cell):
if (index_cell == 0 and index_mol != 0) or (index_cell != 0): if (index_cell == 0 and index_mol != 0) or (index_cell != 0):
for atom in molecule: for atom in molecule:
symbol = atom_symbol[atom.na]
fh.write( fh.write(
f"{float(atom.rx):>10.5f} " f"{float(atom.rx):>10.5f} "
f"{float(atom.ry):>10.5f} " f"{float(atom.ry):>10.5f} "
@@ -134,8 +131,6 @@ class Gaussian:
f"{float(atom.chg):>10.5f}\n" f"{float(atom.chg):>10.5f}\n"
) )
fh.write("\n")
def read_charges_from_gaussian_output(self, cycle, number_of_charges: int) -> List[float]: def read_charges_from_gaussian_output(self, cycle, number_of_charges: int) -> List[float]:
step_dir = Path( step_dir = Path(
self.config.simulation_dir, self.config.simulation_dir,
@@ -156,4 +151,4 @@ class Gaussian:
lines = lines[3:] # Consume 3 more lines lines = lines[3:] # Consume 3 more lines
return list(map(lambda x: float(x.split()[2]), lines[:number_of_charges])) return list(map(lambda x: float(x.split()[2]), lines[:number_of_charges]))

4
crystalpol/polarization.py
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@@ -33,7 +33,7 @@ class Polarization:
cycle = 1 cycle = 1
max_charge_diff = sys.float_info.max max_charge_diff = sys.float_info.max
while max_charge_diff > self.config.charge_tolerance: while max_charge_diff >= self.config.charge_tolerance:
max_charge_diff, charge_diff = self.update_crystal_charges( max_charge_diff, charge_diff = self.update_crystal_charges(
self.gaussian.run(cycle, self.crystal), self.gaussian.run(cycle, self.crystal),
@@ -41,7 +41,7 @@ class Polarization:
Log.make_run( Log.make_run(
cycle, cycle,
max_charge_diff, max_charge_diff if cycle != 1 else 0,
charge_diff, charge_diff,
self.crystal self.crystal
) )

11
crystalpol/shared/config/config.py
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@@ -1,9 +1,8 @@
from dataclasses import dataclass, field, fields from dataclasses import dataclass, field, fields, asdict
@dataclass @dataclass
class Config: class Config:
mem: int mem: int
level: str level: str
n_atoms: int n_atoms: int
@@ -31,13 +30,11 @@ class Config:
f'Memory must be a integer greater than 0.' f'Memory must be a integer greater than 0.'
) )
if self.level is None:
raise ValueError(
f'Invalid value for level. Level must not be none.'
)
if self.n_atoms is None or self.n_atoms <= 0: if self.n_atoms is None or self.n_atoms <= 0:
raise ValueError( raise ValueError(
f'Invalid value for n_atoms: {self.mem},' f'Invalid value for n_atoms: {self.mem},'
f'Number of Atoms must be a integer greater than 0.' f'Number of Atoms must be a integer greater than 0.'
) )
def to_dict(self):
return asdict(self)

3
crystalpol/shared/system/atom.py
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@@ -18,6 +18,7 @@ class Atom:
ry: float, ry: float,
rz: float, rz: float,
na: int = None, na: int = None,
chg: float = None,
symbol: str = None, symbol: str = None,
) -> None: ) -> None:
@@ -42,5 +43,5 @@ class Atom:
self.rx = rx self.rx = rx
self.ry = ry self.ry = ry
self.rz = rz self.rz = rz
self.chg = None self.chg = chg
self.mass = atom_mass[self.na] self.mass = atom_mass[self.na]

2
crystalpol/shared/utils/__init__.py
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@@ -2,4 +2,4 @@ import time
def weekday_date_time(): def weekday_date_time():
return time.strftime("%A, %d %b %Y at %H:%M:%S") return time.strftime("%A, %d %b %Y at %H:%M:%S")

58
crystalpol/shared/utils/log.py
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@@ -1,45 +1,49 @@
import sys from crystalpol.shared.utils import weekday_date_time
from crystalpol.shared.config import Config
import logging import logging
import sys
from crystalpol.shared.utils import weekday_date_time
class Log: class Log:
@staticmethod @staticmethod
def make_header(version: str, config_dict: dict): def make_header(version: str, config_dict: dict, logger=None):
logging.info(
if logger is None:
logger = logging.getLogger()
logger.info(
f"##########################################################################################\n" f"##########################################################################################\n"
f"############## Welcome to CRYSTALPOL version {version} ##############\n" f"############## Welcome to CRYSTALPOL version {version} ##############\n"
f"##########################################################################################\n" f"##########################################################################################\n"
) )
logging.info(f"Your python version is {sys.version}\n") logger.info(f"Your python version is {sys.version}\n")
logging.info(f"Program started on {weekday_date_time()}\n") logger.info(f"Program started on {weekday_date_time()}\n")
logging.info("------------------------------------------------------------------------------------------") logger.info("------------------------------------------------------------------------------------------")
logging.info(" CRYSTALPOL variables being used in this run: ") logger.info(" CRYSTALPOL variables being used in this run: ")
logging.info("------------------------------------------------------------------------------------------\n") logger.info("------------------------------------------------------------------------------------------\n")
for key, value in config_dict.items(): for key, value in config_dict.items():
logging.info(f"\t{key} = {(key if key else 'Not set')}") logger.info(f"\t{key} = {(value if value else 'Not set')}")
logging.info("------------------------------------------------------------------------------------------") logger.info("------------------------------------------------------------------------------------------")
logging.info(f" RUN Results: ") logger.info(f" RUN Results: ")
logging.info("------------------------------------------------------------------------------------------\n") logger.info("------------------------------------------------------------------------------------------\n")
@staticmethod @staticmethod
def make_run(cycle, max_charge_diff, charge_diff, crystal): def make_run(cycle, max_charge_diff, charge_diff, crystal, logger=None):
logging.info(f"cycle: {cycle}")
logging.info(f"\nMax charge diff: {max_charge_diff}")
logging.info(f"Charge Diff: {charge_diff}\n")
logging.info("------------------------------------------------------------------------------------------") if logger is None:
logging.info(f" S rx ry rz chg ") logger = logging.getLogger()
logging.info("------------------------------------------------------------------------------------------")
logger.info(f"cycle: {cycle}")
logger.info(f"\nMax charge diff: {max_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"------------------------------------------------------------------------------------------")
for atom in crystal[0][0]: for atom in crystal[0][0]:
logging.info(f" {atom.symbol} {atom.rx} {atom.ry} {atom.rz} {atom.chg} ") logger.info(
f" {atom.symbol.rjust(2)} {float(atom.rx):.6f} {float(atom.ry):.6f} {float(atom.rz):.6f} {float(atom.chg):.6f} ")
logging.info("\n------------------------------------------------------------------------------------------\n")
logger.info("\n------------------------------------------------------------------------------------------\n")

38
tests/shared/config/test_config.py
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@@ -12,10 +12,44 @@ class TestConfig(unittest.TestCase):
) )
self.assertIsInstance(config, Config) self.assertIsInstance(config, Config)
def test_config_raises_exception(self): def test_config_raises_exception_on_mem_none(self):
with self.assertRaises(ValueError): with self.assertRaises(ValueError):
Config( Config(
mem="1", mem=None,
level="b3lyp/aug-cc-pVDZ", level="b3lyp/aug-cc-pVDZ",
n_atoms=10 n_atoms=10
) )
def test_config_raises_exception_on_mem_zero_or_negative(self):
with self.assertRaises(ValueError):
Config(
mem=0,
level="b3lyp/aug-cc-pVDZ",
n_atoms=10
)
with self.assertRaises(ValueError):
Config(
mem=-1,
level="b3lyp/aug-cc-pVDZ",
n_atoms=10
)
def test_config_raises_exception_on_level_none(self):
with self.assertRaises(ValueError):
Config(
mem=1,
level=None,
n_atoms=10
)
def test_config_raises_exception_on_n_atoms_zero(self):
with self.assertRaises(ValueError):
Config(
mem=1,
level="b3lyp/aug-cc-pVDZ",
n_atoms=0
)

0
tests/shared/utils/__init__.py Normal file
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111
tests/shared/utils/test_log.py Normal file
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@@ -0,0 +1,111 @@
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.utils.log import Log
from io import StringIO
import logging
from unittest import TestCase, mock
class TestLog(TestCase):
def setUp(self):
self.log_stream = StringIO()
logging.basicConfig(
stream=self.log_stream,
format='%(message)s',
level=logging.INFO
)
self.logger = logging.getLogger()
def tearDown(self):
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')
def test_make_header(self, weekday_date_time_mock, sys_mock):
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)
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',
'\tmult = [0, 1]\n',
'------------------------------------------------------------------------------------------\n',
' RUN Results: \n',
'------------------------------------------------------------------------------------------\n', '\n'
]
self.log_stream.seek(0)
self.assertEqual(self.log_stream.readlines(), expected_log_stream)
def test_make_run(self):
Log.make_run(1, 0.000000, [], 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'
]
self.log_stream.seek(0)
self.assertEqual(self.log_stream.readlines(), expected_log_stream)
@staticmethod
def create_crystal():
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
)
)
crystal.add_cell([molecule])
crystal.add_cell([molecule])
return crystal

0
tests/test_files/__init__.py Normal file
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827
tests/test_files/gaussian_output_example.log Normal file
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@@ -0,0 +1,827 @@
Entering Gaussian System, Link 0=g16-step1
Input=simfiles/crystal-01/crystal-01.gjf
Output=simfiles/crystal-01/crystal-01.log
Initial command:
/home/hideyoshi/.local/g16/l1.exe "/scratch/Gau-38148.inp" -scrdir="/scratch/"
Entering Link 1 = /home/hideyoshi/.local/g16/l1.exe PID= 38149.
Copyright (c) 1988-2017, Gaussian, Inc. All Rights Reserved.
This is part of the Gaussian(R) 16 program. It is based on
the Gaussian(R) 09 system (copyright 2009, Gaussian, Inc.),
the Gaussian(R) 03 system (copyright 2003, Gaussian, Inc.),
the Gaussian(R) 98 system (copyright 1998, Gaussian, Inc.),
the Gaussian(R) 94 system (copyright 1995, Gaussian, Inc.),
the Gaussian 92(TM) system (copyright 1992, Gaussian, Inc.),
the Gaussian 90(TM) system (copyright 1990, Gaussian, Inc.),
the Gaussian 88(TM) system (copyright 1988, Gaussian, Inc.),
the Gaussian 86(TM) system (copyright 1986, Carnegie Mellon
University), and the Gaussian 82(TM) system (copyright 1983,
Carnegie Mellon University). Gaussian is a federally registered
trademark of Gaussian, Inc.
This software contains proprietary and confidential information,
including trade secrets, belonging to Gaussian, Inc.
This software is provided under written license and may be
used, copied, transmitted, or stored only in accord with that
written license.
The following legend is applicable only to US Government
contracts under FAR:
RESTRICTED RIGHTS LEGEND
Use, reproduction and disclosure by the US Government is
subject to restrictions as set forth in subparagraphs (a)
and (c) of the Commercial Computer Software - Restricted
Rights clause in FAR 52.227-19.
Gaussian, Inc.
340 Quinnipiac St., Bldg. 40, Wallingford CT 06492
---------------------------------------------------------------
Warning -- This program may not be used in any manner that
competes with the business of Gaussian, Inc. or will provide
assistance to any competitor of Gaussian, Inc. The licensee
of this program is prohibited from giving any competitor of
Gaussian, Inc. access to this program. By using this program,
the user acknowledges that Gaussian, Inc. is engaged in the
business of creating and licensing software in the field of
computational chemistry and represents and warrants to the
licensee that it is not a competitor of Gaussian, Inc. and that
it will not use this program in any manner prohibited above.
---------------------------------------------------------------
Cite this work as:
Gaussian 16, Revision B.01,
M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria,
M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone,
G. A. Petersson, H. Nakatsuji, X. Li, M. Caricato, A. V. Marenich,
J. Bloino, B. G. Janesko, R. Gomperts, B. Mennucci, H. P. Hratchian,
J. V. Ortiz, A. F. Izmaylov, J. L. Sonnenberg, D. Williams-Young,
F. Ding, F. Lipparini, F. Egidi, J. Goings, B. Peng, A. Petrone,
T. Henderson, D. Ranasinghe, V. G. Zakrzewski, J. Gao, N. Rega,
G. Zheng, W. Liang, M. Hada, M. Ehara, K. Toyota, R. Fukuda,
J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai,
T. Vreven, K. Throssell, J. A. Montgomery, Jr., J. E. Peralta,
F. Ogliaro, M. J. Bearpark, J. J. Heyd, E. N. Brothers, K. N. Kudin,
V. N. Staroverov, T. A. Keith, R. Kobayashi, J. Normand,
K. Raghavachari, A. P. Rendell, J. C. Burant, S. S. Iyengar,
J. Tomasi, M. Cossi, J. M. Millam, M. Klene, C. Adamo, R. Cammi,
J. W. Ochterski, R. L. Martin, K. Morokuma, O. Farkas,
J. B. Foresman, and D. J. Fox, Gaussian, Inc., Wallingford CT, 2016.
******************************************
Gaussian 16: EM64L-G16RevB.01 20-Dec-2017
23-Feb-2023
******************************************
%Chk=simfiles/crystal-01/crystal-01.chk
%Mem=24Gb
%Nprocs=20
Will use up to 20 processors via shared memory.
------------------------------------------------------
#P b3lyp/aug-cc-pVDZ Pop=chelpg Density=Current NoSymm
------------------------------------------------------
1/30=1,38=1,172=1/1;
2/12=2,15=1,17=6,18=5,40=1/2;
3/5=16,7=10,11=2,25=1,30=1,74=-5/1,2,3;
4//1;
5/5=2,38=5/2;
6/7=2,8=2,9=2,10=2,15=8,20=3,22=-1,28=1/1,2;
99/5=1,9=1/99;
Leave Link 1 at Thu Feb 23 07:21:23 2023, MaxMem= 3221225472 cpu: 0.3 elap: 0.0
(Enter /home/hideyoshi/.local/g16/l101.exe)
------------------------
Crystal - Cycle number 1
------------------------
Symbolic Z-matrix:
Charge = 0 Multiplicity = 1
Cl 0.52951 -1.62665 1.24734
Cl 0.36293 -1.51155 4.37537
N 3.70316 2.47026 1.67928
N 3.58214 2.53111 3.90653
C 4.1125 3.08953 2.78251
C 5.073 4.21889 2.80434
C 2.86041 1.45634 2.12431
C 2.79065 1.4916 3.51764
C 2.01966 0.58686 4.23407
C 1.33268 -0.36792 3.53324
C 1.40387 -0.4174 2.12743
C 2.1713 0.49075 1.40373
H 2.22113 0.45152 0.47623
H 1.97054 0.6278 5.16261
H 3.80155 2.76937 4.72069
H 5.68239 4.10686 3.53844
H 4.5946 5.04458 2.90832
H 5.56563 4.23595 1.98082
ITRead= 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
MicOpt= -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
NAtoms= 18 NQM= 18 NQMF= 0 NMMI= 0 NMMIF= 0
NMic= 0 NMicF= 0.
Isotopes and Nuclear Properties:
(Nuclear quadrupole moments (NQMom) in fm**2, nuclear magnetic moments (NMagM)
in nuclear magnetons)
Atom 1 2 3 4 5 6 7 8 9 10
IAtWgt= 35 35 14 14 12 12 12 12 12 12
AtmWgt= 34.9688527 34.9688527 14.0030740 14.0030740 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000
NucSpn= 3 3 2 2 0 0 0 0 0 0
AtZEff= -0.0000000 -0.0000000 -0.0000000 -0.0000000 -0.0000000 -0.0000000 -0.0000000 -0.0000000 -0.0000000 -0.0000000
NQMom= -8.1650000 -8.1650000 2.0440000 2.0440000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
NMagM= 0.8218740 0.8218740 0.4037610 0.4037610 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
AtZNuc= 17.0000000 17.0000000 7.0000000 7.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000
Atom 11 12 13 14 15 16 17 18
IAtWgt= 12 12 1 1 1 1 1 1
AtmWgt= 12.0000000 12.0000000 1.0078250 1.0078250 1.0078250 1.0078250 1.0078250 1.0078250
NucSpn= 0 0 1 1 1 1 1 1
AtZEff= -0.0000000 -0.0000000 -0.0000000 -0.0000000 -0.0000000 -0.0000000 -0.0000000 -0.0000000
NQMom= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
NMagM= 0.0000000 0.0000000 2.7928460 2.7928460 2.7928460 2.7928460 2.7928460 2.7928460
AtZNuc= 6.0000000 6.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
Leave Link 101 at Thu Feb 23 07:21:23 2023, MaxMem= 3221225472 cpu: 1.4 elap: 0.1
(Enter /home/hideyoshi/.local/g16/l202.exe)
Input orientation:
---------------------------------------------------------------------
Center Atomic Atomic Coordinates (Angstroms)
Number Number Type X Y Z
---------------------------------------------------------------------
1 17 0 0.529510 -1.626650 1.247340
2 17 0 0.362930 -1.511550 4.375370
3 7 0 3.703160 2.470260 1.679280
4 7 0 3.582140 2.531110 3.906530
5 6 0 4.112500 3.089530 2.782510
6 6 0 5.073000 4.218890 2.804340
7 6 0 2.860410 1.456340 2.124310
8 6 0 2.790650 1.491600 3.517640
9 6 0 2.019660 0.586860 4.234070
10 6 0 1.332680 -0.367920 3.533240
11 6 0 1.403870 -0.417400 2.127430
12 6 0 2.171300 0.490750 1.403730
13 1 0 2.221130 0.451520 0.476230
14 1 0 1.970540 0.627800 5.162610
15 1 0 3.801550 2.769370 4.720690
16 1 0 5.682390 4.106860 3.538440
17 1 0 4.594600 5.044580 2.908320
18 1 0 5.565630 4.235950 1.980820
---------------------------------------------------------------------
Distance matrix (angstroms):
1 2 3 4 5
1 Cl 0.000000
2 Cl 3.134576 0.000000
3 N 5.200317 5.854985 0.000000
4 N 5.803172 5.189048 2.231365 0.000000
5 C 6.118572 6.145439 1.329726 1.362547 0.000000
6 C 7.565573 7.582271 2.489966 2.507207 1.482731
7 C 3.963206 4.484757 1.391515 2.202801 2.160617
8 C 4.471074 3.955810 2.273767 1.363185 2.200246
9 C 4.005088 2.677320 3.592815 2.515698 3.570765
10 C 2.730352 1.719735 4.136618 3.688332 4.499439
11 C 1.732440 2.708127 3.718354 4.074772 4.479326
12 C 2.683899 4.013733 2.518131 3.523854 3.524620
13 H 2.788365 4.744454 2.778318 4.236036 3.981872
14 H 4.742199 2.789440 4.304674 2.792415 4.038933
15 H 6.488097 5.501784 3.057666 0.876222 1.988903
16 H 8.042043 7.782264 3.170534 2.651326 2.017658
17 H 7.986809 7.939906 2.988700 2.887738 2.017540
18 H 7.763413 8.113921 2.584063 3.247933 2.017070
6 7 8 9 10
6 C 0.000000
7 C 3.604120 0.000000
8 C 3.627124 1.395521 0.000000
9 C 4.955669 2.431860 1.387895 0.000000
10 C 5.963230 2.765315 2.362993 1.369200 0.000000
11 C 5.951127 2.373272 2.738635 2.413642 1.408481
12 C 4.927535 1.387974 2.419486 2.836028 2.444465
13 H 5.267479 2.033349 3.264398 3.765670 3.287269
14 H 5.299304 3.272555 2.030925 0.930739 2.013249
15 H 2.718472 3.057937 2.025326 2.859245 4.165086
16 H 0.960630 4.121722 3.898997 5.127367 6.240486
17 H 0.959918 4.061718 4.031026 5.315938 6.350260
18 H 0.959771 3.881370 4.194495 5.564791 6.443872
11 12 13 14 15
11 C 0.000000
12 C 1.391915 0.000000
13 H 2.037007 0.929666 0.000000
14 H 3.259736 3.766731 4.696385 0.000000
15 H 4.757034 4.341894 5.087789 2.852054 0.000000
16 H 6.384795 5.473663 5.892280 5.340376 2.593097
17 H 6.373678 5.373411 5.713547 5.610299 3.014995
18 H 6.244630 5.087340 5.269856 6.005598 3.573475
16 17 18
16 H 0.000000
17 H 1.568329 0.000000
18 H 1.567315 1.567494 0.000000
Symmetry turned off by external request.
Stoichiometry C8H6Cl2N2
Framework group C1[X(C8H6Cl2N2)]
Deg. of freedom 48
Full point group C1 NOp 1
Rotational constants (GHZ): 1.7084125 0.4124606 0.3328115
Leave Link 202 at Thu Feb 23 07:21:23 2023, MaxMem= 3221225472 cpu: 0.0 elap: 0.0
(Enter /home/hideyoshi/.local/g16/l301.exe)
Standard basis: Aug-CC-pVDZ (5D, 7F)
Ernie: Thresh= 0.10000D-02 Tol= 0.10000D-05 Strict=F.
Ernie: 40 primitive shells out of 398 were deleted.
338 basis functions, 658 primitive gaussians, 362 cartesian basis functions
51 alpha electrons 51 beta electrons
nuclear repulsion energy 835.4502353694 Hartrees.
IExCor= 402 DFT=T Ex+Corr=B3LYP ExCW=0 ScaHFX= 0.200000
ScaDFX= 0.800000 0.720000 1.000000 0.810000 ScalE2= 1.000000 1.000000
IRadAn= 5 IRanWt= -1 IRanGd= 0 ICorTp=0 IEmpDi= 4
NAtoms= 18 NActive= 18 NUniq= 18 SFac= 1.00D+00 NAtFMM= 60 NAOKFM=F Big=F
Integral buffers will be 131072 words long.
Raffenetti 2 integral format.
Two-electron integral symmetry is turned off.
Leave Link 301 at Thu Feb 23 07:21:23 2023, MaxMem= 3221225472 cpu: 0.3 elap: 0.0
(Enter /home/hideyoshi/.local/g16/l302.exe)
NPDir=0 NMtPBC= 1 NCelOv= 1 NCel= 1 NClECP= 1 NCelD= 1
NCelK= 1 NCelE2= 1 NClLst= 1 CellRange= 0.0.
One-electron integrals computed using PRISM.
NBasis= 338 RedAO= T EigKep= 1.82D-06 NBF= 338
NBsUse= 337 1.00D-06 EigRej= 8.38D-07 NBFU= 337
Precomputing XC quadrature grid using
IXCGrd= 4 IRadAn= 5 IRanWt= -1 IRanGd= 0 AccXCQ= 0.00D+00.
Generated NRdTot= 0 NPtTot= 0 NUsed= 0 NTot= 32
NSgBfM= 361 361 361 361 361 MxSgAt= 18 MxSgA2= 18.
Leave Link 302 at Thu Feb 23 07:21:23 2023, MaxMem= 3221225472 cpu: 3.5 elap: 0.2
(Enter /home/hideyoshi/.local/g16/l303.exe)
DipDrv: MaxL=1.
Leave Link 303 at Thu Feb 23 07:21:23 2023, MaxMem= 3221225472 cpu: 0.6 elap: 0.0
(Enter /home/hideyoshi/.local/g16/l401.exe)
ExpMin= 2.97D-02 ExpMax= 1.28D+05 ExpMxC= 1.24D+03 IAcc=3 IRadAn= 5 AccDes= 0.00D+00
Harris functional with IExCor= 402 and IRadAn= 5 diagonalized for initial guess.
HarFok: IExCor= 402 AccDes= 0.00D+00 IRadAn= 5 IDoV= 1 UseB2=F ITyADJ=14
ICtDFT= 3500011 ScaDFX= 1.000000 1.000000 1.000000 1.000000
FoFCou: FMM=F IPFlag= 0 FMFlag= 100000 FMFlg1= 0
NFxFlg= 0 DoJE=T BraDBF=F KetDBF=T FulRan=T
wScrn= 0.000000 ICntrl= 500 IOpCl= 0 I1Cent= 200000004 NGrid= 0
NMat0= 1 NMatS0= 1 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0
Symmetry not used in FoFCou.
Harris En= -1338.25918762356
JPrj=0 DoOrth=F DoCkMO=F.
Leave Link 401 at Thu Feb 23 07:21:24 2023, MaxMem= 3221225472 cpu: 16.3 elap: 0.8
(Enter /home/hideyoshi/.local/g16/l502.exe)
Two-electron integral symmetry not used.
Closed shell SCF:
Using DIIS extrapolation, IDIIS= 1040.
NGot= 3221225472 LenX= 3220953610 LenY= 3220822125
Requested convergence on RMS density matrix=1.00D-08 within 128 cycles.
Requested convergence on MAX density matrix=1.00D-06.
Requested convergence on energy=1.00D-06.
No special actions if energy rises.
Fock matrices will be formed incrementally for 20 cycles.
Cycle 1 Pass 1 IDiag 1:
FoFJK: IHMeth= 1 ICntrl= 0 DoSepK=F KAlg= 0 I1Cent= 0 FoldK=F
IRaf= 970000000 NMat= 1 IRICut= 1 DoRegI=T DoRafI=F ISym2E= 0 IDoP0=0 IntGTp=1.
FoFCou: FMM=F IPFlag= 0 FMFlag= 100000 FMFlg1= 0
NFxFlg= 0 DoJE=F BraDBF=F KetDBF=F FulRan=T
wScrn= 0.000000 ICntrl= 0 IOpCl= 0 I1Cent= 0 NGrid= 0
NMat0= 1 NMatS0= 1 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0
Symmetry not used in FoFCou.
E= -1338.02881581095
DIIS: error= 2.39D-02 at cycle 1 NSaved= 1.
NSaved= 1 IEnMin= 1 EnMin= -1338.02881581095 IErMin= 1 ErrMin= 2.39D-02
ErrMax= 2.39D-02 0.00D+00 EMaxC= 1.00D-01 BMatC= 3.23D-01 BMatP= 3.23D-01
IDIUse=3 WtCom= 7.61D-01 WtEn= 2.39D-01
Coeff-Com: 0.100D+01
Coeff-En: 0.100D+01
Coeff: 0.100D+01
Gap= 0.311 Goal= None Shift= 0.000
GapD= 0.311 DampG=1.000 DampE=0.500 DampFc=0.5000 IDamp=-1.
Damping current iteration by 5.00D-01
RMSDP=1.01D-01 MaxDP=6.39D+00 OVMax= 3.33D-01
Cycle 2 Pass 1 IDiag 1:
RMSU= 2.18D-02 CP: 8.49D-01
E= -1338.15214353104 Delta-E= -0.123327720086 Rises=F Damp=T
DIIS: error= 5.84D-03 at cycle 2 NSaved= 2.
NSaved= 2 IEnMin= 2 EnMin= -1338.15214353104 IErMin= 2 ErrMin= 5.84D-03
ErrMax= 5.84D-03 0.00D+00 EMaxC= 1.00D-01 BMatC= 2.60D-02 BMatP= 3.23D-01
IDIUse=3 WtCom= 9.42D-01 WtEn= 5.84D-02
Coeff-Com: 0.116D+00 0.884D+00
Coeff-En: 0.238D+00 0.762D+00
Coeff: 0.124D+00 0.876D+00
Gap= 0.246 Goal= None Shift= 0.000
RMSDP=4.74D-02 MaxDP=3.50D+00 DE=-1.23D-01 OVMax= 2.51D-01
Cycle 3 Pass 1 IDiag 1:
RMSU= 8.33D-03 CP: 6.94D-01 1.14D+00
E= -1338.33065781825 Delta-E= -0.178514287219 Rises=F Damp=F
DIIS: error= 7.44D-03 at cycle 3 NSaved= 3.
NSaved= 3 IEnMin= 3 EnMin= -1338.33065781825 IErMin= 2 ErrMin= 5.84D-03
ErrMax= 7.44D-03 0.00D+00 EMaxC= 1.00D-01 BMatC= 2.85D-02 BMatP= 2.60D-02
IDIUse=3 WtCom= 9.26D-01 WtEn= 7.44D-02
Coeff-Com: 0.156D-01 0.511D+00 0.473D+00
Coeff-En: 0.000D+00 0.000D+00 0.100D+01
Coeff: 0.144D-01 0.473D+00 0.512D+00
Gap= 0.191 Goal= None Shift= 0.000
RMSDP=4.30D-03 MaxDP=3.04D-01 DE=-1.79D-01 OVMax= 6.91D-02
Cycle 4 Pass 1 IDiag 1:
RMSU= 2.43D-03 CP: 7.04D-01 1.15D+00 7.56D-01
E= -1338.35429710968 Delta-E= -0.023639291430 Rises=F Damp=F
DIIS: error= 2.79D-03 at cycle 4 NSaved= 4.
NSaved= 4 IEnMin= 4 EnMin= -1338.35429710968 IErMin= 4 ErrMin= 2.79D-03
ErrMax= 2.79D-03 0.00D+00 EMaxC= 1.00D-01 BMatC= 5.61D-03 BMatP= 2.60D-02
IDIUse=3 WtCom= 9.72D-01 WtEn= 2.79D-02
Coeff-Com: -0.104D-01 0.124D+00 0.322D+00 0.564D+00
Coeff-En: 0.000D+00 0.000D+00 0.184D+00 0.816D+00
Coeff: -0.102D-01 0.121D+00 0.319D+00 0.571D+00
Gap= 0.193 Goal= None Shift= 0.000
RMSDP=1.24D-03 MaxDP=6.68D-02 DE=-2.36D-02 OVMax= 2.69D-02
Cycle 5 Pass 1 IDiag 1:
RMSU= 7.54D-04 CP: 7.04D-01 1.16D+00 8.00D-01 6.41D-01
E= -1338.35922929421 Delta-E= -0.004932184527 Rises=F Damp=F
DIIS: error= 7.66D-04 at cycle 5 NSaved= 5.
NSaved= 5 IEnMin= 5 EnMin= -1338.35922929421 IErMin= 5 ErrMin= 7.66D-04
ErrMax= 7.66D-04 0.00D+00 EMaxC= 1.00D-01 BMatC= 5.62D-04 BMatP= 5.61D-03
IDIUse=3 WtCom= 9.92D-01 WtEn= 7.66D-03
Coeff-Com: -0.731D-02 0.269D-01 0.150D+00 0.353D+00 0.478D+00
Coeff-En: 0.000D+00 0.000D+00 0.000D+00 0.446D-01 0.955D+00
Coeff: -0.725D-02 0.267D-01 0.148D+00 0.350D+00 0.482D+00
Gap= 0.192 Goal= None Shift= 0.000
RMSDP=4.34D-04 MaxDP=3.38D-02 DE=-4.93D-03 OVMax= 8.17D-03
Cycle 6 Pass 1 IDiag 1:
RMSU= 2.58D-04 CP: 7.04D-01 1.15D+00 8.01D-01 6.82D-01 7.42D-01
E= -1338.35979163466 Delta-E= -0.000562340446 Rises=F Damp=F
DIIS: error= 1.76D-04 at cycle 6 NSaved= 6.
NSaved= 6 IEnMin= 6 EnMin= -1338.35979163466 IErMin= 6 ErrMin= 1.76D-04
ErrMax= 1.76D-04 0.00D+00 EMaxC= 1.00D-01 BMatC= 3.04D-05 BMatP= 5.62D-04
IDIUse=3 WtCom= 9.98D-01 WtEn= 1.76D-03
Coeff-Com: -0.252D-02 0.106D-02 0.453D-01 0.126D+00 0.248D+00 0.582D+00
Coeff-En: 0.000D+00 0.000D+00 0.000D+00 0.000D+00 0.000D+00 0.100D+01
Coeff: -0.252D-02 0.106D-02 0.453D-01 0.126D+00 0.247D+00 0.583D+00
Gap= 0.192 Goal= None Shift= 0.000
RMSDP=1.38D-04 MaxDP=1.05D-02 DE=-5.62D-04 OVMax= 2.54D-03
Cycle 7 Pass 1 IDiag 1:
RMSU= 8.36D-05 CP: 7.04D-01 1.15D+00 8.05D-01 6.83D-01 7.07D-01
CP: 6.66D-01
E= -1338.35982004176 Delta-E= -0.000028407103 Rises=F Damp=F
DIIS: error= 5.89D-05 at cycle 7 NSaved= 7.
NSaved= 7 IEnMin= 7 EnMin= -1338.35982004176 IErMin= 7 ErrMin= 5.89D-05
ErrMax= 5.89D-05 0.00D+00 EMaxC= 1.00D-01 BMatC= 3.51D-06 BMatP= 3.04D-05
IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00
Coeff-Com: -0.581D-03-0.207D-02 0.101D-01 0.335D-01 0.834D-01 0.313D+00
Coeff-Com: 0.563D+00
Coeff: -0.581D-03-0.207D-02 0.101D-01 0.335D-01 0.834D-01 0.313D+00
Coeff: 0.563D+00
Gap= 0.192 Goal= None Shift= 0.000
RMSDP=7.45D-05 MaxDP=4.14D-03 DE=-2.84D-05 OVMax= 6.44D-04
Cycle 8 Pass 1 IDiag 1:
RMSU= 3.12D-05 CP: 7.03D-01 1.15D+00 8.07D-01 6.79D-01 6.92D-01
CP: 7.36D-01 9.27D-01
E= -1338.35982355953 Delta-E= -0.000003517770 Rises=F Damp=F
DIIS: error= 1.51D-05 at cycle 8 NSaved= 8.
NSaved= 8 IEnMin= 8 EnMin= -1338.35982355953 IErMin= 8 ErrMin= 1.51D-05
ErrMax= 1.51D-05 0.00D+00 EMaxC= 1.00D-01 BMatC= 1.59D-07 BMatP= 3.51D-06
IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00
Coeff-Com: -0.534D-04-0.104D-02 0.161D-02 0.624D-02 0.190D-01 0.944D-01
Coeff-Com: 0.244D+00 0.636D+00
Coeff: -0.534D-04-0.104D-02 0.161D-02 0.624D-02 0.190D-01 0.944D-01
Coeff: 0.244D+00 0.636D+00
Gap= 0.192 Goal= None Shift= 0.000
RMSDP=1.46D-05 MaxDP=7.03D-04 DE=-3.52D-06 OVMax= 2.89D-04
Cycle 9 Pass 1 IDiag 1:
RMSU= 1.02D-05 CP: 7.03D-01 1.15D+00 8.07D-01 6.80D-01 6.94D-01
CP: 7.35D-01 9.76D-01 9.67D-01
E= -1338.35982368820 Delta-E= -0.000000128671 Rises=F Damp=F
DIIS: error= 7.57D-06 at cycle 9 NSaved= 9.
NSaved= 9 IEnMin= 9 EnMin= -1338.35982368820 IErMin= 9 ErrMin= 7.57D-06
ErrMax= 7.57D-06 0.00D+00 EMaxC= 1.00D-01 BMatC= 5.79D-08 BMatP= 1.59D-07
IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00
Coeff-Com: 0.762D-04-0.337D-03-0.624D-03-0.156D-02-0.158D-02 0.102D-01
Coeff-Com: 0.685D-01 0.411D+00 0.515D+00
Coeff: 0.762D-04-0.337D-03-0.624D-03-0.156D-02-0.158D-02 0.102D-01
Coeff: 0.685D-01 0.411D+00 0.515D+00
Gap= 0.192 Goal= None Shift= 0.000
RMSDP=4.58D-06 MaxDP=2.30D-04 DE=-1.29D-07 OVMax= 1.36D-04
Cycle 10 Pass 1 IDiag 1:
RMSU= 2.41D-06 CP: 7.03D-01 1.15D+00 8.08D-01 6.80D-01 6.93D-01
CP: 7.40D-01 9.84D-01 1.01D+00 7.44D-01
E= -1338.35982375070 Delta-E= -0.000000062500 Rises=F Damp=F
DIIS: error= 2.10D-06 at cycle 10 NSaved= 10.
NSaved=10 IEnMin=10 EnMin= -1338.35982375070 IErMin=10 ErrMin= 2.10D-06
ErrMax= 2.10D-06 0.00D+00 EMaxC= 1.00D-01 BMatC= 3.50D-09 BMatP= 5.79D-08
IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00
Coeff-Com: 0.434D-04-0.609D-04-0.451D-03-0.137D-02-0.262D-02-0.467D-02
Coeff-Com: 0.921D-02 0.135D+00 0.252D+00 0.613D+00
Coeff: 0.434D-04-0.609D-04-0.451D-03-0.137D-02-0.262D-02-0.467D-02
Coeff: 0.921D-02 0.135D+00 0.252D+00 0.613D+00
Gap= 0.192 Goal= None Shift= 0.000
RMSDP=2.01D-06 MaxDP=9.53D-05 DE=-6.25D-08 OVMax= 4.45D-05
Cycle 11 Pass 1 IDiag 1:
RMSU= 8.51D-07 CP: 7.03D-01 1.15D+00 8.08D-01 6.80D-01 6.93D-01
CP: 7.40D-01 9.80D-01 1.01D+00 7.97D-01 8.86D-01
E= -1338.35982375389 Delta-E= -0.000000003187 Rises=F Damp=F
DIIS: error= 9.74D-07 at cycle 11 NSaved= 11.
NSaved=11 IEnMin=11 EnMin= -1338.35982375389 IErMin=11 ErrMin= 9.74D-07
ErrMax= 9.74D-07 0.00D+00 EMaxC= 1.00D-01 BMatC= 8.04D-10 BMatP= 3.50D-09
IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00
Coeff-Com: 0.164D-04 0.102D-04-0.217D-03-0.709D-03-0.148D-02-0.433D-02
Coeff-Com: -0.329D-02 0.309D-01 0.912D-01 0.378D+00 0.510D+00
Coeff: 0.164D-04 0.102D-04-0.217D-03-0.709D-03-0.148D-02-0.433D-02
Coeff: -0.329D-02 0.309D-01 0.912D-01 0.378D+00 0.510D+00
Gap= 0.192 Goal= None Shift= 0.000
RMSDP=9.13D-07 MaxDP=4.84D-05 DE=-3.19D-09 OVMax= 1.40D-05
Cycle 12 Pass 1 IDiag 1:
RMSU= 3.39D-07 CP: 7.03D-01 1.15D+00 8.08D-01 6.80D-01 6.93D-01
CP: 7.40D-01 9.84D-01 1.02D+00 7.92D-01 9.30D-01
CP: 7.03D-01
E= -1338.35982375468 Delta-E= -0.000000000789 Rises=F Damp=F
DIIS: error= 3.21D-07 at cycle 12 NSaved= 12.
NSaved=12 IEnMin=12 EnMin= -1338.35982375468 IErMin=12 ErrMin= 3.21D-07
ErrMax= 3.21D-07 0.00D+00 EMaxC= 1.00D-01 BMatC= 8.46D-11 BMatP= 8.04D-10
IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00
Coeff-Com: -0.127D-05 0.183D-04-0.218D-04-0.965D-04-0.231D-03-0.127D-02
Coeff-Com: -0.335D-02-0.935D-02 0.102D-02 0.933D-01 0.286D+00 0.634D+00
Coeff: -0.127D-05 0.183D-04-0.218D-04-0.965D-04-0.231D-03-0.127D-02
Coeff: -0.335D-02-0.935D-02 0.102D-02 0.933D-01 0.286D+00 0.634D+00
Gap= 0.192 Goal= None Shift= 0.000
RMSDP=2.82D-07 MaxDP=1.50D-05 DE=-7.89D-10 OVMax= 6.90D-06
Cycle 13 Pass 1 IDiag 1:
RMSU= 1.40D-07 CP: 7.03D-01 1.15D+00 8.08D-01 6.80D-01 6.93D-01
CP: 7.40D-01 9.84D-01 1.02D+00 7.97D-01 9.42D-01
CP: 7.22D-01 7.90D-01
E= -1338.35982375479 Delta-E= -0.000000000110 Rises=F Damp=F
DIIS: error= 8.57D-08 at cycle 13 NSaved= 13.
NSaved=13 IEnMin=13 EnMin= -1338.35982375479 IErMin=13 ErrMin= 8.57D-08
ErrMax= 8.57D-08 0.00D+00 EMaxC= 1.00D-01 BMatC= 8.38D-12 BMatP= 8.46D-11
IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00
Coeff-Com: -0.202D-05 0.873D-05 0.420D-05 0.259D-05-0.227D-05-0.286D-03
Coeff-Com: -0.143D-02-0.720D-02-0.666D-02 0.170D-01 0.968D-01 0.322D+00
Coeff-Com: 0.580D+00
Coeff: -0.202D-05 0.873D-05 0.420D-05 0.259D-05-0.227D-05-0.286D-03
Coeff: -0.143D-02-0.720D-02-0.666D-02 0.170D-01 0.968D-01 0.322D+00
Coeff: 0.580D+00
Gap= 0.192 Goal= None Shift= 0.000
RMSDP=7.11D-08 MaxDP=3.46D-06 DE=-1.10D-10 OVMax= 1.34D-06
Cycle 14 Pass 1 IDiag 1:
RMSU= 2.95D-08 CP: 7.03D-01 1.15D+00 8.08D-01 6.80D-01 6.93D-01
CP: 7.40D-01 9.84D-01 1.02D+00 7.97D-01 9.43D-01
CP: 7.35D-01 8.35D-01 8.28D-01
E= -1338.35982375488 Delta-E= -0.000000000095 Rises=F Damp=F
DIIS: error= 3.20D-08 at cycle 14 NSaved= 14.
NSaved=14 IEnMin=14 EnMin= -1338.35982375488 IErMin=14 ErrMin= 3.20D-08
ErrMax= 3.20D-08 0.00D+00 EMaxC= 1.00D-01 BMatC= 1.00D-12 BMatP= 8.38D-12
IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00
Coeff-Com: -0.104D-05 0.218D-05 0.490D-05 0.145D-04 0.295D-04 0.177D-04
Coeff-Com: -0.357D-03-0.280D-02-0.408D-02-0.430D-02 0.119D-01 0.905D-01
Coeff-Com: 0.301D+00 0.608D+00
Coeff: -0.104D-05 0.218D-05 0.490D-05 0.145D-04 0.295D-04 0.177D-04
Coeff: -0.357D-03-0.280D-02-0.408D-02-0.430D-02 0.119D-01 0.905D-01
Coeff: 0.301D+00 0.608D+00
Gap= 0.192 Goal= None Shift= 0.000
RMSDP=1.90D-08 MaxDP=9.94D-07 DE=-9.46D-11 OVMax= 3.64D-07
Cycle 15 Pass 1 IDiag 1:
RMSU= 1.24D-08 CP: 7.03D-01 1.15D+00 8.08D-01 6.80D-01 6.93D-01
CP: 7.40D-01 9.84D-01 1.02D+00 7.97D-01 9.45D-01
CP: 7.37D-01 8.37D-01 8.27D-01 9.59D-01
E= -1338.35982375482 Delta-E= 0.000000000057 Rises=F Damp=F
DIIS: error= 6.38D-09 at cycle 15 NSaved= 15.
NSaved=15 IEnMin=14 EnMin= -1338.35982375488 IErMin=15 ErrMin= 6.38D-09
ErrMax= 6.38D-09 0.00D+00 EMaxC= 1.00D-01 BMatC= 3.85D-14 BMatP= 1.00D-12
IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00
Coeff-Com: -0.157D-06-0.947D-09 0.893D-06 0.376D-05 0.841D-05 0.313D-04
Coeff-Com: 0.972D-05-0.220D-03-0.610D-03-0.260D-02-0.387D-02 0.264D-02
Coeff-Com: 0.462D-01 0.212D+00 0.747D+00
Coeff: -0.157D-06-0.947D-09 0.893D-06 0.376D-05 0.841D-05 0.313D-04
Coeff: 0.972D-05-0.220D-03-0.610D-03-0.260D-02-0.387D-02 0.264D-02
Coeff: 0.462D-01 0.212D+00 0.747D+00
Gap= 0.192 Goal= None Shift= 0.000
RMSDP=4.84D-09 MaxDP=2.02D-07 DE= 5.73D-11 OVMax= 9.71D-08
SCF Done: E(RB3LYP) = -1338.35982375 A.U. after 15 cycles
NFock= 15 Conv=0.48D-08 -V/T= 2.0019
KE= 1.335786554451D+03 PE=-4.830628979661D+03 EE= 1.321032366085D+03
Leave Link 502 at Thu Feb 23 07:22:08 2023, MaxMem= 3221225472 cpu: 869.7 elap: 43.5
(Enter /home/hideyoshi/.local/g16/l601.exe)
Copying SCF densities to generalized density rwf, IOpCl= 0 IROHF=0.
**********************************************************************
Population analysis using the SCF Density.
**********************************************************************
Alpha occ. eigenvalues -- -101.55656-101.55178 -14.39367 -14.32701 -10.27180
Alpha occ. eigenvalues -- -10.25712 -10.25521 -10.23868 -10.22067 -10.19936
Alpha occ. eigenvalues -- -10.19228 -10.17448 -9.47374 -9.46878 -7.23627
Alpha occ. eigenvalues -- -7.23132 -7.22663 -7.22610 -7.22169 -7.22116
Alpha occ. eigenvalues -- -1.05154 -0.92443 -0.90805 -0.86525 -0.84889
Alpha occ. eigenvalues -- -0.80103 -0.76932 -0.72315 -0.67459 -0.63797
Alpha occ. eigenvalues -- -0.61882 -0.57882 -0.52623 -0.50727 -0.49551
Alpha occ. eigenvalues -- -0.48983 -0.47017 -0.45111 -0.45044 -0.43105
Alpha occ. eigenvalues -- -0.40974 -0.40808 -0.40345 -0.35395 -0.33090
Alpha occ. eigenvalues -- -0.32611 -0.31480 -0.30731 -0.28914 -0.24499
Alpha occ. eigenvalues -- -0.23575
Alpha virt. eigenvalues -- -0.04369 -0.02430 -0.00990 -0.00126 0.00038
Alpha virt. eigenvalues -- 0.00938 0.01152 0.02169 0.02863 0.03305
Alpha virt. eigenvalues -- 0.03797 0.04302 0.05550 0.05608 0.06296
Alpha virt. eigenvalues -- 0.06848 0.07244 0.08046 0.08308 0.08574
Alpha virt. eigenvalues -- 0.09015 0.09553 0.09791 0.10875 0.11020
Alpha virt. eigenvalues -- 0.11458 0.11556 0.12399 0.12511 0.12778
Alpha virt. eigenvalues -- 0.13196 0.13821 0.14107 0.14514 0.14925
Alpha virt. eigenvalues -- 0.15616 0.15961 0.16994 0.17241 0.17771
Alpha virt. eigenvalues -- 0.18084 0.18283 0.19013 0.19139 0.19545
Alpha virt. eigenvalues -- 0.19645 0.20082 0.20811 0.21447 0.21841
Alpha virt. eigenvalues -- 0.23052 0.23243 0.23567 0.23898 0.24667
Alpha virt. eigenvalues -- 0.25670 0.25997 0.26574 0.26925 0.27058
Alpha virt. eigenvalues -- 0.27541 0.28620 0.29154 0.29351 0.29935
Alpha virt. eigenvalues -- 0.30395 0.31757 0.32359 0.32713 0.33184
Alpha virt. eigenvalues -- 0.33677 0.34596 0.34774 0.35556 0.35630
Alpha virt. eigenvalues -- 0.35946 0.37471 0.37613 0.38647 0.39077
Alpha virt. eigenvalues -- 0.39843 0.40236 0.40932 0.41909 0.43572
Alpha virt. eigenvalues -- 0.43924 0.44436 0.46077 0.46500 0.46705
Alpha virt. eigenvalues -- 0.47536 0.48335 0.48595 0.49505 0.50439
Alpha virt. eigenvalues -- 0.50806 0.51100 0.51284 0.52108 0.52543
Alpha virt. eigenvalues -- 0.53337 0.54286 0.54747 0.55494 0.55751
Alpha virt. eigenvalues -- 0.57068 0.57823 0.58742 0.59334 0.59580
Alpha virt. eigenvalues -- 0.59882 0.60013 0.60366 0.60905 0.62140
Alpha virt. eigenvalues -- 0.62988 0.63695 0.64258 0.65331 0.65875
Alpha virt. eigenvalues -- 0.66058 0.67265 0.67686 0.68656 0.69138
Alpha virt. eigenvalues -- 0.70904 0.71681 0.72042 0.72624 0.73286
Alpha virt. eigenvalues -- 0.73600 0.74062 0.74738 0.75630 0.76783
Alpha virt. eigenvalues -- 0.78357 0.79230 0.80351 0.80845 0.81497
Alpha virt. eigenvalues -- 0.82192 0.82524 0.83920 0.85294 0.86212
Alpha virt. eigenvalues -- 0.88159 0.89210 0.89596 0.90115 0.91236
Alpha virt. eigenvalues -- 0.91444 0.95248 0.95706 0.96771 0.97593
Alpha virt. eigenvalues -- 0.97842 0.99715 1.00549 1.01604 1.01637
Alpha virt. eigenvalues -- 1.02748 1.04663 1.05699 1.06345 1.08187
Alpha virt. eigenvalues -- 1.09548 1.12001 1.13995 1.15889 1.17383
Alpha virt. eigenvalues -- 1.17953 1.18546 1.18891 1.20126 1.21867
Alpha virt. eigenvalues -- 1.22203 1.23057 1.23941 1.25712 1.26280
Alpha virt. eigenvalues -- 1.26556 1.26912 1.27489 1.27963 1.29611
Alpha virt. eigenvalues -- 1.32415 1.34581 1.35523 1.36582 1.39499
Alpha virt. eigenvalues -- 1.40805 1.41514 1.41986 1.43436 1.43800
Alpha virt. eigenvalues -- 1.44575 1.45016 1.46977 1.48280 1.49100
Alpha virt. eigenvalues -- 1.50411 1.50691 1.51349 1.53879 1.55531
Alpha virt. eigenvalues -- 1.56549 1.58531 1.61824 1.62292 1.64042
Alpha virt. eigenvalues -- 1.65015 1.68931 1.70202 1.70724 1.71645
Alpha virt. eigenvalues -- 1.72660 1.74841 1.76781 1.77814 1.79203
Alpha virt. eigenvalues -- 1.80488 1.81365 1.82373 1.84891 1.86119
Alpha virt. eigenvalues -- 1.88181 1.89865 1.90459 1.91936 1.92027
Alpha virt. eigenvalues -- 1.93713 1.97252 1.98352 2.00046 2.01896
Alpha virt. eigenvalues -- 2.03984 2.05132 2.07048 2.07561 2.08978
Alpha virt. eigenvalues -- 2.12338 2.14306 2.15843 2.16637 2.19132
Alpha virt. eigenvalues -- 2.20040 2.21205 2.22264 2.23773 2.27086
Alpha virt. eigenvalues -- 2.28468 2.29734 2.33122 2.37222 2.39232
Alpha virt. eigenvalues -- 2.43738 2.44337 2.49276 2.51094 2.52818
Alpha virt. eigenvalues -- 2.53997 2.55396 2.59823 2.63745 2.69755
Alpha virt. eigenvalues -- 2.72747 2.73700 2.76824 2.85264 2.89550
Alpha virt. eigenvalues -- 2.92297 2.97450 3.01087 3.02066 3.05422
Alpha virt. eigenvalues -- 3.11372 3.20039 3.21585 3.27848 3.31271
Alpha virt. eigenvalues -- 3.35812 3.38819 3.47012 3.70766 3.78683
Alpha virt. eigenvalues -- 4.41808
Condensed to atoms (all electrons):
1 2 3 4 5 6
1 Cl 17.460587 -0.058224 0.007211 -0.004830 -0.006124 -0.001597
2 Cl -0.058224 17.468438 -0.002680 0.010668 -0.007581 -0.000667
3 N 0.007211 -0.002680 7.877346 0.066096 -0.311852 -0.052899
4 N -0.004830 0.010668 0.066096 7.646857 0.400671 -0.321519
5 C -0.006124 -0.007581 -0.311852 0.400671 9.287405 -1.037623
6 C -0.001597 -0.000667 -0.052899 -0.321519 -1.037623 6.741330
7 C -0.616610 0.321522 -1.301582 -0.401572 0.017671 0.242933
8 C 0.340319 -0.720055 -0.109024 -1.487850 -0.396985 0.151199
9 C -0.453169 0.906961 -0.113436 1.745757 -1.464427 -0.394039
10 C 0.444492 -0.603561 0.117421 -0.369642 0.251010 0.043722
11 C -0.513082 0.508273 -0.207968 0.093833 0.185845 0.081374
12 C 0.787062 -0.423889 1.772681 0.159147 -1.157041 -0.642265
13 H -0.170644 0.012815 -0.230671 -0.029578 0.247747 0.032567
14 H 0.013887 -0.195044 -0.013992 -0.327938 0.287100 0.026003
15 H 0.001259 -0.003064 0.007399 -0.431698 -0.503290 -0.037798
16 H -0.000013 -0.000152 0.149086 -0.165299 0.352718 -0.434189
17 H -0.000057 -0.000111 0.166585 0.119506 -0.190147 -0.120671
18 H -0.000309 0.000172 -0.329858 0.058395 0.998175 -0.741703
7 8 9 10 11 12
1 Cl -0.616610 0.340319 -0.453169 0.444492 -0.513082 0.787062
2 Cl 0.321522 -0.720055 0.906961 -0.603561 0.508273 -0.423889
3 N -1.301582 -0.109024 -0.113436 0.117421 -0.207968 1.772681
4 N -0.401572 -1.487850 1.745757 -0.369642 0.093833 0.159147
5 C 0.017671 -0.396985 -1.464427 0.251010 0.185845 -1.157041
6 C 0.242933 0.151199 -0.394039 0.043722 0.081374 -0.642265
7 C 34.262604 -6.320855 4.488747 -7.689231 7.767674 -28.229380
8 C -6.320855 33.299198 -29.226539 8.575620 -7.793211 4.746425
9 C 4.488747 -29.226539 67.460320 -18.861250 9.379325 -21.266058
10 C -7.689231 8.575620 -18.861250 22.627874 -9.309824 9.407473
11 C 7.767674 -7.793211 9.379325 -9.309824 21.100412 -16.293279
12 C -28.229380 4.746425 -21.266058 9.407473 -16.293279 62.558819
13 H 5.511852 -0.162028 0.637234 -0.852390 2.411283 -9.762159
14 H -0.105853 5.686045 -10.517209 2.858589 -0.879856 0.570246
15 H -0.166232 0.749216 -0.526826 0.060944 -0.045291 0.097757
16 H 0.052888 -0.027598 -0.015821 0.011878 -0.003381 -0.008881
17 H 0.093808 0.092024 -0.060875 0.004600 0.002878 -0.023791
18 H -0.102723 0.027318 0.060719 -0.013654 0.018506 -0.067006
13 14 15 16 17 18
1 Cl -0.170644 0.013887 0.001259 -0.000013 -0.000057 -0.000309
2 Cl 0.012815 -0.195044 -0.003064 -0.000152 -0.000111 0.000172
3 N -0.230671 -0.013992 0.007399 0.149086 0.166585 -0.329858
4 N -0.029578 -0.327938 -0.431698 -0.165299 0.119506 0.058395
5 C 0.247747 0.287100 -0.503290 0.352718 -0.190147 0.998175
6 C 0.032567 0.026003 -0.037798 -0.434189 -0.120671 -0.741703
7 C 5.511852 -0.105853 -0.166232 0.052888 0.093808 -0.102723
8 C -0.162028 5.686045 0.749216 -0.027598 0.092024 0.027318
9 C 0.637234 -10.517209 -0.526826 -0.015821 -0.060875 0.060719
10 C -0.852390 2.858589 0.060944 0.011878 0.004600 -0.013654
11 C 2.411283 -0.879856 -0.045291 -0.003381 0.002878 0.018506
12 C -9.762159 0.570246 0.097757 -0.008881 -0.023791 -0.067006
13 H 4.480448 0.049205 -0.006377 0.002481 0.003242 0.005688
14 H 0.049205 4.653638 0.056292 0.007377 0.002540 0.001876
15 H -0.006377 0.056292 2.295320 -0.020471 0.001405 0.002586
16 H 0.002481 0.007377 -0.020471 2.208589 -0.274233 -0.318386
17 H 0.003242 0.002540 0.001405 -0.274233 1.921413 -0.327958
18 H 0.005688 0.001876 0.002586 -0.318386 -0.327958 2.272657
Mulliken charges:
1
1 Cl -0.230158
2 Cl -0.213819
3 N -0.489860
4 N 0.238997
5 C -0.953271
6 C 2.465843
7 C -1.825659
8 C -1.423218
9 C 4.220587
10 C -0.704072
11 C -0.503512
12 C 3.774138
13 H -1.180716
14 H -1.172905
15 H -0.531129
16 H -0.516594
17 H -0.410158
18 H -0.544494
Sum of Mulliken charges = -0.00000
Mulliken charges with hydrogens summed into heavy atoms:
1
1 Cl -0.230158
2 Cl -0.213819
3 N -0.489860
4 N -0.292132
5 C -0.953271
6 C 0.994597
7 C -1.825659
8 C -1.423218
9 C 3.047682
10 C -0.704072
11 C -0.503512
12 C 2.593422
Electronic spatial extent (au): <R**2>= 7764.1477
Charge= -0.0000 electrons
Dipole moment (field-independent basis, Debye):
X= 2.7395 Y= 3.5706 Z= 3.3308 Tot= 5.5989
Quadrupole moment (field-independent basis, Debye-Ang):
XX= -68.6170 YY= -73.5165 ZZ= -61.6051
XY= 14.4908 XZ= 20.9241 YZ= 19.8337
Traceless Quadrupole moment (field-independent basis, Debye-Ang):
XX= -0.7041 YY= -5.6037 ZZ= 6.3078
XY= 14.4908 XZ= 20.9241 YZ= 19.8337
Octapole moment (field-independent basis, Debye-Ang**2):
XXX= -468.9556 YYY= -106.8486 ZZZ= -585.2890 XYY= -124.9307
XXY= 17.9261 XXZ= -141.4541 XZZ= -76.9527 YZZ= 35.3059
YYZ= -180.7234 XYZ= 78.2906
Hexadecapole moment (field-independent basis, Debye-Ang**3):
XXXX= -3231.4788 YYYY= -1910.6363 ZZZZ= -4129.7027 XXXY= -705.1854
XXXZ= -1101.7994 YYYX= -802.0130 YYYZ= -245.4322 ZZZX= -1010.6523
ZZZY= -59.4145 XXYY= -650.1830 XXZZ= -968.4835 YYZZ= -919.6626
XXYZ= 187.0061 YYXZ= -248.0593 ZZXY= -14.7512
N-N= 8.354502353694D+02 E-N=-4.830628981989D+03 KE= 1.335786554451D+03
No NMR shielding tensors so no spin-rotation constants.
Leave Link 601 at Thu Feb 23 07:22:08 2023, MaxMem= 3221225472 cpu: 1.6 elap: 0.1
(Enter /home/hideyoshi/.local/g16/l602.exe)
FitSet: NAtFit= 18 NAtPot= 18 NAtFrz= 0 MDM= 22 TotChg= 0.00000
Breneman (CHELPG) radii used.
Generate Potential Derived Charges using the Breneman model, NDens= 1.
Grid spacing= 0.300 Box extension= 2.800
NStep X,Y,Z= 38 42 36 Total possible points= 57456
Number of Points to Fit= 11818
**********************************************************************
Electrostatic Properties Using The SCF Density.
**********************************************************************
Atomic Center 1 is at 0.529510 -1.626650 1.247340
Atomic Center 2 is at 0.362930 -1.511550 4.375370
Atomic Center 3 is at 3.703160 2.470260 1.679280
Atomic Center 4 is at 3.582140 2.531110 3.906530
Atomic Center 5 is at 4.112500 3.089530 2.782510
Atomic Center 6 is at 5.073000 4.218890 2.804340
Atomic Center 7 is at 2.860410 1.456340 2.124310
Atomic Center 8 is at 2.790650 1.491600 3.517640
Atomic Center 9 is at 2.019660 0.586860 4.234070
Atomic Center 10 is at 1.332680 -0.367920 3.533240
Atomic Center 11 is at 1.403870 -0.417400 2.127430
Atomic Center 12 is at 2.171300 0.490750 1.403730
Atomic Center 13 is at 2.221130 0.451520 0.476230
Atomic Center 14 is at 1.970540 0.627800 5.162610
Atomic Center 15 is at 3.801550 2.769370 4.720690
Atomic Center 16 is at 5.682390 4.106860 3.538440
Atomic Center 17 is at 4.594600 5.044580 2.908320
Atomic Center 18 is at 5.565630 4.235950 1.980820
11818 points will be used for fitting atomic charges
Fitting point charges to electrostatic potential
Charges from ESP fit, RMS= 0.00445 RRMS= 0.21659:
ESP charges:
1
1 Cl -0.121150
2 Cl -0.107139
3 N -0.684426
4 N -0.516473
5 C 0.512777
6 C -0.083045
7 C 0.397921
8 C 0.129877
9 C -0.214313
10 C 0.036208
11 C 0.109865
12 C -0.287406
13 H 0.184608
14 H 0.158182
15 H 0.362283
16 H 0.021345
17 H 0.035903
18 H 0.064983
Sum of ESP charges = -0.00000
ESP charges with hydrogens summed into heavy atoms:
1
1 Cl -0.121150
2 Cl -0.107139
3 N -0.684426
4 N -0.154190
5 C 0.512777
6 C 0.039187
7 C 0.397921
8 C 0.129877
9 C -0.056131
10 C 0.036208
11 C 0.109865
12 C -0.102798
Charge= -0.00000 Dipole= 2.8484 3.7089 3.2829 Tot= 5.7138
-----------------------------------------------------------------
Electrostatic Properties (Atomic Units)
-----------------------------------------------------------------
Center Electric -------- Electric Field --------
Potential X Y Z
-----------------------------------------------------------------
1 Atom -64.401432
2 Atom -64.396619
3 Atom -18.387902
4 Atom -18.314879
5 Atom -14.676262
6 Atom -14.781825
7 Atom -14.730467
8 Atom -14.711820
9 Atom -14.757462
10 Atom -14.693317
11 Atom -14.694730
12 Atom -14.765077
13 Atom -1.084814
14 Atom -1.072232
15 Atom -0.970686
16 Atom -1.079838
17 Atom -1.081408
18 Atom -1.087271
-----------------------------------------------------------------
Leave Link 602 at Thu Feb 23 07:22:08 2023, MaxMem= 3221225472 cpu: 5.0 elap: 0.3
(Enter /home/hideyoshi/.local/g16/l9999.exe)
1\1\GINC-VALFENDA\SP\RB3LYP\Aug-CC-pVDZ\C8H6Cl2N2\HIDEYOSHI\23-Feb-202
3\0\\#P b3lyp/aug-cc-pVDZ Pop=chelpg Density=Current NoSymm\\Crystal -
Cycle number 1\\0,1\Cl,0,0.52951,-1.62665,1.24734\Cl,0,0.36293,-1.511
55,4.37537\N,0,3.70316,2.47026,1.67928\N,0,3.58214,2.53111,3.90653\C,0
,4.1125,3.08953,2.78251\C,0,5.073,4.21889,2.80434\C,0,2.86041,1.45634,
2.12431\C,0,2.79065,1.4916,3.51764\C,0,2.01966,0.58686,4.23407\C,0,1.3
3268,-0.36792,3.53324\C,0,1.40387,-0.4174,2.12743\C,0,2.1713,0.49075,1
.40373\H,0,2.22113,0.45152,0.47623\H,0,1.97054,0.6278,5.16261\H,0,3.80
155,2.76937,4.72069\H,0,5.68239,4.10686,3.53844\H,0,4.5946,5.04458,2.9
0832\H,0,5.56563,4.23595,1.98082\\Version=EM64L-G16RevB.01\HF=-1338.35
98238\RMSD=4.839e-09\Dipole=1.0777846,1.4047677,1.3104205\Quadrupole=-
0.5234839,-4.1661813,4.6896652,10.7735364,15.5565506,14.7458585\PG=C01
[X(C8H6Cl2N2)]\\@
NEVER LOSE YOUR IGNORANCE, IT CAN'T BE REPLACED.
-- ANDY CAPP
Job cpu time: 0 days 0 hours 14 minutes 59.0 seconds.
Elapsed time: 0 days 0 hours 0 minutes 45.0 seconds.
File lengths (MBytes): RWF= 63 Int= 0 D2E= 0 Chk= 8 Scr= 1
Normal termination of Gaussian 16 at Thu Feb 23 07:22:08 2023.

98
tests/shared/test_gaussian.py → tests/test_gaussian.py
View File

@@ -1,3 +1,5 @@
import os
from crystalpol.shared.system.molecule import Molecule from crystalpol.shared.system.molecule import Molecule
from crystalpol.shared.system.crystal import Crystal from crystalpol.shared.system.crystal import Crystal
from crystalpol.shared.system.atom import Atom from crystalpol.shared.system.atom import Atom
@@ -67,10 +69,39 @@ class TestGaussian(TestCase):
with self.assertRaises(RuntimeError): with self.assertRaises(RuntimeError):
gaussian.create_simulation_dir() gaussian.create_simulation_dir()
# @mock.patch('crystalpol.gaussian.os') @mock.patch('crystalpol.gaussian.os')
def test_create_step_dir(self, os_mock):
os_mock.path.exists.return_value = False
os_mock.makedirs = mock.MagicMock()
gaussian = Gaussian(
Config(
mem=1,
level="b3lyp/aug-cc-pVDZ",
n_atoms=10
)
)
gaussian.create_step_dir(1)
self.assertTrue(os_mock.makedirs.called)
@mock.patch('crystalpol.gaussian.os')
def test_create_step_dir_raises_exception(self, os_mock):
os_mock.path.exists.return_value = True
os_mock.makedirs = mock.MagicMock()
gaussian = Gaussian(
Config(
mem=1,
level="b3lyp/aug-cc-pVDZ",
n_atoms=10
)
)
with self.assertRaises(RuntimeError):
gaussian.create_step_dir(1)
@mock.patch('crystalpol.gaussian.open') @mock.patch('crystalpol.gaussian.open')
def test_make_gaussian_input_cycle_1(self, open_mock): def test_make_gaussian_input_cycle_1(self, open_mock):
open_mock.return_value = StringIO() open_mock.return_value = StringIO()
crystal = self.create_crystal() crystal = self.create_crystal()
@@ -82,7 +113,7 @@ class TestGaussian(TestCase):
n_atoms=10 n_atoms=10
) )
) )
gaussian_input = gaussian.make_gaussian_input(1, Path(), crystal) gaussian_input = gaussian.make_gaussian_input(1, Path('test.gjf'), crystal)
expected_output = """\ expected_output = """\
%Mem=1Gb %Mem=1Gb
%Nprocs=1 %Nprocs=1
@@ -98,7 +129,6 @@ H 0.00000 0.00000 0.00000
@mock.patch('crystalpol.gaussian.open') @mock.patch('crystalpol.gaussian.open')
def test_make_gaussian_input_cycle_2(self, open_mock): def test_make_gaussian_input_cycle_2(self, open_mock):
open_mock.return_value = StringIO() open_mock.return_value = StringIO()
crystal = self.create_crystal() crystal = self.create_crystal()
@@ -110,7 +140,7 @@ H 0.00000 0.00000 0.00000
n_atoms=10 n_atoms=10
) )
) )
gaussian_input = gaussian.make_gaussian_input(2, "test", crystal) gaussian_input = gaussian.make_gaussian_input(2, Path('test.gjf'), crystal)
expected_output = """\ expected_output = """\
%Mem=1Gb %Mem=1Gb
%Nprocs=1 %Nprocs=1
@@ -121,13 +151,11 @@ crystalpol - Cycle number 2
0 1 0 1
H 0.00000 0.00000 0.00000 H 0.00000 0.00000 0.00000
H 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
""" """
self.assertEqual(gaussian_input, expected_output) self.assertEqual(gaussian_input, expected_output)
def test_make_gaussian_charges(self): def test_make_gaussian_charges(self):
file = StringIO() file = StringIO()
crystal = self.create_crystal() crystal = self.create_crystal()
@@ -142,16 +170,19 @@ H 0.00000 0.00000 0.00000
file.seek(0) file.seek(0)
charges_string = file.read() charges_string = file.read()
expected_charges = 'H 0.00000 0.00000 0.00000\n\n' expected_charges = ' 0.00000 0.00000 0.00000 0.00000\n'
self.assertEqual(charges_string, expected_charges) 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.subprocess.call', autospec=True, return_value=0)
@mock.patch('crystalpol.gaussian.Gaussian.create_step_dir')
@mock.patch('crystalpol.gaussian.Gaussian.make_gaussian_input') @mock.patch('crystalpol.gaussian.Gaussian.make_gaussian_input')
def test_run(self, make_gaussian_input_mock, subprocess_call_mock, os_mock): @mock.patch('crystalpol.gaussian.Gaussian.read_charges_from_gaussian_output')
os_mock.path.exists.return_value = False def test_run(self,
read_charges_from_gaussian_output_mock,
make_gaussian_input_mock,
create_step_dir_mock,
subprocess_call_mock):
gaussian = Gaussian( gaussian = Gaussian(
Config( Config(
mem=1, mem=1,
@@ -161,14 +192,20 @@ H 0.00000 0.00000 0.00000
) )
gaussian.run(1, self.create_crystal()) gaussian.run(1, self.create_crystal())
self.assertTrue(read_charges_from_gaussian_output_mock.called)
self.assertTrue(make_gaussian_input_mock.called)
self.assertTrue(create_step_dir_mock.called)
self.assertTrue(subprocess_call_mock.called) 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.subprocess.call', autospec=True, return_value=1)
@mock.patch('crystalpol.gaussian.Gaussian.create_step_dir')
@mock.patch('crystalpol.gaussian.Gaussian.make_gaussian_input') @mock.patch('crystalpol.gaussian.Gaussian.make_gaussian_input')
def test_run_raises_exception(self, subprocess_call_mock, make_gaussian_input_mock, os_mock): @mock.patch('crystalpol.gaussian.Gaussian.read_charges_from_gaussian_output')
os_mock.path.exists.return_value = False def test_run_raises_exception(self,
read_charges_from_gaussian_output_mock,
make_gaussian_input_mock,
create_step_dir_mock,
subprocess_call_mock):
gaussian = Gaussian( gaussian = Gaussian(
Config( Config(
mem=1, mem=1,
@@ -180,9 +217,33 @@ H 0.00000 0.00000 0.00000
with self.assertRaises(RuntimeError): with self.assertRaises(RuntimeError):
gaussian.run(1, self.create_crystal()) gaussian.run(1, self.create_crystal())
@mock.patch('crystalpol.gaussian.open')
def test_read_charges_from_gaussian_output(self, open_mock):
if Path('tests').exists():
os.chdir('tests')
gaussian_output_file = Path('test_files/gaussian_output_example.log')
with open(gaussian_output_file) as output_file:
open_mock.return_value\
.__enter__.return_value\
.readlines.return_value = output_file.readlines()
gaussian = Gaussian(
Config(
mem=1,
level="b3lyp/aug-cc-pVDZ",
n_atoms=10
)
)
charges = gaussian.read_charges_from_gaussian_output(1, 18)
expected_charges = [-0.12115, -0.107139, -0.684426, -0.516473, 0.512777, -0.083045, 0.397921, 0.129877, -0.214313, 0.036208, 0.109865, -0.287406, 0.184608, 0.158182, 0.362283, 0.021345, 0.035903, 0.064983]
self.assertEqual(charges, expected_charges)
@staticmethod @staticmethod
def create_crystal(): def create_crystal():
crystal_structure = [ crystal_structure = [
['H '] ['H ']
] ]
@@ -196,6 +257,7 @@ H 0.00000 0.00000 0.00000
rx=0, rx=0,
ry=0, ry=0,
rz=0, rz=0,
chg=0
) )
) )

21
tests/test_polarization.py
View File

@@ -85,15 +85,26 @@ class TestPolarization(TestCase):
self.assertEqual(len(pol.crystal[0]), 1) self.assertEqual(len(pol.crystal[0]), 1)
@mock.patch('builtins.open', mock.mock_open(read_data=GEOM_DATA)) @mock.patch('builtins.open', mock.mock_open(read_data=GEOM_DATA))
@mock.patch('crystalpol.gaussian.subprocess.call', autospec=True, return_value=0) @mock.patch('crystalpol.polarization.Gaussian')
@mock.patch('crystalpol.gaussian.os') def test_run(self, gaussian_mock):
def test_run(self, os_mock, subprocess_call_mock):
os_mock.path.exists.return_value = False
pol = Polarization("geom_file", "outfile", self.config) pol = Polarization(
"geom_file",
"outfile",
self.config
)
pol.gaussian.run.side_effect = [
[.2, .2, .2, .2],
[.02, .02, .02, .02],
[.02, .02, .02, .02]
]
pol.run() pol.run()
self.assertTrue(pol.gaussian.create_simulation_dir.called)
self.assertTrue(pol.gaussian.run.called)
self.assertIsNotNone(pol.crystal) self.assertIsNotNone(pol.crystal)
self.assertEqual(len(pol.crystal), 2) self.assertEqual(len(pol.crystal), 2)
self.assertEqual(len(pol.crystal[0]), 1) self.assertEqual(len(pol.crystal[0]), 1)