proteindf_tools.gauparam のソースコード
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (C) 2014 The ProteinDF development team.
# see also AUTHORS and README if provided.
#
# This file is a part of the ProteinDF software package.
#
# The ProteinDF is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# The ProteinDF is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with ProteinDF. If not, see <http://www.gnu.org/licenses/>.
from .qmsim import QmSim
[ドキュメント]
class GaussianParam(QmSim):
"""
Set the Gaussian calculation conditions.
"""
def __init__(self):
self._data = {}
self._init_gen_data()
def _init_gen_data(self):
self._gen_data = {}
# DZ
self._gen_data['DZ'] = {}
self._gen_data['DZ']['H']= """
H 0
S 3
1.92406000E+01 3.28280000E-02
2.89920000E+00 2.31208000E-01
6.53400000E-01 8.17238000E-01
S 1
1.77600000E-01 1.00000000E+00
****"""
self._gen_data['DZ']['C'] = """
C 0
S 6
4232.61000000 0.00202900
634.88200000 0.01553500
146.09700000 0.07541100
42.49740000 0.25712100
14.18920000 0.59655500
1.96660000 0.24251700
S 1
5.14770000 1.00000000
S 1
0.49620000 1.00000000
S 1
0.15330000 1.00000000
P 4
18.15570000 0.01853400
3.98640000 0.11544200
1.14290000 0.38620600
0.35940000 0.64008900
P 1
0.11460000 1.00000000
****"""
self._gen_data['DZ']['N'] = """
N 0
S 6
5.90944000E+03 2.00400000E-03
8.87451000E+02 1.53100000E-02
2.04749000E+02 7.42930000E-02
5.98376000E+01 2.53364000E-01
1.99981000E+01 6.00576000E-01
2.68600000E+00 2.45111000E-01
S 1
7.19270000E+00 1.00000000E+00
S 1
7.00000000E-01 1.00000000E+00
S 1
2.13300000E-01 1.00000000E+00
P 4
2.67860000E+01 1.82570000E-02
5.95640000E+00 1.16407000E-01
1.70740000E+00 3.90111000E-01
5.31400000E-01 6.37221000E-01
P 1
1.65400000E-01 1.00000000E+00
****"""
self._gen_data['DZ']['O'] = """
O 0
S 6
7816.54000000 0.00203100
1175.82000000 0.01543600
273.18800000 0.07377100
81.16960000 0.24760600
27.18360000 0.61183200
3.41360000 0.24120500
S 1
9.53220000 1.00000000
S 1
0.93980000 1.00000000
S 1
0.28460000 1.00000000
P 4
35.18320000 0.01958000
7.90400000 0.12418900
2.30510000 0.39472700
0.71710000 0.62737500
P 1
0.21370000 1.00000000
****"""
# DZP
self._gen_data['DZP'] = {}
self._gen_data['DZP']['H'] = """
H 0
S 3
1.92406000E+01 3.28280000E-02
2.89920000E+00 2.31208000E-01
6.53400000E-01 8.17238000E-01
S 1
1.77600000E-01 1.00000000E+00
P 1
1.00000000E+00 1.00000000E+00
****"""
self._gen_data['DZP']['C'] = """
C 0
S 6
4232.61000000 0.00202900
634.88200000 0.01553500
146.09700000 0.07541100
42.49740000 0.25712100
14.18920000 0.59655500
1.96660000 0.24251700
S 1
5.14770000 1.00000000
S 1
0.49620000 1.00000000
S 1
0.15330000 1.00000000
P 4
18.15570000 0.01853400
3.98640000 0.11544200
1.14290000 0.38620600
0.35940000 0.64008900
P 1
0.11460000 1.00000000
D 1
0.75000000 1.00000000
****"""
self._gen_data['DZP']['N'] = """
N 0
S 6
5.90944000E+03 2.00400000E-03
8.87451000E+02 1.53100000E-02
2.04749000E+02 7.42930000E-02
5.98376000E+01 2.53364000E-01
1.99981000E+01 6.00576000E-01
2.68600000E+00 2.45111000E-01
S 1
7.19270000E+00 1.00000000E+00
S 1
7.00000000E-01 1.00000000E+00
S 1
2.13300000E-01 1.00000000E+00
P 4
2.67860000E+01 1.82570000E-02
5.95640000E+00 1.16407000E-01
1.70740000E+00 3.90111000E-01
5.31400000E-01 6.37221000E-01
P 1
1.65400000E-01 1.00000000E+00
D 1
8.00000000E-01 1.00000000E+00
****"""
self._gen_data['DZP']['O'] = """
O 0
S 6
7816.54000000 0.00203100
1175.82000000 0.01543600
273.18800000 0.07377100
81.16960000 0.24760600
27.18360000 0.61183200
3.41360000 0.24120500
S 1
9.53220000 1.00000000
S 1
0.93980000 1.00000000
S 1
0.28460000 1.00000000
P 4
35.18320000 0.01958000
7.90400000 0.12418900
2.30510000 0.39472700
0.71710000 0.62737500
P 1
0.21370000 1.00000000
D 1
0.85000000 1.00000000
****"""
self._gen_data['DZVP'] = {}
self._gen_data['DZVP']['H'] = """
H 0
S 4
5.09991780E+01 9.66050000E-03
7.48321810E+00 7.37289000E-02
1.77746760E+00 2.95858100E-01
5.19329500E-01 7.15905300E-01
S 1
1.54110000E-01 1.00000000E+00
****"""
self._gen_data['DZVP']['C'] = """
C 0
S 6
2808.06450000 0.00201780
421.13828000 0.01543320
95.58661600 0.07558150
26.73900400 0.24782820
8.43282680 0.47937250
2.76058210 0.33383440
S 2
5.44700450 -0.07784080
0.47924220 0.56895600
S 1
0.14615650 1.00000000
P 4
18.13085200 0.01585470
4.09988320 0.09568280
1.18583700 0.30491190
0.36859740 0.49350160
P 1
0.10972000 1.00000000
D 1
0.60000000 1.00000000
****"""
self._gen_data['DZVP']['N'] = """
N 0
S 6
3.84541490E+03 2.01860000E-03
5.77533230E+02 1.54078000E-02
1.31319830E+02 7.53714000E-02
3.68237810E+01 2.48212200E-01
1.16701150E+01 4.79827400E-01
3.85426040E+00 3.31801200E-01
S 2
7.82956110E+00 -7.76669000E-02
6.87735100E-01 5.65459800E-01
S 1
2.04038800E-01 1.00000000E+00
P 4
2.68098410E+01 1.54663000E-02
6.06815400E+00 9.64397000E-02
1.76762560E+00 3.08361000E-01
5.46672700E-01 4.91159700E-01
P 1
1.58728900E-01 1.00000000E+00
D 1
7.00000000E-01 1.00000000E+00
****"""
self._gen_data['DZVP2'] = {}
self._gen_data['DZVP2']['H'] = """
H 0
S 4
5.09991780E+01 9.66050000E-03
7.48321810E+00 7.37289000E-02
1.77746760E+00 2.95858100E-01
5.19329500E-01 7.15905300E-01
S 1
1.54110000E-01 1.00000000E+00
P 1
7.50000000E-01 1.00000000E+00
****"""
self._gen_data['DZVP2']['C'] = """
C 0
S 7
5784.15710000 0.00081900
869.30350000 0.00629350
198.51164000 0.03178120
56.42990100 0.11727340
18.28545700 0.30347630
6.44871460 0.45352140
2.34185960 0.24305910
S 2
5.45953280 -0.07780440
0.47819680 0.57149470
S 1
0.14573010 1.00000000
P 5
34.25856300 0.00580430
7.86389540 0.04064030
2.34451930 0.15502190
0.79617150 0.35314440
0.27268040 0.45500620
P 1
0.08926050 1.00000000
D 1
0.60000000 1.00000000
****"""
self._gen_data['DZVP2']['N'] = """
N 0
S 7
8.10417610E+03 7.96900000E-04
1.21731380E+03 6.12890000E-03
2.77739930E+02 3.10471000E-02
7.88475980E+01 1.15368200E-01
2.55371610E+01 3.02573800E-01
9.00457110E+00 4.55791300E-01
3.28352780E+00 2.43020800E-01
S 2
7.84935730E+00 -7.76364000E-02
6.86223900E-01 5.67981500E-01
S 1
2.03502600E-01 1.00000000E+00
P 5
4.90146080E+01 -5.90070000E-03
1.13166710E+01 -4.16444000E-02
3.40340530E+00 -1.61024900E-01
1.16111070E+00 -3.58353800E-01
3.95335800E-01 -4.48841500E-01
P 1
1.26898100E-01 1.00000000E+00
D 1
7.00000000E-01 1.00000000E+00
****"""
self._gen_data['DZVP2']['O'] = """
O 0
S 7
10814.40200000 0.00078090
1623.75320000 0.00601020
370.18274000 0.03052220
104.97475000 0.11400890
33.98442200 0.30195740
11.98431200 0.45711070
4.38597040 0.24324780
S 2
10.63003400 -0.07876540
0.93985260 0.57063030
S 1
0.27662130 1.00000000
P 5
61.54421800 0.00662380
14.27619400 0.04646420
4.33176790 0.17442290
1.47660430 0.36661150
0.49598570 0.43693610
P 1
0.15448360 1.00000000
D 1
0.80000000 1.00000000
****"""
self._gen_data['cc-pVDZ'] = {}
self._gen_data['cc-pVDZ']['H'] = """
H 0
S 3
13.0100000 0.0196850
1.9620000 0.1379770
0.4446000 0.4781480
S 1
0.1220000 1.0000000
P 1
0.7270000 1.0000000
****"""
self._gen_data['cc-pVDZ']['C'] = """
C 0
S 8
6665.0000000 0.0006920
1000.0000000 0.0053290
228.0000000 0.0270770
64.7100000 0.1017180
21.0600000 0.2747400
7.4950000 0.4485640
2.7970000 0.2850740
0.5215000 0.0152040
S 8
6665.0000000 -0.0001460
1000.0000000 -0.0011540
228.0000000 -0.0057250
64.7100000 -0.0233120
21.0600000 -0.0639550
7.4950000 -0.1499810
2.7970000 -0.1272620
0.5215000 0.5445290
S 1
0.1596000 1.0000000
P 3
9.4390000 0.0381090
2.0020000 0.2094800
0.5456000 0.5085570
P 1
0.1517000 1.0000000
D 1
0.5500000 1.0000000
****"""
self._gen_data['cc-pVDZ']['N'] = """
N 0
S 8
9046.0000000 0.0007000
1357.0000000 0.0053890
309.3000000 0.0274060
87.7300000 0.1032070
28.5600000 0.2787230
10.2100000 0.4485400
3.8380000 0.2782380
0.7466000 0.0154400
S 8
9046.0000000 -0.0001530
1357.0000000 -0.0012080
309.3000000 -0.0059920
87.7300000 -0.0245440
28.5600000 -0.0674590
10.2100000 -0.1580780
3.8380000 -0.1218310
0.7466000 0.5490030
S 1
0.2248000 1.0000000
P 3
13.5500000 0.0399190
2.9170000 0.2171690
0.7973000 0.5103190
P 1
0.2185000 1.0000000
D 1
0.8170000 1.0000000
****"""
self._gen_data['cc-pVDZ']['O'] = """
O 0
S 8
11720.0000000 0.0007100
1759.0000000 0.0054700
400.8000000 0.0278370
113.7000000 0.1048000
37.0300000 0.2830620
13.2700000 0.4487190
5.0250000 0.2709520
1.0130000 0.0154580
S 8
11720.0000000 -0.0001600
1759.0000000 -0.0012630
400.8000000 -0.0062670
113.7000000 -0.0257160
37.0300000 -0.0709240
13.2700000 -0.1654110
5.0250000 -0.1169550
1.0130000 0.5573680
S 1
0.3023000 1.0000000
P 3
17.7000000 0.0430180
3.8540000 0.2289130
1.0460000 0.5087280
P 1
0.2753000 1.0000000
D 1
1.1850000 1.0000000
****"""
# title
def _get_title(self):
return self._data.get('title', '')
def _set_title(self, title):
self._data['title'] = str(title)
title = property(_get_title, _set_title)
# jobtype
def _get_jobtype(self):
return self._data.get('jobtype', 'sp')
def _set_jobtype(self, jobtype):
self._data['jobtype'] = str(jobtype)
jobtype = property(_get_jobtype, _set_jobtype)
# basisset
def _get_basisset(self):
return self._data.get('basisset', '6-31G')
def _set_basisset(self, basisset):
self._data['basisset'] = str(basisset)
basisset = property(_get_basisset, _set_basisset)
# ext_basisset for gen
def _get_ext_basisset(self):
return self._data.get('ext_basisset', '')
def _set_ext_basisset(self, basisset):
self._data['ext_basisset'] = str(basisset)
ext_basisset = property(_get_ext_basisset, _set_ext_basisset)
# charge
def _get_charge(self):
return self._data.get('charge', 0)
def _set_charge(self, charge):
self._data['charge'] = int(charge)
charge = property(_get_charge, _set_charge)
#
[ドキュメント]
def get_inputfile_contents(self):
data = ''
data += "#P {method}/{basisset} {jobtype} \n".format(
method = self.method,
basisset = self.basisset,
jobtype = self.jobtype
)
data += "5D GFPrint GFInput NoSymm \n"
data += "Integral(SG1Grid, BWeights, NoJEngine) NoRaff \n"
data += "\n"
data += "{title} \n".format(title = self.title)
data += "\n"
data += "{charge} 1 \n".format(charge = self.charge)
data += self._get_inputfile_contents_geometry()
if self.basisset == 'gen':
data += self._get_inputfile_contents_basisset_gen()
return data
def _get_inputfile_contents_geometry(self, atom_group = None):
output = ""
if (atom_group == None):
output += self._get_inputfile_contents_geometry(self.molecule)
else:
for key, group in atom_group.groups():
output += self._get_inputfile_contents_geometry(group)
for key, atom in atom_group.atoms():
output += "{} {} {} {}\n".format(
atom.symbol,
atom.xyz.x, atom.xyz.y, atom.xyz.z)
return output
def _get_inputfile_contents_basisset_gen(self):
data = ""
basisset_name = self.ext_basisset
kinds = self.molecule.get_atom_kinds()
for atom in kinds:
data += self._gen_data[basisset_name][atom]
data += "\n\n"
return data