mirror of
https://gitlab.com/scemama/resultsFile.git
synced 2024-12-02 18:48:28 +01:00
Forgot lib
This commit is contained in:
parent
fd24d147cb
commit
a88a846bea
8
.gitignore
vendored
8
.gitignore
vendored
@ -13,14 +13,6 @@ develop-eggs/
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dist/
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downloads/
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eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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*.egg-info/
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.installed.cfg
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*.egg
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# PyInstaller
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# Usually these files are written by a python script from a template
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46
resultsFile/lib/__init__.py
Executable file
46
resultsFile/lib/__init__.py
Executable file
@ -0,0 +1,46 @@
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#!/usr/bin/env python
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# resultsFile is a library which allows to read output files of quantum
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# chemistry codes and write input files.
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# Copyright (C) 2007 Anthony SCEMAMA
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU General Public License as published by
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# the Free Software Foundation; either version 2 of the License, or
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# (at your option) any later version.
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#
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# This program is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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# GNU General Public License for more details.
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#
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# You should have received a copy of the GNU General Public License along
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# with this program; if not, write to the Free Software Foundation, Inc.,
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# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
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#
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# Anthony Scemama
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# LCPQ - IRSAMC
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# Universite Paul Sabatier
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# 118, route de Narbonne
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# 31062 Toulouse Cedex 4
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# scemama@irsamc.ups-tlse.fr
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"""resultsFile library."""
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__author__ = "Anthony SCEMAMA <scemama@irsamc.ups-tlse.fr>"
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__date__ = "20 Nov 2007"
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import os
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wd = os.path.dirname(__file__)
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all = [ i[:-3] for i in os.listdir(wd) if i.endswith(".py") ]
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for mod in all:
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try:
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exec 'from '+mod+' import *'
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except:
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print "Error importing module", mod
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pass
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217
resultsFile/lib/atom.py
Executable file
217
resultsFile/lib/atom.py
Executable file
@ -0,0 +1,217 @@
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#!/usr/bin/env python
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# resultsFile is a library which allows to read output files of quantum
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# chemistry codes and write input files.
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# Copyright (C) 2007 Anthony SCEMAMA
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU General Public License as published by
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# the Free Software Foundation; either version 2 of the License, or
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# (at your option) any later version.
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#
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# This program is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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# GNU General Public License for more details.
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#
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# You should have received a copy of the GNU General Public License along
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# with this program; if not, write to the Free Software Foundation, Inc.,
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# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
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#
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# Anthony Scemama
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# LCPQ - IRSAMC
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# Universite Paul Sabatier
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# 118, route de Narbonne
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# 31062 Toulouse Cedex 4
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# scemama@irsamc.ups-tlse.fr
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from library import *
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from math import *
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class atom(object):
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"""Class for an atom."""
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def __init__(self):
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self._name = None
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self._charge = None
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self._coord = None
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self._basis = None
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def __repr__(self):
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out = "%8s %10.3f %10.6f %10.6f %10.6f"%tuple(\
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[self.name, self.charge]+list(self.coord))
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return out
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def __repr__debug__(self):
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out = ""
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out += "Atom:\n"
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out += " Name : "+str(self.name)+'\n'
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out += " Charge : "+str(self.charge)+'\n'
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out += " Coord : "+str(self.coord)+'\n'
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out += " Basis set : "+str(self.basis)+'\n'
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return out
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def __cmp__(self,other):
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assert ( isinstance(other,atom) )
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if self.charge < other.charge:
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return -1
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elif self.charge > other.charge:
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return 1
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elif self.charge == other.charge:
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return 0
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for i in "name charge coord basis".split():
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exec """
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def get_%(i)s(self): return self._%(i)s
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def set_%(i)s(self,value): self._%(i)s = value
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%(i)s = property(fget=get_%(i)s,fset=set_%(i)s) """%locals()
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class atomDataElement(object):
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"""Atomic database."""
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def __init__(self,symbol,charge,covalR,vdwR,valence,color,mass):
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self.symbol = symbol
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self.charge = int(charge)
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self.covalR = float(covalR)
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self.vdwR = float(vdwR)
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self.mass = float(mass)
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self.valence= int(valence)
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self.color = int(color)
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def __repr__(self):
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out = ""
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out += "%3d "%(self.charge)
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out += "%3s "%(self.symbol)
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out += "%10.6f "%(self.covalR)
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out += "%10.6f "%(self.vdwR)
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out += "%3d "%(self.valence)
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out += "%3d "%(self.color)
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out += "%10.6f "%(self.mass)
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return out
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atomDataText = """
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0 X 0.0 0.75 0 8 0.0
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0 XX 0.0 0.75 0 8 0.0
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1 H 0.370000 1.200000 1 0 1.0079
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2 He 0.700000 1.700000 0 2 4.00260
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3 Li 1.230000 1.700000 1 5 6.941
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4 Be 0.890000 1.700000 2 5 9.01218
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5 B 0.900000 1.700000 3 5 10.81
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6 C 0.850000 1.700000 4 8 12.011
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7 N 0.740000 1.550000 3 3 14.0067
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8 O 0.740000 1.520000 2 1 15.9994
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9 F 0.720000 1.470000 1 7 18.998403
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10 Ne 0.700000 1.700000 0 1 20.179
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11 Na 1.000000 1.700000 1 6 22.98977
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12 Mg 1.360000 1.700000 2 6 24.305
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13 Al 1.250000 1.940000 3 6 26.98154
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14 Si 1.170000 2.100000 4 5 28.0855
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15 P 1.100000 1.800000 3 6 30.97376
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16 S 1.100000 1.800000 6 4 32.06
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17 Cl 0.990000 1.750000 1 6 35.453
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18 Ar 0.700000 1.700000 0 5 39.948
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19 K 2.030000 1.700000 1 5 39.0983
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20 Ca 1.740000 1.700000 2 5 40.08
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21 Sc 1.440000 1.700000 0 5 44.9559
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22 Ti 1.320000 1.700000 0 5 47.90
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23 V 1.220000 1.980000 0 5 50.9415
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24 Cr 0.000000 1.940000 0 5 51.996
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25 Mn 1.160000 1.930000 0 5 54.9380
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26 Fe 0.000000 1.930000 0 5 55.9332
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27 Co 1.150000 1.920000 0 5 58.9332
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28 Ni 1.170000 1.700000 0 5 58.70
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29 Cu 1.250000 1.700000 0 5 63.546
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30 Zn 1.250000 1.700000 0 5 65.38
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31 Ga 1.200000 2.020000 0 0 69.72
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32 Ge 1.210000 1.700000 0 5 72.59
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33 As 1.160000 1.960000 0 1 74.9216
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34 Se 0.700000 1.700000 0 5 78.96
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35 Br 1.240000 2.100000 0 6 79.904
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36 Kr 1.910000 1.700000 0 5 83.80
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37 Rb 1.620000 1.700000 0 5 85.4678
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38 Sr 1.450000 1.700000 0 5 87.62
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39 Y 1.340000 1.700000 0 5 88.9059
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40 Zr 1.290000 2.210000 0 5 91.22
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41 Nb 1.290000 1.700000 0 5 92.9064
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42 Mo 1.240000 2.060000 0 5 95.94
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43 Tc 1.250000 1.700000 0 5 98
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44 Ru 0.000000 2.010000 0 5 101.07
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45 Rh 1.340000 2.010000 0 5 102.9055
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46 Pd 1.410000 2.040000 0 5 106.4
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47 Ag 1.500000 1.700000 0 5 107.868
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48 Cd 1.400000 1.700000 0 5 112.41
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49 In 1.410000 1.700000 0 5 114.82
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50 Sn 1.370000 1.700000 0 5 118.69
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51 Sb 1.330000 1.700000 0 5 121.75
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52 Te 0.700000 1.700000 0 5 127.60
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53 I 1.330000 2.150000 1 6 126.9045
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54 Xe 1.980000 1.700000 0 5 131.30
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55 Cs 1.690000 1.700000 0 5 132.9054
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56 Ba 1.690000 1.700000 0 5 137.33
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57 La 0.000000 0.800000 0 5 138.9055
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58 Ce 1.690000 1.700000 0 5 140.12
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59 Pr 1.690000 1.700000 0 5 140.9077
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60 Nd 1.690000 1.700000 0 5 144.24
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61 Pm 1.690000 1.700000 0 5 145
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62 Sm 1.690000 1.700000 0 5 150.4
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63 Eu 1.690000 1.700000 0 5 151.96
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64 Gd 1.690000 1.700000 0 5 157.25
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65 Tb 1.690000 1.700000 0 5 158.9254
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66 Dy 1.690000 1.700000 0 5 162.50
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67 Ho 1.690000 1.700000 0 5 164.9304
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68 Er 1.690000 1.700000 0 5 167.26
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69 Tm 1.690000 1.700000 0 5 168.9342
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70 Yb 1.690000 1.700000 0 5 173.04
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71 Lu 1.690000 1.700000 0 5 174.967
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72 Hf 1.440000 1.700000 0 5 178.49
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73 Ta 1.340000 1.700000 0 5 180.9479
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74 W 1.300000 1.700000 0 5 183.85
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75 Re 1.280000 1.700000 0 5 186.207
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76 Os 1.260000 2.020000 0 5 190.2
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77 Ir 1.290000 2.030000 0 5 192.22
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78 Pt 1.340000 1.700000 0 5 195.09
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79 Au 1.440000 1.700000 0 9 196.9665
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80 Hg 1.550000 1.700000 0 5 200.59
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81 Tl 1.540000 1.700000 0 5 204.37
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82 Pb 1.520000 1.700000 0 5 207.2
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83 Bi 1.520000 1.700000 0 5 208.9804
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84 Po 1.400000 1.700000 0 5 209
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85 At 0.700000 1.700000 0 5 210
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86 Rn 2.400000 1.700000 0 5 222
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87 Fr 2.000000 1.700000 0 5 223
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88 Ra 1.900000 1.700000 0 5 226.0254
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89 Ac 1.900000 1.700000 0 5 227.0278
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90 Th 1.900000 1.700000 0 5 232.0381
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91 Pa 1.900000 1.700000 0 5 231.0359
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92 U 1.900000 1.700000 0 5 238.029
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93 Np 2.0 2.0 0 5 237.0482
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94 Pu 2.0 2.0 0 5 244
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95 Am 2.0 2.0 0 5 243
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96 Cm 2.0 2.0 0 5 247
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97 Bk 2.0 2.0 0 5 247
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98 Cf 2.0 2.0 0 5 251
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99 Es 2.0 2.0 0 5 254
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100 Fm 2.0 2.0 0 5 257
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101 Md 2.0 2.0 0 5 258
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102 No 2.0 2.0 0 5 259
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103 Lr 2.0 2.0 0 5 260
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"""
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atomData = 110*[None]
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for line in atomDataText.splitlines():
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try:
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charge, symbol, covalR, vdwR, valence, color, mass = line.split()
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at = atomDataElement(symbol,charge,covalR,vdwR,valence,color,mass)
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atomData[int(at.charge)] = at
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except:
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pass
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if __name__ == '__main__':
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for s in atomData:
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print s
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484
resultsFile/lib/basis.py
Executable file
484
resultsFile/lib/basis.py
Executable file
@ -0,0 +1,484 @@
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#!/usr/bin/env python
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# resultsFile is a library which allows to read output files of quantum
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# chemistry codes and write input files.
|
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# Copyright (C) 2007 Anthony SCEMAMA
|
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#
|
||||
# This program 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 2 of the License, or
|
||||
# (at your option) any later version.
|
||||
#
|
||||
# This program 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 this program; if not, write to the Free Software Foundation, Inc.,
|
||||
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
|
||||
#
|
||||
# Anthony Scemama
|
||||
# LCPQ - IRSAMC
|
||||
# Universite Paul Sabatier
|
||||
# 118, route de Narbonne
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# 31062 Toulouse Cedex 4
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# scemama@irsamc.ups-tlse.fr
|
||||
|
||||
|
||||
|
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#import pdb
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from library import *
|
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from math import *
|
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import sys
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|
||||
def normalize_basis_name(s):
|
||||
l = list(s)
|
||||
is_sphe = False
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l.sort()
|
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for i in range(10):
|
||||
if str(i) in l:
|
||||
is_sphe = True
|
||||
if is_sphe:
|
||||
if l[0] == '0':
|
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l.insert(0,'+')
|
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l = [l[-1]]+l[:-1]
|
||||
result = ""
|
||||
for i in l:
|
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result += i
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result = result.lower()
|
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return result
|
||||
|
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|
||||
class primitive(object):
|
||||
"""Class for a primitive basis function."""
|
||||
|
||||
def __init__(self):
|
||||
_center = None
|
||||
_expo = None
|
||||
_sym = None
|
||||
|
||||
def __eq__(self,other):
|
||||
thr = 1.e-6
|
||||
result = True
|
||||
result = result and abs(self.center[0] - other.center[0]) < thr
|
||||
result = result and abs(self.center[1] - other.center[1]) < thr
|
||||
result = result and abs(self.center[2] - other.center[2]) < thr
|
||||
result = result and abs(self.expo - other.expo) < thr
|
||||
result = result and self.sym == other.sym
|
||||
return result
|
||||
|
||||
def __repr__(self):
|
||||
out = "%6s %10.6f %10.6f %10.6f %16.6e"%tuple(
|
||||
[self.sym]+list(self.center)+[self.expo])
|
||||
return out
|
||||
|
||||
def __repr__debug__(self):
|
||||
out = ""
|
||||
out += str(self.sym)+'\t'
|
||||
out += str(self.center)+'\t'
|
||||
out += str(self.expo)
|
||||
return out
|
||||
|
||||
def __cmp__(self,other):
|
||||
assert ( isinstance(other,primitive) )
|
||||
"""Primitive functions are sorted according to the exponents."""
|
||||
if not isinstance(other,primitive):
|
||||
raise TypeError
|
||||
if self.expo < other.expo:
|
||||
return -1
|
||||
elif self.expo > other.expo:
|
||||
return 1
|
||||
elif self.expo == other.expo:
|
||||
return 0
|
||||
|
||||
def get_norm(self):
|
||||
result = sqrt(self.overlap(self))
|
||||
return result
|
||||
|
||||
norm = property (get_norm,None,doc="Sqrt( Integral f^2(R) dR ).")
|
||||
for i in "center expo sym".split():
|
||||
exec """
|
||||
def get_%(i)s(self): return self._%(i)s
|
||||
def set_%(i)s(self,value): self._%(i)s = value
|
||||
%(i)s = property(fget=get_%(i)s,fset=set_%(i)s) """%locals()
|
||||
|
||||
|
||||
#-----------------------
|
||||
|
||||
powersave = { 's':(0,0,0) }
|
||||
|
||||
def powers(sym):
|
||||
if sym in powersave:
|
||||
return powersave[sym]
|
||||
result = (sym.count('x'),sym.count('y'),sym.count('z'))
|
||||
powersave[sym] = result
|
||||
return result
|
||||
|
||||
|
||||
fact_ = [1.]
|
||||
def fact(n):
|
||||
global fact_
|
||||
nstart = len(fact_)
|
||||
if n < nstart :
|
||||
return fact_[n]
|
||||
else:
|
||||
for i in range(nstart,n+1):
|
||||
fact_.append(fact_[i-1]*float(i))
|
||||
return fact_[n]
|
||||
|
||||
def binom(n,m):
|
||||
return fact(n)/(fact(m)*fact(n-m))
|
||||
|
||||
def rintgauss(n):
|
||||
|
||||
def ddfact2(n):
|
||||
if n%2 == 0: print 'error in ddfact2'
|
||||
res=1.
|
||||
for i in range(1,n+1,2):
|
||||
res*=float(i)
|
||||
return res
|
||||
|
||||
res = sqrt(pi)
|
||||
if n == 0: return res
|
||||
elif n == 1: return 0.
|
||||
elif n%2 == 1: return 0.
|
||||
res /= 2.**(n/2)
|
||||
res *= ddfact2(n-1)
|
||||
return res
|
||||
|
||||
|
||||
def Goverlap(fA,fB):
|
||||
fA = spheToCart(fA)
|
||||
fB = spheToCart(fB)
|
||||
if isinstance(fA,contraction):
|
||||
result = fA.overlap(fB)
|
||||
elif isinstance(fB,contraction):
|
||||
result = fB.overlap(fA)
|
||||
else:
|
||||
result = GoverlapCart(fA,fB)
|
||||
return result
|
||||
|
||||
|
||||
def GoverlapCart(fA,fB):
|
||||
gamA=fA.expo
|
||||
gamB=fB.expo
|
||||
gamtot = gamA+gamB
|
||||
SAB=1.0
|
||||
A = fA.center
|
||||
B = fB.center
|
||||
nA = powers(fA.sym)
|
||||
nB = powers(fB.sym)
|
||||
for l in range(3):
|
||||
Al = A[l]
|
||||
Bl = B[l]
|
||||
nAl = nA[l]
|
||||
nBl = nB[l]
|
||||
u=gamA/gamtot*Al+gamB/gamtot*Bl
|
||||
arg=gamtot*u*u-gamA*Al*Al-gamB*Bl*Bl
|
||||
alpha=exp(arg)/gamtot**((1.+float(nAl)+float(nBl))/2.)
|
||||
temp = sqrt(gamtot)
|
||||
wA=temp*(u-Al)
|
||||
wB=temp*(u-Bl)
|
||||
accu=0.
|
||||
for n in range (nAl+1):
|
||||
wAn = wA**n * binom(nAl,n)
|
||||
for m in range (nBl+1):
|
||||
integ=nAl+nBl-n-m
|
||||
accu+=wAn*wB**m*binom(nBl,m)*rintgauss(integ)
|
||||
SAB*=accu*alpha
|
||||
return SAB
|
||||
|
||||
def GoverlapCartNorm2(fA,fB):
|
||||
gamA=fA.expo
|
||||
gamB=fB.expo
|
||||
gamtot = gamA+gamB
|
||||
SAB=1.0
|
||||
nA = powers(fA.sym)
|
||||
nB = powers(fB.sym)
|
||||
for l in range(3):
|
||||
nAl = nA[l]
|
||||
nBl = nB[l]
|
||||
SAB*=rintgauss(nAl+nBl)/(gamA+gamB)**((1.+float(nAl)+float(nBl))/2.)
|
||||
return SAB
|
||||
|
||||
def GoverlapCartNorm(fA):
|
||||
gamA=fA.expo
|
||||
SAB=1.0
|
||||
nA = powers(fA.sym)
|
||||
for l in range(3):
|
||||
nAl = nA[l]
|
||||
SAB*=rintgauss(2*nAl)/(2.*gamA)**(0.5+float(nAl))
|
||||
return SAB
|
||||
|
||||
angular_momentum = {}
|
||||
for i,l in enumerate("spdfghijklmno"):
|
||||
angular_momentum[l]=i
|
||||
|
||||
def get_lm(sym):
|
||||
if 'x' in sym or 'y' in sym or 'z' in sym or sym == 's':
|
||||
return None, None
|
||||
else:
|
||||
return angular_momentum[sym[0]], int(sym[1:])
|
||||
|
||||
def xyz_from_lm(l,m):
|
||||
"""Returns the xyz powers and the coefficients of a spherical function
|
||||
expressed in the cartesian basis"""
|
||||
power = []
|
||||
coef = []
|
||||
absm = abs(m)
|
||||
nb2 = absm
|
||||
nb1 = (l-absm)/2
|
||||
clmt = [ (-0.25)**t * binom(l,t) * binom(l-t,absm+t) for t in xrange(nb1+1) ]
|
||||
mod_absm_2 = absm % 2
|
||||
if m>=0:
|
||||
nb2_start = mod_absm_2
|
||||
elif m<0:
|
||||
nb2_start = (absm+1) % 2
|
||||
if m != 0:
|
||||
norm = 2.**(-absm)/fact(l) * sqrt(2.*abs(fact(l+m)*fact(l-m)))
|
||||
else:
|
||||
norm = 1.
|
||||
for n1 in range(nb2_start,nb2+1,2):
|
||||
k = (absm-n1)/2
|
||||
factor = (-1.)**k * binom(absm,n1) * norm
|
||||
for t in xrange(nb1+1):
|
||||
for n2 in xrange(t+1):
|
||||
coe = clmt[t] * factor * binom(t,n2)
|
||||
ipw = ( n1+2*n2 , absm-n1+2*(t-n2), l-2*t-absm )
|
||||
done = False
|
||||
for i,c in enumerate(coef):
|
||||
if c != 0.:
|
||||
if not done and ipw in power:
|
||||
idx = power.index(ipw)
|
||||
coef[idx] += coe
|
||||
done = True
|
||||
if not done:
|
||||
power.append(ipw)
|
||||
coef.append(coe)
|
||||
return power,coef
|
||||
|
||||
def spheToCart(fA):
|
||||
l,m = get_lm(fA.sym)
|
||||
if l is None:
|
||||
return fA
|
||||
power, coef = xyz_from_lm(l,m)
|
||||
|
||||
contr = contraction()
|
||||
for p,c in zip(power,coef):
|
||||
gauss = gaussian()
|
||||
gauss.center = fA.center
|
||||
gauss.expo = fA.expo
|
||||
gauss.sym = ''
|
||||
for l,letter in enumerate('xyz'):
|
||||
gauss.sym += p[l]*letter
|
||||
contr.append(c,gauss)
|
||||
return contr
|
||||
|
||||
|
||||
class gaussian(primitive):
|
||||
"""Gaussian primitive function."""
|
||||
|
||||
def __init__(self):
|
||||
primitive.__init__(self)
|
||||
|
||||
def overlap(self,other):
|
||||
result = Goverlap(self,other)
|
||||
return result
|
||||
|
||||
def value(self,r):
|
||||
"""Value at r."""
|
||||
x, y, z = r
|
||||
x -= self.center[0]
|
||||
y -= self.center[1]
|
||||
z -= self.center[2]
|
||||
r2 = x**2 + y**2 + z**2
|
||||
px, py, pz = powers(self.sym)
|
||||
P = x**px * y**py * z**pz
|
||||
return P*exp(-self.expo*r2)
|
||||
|
||||
def valuer2(self,r2):
|
||||
"""Value at sqrt(r2)."""
|
||||
return exp(-self.expo*r2)
|
||||
|
||||
#-----------------------
|
||||
|
||||
class contraction(object):
|
||||
"""Contraction of primitive functions."""
|
||||
|
||||
def __init__(self):
|
||||
self._center = None
|
||||
self._prim = []
|
||||
self._coef = []
|
||||
self._sym = None
|
||||
|
||||
def __eq__(self,other):
|
||||
thr = 1.e-6
|
||||
result = True
|
||||
result = result and abs(self._center[0] - other._center[0]) < thr
|
||||
result = result and abs(self._center[1] - other._center[1]) < thr
|
||||
result = result and abs(self._center[2] - other._center[2]) < thr
|
||||
result = result and self._sym == other._sym
|
||||
result = result and len(self._coef) == len(other._coef)
|
||||
if result:
|
||||
for i in range(len(self._coef)):
|
||||
result = result and abs(self._coef[i] - other._coef[i]) < thr
|
||||
if result:
|
||||
for i in range(len(self._prim)):
|
||||
result = result and self._prim[i] == other._prim[i]
|
||||
return result
|
||||
|
||||
def __repr__(self):
|
||||
out = "%6s %10.6f %10.6f %10.6f\n"%tuple(
|
||||
[self.sym]+list(self.center))
|
||||
for i,a in enumerate(self.prim):
|
||||
out += " %16.6e %16.6e\n"%(a.expo,self.coef[i])
|
||||
return out
|
||||
|
||||
def append(self,c,func):
|
||||
if self.sym is None:
|
||||
self.sym = func.sym
|
||||
if self.center is None:
|
||||
self.center = func.center
|
||||
assert ( isinstance(func,primitive) )
|
||||
assert ( self.center == func.center )
|
||||
self._prim.append(func)
|
||||
self._coef.append(c)
|
||||
|
||||
def get_norm(self):
|
||||
sum=0.
|
||||
for i, ci in enumerate(self.coef):
|
||||
for j, cj in enumerate(self.coef):
|
||||
sum += ci*cj*self.prim[i].overlap(self.prim[j])/(self.prim[i].norm*self.prim[j].norm)
|
||||
result = sqrt(sum)
|
||||
return result
|
||||
|
||||
def overlap(self,other0):
|
||||
if isinstance(other0,contraction):
|
||||
other=other0
|
||||
else:
|
||||
other=contraction()
|
||||
other.sym = other0.sym
|
||||
other.center = other0.center
|
||||
other.append(1.,other0)
|
||||
prim = self.prim
|
||||
oprim = other.prim
|
||||
sum = 0.
|
||||
for i, ci in enumerate(self.coef):
|
||||
for j, cj in enumerate(other.coef):
|
||||
sum += ci*cj*prim[i].overlap(oprim[j])
|
||||
return sum
|
||||
|
||||
def get_coef(self):
|
||||
return self._coef
|
||||
coef = property(fget=get_coef)
|
||||
|
||||
def get_center(self):
|
||||
return self._center
|
||||
center = property(fget=get_center)
|
||||
|
||||
def get_prim(self):
|
||||
return self._prim
|
||||
prim = property(fget=get_prim)
|
||||
def normalize(self):
|
||||
coef = self.coef
|
||||
prim = self.prim
|
||||
n = self.norm
|
||||
for i, ci in enumerate(coef):
|
||||
coef[i] /= n
|
||||
|
||||
def value(self,r):
|
||||
"""Value at r."""
|
||||
x, y, z = r
|
||||
x -= self.center[0]
|
||||
y -= self.center[1]
|
||||
z -= self.center[2]
|
||||
r2 = x**2 + y**2 + z**2
|
||||
px, py, pz = powers(self.sym)
|
||||
P = x**px * y**py * z**pz
|
||||
result = 0.
|
||||
for c,chi in zip(self.coef,self.prim):
|
||||
result += c*chi.valuer2(r2)
|
||||
return P*result
|
||||
|
||||
|
||||
for i in "center prim sym coef".split():
|
||||
exec """
|
||||
def get_%(i)s(self): return self._%(i)s
|
||||
def set_%(i)s(self,value): self._%(i)s = value
|
||||
%(i)s = property(fget=get_%(i)s,fset=set_%(i)s) """%locals()
|
||||
|
||||
norm = property (get_norm,None,doc="Sqrt( Integral f^2(R) dR ).")
|
||||
|
||||
|
||||
try:
|
||||
import lib_cython
|
||||
fact = lib_cython.fact
|
||||
binom = lib_cython.binom
|
||||
rintgauss = lib_cython.rintgauss
|
||||
powers = lib_cython.powers
|
||||
GoverlapCart = lib_cython.GoverlapCart
|
||||
GoverlapCartNorm2 = lib_cython.GoverlapCartNorm2
|
||||
except ImportError:
|
||||
pass
|
||||
|
||||
#--------------
|
||||
|
||||
if __name__ == '__main__':
|
||||
for l in range(6):
|
||||
print '---'
|
||||
for m in range(-l,l+1):
|
||||
print "%3d %3d :"%(l,m), xyz_from_lm(l,m)
|
||||
sys.exit(0)
|
||||
|
||||
if __name__ == '__main__':
|
||||
a = gaussian()
|
||||
a.sym = 'f+0'
|
||||
a.expo = 3.
|
||||
a.center = [0.,0.,0.]
|
||||
b = gaussian()
|
||||
b.sym = 'g+2'
|
||||
b.expo = 4.
|
||||
b.center = [0.,0.,0.]
|
||||
x = spheToCart(a)
|
||||
y = spheToCart(a)
|
||||
print x
|
||||
sys.exit(0)
|
||||
print GoverlapCart(a,b)
|
||||
print GoverlapCartNorm2(a,b)
|
||||
print ''
|
||||
for i in range(0,10):
|
||||
print rintgauss(i)
|
||||
sys.exit(0)
|
||||
c = gaussian()
|
||||
c.sym = 's'
|
||||
c.expo = 1.159
|
||||
c.center = [0.,0.,0.]
|
||||
d = contraction()
|
||||
d.append(0.025494863235, a)
|
||||
d.append(0.190362765893, b)
|
||||
d.append(0.852162022245, c)
|
||||
d.normalize()
|
||||
print d
|
||||
sys.exit(0)
|
||||
a = gaussian()
|
||||
a.sym = 'x'
|
||||
a.expo = 1.0
|
||||
a.center = [0.,0.,0.]
|
||||
b = gaussian()
|
||||
b.sym = 'x'
|
||||
b.expo = 2.0
|
||||
b.center = [0.,0.,0.]
|
||||
c = contraction()
|
||||
c.append(1.,a)
|
||||
c.append(2.,b)
|
||||
print c.value( (1.,1.,0.) )
|
||||
print b.overlap(a)
|
||||
print a.overlap(b)
|
||||
print a.norm
|
||||
print c.norm, c.coef
|
||||
c.normalize()
|
||||
print c.norm, c.coef
|
||||
c.normalize()
|
||||
print c.norm, c.coef
|
||||
print Goverlap(a,b)
|
||||
|
76
resultsFile/lib/csf.py
Executable file
76
resultsFile/lib/csf.py
Executable file
@ -0,0 +1,76 @@
|
||||
#!/usr/bin/env python
|
||||
# resultsFile is a library which allows to read output files of quantum
|
||||
# chemistry codes and write input files.
|
||||
# Copyright (C) 2007 Anthony SCEMAMA
|
||||
#
|
||||
# This program 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 2 of the License, or
|
||||
# (at your option) any later version.
|
||||
#
|
||||
# This program 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 this program; if not, write to the Free Software Foundation, Inc.,
|
||||
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
|
||||
#
|
||||
# Anthony Scemama
|
||||
# LCPQ - IRSAMC
|
||||
# Universite Paul Sabatier
|
||||
# 118, route de Narbonne
|
||||
# 31062 Toulouse Cedex 4
|
||||
# scemama@irsamc.ups-tlse.fr
|
||||
|
||||
|
||||
|
||||
from library import *
|
||||
|
||||
class CSF(object):
|
||||
"""Class for an configuration state function."""
|
||||
|
||||
def __init__(self):
|
||||
self._determinants = []
|
||||
self._coefficients = []
|
||||
|
||||
def __repr__(self):
|
||||
out = ""
|
||||
for d,c in zip(self.determinants,self.coefficients):
|
||||
out += "%10.8f\n"%(c,)
|
||||
for spin in d:
|
||||
for orb in d[spin]:
|
||||
out += "%4d "%(orb,)
|
||||
out += "\n"
|
||||
return out
|
||||
|
||||
def __repr__debug__(self):
|
||||
out = ""
|
||||
out += "CSF:\n"
|
||||
out += " Determinants: "+str(self.determinants)+'\n'
|
||||
out += " Coefficients: "+str(self.coefficients)+'\n'
|
||||
return out
|
||||
|
||||
def __cmp__(self,other):
|
||||
assert ( isinstance(other,CSF) )
|
||||
if len(self.coefficients) < len(other.coefficients):
|
||||
return -1
|
||||
elif len(self.coefficients) > len(other.coefficients):
|
||||
return 1
|
||||
elif len(self.coefficients) == len(other.coefficients):
|
||||
return 0
|
||||
|
||||
def append(self,c,up,dn):
|
||||
det = {}
|
||||
det['alpha'] = up
|
||||
det['beta'] = dn
|
||||
self._determinants.append( det )
|
||||
self._coefficients.append( c )
|
||||
|
||||
for i in "determinants coefficients".split():
|
||||
exec """
|
||||
def get_%(i)s(self): return self._%(i)s
|
||||
def set_%(i)s(self,value): self._%(i)s = value
|
||||
%(i)s = property(fget=get_%(i)s,fset=set_%(i)s) """%locals()
|
||||
|
51
resultsFile/lib/cython_setup
Executable file
51
resultsFile/lib/cython_setup
Executable file
@ -0,0 +1,51 @@
|
||||
#!/usr/bin/python
|
||||
# resultsFile is a library which allows to read output files of quantum
|
||||
# chemistry codes and write input files.
|
||||
# Copyright (C) 2007 Anthony SCEMAMA
|
||||
#
|
||||
# This program 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 2 of the License, or
|
||||
# (at your option) any later version.
|
||||
#
|
||||
# This program 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 this program; if not, write to the Free Software Foundation, Inc.,
|
||||
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
|
||||
#
|
||||
# Anthony Scemama
|
||||
# LCPQ - IRSAMC
|
||||
# Universite Paul Sabatier
|
||||
# 118, route de Narbonne
|
||||
# 31062 Toulouse Cedex 4
|
||||
# scemama@irsamc.ups-tlse.fr
|
||||
|
||||
|
||||
|
||||
from distutils.core import setup
|
||||
from distutils.extension import Extension
|
||||
from Cython.Distutils import build_ext
|
||||
|
||||
|
||||
"""
|
||||
./cython_setup build_ext --inplace
|
||||
"""
|
||||
|
||||
ext_modules = [Extension("lib_cython", ["lib_cython.pyx"])]
|
||||
|
||||
import os
|
||||
setup(name="resultsFile",
|
||||
version=os.getenv("VERSION","1.0"),
|
||||
author="Anthony Scemama",
|
||||
author_email="scemama@irsamc.ups-tlse.fr",
|
||||
license="gpl-license",
|
||||
description="Module for I/O on Quantum Chemistry files.",
|
||||
packages=["resultsFile","resultsFile.lib","resultsFile.Modules"],
|
||||
cmdclass = {'build_ext': build_ext},
|
||||
ext_modules = ext_modules
|
||||
)
|
||||
|
119
resultsFile/lib/fortranBinary.py
Executable file
119
resultsFile/lib/fortranBinary.py
Executable file
@ -0,0 +1,119 @@
|
||||
#!/usr/bin/python
|
||||
# resultsFile is a library which allows to read output files of quantum
|
||||
# chemistry codes and write input files.
|
||||
# Copyright (C) 2007 Anthony SCEMAMA
|
||||
#
|
||||
# This program 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 2 of the License, or
|
||||
# (at your option) any later version.
|
||||
#
|
||||
# This program 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 this program; if not, write to the Free Software Foundation, Inc.,
|
||||
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
|
||||
#
|
||||
# Anthony Scemama
|
||||
# LCPQ - IRSAMC
|
||||
# Universite Paul Sabatier
|
||||
# 118, route de Narbonne
|
||||
# 31062 Toulouse Cedex 4
|
||||
# scemama@irsamc.ups-tlse.fr
|
||||
|
||||
|
||||
|
||||
import struct
|
||||
from library import *
|
||||
import sys
|
||||
|
||||
class fortranBinary(object):
|
||||
"""
|
||||
Class for a fortran binary file.
|
||||
Behaves like an array of records.
|
||||
"""
|
||||
|
||||
def __init__(self,name,mode):
|
||||
self._name = name
|
||||
self._mode = mode
|
||||
self._file = None
|
||||
self._recl = None
|
||||
self._form = None
|
||||
|
||||
def get_file(self):
|
||||
if self._file is None:
|
||||
self._file = open(self._name,self._mode)
|
||||
return self._file
|
||||
|
||||
def seek(self,index):
|
||||
self.file.seek(index)
|
||||
|
||||
def next(self):
|
||||
if self.form is None:
|
||||
raise TypeError
|
||||
data = self.file.read(4) # Rec length at the beginning of record
|
||||
if not data: raise IndexError
|
||||
self.recl = struct.unpack('l',data)[0]
|
||||
data = self.file.read(self._recl)
|
||||
data = struct.unpack(self.form,data)
|
||||
self.file.read(4)
|
||||
return list(data)
|
||||
|
||||
def __iter__(self):
|
||||
if self.form is None:
|
||||
raise TypeError
|
||||
self.file.seek(0)
|
||||
while True:
|
||||
data = self.file.read(4) # Rec length at the beginning of record
|
||||
if not data: raise StopIteration
|
||||
self.recl = struct.unpack('l',data)[0]
|
||||
data = self.file.read(self._recl)
|
||||
data = struct.unpack(self.form,data)
|
||||
self.file.read(4)
|
||||
yield list(data)
|
||||
|
||||
def __getitem__(self,index):
|
||||
if self.form is None:
|
||||
raise TypeError
|
||||
self.file.seek(0)
|
||||
for i in range(index-1):
|
||||
data = self.file.read(4) # Rec length at the beginning of record
|
||||
if not data: raise IndexError
|
||||
recl = struct.unpack('l',data)[0]
|
||||
data = self.file.read(recl+4)
|
||||
data = self.file.read(4) # Rec length at the beginning of record
|
||||
if not data: raise IndexError
|
||||
self.recl = struct.unpack('l',data)[0]
|
||||
data = self.file.read(self._recl)
|
||||
data = struct.unpack(self.form,data)
|
||||
self.file.read(4)
|
||||
return list(data)
|
||||
|
||||
def close(self):
|
||||
self._file.close()
|
||||
|
||||
|
||||
# recl = xproperty ( '_recl', doc="Record length")
|
||||
# mode = xproperty ( '_mode', doc="R/W mode")
|
||||
# name = xproperty ( '_name', doc="R/W mode")
|
||||
# file = property ( get_file, doc="Binary file")
|
||||
# form = xproperty ( '_form', doc="Format to read the binary record")
|
||||
for i in "recl mode name file form".split():
|
||||
exec """
|
||||
def get_%(i)s(self): return self._%(i)s
|
||||
def set_%(i)s(self,value): self._%(i)s = value
|
||||
%(i)s = property(fget=get_%(i)s,fset=set_%(i)s) """%locals()
|
||||
|
||||
|
||||
|
||||
if __name__ == '__main__':
|
||||
f = fortranBinary(sys.argv[1],"rb")
|
||||
f.form = 'l'+4*15000*'h'+15000*'d'
|
||||
print f.name
|
||||
print f.mode
|
||||
print f[0]
|
||||
print f[10]
|
||||
print f[0]
|
74
resultsFile/lib/integral.py
Executable file
74
resultsFile/lib/integral.py
Executable file
@ -0,0 +1,74 @@
|
||||
#!/usr/bin/python
|
||||
# resultsFile is a library which allows to read output files of quantum
|
||||
# chemistry codes and write input files.
|
||||
# Copyright (C) 2007 Anthony SCEMAMA
|
||||
#
|
||||
# This program 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 2 of the License, or
|
||||
# (at your option) any later version.
|
||||
#
|
||||
# This program 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 this program; if not, write to the Free Software Foundation, Inc.,
|
||||
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
|
||||
#
|
||||
# Anthony Scemama
|
||||
# LCPQ - IRSAMC
|
||||
# Universite Paul Sabatier
|
||||
# 118, route de Narbonne
|
||||
# 31062 Toulouse Cedex 4
|
||||
# scemama@irsamc.ups-tlse.fr
|
||||
|
||||
|
||||
|
||||
from library import *
|
||||
from math import *
|
||||
|
||||
class integral(object):
|
||||
"""Class for an integral."""
|
||||
|
||||
def __init__(self):
|
||||
self._indices = None
|
||||
self._value = None
|
||||
|
||||
def __repr__(self):
|
||||
out = ""
|
||||
i = self.indices
|
||||
if len(i) == 4:
|
||||
out += "( %4d %4d | %4d %4d )"% tuple( [int(i[k]) for k in range(4)] )
|
||||
elif len(i) == 2:
|
||||
out += "( %4d | h | %4d )"% tuple( [int(i[k]) for k in range(2)] )
|
||||
out += " : %24.16e" % ( self.value )
|
||||
return out
|
||||
|
||||
def __cmp__(self,other):
|
||||
assert ( isinstance(other,integral) )
|
||||
if self._value < other._value:
|
||||
return -1
|
||||
elif self._value > other._value:
|
||||
return 1
|
||||
elif self._value == other._value:
|
||||
return 0
|
||||
|
||||
for i in "indices value".split():
|
||||
exec """
|
||||
def get_%(i)s(self): return self._%(i)s
|
||||
def set_%(i)s(self,value): self._%(i)s = value
|
||||
%(i)s = property(fget=get_%(i)s,fset=set_%(i)s) """%locals()
|
||||
|
||||
|
||||
if __name__ == '__main__':
|
||||
i = integral()
|
||||
i.indices = [1,4]
|
||||
i.value = 1.5
|
||||
print i
|
||||
j = integral()
|
||||
j.indices = [4,3,2,1]
|
||||
j.value = 2.5
|
||||
print j
|
||||
print i<j
|
89
resultsFile/lib/lib_cython.pyx
Normal file
89
resultsFile/lib/lib_cython.pyx
Normal file
@ -0,0 +1,89 @@
|
||||
#!/usr/bin/python
|
||||
from math import *
|
||||
|
||||
powersave = { 's':(0,0,0) }
|
||||
def powers(sym):
|
||||
if sym in powersave:
|
||||
return powersave[sym]
|
||||
result = (sym.count('x'),sym.count('y'),sym.count('z'))
|
||||
powersave[sym] = result
|
||||
return result
|
||||
|
||||
fact_ = [1.]
|
||||
cpdef fact(int n):
|
||||
global fact_
|
||||
cdef int nstart = len(fact_)
|
||||
cdef int i
|
||||
if n >= nstart :
|
||||
for i in range(nstart,n+1):
|
||||
fact_.append(float(fact_[i-1]*i))
|
||||
return fact_[n]
|
||||
|
||||
def binom(int n,int m):
|
||||
return fact(n)/(fact(m)*fact(n-m))
|
||||
|
||||
|
||||
cdef ddfact2(int n):
|
||||
if n%2 == 0: print 'error in ddfact2'
|
||||
cdef double res=1.
|
||||
cdef int i
|
||||
for i in range(1,n+1,2):
|
||||
res*=float(i)
|
||||
return res
|
||||
|
||||
cdef double sqpi = sqrt(pi)
|
||||
|
||||
cpdef rintgauss(int n):
|
||||
res = sqpi
|
||||
if n == 0: return res
|
||||
elif n == 1: return 0.
|
||||
elif n%2 == 1: return 0.
|
||||
res /= 2.**(n/2)
|
||||
res *= ddfact2(n-1)
|
||||
return res
|
||||
|
||||
cpdef GoverlapCart(fA,fB):
|
||||
cdef double gamA=fA.expo
|
||||
cdef double gamB=fB.expo
|
||||
cdef double gamtot = gamA+gamB
|
||||
cdef double SAB=1.0
|
||||
cdef int l, n, m
|
||||
cdef double u, arg, alpha, temp, wA, wB, accu
|
||||
cdef int integ
|
||||
A = fA.center
|
||||
B = fB.center
|
||||
nA = powers(fA.sym)
|
||||
nB = powers(fB.sym)
|
||||
for l in range(3):
|
||||
Al = A[l]
|
||||
Bl = B[l]
|
||||
nAl = nA[l]
|
||||
nBl = nB[l]
|
||||
u=gamA/gamtot*Al+gamB/gamtot*Bl
|
||||
arg=gamtot*u*u-gamA*Al*Al-gamB*Bl*Bl
|
||||
alpha=exp(arg)/gamtot**((1.+float(nAl)+float(nBl))*0.5)
|
||||
temp = sqrt(gamtot)
|
||||
wA=temp*(u-Al)
|
||||
wB=temp*(u-Bl)
|
||||
accu=0.
|
||||
for n in range (nAl+1):
|
||||
for m in range (nBl+1):
|
||||
integ=nAl+nBl-n-m
|
||||
accu+=wA**n*wB**m*binom(nAl,n)*binom(nBl,m)*rintgauss(integ)
|
||||
SAB*=accu*alpha
|
||||
return SAB
|
||||
|
||||
cpdef GoverlapCartNorm2(fA,fB):
|
||||
cdef double gamA=fA.expo
|
||||
cdef double gamB=fB.expo
|
||||
cdef double gamtot = gamA+gamB
|
||||
cdef double SAB=1.0
|
||||
cdef int l
|
||||
nA = powers(fA.sym)
|
||||
nB = powers(fB.sym)
|
||||
for l in range(3):
|
||||
nAl = nA[l]
|
||||
nBl = nB[l]
|
||||
SAB*=rintgauss(nAl+nBl)/(gamA+gamB)**((1.+float(nAl)+float(nBl))/2.)
|
||||
return SAB
|
||||
|
132
resultsFile/lib/library.py
Executable file
132
resultsFile/lib/library.py
Executable file
@ -0,0 +1,132 @@
|
||||
#!/usr/bin/python
|
||||
# resultsFile is a library which allows to read output files of quantum
|
||||
# chemistry codes and write input files.
|
||||
# Copyright (C) 2007 Anthony SCEMAMA
|
||||
#
|
||||
# This program 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 2 of the License, or
|
||||
# (at your option) any later version.
|
||||
#
|
||||
# This program 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 this program; if not, write to the Free Software Foundation, Inc.,
|
||||
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
|
||||
#
|
||||
# Anthony Scemama
|
||||
# LCPQ - IRSAMC
|
||||
# Universite Paul Sabatier
|
||||
# 118, route de Narbonne
|
||||
# 31062 Toulouse Cedex 4
|
||||
# scemama@irsamc.ups-tlse.fr
|
||||
|
||||
|
||||
|
||||
from math import *
|
||||
a0 = 0.529177249
|
||||
|
||||
def prettyPrint(obj,shift=" "):
|
||||
if isinstance(obj,list):
|
||||
for k in obj:
|
||||
prettyPrint(k)
|
||||
elif isinstance(obj,dict):
|
||||
for k in obj:
|
||||
print k
|
||||
prettyPrint(obj[k])
|
||||
else:
|
||||
print str(obj)
|
||||
|
||||
def xproperty(fget, fset=None, fdel=None, doc=None):
|
||||
"""Automatically defines the properties if the functions don't exist."""
|
||||
|
||||
if isinstance(fget,str):
|
||||
attr_name = fget
|
||||
if fset is None:
|
||||
fset = fget
|
||||
fget = lambda obj: getattr(obj, attr_name)
|
||||
|
||||
if isinstance(fset,str):
|
||||
attr_name = fset
|
||||
fset = lambda obj, val: setattr(obj, attr_name, val)
|
||||
|
||||
return property(fget, fset, fdel, doc)
|
||||
|
||||
|
||||
|
||||
def build_get_funcs(var):
|
||||
line = ""
|
||||
line += """def get_"""+var+"""(self):
|
||||
try:
|
||||
getattr(self,'_"""+var+"""')
|
||||
except AttributeError:
|
||||
self._"""+var+""" = None
|
||||
return getattr(self, '_"""+var+"""')\n"""
|
||||
return line
|
||||
|
||||
def build_property(var,txt):
|
||||
line = "def _get_"+var+"(self):\n"
|
||||
line += " return self.get_"+var+"()\n"
|
||||
line += var+" = property(_get_"+var+", fset=None, fdel=None, doc='"+txt+"')\n"
|
||||
return line
|
||||
|
||||
def get_data(var,txt,pos,type=""):
|
||||
line = """def get_%(var)s(self):
|
||||
if self._%(var)s is None:
|
||||
try:
|
||||
self.find_string("%(txt)s")
|
||||
except IndexError:
|
||||
return None
|
||||
pos = self._pos
|
||||
if pos is not None:
|
||||
line = self.text[pos].split()"""
|
||||
if type is "":
|
||||
line += """
|
||||
self._%(var)s = ' '.join(line[%(pos)s])"""
|
||||
else:
|
||||
line += """
|
||||
self._%(var)s = """+type+"""(' '.join(line[%(pos)s]))"""
|
||||
line += """
|
||||
return self._%(var)s"""
|
||||
line = line % {'var': var, 'txt': txt, 'pos': pos}
|
||||
return line
|
||||
|
||||
def init_variable(var,value):
|
||||
assert ( value is not None )
|
||||
line = """def get_"""+var+"""(self):
|
||||
try:
|
||||
getattr(self,'_"""+var+"""')
|
||||
except AttributeError:
|
||||
self._"""+var+""" = None
|
||||
if self._"""+var+""" is None:
|
||||
self._"""+var+""" = """+str(value)+"""
|
||||
return self._"""+var
|
||||
return line
|
||||
|
||||
def cartesianToSpherical(cart):
|
||||
x, y, z = cart
|
||||
r = sqrt(x**2+y**2+z**2)
|
||||
sign = 1.
|
||||
if x != 0.:
|
||||
sign = abs(x)/x
|
||||
theta = atan(y/x)
|
||||
else:
|
||||
sign = 1.
|
||||
theta = atan(pi/2.)
|
||||
if r != 0.:
|
||||
phi = acos(z/r)*sign
|
||||
else:
|
||||
phi = 0.
|
||||
return [r,theta,phi]
|
||||
|
||||
def sphericalToCartesian(sphe):
|
||||
r, theta, phi = sphe
|
||||
x = r*cos(theta)*sin(phi)
|
||||
y = r*sin(theta)*sin(phi)
|
||||
z = r*cos(phi)
|
||||
return [x,y,z]
|
||||
|
||||
|
133
resultsFile/lib/orbital.py
Executable file
133
resultsFile/lib/orbital.py
Executable file
@ -0,0 +1,133 @@
|
||||
#!/usr/bin/env python
|
||||
# resultsFile is a library which allows to read output files of quantum
|
||||
# chemistry codes and write input files.
|
||||
# Copyright (C) 2007 Anthony SCEMAMA
|
||||
#
|
||||
# This program 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 2 of the License, or
|
||||
# (at your option) any later version.
|
||||
#
|
||||
# This program 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 this program; if not, write to the Free Software Foundation, Inc.,
|
||||
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
|
||||
#
|
||||
# Anthony Scemama
|
||||
# LCPQ - IRSAMC
|
||||
# Universite Paul Sabatier
|
||||
# 118, route de Narbonne
|
||||
# 31062 Toulouse Cedex 4
|
||||
# scemama@irsamc.ups-tlse.fr
|
||||
|
||||
|
||||
|
||||
from library import *
|
||||
from math import *
|
||||
|
||||
class orbital(object):
|
||||
"""Class for an orbital."""
|
||||
|
||||
def __init__(self):
|
||||
self._set = None
|
||||
self._eigenvalue = None
|
||||
self._vector = []
|
||||
self._basis = None
|
||||
self._sym = None
|
||||
|
||||
def __repr__(self):
|
||||
out = "%10s %6s %10.6f\n"%(\
|
||||
self.set, self.sym, self.eigenvalue)
|
||||
count=0
|
||||
for c in self.vector:
|
||||
out += "%17.8e "%(c,)
|
||||
count += 1
|
||||
if count == 5:
|
||||
count = 0
|
||||
out += '\n'
|
||||
return out
|
||||
|
||||
def __repr__debug__(self):
|
||||
out = ""
|
||||
out += "Orbital:\n"
|
||||
out += " Set : "+str(self.set)+'\n'
|
||||
out += " Sym : "+str(self.sym)+'\n'
|
||||
out += " Basis : "+str(self.basis)+'\n'
|
||||
out += " Eigenvalue : "+str(self.eigenvalue)+'\n'
|
||||
out += " Vector : "+str(self.vector)+'\n'
|
||||
return out
|
||||
|
||||
def __cmp__(self,other):
|
||||
assert ( isinstance(other,orbital) )
|
||||
if self.eigenvalue < other.eigenvalue:
|
||||
return -1
|
||||
elif self.eigenvalue > other.eigenvalue:
|
||||
return 1
|
||||
elif self.eigenvalue == other.eigenvalue:
|
||||
return 0
|
||||
|
||||
def dot(self,other):
|
||||
assert ( isinstance(other,orbital) )
|
||||
result = 0.
|
||||
for i,j in zip(self.vector,other.vector):
|
||||
result += i*j
|
||||
return sqrt(result)
|
||||
|
||||
def is_ortho(self,other):
|
||||
assert ( isinstance(other,orbital) )
|
||||
if self.dot(other) == 0. :
|
||||
return True
|
||||
else:
|
||||
return False
|
||||
|
||||
def norm(self):
|
||||
return self.dot(self)
|
||||
|
||||
def value(self,r):
|
||||
"""Value at r."""
|
||||
x, y, z = r
|
||||
result = 0.
|
||||
for c,chi in zip(self.vector,self.basis):
|
||||
result += c*chi.value(r)
|
||||
return result
|
||||
|
||||
for i in "eigenvalue vector basis set sym".split():
|
||||
exec """
|
||||
def get_%(i)s(self): return self._%(i)s
|
||||
def set_%(i)s(self,value): self._%(i)s = value
|
||||
%(i)s = property(fget=get_%(i)s,fset=set_%(i)s) """%locals()
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
if __name__ == '__main__':
|
||||
l = []
|
||||
l.append(orbital())
|
||||
l.append(orbital())
|
||||
l.append(orbital())
|
||||
l[0].eigenvalue = 2.
|
||||
l[1].eigenvalue = 1.
|
||||
l[2].eigenvalue = 3.
|
||||
for i in l:
|
||||
print i.eigenvalue
|
||||
l.sort()
|
||||
print ""
|
||||
for i in l:
|
||||
print i.eigenvalue
|
||||
l[0].vector = [1., 0., 0.]
|
||||
l[1].vector = [0., 1., 0.]
|
||||
l[2].vector = [0., 1., 1.]
|
||||
print l[0].is_ortho(l[1])
|
||||
print l[1].is_ortho(l[2])
|
||||
print l[1].dot(l[2])
|
||||
print l[1].dot(l[0])
|
||||
print l[1].norm()
|
||||
print l[2].norm()
|
||||
|
||||
|
||||
|
Loading…
Reference in New Issue
Block a user