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https://gitlab.com/scemama/resultsFile.git
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Python3
This commit is contained in:
parent
c4bbfa23b8
commit
806544a778
@ -27,6 +27,7 @@
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import resultsFile
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from lib import *
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import struct
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import re
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@ -27,6 +27,7 @@
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import resultsFile
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from lib import *
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import struct
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import re
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@ -27,6 +27,7 @@
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import resultsFile
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from lib import *
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import sys
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import struct
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@ -27,6 +27,7 @@
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import resultsFile
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from lib import *
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import struct
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import re
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@ -1,51 +0,0 @@
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#!/usr/bin/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 distutils.core import setup
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from distutils.extension import Extension
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from Cython.Distutils import build_ext
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"""
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./cython_setup build_ext --inplace
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"""
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ext_modules = [Extension("resultsFile_cython", ["resultsFile_cython.pyx"])]
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import os
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setup(name="resultsFile",
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version=os.getenv("VERSION","1.0"),
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author="Anthony Scemama",
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author_email="scemama@irsamc.ups-tlse.fr",
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license="gpl-license",
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description="Module for I/O on Quantum Chemistry files.",
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packages=["resultsFile","resultsFile.lib","resultsFile.Modules"],
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cmdclass = {'build_ext': build_ext},
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ext_modules = ext_modules
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)
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@ -142,7 +142,7 @@ def rintgauss(n):
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if n == 0: return res
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elif n == 1: return 0.
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elif n%2 == 1: return 0.
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res /= 2.**(n/2)
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res /= 2.**(n//2)
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res *= ddfact2(n-1)
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return res
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@ -227,8 +227,11 @@ def xyz_from_lm(l,m):
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coef = []
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absm = abs(m)
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nb2 = absm
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nb1 = (l-absm)/2
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clmt = [ (-0.25)**t * binom(l,t) * binom(l-t,absm+t) for t in range(nb1+1) ]
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nb1 = (l-absm)//2
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clmt = [ (-0.25)**t *
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binom(l,t) *
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binom(l-t,absm+t)
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for t in range(nb1+1) ]
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mod_absm_2 = absm % 2
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if m>=0:
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nb2_start = mod_absm_2
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@ -239,7 +242,7 @@ def xyz_from_lm(l,m):
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else:
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norm = 1.
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for n1 in range(nb2_start,nb2+1,2):
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k = (absm-n1)/2
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k = (absm-n1)//2
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factor = (-1.)**k * binom(absm,n1) * norm
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for t in range(nb1+1):
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for n2 in range(t+1):
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@ -1,89 +0,0 @@
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#!/usr/bin/python
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from math import *
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powersave = { 's':(0,0,0) }
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def powers(sym):
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if sym in powersave:
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return powersave[sym]
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result = (sym.count('x'),sym.count('y'),sym.count('z'))
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powersave[sym] = result
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return result
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fact_ = [1.]
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cpdef fact(int n):
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global fact_
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cdef int nstart = len(fact_)
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cdef int i
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if n >= nstart :
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for i in range(nstart,n+1):
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fact_.append(float(fact_[i-1]*i))
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return fact_[n]
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def binom(int n,int m):
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return fact(n)/(fact(m)*fact(n-m))
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cdef ddfact2(int n):
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if n%2 == 0: print 'error in ddfact2'
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cdef double res=1.
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cdef int i
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for i in range(1,n+1,2):
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res*=float(i)
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return res
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cdef double sqpi = sqrt(pi)
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cpdef rintgauss(int n):
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res = sqpi
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if n == 0: return res
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elif n == 1: return 0.
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elif n%2 == 1: return 0.
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res /= 2.**(n/2)
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res *= ddfact2(n-1)
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return res
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cpdef GoverlapCart(fA,fB):
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cdef double gamA=fA.expo
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cdef double gamB=fB.expo
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cdef double gamtot = gamA+gamB
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cdef double SAB=1.0
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cdef int l, n, m
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cdef double u, arg, alpha, temp, wA, wB, accu
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cdef int integ
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A = fA.center
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B = fB.center
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nA = powers(fA.sym)
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nB = powers(fB.sym)
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for l in range(3):
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Al = A[l]
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Bl = B[l]
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nAl = nA[l]
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nBl = nB[l]
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u=gamA/gamtot*Al+gamB/gamtot*Bl
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arg=gamtot*u*u-gamA*Al*Al-gamB*Bl*Bl
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alpha=exp(arg)/gamtot**((1.+float(nAl)+float(nBl))*0.5)
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temp = sqrt(gamtot)
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wA=temp*(u-Al)
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wB=temp*(u-Bl)
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accu=0.
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for n in range (nAl+1):
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for m in range (nBl+1):
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integ=nAl+nBl-n-m
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accu+=wA**n*wB**m*binom(nAl,n)*binom(nBl,m)*rintgauss(integ)
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SAB*=accu*alpha
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return SAB
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cpdef GoverlapCartNorm2(fA,fB):
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cdef double gamA=fA.expo
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cdef double gamB=fB.expo
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cdef double gamtot = gamA+gamB
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cdef double SAB=1.0
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cdef int l
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nA = powers(fA.sym)
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nB = powers(fB.sym)
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for l in range(3):
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nAl = nA[l]
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nBl = nB[l]
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SAB*=rintgauss(nAl+nBl)/(gamA+gamB)**((1.+float(nAl)+float(nBl))/2.)
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return SAB
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@ -1,241 +0,0 @@
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#!/usr/bin/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 lib import *
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import lib.basis as Basis
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def get_uncontracted_basis(basis):
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uncontr = []
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for contr in basis:
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for b in contr.prim:
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uncontr.append(b)
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return uncontr
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def get_uncontracted_mo_sets(basis,uncontracted_basis,mo_sets,mo_types):
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cdef dict uncontr = {}
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cdef int lenmovector
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cdef int lenbasis = len(basis)
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cdef double ci
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cdef int i, j
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for motype in mo_types:
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uncontr[motype] = []
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for mo in mo_sets[motype]:
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lenmovector = len(mo.vector)
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monew = orbital()
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monew.basis = uncontracted_basis
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monew.eigenvalue = mo.eigenvalue
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monew.set = motype
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v = []
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for i in range(lenbasis):
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contr = basis[i]
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if i<lenmovector:
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ci = mo.vector[i]
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if ci == 0.:
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for j in range(len(contr.prim)):
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v.append(0.)
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else:
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for p, c in zip(contr.prim,contr.coef):
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v.append(c*ci/p.norm)
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monew.vector = v
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uncontr[motype].append(monew)
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return uncontr
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def clean_contractions(basis):
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newbasis = []
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cdef int i, k, l, lenmovector
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idx = range(len(basis))
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for k,b1 in enumerate(basis):
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addBasis=True
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for l, b2 in enumerate(basis[:k]):
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if b2 == b1:
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idx[k] = l
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addBasis=False
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break
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if addBasis:
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newbasis.append(b1)
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self._basis = newbasis
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mo_sets = self.mo_sets
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for motype in self.mo_types:
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for mo in mo_sets[motype]:
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lenmovector = len(mo.vector)
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newvec = [None for i in idx]
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for i in idx:
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newvec[i] = 0.
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for k,l in enumerate(idx):
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if k < lenmovector:
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newvec[l] += mo.vector[k]
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mo.vector = []
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for c in newvec:
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if c is not None:
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mo.vector.append(c)
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# def clean_uncontractions(self):
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# basis = self.uncontracted_basis
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# newbasis = []
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# idx = range(len(basis))
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# for k,b1 in enumerate(basis):
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# addBasis=True
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# for l, b2 in enumerate(basis[:k]):
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# if b2 == b1:
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# idx[k] = l
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# addBasis=False
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# break
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# if addBasis:
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# newbasis.append(b1)
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# self._uncontracted_basis = newbasis
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# mo_sets = self.uncontracted_mo_sets
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# for motype in self.mo_types:
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# for mo in mo_sets[motype]:
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# lenmovector = len(mo.vector)
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# newvec = [None for i in idx]
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# for i in idx:
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# newvec[i] = 0.
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# for k,l in enumerate(idx):
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# if k < lenmovector:
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# newvec[l] += mo.vector[k]
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# mo.vector = []
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# for c in newvec:
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# if c is not None:
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# mo.vector.append(c)
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#
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# def convert_to_cartesian(self):
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# basis = self.basis
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# newbasis = []
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# idx = range(len(basis))
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# map = []
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# weight = []
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# for i,b in enumerate(basis):
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# l, m = Basis.get_lm(b.sym)
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# if l is None:
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# newbasis.append(b)
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# map.append(i)
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# weight.append(1.)
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# else:
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# powers, coefs = xyz_from_lm(l,m)
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# for j,prim in enumerate(b.prim):
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# b.coef[j] /= prim.norm
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# for c, p in zip(coefs, powers):
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# contr = copy.deepcopy(b)
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# sym = ''
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# for l,letter in enumerate('xyz'):
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# sym += p[l]*letter
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# contr.sym = sym
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# for j,prim in enumerate(contr.prim):
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# prim.sym = sym
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# contr.coef[j] *= prim.norm
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# newbasis.append(contr)
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# map.append(i)
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# weight.append(c)
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# mo_sets = self.mo_sets
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# for motype in self.mo_types:
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# for mo in mo_sets[motype]:
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# newvec = []
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# vec = mo.vector
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# for i,w in zip(map,weight):
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# newvec.append(vec[i]*w)
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# mo.vector = newvec
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# same_as = {}
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# for i,b1 in enumerate(newbasis):
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# for j,b2 in enumerate(newbasis[:i]):
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# if b1 == b2:
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# same_as[i] = j
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# weight[j] += weight[i]
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# break
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# to_remove = same_as.keys()
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# to_remove.sort()
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# to_remove.reverse()
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# for i in to_remove:
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# newbasis.pop(i)
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# weight.pop(i)
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# map.pop(i)
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# for motype in self.mo_types:
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# for mo in mo_sets[motype]:
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# for i in to_remove:
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# index = same_as[i]
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# value = mo.vector.pop(i)
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# mo.vector[index] += value
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# self._basis = newbasis
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# self._mo_sets = mo_sets
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# def find_string(self,chars):
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# """Finds the 1st occurence of chars.
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# """
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# self._pos = 0
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# self.find_next_string(chars)
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# def find_last_string(self,chars):
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# """Finds the 1st occurence of chars.
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# """
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# self._pos = len(self.text)-1
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# self.find_prev_string(chars)
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# def find_next_string(self,chars):
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# """Finds the next occurence of chars.
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# """
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# pos = self._pos
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# text = self.text
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# found = False
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# while not found and pos < len(text):
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# if chars in text[pos]:
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# found = True
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# else:
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# pos += 1
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# if not found:
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# raise IndexError
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# self._pos = pos
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# def find_prev_string(self,chars):
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# """Finds the next occurence of chars.
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# """
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# pos = self._pos
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# text = self.text
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# found = False
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# while not found and pos < len(text):
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# if chars in text[pos]:
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# found = True
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# else:
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# pos -= 1
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# if not found:
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# raise IndexError
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# self._pos = pos
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# for i, j in local_vars:
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# if i not in defined_vars:
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# exec build_get_funcs(i) in locals()
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# exec build_property(i,j) in locals()
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# del i,j
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