From 806544a7783331c71dc23dfbe45b9229e8d5bf34 Mon Sep 17 00:00:00 2001
From: Anthony Scemama <scemama@irsamc.ups-tlse.fr>
Date: Mon, 27 Jan 2020 22:12:16 +0100
Subject: [PATCH] Python3

---
 resultsFile/Modules/gaussianFile.py |   1 +
 resultsFile/Modules/molproFile.py   |   1 +
 resultsFile/Modules/wfnFile.py      |   1 +
 resultsFile/Modules/xmvbFile.py     |   1 +
 resultsFile/cython_setup            |  51 ------
 resultsFile/lib/basis.py            |  11 +-
 resultsFile/lib/lib_cython.pyx      |  89 ----------
 resultsFile/resultsFile_cython.pyx  | 241 ----------------------------
 8 files changed, 11 insertions(+), 385 deletions(-)
 delete mode 100755 resultsFile/cython_setup
 delete mode 100644 resultsFile/lib/lib_cython.pyx
 delete mode 100755 resultsFile/resultsFile_cython.pyx

diff --git a/resultsFile/Modules/gaussianFile.py b/resultsFile/Modules/gaussianFile.py
index 5a11426..87b2406 100755
--- a/resultsFile/Modules/gaussianFile.py
+++ b/resultsFile/Modules/gaussianFile.py
@@ -27,6 +27,7 @@
 
 
 import resultsFile
+from lib import *
 
 import struct
 import re
diff --git a/resultsFile/Modules/molproFile.py b/resultsFile/Modules/molproFile.py
index c72725d..93f1ca1 100755
--- a/resultsFile/Modules/molproFile.py
+++ b/resultsFile/Modules/molproFile.py
@@ -27,6 +27,7 @@
 
 
 import resultsFile
+from lib import *
 
 import struct
 import re
diff --git a/resultsFile/Modules/wfnFile.py b/resultsFile/Modules/wfnFile.py
index 54862a8..79b23c7 100755
--- a/resultsFile/Modules/wfnFile.py
+++ b/resultsFile/Modules/wfnFile.py
@@ -27,6 +27,7 @@
 
 
 import resultsFile
+from lib import *
 import sys
 
 import struct
diff --git a/resultsFile/Modules/xmvbFile.py b/resultsFile/Modules/xmvbFile.py
index 058e450..e2cab7d 100755
--- a/resultsFile/Modules/xmvbFile.py
+++ b/resultsFile/Modules/xmvbFile.py
@@ -27,6 +27,7 @@
 
 
 import resultsFile
+from lib import *
 
 import struct
 import re
diff --git a/resultsFile/cython_setup b/resultsFile/cython_setup
deleted file mode 100755
index d2575e3..0000000
--- a/resultsFile/cython_setup
+++ /dev/null
@@ -1,51 +0,0 @@
-#!/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("resultsFile_cython", ["resultsFile_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
-      )
-
diff --git a/resultsFile/lib/basis.py b/resultsFile/lib/basis.py
index 0676bd7..7bd28ee 100755
--- a/resultsFile/lib/basis.py
+++ b/resultsFile/lib/basis.py
@@ -142,7 +142,7 @@ def rintgauss(n):
   if n == 0: return res
   elif n == 1: return 0.
   elif n%2 == 1: return 0.
-  res /= 2.**(n/2)
+  res /= 2.**(n//2)
   res *= ddfact2(n-1)
   return res
 
@@ -227,8 +227,11 @@ def xyz_from_lm(l,m):
   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 range(nb1+1) ]
+  nb1  = (l-absm)//2
+  clmt = [ (-0.25)**t *
+    binom(l,t) *
+    binom(l-t,absm+t)
+    for t in range(nb1+1) ]
   mod_absm_2 = absm % 2
   if m>=0:
     nb2_start = mod_absm_2
@@ -239,7 +242,7 @@ def xyz_from_lm(l,m):
   else:
     norm = 1.
   for n1 in range(nb2_start,nb2+1,2):
-    k = (absm-n1)/2
+    k = (absm-n1)//2
     factor = (-1.)**k * binom(absm,n1) * norm
     for t in range(nb1+1):
       for n2 in range(t+1):
diff --git a/resultsFile/lib/lib_cython.pyx b/resultsFile/lib/lib_cython.pyx
deleted file mode 100644
index 75343c6..0000000
--- a/resultsFile/lib/lib_cython.pyx
+++ /dev/null
@@ -1,89 +0,0 @@
-#!/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
-
diff --git a/resultsFile/resultsFile_cython.pyx b/resultsFile/resultsFile_cython.pyx
deleted file mode 100755
index 825e311..0000000
--- a/resultsFile/resultsFile_cython.pyx
+++ /dev/null
@@ -1,241 +0,0 @@
-#!/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 lib import *
-import lib.basis as Basis
-
-def get_uncontracted_basis(basis):
-   uncontr = []
-   for contr in basis:
-      for b in contr.prim:
-         uncontr.append(b)
-   return uncontr
-
-def get_uncontracted_mo_sets(basis,uncontracted_basis,mo_sets,mo_types):
-   cdef dict uncontr = {}
-   cdef int lenmovector
-   cdef int lenbasis = len(basis)
-   cdef double ci
-   cdef int i, j
-   for motype in mo_types:
-     uncontr[motype] = []
-     for mo in mo_sets[motype]:
-       lenmovector = len(mo.vector)
-       monew = orbital()
-       monew.basis = uncontracted_basis
-       monew.eigenvalue = mo.eigenvalue
-       monew.set = motype
-       v = []
-       for i in range(lenbasis):
-         contr = basis[i]
-         if i<lenmovector:
-           ci = mo.vector[i]
-           if ci == 0.:
-             for j in range(len(contr.prim)):
-                v.append(0.)
-           else:
-             for p, c in zip(contr.prim,contr.coef):
-                v.append(c*ci/p.norm)
-       monew.vector = v
-       uncontr[motype].append(monew)
-   return uncontr
-
-
-def clean_contractions(basis):
-  newbasis = []
-  cdef int i, k, l, lenmovector
-  idx = range(len(basis))
-  for k,b1 in enumerate(basis):
-    addBasis=True
-    for l, b2 in enumerate(basis[:k]):
-      if b2 == b1:
-        idx[k] = l
-        addBasis=False
-        break
-    if addBasis:
-      newbasis.append(b1)
-  self._basis = newbasis 
-
-  mo_sets = self.mo_sets
-  for motype in self.mo_types:
-    for mo in mo_sets[motype]:
-      lenmovector = len(mo.vector)
-      newvec = [None for i in idx]
-      for i in idx:
-        newvec[i] = 0.
-      for k,l in enumerate(idx):
-        if k < lenmovector:
-          newvec[l] += mo.vector[k]
-      mo.vector = []
-      for c in newvec:
-        if c is not None:
-          mo.vector.append(c)
-
-#  def clean_uncontractions(self):
-#    basis = self.uncontracted_basis
-#    newbasis = []
-#    idx = range(len(basis))
-#    for k,b1 in enumerate(basis):
-#      addBasis=True
-#      for l, b2 in enumerate(basis[:k]):
-#        if b2 == b1:
-#          idx[k] = l
-#          addBasis=False
-#          break
-#      if addBasis:
-#        newbasis.append(b1)
-#    self._uncontracted_basis = newbasis 
-
-#    mo_sets = self.uncontracted_mo_sets
-#    for motype in self.mo_types:
-#      for mo in mo_sets[motype]:
-#        lenmovector = len(mo.vector)
-#        newvec = [None for i in idx]
-#        for i in idx:
-#          newvec[i] = 0.
-#        for k,l in enumerate(idx):
-#          if k < lenmovector:
-#            newvec[l] += mo.vector[k]
-#        mo.vector = []
-#        for c in newvec:
-#          if c is not None:
-#            mo.vector.append(c)
-#      
-#  def convert_to_cartesian(self):
-#    basis = self.basis
-#    newbasis = []
-#    idx = range(len(basis))
-#    map = []
-#    weight = []
-#    for i,b in enumerate(basis):
-#      l, m = Basis.get_lm(b.sym)
-#      if l is None:
-#        newbasis.append(b)
-#        map.append(i)
-#        weight.append(1.)
-#      else:
-#        powers, coefs = xyz_from_lm(l,m)
-#        for j,prim in enumerate(b.prim):
-#          b.coef[j] /= prim.norm
-#        for c, p in zip(coefs, powers):
-#          contr = copy.deepcopy(b)
-#          sym = ''
-#          for l,letter in enumerate('xyz'):
-#            sym += p[l]*letter
-#          contr.sym = sym
-#          for j,prim in enumerate(contr.prim):
-#            prim.sym = sym
-#            contr.coef[j] *= prim.norm
-#          newbasis.append(contr)
-#          map.append(i)
-#          weight.append(c)
-
-#    mo_sets = self.mo_sets
-#    for motype in self.mo_types:
-#      for mo in mo_sets[motype]:
-#        newvec = []
-#        vec = mo.vector
-#        for i,w in zip(map,weight):
-#          newvec.append(vec[i]*w)
-#        mo.vector = newvec
-
-#    same_as = {}
-#    for i,b1 in enumerate(newbasis):
-#      for j,b2 in enumerate(newbasis[:i]):
-#        if b1 == b2:
-#         same_as[i] = j
-#         weight[j] += weight[i]
-#         break
-#    to_remove = same_as.keys()
-#    to_remove.sort()
-#    to_remove.reverse()
-#    for i in to_remove:
-#      newbasis.pop(i)
-#      weight.pop(i)
-#      map.pop(i)
-
-
-#    for motype in self.mo_types:
-#      for mo in mo_sets[motype]:
-#        for i in to_remove:
-#          index = same_as[i]
-#          value = mo.vector.pop(i)
-#          mo.vector[index] += value
-
-#    self._basis = newbasis
-#    self._mo_sets = mo_sets
-
-#  def find_string(self,chars):
-#      """Finds the 1st occurence of chars.
-#      """
-#      self._pos = 0
-#      self.find_next_string(chars)
-
-#  def find_last_string(self,chars):
-#      """Finds the 1st occurence of chars.
-#      """
-#      self._pos = len(self.text)-1
-#      self.find_prev_string(chars)
-
-#  def find_next_string(self,chars):
-#      """Finds the next occurence of chars.
-#      """
-#      pos  = self._pos
-#      text = self.text
-#      found = False
-#      while not found and pos < len(text):
-#         if chars in text[pos]:
-#            found = True
-#         else:
-#            pos += 1
-#      if not found:
-#         raise IndexError
-#      self._pos = pos
-
-#  def find_prev_string(self,chars):
-#      """Finds the next occurence of chars.
-#      """
-#      pos  = self._pos
-#      text = self.text
-#      found = False
-#      while not found and pos < len(text):
-#         if chars in text[pos]:
-#            found = True
-#         else:
-#            pos -= 1
-#      if not found:
-#         raise IndexError
-#      self._pos = pos
-
-
-#  for i, j in local_vars:
-#     if i not in defined_vars:
-#        exec build_get_funcs(i) in locals()
-#     exec build_property(i,j) in locals()
-#  del i,j
-
-