Updated for 2020

EZFIO.tar.gz

@@ -1 +0,0 @@
-EZFIO.1.0.20.tar.gz

Makefile

@@ -9,13 +9,13 @@ EZFIO.tar.gz:
 
 EZFIO/config/eplf.config: EZFIO.tar.gz
 	tar -zxf EZFIO.tar.gz
-	cd EZFIO ; IRPF90="`echo $(IRPF90) | cut -f 1`" ./configure
+	cd EZFIO 
 	if [ -e $@ ] ; then rm $@ ; fi
 	ln -s $$PWD/eplf.config $@
 	touch EZFIO/config/eplf.config
 
 EZFIO/lib/libezfio.so: EZFIO/config/eplf.config
-	make -C EZFIO/
+	$(MAKE) -C EZFIO/
 	cp EZFIO/Python/ezfio.py scripts/
 
 bin/ezfio.py: EZFIO/lib/libezfio.so

README

@@ -1,47 +0,0 @@
-+==============================================================================+
-|                                  EPLF                                        |
-+==============================================================================+
-
-Dependencies:
--------------
-
-- EZFIO library : http://ezfio.sourceforge.net
-- IRPF90 : http://irpf90.sourceforge.net
-- Python > 2.3
-- Any Fortran 90 compiler (gfortran, for example)
-
-Installing EPLF:
-------------------
-
-- As the super-user, run
-./eplf.install
-
-
-Using EPLF:
--------------
-
- With Gaussian:
- --------------
-
- 1 - Add the following keywords to your Gaussian input:
- # GFPRINT pop=Full 6d 10f
- 
- 2 - Run Gaussian. You obtain an output file (x.out)
-
- 3 - Run the eplf_input.py script:
- eplf_input.py x.out
-
- 4 - You now have a QCIO directory which contains the wave function data.
-
- 5 - Run eplf to get a cube file
-
-
-
-Web Site:
-http://eplf.sourceforge.net
-
-Author:
-Anthony Scemama, LCPQ-IRSAMC, CNRS-Universite Paul Sabatier
-scemama@irsamc.ups-tlse.fr
-http://sourceforge.net/userapps/mediawiki/scemama
-

README.org

@@ -0,0 +1,101 @@
+#+TITLE: EPLF
+#+AUTHOR: Anthony Scemama
+#+EMAIL: scemama@irsamc.ups-tlse.fr
+#+date: 2020-06-02
+
+Computes the Electron Pair Localization Function.
+
+* Dependencies
+
+    - Python3
+    - resultsFile : https://gitlab.com/scemama/resultsFile
+    - IRPF90 : http://irpf90.ups-tlse.fr
+    - GFortran or Intel Fortran
+
+ =resultsFile= and =IRPF90= can both be installed with pip.
+
+  #+begin_src shell 
+  python3 -m pip install resultsFile
+  python3 -m pip install irpf90
+  #+end_src
+  
+ =./configure= should detect suitable defaults for your system. You can 
+  update the =make.config= file if you want. It is important to give the
+  Fortran compiler the option to accept infinitely long lines (with
+  gfortran, the option is =-ffree-line-length-none=).
+  The =configure= script will also create a file =$HOME/.eplfrc= that you
+  will need to source before running the program.
+
+* Using EPLF
+
+ GAMESS or Gaussian can be used to produce the wave function.
+ With Gaussian, the following keywords are required:
+ #+begin_example
+ # GFPRINT pop=Full 6d 10f
+ #+end_example
+
+ Go into the =test= directory and execute the following commands to make
+ a test run with an Gaussian output file.
+
+ 1. Run the =eplf_input.py= script to convert the output file into an
+    EZFIO directory containing all the data required for the
+    computation:
+
+    #+begin_src shell 
+    eplf_input.py c2h.out
+    #+end_src
+   
+    The =c2h.out.ezfio= directory is produced.
+   
+ 2. Edit the parameters by running =eplf_edit.py=
+   
+    #+begin_src shell 
+    eplf_edit.py c2h.out.ezfio
+    #+end_src
+
+    The editor defined with the =$EDITOR= environment variable will open
+    and let you change the parameters. To compute the density and the
+    EPLF, just add an =X= character between the brackets next to =eplf=
+    and =density=:
+
+    #+begin_example
+    ( ) density ->   (X) density
+    ( ) eplf    ->   (X) eplf
+    #+end_example
+
+ 3. Run the program to compute the data and save it in the EZFIO directory
+
+    #+begin_src shell
+    eplf c2h.out.ezfio
+    #+end_src
+    
+    If the program is compiled with MPI, run
+
+    #+begin_src shell
+    mpirun eplf c2h.out.ezfio
+    #+end_src
+
+ 4. Now you can convert the data into cube files as:
+    #+begin_src shell 
+    to_cube.py c2h.out.ezfio density
+    to_cube.py c2h.out.ezfio eplf
+    #+end_src
+
+    The parameters of the grid can be changed by first clearing the
+    data, and the updating the grid parameters. This can be done with
+ =eplf_edit.py= by un-commenting the lines =clear(all)=
+    and =edit(grid_parameters)=.
+
+* References
+
+  Scemama, A., Chaquin, P., Caffarel, M. (2004).
+  "Electron pair localization function: A practical tool to visualize electron
+  localization in molecules from quantum Monte Carlo data".
+ /J. Chem. Phys./ *121* (4), 1725–1735. doi: 10.1063/1.1765098
+
+  Scemama, A., Caffarel, M., Chaudret, R., & Piquemal, J.-P. (2011),
+  "Electron Pair Localization Function (EPLF) for Density Functional
+  Theory and ab Initio Wave Function-Based Methods: A New Tool for
+  Chemical Interpretation".
+ /J. Chem. Theory Comput./ *7* (3), 618–624. doi: 10.1021/ct1005938
+  

configure.ac

@@ -31,7 +31,7 @@ AC_REVISION([$Revision: $VERSION $])
 
 AC_PREREQ([2.50])
 
-AC_INIT([EPLF], [], [scemama@irsamc.ups-tlse.fr],[eplf],[http://eplf.sourceforge.net])
+AC_INIT([EPLF], [], [scemama@irsamc.ups-tlse.fr],[eplf],[https://gitlab.com/scemama/eplf])
 
 AC_SYS_LONG_FILE_NAMES
 
@@ -53,75 +53,18 @@ AC_PROG_CC
 # Check for curl
 AC_CHECK_PROGS([CURL],[curl],[])
 
-######################################################
-# Define download function
-AC_DEFUN([AC_DOWNLOAD],[{
- # AC_DOWNLOAD ( VARIABLE, name, url )
- WHERE=
- if [[ ! -z $CURL ]] ; then
-   echo ""
-   echo "**************************"
-   echo $1 is not installed
-   echo "**************************"
-   echo "Do you want to download it?"
-   select x in yes no
-   do
-    if [[ ! -z $x ]] ; then
-      break
-    fi
-   done
-   if [[ $x == yes ]] ; then
-      if [[ ! -d "Downloads" ]] ; then
-        mkdir $EPLF_PATH/Downloads
-      fi
-      cd $EPLF_PATH/Downloads
-      mkdir $EPLF_PATH/Downloads/tmp
-      cd $EPLF_PATH/Downloads/tmp
-      $CURL -L "$3" -o $2 && mv $2 .. && WHERE=$2
-      cd $EPLF_PATH
-      rm -rf $EPLF_PATH/Downloads/tmp
-   fi
-   if [[ ! -z $WHERE ]] ; then
-      echo $2 was downloaded to Downloads/$WHERE.
-      $1=1
-   else
-      AC_MSG_ERROR([$2 should be installed. You can download it at
-    $3])
-   fi
- else
-    AC_MSG_ERROR([Please download $2 at
-    $3])
- fi
-}])
-
 ######################################################
 # Check for python
-AC_CHECK_PROGS([PYTHON],[python],[])
+AC_CHECK_PROGS([PYTHON],[python3],[])
 if [[ -z $PYTHON ]] ; then
-  AC_MSG_ERROR([Python should be installed:
+  AC_MSG_ERROR([Python3 should be installed])
-  http://www.python.org])
 fi
 
 ######################################################
 # IRPF90 compiler
 AC_CHECK_PROGS([IRPF90],[irpf90],[])
 if [[ -z $IRPF90 ]] ; then
-  AC_DOWNLOAD([IRPF90],[irpf90.gz],[http://sourceforge.net/projects/irpf90/files/irpf90-1.1.57-noarch.exe.gz/download])
+  AC_MSG_ERROR([IRPF90 should be installed: python3 -m pip install irpf90])
-  gunzip Downloads/irpf90.gz
-  mv Downloads/irpf90 bin/
-  chmod +x bin/irpf90
-  IRPF90=$EPLF_PATH/bin/irpf90
-fi
-
-######################################################
-# EZFIO
-EZFIO=`ls EZFIO*.tar.gz | tail -1`
-if [[ -z $EZFIO ]] ; then
-  AC_DOWNLOAD([EZFIO],[EZFIO.tar.gz],[http://sourceforge.net/projects/ezfio/files/latest])
-  if [[ -z $EZFIO ]] ; then
-    AC_MSG_ERROR([Download EZFIO.tar.gz into $PWD and run this configure script again.])
-  fi
-  mv Downloads/EZFIO*.tar.gz EZFIO.tar.gz
 fi
 
 ######################################################
@@ -165,24 +108,26 @@ AC_FC_FREEFORM
 
 case $FC in
     mpif90*)
-       FCFLAGS="-O3"
+       FCFLAGS="-fPIC -O2 -ffree-line-length-none -ffast-math "
        IRPF90="$IRPF90 -DMPI"
        ;;
     ifort*)
-       FCFLAGS="-O3 -axSSE2,AVX -ip"
+       FCFLAGS="-O2 -xHost -ip"
        if test $STATIC == 1 ; then
          FCFLAGS="$FCFLAGS -static-intel -static-libgcc -static"
        fi
        ;;
     gfortran*)
-       FCFLAGS="-fPIC -O3 -ffast-math"
+       FCFLAGS="-fPIC -O2 -ffast-math -ffree-line-length-none"
        if test $STATIC == 0 ; then
          FCFLAGS="$FCFLAGS -static-libgcc -static"
        fi
        ;;
 esac
 
-AC_SUBST(IRPF90)
+AC_SUBST([FC])
+AC_SUBST([IRPF90])
+AC_SUBST([FCFLAGS])
 
 # Write make.config
 

eplf.config

@@ -1,7 +1,7 @@
 electrons
   elec_alpha_num      integer
   elec_beta_num       integer
-  elec_num            integer           = electrons_elec_alpha_num + electrons_elec_beta_num
+  elec_num            integer           
 
 nuclei
   nucl_num            integer
@@ -18,7 +18,7 @@ ao_basis
   ao_prim_num        integer       (ao_basis_ao_num)
   ao_nucl            integer       (ao_basis_ao_num)
   ao_power           integer       (ao_basis_ao_num,3)
-  ao_prim_num_max    integer       = maxval(ao_basis_ao_prim_num)
+  ao_prim_num_max    integer       
   ao_coef            real          (ao_basis_ao_num,ao_basis_ao_prim_num_max)
   ao_expo            real          (ao_basis_ao_num,ao_basis_ao_prim_num_max)
 
@@ -26,9 +26,9 @@ mo_basis
   mo_tot_num         integer
   mo_coef            real              (ao_basis_ao_num,mo_basis_mo_tot_num)
   mo_classif         character         (mo_basis_mo_tot_num)
-  mo_closed_num      integer           =n_count_ch(mo_basis_mo_classif,size(mo_basis_mo_classif),'c')
+  mo_closed_num      integer           
-  mo_active_num      integer           =n_count_ch(mo_basis_mo_classif,size(mo_basis_mo_classif),'a')
+  mo_active_num      integer           
-  mo_virtual_num     integer           =n_count_ch(mo_basis_mo_classif,size(mo_basis_mo_classif),'v')
+  mo_virtual_num     integer           
   mo_energy          real              (mo_basis_mo_tot_num)
   mo_occ             real              (mo_basis_mo_tot_num)
 

make.config.in

@@ -2,3 +2,4 @@ IRPF90 = @IRPF90@
 FC     = @FC@
 FCFLAGS= @FCFLAGS@
 LIB    = @LIB@
+export FC FCFLAGS IRPF90

scripts/eplf_edit.py

@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/env python3
 
 from math import *
 
@@ -25,7 +25,7 @@ class Cleaner(object):
   def action(self):
     raise TypeError
   def clean(self):
-    print "Removing "+self.name
+    print("Removing "+self.name)
     self.action()
 
 class GridDataCleaner(Cleaner):
@@ -40,7 +40,7 @@ class AllCleaner(Cleaner):
 def clear(x,inp):
   d = { "all": AllCleaner,
       }
-  if x in d.keys():
+  if x in list(d.keys()):
     type = d[x]
   else:
     type = GridDataCleaner
@@ -58,7 +58,7 @@ class Editor(object):
   def action(self):
     raise TypeError
   def edit(self):
-    print "Editing "+self.name
+    print("Editing "+self.name)
     self.action()
     
 class GeometryEditor(Editor):
@@ -68,26 +68,26 @@ class GeometryEditor(Editor):
     edit_temp_file(self.inp,self.write_geom_file,self.read_geom_file)
 
   def write_geom_file(self,file,inp):
-    print >>file, "###########################"
+    print("###########################", file=file)
-    print >>file, "# Geometry : %s"%(inp.name)
+    print("# Geometry : %s"%(inp.name), file=file)
-    print >>file, "###########################"
+    print("###########################", file=file)
-    print >>file, ""
+    print("", file=file)
     fields = "Charge X Y Z"
     format = "%10.1f "+"%10.6f "*3
     fields = fields.split()
-    print >>file, " ".join(["#"]+map(lambda x: x.center(10),fields))
+    print(" ".join(["#"]+[x.center(10) for x in fields]), file=file)
-    print >>file, "# "+"-"*11*len(fields)+"\n"
+    print("# "+"-"*11*len(fields)+"\n", file=file)
     charge = self.charge
     coord = self.coord
-    for i in xrange(len(charge)):
+    for i in range(len(charge)):
       buffer = [ charge[i], coord[0][i], coord[1][i], coord[2][i] ]
-      print >>file, "  "+format%tuple(buffer)
+      print("  "+format%tuple(buffer), file=file)
 
   def read_geom_file(self,file,inp):
     lines = file.readlines()
-    lines = filter(lambda x: len(x.strip())>0,lines)
+    lines = [x for x in lines if len(x.strip())>0]
-    lines = filter(lambda x: not x.startswith("#"),lines)
+    lines = [x for x in lines if not x.startswith("#")]
-    lines = map(lambda x: x.split(),lines)
+    lines = [x.split() for x in lines]
     coord = [ [], [], [] ]
     charge = []
     for line in lines:
@@ -106,42 +106,42 @@ class GridEditor(Editor):
     edit_temp_file(self.inp,self.write_grid_file,self.read_grid_file)
 
   def write_grid_file(self,file,inp):
-    print >>file, "###########################"
+    print("###########################", file=file)
-    print >>file, "# Grid : %s"%(inp.name)
+    print("# Grid : %s"%(inp.name), file=file)
-    print >>file, "###########################"
+    print("###########################", file=file)
-    print >>file, ""
+    print("", file=file)
-    print >>file, "# Number of points along x, y, z"
+    print("# Number of points along x, y, z", file=file)
     if self.point_num is None:
-      print >>file, "Default"
+      print("Default", file=file)
     else:
-      print >>file, "%d %d %d"%tuple(self.point_num)
+      print("%d %d %d"%tuple(self.point_num), file=file)
-    print >>file, ""
+    print("", file=file)
-    print >>file, "# Coordinates of the origin (x,y,z)"
+    print("# Coordinates of the origin (x,y,z)", file=file)
     if self.origin is None:
-      print >>file, "Default"
+      print("Default", file=file)
     else:
-      print >>file, "%f %f %f"%tuple(self.origin)
+      print("%f %f %f"%tuple(self.origin), file=file)
-    print >>file, ""
+    print("", file=file)
-    print >>file, "# Coordinates of the opposite point (x,y,z)"
+    print("# Coordinates of the opposite point (x,y,z)", file=file)
     if self.opposite is None:
-      print >>file, "Default"
+      print("Default", file=file)
     else:
-      print >>file, "%f %f %f"%tuple(self.opposite)
+      print("%f %f %f"%tuple(self.opposite), file=file)
-    print >>file, ""
+    print("", file=file)
-    print >>file, "# Step sizes (x,y,z)"
+    print("# Step sizes (x,y,z)", file=file)
     if self.step_size is None:
-      print >>file, "Default"
+      print("Default", file=file)
     else:
-      print >>file, "%f %f %f"%tuple(self.step_size)
+      print("%f %f %f"%tuple(self.step_size), file=file)
 
   def read_grid_file(self,file,inp):
     lines = file.readlines()
-    lines = filter(lambda x: len(x.strip())>0,lines)
+    lines = [x for x in lines if len(x.strip())>0]
-    lines = filter(lambda x: not x.startswith("#"),lines)
+    lines = [x for x in lines if not x.startswith("#")]
 
     buffer = lines.pop(0).lower().split()
     if buffer[0] != "default":
-      self.inp.point_num = map(int,buffer)
+      self.inp.point_num = list(map(int,buffer))
     else:
       try:
        os.remove("%s/grid/point_num.gz"%self.inp.name)
@@ -150,7 +150,7 @@ class GridEditor(Editor):
 
     buffer = lines.pop(0).lower().split()
     if buffer[0] != "default":
-      self.inp.origin = map(float,buffer)
+      self.inp.origin = list(map(float,buffer))
     else:
       try:
        os.remove("%s/grid/origin.gz"%self.inp.name)
@@ -159,7 +159,7 @@ class GridEditor(Editor):
 
     buffer = lines.pop(0).lower().split()
     if buffer[0] != "default":
-      self.inp.opposite = map(float,buffer)
+      self.inp.opposite = list(map(float,buffer))
     else:
       try:
        os.remove("%s/grid/opposite.gz"%self.inp.name)
@@ -187,31 +187,31 @@ def edit(x,inp):
 #############################
 
 def write_main_file(file,inp):
-  print >>file, "####################"
+  print("####################", file=file)
-  print >>file, "# %s"%(inp.name)
+  print("# %s"%(inp.name), file=file)
-  print >>file, "####################"
+  print("####################", file=file)
-  print >>file, ""
+  print("", file=file)
-  compute = filter(lambda x: x.startswith("compute"),rw_data)
+  compute = [x for x in rw_data if x.startswith("compute")]
-  print >>file, "# Clear"
+  print("# Clear", file=file)
-  print >>file, "# --------------------\n"
+  print("# --------------------\n", file=file)
-  print >>file, '# clear(all)'
+  print('# clear(all)', file=file)
   for p in compute:
-    print >>file, '# clear(%s)'%(p[8:])
+    print('# clear(%s)'%(p[8:]), file=file)
-  print >>file, ""
+  print("", file=file)
-  print >>file, "# Computation"
+  print("# Computation", file=file)
-  print >>file, "# --------------------\n"
+  print("# --------------------\n", file=file)
-  print >>file, "nproc = %d"%(inp.nproc)
+  print("nproc = %d"%(inp.nproc), file=file)
-  print >>file, ""
+  print("", file=file)
   for p in compute:
     x = ' '
-    exec "if inp.%s: x = 'X'"%(p)
+    exec("if inp.%s: x = 'X'"%(p))
-    print >>file, "(%s) %s"%(x,p[8:])
+    print("(%s) %s"%(x,p[8:]), file=file)
-  print >>file, ""
+  print("", file=file)
-  print >>file, "# Edit"
+  print("# Edit", file=file)
-  print >>file, "# --------------------\n"
+  print("# --------------------\n", file=file)
-  print >>file, '# edit(geometry)'
+  print('# edit(geometry)', file=file)
-  print >>file, '# edit(grid_parameters)'
+  print('# edit(grid_parameters)', file=file)
-  print >>file, ""
+  print("", file=file)
 
 
 ## Execute temporary input file
@@ -235,7 +235,7 @@ def read_main_file(file,inp):
       line = line.replace("(","('").replace(")","',inp)").lower()
     else:
       line = "inp."+line
-    exec line
+    exec(line)
 
 
 def edit_temp_file(input_file,write_file,read_file,saved_file=None):
@@ -282,14 +282,14 @@ $RUNCOMMAND
     else:
       command = "${EPLF_MPIRUN} -np %d "%(inp.nproc)+command
   buffer = buffer.replace("$RUNCOMMAND",command)
-  print >>file, buffer
+  print(buffer, file=file)
   file.close()
-  os.chmod(run_script,0744)
+  os.chmod(run_script,0o744)
 
 
 def main():
   if len(sys.argv) not in [2,3]:
-    print "Syntax : %s <EZFIO_File> [input_file]"%(sys.argv[0])
+    print("Syntax : %s <EZFIO_File> [input_file]"%(sys.argv[0]))
     sys.exit(1)
   inp = InputFile(sys.argv[1])
   if len(sys.argv) == 3:

scripts/input_wrapper.py

@@ -361,10 +361,10 @@ class InputFile(object):
 
   # Build the corresponding properties
   for i in ro_data:
-    exec "%s = property(fget=get_%s,fset=None)"%(i,i)
+    exec("%s = property(fget=get_%s,fset=None)"%(i,i))
     
   for i in rw_data_full:
-    exec "%s = property(fget=get_%s,fset=set_%s)"%(i,i,i)
+    exec("%s = property(fget=get_%s,fset=set_%s)"%(i,i,i))
 
 
 

scripts/reduce_ndets.py

@@ -14,16 +14,16 @@ if len(sys.argv) == 2:
 elif len(sys.argv) == 3:
    det_thr=float(sys.argv[2])
 else:
-   print "usage: "+sys.argv[0]+" file.out det_threshold"
+   print("usage: "+sys.argv[0]+" file.out det_threshold")
    sys.exit(2)
 
 def reduce_dets():
   ezfio.set_file(firstArg)
   os.system ("cp -r %s/determinants %s/determinants.bak"%(firstArg,firstArg))
-  print "Initial number of determinants: ",ezfio.determinants_det_num 
+  print("Initial number of determinants: ",ezfio.determinants_det_num) 
   coef = ezfio.determinants_det_coef 
-  norm = sum( map(lambda x: x*x,coef) )
+  norm = sum( [x*x for x in coef] )
-  print "Norm of the initial wave function: ", sqrt(norm)
+  print("Norm of the initial wave function: ", sqrt(norm))
   dets_a, dets_b = ezfio.determinants_det_occ
 
   to_remove = []
@@ -37,9 +37,9 @@ def reduce_dets():
     coef.pop(i)
     dets_a.pop(i)
     dets_b.pop(i)
-  print "New number of determinants: ", len(coef)
+  print("New number of determinants: ", len(coef))
-  norm = sum( map(lambda x: x*x,coef) )
+  norm = sum( [x*x for x in coef] )
-  print "Norm of the new wave function: ", sqrt(norm)
+  print("Norm of the new wave function: ", sqrt(norm))
   ezfio.determinants_det_num = len(coef)
   ezfio.determinants_det_coef = coef
   ezfio.determinants_det_occ = dets_a+dets_b

scripts/to_cube.py

@@ -8,7 +8,7 @@ import common
 try:
    x, filename, grid_type = sys.argv
 except ValueError:
-   print "usage: "+sys.argv[0]+" filename grid_type"
+   print("usage: "+sys.argv[0]+" filename grid_type")
    sys.exit(2)
 
 
@@ -17,28 +17,28 @@ from ezfio import ezfio
 def main():
   ezfio.set_file(filename)
   file = open("%s_%s.cube"%(filename,grid_type),"w")
-  print >>file, " Cube File"
+  print(" Cube File", file=file)
-  print >>file, filename, grid_type
+  print(filename, grid_type, file=file)
   data = [ ezfio.nuclei_nucl_num ]+ezfio.grid_origin
-  print >>file, "%5d%12.6f%12.6f%12.6f" % tuple(data)
+  print("%5d%12.6f%12.6f%12.6f" % tuple(data), file=file)
   data = [ ezfio.grid_num_x, ezfio.grid_step_size[0],0.,0. ]
-  print >>file, "%5d%12.6f%12.6f%12.6f" % tuple(data)
+  print("%5d%12.6f%12.6f%12.6f" % tuple(data), file=file)
   data = [ ezfio.grid_num_y, 0., ezfio.grid_step_size[1],0. ]
-  print >>file, "%5d%12.6f%12.6f%12.6f" % tuple(data)
+  print("%5d%12.6f%12.6f%12.6f" % tuple(data), file=file)
   data = [ ezfio.grid_num_z, 0.,0., ezfio.grid_step_size[2] ]
-  print >>file, "%5d%12.6f%12.6f%12.6f" % tuple(data)
+  print("%5d%12.6f%12.6f%12.6f" % tuple(data), file=file)
 
   charge = ezfio.nuclei_nucl_charge
   coord = ezfio.nuclei_nucl_coord
   for i in range(ezfio.nuclei_nucl_num):
     data = [ charge[i], charge[i], coord[0][i], coord[1][i], coord[2][i] ]
-    print >>file, "%5d%12.6f%12.6f%12.6f%12.6f" % tuple(data)
+    print("%5d%12.6f%12.6f%12.6f%12.6f" % tuple(data), file=file)
 
   data = getattr(ezfio,"grid_data_%s"%grid_type)
-  for i in xrange(0,ezfio.grid_num_x):
+  for i in range(0,ezfio.grid_num_x):
-   for j in xrange(0,ezfio.grid_num_y):
+   for j in range(0,ezfio.grid_num_y):
-    for k in xrange(0,ezfio.grid_num_z,6):
+    for k in range(0,ezfio.grid_num_z,6):
-     for l in xrange(k,min(ezfio.grid_num_z,k+6)):
+     for l in range(k,min(ezfio.grid_num_z,k+6)):
       file.write (" %12.5E"%data[l][j][i])
      file.write ("\n")
   file.close()

scripts/to_ezfio.py

@@ -1,9 +1,9 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 import common
 import sys,os,time
+from functools import reduce
 
-sys.path = [ "/home/scemama/resultsFile" ]+sys.path
 from resultsFile import *
 
 # Check command line
@@ -14,14 +14,14 @@ if len(sys.argv) == 2:
 elif len(sys.argv) == 3:
    State=int(sys.argv[2])
 else:
-   print "usage: "+sys.argv[0]+" file.out"
+   print("usage: "+sys.argv[0]+" file.out")
    sys.exit(2)
 
 firstArg = sys.argv[1]
 
 file = getFile(firstArg)
 file.convert_to_cartesian()
-print firstArg, 'recognized as', str(file).split('.')[-1].split()[0]
+print(firstArg, 'recognized as', str(file).split('.')[-1].split()[0])
 
 from ezfio import ezfio
 
@@ -31,6 +31,7 @@ def write_ezfioFile(res,filename):
 # Electrons
   ezfio.electrons_elec_alpha_num = res.num_alpha
   ezfio.electrons_elec_beta_num = res.num_beta
+  ezfio.electrons_elec_num = res.num_beta + res.num_alpha
 
 # Nuclei
   ezfio.nuclei_nucl_num = len(res.geometry)
@@ -70,16 +71,17 @@ def write_ezfioFile(res,filename):
          at.append(i+1)
     num_prim.append(len(b.prim))
     s = b.sym
-    power_x.append( string.count(s,"x") ) 
+    power_x.append( s.count("x") ) 
-    power_y.append( string.count(s,"y") )
+    power_y.append( s.count("y") )
-    power_z.append( string.count(s,"z") )
+    power_z.append( s.count("z") )
     coefficient.append(  b.coef )
     exponent.append( [ p.expo for p in b.prim ] )
   ezfio.ao_basis_ao_num = len(res.basis)
   ezfio.ao_basis_ao_nucl = at
   ezfio.ao_basis_ao_prim_num = num_prim
   ezfio.ao_basis_ao_power = power_x+power_y+power_z
-  prim_num_max = ezfio.get_ao_basis_ao_prim_num_max()
+  prim_num_max = max(num_prim)
+  ezfio.ao_basis_ao_prim_num_max = prim_num_max
   len_res_basis = len(res.basis)
   for i in range(len(res.basis)):
     coefficient[i] += [ 0. for j in range(len(coefficient[i]),prim_num_max) ]
@@ -165,8 +167,12 @@ def write_ezfioFile(res,filename):
 
   coef = reduce(lambda x, y: x+y,res.det_coefficients,[])
 
+  ezfio.mo_basis_mo_closed_num  = len(res.closed_mos)
+  ezfio.mo_basis_mo_active_num  = len(res.active_mos)
+  ezfio.mo_basis_mo_virtual_num = len(res.virtual_mos)
+
   if len(dets_a[0]) > 0:
-   for i in xrange(len(coef),0,-1):
+   for i in range(len(coef),0,-1):
      i -= 1
      if abs(coef[i]) < det_thr :
        dets_a.pop(i)
@@ -183,7 +189,7 @@ def write_ezfioFile(res,filename):
 
   ezfio.compute_eplf = True
   for i in "density density_lapl elf elf_grad eplf_lapl density_grad elf_grad elf_lapl eplf_grad".split():
-    exec "ezfio.compute_%s = False" % i
+    exec("ezfio.compute_%s = False" % i)
 
 
 def main():