Added to_cube.py

Makefile

@@ -2,7 +2,7 @@
 all: bin/eplf
 
 EZFIO/config/eplf.config: EZFIO.tar.gz
-	tar -zxvf EZFIO.tar.gz
+	tar -zxf EZFIO.tar.gz
 	cd EZFIO ; ./configure
 	if [ -e $@ ] ; then rm $@ ; fi
 	ln -s $$PWD/eplf.config $@
@@ -16,7 +16,6 @@ bin/ezfio.py: EZFIO/lib/libezfio.so
 
 bin/eplf: EZFIO/lib/libezfio.so
 	make -C src
-	mv src/eplf bin
 
 clean:
 	- rm -rf EZFIO

bin/common.py

@@ -0,0 +1,5 @@
+#!/usr/bin/env python
+
+import sys, os
+wd = os.path.dirname(__file__)
+sys.path = [ wd+"/../EZFIO/Python" ]+sys.path

bin/to_cube.py

@@ -0,0 +1,46 @@
+#!/usr/bin/env python
+
+import sys
+import common
+
+# Check command line
+
+try:
+   x, filename, grid_type = sys.argv
+except ValueError:
+   print "usage: "+sys.argv[0]+" filename grid_type"
+   sys.exit(2)
+
+
+from ezfio import ezfio
+
+def main():
+  ezfio.set_file(filename)
+  file = open("%s_%s.cube"%(filename,grid_type),"w")
+  print >>file, " Cube File"
+  print >>file, filename, grid_type
+  data = [ ezfio.nuclei_nucl_num ]+ezfio.grid_origin
+  print >>file, "%5d%12.6f%12.6f%12.6f" % tuple(data)
+  data = [ ezfio.grid_num_x, ezfio.grid_step_size[0],0.,0. ]
+  print >>file, "%5d%12.6f%12.6f%12.6f" % tuple(data)
+  data = [ ezfio.grid_num_y, 0., ezfio.grid_step_size[1],0. ]
+  print >>file, "%5d%12.6f%12.6f%12.6f" % tuple(data)
+  data = [ ezfio.grid_num_z, 0.,0., ezfio.grid_step_size[2] ]
+  print >>file, "%5d%12.6f%12.6f%12.6f" % tuple(data)
+
+  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)
+
+  data = getattr(ezfio,"grid_data_%s"%grid_type)
+  for i in xrange(0,ezfio.grid_num_x):
+   for j in xrange(0,ezfio.grid_num_y):
+    for k in xrange(0,ezfio.grid_num_z,6):
+     for l in xrange(k,min(ezfio.grid_num_z,k+6)):
+      file.write (" %12.5E"%data[l][j][i])
+     file.write ("\n")
+  file.close()
+
+main()

bin/to_ezfio.py

@@ -1,11 +1,9 @@
 #!/usr/bin/env python
 
+import common
 import sys,os,time
 
-wd = os.path.dirname(__file__)
 sys.path = [ "/home/scemama/resultsFile" ]+sys.path
-sys.path = [ wd+"/../EZFIO/Python" ]+sys.path
-
 from resultsFile import *
 
 # Check command line
@@ -29,11 +27,11 @@ def write_ezfioFile(res,filename):
   ezfio.set_file(filename)
 
 # Electrons
-  ezfio.set_electrons_elec_alpha_num(res.num_alpha)
-  ezfio.set_electrons_elec_beta_num(res.num_beta)
+  ezfio.electrons_elec_alpha_num = res.num_alpha
+  ezfio.electrons_elec_beta_num = res.num_beta
 
 # Nuclei
-  ezfio.set_nuclei_nucl_num(len(res.geometry))
+  ezfio.nuclei_nucl_num = len(res.geometry)
   charge = []
   coord = []
   coord_x = []
@@ -49,8 +47,8 @@ def write_ezfioFile(res,filename):
       coord_x.append(a.coord[0]/a0)
       coord_y.append(a.coord[1]/a0)
       coord_z.append(a.coord[2]/a0)
-  ezfio.set_nuclei_nucl_charge(charge)
-  ezfio.set_nuclei_nucl_coord(coord_x+coord_y+coord_z)
+  ezfio.nuclei_nucl_charge = charge
+  ezfio.nuclei_nucl_coord = coord_x+coord_y+coord_z
 
 # AO Basis
   import string
@@ -87,10 +85,10 @@ def write_ezfioFile(res,filename):
   if not is_cartesian:
      print 'Only cartesian basis functions work...'
      sys.exit(0)
-  ezfio.set_ao_basis_ao_num(len(res.basis))
-  ezfio.set_ao_basis_ao_nucl(at)
-  ezfio.set_ao_basis_ao_prim_num(num_prim)
-  ezfio.set_ao_basis_ao_power(power_x+power_y+power_z)
+  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()
   len_res_basis = len(res.basis)
   for i in range(len(res.basis)):
@@ -104,17 +102,17 @@ def write_ezfioFile(res,filename):
    for j in range(i,len(coefficient),prim_num_max):
     coef.append ( coefficient[j] )
     expo.append ( exponent[j] )
-  ezfio.set_ao_basis_ao_coef(coef)
-  ezfio.set_ao_basis_ao_expo(expo)
+  ezfio.ao_basis_ao_coef = coef
+  ezfio.ao_basis_ao_expo = expo
 
 # MOs
   NumOrbSym = [ s[1] for s in res.symmetries ]
   mo_tot_num = sum(NumOrbSym)
-  ezfio.set_mo_basis_mo_tot_num(mo_tot_num)
+  ezfio.mo_basis_mo_tot_num = mo_tot_num
 
   MoTag = res.mo_types[-1]
   if res.occ_num.keys != []:
-    ezfio.set_mo_basis_mo_occ(res.occ_num[MoTag])
+    ezfio.mo_basis_mo_occ = res.occ_num[MoTag]
 
   mo = res.mo_sets[MoTag]
   if len(mo) < mo_tot_num:
@@ -124,20 +122,20 @@ def write_ezfioFile(res,filename):
     while len(mo) < mo_tot_num:
       mo.append(newmo)
   Energies  = [ m.eigenvalue for m in mo ]
-  ezfio.set_mo_basis_mo_energy(Energies)
+  ezfio.mo_basis_mo_energy = Energies
 
   if res.occ_num is not None:
     OccNum    = res.occ_num[MoTag]
     while len(OccNum) < mo_tot_num:
       OccNum.append(0.)
-    ezfio.set_mo_basis_mo_occ(OccNum)
+    ezfio.mo_basis_mo_occ = OccNum
 
   cls       = [ "v" for i in mo ]
   for i in res.closed_mos:
     cls[i] = 'c'
   for i in res.active_mos:
     cls[i] = 'a'
-  ezfio.set_mo_basis_mo_classif(cls)
+  ezfio.mo_basis_mo_classif = cls
 
   MoMatrix = []
   for m in mo:
@@ -145,7 +143,7 @@ def write_ezfioFile(res,filename):
          MoMatrix.append(coef)
   while len(MoMatrix) < len(mo[0].vector)**2:
     MoMatrix.append(0.)
-  ezfio.set_mo_basis_mo_coef(MoMatrix)
+  ezfio.mo_basis_mo_coef = MoMatrix
 
 # Determinants
   closed_mos = res.closed_mos
@@ -169,17 +167,18 @@ def write_ezfioFile(res,filename):
   coef = reduce(lambda x, y: x+y,res.det_coefficients,[])
 
   if len(dets_a[0]) > 0:
-   ezfio.set_determinants_det_num(len(dets_a))
-   ezfio.set_determinants_det_coef(coef)
-   ezfio.set_determinants_det_occ(dets_a+dets_b)
+   ezfio.determinants_det_num = len(dets_a)
+   ezfio.determinants_det_coef = coef
+   ezfio.determinants_det_occ = dets_a+dets_b
   else:
-   ezfio.set_determinants_det_num(1)
-   ezfio.set_determinants_det_coef([1.])
-   ezfio.set_determinants_det_occ(dets_a+dets_b)
+   ezfio.determinants_det_num = 1
+   ezfio.determinants_det_coef = [1.]
+   ezfio.determinants_det_occ = dets_a+dets_b
 
 
-  ezfio.set_compute_eplf(True)
+  ezfio.compute_eplf = True
   for i in "density density_lapl elf_grad eplf_lapl density_grad elf_grad elf_lapl eplf_grad".split():
-    exec "ezfio.set_compute_%s(False)" % i
+    exec "ezfio.compute_%s = False" % i
 
 write_ezfioFile(file,firstArg+".ezfio")
+

eplf.config

@@ -37,9 +37,9 @@ grid
  step_size           real (3)
  origin              real (3)
  opposite            real (3)
- num_x               integer           = grid_point_num(1)
- num_y               integer           = grid_point_num(2)
- num_z               integer           = grid_point_num(3)
+ num_x               integer           = at(grid_point_num,1)
+ num_y               integer           = at(grid_point_num,2)
+ num_z               integer           = at(grid_point_num,3)
 
 grid_data
  eplf                real (grid_num_x,grid_num_y,grid_num_z)

src/Makefile

@@ -4,7 +4,7 @@ SRC=
 OBJ=
 
 eplf: main
-	mv main eplf
+	mv main ../bin/eplf
 
 include irpf90.make
 

src/elf_function.irp.f

@@ -1,7 +1,7 @@
 BEGIN_PROVIDER [ double precision, kinetic_energy_alpha_p ]
  implicit none
  BEGIN_DOC  
-! Kinetic Energy
+! Alpha Kinetic Energy
  END_DOC
 
  kinetic_energy_alpha_p = 0.d0
@@ -18,7 +18,7 @@ END_PROVIDER
 BEGIN_PROVIDER [ double precision, kinetic_energy_beta_p ]
  implicit none
  BEGIN_DOC  
-! Kinetic Energy
+! Beta Kinetic Energy
  END_DOC
 
  kinetic_energy_beta_p = 0.d0
@@ -35,6 +35,7 @@ END_PROVIDER
 BEGIN_PROVIDER [ double precision, kinetic_energy_p ]
  implicit none
  BEGIN_DOC  
+! Kinetic energy
  END_DOC
  kinetic_energy_p = kinetic_energy_alpha_p + kinetic_energy_beta_p
 END_PROVIDER

src/ezfio_interface.irp.f

@@ -92,6 +92,20 @@ subroutine get_$X(res)
  IRP_ENDIF
 !$OMP END CRITICAL (ezfio_critical)
 
+end
+
+subroutine set_$X(res)
+ $T :: res$D
+ implicit none
+ integer :: ierr
+ logical :: exists
+!$OMP CRITICAL (ezfio_critical)
+ PROVIDE ezfio_filename
+ if (mpi_master) then
+   call ezfio_set_$X(res)
+ endif
+!$OMP END CRITICAL (ezfio_critical)
+
 end
 """
 

src/grid.irp.f

@@ -60,10 +60,10 @@
  grid_y_num = Npoints(2)
  grid_z_num = Npoints(3)
 
- call get_grid_point_num(Npoints)
- call get_grid_origin(origin)
- call get_grid_opposite(opposite)
- call get_grid_step_size(step_size)
+ call set_grid_point_num(Npoints)
+ call set_grid_origin(origin)
+ call set_grid_opposite(opposite)
+ call set_grid_step_size(step_size)
 
 END_PROVIDER