Install resultsFile

Makefile

@@ -44,6 +44,11 @@ emsl: EMSL_Basis
 binary: 
 	$(QPACKAGE_ROOT)/scripts/make_binary.sh
 
+resultsFile: 
+	$(info $(BLUE)===== Fetching resultsFile from the web ===== $(BLACK))
+	@sleep 1
+	$(QPACKAGE_ROOT)/scripts/install_resultsFile.sh
+
 EZFIO: bin/irpf90
 	$(info $(BLUE)===== Fetching EZFIO from the web ===== $(BLACK))
 	@sleep 1

scripts/install_emsl.sh

@@ -4,10 +4,10 @@
 # Mon Jan 12 12:57:19 CET 2015
 
 BASE="EMSL_Basis_Set_Exchange_Local"
-URL="https://github.com/LCPQ/EMSL_Basis_Set_Exchange_Local/archive/master.tar.gz"
+URL="https://github.com/LCPQ/${BASE}/archive/master.tar.gz"
 
-${QPACKAGE_ROOT}/scripts/fetch_from_web.py ${URL} ${QPACKAGE_ROOT}/EMSL_Basis.tar.gz
+${QPACKAGE_ROOT}/scripts/fetch_from_web.py ${URL} ${QPACKAGE_ROOT}/${BASE}.tar.gz
-tar -zxf EMSL_Basis.tar.gz && rm EMSL_Basis.tar.gz ||exit 1
+tar -zxf ${BASE}.tar.gz && rm ${BASE}.tar.gz ||exit 1
-mv EMSL_Basis_Set_Exchange_Local-master EMSL_Basis
+mv ${BASE}-master EMSL_Basis
 
 

scripts/install_resultsFile.sh

@@ -0,0 +1,12 @@
+#!/bin/bash
+#
+# Installs the resultsFile Python library
+# Mon Jan 19 15:08:18 CET 2015
+
+URL="https://github.com/LCPQ/resultsFile/archive/master.tar.gz"
+
+${QPACKAGE_ROOT}/scripts/fetch_from_web.py ${URL} ${QPACKAGE_ROOT}/resultsFile.tar.gz
+tar -zxf resultsFile.tar.gz && rm resultsFile.tar.gz ||exit 1
+mv resultsFile-master resultsFile
+
+

scripts/qp_convert.py

@@ -0,0 +1,293 @@
+#!/usr/bin/env python
+
+import sys,os
+try:
+  QPACKAGE_ROOT = os.environ["QPACKAGE_ROOT"]
+except:
+  print "Error: QPACKAGE_ROOT environment variable not found."
+  sys.exit(1)
+
+sys.path =  [ QPACKAGE_ROOT+"/EZFIO/Python", QPACKAGE_ROOT+"/resultsFile" ]+sys.path
+from ezfio import ezfio
+import ezfio as ez
+print "EZFIO: ", os.path.dirname(ez.__file__)
+
+try:
+  from resultsFile import *
+except:
+  print "Error: resultsFile Python library not installed"
+  sys.exit(1)
+
+
+def write_ezfioFile(res,filename):
+  res.clean_uncontractions()
+  ezfio.set_file(filename)
+
+# Electrons
+  ezfio.set_electrons_elec_alpha_num(res.num_alpha)
+  ezfio.set_electrons_elec_beta_num(res.num_beta)
+
+# Nuclei
+  ezfio.set_nuclei_nucl_num(len(res.geometry))
+  charge = []
+  coord = []
+  coord_x = []
+  coord_y = []
+  coord_z = []
+  for a in res.geometry:
+    charge.append(a.charge)
+    if res.units == 'BOHR':
+      coord_x.append(a.coord[0])
+      coord_y.append(a.coord[1])
+      coord_z.append(a.coord[2])
+    else:
+      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)
+  label = map(lambda x: x.name, res.geometry)
+  ezfio.set_nuclei_nucl_label(label)
+  ezfio.set_nuclei_nucl_coord(coord_x+coord_y+coord_z)
+
+# Basis
+  basis = res.uncontracted_basis
+  geom  = res.geometry
+
+# MO 
+  MoTag = res.determinants_mo_type
+  ezfio.set_mo_basis_mo_label('Orthonormalized')
+  MO_type = MoTag
+  allMOs = res.uncontracted_mo_sets[MO_type]
+
+
+  closed = [ (allMOs[i].eigenvalue,i) for i  in res.closed_mos ]
+  active = [ (allMOs[i].eigenvalue,i) for i  in res.active_mos ]
+  virtual =[ (allMOs[i].eigenvalue,i) for i  in res.virtual_mos ]
+
+# closed.sort()
+# active.sort()
+# virtual.sort()
+  closed = map( lambda x: x[1], closed)
+  active = map( lambda x: x[1], active)
+  virtual = map( lambda x: x[1], virtual)
+  MOindices = closed + active + virtual
+
+  MOs = []
+  for i in MOindices:
+    MOs.append(allMOs[i])
+
+  mo_tot_num = len(MOs)
+  while len(MOindices) < mo_tot_num:
+    MOindices.append(len(MOindices))
+
+  MOmap = list(MOindices)
+  for i in range(len(MOindices)):
+    MOmap[i] = MOindices.index(i)
+
+  energies = []
+  for i in xrange(mo_tot_num):
+    energies.append(MOs[i].eigenvalue)
+
+  if res.occ_num is not None:
+    OccNum    = []
+    for i in MOindices:
+      OccNum.append(res.occ_num[MO_type][i])
+
+    while len(OccNum) < mo_tot_num:
+      OccNum.append(0.)
+
+  MoMatrix = []
+  sym0 = [ i.sym for i in res.mo_sets[MO_type] ]
+  sym  = [ i.sym for i in res.mo_sets[MO_type] ]
+  for i in xrange(len(sym)):
+    sym[MOmap[i]] = sym0[i]
+
+  MoMatrix = []
+  for i in xrange(len(MOs)):
+     m = MOs[i]
+     for coef in m.vector:
+         MoMatrix.append(coef)
+
+  while len(MoMatrix) < len(MOs[0].vector)**2:
+    MoMatrix.append(0.)
+
+  ezfio.set_mo_basis_mo_tot_num(mo_tot_num)
+  ezfio.set_mo_basis_mo_occ(OccNum)
+
+
+  res.clean_contractions()
+  # AO Basis
+  import string
+  at = []
+  num_prim = []
+  magnetic_number = []
+  angular_number = []
+  power_x = []
+  power_y = []
+  power_z = []
+  coefficient = []
+  exponent = []
+  res.convert_to_cartesian()
+  for b in res.basis:
+    c = b.center
+    for i,atom in enumerate(res.geometry):
+      if atom.coord == c:
+         at.append(i+1)
+    num_prim.append(len(b.prim))
+    s = b.sym
+    power_x.append( string.count(s,"x") )
+    power_y.append( string.count(s,"y") )
+    power_z.append( string.count(s,"z") )
+    coefficient.append(  b.coef )
+    exponent.append( [ p.expo for p in b.prim ] )
+  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)
+  prim_num_max = ezfio.get_ao_basis_ao_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) ]
+    exponent[i]    += [ 0. for j in range(len(exponent[i]),prim_num_max) ]
+  coefficient = reduce(lambda x, y: x+y, coefficient, [])
+  exponent = reduce(lambda x, y: x+y, exponent, [])
+  coef = []
+  expo = []
+  for i in range(prim_num_max):
+   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.set_ao_basis_ao_basis("Read by resultsFile")
+
+# Apply threshold to determinants
+  if len(res.determinants) == 1:
+    sorted_determinants = [ (-1.,1.,res.determinants[0]) ]
+  else:
+    sorted_determinants = []
+    for i,j in zip(res.det_coefficients[0],res.determinants):
+      sorted_determinants.append((-abs(i),i,j))
+  sorted_determinants.sort()
+  norm = 0.0
+  for length, (a,b,c) in enumerate(sorted_determinants):
+    if -a < det_threshold:
+      length -=1
+      break
+    norm += a**2
+  norm = sqrt(norm)
+  length += 1
+  for i in xrange(length):
+    a = sorted_determinants[i]
+    sorted_determinants[i] = (a[0],a[1]/norm,a[2])
+  sorted_determinants = sorted_determinants[:length]
+
+# MOs
+  mo_tot_num = len(res.mo_sets[MoTag])
+  closed_mos = res.closed_mos
+  active_mos = res.active_mos
+  virtual_mos = res.virtual_mos
+  to_remove = []
+  to_add = []
+  for i in active_mos:
+    found = False
+    for (a,b,c) in sorted_determinants:
+      if i in c['alpha']+c['beta']:
+        found = True
+        break
+    if not found:
+      to_remove.append(i)
+      to_add.append(i)
+  virtual_mos = to_add + virtual_mos
+  for i in active_mos:
+    always = True
+    for (a,b,c) in sorted_determinants:
+      if not (i in c['alpha'] and i in c['beta']):
+        always = False
+        break
+    if always:
+      to_remove.append(i)
+      closed_mos.append(i)
+  for i in to_remove:
+    active_mos.remove(i)
+
+
+  MOindices = closed_mos + active_mos + virtual_mos
+  while len(MOindices) < mo_tot_num:
+    MOindices.append(len(MOindices))
+  MOmap = list(MOindices)
+  for i in range(len(MOindices)):
+    MOmap[i] = MOindices.index(i)
+
+
+  ezfio.set_mo_basis_mo_tot_num(mo_tot_num)
+
+  mo = []
+  for i in MOindices:
+    mo.append(res.mo_sets[MoTag][i])
+
+  if len(mo) < mo_tot_num:
+    newmo = orbital()
+    newmo.eigenvalue = 0.
+    newmo.vector = [0. for i in range(mo_tot_num)]
+    newmo.vector[len(mo)] = 1.
+    while len(mo) < mo_tot_num:
+      mo.append(newmo)
+  Energies  = [ m.eigenvalue for m in mo ]
+
+  if res.occ_num is not None:
+    OccNum    = []
+    for i in MOindices:
+      OccNum.append(res.occ_num[MoTag][i])
+
+    while len(OccNum) < mo_tot_num:
+      OccNum.append(0.)
+    ezfio.set_mo_basis_mo_occ(OccNum)
+
+  cls = [ "v" for i in mo ]
+  for i in closed_mos:
+    cls[MOmap[i]] = 'c'
+  for i in active_mos:
+    cls[MOmap[i]] = 'a'
+
+  sym0 = [ i.sym for i in res.mo_sets[MoTag] ]
+  sym  = [ i.sym for i in res.mo_sets[MoTag] ]
+  for i in xrange(len(sym)):
+    sym[MOmap[i]] = sym0[i]
+
+  MoMatrix = []
+  for m in mo:
+     for coef in m.vector:
+         MoMatrix.append(coef)
+  while len(MoMatrix) < len(mo[0].vector)**2:
+    MoMatrix.append(0.)
+  ezfio.set_mo_basis_mo_coef(MoMatrix)
+  del MoMatrix
+
+
+
+if __name__ == '__main__':
+  # Check command line
+
+  det_threshold = 0.
+
+  if len(sys.argv) == 2:
+   State=0
+  elif len(sys.argv) == 3:
+   State=int(sys.argv[2])
+  else:
+   print "usage: "+sys.argv[0]+" file.out [state]"
+   sys.exit(2)
+
+  firstArg = sys.argv[1]
+
+  file = getFile(firstArg)
+  print firstArg, 'recognized as', str(file).split('.')[-1].split()[0]
+
+  filename = firstArg+".ezfio"
+  write_ezfioFile(file,filename)
+
+
+
+
+

setup_environment.sh

@@ -47,7 +47,7 @@ source quantum_package.rc
 make EZFIO
 if [[ ! -d ${QPACKAGE_ROOT}/EZFIO ]]
 then
-  echo $RED "Error in IRPF90 installation" $BLACK
+  echo $RED "Error in EZFIO installation" $BLACK
   exit 1
 fi
 
@@ -58,6 +58,14 @@ then
   exit 1
 fi
 
+make resultsFile
+if [[ ! -d ${QPACKAGE_ROOT}/resultsFile ]]
+then
+  echo $RED "Error in resultsFile installation" $BLACK
+  exit 1
+fi
+
+
 echo $RED "
 =======================================================
 To complete the installation, add the following line to