Merge Anouar (#69)

* Converter for Pyscf

* Scripts to read integrals and metadata and generates fake ezfio

* update README

* Trying to fix jbuilder bug in OCaml installation

* Do AO->MO  transformation from pyscf in QP

* Optimization of reader due to format creux

* Optimization of reader due to format creux 2

plugins/QMC/qp_convert_qmcpack_to_ezfio.py

@@ -333,11 +333,14 @@ if do_pseudo:
 # |_/ (/_ |_ 
 #
 
+
 psi_coef = ezfio.get_determinants_psi_coef()
 psi_det = ezfio.get_determinants_psi_det()
 bit_kind = ezfio.get_determinants_bit_kind()
 
 
+nexcitedstate = ezfio.get_determinants_n_states()
+
 print ""
 print "BEGIN_DET"
 print ""
@@ -349,7 +352,11 @@ if "QP_STATE" in os.environ:
   state = int(os.environ["QP_STATE"])-1
 else:
   state = 0
-psi_coef = psi_coef[state]
+
+psi_coef_small = psi_coef[state]
+
+
+
 
 encode = 8*bit_kind
 
@@ -359,11 +366,35 @@ def bindigits(n, bits):
 
 decode = lambda det: ''.join(bindigits(i,encode)[::-1] for i in det)[:mo_num]
 
-for coef, (det_a, det_b) in zip(psi_coef, psi_det):
+MultiDetAlpha = []
+MultiDetBeta = []
+for coef, (det_a, det_b) in zip(psi_coef_small, psi_det):
 
         print coef
-        print decode(det_a)
-        print decode(det_b)
+        MyDetA=decode(det_a)
+        MyDetB=decode(det_b)
+        print MyDetA 
+        print MyDetB
         print ''
-
+        MultiDetAlpha.append( det_a  )
+	MultiDetBeta.append( det_b  )
 print "END_DET"
+
+import h5py
+H5_qmcpack=h5py.File('MultiDet.h5','w')
+groupMultiDet=H5_qmcpack.create_group("MultiDet")
+groupMultiDet.create_dataset("NbDet",(1,),dtype="f8",data=len(psi_coef_small))
+
+groupMultiDet.create_dataset("Coeff",(len(psi_coef_small),),dtype="f8",data=psi_coef)
+groupMultiDet.create_dataset("nstate",(1,),dtype="i4",data=len(MyDetA))
+groupMultiDet.create_dataset("nexcitedstate",(1,),dtype="i4",data=nexcitedstate)
+groupMultiDet.create_dataset("Nbits",(1,),dtype="i4",data=len(det_a))
+
+print "temp=",MultiDetAlpha[0]
+mylen="S"+str(len(MyDetA))
+groupMultiDet.create_dataset("CI_Alpha",(len(psi_coef_small),len(det_a)),dtype='i8',data=MultiDetAlpha)
+
+mylen="S"+str(len(MyDetB))
+groupMultiDet.create_dataset("CI_Beta",(len(psi_coef_small),len(det_b)),dtype='i8',data=MultiDetBeta)
+
+H5_qmcpack.close()

plugins/pyscf/NEEDED_CHILDREN_MODULES

@@ -0,0 +1 @@
+

plugins/pyscf/PyscfToQp.py

@@ -0,0 +1,137 @@
+
+import numpy,re,sys
+
+def pyscf2QP(cell,mf, kpts=[], int_threshold = 1E-15):
+   # The integral will be not printed in they are bellow that
+
+
+  PBC=False
+  ComputeMode= re.split('[. ]', str(mf))
+  print 'ComputeMode=',ComputeMode
+
+  for n in ComputeMode:
+     if n in ("UHF","KUHF","UKS"):
+           sys.exit('Unrestricted calculation unsupported in Quantum Package')
+     if n == "pbc":
+           PBC=True
+
+  if PBC and len(kpts) == 0:
+	sys.exit("ERROR (read!): You need to specify explicit the list of K-point (including gamma)")
+
+  print 'Performing PBC?:',PBC
+  if PBC:
+      from pyscf.pbc import ao2mo
+      from pyscf.pbc import tools
+  else:
+      from pyscf import ao2mo
+
+  natom = len(cell.atom_coords())
+  print 'n_atom',   natom
+  print 'num_elec', cell.nelectron
+  print 'nucl_num', len(cell.atom_coords())
+
+
+  print ''
+  mo_coeff = mf.mo_coeff # List of mo_coeff for each k-point
+  if not PBC:
+      nmo = mo_coeff.shape[1]
+  else:
+    nmo = mo_coeff[0].shape[1]
+  
+
+  # Wrote all the parameter need to creat a dummy EZFIO folder who will containt the integral after.
+  # More an implentation detail than a real thing
+  with open('param','w') as f:
+        f.write(' '.join(map(str,(cell.nelectron, nmo, natom))))
+  #                             _                             
+  # |\ |      _ |  _   _. ._   |_)  _  ._      |  _ o  _  ._  
+  # | \| |_| (_ | (/_ (_| |    | \ (/_ |_) |_| | _> | (_) | | 
+  #                                    |                      
+  
+  print 'mf, cell', mf.energy_nuc(), cell.energy_nuc()
+  shift = tools.pbc.madelung(cell, numpy.zeros(3))*cell.nelectron * -.5 if PBC else 0
+  e_nuc = cell.energy_nuc() + shift
+
+  print 'nucl_repul', e_nuc
+  with open('e_nuc','w') as f:
+         f.write(str(e_nuc))
+ 
+ 
+  from itertools import product
+ 
+  # ___                                              
+  #  |  ._ _|_  _   _  ._ _. |  _   |\/|  _  ._   _  
+  # _|_ | | |_ (/_ (_| | (_| | _>   |  | (_) | | (_) 
+  #                 _|                              
+  
+  if PBC:
+        h_ao = ('kinetic', mf.get_hcore(kpts=kpts) ) # Give only one k point ?
+        dummy_ao = ('nuclear', numpy.zeros( (len(kpts),nmo,nmo), dtype=numpy.float ))
+  else:
+        h_ao = ('kinetic', mf.get_hcore() )
+        dummy_ao = ('nuclear', numpy.zeros( (nmo,nmo), dtype=numpy.float ))
+    
+  def gen_mono_MO(mo_coeff,l_int,shift=0):
+         # 2Id transfortion Transformation. For now we handle only one or zero K point.
+         print 'l_int.shape=',l_int.shape
+ 
+         l_int_mo = reduce(numpy.dot, (mo_coeff.T, l_int, mo_coeff)) #This formula is only right for one kpt.
+ 
+	 print 'l_int_mo=',l_int_mo
+
+         for i,j in product(range(nmo), repeat=2):
+                 int_ = l_int_mo[i,j]
+                 yield (i+1+shift,j+1+shift, int_)
+ 
+  # Print 
+  for name, ao in (h_ao,dummy_ao):
+         with open('%s_mo' % name,'w') as f:
+		 print '%s_mo' % name
+		 if not PBC:
+                 	for mono in gen_mono_MO(mo_coeff,ao):
+                        	 f.write('%s %s %s\n'% mono)
+ 		 else:
+			for i,(m,a) in enumerate(zip(mo_coeff,ao)):
+			   for mono in gen_mono_MO(m,a,i):
+                                 f.write('%s %s %s\n'% mono)
+
+  # ___                              _    
+  #  |  ._ _|_  _   _  ._ _. |  _   |_) o 
+  # _|_ | | |_ (/_ (_| | (_| | _>   |_) | 
+  #                 _|                    
+  #
+
+  def ao2mo_amazing(mo_coeff):
+	if PBC:
+		eri_4d= mf.with_df.ao2mo(mo_coeff,compact=False)
+	else:
+		eri_4d= ao2mo.kernel(cell,mo_coeff,compact=False)
+	
+	return eri_4d.reshape((nmo,)*4)
+
+
+  def write_amazing(eri_4d, shift=0):
+
+    # HANDLE 8 FOLD by Scemama way. Maybe we can use compact=True
+    for l in range(nmo):
+      for k in range(nmo):
+        for j in range(l,nmo):
+                for i in range(max(j,k),nmo):
+                        v = eri_4d[i,k,j,l]
+                        if abs(v) > int_threshold:
+                              f.write('%s %s %s %s %s\n' % (i+1+shift,j+1+shift,k+1+shift,l+1+shift,v))
+
+
+  if PBC: 
+     eri_4d= mf.with_df.ao2mo(mo_coeff[0],compact=False)
+  else: #Molecular
+     eri_4d= ao2mo.kernel(cell,mo_coeff,compact=False)
+
+  eri_4d = eri_4d.reshape((nmo,)*4)
+
+  f = open('bielec_mo','w')
+  for i,mc in enumerate(mo_coeff):
+	eri = ao2mo_amazing(mc)
+	write_amazing(eri, nmo*i)
+
+

plugins/pyscf/README.rst

@@ -0,0 +1,21 @@
+=====
+pyscf
+=====
+Converter from Pyscf to Quatum Package for Molecules AND Solids
+Import this script in your Pyscf input. 
+
+
+Use as follow:
+```
+   from MolPyscfToQP import pyscf2QP
+   pyscf2QP(cell,mf,kpts=kpts,int_threshold = 1E-15)
+
+```
+Needed Modules
+==============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+Documentation
+=============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.

plugins/pyscf/pyscf.main.irp.f

@@ -0,0 +1,38 @@
+program pyscf
+  implicit none
+  BEGIN_DOC
+! TODO
+  END_DOC
+  print *, '  _/                              '
+  print *, ' -:\_?,     _Jm####La             '
+  print *, 'J"(:" >  _]#AZ#Z#UUZ##,           '
+  print *, '_,::./   %(|i%12XmX1*1XL      _?, '
+  print *, '  \..\ _\(vmWQwodY+ia%lnL  _",/ ( '
+  print *, '   .:< ]J=mQD?WXn<uQWmmvd, -.-:=!'
+  print *, '   "{Z jC]QW|=3Zv)Bi3BmXv3  =   _7'
+  print *, '    ]h[Z6)WQ;)jZs]C;|$BZv+, : ./  '
+  print *, '    -#sJX%$Wmm#ev]hinW#Xi:` c ;   '
+  print *, '     #X#X23###1}vI$WWmX1>|,)nr"   '
+  print *, '     4XZ#Xov1v}=)vnXAX1nnv;1n"    '
+  print *, '     ]XX#ZXoovvvivnnnlvvo2*i7     '
+  print *, '     "23Z#1S2oo2XXSnnnoSo2>v"     '
+  print *, '      miX#L -~`""!!1}oSoe|i7      '
+  print *, '      4cn#m,        v221=|v[      '
+  print *, '      ]hI3Zma,;..__wXSe=+vo       '
+  print *, '      ]Zov*XSUXXZXZXSe||vo2       '
+  print *, '      ]Z#><iiii|i||||==vn2(       '
+  print *, '      ]Z#i<ii||+|=||=:{no2[       '
+  print *, '      ]ZUsiiiiivi|=||=vo22[       '
+  print *, '      ]XZvlliiIi|i=|+|vooo        '
+  print *, '      =v1llli||||=|||||lii(       '
+  print *, '      ]iillii||||||||=>=|<        '
+  print *, '      -ziiiii||||||+||==+>        '
+  print *, '       -%|+++||=|=+|=|==/         '
+  print *, '        -a>====+|====-:-          '
+  print *, '          "~,- --   /-            '
+  print *, '            -.     )>             '
+  print *, '           .~      +-             '
+  print *, '           . .... : .             '
+  print *, '            -------~              '
+  print *, ''
+end

plugins/read_integral/Gen_Ezfio_from_integral.sh

@@ -0,0 +1,17 @@
+#!/bin/bash
+
+ezfio=$1
+# Create the integral
+echo 'Create Integral'
+
+echo 'Create EZFIO'
+read nel nmo natom <<< $(cat param) 
+read e_nucl <<< $(cat e_nuc)
+./create_ezfio.py $ezfio $nel $natom $nmo $e_nucl
+#Handle the orbital consitensy check
+qp_edit -c $ezfio &> /dev/null
+cp $ezfio/{ao,mo}_basis/ao_md5 
+
+#Read the integral
+echo 'Read Integral'
+qp_run read_integrals_mo $ezfio 

plugins/read_integral/README.rst

@@ -3,6 +3,7 @@ read_integral
 =============
 
 Warning: CAN NOT CHANGE THE NUMBER OF MO !
+Scripts to read integrals and metadata and generates fake ezfio
 
 Needed Modules
 ==============

plugins/read_integral/create_ezfio.py

@@ -0,0 +1,48 @@
+#!/usr/bin/env python
+from ezfio import ezfio
+
+import sys
+filename = sys.argv[1]
+num_elec, nucl_num, mo_tot_num = map(int,sys.argv[2:5])
+
+nuclear_repulsion = float(sys.argv[5])
+ezfio.set_file(filename)
+
+#Important !
+import math
+ezfio.electrons_elec_alpha_num = int(math.ceil(num_elec / 2.))
+ezfio.electrons_elec_beta_num = int(math.floor(num_elec / 2.))
+
+
+#Important
+ezfio.set_nuclei_nucl_num(nucl_num)
+ezfio.set_nuclei_nucl_charge([0.]*nucl_num)
+ezfio.set_nuclei_nucl_coord( [ [0.], [0.], [0.] ]*nucl_num )
+ezfio.set_nuclei_nucl_label( ['He'] * nucl_num )
+
+ezfio.set_nuclei_disk_access_nuclear_repulsion('Read')
+ezfio.set_nuclei_nuclear_repulsion(nuclear_repulsion)
+
+# Ao num
+ao_num = mo_tot_num
+ezfio.set_ao_basis_ao_basis("Dummy one. We read MO")
+ezfio.set_ao_basis_ao_num(ao_num)
+ezfio.set_ao_basis_ao_nucl([1]*ao_num) #Maybe put a realy incorrect stuff
+
+#Just need one
+ao_prim_num_max  = 5
+
+d = [ [0] *ao_prim_num_max]*ao_num
+ezfio.set_ao_basis_ao_prim_num([ao_prim_num_max]*ao_num)
+ezfio.set_ao_basis_ao_power(d)
+ezfio.set_ao_basis_ao_coef(d)
+ezfio.set_ao_basis_ao_expo(d)
+
+#Dummy one
+ao_md5 = '3b8b464dfc95f282129bde3efef3c502'
+ezfio.set_ao_basis_ao_md5(ao_md5)
+ezfio.set_mo_basis_ao_md5(ao_md5)
+
+
+ezfio.set_mo_basis_mo_tot_num(mo_tot_num)
+ezfio.set_mo_basis_mo_coef([ [0]*mo_tot_num] * ao_num)

plugins/read_integral/read_integrals_achocol.irp.f

@@ -0,0 +1,47 @@
+program read_integrals
+
+  PROVIDE ezfio_filename
+  call ezfio_set_integrals_monoelec_disk_access_ao_one_integrals("None")
+  call run
+end
+
+subroutine run
+  use map_module
+  implicit none
+  
+  integer :: iunit
+  integer :: getunitandopen
+
+  integer ::i,j,k,l
+  double precision :: integral
+  double precision, allocatable :: A(:,:)
+
+  integer             :: n_integrals 
+  integer(key_kind), allocatable   :: buffer_i(:) 
+  real(integral_kind), allocatable :: buffer_values(:)
+  integer(key_kind)  :: key
+   
+  call ezfio_set_integrals_monoelec_disk_access_ao_one_integrals("Read")
+
+  allocate(buffer_i(ao_num**4/8), buffer_values(ao_num**4/8))
+   
+  iunit = getunitandopen('bielec_ao','r')
+  n_integrals=0
+  do 
+    read (iunit,*,end=13) i,j,k,l, integral
+    n_integrals += 1
+    call bielec_integrals_index(i, j, k, l, buffer_i(n_integrals) )
+    buffer_values(n_integrals) = integral
+  enddo
+  13 continue
+  close(iunit)
+  
+  call insert_into_ao_integrals_map(n_integrals,buffer_i,buffer_values)
+
+  call map_sort(ao_integrals_map)
+  call map_unique(ao_integrals_map)
+
+  call map_save_to_disk(trim(ezfio_filename)//'/work/ao_ints',ao_integrals_map)
+  call ezfio_set_integrals_bielec_disk_access_ao_integrals('Read')
+
+end

plugins/read_integral/read_integrals_mo_chocol.irp.f

@@ -0,0 +1,86 @@
+program read_integrals
+  BEGIN_DOC
+! Reads the integrals from the following files:
+! - kinetic_mo
+! - nuclear_mo
+! - bielec_mo
+  END_DOC
+
+  integer :: iunit
+  integer :: getunitandopen
+  integer :: i,j,n
+
+  PROVIDE ezfio_filename
+  call ezfio_set_integrals_monoelec_disk_access_mo_one_integrals("None")
+
+  logical :: has
+  call ezfio_has_mo_basis_mo_tot_num(has)
+  if (.not.has) then
+
+    iunit = getunitandopen('nuclear_mo','r')
+    n=0
+    do 
+      read (iunit,*,end=12) i
+      n = max(n,i)
+    enddo
+    12 continue
+    close(iunit)
+    call ezfio_set_mo_basis_mo_tot_num(n)
+
+    call ezfio_has_ao_basis_ao_num(has)
+    mo_label = "None"
+    if (has) then
+      call huckel_guess
+    else
+      call ezfio_set_ao_basis_ao_num(n)
+    endif
+  endif
+  call run
+end
+
+subroutine run
+  use map_module
+  implicit none
+  
+  integer :: iunit
+  integer :: getunitandopen
+
+  integer ::i,j,k,l
+  double precision :: integral
+  double precision, allocatable :: A(:,:)
+
+  integer             :: n_integrals 
+  integer(key_kind), allocatable   :: buffer_i(:) 
+  real(integral_kind), allocatable :: buffer_values(:)
+  integer(key_kind)  :: key
+   
+  call ezfio_get_mo_basis_mo_tot_num(mo_tot_num)
+
+  allocate (A(mo_tot_num,mo_tot_num))
+  A = 0.d0
+  
+  iunit = getunitandopen('kinetic_mo','r')
+  do 
+    read (iunit,*,end=10) i,j, integral
+    A(i,j) = integral
+  enddo
+  10 continue
+  close(iunit)
+  call write_one_e_integrals('mo_kinetic_integral', A, size(A,1), size(A,2))
+
+
+  iunit = getunitandopen('nuclear_mo','r')
+  do 
+    read (iunit,*,end=12) i,j, integral
+    A(i,j) = integral
+  enddo
+  12 continue
+  close(iunit)
+  call write_one_e_integrals('mo_ne_integral', A, size(A,1), size(A,2))
+
+  call write_one_e_integrals('mo_pseudo_integral', mo_pseudo_integral,&
+        size(mo_pseudo_integral,1), size(mo_pseudo_integral,2))
+
+
+  call ezfio_set_integrals_monoelec_disk_access_mo_one_integrals("Read")
+end