Added MOs and bitmasks

.gitignore

@@ -1,3 +1,3 @@
-sci.rc
+quantum_package.rc
 EZFIO
 irpf90

Makefile

@@ -23,5 +23,5 @@ doc:
 	$(MAKE) -C doc
 
 src: irpf90 EZFIO
-	export SCI_ROOT=$$PWD ; \
+	export QPACKAGE_ROOT=$$PWD ; \
 	$(MAKE) -C src

scripts/check_dependencies.sh

@@ -32,7 +32,7 @@ fi
 
 for d in $COMMAND_LINE
 do
-  if [[ ! -d ${SCI_ROOT}/src/$d ]]
+  if [[ ! -d ${QPACKAGE_ROOT}/src/$d ]]
   then
     echo Error: Directory $d does not exist 
     exit 2
@@ -44,7 +44,7 @@ DEPS_LONG=""
 for i in $COMMAND_LINE
 do
   DEPS_LONG+=" $i "
-  DEPS_LONG+=$(grep -e '^INCLUDE_DIRS' ${SCI_ROOT}/src/${i}/Makefile 2>/dev/null | cut -d '=' -f 2)
+  DEPS_LONG+=$(grep -e '^INCLUDE_DIRS' ${QPACKAGE_ROOT}/src/${i}/Makefile 2>/dev/null | cut -d '=' -f 2)
 done
 
 DEPS=$(unique_list $DEPS_LONG)

scripts/create_Makefile.sh

@@ -11,7 +11,7 @@ DEPS_LONG=""
 for i in $@
 do
   DEPS_LONG+=" $i "
-  DEPS_LONG+=$(grep 'INCLUDE_DIRS' ${SCI_ROOT}/src/${i}/Makefile 2>/dev/null | cut -d '=' -f 2)
+  DEPS_LONG+=$(grep 'INCLUDE_DIRS' ${QPACKAGE_ROOT}/src/${i}/Makefile 2>/dev/null | cut -d '=' -f 2)
 done
 
 DEPS=($(
@@ -34,15 +34,15 @@ SRC=
 OBJ=
 
 include Makefile.depend
-include \$(SCI_ROOT)/src/Makefile.config
+include \$(QPACKAGE_ROOT)/src/Makefile.config
-include \$(SCI_ROOT)/src/Makefile.common
+include \$(QPACKAGE_ROOT)/src/Makefile.common
 include irpf90.make
 
 irpf90.make: \$(filter-out IRPF90_temp/%, \$(wildcard */*.irp.f)) \$(wildcard *.irp.f) \$(wildcard *.inc.f) Makefile \$(EZFIO)
 	\$(IRPF90)
 
 Makefile.depend: Makefile
-	\$(SCI_ROOT)/scripts/create_Makefile_depend.sh
+	\$(QPACKAGE_ROOT)/scripts/create_Makefile_depend.sh
 EOF
 
 

scripts/create_Makefile_depend.sh

@@ -13,12 +13,12 @@ DEPS=$(grep "INCLUDE_DIRS" Makefile 2>/dev/null | cut -d '=' -f 2)
 for M in ${DEPS}
 do
   # X is the list of external source files
-  X=$(grep 'SRC=' ${SCI_ROOT}/src/${M}/Makefile 2>/dev/null |cut -d '=' -f 2) 
+  X=$(grep 'SRC=' ${QPACKAGE_ROOT}/src/${M}/Makefile 2>/dev/null |cut -d '=' -f 2) 
   for f in ${X}
   do
     SRC+=" ${M}/${f}"
   done
-  X=$(grep 'OBJ=' ${SCI_ROOT}/src/${M}/Makefile 2>/dev/null |cut -d '=' -f 2) 
+  X=$(grep 'OBJ=' ${QPACKAGE_ROOT}/src/${M}/Makefile 2>/dev/null |cut -d '=' -f 2) 
   for f in ${X}
   do
     OBJ+=" IRPF90_temp/${M}/${f/IRPF90_temp//}"

scripts/create_module.sh

@@ -23,6 +23,6 @@ mkdir ${MODULE}
 cd ${MODULE}
 
 # Create the Makefile
-${SCI_ROOT}/create_Makefile.sh
+${QPACKAGE_ROOT}/create_Makefile.sh
 
 

setup_environment.sh

@@ -1,19 +1,19 @@
 #!/bin/bash
 
-SCI_ROOT=${PWD}
+QPACKAGE_ROOT=${PWD}
 
 IRPF90=$(which irpf90) 
 
 if [[ -z ${IRPF90} ]] ;
 then
     make irpf90
-    IRPF90=${SCI_ROOT}/irpf90/bin/irpf90
+    IRPF90=${QPACKAGE_ROOT}/irpf90/bin/irpf90
 fi
 make EZFIO
 
-cat << EOF > sci.rc
+cat << EOF > quantum_package.rc
 export IRPF90=${IRPF90}
-export SCI_ROOT=${SCI_ROOT}
+export QPACKAGE_ROOT=${QPACKAGE_ROOT}
-export PATH+=:${SCI_ROOT}/scripts
+export PATH+=:${QPACKAGE_ROOT}/scripts
-export PATH+=:${SCI_ROOT}/bin
+export PATH+=:${QPACKAGE_ROOT}/bin
 EOF

src/.gitignore

@@ -0,0 +1,9 @@
+Makefile.config
+*IRPF90_temp
+*IRPF90_man
+*irpf90.make
+*irpf90_entities
+*tags
+*.o
+*.mod
+*/Makefile.depend

src/AOs/Makefile

@@ -1,9 +1,20 @@
 default: all
-INCLUDE_DIRS = Ezfio_files Utils Nuclei
 
-include ../Makefile.config
+# Define here all other modules on which the current module depends
-include ../Makefile.common
+INCLUDE_DIRS = Ezfio_files Nuclei Utils
+
+# Define here all new external source files and objects.Don't forget to prefix the
+# object files with IRPF90_temp/
+SRC=
+OBJ=
+
+include Makefile.depend
+include $(QPACKAGE_ROOT)/src/Makefile.config
+include $(QPACKAGE_ROOT)/src/Makefile.common
 include irpf90.make
 
 irpf90.make: $(filter-out IRPF90_temp/%, $(wildcard */*.irp.f)) $(wildcard *.irp.f) $(wildcard *.inc.f) Makefile $(EZFIO)
 	$(IRPF90)
+
+Makefile.depend: Makefile
+	$(QPACKAGE_ROOT)/scripts/create_Makefile_depend.sh

src/Bitmask/Makefile

@@ -0,0 +1,20 @@
+default: all
+
+# Define here all other modules on which the current module depends
+INCLUDE_DIRS = AOs Electrons Ezfio_files MOs Nuclei Utils
+
+# Define here all new external source files and objects.Don't forget to prefix the
+# object files with IRPF90_temp/
+SRC=bitmasks_module.f90
+OBJ=IRPF90_temp/bitmasks_module.o
+
+include Makefile.depend
+include $(QPACKAGE_ROOT)/src/Makefile.config
+include $(QPACKAGE_ROOT)/src/Makefile.common
+include irpf90.make
+
+irpf90.make: $(filter-out IRPF90_temp/%, $(wildcard */*.irp.f)) $(wildcard *.irp.f) $(wildcard *.inc.f) Makefile $(EZFIO)
+	$(IRPF90)
+
+Makefile.depend: Makefile
+	$(QPACKAGE_ROOT)/scripts/create_Makefile_depend.sh

src/Bitmask/bitmasks.irp.f

@@ -0,0 +1,57 @@
+use bitmasks
+
+BEGIN_PROVIDER [ integer, N_int ]
+  implicit none
+  BEGIN_DOC
+  ! Number of 64-bit integers needed to represent determinants as binary strings
+  END_DOC
+  N_int = (mo_tot_num-1)/bit_kind_size + 1
+END_PROVIDER
+
+
+BEGIN_PROVIDER [ integer(bit_kind), full_ijkl_bitmask, (N_int,4) ]
+  implicit none
+  BEGIN_DOC
+  ! Bitmask to include all possible <ij|kl> integrals
+  END_DOC
+  
+  integer                        :: i,j,n
+  n = mod(mo_tot_num-1,bit_kind_size)+1
+  full_ijkl_bitmask = 0_bit_kind
+  do j=1,4
+    do i=1,N_int-1
+      full_ijkl_bitmask(i,j) = not(0_bit_kind)
+    enddo
+    do i=1,n
+      full_ijkl_bitmask(N_int,j) = ibset(full_ijkl_bitmask(N_int,j),i-1)
+    enddo
+  enddo
+END_PROVIDER
+
+
+BEGIN_PROVIDER [ integer(bit_kind), HF_bitmask, (N_int,2)]
+  implicit none
+  BEGIN_DOC
+  ! Hartree Fock bit mask
+  END_DOC
+  integer                        :: i,j,n
+  integer                        :: occ(elec_alpha_num)
+
+  HF_bitmask = 0_bit_kind
+  do i=1,elec_alpha_num
+   occ(i) = i 
+  enddo
+  call list_to_bitstring( HF_bitmask(1,1), occ, elec_alpha_num, N_int)
+  ! elec_alpha_num <= elec_beta_num, so occ is already OK.
+  call list_to_bitstring( HF_bitmask(1,2), occ, elec_beta_num, N_int)
+
+END_PROVIDER
+
+BEGIN_PROVIDER [ integer(bit_kind), ref_bitmask, (N_int,2)]
+ implicit none
+ BEGIN_DOC
+! Reference bit mask, used in Slater rules, chosen as Hartree-Fock bitmask
+ END_DOC
+ ref_bitmask = HF_bitmask
+END_PROVIDER
+

src/Bitmask/bitmasks_module.f90

@@ -0,0 +1,5 @@
+module bitmasks
+  integer, parameter             :: bit_kind_shift = 6   ! 5: 32 bits, 6: 64 bits
+  integer, parameter             :: bit_kind_size = 64
+  integer, parameter             :: bit_kind = 64/8
+end module

src/Bitmask/bitmasks_routines.irp.f

@@ -0,0 +1,94 @@
+subroutine bitstring_to_list( string, list, n_elements, Nint)
+  use bitmasks
+  implicit none
+  BEGIN_DOC
+  ! Gives the inidices(+1) of the bits set to 1 in the bit string
+  END_DOC
+  integer, intent(in)            :: Nint
+  integer(bit_kind), intent(in)  :: string(Nint)
+  integer, intent(out)           :: list(Nint*bit_kind_size)
+  integer, intent(out)           :: n_elements
+  
+  integer                        :: i, ishift
+  integer(bit_kind)              :: l
+  
+  n_elements = 0
+  ishift = 2
+  do i=1,Nint
+    l = string(i)
+    do while (l /= 0_bit_kind)
+      n_elements = n_elements+1
+      list(n_elements) = ishift+popcnt(l-1_bit_kind) - popcnt(l)
+      l = iand(l,l-1_bit_kind)
+    enddo
+    ishift = ishift + bit_kind_size
+  enddo
+  
+end
+
+subroutine list_to_bitstring( string, list, n_elements, Nint)
+  use bitmasks
+  implicit none
+  integer, intent(in)            :: Nint
+  integer(bit_kind), intent(out) :: string(Nint)
+  integer, intent(in)            :: list(Nint*bit_kind_size)
+  integer, intent(in)            :: n_elements
+  
+  
+  integer                        :: i, j
+  integer                        :: ipos, iint
+  BEGIN_DOC
+  ! return the physical string "string(N_int,2)" from the array of occupations "list(N_int*bit_kind_size,2)
+  !                              list
+  !                                       <== ipos ==>
+  !                                                  |
+  !                                                  v
+  !string :|------------------------|-------------------------|------------------------|
+  !        <==== bit_kind_size ====> <==== bit_kind_size ====> <==== bit_kind_size ====>
+  !        {        iint            } {         iint         } {         iint         }
+  END_DOC
+  
+  string = 0_bit_kind
+  
+  do i=1,n_elements
+    iint = ishft(list(i)-1,-bit_kind_shift) + 1
+    ipos = list(i)-ishft((iint-1),bit_kind_shift)-1
+    string(iint) = ibset( string(iint), ipos )
+  enddo
+  
+end
+
+
+subroutine write_bitstring( iunit, string, Nint )
+  implicit none
+   use bitmasks
+  integer, intent(in)            :: iunit
+  integer, intent(in)            :: Nint
+  integer(bit_kind), intent(in)  :: string(Nint)
+  
+  integer                        :: i, j, ibuf
+  integer(bit_kind)              :: itemp
+  character*(1)                  :: buffer(Nint*bit_kind_size+2)
+  
+  ibuf = 1
+  buffer(ibuf) = '|'
+  ibuf = ibuf+1
+  do i=1,Nint
+    itemp = 1_bit_kind
+    do j=1,bit_kind_size
+      if (iand(itemp,string(i)) == itemp) then
+        buffer(ibuf) = '+'
+      else
+        buffer(ibuf) = '-'
+      endif
+      ibuf = ibuf+1
+      itemp = ishft(itemp,1)
+    enddo
+  enddo
+  buffer(ibuf) = '|'
+  write(iunit,'(100A)') buffer(1:ibuf)
+  
+end
+
+
+

src/Electrons/Makefile

@@ -0,0 +1,20 @@
+default: all
+
+# Define here all other modules on which the current module depends
+INCLUDE_DIRS = Ezfio_files
+
+# Define here all new external source files and objects.Don't forget to prefix the
+# object files with IRPF90_temp/
+SRC=
+OBJ=
+
+include Makefile.depend
+include $(QPACKAGE_ROOT)/src/Makefile.config
+include $(QPACKAGE_ROOT)/src/Makefile.common
+include irpf90.make
+
+irpf90.make: $(filter-out IRPF90_temp/%, $(wildcard */*.irp.f)) $(wildcard *.irp.f) $(wildcard *.inc.f) Makefile $(EZFIO)
+	$(IRPF90)
+
+Makefile.depend: Makefile
+	$(QPACKAGE_ROOT)/scripts/create_Makefile_depend.sh

src/Ezfio_files/Makefile

@@ -1,8 +1,20 @@
 default: all
 
-include ../Makefile.config
+# Define here all other modules on which the current module depends
-include ../Makefile.common
+INCLUDE_DIRS = 
+
+# Define here all new external source files and objects.Don't forget to prefix the
+# object files with IRPF90_temp/
+SRC=
+OBJ=
+
+include Makefile.depend
+include $(QPACKAGE_ROOT)/src/Makefile.config
+include $(QPACKAGE_ROOT)/src/Makefile.common
 include irpf90.make
 
 irpf90.make: $(filter-out IRPF90_temp/%, $(wildcard */*.irp.f)) $(wildcard *.irp.f) $(wildcard *.inc.f) Makefile $(EZFIO)
 	$(IRPF90)
+
+Makefile.depend: Makefile
+	$(QPACKAGE_ROOT)/scripts/create_Makefile_depend.sh

src/MOs/Makefile

@@ -0,0 +1,20 @@
+default: all
+
+# Define here all other modules on which the current module depends
+INCLUDE_DIRS = AOs Ezfio_files Nuclei Utils
+
+# Define here all new external source files and objects.Don't forget to prefix the
+# object files with IRPF90_temp/
+SRC=
+OBJ=
+
+include Makefile.depend
+include $(QPACKAGE_ROOT)/src/Makefile.config
+include $(QPACKAGE_ROOT)/src/Makefile.common
+include irpf90.make
+
+irpf90.make: $(filter-out IRPF90_temp/%, $(wildcard */*.irp.f)) $(wildcard *.irp.f) $(wildcard *.inc.f) Makefile $(EZFIO)
+	$(IRPF90)
+
+Makefile.depend: Makefile
+	$(QPACKAGE_ROOT)/scripts/create_Makefile_depend.sh

src/MOs/mos.ezfio_config

@@ -0,0 +1,8 @@
+mo_basis
+  mo_tot_num         integer
+  mo_coef            double precision  (ao_basis_ao_num,mo_basis_mo_tot_num)
+  mo_energy          double precision (mo_basis_mo_tot_num)
+  mo_occ             double precision (mo_basis_mo_tot_num)
+  mo_symmetry        character*(8)     (mo_basis_mo_tot_num)
+  mo_label           character*(64)
+

src/MOs/mos.irp.f

@@ -0,0 +1,94 @@
+BEGIN_PROVIDER [ integer, mo_tot_num ]
+  implicit none
+  BEGIN_DOC
+  ! Total number of molecular orbitals and the size of the keys corresponding
+  END_DOC
+  PROVIDE ezfio_filename
+  call ezfio_get_mo_basis_mo_tot_num(mo_tot_num)
+  ASSERT (mo_tot_num > 0)
+END_PROVIDER
+
+
+BEGIN_PROVIDER [ integer, mo_tot_num_align ]
+  implicit none
+  BEGIN_DOC
+  ! Aligned variable for dimensioning of arrays
+  END_DOC
+  integer                        :: align_double
+  mo_tot_num_align = align_double(mo_tot_num)
+END_PROVIDER
+
+
+BEGIN_PROVIDER [ character*(64), mo_label ]
+  implicit none
+  BEGIN_DOC
+  ! Label characterizing the MOS (local, canonical, natural, etc)
+  END_DOC
+  logical                        :: exists
+  PROVIDE ezfio_filename
+  call ezfio_has_mo_basis_mo_label(exists)
+  if (exists) then
+    call ezfio_get_mo_basis_mo_label(mo_label)
+  else
+    mo_label = 'no_label'
+    call ezfio_set_mo_basis_mo_label(mo_label)
+  endif
+  
+END_PROVIDER
+
+
+BEGIN_PROVIDER [ double precision, mo_energy, (mo_tot_num) ]
+  implicit none
+  BEGIN_DOC
+  ! Fock diagonal elements
+  END_DOC
+  PROVIDE ezfio_filename
+  mo_energy = 0.d0
+  call ezfio_get_mo_basis_mo_energy(mo_energy)
+END_PROVIDER
+
+
+BEGIN_PROVIDER [ double precision, mo_coef, (ao_num_align,mo_tot_num) ]
+  implicit none
+  BEGIN_DOC
+  ! Molecular orbital coefficients on AO basis set
+  ! mo_coef(i,j) = coefficient of the ith ao on the jth mo
+  END_DOC
+  integer                        :: i, j
+  double precision, allocatable  :: buffer(:,:)
+  !DIR$ ATTRIBUTES ALIGN : $IRP_ALIGN :: buffer
+  
+  PROVIDE ezfio_filename
+  allocate(buffer(ao_num,mo_tot_num))
+  buffer = 0.d0
+  call ezfio_get_mo_basis_mo_coef(buffer)
+  do i=1,mo_tot_num
+    do j=1,ao_num
+      mo_coef(j,i) = buffer(j,i)
+    enddo
+    do j=ao_num+1,ao_num_align
+      mo_coef(j,i) = 0.d0
+    enddo
+  enddo
+  deallocate(buffer)
+  
+END_PROVIDER
+
+BEGIN_PROVIDER [ double precision, mo_coef_transp, (mo_tot_num_align,ao_num) ]
+  implicit none
+  BEGIN_DOC
+  ! Molecular orbital coefficients on AO basis set
+  END_DOC
+  integer                        :: i, j
+  
+  do j=1,ao_num
+    do i=1,mo_tot_num
+      mo_coef_transp(i,j) = mo_coef(j,i)
+    enddo
+    do i=mo_tot_num+1,mo_tot_num_align
+      mo_coef_transp(i,j) = 0.d0
+    enddo
+  enddo
+  
+END_PROVIDER
+

src/MOs/utils.irp.f

@@ -0,0 +1,48 @@
+subroutine save_mos
+  implicit none
+  double precision, allocatable  :: buffer(:,:)
+  integer                        :: i,j
+  
+  call system('save_current_mos.sh '//trim(ezfio_filename))
+  
+  call ezfio_set_mo_basis_mo_label(mo_label)
+  allocate ( buffer(ao_num,mo_tot_num) )
+  buffer = 0.d0
+  do j = 1, mo_tot_num
+    do i = 1, ao_num
+      buffer(i,j) = mo_coef(i,j)
+    enddo
+  enddo
+  call ezfio_set_mo_basis_mo_coef(buffer)
+  deallocate (buffer)
+  
+end
+
+subroutine mo_as_eigvectors_of_mo_matrix(matrix,n,m,label)
+  implicit none
+  integer,intent(in)             :: n,m
+  character*(64), intent(in)     :: label
+  double precision, intent(in)   :: matrix(n,m)
+  
+  double precision, allocatable  :: mo_coef_new(:,:), R(:,:),eigvalues(:)
+  !DIR$ ATTRIBUTES ALIGN : $IRP_ALIGN :: mo_coef_new, R
+  
+  if (m /= mo_tot_num) then
+    print *, irp_here, ': Error : m/= mo_tot_num'
+  endif
+  allocate(R(n,m))
+  allocate(mo_coef_new(ao_num_align,m),eigvalues(m))
+  mo_coef_new = mo_coef
+  
+  call jacobi_lapack(eigvalues,R,matrix,size(matrix,1),size(matrix,2))
+  integer :: i
+  do i = 1, m
+   print*,'eigvalues(i) = ',eigvalues(i)
+  enddo
+  
+  call dgemm('N','N',ao_num,m,m,1.d0,mo_coef_new,size(mo_coef_new,1),R,size(R,1),0.d0,mo_coef,size(mo_coef,1))
+  deallocate(mo_coef_new,R,eigvalues)
+  
+  mo_label = label
+  SOFT_TOUCH mo_coef
+end

src/Makefile

@@ -1,13 +1,13 @@
 default: all
-INCLUDE_DIRS = Ezfio_files Nuclei Utils AOs Electrons # MonoInts BiInts MOs Output Bitmask
+INCLUDE_DIRS = Ezfio_files Nuclei Utils AOs Electrons MonoInts BiInts MOs Output Bitmask
 
 include Makefile.common
 include Makefile.config
 
 LIB+=$(MKL) 
 
-SRC=#BiInts/map_module.f90 Bitmask/bitmasks_module.f90
+SRC=BiInts/map_module.f90 Bitmask/bitmasks_module.f90
-OBJ=#IRPF90_temp/BiInts/map_module.o IRPF90_temp/Bitmask/bitmasks_module.o
+OBJ=IRPF90_temp/BiInts/map_module.o IRPF90_temp/Bitmask/bitmasks_module.o
 PYTHON_SCRIPTS=
 
 include irpf90.make
@@ -17,5 +17,7 @@ irpf90.make: $(filter-out IRPF90_temp/%, $(wildcard */*.irp.f)) $(wildcard *.irp
 	$(IRPF90)
 
 all_clean:
-	for i in */ ; do $(MAKE) -C $$i veryclean clean_links ; done
+	for i in */ ; do unset INCLUDE_DIRS ; $(MAKE) -C $$i veryclean && $(MAKE) -C $$i clean_links ; done
 
+all_modules:
+	for i in */ ; do unset INCLUDE_DIRS ; $(MAKE) -C $$i || exit 1 ; done

src/Makefile.common

@@ -1,7 +1,15 @@
-ifndef SCI_ROOT
+ifndef QPACKAGE_ROOT
-$(error SCI_ROOT undefined. Run the setup_environment.sh script)
+$(error QPACKAGE_ROOT undefined. Run the setup_environment.sh script)
 endif
 
+INCLUDE_DIRS_OK=$(shell X=`$(QPACKAGE_ROOT)/scripts/check_dependencies.sh $(INCLUDE_DIRS)` && echo OK || echo $$X)
+ifneq ($(INCLUDE_DIRS_OK),OK)
+  $(info ---------------------)
+  $(info Your INCLUDE_DIRS variable is inconsistent. It should be:)
+  $(info INCLUDE_DIRS = $(INCLUDE_DIRS_OK))
+  $(info ---------------------)
+  $(error )
+endif
 
 IRP_VERSION_OK=$(shell $(IRPF90) -v | python -c "import sys ; print float(sys.stdin.readline().rsplit('.',1)[0]) >= 1.3")
 ifeq ($(IRP_VERSION_OK),False)
@@ -9,25 +17,25 @@ $(error 'IRPF90 version >= 1.3 is required')
 endif
 
 
-MAKEFILE_OK=$(shell ls $(SCI_ROOT)/src/Makefile.config 2> /dev/null && echo True || echo False)
+MAKEFILE_OK=$(shell ls $(QPACKAGE_ROOT)/src/Makefile.config 2> /dev/null && echo True || echo False)
 ifeq ($(MAKEFILE_OK),False)
 $(error 'Makefile.config is not present. Please modify Makefile.config.example to create Makefile.config')
 endif
 
 
-EZFIO_DIR=$(SCI_ROOT)/EZFIO
+EZFIO_DIR=$(QPACKAGE_ROOT)/EZFIO
 EZFIO=$(EZFIO_DIR)/lib/libezfio_irp.a
 
-$(EZFIO): $(wildcard $(SCI_ROOT)/src/*.ezfio_config) $(wildcard $(SCI_ROOT)/src/*/*.ezfio_config)
+$(EZFIO): $(wildcard $(QPACKAGE_ROOT)/src/*.ezfio_config) $(wildcard $(QPACKAGE_ROOT)/src/*/*.ezfio_config)
 	@echo Building EZFIO library
-	@cp $(wildcard $(SCI_ROOT)/src/*.ezfio_config) $(wildcard $(SCI_ROOT)/src/*/*.ezfio_config) $(EZFIO_DIR)/config 
+	@cp $(wildcard $(QPACKAGE_ROOT)/src/*.ezfio_config) $(wildcard $(QPACKAGE_ROOT)/src/*/*.ezfio_config) $(EZFIO_DIR)/config 
 	@cd $(EZFIO_DIR) ; export FC="$(FC)" ; export FCFLAGS="$(FCFLAGS)" ; export IRPF90="$(IRPF90)" ; $(MAKE) ; $(MAKE) Python
 
 INCLUDE_DIRS+=include
 
 
-ifneq ($(PWD),$(SCI_ROOT)/src)
+ifneq ($(PWD),$(QPACKAGE_ROOT)/src)
-$(shell $(SCI_ROOT)/scripts/prepare_module.sh $(INCLUDE_DIRS))
+$(shell $(QPACKAGE_ROOT)/scripts/prepare_module.sh $(INCLUDE_DIRS))
 clean_links:
 	rm $(INCLUDE_DIRS) $$(basename $$PWD)
 else

src/Nuclei/Makefile

@@ -1,9 +1,20 @@
 default: all
+
+# Define here all other modules on which the current module depends
 INCLUDE_DIRS = Ezfio_files Utils
 
-include ../Makefile.config
+# Define here all new external source files and objects.Don't forget to prefix the
-include ../Makefile.common
+# object files with IRPF90_temp/
+SRC=
+OBJ=
+
+include Makefile.depend
+include $(QPACKAGE_ROOT)/src/Makefile.config
+include $(QPACKAGE_ROOT)/src/Makefile.common
 include irpf90.make
 
 irpf90.make: $(filter-out IRPF90_temp/%, $(wildcard */*.irp.f)) $(wildcard *.irp.f) $(wildcard *.inc.f) Makefile $(EZFIO)
 	$(IRPF90)
+
+Makefile.depend: Makefile
+	$(QPACKAGE_ROOT)/scripts/create_Makefile_depend.sh

src/Output/Makefile

@@ -0,0 +1,20 @@
+default: all
+
+# Define here all other modules on which the current module depends
+INCLUDE_DIRS = 
+
+# Define here all new external source files and objects.Don't forget to prefix the
+# object files with IRPF90_temp/
+SRC=
+OBJ=
+
+include Makefile.depend
+include $(QPACKAGE_ROOT)/src/Makefile.config
+include $(QPACKAGE_ROOT)/src/Makefile.common
+include irpf90.make
+
+irpf90.make: $(filter-out IRPF90_temp/%, $(wildcard */*.irp.f)) $(wildcard *.irp.f) $(wildcard *.inc.f) Makefile $(EZFIO)
+	$(IRPF90)
+
+Makefile.depend: Makefile
+	$(QPACKAGE_ROOT)/scripts/create_Makefile_depend.sh

src/Output/output.ezfio_config

@@ -0,0 +1,3 @@
+output
+  empty              logical
+

src/Output/output.irp.f

@@ -0,0 +1,22 @@
+BEGIN_TEMPLATE
+
+BEGIN_PROVIDER [ integer, output_$NAME ]
+  implicit none
+  BEGIN_DOC  
+!  Output file for $NAME
+  END_DOC
+  integer :: getUnitAndOpen
+  call ezfio_set_output_empty(.False.)
+  output_$NAME = getUnitAndOpen(trim(ezfio_filename)//'/output/'//'$NAME','w')
+END_PROVIDER
+
+SUBST [ NAME ]
+
+AO            ;;
+MO            ;;
+AO_integrals  ;;
+MO_integrals  ;;
+
+END_TEMPLATE
+
+

src/Utils/Makefile

@@ -0,0 +1,20 @@
+default: all
+
+# Define here all other modules on which the current module depends
+INCLUDE_DIRS = 
+
+# Define here all new external source files and objects.Don't forget to prefix the
+# object files with IRPF90_temp/
+SRC=
+OBJ=
+
+include Makefile.depend
+include $(QPACKAGE_ROOT)/src/Makefile.config
+include $(QPACKAGE_ROOT)/src/Makefile.common
+include irpf90.make
+
+irpf90.make: $(filter-out IRPF90_temp/%, $(wildcard */*.irp.f)) $(wildcard *.irp.f) $(wildcard *.inc.f) Makefile $(EZFIO)
+	$(IRPF90)
+
+Makefile.depend: Makefile
+	$(QPACKAGE_ROOT)/scripts/create_Makefile_depend.sh