Merge branch 'dev-lcpq' of github.com:QuantumPackage/qp2 into dev-lcpq

bin/qp_plugins

@@ -3,7 +3,7 @@
 """
 Usage:
        qp_plugins list [-iuq]
-       qp_plugins download <url>
+       qp_plugins download <url> [-n <name>]
        qp_plugins install <name>...
        qp_plugins uninstall <name>
        qp_plugins create -n <name> [-r <repo>] [<needed_modules>...]
@@ -186,7 +186,10 @@ def main(arguments):
                       url.endswith(".zip"))
         os.chdir(QP_PLUGINS)
         if is_repo:
-            subprocess.check_call(["git", "clone", url])
+            git_cmd=["git", "clone", url]
+            if arguments["--name"]:
+               git_cmd.append(arguments["--name"])
+            subprocess.check_call(git_cmd)
         else:
             filename = url.split('/')[-1]
 

configure

@@ -60,7 +60,7 @@ function execute () {
 }
 
 PACKAGES=""
-OCAML_PACKAGES="ocamlbuild cryptokit zmq sexplib ppx_sexp_conv ppx_deriving getopt"
+OCAML_PACKAGES="ocamlbuild cryptokit zmq sexplib.v0.11.0 ppx_sexp_conv ppx_deriving getopt"
 
 while true ; do
     case "$1" in

docs/source/research.bib

@@ -19,21 +19,23 @@ Programs}},
 	url = {https://arxiv.org/abs/1812.06902}
 }
 
-@article{Loos2019Jan,
+
+%%%% PUBLISHED PAPERS
+
+@article{Loos2019Mar,
         author = {Loos, Pierre-Fran\c{c}ois and Boggio-Pasqua, Martial and Scemama, Anthony and Caffarel, Michel and Jacquemin, Denis},
         title = {{Reference Energies for Double Excitations}},
         journal = {J. Chem. Theory Comput.},
+        volume = {15},
+        number = {3},
+        pages = {1939--1956},
         year = {2019},
-        month = {Jan},
+        month = {Mar},
         issn = {1549-9618},
         publisher = {American Chemical Society},
         doi = {10.1021/acs.jctc.8b01205}
 }
 
-
-
-
-%%%% PUBLISHED PAPERS
 @article{PinedaFlores2019Feb,
         author = {Pineda Flores, Sergio and Neuscamman, Eric},
         title = {{Excited State Specific Multi-Slater Jastrow Wave Functions}},

ocaml/.gitignore

@@ -1,38 +0,0 @@
-_build
-element_create_db
-element_create_db.byte
-ezfio.ml
-.gitignore
-Git.ml
-Input_ao_one_e_ints.ml
-Input_ao_two_e_erf_ints.ml
-Input_ao_two_e_ints.ml
-Input_auto_generated.ml
-Input_becke_numerical_grid.ml
-Input_champ.ml
-Input_davidson.ml
-Input_density_for_dft.ml
-Input_determinants.ml
-Input_dft_keywords.ml
-Input_dressing.ml
-Input_mo_one_e_ints.ml
-Input_mo_two_e_erf_ints.ml
-Input_mo_two_e_ints.ml
-Input_nuclei.ml
-Input_perturbation.ml
-Input_pseudo.ml
-Input_scf_utils.ml
-Input_variance.ml
-qp_create_ezfio
-qp_create_ezfio.native
-qp_edit
-qp_edit.ml
-qp_edit.native
-qp_print_basis
-qp_print_basis.native
-qp_run
-qp_run.native
-qp_set_mo_class
-qp_set_mo_class.native
-qptypes_generator.byte
-Qptypes.ml

src/becke_numerical_grid/grid_becke.irp.f

@@ -195,6 +195,20 @@ BEGIN_PROVIDER [double precision, weight_at_r, (n_points_integration_angular,n_p
         enddo
         accu = 1.d0/accu
         weight_at_r(l,k,j) = tmp_array(j) * accu
+        if(isnan(weight_at_r(l,k,j)))then
+         print*,'isnan(weight_at_r(l,k,j))'
+         print*,l,k,j
+         accu = 0.d0
+         do i = 1, nucl_num
+           ! function defined for each atom "i" by equation (13) and (21) with k == 3
+           tmp_array(i) = cell_function_becke(r,i) ! P_n(r)
+           print*,i,tmp_array(i)
+           ! Then you compute the summ the P_n(r) function for each of the "r" points
+           accu += tmp_array(i)
+         enddo
+         write(*,'(100(F16.10,X))')tmp_array(j) , accu
+          stop
+        endif
       enddo
     enddo
   enddo
@@ -221,6 +235,12 @@ BEGIN_PROVIDER [double precision, final_weight_at_r, (n_points_integration_angul
         contrib_integration = derivative_knowles_function(alpha_knowles(int(nucl_charge(j))),m_knowles,x)&
             *knowles_function(alpha_knowles(int(nucl_charge(j))),m_knowles,x)**2
         final_weight_at_r(k,i,j) = weights_angular_points(k)  * weight_at_r(k,i,j) * contrib_integration * dr_radial_integral
+        if(isnan(final_weight_at_r(k,i,j)))then
+         print*,'isnan(final_weight_at_r(k,i,j))' 
+         print*,k,i,j
+         write(*,'(100(F16.10,X))')weights_angular_points(k)  , weight_at_r(k,i,j) , contrib_integration , dr_radial_integral
+         stop 
+        endif
       enddo
     enddo
   enddo

src/becke_numerical_grid/step_function_becke.irp.f

@@ -31,6 +31,10 @@ double precision function cell_function_becke(r,atom_number)
   double precision               :: mu_ij,nu_ij
   double precision               :: distance_i,distance_j,step_function_becke
   integer                        :: j
+  if(int(nucl_charge(atom_number))==0)then
+   cell_function_becke = 0.d0
+   return
+  endif
   distance_i = (r(1) - nucl_coord_transp(1,atom_number) ) * (r(1) - nucl_coord_transp(1,atom_number))
   distance_i += (r(2) - nucl_coord_transp(2,atom_number) ) * (r(2) - nucl_coord_transp(2,atom_number))
   distance_i += (r(3) - nucl_coord_transp(3,atom_number) ) * (r(3) - nucl_coord_transp(3,atom_number))
@@ -38,6 +42,7 @@ double precision function cell_function_becke(r,atom_number)
   cell_function_becke = 1.d0
   do j = 1, nucl_num
     if(j==atom_number)cycle
+    if(int(nucl_charge(j))==0)cycle
     distance_j = (r(1) - nucl_coord_transp(1,j) ) * (r(1) - nucl_coord_transp(1,j))
     distance_j+= (r(2) - nucl_coord_transp(2,j) ) * (r(2) - nucl_coord_transp(2,j))
     distance_j+= (r(3) - nucl_coord_transp(3,j) ) * (r(3) - nucl_coord_transp(3,j))

src/density_for_dft/EZFIO.cfg

@@ -16,3 +16,10 @@ doc: Type of density
 doc: if [no_core_dm] then all elements of the density matrix involving at least one orbital set as core are set to zero
 interface: ezfio, provider, ocaml
 default: full_density
+
+[normalize_dm]
+type: logical
+doc: Type of density
+doc: if .True., then you normalize the no_core_dm to elec_alpha_num - n_core_orb  and elec_beta_num - n_core_orb
+interface: ezfio, provider, ocaml
+default: True

src/density_for_dft/density_for_dft.irp.f

@@ -21,13 +21,28 @@ BEGIN_PROVIDER [double precision, one_e_dm_mo_alpha_for_dft, (mo_num,mo_num, N_s
  endif
  
  if(no_core_density .EQ. "no_core_dm")then
-  integer :: i,j
+  integer :: ii,i,j
-  do i = 1, n_core_orb
+  do ii = 1, n_core_orb
+   i = list_core(ii)
    do j = 1, mo_num
     one_e_dm_mo_alpha_for_dft(j,i,:) = 0.d0
     one_e_dm_mo_alpha_for_dft(i,j,:) = 0.d0
    enddo
   enddo
+  if(normalize_dm)then
+   double precision :: elec_alpha_frozen_num, elec_alpha_valence(N_states)
+   elec_alpha_frozen_num = elec_alpha_num - n_core_orb 
+   elec_alpha_valence = 0.d0
+   integer :: istate 
+   do istate = 1, N_states
+    do i = 1, mo_num
+     elec_alpha_valence(istate) += one_e_dm_mo_alpha_for_dft(i,i,istate)
+    enddo
+    elec_alpha_valence(istate) = elec_alpha_frozen_num/elec_alpha_valence(istate)
+    one_e_dm_mo_alpha_for_dft(:,:,istate) = one_e_dm_mo_alpha_for_dft(:,:,istate) * elec_alpha_valence(istate)
+   enddo 
+   
+  endif
  endif
 
 END_PROVIDER
@@ -55,13 +70,27 @@ BEGIN_PROVIDER [double precision, one_e_dm_mo_beta_for_dft, (mo_num,mo_num, N_st
  endif
 
  if(no_core_density .EQ. "no_core_dm")then
-  integer :: i,j
+  integer :: ii,i,j
-  do i = 1, n_core_orb
+  do ii = 1, n_core_orb
+   i = list_core(ii)
    do j = 1, mo_num
     one_e_dm_mo_beta_for_dft(j,i,:) = 0.d0
     one_e_dm_mo_beta_for_dft(i,j,:) = 0.d0
    enddo
   enddo
+  if(normalize_dm)then
+   double precision :: elec_beta_valence(N_states),elec_beta_frozen_num
+   elec_beta_frozen_num = elec_beta_num - n_core_orb 
+   elec_beta_valence = 0.d0
+   integer :: istate 
+   do istate = 1, N_states
+    do i = 1, mo_num
+     elec_beta_valence(istate) += one_e_dm_mo_beta_for_dft(i,i,istate)
+    enddo
+    elec_beta_valence(istate) = elec_beta_frozen_num/elec_beta_valence(istate)
+    one_e_dm_mo_beta_for_dft(:,:,istate) = one_e_dm_mo_beta_for_dft(:,:,istate) * elec_beta_valence(istate)
+   enddo 
+  endif
  endif
 END_PROVIDER
 
@@ -119,3 +148,65 @@ END_PROVIDER
   one_body_dm_mo_beta_one_det(i,i, 1:N_states) = 1.d0
  enddo
 END_PROVIDER
+
+
+
+
+BEGIN_PROVIDER [double precision, one_e_dm_mo_alpha_for_dft_no_core, (mo_num,mo_num, N_states)]
+ implicit none
+ BEGIN_DOC
+! density matrix for alpha electrons in the MO basis without the core orbitals
+ END_DOC
+ one_e_dm_mo_alpha_for_dft_no_core = one_e_dm_mo_alpha_for_dft 
+
+ integer :: ii,i,j
+ do ii = 1, n_core_orb
+  i = list_core(ii)
+  do j = 1, mo_num
+   one_e_dm_mo_alpha_for_dft_no_core(j,i,:) = 0.d0
+   one_e_dm_mo_alpha_for_dft_no_core(i,j,:) = 0.d0
+  enddo
+ enddo
+
+END_PROVIDER
+
+BEGIN_PROVIDER [double precision, one_e_dm_mo_beta_for_dft_no_core, (mo_num,mo_num, N_states)]
+ implicit none
+ BEGIN_DOC
+! density matrix for beta  electrons in the MO basis without the core orbitals 
+ END_DOC
+ one_e_dm_mo_beta_for_dft_no_core = one_e_dm_mo_beta_for_dft 
+ integer :: ii,i,j
+ do ii = 1, n_core_orb
+  i = list_core(ii)
+  do j = 1, mo_num
+   one_e_dm_mo_beta_for_dft_no_core(j,i,:) = 0.d0
+   one_e_dm_mo_beta_for_dft_no_core(i,j,:) = 0.d0
+  enddo
+ enddo
+END_PROVIDER
+
+ BEGIN_PROVIDER [ double precision, one_e_dm_alpha_ao_for_dft_no_core, (ao_num,ao_num,N_states) ]
+&BEGIN_PROVIDER [ double precision, one_e_dm_beta_ao_for_dft_no_core, (ao_num,ao_num,N_states) ]
+ BEGIN_DOC
+! one body density matrix on the AO basis based on one_e_dm_mo_alpha_for_dft_no_core
+ END_DOC
+ implicit none
+ integer :: istate
+ double precision :: mo_alpha,mo_beta
+
+ one_e_dm_alpha_ao_for_dft_no_core = 0.d0
+ one_e_dm_beta_ao_for_dft_no_core = 0.d0
+ do istate = 1, N_states
+  call mo_to_ao_no_overlap( one_e_dm_mo_alpha_for_dft_no_core(1,1,istate), &
+                            size(one_e_dm_mo_alpha_for_dft_no_core,1),     &
+                            one_e_dm_alpha_ao_for_dft_no_core(1,1,istate), &
+                            size(one_e_dm_alpha_ao_for_dft_no_core,1) )
+  call mo_to_ao_no_overlap( one_e_dm_mo_beta_for_dft_no_core(1,1,istate), &
+                            size(one_e_dm_mo_beta_for_dft_no_core,1),     &
+                            one_e_dm_beta_ao_for_dft_no_core(1,1,istate), &
+                            size(one_e_dm_beta_ao_for_dft_no_core,1) )
+ enddo
+
+END_PROVIDER
+

src/dft_utils_in_r/dm_in_r.irp.f

@@ -109,6 +109,90 @@ end
    grad_dm_b *= 2.d0
  end
 
+subroutine dm_dft_alpha_beta_no_core_at_r(r,dm_a,dm_b)
+ implicit none
+ BEGIN_DOC
+! input: r(1) ==> r(1) = x, r(2) = y, r(3) = z
+! output : dm_a = alpha density evaluated at r(3) without the core orbitals 
+! output : dm_b = beta  density evaluated at r(3) without the core orbitals 
+ END_DOC
+ double precision, intent(in) :: r(3)
+ double precision, intent(out) :: dm_a(N_states),dm_b(N_states)
+ integer :: istate
+ double precision  :: aos_array(ao_num),aos_array_bis(ao_num),u_dot_v
+ call give_all_aos_at_r(r,aos_array)
+ do istate = 1, N_states
+  aos_array_bis = aos_array
+  ! alpha density
+  call dgemv('N',ao_num,ao_num,1.d0,one_e_dm_alpha_ao_for_dft_no_core(1,1,istate),ao_num,aos_array,1,0.d0,aos_array_bis,1)
+  dm_a(istate) = u_dot_v(aos_array,aos_array_bis,ao_num)
+  ! beta density
+  aos_array_bis = aos_array
+  call dgemv('N',ao_num,ao_num,1.d0,one_e_dm_beta_ao_for_dft_no_core(1,1,istate),ao_num,aos_array,1,0.d0,aos_array_bis,1)
+  dm_b(istate) = u_dot_v(aos_array,aos_array_bis,ao_num)
+ enddo
+end
+
+ subroutine dens_grad_a_b_no_core_and_aos_grad_aos_at_r(r,dm_a,dm_b, grad_dm_a, grad_dm_b, aos_array, grad_aos_array)
+ implicit none
+ BEGIN_DOC
+! input:
+!
+! * r(1) ==> r(1) = x, r(2) = y, r(3) = z
+!
+! output:
+!
+! * dm_a = alpha density evaluated at r without the core orbitals 
+! * dm_b = beta  density evaluated at r without the core orbitals 
+! * aos_array(i) = ao(i) evaluated at r without the core orbitals 
+! * grad_dm_a(1) = X gradient of the alpha density evaluated in r without the core orbitals 
+! * grad_dm_a(1) = X gradient of the beta  density evaluated in r without the core orbitals 
+! * grad_aos_array(1) = X gradient of the aos(i) evaluated at r
+!
+ END_DOC
+ double precision, intent(in)  :: r(3)
+ double precision, intent(out) :: dm_a(N_states),dm_b(N_states)
+ double precision, intent(out) :: grad_dm_a(3,N_states),grad_dm_b(3,N_states)
+ double precision, intent(out) :: grad_aos_array(3,ao_num)
+ integer :: i,j,istate
+ double precision  :: aos_array(ao_num),aos_array_bis(ao_num),u_dot_v
+ double precision  :: aos_grad_array(ao_num,3), aos_grad_array_bis(ao_num,3)
+
+ call give_all_aos_and_grad_at_r(r,aos_array,grad_aos_array)
+ do i = 1, ao_num
+  do j = 1, 3
+   aos_grad_array(i,j) =  grad_aos_array(j,i)
+  enddo
+ enddo
+
+ do istate = 1, N_states
+   ! alpha density
+   ! aos_array_bis = \rho_ao * aos_array
+   call dsymv('U',ao_num,1.d0,one_e_dm_alpha_ao_for_dft_no_core(1,1,istate),size(one_e_dm_alpha_ao_for_dft_no_core,1),aos_array,1,0.d0,aos_array_bis,1)
+   dm_a(istate) = u_dot_v(aos_array,aos_array_bis,ao_num)
+
+   ! grad_dm(1) = \sum_i aos_grad_array(i,1) * aos_array_bis(i)
+   grad_dm_a(1,istate) = u_dot_v(aos_grad_array(1,1),aos_array_bis,ao_num)
+   grad_dm_a(2,istate) = u_dot_v(aos_grad_array(1,2),aos_array_bis,ao_num)
+   grad_dm_a(3,istate) = u_dot_v(aos_grad_array(1,3),aos_array_bis,ao_num)
+   ! aos_grad_array_bis = \rho_ao * aos_grad_array
+
+   ! beta density
+   call dsymv('U',ao_num,1.d0,one_e_dm_beta_ao_for_dft_no_core(1,1,istate),size(one_e_dm_beta_ao_for_dft_no_core,1),aos_array,1,0.d0,aos_array_bis,1)
+   dm_b(istate) = u_dot_v(aos_array,aos_array_bis,ao_num)
+
+   ! grad_dm(1) = \sum_i aos_grad_array(i,1) * aos_array_bis(i)
+   grad_dm_b(1,istate) = u_dot_v(aos_grad_array(1,1),aos_array_bis,ao_num)
+   grad_dm_b(2,istate) = u_dot_v(aos_grad_array(1,2),aos_array_bis,ao_num)
+   grad_dm_b(3,istate) = u_dot_v(aos_grad_array(1,3),aos_array_bis,ao_num)
+   ! aos_grad_array_bis = \rho_ao * aos_grad_array
+ enddo
+   grad_dm_a *= 2.d0
+   grad_dm_b *= 2.d0
+ end
+
+
+
  BEGIN_PROVIDER [double precision, one_e_dm_alpha_in_r, (n_points_integration_angular,n_points_radial_grid,nucl_num,N_states) ]
 &BEGIN_PROVIDER [double precision, one_e_dm_beta_in_r, (n_points_integration_angular,n_points_radial_grid,nucl_num,N_states) ]
  implicit none
@@ -143,6 +227,8 @@ END_PROVIDER
 
  BEGIN_PROVIDER [double precision, one_e_dm_alpha_at_r, (n_points_final_grid,N_states) ]
 &BEGIN_PROVIDER [double precision, one_e_dm_beta_at_r, (n_points_final_grid,N_states) ]
+&BEGIN_PROVIDER [double precision, elec_beta_num_grid_becke , (N_states) ]
+&BEGIN_PROVIDER [double precision, elec_alpha_num_grid_becke , (N_states) ]
  implicit none
  BEGIN_DOC
 ! one_e_dm_alpha_at_r(i,istate) = n_alpha(r_i,istate)
@@ -209,3 +295,44 @@ END_PROVIDER
  enddo
 
 END_PROVIDER
+
+
+ BEGIN_PROVIDER [double precision, one_e_dm_no_core_and_grad_alpha_in_r, (4,n_points_final_grid,N_states) ]
+&BEGIN_PROVIDER [double precision, one_e_dm_no_core_and_grad_beta_in_r,  (4,n_points_final_grid,N_states) ]
+ BEGIN_DOC
+! one_e_dm_no_core_and_grad_alpha_in_r(1,i,i_state) = d\dx n_alpha(r_i,istate) without core orbitals 
+! one_e_dm_no_core_and_grad_alpha_in_r(2,i,i_state) = d\dy n_alpha(r_i,istate) without core orbitals 
+! one_e_dm_no_core_and_grad_alpha_in_r(3,i,i_state) = d\dz n_alpha(r_i,istate) without core orbitals 
+! one_e_dm_no_core_and_grad_alpha_in_r(4,i,i_state) = n_alpha(r_i,istate) without core orbitals 
+! where r_i is the ith point of the grid and istate is the state number
+ END_DOC
+ implicit none
+ integer :: i,j,k,l,m,istate
+ double precision :: contrib
+ double precision :: r(3)
+ double precision, allocatable :: aos_array(:),grad_aos_array(:,:)
+ double precision, allocatable :: dm_a(:),dm_b(:), dm_a_grad(:,:), dm_b_grad(:,:)
+ allocate(dm_a(N_states),dm_b(N_states), dm_a_grad(3,N_states), dm_b_grad(3,N_states))
+ allocate(aos_array(ao_num),grad_aos_array(3,ao_num))
+ do istate = 1, N_states
+  do i = 1, n_points_final_grid
+  r(1) = final_grid_points(1,i)
+  r(2) = final_grid_points(2,i)
+  r(3) = final_grid_points(3,i)
+ !!!! Works also with the ao basis
+   call dens_grad_a_b_no_core_and_aos_grad_aos_at_r(r,dm_a,dm_b,  dm_a_grad, dm_b_grad, aos_array, grad_aos_array)
+   one_e_dm_no_core_and_grad_alpha_in_r(1,i,istate)  =  dm_a_grad(1,istate)
+   one_e_dm_no_core_and_grad_alpha_in_r(2,i,istate)  =  dm_a_grad(2,istate)
+   one_e_dm_no_core_and_grad_alpha_in_r(3,i,istate)  =  dm_a_grad(3,istate)
+   one_e_dm_no_core_and_grad_alpha_in_r(4,i,istate)  =  dm_a(istate)
+
+   one_e_dm_no_core_and_grad_beta_in_r(1,i,istate)  =  dm_b_grad(1,istate)
+   one_e_dm_no_core_and_grad_beta_in_r(2,i,istate)  =  dm_b_grad(2,istate)
+   one_e_dm_no_core_and_grad_beta_in_r(3,i,istate)  =  dm_b_grad(3,istate)
+   one_e_dm_no_core_and_grad_beta_in_r(4,i,istate)  =  dm_b(istate)
+  enddo
+ enddo
+
+END_PROVIDER
+
+

src/nuclei/atomic_radii.irp.f

@@ -1,4 +1,4 @@
-BEGIN_PROVIDER [ double precision, slater_bragg_radii, (100)]
+BEGIN_PROVIDER [ double precision, slater_bragg_radii, (0:100)]
  implicit none
  BEGIN_DOC
  ! atomic radii in Angstrom defined in table I of JCP 41, 3199 (1964) Slater
@@ -54,10 +54,10 @@ BEGIN_PROVIDER [ double precision, slater_bragg_radii, (100)]
 
 END_PROVIDER
 
-BEGIN_PROVIDER [double precision, slater_bragg_radii_ua, (100)]
+BEGIN_PROVIDER [double precision, slater_bragg_radii_ua, (0:100)]
  implicit none
  integer :: i
- do i = 1, 100
+ do i = 0, 100
   slater_bragg_radii_ua(i) = slater_bragg_radii(i) * 1.889725989d0
  enddo
 END_PROVIDER