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

* Adding Basis Sets and ECP from NCSU. When available He core ECP are chosen instead of large core. This applies to Na Mg Al Si P S Cl and Ar

*  ECP from ncsu

* Update Readme file with description of Basis Set

config/ifort_avx.cfg

@@ -32,7 +32,7 @@ OPENMP  : 1          ; Append OpenMP flags
 #
 [OPT]
 FC       : -traceback
-FCFLAGS  : -xAVX -O2 -ip -ftz -g 
+FCFLAGS  : -march=corei7-avx -O2 -ip -ftz -g 
 
 # Profiling flags
 #################

config/ifort_avx_mpi.cfg

@@ -31,14 +31,14 @@ OPENMP  : 1          ; Append OpenMP flags
 # -ftz                       : Flushes denormal results to zero
 #
 [OPT]
-FCFLAGS  : -xAVX -O2 -ip -ftz -g -traceback  
+FCFLAGS  : -march=corei7-avx -O2 -ip -ftz -g -traceback  
 
 # Profiling flags
 #################
 #
 [PROFILE]
 FC       : -p -g
-FCFLAGS  : -xSSE4.2 -O2 -ip -ftz 
+FCFLAGS  : -march=corei7 -O2 -ip -ftz 
 
 
 # Debugging flags

src/ao_two_e_erf_ints/two_e_integrals_erf.irp.f

@@ -15,6 +15,8 @@ double precision function ao_two_e_integral_erf(i,j,k,l)
   double precision               :: Q_new(0:max_dim,3),Q_center(3),fact_q,qq
   integer                        :: iorder_p(3), iorder_q(3)
   double precision               :: ao_two_e_integral_schwartz_accel_erf
+  
+  provide mu_erf
 
    if (ao_prim_num(i) * ao_prim_num(j) * ao_prim_num(k) * ao_prim_num(l) > 1024 ) then
      ao_two_e_integral_erf = ao_two_e_integral_schwartz_accel_erf(i,j,k,l)

src/ao_two_e_ints/map_integrals.irp.f

@@ -279,6 +279,100 @@ subroutine get_ao_two_e_integrals_non_zero(j,k,l,sze,out_val,out_val_index,non_z
 end
 
 
+subroutine get_ao_two_e_integrals_non_zero_jl(j,l,thresh,sze_max,sze,out_val,out_val_index,non_zero_int)
+  use map_module
+  implicit none
+  BEGIN_DOC
+  ! Gets multiple AO bi-electronic integral from the AO map .
+  ! All non-zero i are retrieved for j,k,l fixed.
+  END_DOC
+  double precision, intent(in)   :: thresh
+  integer, intent(in)            :: j,l, sze,sze_max
+  real(integral_kind), intent(out) :: out_val(sze_max)
+  integer, intent(out)           :: out_val_index(2,sze_max),non_zero_int
+
+  integer                        :: i,k
+  integer(key_kind)              :: hash
+  double precision               :: tmp
+
+  PROVIDE ao_two_e_integrals_in_map
+  non_zero_int = 0
+  if (ao_overlap_abs(j,l) < thresh) then
+    out_val = 0.d0
+    return
+  endif
+
+  non_zero_int = 0
+  do k = 1, sze
+   do i = 1, sze
+     integer, external :: ao_l4
+     double precision, external :: ao_two_e_integral
+     !DIR$ FORCEINLINE
+     if (ao_two_e_integral_schwartz(i,k)*ao_two_e_integral_schwartz(j,l) < thresh) then
+       cycle
+     endif
+     call two_e_integrals_index(i,j,k,l,hash)
+     call map_get(ao_integrals_map, hash,tmp)
+     if (dabs(tmp) < thresh ) cycle
+     non_zero_int = non_zero_int+1
+     out_val_index(1,non_zero_int) = i
+     out_val_index(2,non_zero_int) = k
+     out_val(non_zero_int) = tmp
+   enddo
+  enddo
+
+end
+
+
+subroutine get_ao_two_e_integrals_non_zero_jl_from_list(j,l,thresh,list,n_list,sze_max,out_val,out_val_index,non_zero_int)
+  use map_module
+  implicit none
+  BEGIN_DOC
+  ! Gets multiple AO two-electron integrals from the AO map .
+  ! All non-zero i are retrieved for j,k,l fixed.
+  END_DOC
+  double precision, intent(in)   :: thresh
+  integer, intent(in)            :: sze_max
+  integer, intent(in)            :: j,l, n_list,list(2,sze_max)
+  real(integral_kind), intent(out) :: out_val(sze_max)
+  integer, intent(out)           :: out_val_index(2,sze_max),non_zero_int
+
+  integer                        :: i,k
+  integer(key_kind)              :: hash
+  double precision               :: tmp
+
+  PROVIDE ao_two_e_integrals_in_map
+  non_zero_int = 0
+  if (ao_overlap_abs(j,l) < thresh) then
+    out_val = 0.d0
+    return
+  endif
+
+  non_zero_int = 0
+ integer :: kk
+  do kk = 1, n_list
+   k = list(1,kk)
+   i = list(2,kk)
+   integer, external :: ao_l4
+   double precision, external :: ao_two_e_integral
+   !DIR$ FORCEINLINE
+   if (ao_two_e_integral_schwartz(i,k)*ao_two_e_integral_schwartz(j,l) < thresh) then
+     cycle
+   endif
+   call two_e_integrals_index(i,j,k,l,hash)
+   call map_get(ao_integrals_map, hash,tmp)
+   if (dabs(tmp) < thresh ) cycle
+   non_zero_int = non_zero_int+1
+   out_val_index(1,non_zero_int) = i
+   out_val_index(2,non_zero_int) = k
+   out_val(non_zero_int) = tmp
+  enddo
+
+end
+
+
+
+
 function get_ao_map_size()
   implicit none
   integer (map_size_kind) :: get_ao_map_size

src/becke_numerical_grid/EZFIO.cfg

@@ -8,3 +8,9 @@ default: 2
 type: integer
 doc: Total number of grid points 
 interface: ezfio
+
+[thresh_grid]
+type: double precision
+doc: threshold on the weight of a given grid point
+interface: ezfio,provider,ocaml
+default: 1.e-20

src/becke_numerical_grid/atomic_number.irp.f

@@ -0,0 +1,9 @@
+BEGIN_PROVIDER [ integer, grid_atomic_number, (nucl_num) ]
+ implicit none
+ BEGIN_DOC
+ ! Atomic number used to adjust the grid
+ END_DOC
+ grid_atomic_number(:) = max(1,int(nucl_charge(:)))
+
+END_PROVIDER
+

src/becke_numerical_grid/grid_becke.irp.f

@@ -146,7 +146,7 @@ BEGIN_PROVIDER [double precision, grid_points_per_atom, (3,n_points_integration_
       x = grid_points_radial(j)
 
       ! value of the radial coordinate for the integration
-      r = knowles_function(alpha_knowles(int(nucl_charge(i))),m_knowles,x)
+      r = knowles_function(alpha_knowles(grid_atomic_number(i)),m_knowles,x)
 
       ! explicit values of the grid points centered around each atom
       do k = 1, n_points_integration_angular
@@ -232,8 +232,8 @@ BEGIN_PROVIDER [double precision, final_weight_at_r, (n_points_integration_angul
     do i = 1, n_points_radial_grid -1 !for each radial grid attached to the "jth" atom
       x = grid_points_radial(i) ! x value for the mapping of the [0, +\infty] to [0,1]
       do k = 1, n_points_integration_angular  ! for each angular point attached to the "jth" atom
-        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
+        contrib_integration = derivative_knowles_function(alpha_knowles(grid_atomic_number(j)),m_knowles,x)&
+            *knowles_function(alpha_knowles(grid_atomic_number(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))' 

src/becke_numerical_grid/grid_becke_per_atom.irp.f

@@ -0,0 +1,53 @@
+
+
+ BEGIN_PROVIDER [integer, n_pts_per_atom, (nucl_num)]
+&BEGIN_PROVIDER [integer, n_pts_max_per_atom]
+  BEGIN_DOC
+  ! Number of points which are non zero
+  END_DOC
+  integer                        :: i,j,k,l
+  n_pts_per_atom = 0
+  do j = 1, nucl_num
+    do i = 1, n_points_radial_grid -1
+      do k = 1, n_points_integration_angular
+        if(dabs(final_weight_at_r(k,i,j)) < thresh_grid)then
+          cycle
+        endif
+        n_pts_per_atom(j) += 1
+      enddo
+    enddo
+  enddo
+  n_pts_max_per_atom = maxval(n_pts_per_atom)
+END_PROVIDER
+
+ BEGIN_PROVIDER [double precision, final_grid_points_per_atom, (3,n_pts_max_per_atom,nucl_num)]
+&BEGIN_PROVIDER [double precision, final_weight_at_r_vector_per_atom, (n_pts_max_per_atom,nucl_num) ]
+&BEGIN_PROVIDER [integer, index_final_points_per_atom, (3,n_pts_max_per_atom,nucl_num) ]
+&BEGIN_PROVIDER [integer, index_final_points_per_atom_reverse, (n_points_integration_angular,n_points_radial_grid,nucl_num) ]
+ implicit none
+ integer                        :: i,j,k,l,i_count(nucl_num)
+ double precision               :: r(3)
+ i_count = 0
+  do j = 1, nucl_num
+    do i = 1, n_points_radial_grid -1
+      do k = 1, n_points_integration_angular
+        if(dabs(final_weight_at_r(k,i,j)) < thresh_grid)then
+          cycle
+        endif
+        i_count(j) += 1
+        final_grid_points_per_atom(1,i_count(j),j) = grid_points_per_atom(1,k,i,j)
+        final_grid_points_per_atom(2,i_count(j),j) = grid_points_per_atom(2,k,i,j)
+        final_grid_points_per_atom(3,i_count(j),j) = grid_points_per_atom(3,k,i,j)
+        final_weight_at_r_vector_per_atom(i_count(j),j) = final_weight_at_r(k,i,j)
+        index_final_points_per_atom(1,i_count(j),j) = k
+        index_final_points_per_atom(2,i_count(j),j) = i
+        index_final_points_per_atom(3,i_count(j),j) = j
+        index_final_points_per_atom_reverse(k,i,j) = i_count(j)
+      enddo
+    enddo
+  enddo
+
+
+
+
+END_PROVIDER 

src/becke_numerical_grid/grid_becke_vector.irp.f

@@ -1,5 +1,6 @@
 
 BEGIN_PROVIDER [integer, n_points_final_grid]
+  implicit none
   BEGIN_DOC
   ! Number of points which are non zero
   END_DOC
@@ -8,9 +9,9 @@ BEGIN_PROVIDER [integer, n_points_final_grid]
   do j = 1, nucl_num
     do i = 1, n_points_radial_grid -1
       do k = 1, n_points_integration_angular
-!       if(dabs(final_weight_at_r(k,i,j)) < 1.d-30)then
-!         cycle
-!       endif
+        if(dabs(final_weight_at_r(k,i,j)) < thresh_grid)then
+          cycle
+        endif
         n_points_final_grid += 1
       enddo
     enddo
@@ -39,9 +40,9 @@ END_PROVIDER
   do j = 1, nucl_num
     do i = 1, n_points_radial_grid -1
       do k = 1, n_points_integration_angular
-       !if(dabs(final_weight_at_r(k,i,j)) < 1.d-30)then
-       !  cycle
-       !endif
+        if(dabs(final_weight_at_r(k,i,j)) < thresh_grid)then
+          cycle
+        endif
         i_count += 1
         final_grid_points(1,i_count) = grid_points_per_atom(1,k,i,j)
         final_grid_points(2,i_count) = grid_points_per_atom(2,k,i,j)

src/becke_numerical_grid/step_function_becke.irp.f

@@ -31,10 +31,6 @@ 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))
@@ -42,7 +38,6 @@ 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/dft_utils_in_r/ao_in_r.irp.f

@@ -121,3 +121,26 @@
  enddo
  END_PROVIDER
 
+
+ BEGIN_PROVIDER[double precision, aos_in_r_array_per_atom, (ao_num,n_pts_max_per_atom,nucl_num)]
+&BEGIN_PROVIDER[double precision, aos_in_r_array_per_atom_transp, (n_pts_max_per_atom,ao_num,nucl_num)]
+ implicit none
+ BEGIN_DOC
+ ! aos_in_r_array_per_atom(i,j,k)        = value of the ith ao on the jth grid point attached on the kth atom 
+ END_DOC
+ integer :: i,j,k
+ double precision :: aos_array(ao_num), r(3)
+ do k = 1, nucl_num
+  do i = 1, n_pts_per_atom(k)
+   r(1) = final_grid_points_per_atom(1,i,k)
+   r(2) = final_grid_points_per_atom(2,i,k)
+   r(3) = final_grid_points_per_atom(3,i,k)
+   call give_all_aos_at_r(r,aos_array)
+   do j = 1, ao_num
+    aos_in_r_array_per_atom(j,i,k) = aos_array(j)
+    aos_in_r_array_per_atom_transp(i,j,k) = aos_array(j)
+   enddo
+  enddo
+ enddo
+ END_PROVIDER
+

src/nuclei/atomic_radii.irp.f

@@ -66,7 +66,7 @@ BEGIN_PROVIDER [double precision, slater_bragg_radii_per_atom, (nucl_num)]
  implicit none
  integer :: i
  do i = 1, nucl_num
-  slater_bragg_radii_per_atom(i) = slater_bragg_radii(int(nucl_charge(i)))
+  slater_bragg_radii_per_atom(i) = slater_bragg_radii(max(1,int(nucl_charge(i))))
  enddo
 END_PROVIDER
 
@@ -74,7 +74,7 @@ BEGIN_PROVIDER [double precision, slater_bragg_radii_per_atom_ua, (nucl_num)]
  implicit none
  integer :: i
  do i = 1, nucl_num
-  slater_bragg_radii_per_atom_ua(i) = slater_bragg_radii_ua(int(nucl_charge(i)))
+  slater_bragg_radii_per_atom_ua(i) = slater_bragg_radii_ua(max(1,int(nucl_charge(i))))
  enddo
 END_PROVIDER