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added point charges with the python script to write the point charges
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@ -106,3 +106,21 @@ interface: ezfio,provider,ocaml
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default: 1.e-15
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ezfio_name: threshold_ao
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[n_pts_charge]
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type: integer
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doc: Number of point charges to be added to the potential
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interface: ezfio
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default: 0
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[pts_charge_z]
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type: double precision
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doc: Charge associated to each point charge
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interface: ezfio
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size: (ao_one_e_ints.n_pts_charge)
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[pts_charge_coord]
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type: double precision
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doc: Coordinate of each point charge.
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interface: ezfio
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size: (ao_one_e_ints.n_pts_charge,3)
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272
src/ao_one_e_ints/point_charges.irp.f
Normal file
272
src/ao_one_e_ints/point_charges.irp.f
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@ -0,0 +1,272 @@
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! ---
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BEGIN_PROVIDER [ integer, n_pts_charge ]
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implicit none
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BEGIN_DOC
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! Number of point charges to be added to the potential
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END_DOC
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logical :: has
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PROVIDE ezfio_filename
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if (mpi_master) then
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call ezfio_has_ao_one_e_ints_n_pts_charge(has)
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if (has) then
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write(6,'(A)') '.. >>>>> [ IO READ: n_pts_charge ] <<<<< ..'
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call ezfio_get_ao_one_e_ints_n_pts_charge(n_pts_charge)
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else
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print *, 'ao_one_e_ints/n_pts_charge not found in EZFIO file'
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stop 1
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endif
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endif
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IRP_IF MPI_DEBUG
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print *, irp_here, mpi_rank
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call MPI_BARRIER(MPI_COMM_WORLD, ierr)
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IRP_ENDIF
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IRP_IF MPI
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include 'mpif.h'
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integer :: ierr
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call MPI_BCAST( n_pts_charge, 1, MPI_INTEGER, 0, MPI_COMM_WORLD, ierr)
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if (ierr /= MPI_SUCCESS) then
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stop 'Unable to read n_pts_charge with MPI'
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endif
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IRP_ENDIF
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call write_time(6)
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END_PROVIDER
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BEGIN_PROVIDER [ double precision, pts_charge_z, (n_pts_charge) ]
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BEGIN_DOC
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! Charge associated to each point charge.
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END_DOC
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implicit none
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logical :: exists
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PROVIDE ezfio_filename
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if (mpi_master) then
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call ezfio_has_ao_one_e_ints_pts_charge_z(exists)
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endif
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IRP_IF MPI_DEBUG
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print *, irp_here, mpi_rank
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call MPI_BARRIER(MPI_COMM_WORLD, ierr)
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IRP_ENDIF
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IRP_IF MPI
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include 'mpif.h'
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integer :: ierr
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call MPI_BCAST(pts_charge_z, (n_pts_charge), MPI_DOUBLE_PRECISION, 0, MPI_COMM_WORLD, ierr)
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if (ierr /= MPI_SUCCESS) then
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stop 'Unable to read pts_charge_z with MPI'
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endif
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IRP_ENDIF
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if (exists) then
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if (mpi_master) then
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write(6,'(A)') '.. >>>>> [ IO READ: pts_charge_z ] <<<<< ..'
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call ezfio_get_ao_one_e_ints_pts_charge_z(pts_charge_z)
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IRP_IF MPI
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call MPI_BCAST(pts_charge_z, (n_pts_charge), MPI_DOUBLE_PRECISION, 0, MPI_COMM_WORLD, ierr)
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if (ierr /= MPI_SUCCESS) then
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stop 'Unable to read pts_charge_z with MPI'
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endif
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IRP_ENDIF
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endif
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else
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integer :: i
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do i = 1, n_pts_charge
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pts_charge_z(i) = 0.d0
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enddo
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endif
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print*,'Point charges '
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do i = 1, n_pts_charge
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print*,'i,pts_charge_z(i)',i,pts_charge_z(i)
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enddo
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END_PROVIDER
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BEGIN_PROVIDER [ double precision, pts_charge_coord, (n_pts_charge,3) ]
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BEGIN_DOC
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! Coordinates of each point charge.
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END_DOC
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implicit none
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logical :: exists
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PROVIDE ezfio_filename
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if (mpi_master) then
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call ezfio_has_ao_one_e_ints_pts_charge_coord(exists)
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endif
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IRP_IF MPI_DEBUG
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print *, irp_here, mpi_rank
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call MPI_BARRIER(MPI_COMM_WORLD, ierr)
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IRP_ENDIF
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IRP_IF MPI
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include 'mpif.h'
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integer :: ierr
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call MPI_BCAST(pts_charge_coord, (n_pts_charge), MPI_DOUBLE_PRECISION, 0, MPI_COMM_WORLD, ierr)
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if (ierr /= MPI_SUCCESS) then
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stop 'Unable to read pts_charge_coord with MPI'
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endif
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IRP_ENDIF
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if (exists) then
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if (mpi_master) then
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double precision, allocatable :: buffer(:,:)
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allocate (buffer(n_pts_charge,3))
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write(6,'(A)') '.. >>>>> [ IO READ: pts_charge_coord ] <<<<< ..'
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call ezfio_get_ao_one_e_ints_pts_charge_coord(buffer)
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integer :: i,j
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do i=1,3
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do j=1,n_pts_charge
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pts_charge_coord(j,i) = buffer(j,i)
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enddo
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enddo
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deallocate(buffer)
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IRP_IF MPI
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call MPI_BCAST(pts_charge_coord, (n_pts_charge), MPI_DOUBLE_PRECISION, 0, MPI_COMM_WORLD, ierr)
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if (ierr /= MPI_SUCCESS) then
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stop 'Unable to read pts_charge_coord with MPI'
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endif
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IRP_ENDIF
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endif
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else
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do i = 1, n_pts_charge
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pts_charge_coord(i,:) = 0.d0
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enddo
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endif
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print*,'Coordinates for the point charges '
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do i = 1, n_pts_charge
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write(*,'(I3,X,3(F16.8,X))'),i,pts_charge_coord(i,1:3)
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enddo
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END_PROVIDER
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! ---
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BEGIN_PROVIDER [ double precision, ao_integrals_pt_chrg, (ao_num,ao_num)]
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BEGIN_DOC
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! Point charge-electron interaction, in the |AO| basis set.
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!
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! :math:`\langle \chi_i | -\sum_A \frac{1}{|r-R_A|} | \chi_j \rangle`
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!
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! These integrals also contain the pseudopotential integrals.
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END_DOC
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implicit none
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integer :: num_A, num_B, power_A(3), power_B(3)
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integer :: i, j, k, l, n_pt_in, m
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double precision :: alpha, beta
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double precision :: A_center(3),B_center(3),C_center(3)
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double precision :: overlap_x,overlap_y,overlap_z,overlap,dx,NAI_pol_mult
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ao_integrals_pt_chrg = 0.d0
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! if (read_ao_integrals_pt_chrg) then
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!
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! call ezfio_get_ao_one_e_ints_ao_integrals_pt_chrg(ao_integrals_pt_chrg)
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! print *, 'AO N-e integrals read from disk'
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!
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! else
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! if(use_cosgtos) then
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! !print *, " use_cosgtos for ao_integrals_pt_chrg ?", use_cosgtos
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!
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! do j = 1, ao_num
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! do i = 1, ao_num
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! ao_integrals_pt_chrg(i,j) = ao_integrals_pt_chrg_cosgtos(i,j)
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! enddo
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! enddo
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!
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! else
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!$OMP PARALLEL &
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!$OMP DEFAULT (NONE) &
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!$OMP PRIVATE (i,j,k,l,m,alpha,beta,A_center,B_center,C_center,power_A,power_B,&
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!$OMP num_A,num_B,Z,c,c1,n_pt_in) &
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!$OMP SHARED (ao_num,ao_prim_num,ao_expo_ordered_transp,ao_power,ao_nucl,pts_charge_coord,ao_coef_normalized_ordered_transp,&
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!$OMP n_pt_max_integrals,ao_integrals_pt_chrg,n_pts_charge,pts_charge_z)
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n_pt_in = n_pt_max_integrals
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!$OMP DO SCHEDULE (dynamic)
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do j = 1, ao_num
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num_A = ao_nucl(j)
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power_A(1:3)= ao_power(j,1:3)
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A_center(1:3) = pts_charge_coord(num_A,1:3)
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do i = 1, ao_num
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num_B = ao_nucl(i)
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power_B(1:3)= ao_power(i,1:3)
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B_center(1:3) = pts_charge_coord(num_B,1:3)
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do l=1,ao_prim_num(j)
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alpha = ao_expo_ordered_transp(l,j)
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do m=1,ao_prim_num(i)
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beta = ao_expo_ordered_transp(m,i)
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double precision :: c, c1
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c = 0.d0
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do k = 1, n_pts_charge
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double precision :: Z
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Z = pts_charge_z(k)
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C_center(1:3) = pts_charge_coord(k,1:3)
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c1 = NAI_pol_mult( A_center, B_center, power_A, power_B &
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, alpha, beta, C_center, n_pt_in )
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c = c - Z * c1
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enddo
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ao_integrals_pt_chrg(i,j) = ao_integrals_pt_chrg(i,j) &
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+ ao_coef_normalized_ordered_transp(l,j) &
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* ao_coef_normalized_ordered_transp(m,i) * c
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enddo
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enddo
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enddo
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enddo
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!$OMP END DO
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!$OMP END PARALLEL
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! endif
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! IF(do_pseudo) THEN
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! ao_integrals_pt_chrg += ao_pseudo_integrals
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! ENDIF
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! endif
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! if (write_ao_integrals_pt_chrg) then
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! call ezfio_set_ao_one_e_ints_ao_integrals_pt_chrg(ao_integrals_pt_chrg)
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! print *, 'AO N-e integrals written to disk'
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! endif
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END_PROVIDER
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73
src/ao_one_e_ints/write_pt_charges.py
Executable file
73
src/ao_one_e_ints/write_pt_charges.py
Executable file
@ -0,0 +1,73 @@
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#!/usr/bin/env python
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import os
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import sys
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def zip_in_ezfio(ezfio,tmp):
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tmpzip=tmp+".gz"
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cmdzip="gzip -c "+tmp+" > "+tmpzip
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os.system(cmdzip)
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os.system("rm "+tmp)
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cmdmv="mv "+tmpzip+" "+EZFIO+"/ao_one_e_ints/"+tmpzip
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os.system(cmdmv)
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def mv_in_ezfio(ezfio,tmp):
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cmdmv="mv "+tmp+" "+EZFIO+"/ao_one_e_ints/"+tmp
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os.system(cmdmv)
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# Getting the EZFIO
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EZFIO=sys.argv[1]
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EZFIO=EZFIO.replace("/", "")
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print(EZFIO)
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# Reading the point charges and convert the Angstrom geometry in Bohr for QP
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f = open('point_charges.xyz','r')
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lines = f.readlines()
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convert_angs_to_bohr=1.88973
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n_charges=0
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coord_x=[]
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coord_y=[]
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coord_z=[]
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charges=[]
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for line in lines:
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data = line.split()
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if(len(data)>0):
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n_charges += 1
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charges.append(str(data[0]))
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coord_x.append(str(convert_angs_to_bohr*float(data[1])))
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coord_y.append(str(convert_angs_to_bohr*float(data[2])))
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coord_z.append(str(convert_angs_to_bohr*float(data[3])))
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# Write the file containing the number of charges and set in EZFIO folder
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tmp="n_pts_charge"
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fncharges = open(tmp,'w')
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fncharges.write(" "+str(n_charges)+'\n')
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fncharges.close()
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mv_in_ezfio(EZFIO,tmp)
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# Write the file containing the charges and set in EZFIO folder
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tmp="pts_charge_z"
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fcharges = open(tmp,'w')
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fcharges.write(" 1\n")
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fcharges.write(" "+str(n_charges)+'\n')
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for i in range(n_charges):
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fcharges.write(charges[i]+'\n')
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fcharges.close()
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zip_in_ezfio(EZFIO,tmp)
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# Write the file containing the charge coordinates and set in EZFIO folder
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tmp="pts_charge_coord"
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fcoord = open(tmp,'w')
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fcoord.write(" 2\n")
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fcoord.write(" "+str(n_charges)+' 3\n')
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#fcoord.write(" "+' 3 '+str(n_charges)+' \n')
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for i in range(n_charges):
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fcoord.write(' '+coord_x[i]+'\n')
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for i in range(n_charges):
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fcoord.write(' '+coord_y[i]+'\n')
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for i in range(n_charges):
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fcoord.write(' '+coord_z[i]+'\n')
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fcoord.close()
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zip_in_ezfio(EZFIO,tmp)
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