mirror of
https://github.com/QuantumPackage/qp2.git
synced 2024-09-01 21:53:40 +02:00
added point charges with the python script to write the point charges
This commit is contained in:
parent
6d7c7ab335
commit
7eb14fc0f8
@ -106,3 +106,21 @@ interface: ezfio,provider,ocaml
|
||||
default: 1.e-15
|
||||
ezfio_name: threshold_ao
|
||||
|
||||
[n_pts_charge]
|
||||
type: integer
|
||||
doc: Number of point charges to be added to the potential
|
||||
interface: ezfio
|
||||
default: 0
|
||||
|
||||
[pts_charge_z]
|
||||
type: double precision
|
||||
doc: Charge associated to each point charge
|
||||
interface: ezfio
|
||||
size: (ao_one_e_ints.n_pts_charge)
|
||||
|
||||
[pts_charge_coord]
|
||||
type: double precision
|
||||
doc: Coordinate of each point charge.
|
||||
interface: ezfio
|
||||
size: (ao_one_e_ints.n_pts_charge,3)
|
||||
|
||||
|
272
src/ao_one_e_ints/point_charges.irp.f
Normal file
272
src/ao_one_e_ints/point_charges.irp.f
Normal file
@ -0,0 +1,272 @@
|
||||
|
||||
! ---
|
||||
|
||||
|
||||
BEGIN_PROVIDER [ integer, n_pts_charge ]
|
||||
implicit none
|
||||
BEGIN_DOC
|
||||
! Number of point charges to be added to the potential
|
||||
END_DOC
|
||||
|
||||
logical :: has
|
||||
PROVIDE ezfio_filename
|
||||
if (mpi_master) then
|
||||
|
||||
call ezfio_has_ao_one_e_ints_n_pts_charge(has)
|
||||
if (has) then
|
||||
write(6,'(A)') '.. >>>>> [ IO READ: n_pts_charge ] <<<<< ..'
|
||||
call ezfio_get_ao_one_e_ints_n_pts_charge(n_pts_charge)
|
||||
else
|
||||
print *, 'ao_one_e_ints/n_pts_charge not found in EZFIO file'
|
||||
stop 1
|
||||
endif
|
||||
endif
|
||||
IRP_IF MPI_DEBUG
|
||||
print *, irp_here, mpi_rank
|
||||
call MPI_BARRIER(MPI_COMM_WORLD, ierr)
|
||||
IRP_ENDIF
|
||||
IRP_IF MPI
|
||||
include 'mpif.h'
|
||||
integer :: ierr
|
||||
call MPI_BCAST( n_pts_charge, 1, MPI_INTEGER, 0, MPI_COMM_WORLD, ierr)
|
||||
if (ierr /= MPI_SUCCESS) then
|
||||
stop 'Unable to read n_pts_charge with MPI'
|
||||
endif
|
||||
IRP_ENDIF
|
||||
|
||||
call write_time(6)
|
||||
|
||||
END_PROVIDER
|
||||
|
||||
BEGIN_PROVIDER [ double precision, pts_charge_z, (n_pts_charge) ]
|
||||
|
||||
BEGIN_DOC
|
||||
! Charge associated to each point charge.
|
||||
END_DOC
|
||||
|
||||
implicit none
|
||||
logical :: exists
|
||||
|
||||
PROVIDE ezfio_filename
|
||||
|
||||
if (mpi_master) then
|
||||
call ezfio_has_ao_one_e_ints_pts_charge_z(exists)
|
||||
endif
|
||||
|
||||
IRP_IF MPI_DEBUG
|
||||
print *, irp_here, mpi_rank
|
||||
call MPI_BARRIER(MPI_COMM_WORLD, ierr)
|
||||
IRP_ENDIF
|
||||
|
||||
IRP_IF MPI
|
||||
include 'mpif.h'
|
||||
integer :: ierr
|
||||
call MPI_BCAST(pts_charge_z, (n_pts_charge), MPI_DOUBLE_PRECISION, 0, MPI_COMM_WORLD, ierr)
|
||||
if (ierr /= MPI_SUCCESS) then
|
||||
stop 'Unable to read pts_charge_z with MPI'
|
||||
endif
|
||||
IRP_ENDIF
|
||||
|
||||
if (exists) then
|
||||
|
||||
if (mpi_master) then
|
||||
write(6,'(A)') '.. >>>>> [ IO READ: pts_charge_z ] <<<<< ..'
|
||||
call ezfio_get_ao_one_e_ints_pts_charge_z(pts_charge_z)
|
||||
IRP_IF MPI
|
||||
call MPI_BCAST(pts_charge_z, (n_pts_charge), MPI_DOUBLE_PRECISION, 0, MPI_COMM_WORLD, ierr)
|
||||
if (ierr /= MPI_SUCCESS) then
|
||||
stop 'Unable to read pts_charge_z with MPI'
|
||||
endif
|
||||
IRP_ENDIF
|
||||
endif
|
||||
|
||||
else
|
||||
|
||||
integer :: i
|
||||
do i = 1, n_pts_charge
|
||||
pts_charge_z(i) = 0.d0
|
||||
enddo
|
||||
|
||||
endif
|
||||
print*,'Point charges '
|
||||
do i = 1, n_pts_charge
|
||||
print*,'i,pts_charge_z(i)',i,pts_charge_z(i)
|
||||
enddo
|
||||
|
||||
END_PROVIDER
|
||||
|
||||
|
||||
BEGIN_PROVIDER [ double precision, pts_charge_coord, (n_pts_charge,3) ]
|
||||
|
||||
BEGIN_DOC
|
||||
! Coordinates of each point charge.
|
||||
END_DOC
|
||||
|
||||
implicit none
|
||||
logical :: exists
|
||||
|
||||
PROVIDE ezfio_filename
|
||||
|
||||
if (mpi_master) then
|
||||
call ezfio_has_ao_one_e_ints_pts_charge_coord(exists)
|
||||
endif
|
||||
|
||||
IRP_IF MPI_DEBUG
|
||||
print *, irp_here, mpi_rank
|
||||
call MPI_BARRIER(MPI_COMM_WORLD, ierr)
|
||||
IRP_ENDIF
|
||||
|
||||
IRP_IF MPI
|
||||
include 'mpif.h'
|
||||
integer :: ierr
|
||||
call MPI_BCAST(pts_charge_coord, (n_pts_charge), MPI_DOUBLE_PRECISION, 0, MPI_COMM_WORLD, ierr)
|
||||
if (ierr /= MPI_SUCCESS) then
|
||||
stop 'Unable to read pts_charge_coord with MPI'
|
||||
endif
|
||||
IRP_ENDIF
|
||||
|
||||
if (exists) then
|
||||
|
||||
if (mpi_master) then
|
||||
double precision, allocatable :: buffer(:,:)
|
||||
allocate (buffer(n_pts_charge,3))
|
||||
write(6,'(A)') '.. >>>>> [ IO READ: pts_charge_coord ] <<<<< ..'
|
||||
call ezfio_get_ao_one_e_ints_pts_charge_coord(buffer)
|
||||
integer :: i,j
|
||||
do i=1,3
|
||||
do j=1,n_pts_charge
|
||||
pts_charge_coord(j,i) = buffer(j,i)
|
||||
enddo
|
||||
enddo
|
||||
deallocate(buffer)
|
||||
IRP_IF MPI
|
||||
call MPI_BCAST(pts_charge_coord, (n_pts_charge), MPI_DOUBLE_PRECISION, 0, MPI_COMM_WORLD, ierr)
|
||||
if (ierr /= MPI_SUCCESS) then
|
||||
stop 'Unable to read pts_charge_coord with MPI'
|
||||
endif
|
||||
IRP_ENDIF
|
||||
endif
|
||||
|
||||
else
|
||||
|
||||
do i = 1, n_pts_charge
|
||||
pts_charge_coord(i,:) = 0.d0
|
||||
enddo
|
||||
|
||||
endif
|
||||
print*,'Coordinates for the point charges '
|
||||
do i = 1, n_pts_charge
|
||||
write(*,'(I3,X,3(F16.8,X))'),i,pts_charge_coord(i,1:3)
|
||||
enddo
|
||||
|
||||
END_PROVIDER
|
||||
|
||||
! ---
|
||||
|
||||
BEGIN_PROVIDER [ double precision, ao_integrals_pt_chrg, (ao_num,ao_num)]
|
||||
|
||||
BEGIN_DOC
|
||||
! Point charge-electron interaction, in the |AO| basis set.
|
||||
!
|
||||
! :math:`\langle \chi_i | -\sum_A \frac{1}{|r-R_A|} | \chi_j \rangle`
|
||||
!
|
||||
! These integrals also contain the pseudopotential integrals.
|
||||
END_DOC
|
||||
|
||||
implicit none
|
||||
integer :: num_A, num_B, power_A(3), power_B(3)
|
||||
integer :: i, j, k, l, n_pt_in, m
|
||||
double precision :: alpha, beta
|
||||
double precision :: A_center(3),B_center(3),C_center(3)
|
||||
double precision :: overlap_x,overlap_y,overlap_z,overlap,dx,NAI_pol_mult
|
||||
|
||||
ao_integrals_pt_chrg = 0.d0
|
||||
|
||||
! if (read_ao_integrals_pt_chrg) then
|
||||
!
|
||||
! call ezfio_get_ao_one_e_ints_ao_integrals_pt_chrg(ao_integrals_pt_chrg)
|
||||
! print *, 'AO N-e integrals read from disk'
|
||||
!
|
||||
! else
|
||||
|
||||
! if(use_cosgtos) then
|
||||
! !print *, " use_cosgtos for ao_integrals_pt_chrg ?", use_cosgtos
|
||||
!
|
||||
! do j = 1, ao_num
|
||||
! do i = 1, ao_num
|
||||
! ao_integrals_pt_chrg(i,j) = ao_integrals_pt_chrg_cosgtos(i,j)
|
||||
! enddo
|
||||
! enddo
|
||||
!
|
||||
! else
|
||||
|
||||
!$OMP PARALLEL &
|
||||
!$OMP DEFAULT (NONE) &
|
||||
!$OMP PRIVATE (i,j,k,l,m,alpha,beta,A_center,B_center,C_center,power_A,power_B,&
|
||||
!$OMP num_A,num_B,Z,c,c1,n_pt_in) &
|
||||
!$OMP SHARED (ao_num,ao_prim_num,ao_expo_ordered_transp,ao_power,ao_nucl,pts_charge_coord,ao_coef_normalized_ordered_transp,&
|
||||
!$OMP n_pt_max_integrals,ao_integrals_pt_chrg,n_pts_charge,pts_charge_z)
|
||||
|
||||
n_pt_in = n_pt_max_integrals
|
||||
|
||||
!$OMP DO SCHEDULE (dynamic)
|
||||
|
||||
do j = 1, ao_num
|
||||
num_A = ao_nucl(j)
|
||||
power_A(1:3)= ao_power(j,1:3)
|
||||
A_center(1:3) = pts_charge_coord(num_A,1:3)
|
||||
|
||||
do i = 1, ao_num
|
||||
|
||||
num_B = ao_nucl(i)
|
||||
power_B(1:3)= ao_power(i,1:3)
|
||||
B_center(1:3) = pts_charge_coord(num_B,1:3)
|
||||
|
||||
do l=1,ao_prim_num(j)
|
||||
alpha = ao_expo_ordered_transp(l,j)
|
||||
|
||||
do m=1,ao_prim_num(i)
|
||||
beta = ao_expo_ordered_transp(m,i)
|
||||
|
||||
double precision :: c, c1
|
||||
c = 0.d0
|
||||
|
||||
do k = 1, n_pts_charge
|
||||
double precision :: Z
|
||||
Z = pts_charge_z(k)
|
||||
|
||||
C_center(1:3) = pts_charge_coord(k,1:3)
|
||||
|
||||
c1 = NAI_pol_mult( A_center, B_center, power_A, power_B &
|
||||
, alpha, beta, C_center, n_pt_in )
|
||||
|
||||
c = c - Z * c1
|
||||
|
||||
enddo
|
||||
ao_integrals_pt_chrg(i,j) = ao_integrals_pt_chrg(i,j) &
|
||||
+ ao_coef_normalized_ordered_transp(l,j) &
|
||||
* ao_coef_normalized_ordered_transp(m,i) * c
|
||||
enddo
|
||||
enddo
|
||||
enddo
|
||||
enddo
|
||||
|
||||
!$OMP END DO
|
||||
!$OMP END PARALLEL
|
||||
|
||||
! endif
|
||||
|
||||
|
||||
! IF(do_pseudo) THEN
|
||||
! ao_integrals_pt_chrg += ao_pseudo_integrals
|
||||
! ENDIF
|
||||
|
||||
! endif
|
||||
|
||||
|
||||
! if (write_ao_integrals_pt_chrg) then
|
||||
! call ezfio_set_ao_one_e_ints_ao_integrals_pt_chrg(ao_integrals_pt_chrg)
|
||||
! print *, 'AO N-e integrals written to disk'
|
||||
! endif
|
||||
|
||||
END_PROVIDER
|
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 @@
|
||||
#!/usr/bin/env python
|
||||
import os
|
||||
import sys
|
||||
|
||||
|
||||
def zip_in_ezfio(ezfio,tmp):
|
||||
tmpzip=tmp+".gz"
|
||||
cmdzip="gzip -c "+tmp+" > "+tmpzip
|
||||
os.system(cmdzip)
|
||||
os.system("rm "+tmp)
|
||||
cmdmv="mv "+tmpzip+" "+EZFIO+"/ao_one_e_ints/"+tmpzip
|
||||
os.system(cmdmv)
|
||||
|
||||
def mv_in_ezfio(ezfio,tmp):
|
||||
cmdmv="mv "+tmp+" "+EZFIO+"/ao_one_e_ints/"+tmp
|
||||
os.system(cmdmv)
|
||||
|
||||
|
||||
# Getting the EZFIO
|
||||
EZFIO=sys.argv[1]
|
||||
EZFIO=EZFIO.replace("/", "")
|
||||
print(EZFIO)
|
||||
|
||||
# Reading the point charges and convert the Angstrom geometry in Bohr for QP
|
||||
f = open('point_charges.xyz','r')
|
||||
lines = f.readlines()
|
||||
convert_angs_to_bohr=1.88973
|
||||
n_charges=0
|
||||
coord_x=[]
|
||||
coord_y=[]
|
||||
coord_z=[]
|
||||
charges=[]
|
||||
for line in lines:
|
||||
data = line.split()
|
||||
if(len(data)>0):
|
||||
n_charges += 1
|
||||
charges.append(str(data[0]))
|
||||
coord_x.append(str(convert_angs_to_bohr*float(data[1])))
|
||||
coord_y.append(str(convert_angs_to_bohr*float(data[2])))
|
||||
coord_z.append(str(convert_angs_to_bohr*float(data[3])))
|
||||
|
||||
# Write the file containing the number of charges and set in EZFIO folder
|
||||
tmp="n_pts_charge"
|
||||
fncharges = open(tmp,'w')
|
||||
fncharges.write(" "+str(n_charges)+'\n')
|
||||
fncharges.close()
|
||||
mv_in_ezfio(EZFIO,tmp)
|
||||
|
||||
# Write the file containing the charges and set in EZFIO folder
|
||||
tmp="pts_charge_z"
|
||||
fcharges = open(tmp,'w')
|
||||
fcharges.write(" 1\n")
|
||||
fcharges.write(" "+str(n_charges)+'\n')
|
||||
for i in range(n_charges):
|
||||
fcharges.write(charges[i]+'\n')
|
||||
fcharges.close()
|
||||
zip_in_ezfio(EZFIO,tmp)
|
||||
|
||||
# Write the file containing the charge coordinates and set in EZFIO folder
|
||||
tmp="pts_charge_coord"
|
||||
fcoord = open(tmp,'w')
|
||||
fcoord.write(" 2\n")
|
||||
fcoord.write(" "+str(n_charges)+' 3\n')
|
||||
#fcoord.write(" "+' 3 '+str(n_charges)+' \n')
|
||||
for i in range(n_charges):
|
||||
fcoord.write(' '+coord_x[i]+'\n')
|
||||
for i in range(n_charges):
|
||||
fcoord.write(' '+coord_y[i]+'\n')
|
||||
for i in range(n_charges):
|
||||
fcoord.write(' '+coord_z[i]+'\n')
|
||||
fcoord.close()
|
||||
zip_in_ezfio(EZFIO,tmp)
|
||||
|
Loading…
Reference in New Issue
Block a user