qmckl/org/examples.org

#+TITLE: Code examples
#+SETUPFILE: ../tools/theme.setup
#+INCLUDE: ../tools/lib.org
  
In this section, we present examples of usage of QMCkl.
For simplicity, we assume that the wave function parameters are stored
in a [[https://github.com/TREX-CoE/trexio][TREXIO]] file.

* Python

** Check numerically that MOs are orthonormal

   In this example, we will compute the numerically the overlap
   between the molecular orbitals:
   
   \[
      S_{ij} = \int \phi_i(\mathbf{r}) \phi_j(\mathbf{r})
   \text{d}\mathbf{r} \sim \sum_{k=1}^{N} \phi_i(\mathbf{r}_k)
   \phi_j(\mathbf{r}_k) \delta \mathbf{r}
   \]
   

   #+begin_src python :session 
import numpy as np
import qmckl
   #+end_src

   #+RESULTS:
   

   First, we create a context for the QMCkl calculation, and load the
   wave function stored in =h2o_5z.h5= inside it:
   
   #+begin_src python :session 
trexio_filename = "..//share/qmckl/test_data/h2o_5z.h5"

context = qmckl.context_create()
qmckl.trexio_read(context, trexio_filename)
   #+end_src

   #+RESULTS:
   : None

   We now define the grid points as a regular grid around the
   molecule.

   We fetch the nuclear coordinates from the context,
   
   #+begin_src python :session :results output
nucl_num = qmckl.get_nucleus_num(context)

nucl_charge = qmckl.get_nucleus_charge(context, nucl_num)

nucl_coord = qmckl.get_nucleus_coord(context, 'N', nucl_num*3)
nucl_coord = np.reshape(nucl_coord, (3, nucl_num))

for i in range(nucl_num):
    print("%d  %+f %+f %+f"%(int(nucl_charge[i]),
                             nucl_coord[i,0],
                             nucl_coord[i,1],
                             nucl_coord[i,2]) )
   #+end_src

   #+RESULTS:
   : 8  +0.000000 +0.000000 +0.000000
   : 1  -1.430429 +0.000000 -1.107157
   : 1  +1.430429 +0.000000 -1.107157

   and compute the coordinates of the grid points:
   
   #+begin_src python :session
nx = ( 40, 40, 40 )
point_num = nx[0] * nx[1] * nx[2]

rmin  = np.array( list([ np.min(nucl_coord[:,a]) for a in range(3) ]) )
rmax  = np.array( list([ np.max(nucl_coord[:,a]) for a in range(3) ]) )

shift = np.array([5.,5.,5.])

linspace = [ None for i in range(3) ]
step     = [ None for i in range(3) ]
for a in range(3):
    linspace[a], step[a] = np.linspace(rmin[a]-shift[a],
                                       rmax[a]+shift[a],
                                       num=nx[a],
                                       retstep=True)

dr = step[0] * step[1] * step[2]
dr
   #+end_src

   #+RESULTS:
   : 0.024081249137090373
   
   Now the grid is ready, we can create the list of grid points on
   which the MOs will be evaluated, and transfer them to the QMCkl
   context:

   #+begin_src python :session
point = []
for x in linspace[0]:
    for y in linspace[1]:
        for z in linspace[2]:
            point += [x, y, z]

#point = np.array(point)
qmckl.set_point(context, 'N', point, len(point)/3)
   #+end_src

   #+RESULTS:
   
   Then, will first evaluate all the MOs at the grid points, and then we will
   compute the overlap between all the MOs.

* Fortran
** Checking errors

   All QMCkl functions return an error code. A convenient way to handle
   errors is to write an error-checking function that displays the
   error in text format and exits the program.

   #+NAME: qmckl_check_error
   #+begin_src f90 
subroutine qmckl_check_error(rc, message)
  use qmckl
  implicit none
  integer(qmckl_exit_code), intent(in) :: rc
  character(len=*)        , intent(in) :: message
  character(len=128)                   :: str_buffer
  if (rc /= QMCKL_SUCCESS) then
     print *, message
     call qmckl_string_of_error(rc, str_buffer)
     print *, str_buffer
     call exit(rc)
  end if
end subroutine qmckl_check_error
   #+end_src
  
** Computing an atomic orbital on a grid
   :PROPERTIES:
   :header-args: :tangle ao_grid.f90
   :END:

   The following program, in Fortran, computes the values of an atomic
   orbital on a regular 3-dimensional grid. The 100^3 grid points are
   automatically defined, such that the molecule fits in a box with 5
   atomic units in the borders.

   This program uses the ~qmckl_check_error~ function defined above.
  
   To use this program, run
  
   #+begin_src bash :tangle no
$ ao_grid <trexio_file> <AO_id> <point_num>
   #+end_src

  
   #+begin_src f90  :noweb yes
<<qmckl_check_error>>

program ao_grid
  use qmckl
  implicit none

  integer(qmckl_context)    :: qmckl_ctx  ! QMCkl context
  integer(qmckl_exit_code)  :: rc         ! Exit code of QMCkl functions

  character(len=128)            :: trexio_filename
  character(len=128)            :: str_buffer
  integer                       :: ao_id
  integer                       :: point_num_x

  integer(c_int64_t)            :: nucl_num
  double precision, allocatable :: nucl_coord(:,:)

  integer(c_int64_t)            :: point_num
  integer(c_int64_t)            :: ao_num
  integer(c_int64_t)            :: ipoint, i, j, k
  double precision              :: x, y, z, dr(3)
  double precision              :: rmin(3), rmax(3)
  double precision, allocatable :: points(:,:)
  double precision, allocatable :: ao_vgl(:,:,:)
   #+end_src

   Start by fetching the command-line arguments:

   #+begin_src f90 
  if (iargc() /= 3) then
     print *, 'Syntax: ao_grid <trexio_file> <AO_id> <point_num>'
     call exit(-1)
  end if
  call getarg(1, trexio_filename)
  call getarg(2, str_buffer)
  read(str_buffer, *) ao_id
  call getarg(3, str_buffer)
  read(str_buffer, *) point_num_x

  if (point_num_x < 0 .or. point_num_x > 300) then
     print *, 'Error: 0 < point_num < 300'
     call exit(-1)
  end if
   #+end_src

   Create the QMCkl context and initialize it with the wave function
   present in the TREXIO file:

   #+begin_src f90 
  qmckl_ctx = qmckl_context_create()
  rc  = qmckl_trexio_read(qmckl_ctx, trexio_filename, 1_8*len(trim(trexio_filename)))
  call qmckl_check_error(rc, 'Read TREXIO')
   #+end_src

   We need to check that ~ao_id~ is in the range, so we get the total
   number of AOs from QMCkl:
  
   #+begin_src f90 
  rc = qmckl_get_ao_basis_ao_num(qmckl_ctx, ao_num)
  call qmckl_check_error(rc, 'Getting ao_num')

  if (ao_id < 0 .or. ao_id > ao_num) then
     print *, 'Error: 0 < ao_id < ', ao_num
     call exit(-1)
  end if
   #+end_src

   Now we will compute the limits of the box in which the molecule fits.
   For that, we first need to ask QMCkl the coordinates of nuclei.

   #+begin_src f90 
  rc = qmckl_get_nucleus_num(qmckl_ctx, nucl_num)
  call qmckl_check_error(rc, 'Get nucleus num')

  allocate( nucl_coord(3, nucl_num) )
  rc = qmckl_get_nucleus_coord(qmckl_ctx, 'N', nucl_coord, 3_8*nucl_num)
  call qmckl_check_error(rc, 'Get nucleus coord')
   #+end_src

   We now compute the coordinates of opposite points of the box, and
   the distance between points along the 3 directions:

   #+begin_src f90 
  rmin(1) = minval( nucl_coord(1,:) ) - 5.d0
  rmin(2) = minval( nucl_coord(2,:) ) - 5.d0
  rmin(3) = minval( nucl_coord(3,:) ) - 5.d0
     
  rmax(1) = maxval( nucl_coord(1,:) ) + 5.d0
  rmax(2) = maxval( nucl_coord(2,:) ) + 5.d0
  rmax(3) = maxval( nucl_coord(3,:) ) + 5.d0

  dr(1:3) = (rmax(1:3) - rmin(1:3)) / dble(point_num_x-1)
   #+end_src

   We now produce the list of point coordinates where the AO will be
   evaluated:
  
   #+begin_src f90 
  point_num = point_num_x**3
  allocate( points(point_num, 3) )
  ipoint=0
  z = rmin(3)
  do k=1,point_num_x
     y = rmin(2)
     do j=1,point_num_x
        x = rmin(1)
        do i=1,point_num_x
           ipoint = ipoint+1
           points(ipoint,1) = x
           points(ipoint,2) = y
           points(ipoint,3) = z
           x = x + dr(1)
        end do
        y = y + dr(2)
     end do
     z = z + dr(3)
  end do
   #+end_src
  
   We give the points to QMCkl:

   #+begin_src f90 
  rc = qmckl_set_point(qmckl_ctx, 'T', points, point_num)
  call qmckl_check_error(rc, 'Setting points')
   #+end_src

   We allocate the space required to retrieve the values, gradients and
   Laplacian of all AOs, and ask to retrieve the values of the
   AOs computed at the point positions. 
  
   #+begin_src f90 
  allocate( ao_vgl(ao_num, 5, point_num) )
  rc = qmckl_get_ao_basis_ao_vgl(qmckl_ctx, ao_vgl, ao_num*5_8*point_num)
  call qmckl_check_error(rc, 'Setting points')
   #+end_src

   We finally print the value of the AO:

   #+begin_src f90 
  do ipoint=1, point_num
     print '(3(F16.10,X),E20.10)', points(ipoint, 1:3), ao_vgl(ao_id,1,ipoint)
  end do
   #+end_src

   #+begin_src f90 
  deallocate( nucl_coord, points, ao_vgl )
end program ao_grid
   #+end_src