mirror of
https://github.com/TREX-CoE/qmckl.git
synced 2025-01-03 10:06:09 +01:00
Fix tests
This commit is contained in:
parent
e00e034497
commit
bd299126c1
224
org/examples.org
224
org/examples.org
@ -3,17 +3,124 @@
|
||||
#+INCLUDE: ../tools/lib.org
|
||||
|
||||
In this section, we present examples of usage of QMCkl.
|
||||
For simplicity, we assume that the wave function parameters are stores
|
||||
For simplicity, we assume that the wave function parameters are stored
|
||||
in a [[https://github.com/TREX-CoE/trexio][TREXIO]] file.
|
||||
|
||||
* Checking errors
|
||||
* Python
|
||||
|
||||
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.
|
||||
** Check numerically that MOs are orthonormal
|
||||
|
||||
#+NAME: qmckl_check_error
|
||||
#+begin_src f90
|
||||
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
|
||||
@ -27,28 +134,28 @@ subroutine qmckl_check_error(rc, message)
|
||||
call exit(rc)
|
||||
end if
|
||||
end subroutine qmckl_check_error
|
||||
#+end_src
|
||||
#+end_src
|
||||
|
||||
* Computing an atomic orbital on a grid
|
||||
:PROPERTIES:
|
||||
:header-args: :tangle ao_grid.f90
|
||||
:END:
|
||||
** 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.
|
||||
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.
|
||||
This program uses the ~qmckl_check_error~ function defined above.
|
||||
|
||||
To use this program, run
|
||||
To use this program, run
|
||||
|
||||
#+begin_src bash :tangle no
|
||||
#+begin_src bash :tangle no
|
||||
$ ao_grid <trexio_file> <AO_id> <point_num>
|
||||
#+end_src
|
||||
#+end_src
|
||||
|
||||
|
||||
#+begin_src f90 :noweb yes
|
||||
#+begin_src f90 :noweb yes
|
||||
<<qmckl_check_error>>
|
||||
|
||||
program ao_grid
|
||||
@ -73,11 +180,11 @@ program ao_grid
|
||||
double precision :: rmin(3), rmax(3)
|
||||
double precision, allocatable :: points(:,:)
|
||||
double precision, allocatable :: ao_vgl(:,:,:)
|
||||
#+end_src
|
||||
#+end_src
|
||||
|
||||
Start by fetching the command-line arguments:
|
||||
Start by fetching the command-line arguments:
|
||||
|
||||
#+begin_src f90
|
||||
#+begin_src f90
|
||||
if (iargc() /= 3) then
|
||||
print *, 'Syntax: ao_grid <trexio_file> <AO_id> <point_num>'
|
||||
call exit(-1)
|
||||
@ -92,21 +199,21 @@ program ao_grid
|
||||
print *, 'Error: 0 < point_num < 300'
|
||||
call exit(-1)
|
||||
end if
|
||||
#+end_src
|
||||
#+end_src
|
||||
|
||||
Create the QMCkl context and initialize it with the wave function
|
||||
present in the TREXIO file:
|
||||
Create the QMCkl context and initialize it with the wave function
|
||||
present in the TREXIO file:
|
||||
|
||||
#+begin_src f90
|
||||
#+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
|
||||
#+end_src
|
||||
|
||||
We need to check that ~ao_id~ is in the range, so we get the total
|
||||
number of AOs from QMCkl:
|
||||
We need to check that ~ao_id~ is in the range, so we get the total
|
||||
number of AOs from QMCkl:
|
||||
|
||||
#+begin_src f90
|
||||
#+begin_src f90
|
||||
rc = qmckl_get_ao_basis_ao_num(qmckl_ctx, ao_num)
|
||||
call qmckl_check_error(rc, 'Getting ao_num')
|
||||
|
||||
@ -114,24 +221,24 @@ program ao_grid
|
||||
print *, 'Error: 0 < ao_id < ', ao_num
|
||||
call exit(-1)
|
||||
end if
|
||||
#+end_src
|
||||
#+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.
|
||||
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
|
||||
#+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
|
||||
#+end_src
|
||||
|
||||
We now compute the coordinates of opposite points of the box, and
|
||||
the distance between points along the 3 directions:
|
||||
We now compute the coordinates of opposite points of the box, and
|
||||
the distance between points along the 3 directions:
|
||||
|
||||
#+begin_src f90
|
||||
#+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
|
||||
@ -141,12 +248,12 @@ program ao_grid
|
||||
rmax(3) = maxval( nucl_coord(3,:) ) + 5.d0
|
||||
|
||||
dr(1:3) = (rmax(1:3) - rmin(1:3)) / dble(point_num_x-1)
|
||||
#+end_src
|
||||
#+end_src
|
||||
|
||||
We now produce the list of point coordinates where the AO will be
|
||||
evaluated:
|
||||
We now produce the list of point coordinates where the AO will be
|
||||
evaluated:
|
||||
|
||||
#+begin_src f90
|
||||
#+begin_src f90
|
||||
point_num = point_num_x**3
|
||||
allocate( points(point_num, 3) )
|
||||
ipoint=0
|
||||
@ -166,34 +273,35 @@ program ao_grid
|
||||
end do
|
||||
z = z + dr(3)
|
||||
end do
|
||||
#+end_src
|
||||
#+end_src
|
||||
|
||||
We give the points to QMCkl:
|
||||
We give the points to QMCkl:
|
||||
|
||||
#+begin_src f90
|
||||
#+begin_src f90
|
||||
rc = qmckl_set_point(qmckl_ctx, 'T', points, point_num)
|
||||
call qmckl_check_error(rc, 'Setting points')
|
||||
#+end_src
|
||||
#+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.
|
||||
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
|
||||
#+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
|
||||
#+end_src
|
||||
|
||||
We finally print the value of the AO:
|
||||
We finally print the value of the AO:
|
||||
|
||||
#+begin_src f90
|
||||
#+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
|
||||
#+end_src
|
||||
|
||||
#+begin_src f90
|
||||
#+begin_src f90
|
||||
deallocate( nucl_coord, points, ao_vgl )
|
||||
end program ao_grid
|
||||
#+end_src
|
||||
#+end_src
|
||||
|
||||
|
||||
@ -1289,7 +1289,7 @@ end function qmckl_compute_local_energy_f
|
||||
|
||||
double local_energy[chbrclf_walk_num];
|
||||
|
||||
rc = qmckl_get_local_energy(context, &(local_energy[0]), walk_num);
|
||||
rc = qmckl_get_local_energy(context, &(local_energy[0]), chbrclf_walk_num);
|
||||
assert (rc == QMCKL_SUCCESS);
|
||||
|
||||
#+end_src
|
||||
|
||||
Loading…
Reference in New Issue
Block a user