mirror of
https://github.com/TREX-CoE/qmckl.git
synced 2024-08-16 18:38:28 +02:00
Fix tests
This commit is contained in:
parent
e00e034497
commit
bd299126c1
114
org/examples.org
114
org/examples.org
@ -3,10 +3,117 @@
|
|||||||
#+INCLUDE: ../tools/lib.org
|
#+INCLUDE: ../tools/lib.org
|
||||||
|
|
||||||
In this section, we present examples of usage of QMCkl.
|
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.
|
in a [[https://github.com/TREX-CoE/trexio][TREXIO]] file.
|
||||||
|
|
||||||
* Checking errors
|
* 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
|
All QMCkl functions return an error code. A convenient way to handle
|
||||||
errors is to write an error-checking function that displays the
|
errors is to write an error-checking function that displays the
|
||||||
@ -29,7 +136,7 @@ subroutine qmckl_check_error(rc, message)
|
|||||||
end subroutine qmckl_check_error
|
end subroutine qmckl_check_error
|
||||||
#+end_src
|
#+end_src
|
||||||
|
|
||||||
* Computing an atomic orbital on a grid
|
** Computing an atomic orbital on a grid
|
||||||
:PROPERTIES:
|
:PROPERTIES:
|
||||||
:header-args: :tangle ao_grid.f90
|
:header-args: :tangle ao_grid.f90
|
||||||
:END:
|
:END:
|
||||||
@ -197,3 +304,4 @@ program ao_grid
|
|||||||
deallocate( nucl_coord, points, ao_vgl )
|
deallocate( nucl_coord, points, ao_vgl )
|
||||||
end program ao_grid
|
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];
|
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);
|
assert (rc == QMCKL_SUCCESS);
|
||||||
|
|
||||||
#+end_src
|
#+end_src
|
||||||
|
Loading…
Reference in New Issue
Block a user