Fix tests

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
+** Check numerically that MOs are orthonormal
-  errors is to write an error-checking function that displays the
-  error in text format and exits the program.
 
-  #+NAME: qmckl_check_error
+   In this example, we will compute the numerically the overlap
-  #+begin_src f90 
+   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
+** Computing an atomic orbital on a grid
-  :PROPERTIES:
+   :PROPERTIES:
-  :header-args: :tangle ao_grid.f90
+   :header-args: :tangle ao_grid.f90
-  :END:
+   :END:
 
-  The following program, in Fortran, computes the values of an atomic
+   The following program, in Fortran, computes the values of an atomic
-  orbital on a regular 3-dimensional grid. The 100^3 grid points are
+   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
+   automatically defined, such that the molecule fits in a box with 5
-  atomic units in the borders.
+   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
+   Create the QMCkl context and initialize it with the wave function
-  present in the TREXIO file:
+   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
+   We need to check that ~ao_id~ is in the range, so we get the total
-  number of AOs from QMCkl:
+   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.
+   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.
+   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
+   We now compute the coordinates of opposite points of the box, and
-  the distance between points along the 3 directions:
+   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
+   We now produce the list of point coordinates where the AO will be
-  evaluated:
+   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
+   We allocate the space required to retrieve the values, gradients and
-  Laplacian of all AOs, and ask to retrieve the values of the
+   Laplacian of all AOs, and ask to retrieve the values of the
-  AOs computed at the point positions. 
+   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
+

org/qmckl_local_energy.org

@@ -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