Fix tests

org/examples.org

@@ -3,10 +3,117 @@
 #+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
+
+** 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
@@ -29,7 +136,7 @@ subroutine qmckl_check_error(rc, message)
 end subroutine qmckl_check_error
    #+end_src
   
-* Computing an atomic orbital on a grid
+** Computing an atomic orbital on a grid
    :PROPERTIES:
    :header-args: :tangle ao_grid.f90
    :END:
@@ -197,3 +304,4 @@ program ao_grid
   deallocate( nucl_coord, points, ao_vgl )
 end program ao_grid
    #+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