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Fix tests
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org/examples.org
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org/examples.org
@ -3,17 +3,124 @@
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#+INCLUDE: ../tools/lib.org
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In this section, we present examples of usage of QMCkl.
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For simplicity, we assume that the wave function parameters are stores
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For simplicity, we assume that the wave function parameters are stored
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in a [[https://github.com/TREX-CoE/trexio][TREXIO]] file.
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* Checking errors
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* Python
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All QMCkl functions return an error code. A convenient way to handle
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errors is to write an error-checking function that displays the
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error in text format and exits the program.
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** Check numerically that MOs are orthonormal
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#+NAME: qmckl_check_error
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#+begin_src f90
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In this example, we will compute the numerically the overlap
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between the molecular orbitals:
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\[
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S_{ij} = \int \phi_i(\mathbf{r}) \phi_j(\mathbf{r})
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\text{d}\mathbf{r} \sim \sum_{k=1}^{N} \phi_i(\mathbf{r}_k)
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\phi_j(\mathbf{r}_k) \delta \mathbf{r}
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\]
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#+begin_src python :session
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import numpy as np
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import qmckl
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#+end_src
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#+RESULTS:
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First, we create a context for the QMCkl calculation, and load the
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wave function stored in =h2o_5z.h5= inside it:
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#+begin_src python :session
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trexio_filename = "..//share/qmckl/test_data/h2o_5z.h5"
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context = qmckl.context_create()
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qmckl.trexio_read(context, trexio_filename)
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#+end_src
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#+RESULTS:
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: None
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We now define the grid points as a regular grid around the
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molecule.
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We fetch the nuclear coordinates from the context,
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#+begin_src python :session :results output
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nucl_num = qmckl.get_nucleus_num(context)
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nucl_charge = qmckl.get_nucleus_charge(context, nucl_num)
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nucl_coord = qmckl.get_nucleus_coord(context, 'N', nucl_num*3)
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nucl_coord = np.reshape(nucl_coord, (3, nucl_num))
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for i in range(nucl_num):
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print("%d %+f %+f %+f"%(int(nucl_charge[i]),
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nucl_coord[i,0],
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nucl_coord[i,1],
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nucl_coord[i,2]) )
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#+end_src
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#+RESULTS:
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: 8 +0.000000 +0.000000 +0.000000
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: 1 -1.430429 +0.000000 -1.107157
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: 1 +1.430429 +0.000000 -1.107157
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and compute the coordinates of the grid points:
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#+begin_src python :session
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nx = ( 40, 40, 40 )
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point_num = nx[0] * nx[1] * nx[2]
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rmin = np.array( list([ np.min(nucl_coord[:,a]) for a in range(3) ]) )
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rmax = np.array( list([ np.max(nucl_coord[:,a]) for a in range(3) ]) )
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shift = np.array([5.,5.,5.])
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linspace = [ None for i in range(3) ]
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step = [ None for i in range(3) ]
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for a in range(3):
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linspace[a], step[a] = np.linspace(rmin[a]-shift[a],
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rmax[a]+shift[a],
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num=nx[a],
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retstep=True)
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dr = step[0] * step[1] * step[2]
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dr
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#+end_src
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#+RESULTS:
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: 0.024081249137090373
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Now the grid is ready, we can create the list of grid points on
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which the MOs will be evaluated, and transfer them to the QMCkl
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context:
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#+begin_src python :session
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point = []
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for x in linspace[0]:
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for y in linspace[1]:
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for z in linspace[2]:
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point += [x, y, z]
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#point = np.array(point)
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qmckl.set_point(context, 'N', point, len(point)/3)
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#+end_src
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#+RESULTS:
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Then, will first evaluate all the MOs at the grid points, and then we will
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compute the overlap between all the MOs.
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* Fortran
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** Checking errors
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All QMCkl functions return an error code. A convenient way to handle
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errors is to write an error-checking function that displays the
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error in text format and exits the program.
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#+NAME: qmckl_check_error
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#+begin_src f90
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subroutine qmckl_check_error(rc, message)
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use qmckl
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implicit none
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@ -27,28 +134,28 @@ subroutine qmckl_check_error(rc, message)
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call exit(rc)
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end if
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end subroutine qmckl_check_error
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#+end_src
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#+end_src
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* Computing an atomic orbital on a grid
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:PROPERTIES:
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:header-args: :tangle ao_grid.f90
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:END:
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** Computing an atomic orbital on a grid
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:PROPERTIES:
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:header-args: :tangle ao_grid.f90
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:END:
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The following program, in Fortran, computes the values of an atomic
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orbital on a regular 3-dimensional grid. The 100^3 grid points are
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automatically defined, such that the molecule fits in a box with 5
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atomic units in the borders.
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The following program, in Fortran, computes the values of an atomic
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orbital on a regular 3-dimensional grid. The 100^3 grid points are
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automatically defined, such that the molecule fits in a box with 5
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atomic units in the borders.
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This program uses the ~qmckl_check_error~ function defined above.
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This program uses the ~qmckl_check_error~ function defined above.
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To use this program, run
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To use this program, run
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#+begin_src bash :tangle no
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#+begin_src bash :tangle no
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$ ao_grid <trexio_file> <AO_id> <point_num>
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#+end_src
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#+end_src
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#+begin_src f90 :noweb yes
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#+begin_src f90 :noweb yes
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<<qmckl_check_error>>
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program ao_grid
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@ -73,11 +180,11 @@ program ao_grid
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double precision :: rmin(3), rmax(3)
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double precision, allocatable :: points(:,:)
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double precision, allocatable :: ao_vgl(:,:,:)
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#+end_src
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#+end_src
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Start by fetching the command-line arguments:
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Start by fetching the command-line arguments:
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#+begin_src f90
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#+begin_src f90
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if (iargc() /= 3) then
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print *, 'Syntax: ao_grid <trexio_file> <AO_id> <point_num>'
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call exit(-1)
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@ -92,21 +199,21 @@ program ao_grid
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print *, 'Error: 0 < point_num < 300'
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call exit(-1)
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end if
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#+end_src
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#+end_src
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Create the QMCkl context and initialize it with the wave function
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present in the TREXIO file:
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Create the QMCkl context and initialize it with the wave function
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present in the TREXIO file:
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#+begin_src f90
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#+begin_src f90
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qmckl_ctx = qmckl_context_create()
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rc = qmckl_trexio_read(qmckl_ctx, trexio_filename, 1_8*len(trim(trexio_filename)))
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call qmckl_check_error(rc, 'Read TREXIO')
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#+end_src
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#+end_src
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We need to check that ~ao_id~ is in the range, so we get the total
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number of AOs from QMCkl:
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We need to check that ~ao_id~ is in the range, so we get the total
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number of AOs from QMCkl:
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#+begin_src f90
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#+begin_src f90
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rc = qmckl_get_ao_basis_ao_num(qmckl_ctx, ao_num)
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call qmckl_check_error(rc, 'Getting ao_num')
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@ -114,24 +221,24 @@ program ao_grid
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print *, 'Error: 0 < ao_id < ', ao_num
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call exit(-1)
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end if
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#+end_src
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#+end_src
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Now we will compute the limits of the box in which the molecule fits.
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For that, we first need to ask QMCkl the coordinates of nuclei.
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Now we will compute the limits of the box in which the molecule fits.
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For that, we first need to ask QMCkl the coordinates of nuclei.
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#+begin_src f90
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#+begin_src f90
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rc = qmckl_get_nucleus_num(qmckl_ctx, nucl_num)
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call qmckl_check_error(rc, 'Get nucleus num')
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allocate( nucl_coord(3, nucl_num) )
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rc = qmckl_get_nucleus_coord(qmckl_ctx, 'N', nucl_coord, 3_8*nucl_num)
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call qmckl_check_error(rc, 'Get nucleus coord')
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#+end_src
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#+end_src
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We now compute the coordinates of opposite points of the box, and
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the distance between points along the 3 directions:
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We now compute the coordinates of opposite points of the box, and
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the distance between points along the 3 directions:
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#+begin_src f90
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#+begin_src f90
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rmin(1) = minval( nucl_coord(1,:) ) - 5.d0
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rmin(2) = minval( nucl_coord(2,:) ) - 5.d0
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rmin(3) = minval( nucl_coord(3,:) ) - 5.d0
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@ -141,12 +248,12 @@ program ao_grid
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rmax(3) = maxval( nucl_coord(3,:) ) + 5.d0
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dr(1:3) = (rmax(1:3) - rmin(1:3)) / dble(point_num_x-1)
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#+end_src
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#+end_src
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We now produce the list of point coordinates where the AO will be
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evaluated:
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We now produce the list of point coordinates where the AO will be
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evaluated:
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#+begin_src f90
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#+begin_src f90
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point_num = point_num_x**3
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allocate( points(point_num, 3) )
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ipoint=0
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@ -166,34 +273,35 @@ program ao_grid
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end do
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z = z + dr(3)
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end do
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#+end_src
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#+end_src
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We give the points to QMCkl:
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We give the points to QMCkl:
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#+begin_src f90
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#+begin_src f90
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rc = qmckl_set_point(qmckl_ctx, 'T', points, point_num)
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call qmckl_check_error(rc, 'Setting points')
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#+end_src
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#+end_src
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We allocate the space required to retrieve the values, gradients and
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Laplacian of all AOs, and ask to retrieve the values of the
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AOs computed at the point positions.
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We allocate the space required to retrieve the values, gradients and
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Laplacian of all AOs, and ask to retrieve the values of the
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AOs computed at the point positions.
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#+begin_src f90
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#+begin_src f90
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allocate( ao_vgl(ao_num, 5, point_num) )
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rc = qmckl_get_ao_basis_ao_vgl(qmckl_ctx, ao_vgl, ao_num*5_8*point_num)
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call qmckl_check_error(rc, 'Setting points')
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#+end_src
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#+end_src
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We finally print the value of the AO:
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We finally print the value of the AO:
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#+begin_src f90
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#+begin_src f90
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do ipoint=1, point_num
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print '(3(F16.10,X),E20.10)', points(ipoint, 1:3), ao_vgl(ao_id,1,ipoint)
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end do
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#+end_src
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#+end_src
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#+begin_src f90
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#+begin_src f90
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deallocate( nucl_coord, points, ao_vgl )
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end program ao_grid
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#+end_src
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#+end_src
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@ -1289,7 +1289,7 @@ end function qmckl_compute_local_energy_f
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double local_energy[chbrclf_walk_num];
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rc = qmckl_get_local_energy(context, &(local_energy[0]), walk_num);
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rc = qmckl_get_local_energy(context, &(local_energy[0]), chbrclf_walk_num);
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assert (rc == QMCKL_SUCCESS);
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#+end_src
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