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Added Python example.
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@ -7,10 +7,9 @@ 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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in a [[https://github.com/TREX-CoE/trexio][TREXIO]] file.
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* Python
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* Python
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** Check numerically that MOs are orthonormal
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** Check numerically that MOs are orthonormal
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In this example, we will compute the numerically the overlap
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In this example, we will compute numerically the overlap
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between the molecular orbitals:
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between the molecular orbitals:
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\[
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\[
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@ -18,6 +17,11 @@ in a [[https://github.com/TREX-CoE/trexio][TREXIO]] file.
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\text{d}\mathbf{r} \sim \sum_{k=1}^{N} \phi_i(\mathbf{r}_k)
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\text{d}\mathbf{r} \sim \sum_{k=1}^{N} \phi_i(\mathbf{r}_k)
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\phi_j(\mathbf{r}_k) \delta \mathbf{r}
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\phi_j(\mathbf{r}_k) \delta \mathbf{r}
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\]
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\]
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\[
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S_{ij} = \langle \phi_i | \phi_j \rangle
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\sim \sum_{k=1}^{N} \langle \phi_i | \mathbf{r}_k \rangle
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\langle \mathbf{r}_k | \phi_j \rangle
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\]
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#+begin_src python :session
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#+begin_src python :session
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@ -27,9 +31,9 @@ import qmckl
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#+RESULTS:
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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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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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wave function stored in =h2o_5z.h5= inside it. It is a Hartree-Fock
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determinant for the water molecule in the cc-pV5Z basis set.
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#+begin_src python :session
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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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trexio_filename = "..//share/qmckl/test_data/h2o_5z.h5"
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@ -41,12 +45,12 @@ qmckl.trexio_read(context, trexio_filename)
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#+RESULTS:
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#+RESULTS:
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: None
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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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We now define the grid points $\mathbf{r}_k$ as a regular grid around the
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molecule.
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molecule.
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We fetch the nuclear coordinates from the context,
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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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#+begin_src python :session :results output :export both
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nucl_num = qmckl.get_nucleus_num(context)
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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_charge = qmckl.get_nucleus_charge(context, nucl_num)
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@ -61,21 +65,22 @@ for i in range(nucl_num):
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nucl_coord[i,2]) )
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nucl_coord[i,2]) )
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#+end_src
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#+end_src
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#+RESULTS:
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#+begin_example
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: 8 +0.000000 +0.000000 +0.000000
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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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: 1 +1.430429 +0.000000 -1.107157
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1 +1.430429 +0.000000 -1.107157
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#+end_example
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and compute the coordinates of the grid points:
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and compute the coordinates of the grid points:
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#+begin_src python :session
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#+begin_src python :session
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nx = ( 40, 40, 40 )
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nx = ( 120, 120, 120 )
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shift = np.array([5.,5.,5.])
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point_num = nx[0] * nx[1] * nx[2]
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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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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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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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linspace = [ None for i in range(3) ]
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step = [ None for i in range(3) ]
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step = [ None for i in range(3) ]
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@ -86,15 +91,13 @@ for a in range(3):
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retstep=True)
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retstep=True)
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dr = step[0] * step[1] * step[2]
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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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#+end_src
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#+RESULTS:
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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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Now the grid is ready, we can create the list of grid points
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which the MOs will be evaluated, and transfer them to the QMCkl
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$\mathbf{r}_k$ on which the MOs $\phi_i$ will be evaluated, and
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context:
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transfer them to the QMCkl context:
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#+begin_src python :session
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#+begin_src python :session
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point = []
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point = []
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@ -104,13 +107,63 @@ for x in linspace[0]:
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point += [ [x, y, z] ]
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point += [ [x, y, z] ]
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point = np.array(point)
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point = np.array(point)
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qmckl.set_point(context, 'N', len(point), point)
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point_num = len(point)
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qmckl.set_point(context, 'N', point_num, np.reshape(point, (point_num*3)))
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#+end_src
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#+end_src
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#+RESULTS:
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#+RESULTS:
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: None
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Then, will first evaluate all the MOs at the grid points, and then we will
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Then, we evaluate all the MOs at the grid points (and time the execution),
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compute the overlap between all the MOs.
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and thus obtain the matrix $M_{ki} = \langle \mathbf{r}_k | \phi_i \rangle =
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\phi_i(\mathbf{r}_k)$.
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#+begin_src python :session :results output :export both
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import time
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mo_num = qmckl.get_mo_basis_mo_num(context)
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before = time.time()
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mo_value = qmckl.get_mo_basis_mo_value(context, point_num*mo_num)
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after = time.time()
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mo_value = np.reshape( mo_value, (point_num, mo_num) )
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print("Number of MOs: ", mo_num)
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print("Number of grid points: ", point_num)
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print("Execution time : ", (after - before), "seconds")
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#+end_src
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#+begin_example
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Number of MOs: 201
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Number of grid points: 1728000
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Execution time : 3.511528968811035 seconds
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#+end_example
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and finally we compute the overlap between all the MOs as
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$M^\dagger M$.
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#+begin_src python :session :results output
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overlap = mo_value.T @ mo_value * dr
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print (overlap)
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#+end_src
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#+begin_example
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[[ 9.88693941e-01 2.34719693e-03 -1.50518232e-08 ... 3.12084178e-09
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-5.81064929e-10 3.70130091e-02]
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[ 2.34719693e-03 9.99509628e-01 3.18930040e-09 ... -2.46888958e-10
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-1.06064273e-09 -7.65567973e-03]
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[-1.50518232e-08 3.18930040e-09 9.99995073e-01 ... -5.84882580e-06
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-1.21598117e-06 4.59036468e-08]
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...
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[ 3.12084178e-09 -2.46888958e-10 -5.84882580e-06 ... 1.00019107e+00
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-2.03342837e-04 -1.36954855e-08]
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[-5.81064929e-10 -1.06064273e-09 -1.21598117e-06 ... -2.03342837e-04
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9.99262427e-01 1.18264754e-09]
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[ 3.70130091e-02 -7.65567973e-03 4.59036468e-08 ... -1.36954855e-08
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1.18264754e-09 8.97215950e-01]]
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#+end_example
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* Fortran
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* Fortran
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** Checking errors
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** Checking errors
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@ -278,7 +331,7 @@ program ao_grid
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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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rc = qmckl_set_point(qmckl_ctx, 'T', point_num, points, size(points)*1_8 )
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call qmckl_check_error(rc, 'Setting points')
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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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@ -292,11 +345,11 @@ program ao_grid
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call qmckl_check_error(rc, 'Setting points')
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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 and Laplacian 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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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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print '(3(F10.6,X),2(E20.10,X))', points(ipoint, 1:3), ao_vgl(ao_id,1,ipoint), ao_vgl(ao_id,5,ipoint)
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end do
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end do
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#+end_src
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#+end_src
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