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667 lines
12 KiB
ReStructuredText
667 lines
12 KiB
ReStructuredText
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.. _module_nuclei:
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.. program:: nuclei
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.. default-role:: option
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======
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nuclei
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======
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This module contains data relative to the nuclei (coordinates, charge,
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nuclear repulsion energy, etc).
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The coordinates are expressed in atomic units.
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EZFIO parameters
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----------------
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.. option:: nucl_num
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Number of nuclei
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.. option:: nucl_label
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Nuclear labels
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.. option:: nucl_charge
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Nuclear charges
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.. option:: nucl_coord
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Nuclear coordinates in the format (:, {x,y,z})
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.. option:: disk_access_nuclear_repulsion
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Read/Write Nuclear Repulsion from/to disk [ Write | Read | None ]
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Default: None
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.. option:: nuclear_repulsion
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Nuclear repulsion (Computed automaticaly or Read in the |EZFIO|)
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Providers
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---------
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.. c:var:: center_of_mass
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File : :file:`nuclei/nuclei.irp.f`
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.. code:: fortran
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double precision, allocatable :: center_of_mass (3)
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Center of mass of the molecule
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Needs:
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.. hlist::
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:columns: 3
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* :c:data:`element_name`
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* :c:data:`nucl_charge`
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* :c:data:`nucl_coord`
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* :c:data:`nucl_num`
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Needed by:
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.. hlist::
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:columns: 3
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* :c:data:`inertia_tensor`
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.. c:var:: element_mass
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File : :file:`nuclei/nuclei.irp.f`
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.. code:: fortran
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character*(4), allocatable :: element_name (0:127)
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double precision, allocatable :: element_mass (0:127)
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Array of the name of element, sorted by nuclear charge (integer)
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Needs:
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.. hlist::
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:columns: 3
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* :c:data:`mpi_master`
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Needed by:
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.. hlist::
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:columns: 3
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* :c:data:`center_of_mass`
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* :c:data:`inertia_tensor`
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.. c:var:: element_name
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File : :file:`nuclei/nuclei.irp.f`
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.. code:: fortran
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character*(4), allocatable :: element_name (0:127)
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double precision, allocatable :: element_mass (0:127)
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Array of the name of element, sorted by nuclear charge (integer)
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Needs:
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.. hlist::
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:columns: 3
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* :c:data:`mpi_master`
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Needed by:
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.. hlist::
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:columns: 3
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* :c:data:`center_of_mass`
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* :c:data:`inertia_tensor`
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.. c:var:: inertia_tensor
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File : :file:`nuclei/inertia.irp.f`
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.. code:: fortran
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double precision, allocatable :: inertia_tensor (3,3)
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Inertia tensor
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Needs:
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.. hlist::
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:columns: 3
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* :c:data:`center_of_mass`
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* :c:data:`element_name`
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* :c:data:`nucl_charge`
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* :c:data:`nucl_coord`
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* :c:data:`nucl_num`
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Needed by:
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.. hlist::
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:columns: 3
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* :c:data:`inertia_tensor_eigenvectors`
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.. c:var:: inertia_tensor_eigenvalues
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File : :file:`nuclei/inertia.irp.f`
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.. code:: fortran
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double precision, allocatable :: inertia_tensor_eigenvectors (3,3)
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double precision, allocatable :: inertia_tensor_eigenvalues (3)
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Eigenvectors/eigenvalues of the inertia_tensor. Used to find normal orientation.
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Needs:
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.. hlist::
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:columns: 3
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* :c:data:`inertia_tensor`
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.. c:var:: inertia_tensor_eigenvectors
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File : :file:`nuclei/inertia.irp.f`
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.. code:: fortran
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double precision, allocatable :: inertia_tensor_eigenvectors (3,3)
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double precision, allocatable :: inertia_tensor_eigenvalues (3)
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Eigenvectors/eigenvalues of the inertia_tensor. Used to find normal orientation.
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Needs:
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.. hlist::
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:columns: 3
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* :c:data:`inertia_tensor`
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.. c:var:: nucl_coord
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File : :file:`nuclei/nuclei.irp.f`
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.. code:: fortran
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double precision, allocatable :: nucl_coord (nucl_num,3)
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Nuclear coordinates in the format (:, {x,y,z})
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Needs:
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.. hlist::
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:columns: 3
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* :c:data:`ezfio_filename`
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* :c:data:`mpi_master`
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* :c:data:`nucl_charge`
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* :c:data:`nucl_label`
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* :c:data:`nucl_num`
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* :c:data:`output_wall_time_0`
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Needed by:
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.. hlist::
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:columns: 3
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* :c:data:`ao_deriv2_x`
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* :c:data:`ao_deriv_1_x`
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* :c:data:`ao_dipole_x`
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* :c:data:`ao_integrals_n_e`
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* :c:data:`ao_integrals_n_e_per_atom`
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* :c:data:`ao_overlap`
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* :c:data:`ao_overlap_abs`
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* :c:data:`ao_pseudo_integrals_local`
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* :c:data:`ao_pseudo_integrals_non_local`
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* :c:data:`ao_spread_x`
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* :c:data:`ao_two_e_integral_alpha`
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* :c:data:`ao_two_e_integral_erf_schwartz`
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* :c:data:`ao_two_e_integral_schwartz`
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* :c:data:`ao_two_e_integrals_erf_in_map`
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* :c:data:`ao_two_e_integrals_in_map`
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* :c:data:`center_of_mass`
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* :c:data:`inertia_tensor`
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* :c:data:`nucl_coord_transp`
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* :c:data:`nucl_dist_2`
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* :c:data:`nuclear_repulsion`
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.. c:var:: nucl_coord_transp
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File : :file:`nuclei/nuclei.irp.f`
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.. code:: fortran
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double precision, allocatable :: nucl_coord_transp (3,nucl_num)
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Transposed array of nucl_coord
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Needs:
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.. hlist::
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:columns: 3
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* :c:data:`nucl_coord`
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* :c:data:`nucl_num`
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.. c:var:: nucl_dist
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File : :file:`nuclei/nuclei.irp.f`
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.. code:: fortran
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double precision, allocatable :: nucl_dist_2 (nucl_num,nucl_num)
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double precision, allocatable :: nucl_dist_vec_x (nucl_num,nucl_num)
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double precision, allocatable :: nucl_dist_vec_y (nucl_num,nucl_num)
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double precision, allocatable :: nucl_dist_vec_z (nucl_num,nucl_num)
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double precision, allocatable :: nucl_dist (nucl_num,nucl_num)
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nucl_dist : Nucleus-nucleus distances
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nucl_dist_2 : Nucleus-nucleus distances squared
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nucl_dist_vec : Nucleus-nucleus distances vectors
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Needs:
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.. hlist::
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:columns: 3
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* :c:data:`nucl_coord`
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* :c:data:`nucl_num`
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Needed by:
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.. hlist::
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:columns: 3
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* :c:data:`nucl_dist_inv`
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.. c:var:: nucl_dist_2
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File : :file:`nuclei/nuclei.irp.f`
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.. code:: fortran
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double precision, allocatable :: nucl_dist_2 (nucl_num,nucl_num)
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double precision, allocatable :: nucl_dist_vec_x (nucl_num,nucl_num)
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double precision, allocatable :: nucl_dist_vec_y (nucl_num,nucl_num)
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double precision, allocatable :: nucl_dist_vec_z (nucl_num,nucl_num)
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double precision, allocatable :: nucl_dist (nucl_num,nucl_num)
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nucl_dist : Nucleus-nucleus distances
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nucl_dist_2 : Nucleus-nucleus distances squared
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nucl_dist_vec : Nucleus-nucleus distances vectors
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Needs:
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.. hlist::
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:columns: 3
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* :c:data:`nucl_coord`
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* :c:data:`nucl_num`
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Needed by:
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.. hlist::
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:columns: 3
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* :c:data:`nucl_dist_inv`
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.. c:var:: nucl_dist_inv
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File : :file:`nuclei/nuclei.irp.f`
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.. code:: fortran
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double precision, allocatable :: nucl_dist_inv (nucl_num,nucl_num)
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Inverse of the distance between nucleus I and nucleus J
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Needs:
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.. hlist::
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:columns: 3
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* :c:data:`nucl_dist_2`
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* :c:data:`nucl_num`
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.. c:var:: nucl_dist_vec_x
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File : :file:`nuclei/nuclei.irp.f`
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.. code:: fortran
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double precision, allocatable :: nucl_dist_2 (nucl_num,nucl_num)
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double precision, allocatable :: nucl_dist_vec_x (nucl_num,nucl_num)
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double precision, allocatable :: nucl_dist_vec_y (nucl_num,nucl_num)
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double precision, allocatable :: nucl_dist_vec_z (nucl_num,nucl_num)
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double precision, allocatable :: nucl_dist (nucl_num,nucl_num)
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nucl_dist : Nucleus-nucleus distances
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nucl_dist_2 : Nucleus-nucleus distances squared
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nucl_dist_vec : Nucleus-nucleus distances vectors
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Needs:
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.. hlist::
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:columns: 3
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* :c:data:`nucl_coord`
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* :c:data:`nucl_num`
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Needed by:
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.. hlist::
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:columns: 3
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* :c:data:`nucl_dist_inv`
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.. c:var:: nucl_dist_vec_y
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File : :file:`nuclei/nuclei.irp.f`
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.. code:: fortran
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double precision, allocatable :: nucl_dist_2 (nucl_num,nucl_num)
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double precision, allocatable :: nucl_dist_vec_x (nucl_num,nucl_num)
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double precision, allocatable :: nucl_dist_vec_y (nucl_num,nucl_num)
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double precision, allocatable :: nucl_dist_vec_z (nucl_num,nucl_num)
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double precision, allocatable :: nucl_dist (nucl_num,nucl_num)
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nucl_dist : Nucleus-nucleus distances
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|
|
nucl_dist_2 : Nucleus-nucleus distances squared
|
||
|
|
nucl_dist_vec : Nucleus-nucleus distances vectors
|
||
|
|
|
||
|
|
Needs:
|
||
|
|
|
||
|
|
.. hlist::
|
||
|
|
:columns: 3
|
||
|
|
|
||
|
|
* :c:data:`nucl_coord`
|
||
|
|
* :c:data:`nucl_num`
|
||
|
|
|
||
|
|
Needed by:
|
||
|
|
|
||
|
|
.. hlist::
|
||
|
|
:columns: 3
|
||
|
|
|
||
|
|
* :c:data:`nucl_dist_inv`
|
||
|
|
|
||
|
|
|
||
|
|
.. c:var:: nucl_dist_vec_z
|
||
|
|
|
||
|
|
|
||
|
|
File : :file:`nuclei/nuclei.irp.f`
|
||
|
|
|
||
|
|
.. code:: fortran
|
||
|
|
|
||
|
|
double precision, allocatable :: nucl_dist_2 (nucl_num,nucl_num)
|
||
|
|
double precision, allocatable :: nucl_dist_vec_x (nucl_num,nucl_num)
|
||
|
|
double precision, allocatable :: nucl_dist_vec_y (nucl_num,nucl_num)
|
||
|
|
double precision, allocatable :: nucl_dist_vec_z (nucl_num,nucl_num)
|
||
|
|
double precision, allocatable :: nucl_dist (nucl_num,nucl_num)
|
||
|
|
|
||
|
|
|
||
|
|
nucl_dist : Nucleus-nucleus distances
|
||
|
|
nucl_dist_2 : Nucleus-nucleus distances squared
|
||
|
|
nucl_dist_vec : Nucleus-nucleus distances vectors
|
||
|
|
|
||
|
|
Needs:
|
||
|
|
|
||
|
|
.. hlist::
|
||
|
|
:columns: 3
|
||
|
|
|
||
|
|
* :c:data:`nucl_coord`
|
||
|
|
* :c:data:`nucl_num`
|
||
|
|
|
||
|
|
Needed by:
|
||
|
|
|
||
|
|
.. hlist::
|
||
|
|
:columns: 3
|
||
|
|
|
||
|
|
* :c:data:`nucl_dist_inv`
|
||
|
|
|
||
|
|
|
||
|
|
.. c:var:: nuclear_repulsion
|
||
|
|
|
||
|
|
|
||
|
|
File : :file:`nuclei/nuclei.irp.f`
|
||
|
|
|
||
|
|
.. code:: fortran
|
||
|
|
|
||
|
|
double precision :: nuclear_repulsion
|
||
|
|
|
||
|
|
|
||
|
|
Nuclear repulsion energy
|
||
|
|
|
||
|
|
Needs:
|
||
|
|
|
||
|
|
.. hlist::
|
||
|
|
:columns: 3
|
||
|
|
|
||
|
|
* :c:data:`disk_access_nuclear_repulsion`
|
||
|
|
* :c:data:`mpi_master`
|
||
|
|
* :c:data:`nucl_charge`
|
||
|
|
* :c:data:`nucl_coord`
|
||
|
|
* :c:data:`nucl_num`
|
||
|
|
* :c:data:`output_wall_time_0`
|
||
|
|
|
||
|
|
Needed by:
|
||
|
|
|
||
|
|
.. hlist::
|
||
|
|
:columns: 3
|
||
|
|
|
||
|
|
* :c:data:`ci_energy`
|
||
|
|
* :c:data:`core_energy`
|
||
|
|
* :c:data:`core_energy_erf`
|
||
|
|
* :c:data:`hf_energy`
|
||
|
|
* :c:data:`psi_energy_with_nucl_rep`
|
||
|
|
* :c:data:`pt2_e0_denominator`
|
||
|
|
* :c:data:`scf_energy`
|
||
|
|
|
||
|
|
|
||
|
|
.. c:var:: slater_bragg_radii
|
||
|
|
|
||
|
|
|
||
|
|
File : :file:`nuclei/atomic_radii.irp.f`
|
||
|
|
|
||
|
|
.. code:: fortran
|
||
|
|
|
||
|
|
double precision, allocatable :: slater_bragg_radii (100)
|
||
|
|
|
||
|
|
|
||
|
|
atomic radii in Angstrom defined in table I of JCP 41, 3199 (1964) Slater
|
||
|
|
execpt for the Hydrogen atom where we took the value of Becke (1988, JCP)
|
||
|
|
|
||
|
|
Needed by:
|
||
|
|
|
||
|
|
.. hlist::
|
||
|
|
:columns: 3
|
||
|
|
|
||
|
|
* :c:data:`slater_bragg_radii_per_atom`
|
||
|
|
* :c:data:`slater_bragg_radii_ua`
|
||
|
|
|
||
|
|
|
||
|
|
.. c:var:: slater_bragg_radii_per_atom
|
||
|
|
|
||
|
|
|
||
|
|
File : :file:`nuclei/atomic_radii.irp.f`
|
||
|
|
|
||
|
|
.. code:: fortran
|
||
|
|
|
||
|
|
double precision, allocatable :: slater_bragg_radii_per_atom (nucl_num)
|
||
|
|
|
||
|
|
|
||
|
|
|
||
|
|
Needs:
|
||
|
|
|
||
|
|
.. hlist::
|
||
|
|
:columns: 3
|
||
|
|
|
||
|
|
* :c:data:`nucl_charge`
|
||
|
|
* :c:data:`nucl_num`
|
||
|
|
* :c:data:`slater_bragg_radii`
|
||
|
|
|
||
|
|
Needed by:
|
||
|
|
|
||
|
|
.. hlist::
|
||
|
|
:columns: 3
|
||
|
|
|
||
|
|
* :c:data:`slater_bragg_type_inter_distance`
|
||
|
|
|
||
|
|
|
||
|
|
.. c:var:: slater_bragg_radii_per_atom_ua
|
||
|
|
|
||
|
|
|
||
|
|
File : :file:`nuclei/atomic_radii.irp.f`
|
||
|
|
|
||
|
|
.. code:: fortran
|
||
|
|
|
||
|
|
double precision, allocatable :: slater_bragg_radii_per_atom_ua (nucl_num)
|
||
|
|
|
||
|
|
|
||
|
|
|
||
|
|
Needs:
|
||
|
|
|
||
|
|
.. hlist::
|
||
|
|
:columns: 3
|
||
|
|
|
||
|
|
* :c:data:`nucl_charge`
|
||
|
|
* :c:data:`nucl_num`
|
||
|
|
* :c:data:`slater_bragg_radii_ua`
|
||
|
|
|
||
|
|
Needed by:
|
||
|
|
|
||
|
|
.. hlist::
|
||
|
|
:columns: 3
|
||
|
|
|
||
|
|
* :c:data:`slater_bragg_type_inter_distance_ua`
|
||
|
|
|
||
|
|
|
||
|
|
.. c:var:: slater_bragg_radii_ua
|
||
|
|
|
||
|
|
|
||
|
|
File : :file:`nuclei/atomic_radii.irp.f`
|
||
|
|
|
||
|
|
.. code:: fortran
|
||
|
|
|
||
|
|
double precision, allocatable :: slater_bragg_radii_ua (100)
|
||
|
|
|
||
|
|
|
||
|
|
|
||
|
|
Needs:
|
||
|
|
|
||
|
|
.. hlist::
|
||
|
|
:columns: 3
|
||
|
|
|
||
|
|
* :c:data:`slater_bragg_radii`
|
||
|
|
|
||
|
|
Needed by:
|
||
|
|
|
||
|
|
.. hlist::
|
||
|
|
:columns: 3
|
||
|
|
|
||
|
|
* :c:data:`slater_bragg_radii_per_atom_ua`
|
||
|
|
|
||
|
|
|
||
|
|
.. c:var:: slater_bragg_type_inter_distance
|
||
|
|
|
||
|
|
|
||
|
|
File : :file:`nuclei/atomic_radii.irp.f`
|
||
|
|
|
||
|
|
.. code:: fortran
|
||
|
|
|
||
|
|
double precision, allocatable :: slater_bragg_type_inter_distance (nucl_num,nucl_num)
|
||
|
|
|
||
|
|
|
||
|
|
|
||
|
|
Needs:
|
||
|
|
|
||
|
|
.. hlist::
|
||
|
|
:columns: 3
|
||
|
|
|
||
|
|
* :c:data:`nucl_num`
|
||
|
|
* :c:data:`slater_bragg_radii_per_atom`
|
||
|
|
|
||
|
|
|
||
|
|
|
||
|
|
.. c:var:: slater_bragg_type_inter_distance_ua
|
||
|
|
|
||
|
|
|
||
|
|
File : :file:`nuclei/atomic_radii.irp.f`
|
||
|
|
|
||
|
|
.. code:: fortran
|
||
|
|
|
||
|
|
double precision, allocatable :: slater_bragg_type_inter_distance_ua (nucl_num,nucl_num)
|
||
|
|
|
||
|
|
|
||
|
|
|
||
|
|
Needs:
|
||
|
|
|
||
|
|
.. hlist::
|
||
|
|
:columns: 3
|
||
|
|
|
||
|
|
* :c:data:`nucl_num`
|
||
|
|
* :c:data:`slater_bragg_radii_per_atom_ua`
|
||
|
|
|
||
|
|
|