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Develop (#15) * fixed laplacian of aos * corrected the laplacians of aos * added dft_one_e * added new feature for new dft functionals * changed the configure to add new functionals * changed the configure * added dft_one_e/README.rst * added README.rst in new_functionals * added source/programmers_guide/new_ks.rst * Thesis Yann * Added gmp installation in configure * improved qp_e_conv_fci * Doc * Typos * Added variance_max * Fixed completion in qp_create * modif TODO * fixed DFT potential for n_states gt 1 * improved pot pbe * trying to improve sr PBE * fixed potential pbe * fixed the vxc smashed for pbe sr and normal * Comments in selection * bug fixed by peter * Fixed bug with zero beta electrons * Update README.rst * Update e_xc_new_func.irp.f * Update links.rst * Update quickstart.rst * Update quickstart.rst * updated cipsi * Fixed energies of non-expected s2 (#9) * Moved diag_algorithm in Davdison * Add print_ci_vector in tools (#11) * Fixed energies of non-expected s2 * Moved diag_algorithm in Davdison * Fixed travis * Added print_ci_vector * Documentation * Cleaned qp_set_mo_class.ml * Removed Core in taskserver * Merge develop-toto and manus (#12) * Fixed energies of non-expected s2 * Moved diag_algorithm in Davdison * Fixed travis * Added print_ci_vector * Documentation * Cleaned qp_set_mo_class.ml * Removed Core in taskserver * Frozen core for heavy atoms * Improved molden module * In sync with manus * Fixed some of the documentation errors * Develop toto (#13) * Fixed energies of non-expected s2 * Moved diag_algorithm in Davdison * Fixed travis * Added print_ci_vector * Documentation * Cleaned qp_set_mo_class.ml * Removed Core in taskserver * Frozen core for heavy atoms * Improved molden module * In sync with manus * Fixed some of the documentation errors * Develop manus (#14) * modified printing for rpt2 * Comment * Fixed plugins * Scripting for functionals * Documentation * Develop (#10) * fixed laplacian of aos * corrected the laplacians of aos * added dft_one_e * added new feature for new dft functionals * changed the configure to add new functionals * changed the configure * added dft_one_e/README.rst * added README.rst in new_functionals * added source/programmers_guide/new_ks.rst * Thesis Yann * Added gmp installation in configure * improved qp_e_conv_fci * Doc * Typos * Added variance_max * Fixed completion in qp_create * modif TODO * fixed DFT potential for n_states gt 1 * improved pot pbe * trying to improve sr PBE * fixed potential pbe * fixed the vxc smashed for pbe sr and normal * Comments in selection * bug fixed by peter * Fixed bug with zero beta electrons * Update README.rst * Update e_xc_new_func.irp.f * Update links.rst * Update quickstart.rst * Update quickstart.rst * updated cipsi * Fixed energies of non-expected s2 (#9) * Moved diag_algorithm in Davdison * some modifs * modified gfortran_debug.cfg * fixed automatization of functionals * modified e_xc_general.irp.f * minor modifs in ref_bitmask.irp.f * modifying functionals * rs_ks_scf and ks_scf compiles with the automatic handling of functionals * removed prints * fixed configure * fixed the new functionals * Merge toto * modified automatic functionals * Changed python into python2 * from_xyz suppressed * Cleaning repo * Update README.md * Update README.md * Contributors * Update GITHUB.md * bibtex
2019-03-07 16:29:06 +01:00
.. _module_nuclei:
.. program:: nuclei
.. default-role:: option
======
nuclei
======
This module contains data relative to the nuclei (coordinates, charge,
nuclear repulsion energy, etc).
The coordinates are expressed in atomic units.
EZFIO parameters
----------------
.. option:: nucl_num
Number of nuclei
.. option:: nucl_label
Nuclear labels
.. option:: nucl_charge
Nuclear charges
.. option:: nucl_coord
Nuclear coordinates in the format (:, {x,y,z})
.. option:: disk_access_nuclear_repulsion
Read/Write Nuclear Repulsion from/to disk [ Write | Read | None ]
Default: None
.. option:: nuclear_repulsion
Nuclear repulsion (Computed automaticaly or Read in the |EZFIO|)
Providers
---------
.. c:var:: center_of_mass
File : :file:`nuclei/nuclei.irp.f`
.. code:: fortran
double precision, allocatable :: center_of_mass (3)
Center of mass of the molecule
Needs:
.. hlist::
:columns: 3
* :c:data:`element_name`
* :c:data:`nucl_charge`
* :c:data:`nucl_coord`
* :c:data:`nucl_num`
Needed by:
.. hlist::
:columns: 3
* :c:data:`inertia_tensor`
.. c:var:: element_mass
File : :file:`nuclei/nuclei.irp.f`
.. code:: fortran
character*(4), allocatable :: element_name (0:127)
double precision, allocatable :: element_mass (0:127)
Array of the name of element, sorted by nuclear charge (integer)
Needs:
.. hlist::
:columns: 3
* :c:data:`mpi_master`
Needed by:
.. hlist::
:columns: 3
* :c:data:`center_of_mass`
* :c:data:`inertia_tensor`
.. c:var:: element_name
File : :file:`nuclei/nuclei.irp.f`
.. code:: fortran
character*(4), allocatable :: element_name (0:127)
double precision, allocatable :: element_mass (0:127)
Array of the name of element, sorted by nuclear charge (integer)
Needs:
.. hlist::
:columns: 3
* :c:data:`mpi_master`
Needed by:
.. hlist::
:columns: 3
* :c:data:`center_of_mass`
* :c:data:`inertia_tensor`
.. c:var:: inertia_tensor
File : :file:`nuclei/inertia.irp.f`
.. code:: fortran
double precision, allocatable :: inertia_tensor (3,3)
Inertia tensor
Needs:
.. hlist::
:columns: 3
* :c:data:`center_of_mass`
* :c:data:`element_name`
* :c:data:`nucl_charge`
* :c:data:`nucl_coord`
* :c:data:`nucl_num`
Needed by:
.. hlist::
:columns: 3
* :c:data:`inertia_tensor_eigenvectors`
.. c:var:: inertia_tensor_eigenvalues
File : :file:`nuclei/inertia.irp.f`
.. code:: fortran
double precision, allocatable :: inertia_tensor_eigenvectors (3,3)
double precision, allocatable :: inertia_tensor_eigenvalues (3)
Eigenvectors/eigenvalues of the inertia_tensor. Used to find normal orientation.
Needs:
.. hlist::
:columns: 3
* :c:data:`inertia_tensor`
.. c:var:: inertia_tensor_eigenvectors
File : :file:`nuclei/inertia.irp.f`
.. code:: fortran
double precision, allocatable :: inertia_tensor_eigenvectors (3,3)
double precision, allocatable :: inertia_tensor_eigenvalues (3)
Eigenvectors/eigenvalues of the inertia_tensor. Used to find normal orientation.
Needs:
.. hlist::
:columns: 3
* :c:data:`inertia_tensor`
.. c:var:: nucl_coord
File : :file:`nuclei/nuclei.irp.f`
.. code:: fortran
double precision, allocatable :: nucl_coord (nucl_num,3)
Nuclear coordinates in the format (:, {x,y,z})
Needs:
.. hlist::
:columns: 3
* :c:data:`ezfio_filename`
* :c:data:`mpi_master`
* :c:data:`nucl_charge`
* :c:data:`nucl_label`
* :c:data:`nucl_num`
* :c:data:`output_wall_time_0`
Needed by:
.. hlist::
:columns: 3
* :c:data:`ao_deriv2_x`
* :c:data:`ao_deriv_1_x`
* :c:data:`ao_dipole_x`
* :c:data:`ao_integrals_n_e`
* :c:data:`ao_integrals_n_e_per_atom`
* :c:data:`ao_overlap`
* :c:data:`ao_overlap_abs`
* :c:data:`ao_pseudo_integrals_local`
* :c:data:`ao_pseudo_integrals_non_local`
* :c:data:`ao_spread_x`
* :c:data:`ao_two_e_integral_alpha`
* :c:data:`ao_two_e_integral_erf_schwartz`
* :c:data:`ao_two_e_integral_schwartz`
* :c:data:`ao_two_e_integrals_erf_in_map`
* :c:data:`ao_two_e_integrals_in_map`
* :c:data:`center_of_mass`
* :c:data:`inertia_tensor`
* :c:data:`nucl_coord_transp`
* :c:data:`nucl_dist_2`
* :c:data:`nuclear_repulsion`
.. c:var:: nucl_coord_transp
File : :file:`nuclei/nuclei.irp.f`
.. code:: fortran
double precision, allocatable :: nucl_coord_transp (3,nucl_num)
Transposed array of nucl_coord
Needs:
.. hlist::
:columns: 3
* :c:data:`nucl_coord`
* :c:data:`nucl_num`
.. c:var:: nucl_dist
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:: nucl_dist_2
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:: nucl_dist_inv
File : :file:`nuclei/nuclei.irp.f`
.. code:: fortran
double precision, allocatable :: nucl_dist_inv (nucl_num,nucl_num)
Inverse of the distance between nucleus I and nucleus J
Needs:
.. hlist::
:columns: 3
* :c:data:`nucl_dist_2`
* :c:data:`nucl_num`
.. c:var:: nucl_dist_vec_x
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:: nucl_dist_vec_y
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:: 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`