mirror of
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synced 2024-11-16 11:03:49 +01:00
8b22e38c9c
* 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
667 lines
12 KiB
ReStructuredText
667 lines
12 KiB
ReStructuredText
.. _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
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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_z
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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:: nuclear_repulsion
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File : :file:`nuclei/nuclei.irp.f`
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.. code:: fortran
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double precision :: nuclear_repulsion
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Nuclear repulsion energy
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Needs:
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.. hlist::
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:columns: 3
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* :c:data:`disk_access_nuclear_repulsion`
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* :c:data:`mpi_master`
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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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* :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:`ci_energy`
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* :c:data:`core_energy`
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* :c:data:`core_energy_erf`
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* :c:data:`hf_energy`
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* :c:data:`psi_energy_with_nucl_rep`
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* :c:data:`pt2_e0_denominator`
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* :c:data:`scf_energy`
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.. c:var:: slater_bragg_radii
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File : :file:`nuclei/atomic_radii.irp.f`
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.. code:: fortran
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double precision, allocatable :: slater_bragg_radii (100)
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atomic radii in Angstrom defined in table I of JCP 41, 3199 (1964) Slater
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execpt for the Hydrogen atom where we took the value of Becke (1988, JCP)
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Needed by:
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.. hlist::
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:columns: 3
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* :c:data:`slater_bragg_radii_per_atom`
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* :c:data:`slater_bragg_radii_ua`
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.. c:var:: slater_bragg_radii_per_atom
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File : :file:`nuclei/atomic_radii.irp.f`
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.. code:: fortran
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double precision, allocatable :: slater_bragg_radii_per_atom (nucl_num)
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Needs:
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.. hlist::
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:columns: 3
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* :c:data:`nucl_charge`
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* :c:data:`nucl_num`
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* :c:data:`slater_bragg_radii`
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Needed by:
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.. hlist::
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:columns: 3
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* :c:data:`slater_bragg_type_inter_distance`
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.. c:var:: slater_bragg_radii_per_atom_ua
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File : :file:`nuclei/atomic_radii.irp.f`
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.. code:: fortran
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double precision, allocatable :: slater_bragg_radii_per_atom_ua (nucl_num)
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Needs:
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.. hlist::
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:columns: 3
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* :c:data:`nucl_charge`
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* :c:data:`nucl_num`
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* :c:data:`slater_bragg_radii_ua`
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Needed by:
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.. hlist::
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:columns: 3
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* :c:data:`slater_bragg_type_inter_distance_ua`
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.. c:var:: slater_bragg_radii_ua
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File : :file:`nuclei/atomic_radii.irp.f`
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.. code:: fortran
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double precision, allocatable :: slater_bragg_radii_ua (100)
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Needs:
|
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|
.. hlist::
|
|
:columns: 3
|
|
|
|
* :c:data:`slater_bragg_radii`
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|
|
|
Needed by:
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|
|
.. hlist::
|
|
:columns: 3
|
|
|
|
* :c:data:`slater_bragg_radii_per_atom_ua`
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.. c:var:: slater_bragg_type_inter_distance
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File : :file:`nuclei/atomic_radii.irp.f`
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.. code:: fortran
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double precision, allocatable :: slater_bragg_type_inter_distance (nucl_num,nucl_num)
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Needs:
|
|
|
|
.. hlist::
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|
:columns: 3
|
|
|
|
* :c:data:`nucl_num`
|
|
* :c:data:`slater_bragg_radii_per_atom`
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.. c:var:: slater_bragg_type_inter_distance_ua
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File : :file:`nuclei/atomic_radii.irp.f`
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.. code:: fortran
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|
double precision, allocatable :: slater_bragg_type_inter_distance_ua (nucl_num,nucl_num)
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Needs:
|
|
|
|
.. hlist::
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|
:columns: 3
|
|
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|
* :c:data:`nucl_num`
|
|
* :c:data:`slater_bragg_radii_per_atom_ua`
|
|
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|