This module is used to efficiently handle the topological problem of
finding all the atom pairs in the molecule separated by exactly n bonds.
To do so the molecule is tought as an undirected unweighted graph,
represented in memory with a boolean adjacency matrix. Since this matrix
is sparse and symmetric, it is effeciently represented in the Yale format
(sometime referred as compressed sparse row, CSR) omitting the value
array.
From the adjacency matrix , the matrix containing the atom
pairs separated by exactly n bonds are computed according the following
recoursive formula:
Note that in this context since we are manipulating boolean matrices,
the product is replaced by logical and, sum by logical or, and - by
The module contains all the routines needed to perform such operations,
including the linear scaling multiplication between sparse matrices.
Uses
module~~mod_adjacency_mat~~UsesGraph
module~mod_adjacency_mat
mod_adjacency_mat
module~mod_memory
mod_memory
module~mod_adjacency_mat->module~mod_memory
module~mod_io
mod_io
module~mod_memory->module~mod_io
module~mod_constants
mod_constants
module~mod_memory->module~mod_constants
iso_c_binding
iso_c_binding
module~mod_memory->iso_c_binding
module~mod_io->module~mod_constants
module~mod_constants->iso_c_binding
Nodes of different colours represent the following:
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Module
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Subroutine
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Program
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Solid arrows point from a submodule to the (sub)module which it is
descended from. Dashed arrows point from a module or program unit to
modules which it uses.
Used by
module~~mod_adjacency_mat~~UsedByGraph
module~mod_adjacency_mat
mod_adjacency_mat
proc~make_screening_lists
make_screening_lists
proc~make_screening_lists->module~mod_adjacency_mat
module~mod_tree
mod_tree
module~mod_tree->module~mod_adjacency_mat
proc~guess_connectivity
guess_connectivity
proc~guess_connectivity->module~mod_adjacency_mat
module~mod_mmpol
mod_mmpol
module~mod_mmpol->module~mod_adjacency_mat
module~mod_nonbonded
mod_nonbonded
module~mod_mmpol->module~mod_nonbonded
module~mod_electrostatics
mod_electrostatics
module~mod_mmpol->module~mod_electrostatics
module~mod_topology
mod_topology
module~mod_mmpol->module~mod_topology
module~mod_link_atom
mod_link_atom
module~mod_mmpol->module~mod_link_atom
module~mod_bonded
mod_bonded
module~mod_mmpol->module~mod_bonded
module~mod_nonbonded->module~mod_adjacency_mat
module~mod_nonbonded->module~mod_topology
module~mod_neighbor_list
mod_neighbor_list
module~mod_nonbonded->module~mod_neighbor_list
proc~mmpol_init_from_hdf5
mmpol_init_from_hdf5
proc~mmpol_init_from_hdf5->module~mod_adjacency_mat
proc~mmpol_init_from_hdf5->module~mod_mmpol
proc~mmpol_init_from_hdf5->module~mod_nonbonded
proc~mmpol_init_from_hdf5->module~mod_electrostatics
proc~mmpol_init_from_hdf5->module~mod_bonded
proc~tree_populate_farnear_lists
tree_populate_farnear_lists
proc~tree_populate_farnear_lists->module~mod_adjacency_mat
proc~electrostatics_terminate
electrostatics_terminate
proc~electrostatics_terminate->module~mod_adjacency_mat
proc~init_as_octatree
init_as_octatree
proc~init_as_octatree->module~mod_adjacency_mat
proc~build_pg_adjacency_matrix
build_pg_adjacency_matrix
proc~build_pg_adjacency_matrix->module~mod_adjacency_mat
proc~mmpol_init_from_mmp
mmpol_init_from_mmp
proc~mmpol_init_from_mmp->module~mod_adjacency_mat
proc~mmpol_init_from_mmp->module~mod_mmpol
proc~mmpol_init_from_mmp->module~mod_electrostatics
proc~populate_level_list
populate_level_list
proc~populate_level_list->module~mod_adjacency_mat
proc~nl_terminate
nl_terminate
proc~nl_terminate->module~mod_adjacency_mat
proc~init_as_ribtree
init_as_ribtree
proc~init_as_ribtree->module~mod_adjacency_mat
proc~free_tree
free_tree
proc~free_tree->module~mod_adjacency_mat
module~mod_electrostatics->module~mod_adjacency_mat
module~mod_electrostatics->module~mod_topology
module~fmmlib_interface
fmmlib_interface
module~mod_electrostatics->module~fmmlib_interface
proc~tree_populate_farnear_lists_safe
tree_populate_farnear_lists_safe
proc~tree_populate_farnear_lists_safe->module~mod_adjacency_mat
proc~topology_terminate
topology_terminate
proc~topology_terminate->module~mod_adjacency_mat
proc~mmpol_prepare
mmpol_prepare
proc~mmpol_prepare->module~mod_adjacency_mat
proc~mmpol_prepare->module~mod_electrostatics
proc~nl_update
nl_update
proc~nl_update->module~mod_adjacency_mat
module~mod_topology->module~mod_adjacency_mat
module~mod_neighbor_list->module~mod_adjacency_mat
proc~check_conn_matrix
check_conn_matrix
proc~check_conn_matrix->module~mod_adjacency_mat
proc~create_new_bond
create_new_bond
proc~create_new_bond->module~mod_adjacency_mat
proc~qm_helper_update_coord
qm_helper_update_coord
proc~qm_helper_update_coord->module~mod_adjacency_mat
proc~qm_helper_update_coord->module~mod_topology
proc~ommp_system_from_qm_helper
ommp_system_from_qm_helper
proc~ommp_system_from_qm_helper->module~mod_adjacency_mat
proc~ommp_system_from_qm_helper->module~mod_mmpol
proc~ommp_system_from_qm_helper->module~mod_topology
module~mod_prm
mod_prm
proc~ommp_system_from_qm_helper->module~mod_prm
proc~vdw_terminate
vdw_terminate
proc~vdw_terminate->module~mod_adjacency_mat
proc~vdw_terminate->module~mod_neighbor_list
proc~mmpol_init_from_xyz
mmpol_init_from_xyz
proc~mmpol_init_from_xyz->module~mod_adjacency_mat
proc~mmpol_init_from_xyz->module~mod_mmpol
proc~mmpol_init_from_xyz->module~mod_electrostatics
proc~mmpol_init_from_xyz->module~mod_topology
proc~mmpol_init_from_xyz->module~mod_prm
proc~fmm_make_neigh_list
fmm_make_neigh_list
proc~fmm_make_neigh_list->module~mod_adjacency_mat
proc~allocate_tree
allocate_tree
proc~allocate_tree->module~mod_adjacency_mat
proc~vdw_init
vdw_init
proc~vdw_init->module~mod_neighbor_list
proc~r1_hdf5_read_array
r1_hdf5_read_array
proc~r1_hdf5_read_array->module~mod_mmpol
proc~i1_hdf5_read_array
i1_hdf5_read_array
proc~i1_hdf5_read_array->module~mod_mmpol
proc~ommp_potential_mm2ext
ommp_potential_mm2ext
proc~ommp_potential_mm2ext->module~mod_electrostatics
proc~ommp_qm_helper_set_frozen_atoms
ommp_qm_helper_set_frozen_atoms
proc~ommp_qm_helper_set_frozen_atoms->module~mod_topology
proc~ommp_turn_pol_off
ommp_turn_pol_off
proc~ommp_turn_pol_off->module~mod_electrostatics
proc~add_link_atom
add_link_atom
proc~add_link_atom->module~mod_topology
module~mod_iohdf5
mod_iohdf5
module~mod_iohdf5->module~mod_mmpol
module~mod_iohdf5->module~mod_nonbonded
module~mod_iohdf5->module~mod_electrostatics
module~mod_iohdf5->module~mod_topology
module~mod_iohdf5->module~mod_bonded
proc~ommp_field_pol2ext
ommp_field_pol2ext
proc~ommp_field_pol2ext->module~mod_electrostatics
proc~init_bonded_for_link_atom
init_bonded_for_link_atom
proc~init_bonded_for_link_atom->module~mod_topology
proc~init_bonded_for_link_atom->module~mod_prm
proc~init_bonded_for_link_atom->module~mod_bonded
module~mod_octatree
mod_octatree
module~mod_octatree->module~mod_tree
proc~free_fmm
free_fmm
proc~free_fmm->module~mod_tree
proc~r3_hdf5_read_array
r3_hdf5_read_array
proc~r3_hdf5_read_array->module~mod_mmpol
proc~l1_hdf5_read_array
l1_hdf5_read_array
proc~l1_hdf5_read_array->module~mod_mmpol
proc~electrostatic_for_ene
electrostatic_for_ene
proc~electrostatic_for_ene->module~mod_electrostatics
proc~init_vdw_for_link_atom
init_vdw_for_link_atom
proc~init_vdw_for_link_atom->module~mod_topology
module~mod_polarization
mod_polarization
module~mod_polarization->module~mod_mmpol
module~mod_polarization->module~mod_electrostatics
proc~dipole_t
dipole_T
proc~dipole_t->module~mod_electrostatics
proc~qm_helper_init
qm_helper_init
proc~qm_helper_init->module~mod_topology
module~mod_qm_helper
mod_qm_helper
module~mod_qm_helper->module~mod_mmpol
module~mod_qm_helper->module~mod_nonbonded
module~mod_qm_helper->module~mod_topology
proc~qm_helper_terminate
qm_helper_terminate
proc~qm_helper_terminate->module~mod_nonbonded
proc~qm_helper_terminate->module~mod_topology
proc~ommp_vdw_geomgrad
ommp_vdw_geomgrad
proc~ommp_vdw_geomgrad->module~mod_nonbonded
proc~ommp_get_vdw_energy
ommp_get_vdw_energy
proc~ommp_get_vdw_energy->module~mod_nonbonded
proc~ommp_potential_pol2ext
ommp_potential_pol2ext
proc~ommp_potential_pol2ext->module~mod_electrostatics
module~mod_fmm
mod_fmm
module~mod_fmm->module~mod_tree
proc~ommp_set_frozen_atoms
ommp_set_frozen_atoms
proc~ommp_set_frozen_atoms->module~mod_topology
proc~ommp_full_geomgrad
ommp_full_geomgrad
proc~ommp_full_geomgrad->module~mod_nonbonded
module~mod_geomgrad
mod_geomgrad
proc~ommp_full_geomgrad->module~mod_geomgrad
proc~ommp_set_default_matv
ommp_set_default_matv
proc~ommp_set_default_matv->module~mod_electrostatics
proc~c_ommp_field_mm2ext
C_ommp_field_mm2ext
proc~c_ommp_field_mm2ext->module~mod_electrostatics
proc~qm_helper_vdw_geomgrad
qm_helper_vdw_geomgrad
proc~qm_helper_vdw_geomgrad->module~mod_mmpol
proc~qm_helper_vdw_geomgrad->module~mod_nonbonded
proc~qm_helper_vdw_geomgrad->module~mod_link_atom
proc~ommp_create_link_atom
ommp_create_link_atom
proc~ommp_create_link_atom->module~mod_mmpol
proc~ommp_create_link_atom->module~mod_nonbonded
proc~ommp_create_link_atom->module~mod_topology
proc~ommp_create_link_atom->module~mod_qm_helper
proc~ommp_create_link_atom->module~mod_link_atom
proc~ommp_set_default_solver
ommp_set_default_solver
proc~ommp_set_default_solver->module~mod_electrostatics
proc~ommp_field_mmpol2ext
ommp_field_mmpol2ext
proc~ommp_field_mmpol2ext->module~mod_electrostatics
proc~i3_hdf5_read_array
i3_hdf5_read_array
proc~i3_hdf5_read_array->module~mod_mmpol
proc~rotation_geomgrad
rotation_geomgrad
proc~rotation_geomgrad->module~mod_electrostatics
proc~ommp_set_external_field
ommp_set_external_field
proc~ommp_set_external_field->module~mod_electrostatics
proc~ommp_set_external_field->module~mod_polarization
proc~assign_mpoles
assign_mpoles
proc~assign_mpoles->module~mod_electrostatics
proc~c_ommp_set_fmm_min_cell_size
C_ommp_set_fmm_min_cell_size
proc~c_ommp_set_fmm_min_cell_size->module~mod_electrostatics
proc~assign_pol
assign_pol
proc~assign_pol->module~mod_electrostatics
module~mod_prm->module~mod_electrostatics
module~mod_prm->module~mod_topology
module~mod_prm->module~mod_bonded
proc~vdw_set_cutoff
vdw_set_cutoff
proc~vdw_set_cutoff->module~mod_neighbor_list
module~mod_inputloader
mod_inputloader
module~mod_inputloader->module~mod_mmpol
proc~r2_hdf5_read_array
r2_hdf5_read_array
proc~r2_hdf5_read_array->module~mod_mmpol
proc~i2_hdf5_read_array
i2_hdf5_read_array
proc~i2_hdf5_read_array->module~mod_mmpol
proc~qm_helper_link_atom_geomgrad
qm_helper_link_atom_geomgrad
proc~qm_helper_link_atom_geomgrad->module~mod_mmpol
proc~qm_helper_link_atom_geomgrad->module~mod_link_atom
proc~c_ommp_update_coordinates
C_ommp_update_coordinates
proc~c_ommp_update_coordinates->module~mod_mmpol
proc~ommp_get_polelec_energy
ommp_get_polelec_energy
proc~ommp_get_polelec_energy->module~mod_electrostatics
proc~ommp_get_polelec_energy->module~mod_polarization
proc~electrostatic_for_grad
electrostatic_for_grad
proc~electrostatic_for_grad->module~mod_electrostatics
proc~c_ommp_set_fmm_distance
C_ommp_set_fmm_distance
proc~c_ommp_set_fmm_distance->module~mod_electrostatics
proc~init_eel_for_link_atom
init_eel_for_link_atom
proc~init_eel_for_link_atom->module~mod_electrostatics
proc~init_eel_for_link_atom->module~mod_prm
proc~c_ommp_field_pol2ext
C_ommp_field_pol2ext
proc~c_ommp_field_pol2ext->module~mod_electrostatics
proc~ommp_get_fixedelec_energy
ommp_get_fixedelec_energy
proc~ommp_get_fixedelec_energy->module~mod_electrostatics
proc~l2_hdf5_read_array
l2_hdf5_read_array
proc~l2_hdf5_read_array->module~mod_mmpol
proc~vdw_geomgrad
vdw_geomgrad
proc~vdw_geomgrad->module~mod_neighbor_list
proc~ommp_set_vdw_cutoff
ommp_set_vdw_cutoff
proc~ommp_set_vdw_cutoff->module~mod_nonbonded
proc~ommp_potential_mmpol2ext
ommp_potential_mmpol2ext
proc~ommp_potential_mmpol2ext->module~mod_electrostatics
module~fmmlib_interface->module~mod_tree
module~fmmlib_interface->module~mod_octatree
module~fmmlib_interface->module~mod_fmm
module~mod_ribtree
mod_ribtree
module~fmmlib_interface->module~mod_ribtree
proc~qm_helper_init_vdw
qm_helper_init_vdw
proc~qm_helper_init_vdw->module~mod_nonbonded
proc~update_coordinates
update_coordinates
proc~update_coordinates->module~mod_electrostatics
proc~update_coordinates->module~mod_link_atom
proc~init_link_atom
init_link_atom
proc~init_link_atom->module~mod_topology
proc~qm_helper_vdw_energy
qm_helper_vdw_energy
proc~qm_helper_vdw_energy->module~mod_mmpol
proc~qm_helper_vdw_energy->module~mod_nonbonded
proc~qm_helper_vdw_energy->module~mod_link_atom
proc~rotate_multipoles
rotate_multipoles
proc~rotate_multipoles->module~mod_electrostatics
module~mod_solvers
mod_solvers
module~mod_solvers->module~mod_electrostatics
module~mod_link_atom->module~mod_nonbonded
module~mod_link_atom->module~mod_topology
module~mod_link_atom->module~mod_bonded
proc~polelec_geomgrad
polelec_geomgrad
proc~polelec_geomgrad->module~mod_electrostatics
proc~polelec_geomgrad->module~mod_polarization
proc~vdw_potential
vdw_potential
proc~vdw_potential->module~mod_neighbor_list
proc~mmpol_init
mmpol_init
proc~mmpol_init->module~mod_electrostatics
proc~assign_vdw
assign_vdw
proc~assign_vdw->module~mod_nonbonded
proc~ommp_field_mm2ext
ommp_field_mm2ext
proc~ommp_field_mm2ext->module~mod_electrostatics
proc~tmatvec_otf
TMatVec_otf
proc~tmatvec_otf->module~mod_electrostatics
module~mod_bonded->module~mod_topology
proc~mmpol_terminate
mmpol_terminate
proc~mmpol_terminate->module~mod_nonbonded
proc~mmpol_terminate->module~mod_electrostatics
proc~mmpol_terminate->module~mod_bonded
module~mod_geomgrad->module~mod_mmpol
module~mod_geomgrad->module~mod_topology
proc~ommp_terminate
ommp_terminate
proc~ommp_terminate->module~mod_mmpol
module~ommp_interface
ommp_interface
module~ommp_interface->module~mod_mmpol
module~ommp_interface->module~mod_electrostatics
module~ommp_interface->module~mod_topology
module~ommp_interface->module~mod_iohdf5
module~ommp_interface->module~mod_qm_helper
module~mod_ribtree->module~mod_tree
proc~fixedelec_geomgrad
fixedelec_geomgrad
proc~fixedelec_geomgrad->module~mod_electrostatics
proc~ommp_fixedelec_geomgrad
ommp_fixedelec_geomgrad
proc~ommp_fixedelec_geomgrad->module~mod_geomgrad
proc~assign_pitors
assign_pitors
proc~assign_pitors->module~mod_bonded
module~mod_ommp_c_interface
mod_ommp_C_interface
module~mod_ommp_c_interface->module~ommp_interface
proc~assign_tortors
assign_tortors
proc~assign_tortors->module~mod_bonded
proc~c_ommp_qm_helper_use_frozen
C_ommp_qm_helper_use_frozen
proc~c_ommp_qm_helper_use_frozen->module~mod_qm_helper
proc~c_ommp_qm_helper_get_cqm
C_ommp_qm_helper_get_cqm
proc~c_ommp_qm_helper_get_cqm->module~mod_qm_helper
proc~c_ommp_qm_helper_get_e_p2n
C_ommp_qm_helper_get_E_p2n
proc~c_ommp_qm_helper_get_e_p2n->module~mod_qm_helper
proc~c_ommp_qm_helper_get_h_n2m
C_ommp_qm_helper_get_H_n2m
proc~c_ommp_qm_helper_get_h_n2m->module~mod_qm_helper
proc~c_ommp_qm_helper_get_v_m2n
C_ommp_qm_helper_get_V_m2n
proc~c_ommp_qm_helper_get_v_m2n->module~mod_qm_helper
proc~ommp_qm_helper_vdw_energy
ommp_qm_helper_vdw_energy
proc~ommp_qm_helper_vdw_energy->module~mod_qm_helper
proc~ommp_terminate_qm_helper
ommp_terminate_qm_helper
proc~ommp_terminate_qm_helper->module~mod_qm_helper
proc~ommp_qm_helper_vdw_geomgrad
ommp_qm_helper_vdw_geomgrad
proc~ommp_qm_helper_vdw_geomgrad->module~mod_qm_helper
proc~c_ommp_qm_helper_get_e_n2p
C_ommp_qm_helper_get_E_n2p
proc~c_ommp_qm_helper_get_e_n2p->module~mod_qm_helper
proc~c_ommp_qm_helper_get_v_p2n
C_ommp_qm_helper_get_V_p2n
proc~c_ommp_qm_helper_get_v_p2n->module~mod_qm_helper
proc~qm_helper_init_vdw_prm
qm_helper_init_vdw_prm
proc~qm_helper_init_vdw_prm->module~mod_prm
proc~ommp_angle_geomgrad
ommp_angle_geomgrad
proc~ommp_angle_geomgrad->module~mod_link_atom
proc~ommp_angle_geomgrad->module~mod_bonded
proc~assign_torsion
assign_torsion
proc~assign_torsion->module~mod_bonded
proc~assign_bond
assign_bond
proc~assign_bond->module~mod_bonded
proc~ommp_angtor_geomgrad
ommp_angtor_geomgrad
proc~ommp_angtor_geomgrad->module~mod_bonded
proc~ommp_get_full_bnd_energy
ommp_get_full_bnd_energy
proc~ommp_get_full_bnd_energy->module~mod_link_atom
proc~ommp_get_full_bnd_energy->module~mod_bonded
proc~link_atom_torsion_geomgrad
link_atom_torsion_geomgrad
proc~link_atom_torsion_geomgrad->module~mod_bonded
proc~ommp_init_xyz
ommp_init_xyz
proc~ommp_init_xyz->module~mod_inputloader
proc~ommp_strtor_geomgrad
ommp_strtor_geomgrad
proc~ommp_strtor_geomgrad->module~mod_bonded
proc~c_ommp_full_geomgrad
C_ommp_full_geomgrad
proc~c_ommp_full_geomgrad->module~ommp_interface
proc~ommp_full_bnd_geomgrad
ommp_full_bnd_geomgrad
proc~ommp_full_bnd_geomgrad->module~mod_link_atom
proc~ommp_full_bnd_geomgrad->module~mod_bonded
proc~ommp_get_strbnd_energy
ommp_get_strbnd_energy
proc~ommp_get_strbnd_energy->module~mod_bonded
proc~ommp_get_imptorsion_energy
ommp_get_imptorsion_energy
proc~ommp_get_imptorsion_energy->module~mod_bonded
proc~c_ommp_qm_helper_get_frozen
C_ommp_qm_helper_get_frozen
proc~c_ommp_qm_helper_get_frozen->module~mod_qm_helper
proc~polarization
polarization
proc~polarization->module~mod_solvers
proc~ommp_get_opb_energy
ommp_get_opb_energy
proc~ommp_get_opb_energy->module~mod_bonded
proc~ommp_bond_geomgrad
ommp_bond_geomgrad
proc~ommp_bond_geomgrad->module~mod_link_atom
proc~ommp_bond_geomgrad->module~mod_bonded
proc~assign_urey
assign_urey
proc~assign_urey->module~mod_bonded
proc~ommp_get_pitors_energy
ommp_get_pitors_energy
proc~ommp_get_pitors_energy->module~mod_bonded
proc~ommp_torsion_geomgrad
ommp_torsion_geomgrad
proc~ommp_torsion_geomgrad->module~mod_link_atom
proc~ommp_torsion_geomgrad->module~mod_bonded
proc~ommp_init_mmp
ommp_init_mmp
proc~ommp_init_mmp->module~mod_inputloader
proc~ommp_imptorsion_geomgrad
ommp_imptorsion_geomgrad
proc~ommp_imptorsion_geomgrad->module~mod_bonded
proc~assign_imptorsion
assign_imptorsion
proc~assign_imptorsion->module~mod_bonded
proc~ommp_opb_geomgrad
ommp_opb_geomgrad
proc~ommp_opb_geomgrad->module~mod_bonded
proc~assign_opb
assign_opb
proc~assign_opb->module~mod_bonded
proc~link_atom_bond_geomgrad
link_atom_bond_geomgrad
proc~link_atom_bond_geomgrad->module~mod_bonded
proc~ommp_polelec_geomgrad
ommp_polelec_geomgrad
proc~ommp_polelec_geomgrad->module~mod_geomgrad
proc~c_ommp_qm_helper_get_g_n2p
C_ommp_qm_helper_get_G_n2p
proc~c_ommp_qm_helper_get_g_n2p->module~mod_qm_helper
proc~ommp_qm_helper_link_atom_geomgrad
ommp_qm_helper_link_atom_geomgrad
proc~ommp_qm_helper_link_atom_geomgrad->module~mod_qm_helper
proc~ommp_init_qm_helper
ommp_init_qm_helper
proc~ommp_init_qm_helper->module~mod_qm_helper
proc~c_ommp_qm_helper_get_e_n2m
C_ommp_qm_helper_get_E_n2m
proc~c_ommp_qm_helper_get_e_n2m->module~mod_qm_helper
proc~c_ommp_qm_helper_get_g_n2m
C_ommp_qm_helper_get_G_n2m
proc~c_ommp_qm_helper_get_g_n2m->module~mod_qm_helper
proc~c_ommp_qm_helper_use_nonbonded
C_ommp_qm_helper_use_nonbonded
proc~c_ommp_qm_helper_use_nonbonded->module~mod_qm_helper
proc~ommp_update_link_atoms_position
ommp_update_link_atoms_position
proc~ommp_update_link_atoms_position->module~mod_qm_helper
proc~ommp_update_link_atoms_position->module~mod_link_atom
proc~ommp_qm_helper_update_coord
ommp_qm_helper_update_coord
proc~ommp_qm_helper_update_coord->module~mod_qm_helper
proc~c_ommp_qm_helper_get_npol
C_ommp_qm_helper_get_npol
proc~c_ommp_qm_helper_get_npol->module~mod_qm_helper
proc~c_ommp_qm_helper_get_nmm
C_ommp_qm_helper_get_nmm
proc~c_ommp_qm_helper_get_nmm->module~mod_qm_helper
proc~ommp_get_bond_energy
ommp_get_bond_energy
proc~ommp_get_bond_energy->module~mod_link_atom
proc~ommp_get_bond_energy->module~mod_bonded
proc~c_ommp_qm_helper_get_e_m2n
C_ommp_qm_helper_get_E_m2n
proc~c_ommp_qm_helper_get_e_m2n->module~mod_qm_helper
proc~assign_angle
assign_angle
proc~assign_angle->module~mod_bonded
proc~ommp_get_link_atom_coordinates
ommp_get_link_atom_coordinates
proc~ommp_get_link_atom_coordinates->module~mod_link_atom
proc~link_atom_angle_geomgrad
link_atom_angle_geomgrad
proc~link_atom_angle_geomgrad->module~mod_bonded
proc~c_ommp_qm_helper_get_qm_atoms
C_ommp_qm_helper_get_qm_atoms
proc~c_ommp_qm_helper_get_qm_atoms->module~mod_qm_helper
proc~ommp_get_tortor_energy
ommp_get_tortor_energy
proc~ommp_get_tortor_energy->module~mod_bonded
proc~ommp_pitors_geomgrad
ommp_pitors_geomgrad
proc~ommp_pitors_geomgrad->module~mod_bonded
proc~assign_strbnd
assign_strbnd
proc~assign_strbnd->module~mod_bonded
proc~ommp_tortor_geomgrad
ommp_tortor_geomgrad
proc~ommp_tortor_geomgrad->module~mod_bonded
proc~ommp_get_angle_energy
ommp_get_angle_energy
proc~ommp_get_angle_energy->module~mod_link_atom
proc~ommp_get_angle_energy->module~mod_bonded
proc~ommp_get_angtor_energy
ommp_get_angtor_energy
proc~ommp_get_angtor_energy->module~mod_bonded
proc~assign_angtor
assign_angtor
proc~assign_angtor->module~mod_bonded
proc~ommp_get_urey_energy
ommp_get_urey_energy
proc~ommp_get_urey_energy->module~mod_bonded
proc~ommp_urey_geomgrad
ommp_urey_geomgrad
proc~ommp_urey_geomgrad->module~mod_bonded
proc~ommp_get_torsion_energy
ommp_get_torsion_energy
proc~ommp_get_torsion_energy->module~mod_link_atom
proc~ommp_get_torsion_energy->module~mod_bonded
proc~c_ommp_get_opb_energy
C_ommp_get_opb_energy
proc~c_ommp_get_opb_energy->module~mod_bonded
proc~ommp_strbnd_geomgrad
ommp_strbnd_geomgrad
proc~ommp_strbnd_geomgrad->module~mod_bonded
proc~c_ommp_terminate_qm_helper
C_ommp_terminate_qm_helper
proc~c_ommp_terminate_qm_helper->module~mod_qm_helper
proc~ommp_get_strtor_energy
ommp_get_strtor_energy
proc~ommp_get_strtor_energy->module~mod_bonded
proc~assign_strtor
assign_strtor
proc~assign_strtor->module~mod_bonded
Nodes of different colours represent the following:
Graph Key
Module
Module
Submodule
Submodule
Subroutine
Subroutine
Function
Function
Program
Program
This Page's Entity
This Page's Entity
Solid arrows point from a submodule to the (sub)module which it is
descended from. Dashed arrows point from a module or program unit to
modules which it uses.
Derived Types
Describe a square boolean sparse matrix n x n.
Components
Type
Visibility Attributes
Name
Initial
public
::
n
Dimension of the matrix
public,
allocatable
::
ri (:)
Row index vector, always dimensioned n+1
public,
allocatable
::
ci (:)
Column index vector, dimension number of non-zero elements
Subroutines
Arguments
Type
Intent Optional Attributes
Name
yale_sparse ),
intent(inout)
::
m
Matrix to be initialized
intent(in)
::
n
Major dimension for the matrix
intent(in)
::
nnz
Number of nonzero element for the matrix
Copy boolean sparse matrix in yale format f to t.
Arguments
Type
Intent Optional Attributes
Name
yale_sparse ),
intent(in)
::
f
Matrix to copy
yale_sparse ),
intent(out)
::
t
Destination matrix
Deallocate a boolean sparse matrix (in Yale format)
Arguments
Type
Intent Optional Attributes
Name
yale_sparse ),
intent(inout)
::
m
Matrix to free
Create adjacency matrix from connectivity lists.
Arguments
Type
Intent Optional Attributes
Name
intent(inout)
::
i12 (:,:)
Indices of connected atoms for each atom in the molecule
yale_sparse ),
intent(out)
::
sparse
Adjacency matrix in Yale format ()
Reshape a boolean sparse matrix in Yale format to accomodate a
larger number of non-zero elements or to trim unused non-zero
elements after a guess allocation.
Arguments
Type
Intent Optional Attributes
Name
yale_sparse ),
intent(inout)
::
m
Matrix to be reshaped
intent(in)
::
nnz
New shape for the matrix
Performs the operation on boolean
sparse matrices; product correspond to logical and while sum
correspond to logical or.
Arguments
Type
Intent Optional Attributes
Name
yale_sparse ),
intent(in)
::
sp1
Input matrices (sparse boolean matrices in Yale format)
yale_sparse ),
intent(in)
::
sp2
Input matrices (sparse boolean matrices in Yale format)
yale_sparse ),
intent(out)
::
res
Output matrix (sparse boolean matrices in Yale format)
private subroutine mat_mult (sp1, sp2, res)
Performs the operation on boolean
sparse matrices; product correspond to logical and while sum
correspond to logical or.
Arguments
Type
Intent Optional Attributes
Name
yale_sparse ),
intent(in)
::
sp1
Input matrices (sparse boolean matrices in Yale format)
yale_sparse ),
intent(in)
::
sp2
Input matrices (sparse boolean matrices in Yale format)
yale_sparse ),
intent(out)
::
res
Output matrix (sparse boolean matrices in Yale format)
Performs the operation on
boolean sparse matrices.
Read more… Arguments
Type
Intent Optional Attributes
Name
yale_sparse ),
intent(in)
::
sp1
Input matrices (sparse boolean matrices in Yale format)
yale_sparse ),
intent(in)
::
sp2
Input matrices (sparse boolean matrices in Yale format)
yale_sparse ),
intent(out)
::
res
Output matrix (sparse boolean matrices in Yale format)
Create an identity matrix (boolean sparse, represented in
Yale format) of dimension .
Arguments
Type
Intent Optional Attributes
Name
intent(in)
::
n
Rank of the output matrix
yale_sparse ),
intent(out)
::
res
Output matrix
Build connectivity matrices up to
starting from . Results are stored in an
array of boolean sparse matrix in Yale format in such a way that
; since FORTRAN is 1-based the useless
is not stored.
Arguments
Type
Intent Optional Attributes
Name
yale_sparse ),
intent(in)
::
adj
Adjacency matrix in Yale format
intent(in)
::
n
Maximum level of connectivity that should be computed
yale_sparse ),
intent(out),
allocatable
::
res (:)
Results connectivity matrices
::
start_id
Specifies if the first matrix allocated res(1) should be the
identity (true) or the adjacency (false).
Takes as argument an array of group index for each
atom, and create a list of atms in each group using the
sparse matrix format (saved as Yale format).
This is used by cell lists, polarization group etc.
Arguments
Type
Intent Optional Attributes
Name
intent(in)
::
a2g (:)
Index of polarization group for each MM atom
yale_sparse ),
intent(out)
::
g2a
Indices of atoms included in each polarization group;
Atom indeces for the n-th group are found at
pg2mm%ci(pg2mm%ri(n):pg2mm%ri(n+1)-1)
intent(in),
optional
::
ng_in
Number of groups if it is not provided in input it is
assumed that the number of group equals the largest group
index, that is no empty groups are present after the one
with the largest index.
This subroutine takes as input a sparse matrix (rank [n]) in an
uncompressed yale format [uc_list], as a rectangular
matrix ([n] x max_el_per_row) and the actual number of items
[nit] for each row (remaining
elements are not considered) and compress in a Yale format
sparse matrix [s].
The task is parallelized to handle large matrices.
Arguments
Type
Intent Optional Attributes
Name
intent(in)
::
n
Rank of matrix
intent(in)
::
uc_list (:,:)
Uncompressed list/boolean sparse matrix
intent(in)
::
nit (n)
Number of elements for each row of [uc_list]
yale_sparse ),
intent(out)
::
s
Output sparse matrix
Compress the data in uc_data to the same Yale sparse
format described in s
Arguments
Type
Intent Optional Attributes
Name
yale_sparse ),
intent(in)
::
s
Input Yale format binary matrix/sparse list
intent(in)
::
uc_data (:,:)
Uncompressed data in input
intent(out),
allocatable
::
c_data (:)
Compressed data in output