guess_connectivity Subroutine

public subroutine guess_connectivity(top, exclude_list)

Uses

  • proc~~guess_connectivity~~UsesGraph proc~guess_connectivity guess_connectivity module~mod_io mod_io proc~guess_connectivity->module~mod_io module~mod_adjacency_mat mod_adjacency_mat proc~guess_connectivity->module~mod_adjacency_mat module~mod_memory mod_memory proc~guess_connectivity->module~mod_memory module~mod_constants mod_constants proc~guess_connectivity->module~mod_constants module~mod_io->module~mod_constants module~mod_adjacency_mat->module~mod_memory module~mod_memory->module~mod_io module~mod_memory->module~mod_constants iso_c_binding iso_c_binding module~mod_memory->iso_c_binding module~mod_constants->iso_c_binding

This subroutine guess the connectivity of the system from the coordinates and the atomic number of its atoms. It is based on distances and atomic radii, so it can easily fail on distorted geometries. It should be used only when the the bonds of the molecule are not availble in any other way; it is often used to assign connectivity to a QM part that does not have any. H B C N O F Si P S Cl As Se Br Te I

Arguments

Type IntentOptional Attributes Name
type(ommp_topology_type), intent(inout) :: top

Topology for which connectivity should be guessed.
integer(kind=ip), intent(in), optional :: exclude_list(:)

List of atoms that should not be connected when guessing the topology, this is used for LA that could have an ambiguous or not defined position.

Calls

proc~~guess_connectivity~~CallsGraph proc~guess_connectivity guess_connectivity proc~fatal_error fatal_error proc~guess_connectivity->proc~fatal_error interface~mallocate mallocate proc~guess_connectivity->interface~mallocate proc~ommp_message ommp_message proc~guess_connectivity->proc~ommp_message interface~mfree mfree proc~guess_connectivity->interface~mfree proc~adj_mat_from_conn adj_mat_from_conn proc~guess_connectivity->proc~adj_mat_from_conn proc~fatal_error->proc~ommp_message proc~close_output close_output proc~fatal_error->proc~close_output proc~i_alloc1 i_alloc1 interface~mallocate->proc~i_alloc1 proc~i_alloc3 i_alloc3 interface~mallocate->proc~i_alloc3 proc~l_alloc2 l_alloc2 interface~mallocate->proc~l_alloc2 proc~r_alloc3 r_alloc3 interface~mallocate->proc~r_alloc3 proc~i_alloc2 i_alloc2 interface~mallocate->proc~i_alloc2 proc~r_alloc1 r_alloc1 interface~mallocate->proc~r_alloc1 proc~r_alloc2 r_alloc2 interface~mallocate->proc~r_alloc2 proc~l_alloc1 l_alloc1 interface~mallocate->proc~l_alloc1 proc~l_free1 l_free1 interface~mfree->proc~l_free1 proc~i_free2 i_free2 interface~mfree->proc~i_free2 proc~r_free3 r_free3 interface~mfree->proc~r_free3 proc~r_free2 r_free2 interface~mfree->proc~r_free2 proc~i_free1 i_free1 interface~mfree->proc~i_free1 proc~r_free1 r_free1 interface~mfree->proc~r_free1 proc~l_free2 l_free2 interface~mfree->proc~l_free2 proc~i_free3 i_free3 interface~mfree->proc~i_free3 proc~adj_mat_from_conn->interface~mallocate proc~adj_mat_from_conn->interface~mfree proc~compress_list compress_list proc~adj_mat_from_conn->proc~compress_list proc~sort_ivec_inplace sort_ivec_inplace proc~adj_mat_from_conn->proc~sort_ivec_inplace proc~compress_list->interface~mallocate proc~compress_list->interface~mfree proc~chk_free chk_free proc~l_free1->proc~chk_free proc~i_free2->proc~chk_free proc~r_free3->proc~chk_free proc~close_output->proc~ommp_message proc~chk_alloc chk_alloc proc~i_alloc1->proc~chk_alloc proc~memory_init memory_init proc~i_alloc1->proc~memory_init proc~i_alloc3->proc~chk_alloc proc~i_alloc3->proc~memory_init proc~l_alloc2->proc~chk_alloc proc~l_alloc2->proc~memory_init proc~r_free2->proc~chk_free proc~i_free1->proc~chk_free proc~sort_ivec_inplace->interface~mfree proc~sort_ivec sort_ivec proc~sort_ivec_inplace->proc~sort_ivec proc~r_alloc3->proc~chk_alloc proc~r_alloc3->proc~memory_init proc~i_alloc2->proc~chk_alloc proc~i_alloc2->proc~memory_init proc~r_alloc1->proc~chk_alloc proc~r_alloc1->proc~memory_init proc~r_alloc2->proc~chk_alloc proc~r_alloc2->proc~memory_init proc~l_alloc1->proc~chk_alloc proc~l_alloc1->proc~memory_init proc~r_free1->proc~chk_free proc~l_free2->proc~chk_free proc~i_free3->proc~chk_free proc~chk_free->proc~fatal_error proc~chk_alloc->proc~fatal_error proc~sort_ivec->interface~mallocate proc~sort_ivec->interface~mfree

Called by

proc~~guess_connectivity~~CalledByGraph proc~guess_connectivity guess_connectivity proc~qm_helper_update_coord qm_helper_update_coord proc~qm_helper_update_coord->proc~guess_connectivity proc~qm_helper_init qm_helper_init proc~qm_helper_init->proc~guess_connectivity proc~ommp_create_link_atom ommp_create_link_atom proc~ommp_create_link_atom->proc~qm_helper_update_coord proc~ommp_update_link_atoms_position ommp_update_link_atoms_position proc~ommp_update_link_atoms_position->proc~qm_helper_update_coord proc~ommp_init_qm_helper ommp_init_qm_helper proc~ommp_init_qm_helper->proc~qm_helper_init proc~ommp_qm_helper_update_coord ommp_qm_helper_update_coord proc~ommp_qm_helper_update_coord->proc~qm_helper_update_coord proc~c_ommp_create_link_atom C_ommp_create_link_atom proc~c_ommp_create_link_atom->proc~ommp_create_link_atom proc~c_ommp_update_link_atoms_position C_ommp_update_link_atoms_position proc~c_ommp_update_link_atoms_position->proc~ommp_update_link_atoms_position proc~c_ommp_qm_helper_update_coord C_ommp_qm_helper_update_coord proc~c_ommp_qm_helper_update_coord->proc~ommp_qm_helper_update_coord proc~c_ommp_init_qm_helper C_ommp_init_qm_helper proc~c_ommp_init_qm_helper->proc~ommp_init_qm_helper

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