mod_tree Module


Uses

  • module~~mod_tree~~UsesGraph module~mod_tree mod_tree module~mod_fmm_utils mod_fmm_utils module~mod_tree->module~mod_fmm_utils module~mod_adjacency_mat mod_adjacency_mat module~mod_tree->module~mod_adjacency_mat module~mod_constants mod_constants module~mod_tree->module~mod_constants module~mod_fmm_utils->module~mod_constants module~mod_memory mod_memory module~mod_adjacency_mat->module~mod_memory iso_c_binding iso_c_binding module~mod_constants->iso_c_binding module~mod_memory->module~mod_constants module~mod_memory->iso_c_binding module~mod_io mod_io module~mod_memory->module~mod_io module~mod_io->module~mod_constants

Used by

  • module~~mod_tree~~UsedByGraph module~mod_tree mod_tree module~fmmlib_interface fmmlib_interface module~fmmlib_interface->module~mod_tree module~mod_ribtree mod_ribtree module~fmmlib_interface->module~mod_ribtree module~mod_octatree mod_octatree module~fmmlib_interface->module~mod_octatree module~mod_fmm mod_fmm module~fmmlib_interface->module~mod_fmm module~mod_ribtree->module~mod_tree module~mod_octatree->module~mod_tree proc~free_fmm free_fmm proc~free_fmm->module~mod_tree module~mod_fmm->module~mod_tree module~mod_electrostatics mod_electrostatics module~mod_electrostatics->module~fmmlib_interface proc~mmpol_init mmpol_init proc~mmpol_init->module~mod_electrostatics 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~ommp_get_polelec_energy ommp_get_polelec_energy proc~ommp_get_polelec_energy->module~mod_electrostatics module~mod_polarization mod_polarization proc~ommp_get_polelec_energy->module~mod_polarization proc~mmpol_init_from_xyz mmpol_init_from_xyz proc~mmpol_init_from_xyz->module~mod_electrostatics module~mod_mmpol mod_mmpol proc~mmpol_init_from_xyz->module~mod_mmpol module~mod_prm mod_prm proc~mmpol_init_from_xyz->module~mod_prm module~mod_mmpol->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~mmpol_init_from_mmp mmpol_init_from_mmp proc~mmpol_init_from_mmp->module~mod_electrostatics proc~mmpol_init_from_mmp->module~mod_mmpol proc~rotate_multipoles rotate_multipoles proc~rotate_multipoles->module~mod_electrostatics proc~mmpol_init_from_hdf5 mmpol_init_from_hdf5 proc~mmpol_init_from_hdf5->module~mod_electrostatics proc~mmpol_init_from_hdf5->module~mod_mmpol proc~assign_mpoles assign_mpoles proc~assign_mpoles->module~mod_electrostatics proc~ommp_potential_mm2ext ommp_potential_mm2ext proc~ommp_potential_mm2ext->module~mod_electrostatics proc~fixedelec_geomgrad fixedelec_geomgrad proc~fixedelec_geomgrad->module~mod_electrostatics proc~ommp_get_fixedelec_energy ommp_get_fixedelec_energy proc~ommp_get_fixedelec_energy->module~mod_electrostatics module~mod_solvers mod_solvers module~mod_solvers->module~mod_electrostatics proc~tmatvec_otf TMatVec_otf proc~tmatvec_otf->module~mod_electrostatics proc~c_ommp_field_mm2ext C_ommp_field_mm2ext proc~c_ommp_field_mm2ext->module~mod_electrostatics proc~ommp_turn_pol_off ommp_turn_pol_off proc~ommp_turn_pol_off->module~mod_electrostatics proc~c_ommp_field_pol2ext C_ommp_field_pol2ext proc~c_ommp_field_pol2ext->module~mod_electrostatics module~ommp_interface ommp_interface module~ommp_interface->module~mod_electrostatics module~ommp_interface->module~mod_mmpol module~mod_iohdf5 mod_iohdf5 module~ommp_interface->module~mod_iohdf5 module~mod_qm_helper mod_qm_helper module~ommp_interface->module~mod_qm_helper module~mod_iohdf5->module~mod_electrostatics module~mod_iohdf5->module~mod_mmpol proc~ommp_set_default_matv ommp_set_default_matv proc~ommp_set_default_matv->module~mod_electrostatics proc~ommp_field_mm2ext ommp_field_mm2ext proc~ommp_field_mm2ext->module~mod_electrostatics proc~ommp_field_pol2ext ommp_field_pol2ext proc~ommp_field_pol2ext->module~mod_electrostatics proc~ommp_potential_mmpol2ext ommp_potential_mmpol2ext proc~ommp_potential_mmpol2ext->module~mod_electrostatics proc~mmpol_terminate mmpol_terminate proc~mmpol_terminate->module~mod_electrostatics proc~ommp_set_default_solver ommp_set_default_solver proc~ommp_set_default_solver->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~ommp_field_mmpol2ext ommp_field_mmpol2ext proc~ommp_field_mmpol2ext->module~mod_electrostatics proc~update_coordinates update_coordinates proc~update_coordinates->module~mod_electrostatics proc~electrostatic_for_ene electrostatic_for_ene proc~electrostatic_for_ene->module~mod_electrostatics proc~ommp_potential_pol2ext ommp_potential_pol2ext proc~ommp_potential_pol2ext->module~mod_electrostatics proc~rotation_geomgrad rotation_geomgrad proc~rotation_geomgrad->module~mod_electrostatics proc~mmpol_prepare mmpol_prepare proc~mmpol_prepare->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 module~mod_polarization->module~mod_electrostatics module~mod_polarization->module~mod_mmpol proc~dipole_t dipole_T proc~dipole_t->module~mod_electrostatics proc~assign_pol assign_pol proc~assign_pol->module~mod_electrostatics proc~polelec_geomgrad polelec_geomgrad proc~polelec_geomgrad->module~mod_electrostatics proc~polelec_geomgrad->module~mod_polarization module~mod_prm->module~mod_electrostatics proc~polarization polarization proc~polarization->module~mod_solvers proc~ommp_system_from_qm_helper ommp_system_from_qm_helper proc~ommp_system_from_qm_helper->module~mod_mmpol proc~ommp_system_from_qm_helper->module~mod_prm proc~qm_helper_link_atom_geomgrad qm_helper_link_atom_geomgrad proc~qm_helper_link_atom_geomgrad->module~mod_mmpol module~mod_inputloader mod_inputloader module~mod_inputloader->module~mod_mmpol proc~r1_hdf5_read_array r1_hdf5_read_array proc~r1_hdf5_read_array->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~i1_hdf5_read_array i1_hdf5_read_array proc~i1_hdf5_read_array->module~mod_mmpol module~mod_qm_helper->module~mod_mmpol proc~qm_helper_vdw_energy qm_helper_vdw_energy proc~qm_helper_vdw_energy->module~mod_mmpol proc~qm_helper_init_vdw_prm qm_helper_init_vdw_prm proc~qm_helper_init_vdw_prm->module~mod_prm proc~init_bonded_for_link_atom init_bonded_for_link_atom proc~init_bonded_for_link_atom->module~mod_prm proc~l1_hdf5_read_array l1_hdf5_read_array proc~l1_hdf5_read_array->module~mod_mmpol proc~i3_hdf5_read_array i3_hdf5_read_array proc~i3_hdf5_read_array->module~mod_mmpol proc~ommp_terminate ommp_terminate proc~ommp_terminate->module~mod_mmpol proc~qm_helper_vdw_geomgrad qm_helper_vdw_geomgrad proc~qm_helper_vdw_geomgrad->module~mod_mmpol module~mod_geomgrad mod_geomgrad module~mod_geomgrad->module~mod_mmpol proc~ommp_create_link_atom ommp_create_link_atom proc~ommp_create_link_atom->module~mod_mmpol proc~ommp_create_link_atom->module~mod_qm_helper proc~r3_hdf5_read_array r3_hdf5_read_array proc~r3_hdf5_read_array->module~mod_mmpol proc~l2_hdf5_read_array l2_hdf5_read_array proc~l2_hdf5_read_array->module~mod_mmpol proc~c_ommp_full_geomgrad C_ommp_full_geomgrad proc~c_ommp_full_geomgrad->module~ommp_interface proc~c_ommp_update_coordinates C_ommp_update_coordinates proc~c_ommp_update_coordinates->module~mod_mmpol module~mod_ommp_c_interface mod_ommp_C_interface module~mod_ommp_c_interface->module~ommp_interface proc~ommp_fixedelec_geomgrad ommp_fixedelec_geomgrad proc~ommp_fixedelec_geomgrad->module~mod_geomgrad 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_v_m2n C_ommp_qm_helper_get_V_m2n proc~c_ommp_qm_helper_get_v_m2n->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~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_frozen C_ommp_qm_helper_get_frozen proc~c_ommp_qm_helper_get_frozen->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~ommp_full_geomgrad ommp_full_geomgrad proc~ommp_full_geomgrad->module~mod_geomgrad 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_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~ommp_init_mmp ommp_init_mmp proc~ommp_init_mmp->module~mod_inputloader 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_init_xyz ommp_init_xyz proc~ommp_init_xyz->module~mod_inputloader proc~ommp_qm_helper_update_coord ommp_qm_helper_update_coord proc~ommp_qm_helper_update_coord->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_update_link_atoms_position ommp_update_link_atoms_position proc~ommp_update_link_atoms_position->module~mod_qm_helper 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~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~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_terminate_qm_helper C_ommp_terminate_qm_helper proc~c_ommp_terminate_qm_helper->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~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

Contents

Derived Types

Subroutines


Derived Types

type, public ::  fmm_tree_type

Data structore to represent the tree for storing sources and targets of the fmm problem

Components

Type Visibility Attributes Name Initial
integer(kind=ip), public :: tree_degree = 0

Maximum number of children for each node
integer(kind=ip), public :: n_nodes = 0

Number of nodes in the tree
integer(kind=ip), public :: breadth = 0

Number of levels in the tree
integer(kind=ip), public, allocatable :: children(:,:)

For each node in the tree, its children (0 is the null element)
integer(kind=ip), public, allocatable :: parent(:)

For each node in the tree, its parent (0 is the null element)
integer(kind=ip), public, allocatable :: node_level(:)

For each node the level of the tree in which it is located (1-based)
logical(kind=lp), public, allocatable :: is_leaf(:)

For each node true if is a leaf and false otherwise
type(yale_sparse), public :: level_list

For each level, the list of the nodes contained
integer(kind=ip), public :: n_particles = 0

Number of particles stored in the tree
real(kind=rp), public, pointer :: particles_coords(:,:)

Pointer to particle coordinates
type(yale_sparse), public :: particle_list

List of particles contained in each node, for all non-leaf nodes this list should be empty
integer(kind=ip), public, allocatable :: particle_to_node(:)
real(kind=rp), public, allocatable :: node_centroid(:,:)

For each node its centroid (in cartesian coordinates)
real(kind=rp), public, allocatable :: node_dimension(:)

For each node, its dimension (or radius)
type(yale_sparse), public :: near_nl

List of nodes pair eligible for near-field
type(yale_sparse), public :: far_nl

List of nodes pair eligible for far-field

Subroutines

public subroutine allocate_tree(t)

Given a tree with all the dimension set, it allocates all the required arrays and data stractures for populating the tree

Arguments

Type IntentOptional Attributes Name
type(fmm_tree_type), intent(inout) :: t

public subroutine free_tree(t)

Frees all allocatable quantities contained inside a tree

Arguments

Type IntentOptional Attributes Name
type(fmm_tree_type), intent(inout) :: t

public subroutine print_tree(t)

Arguments

Type IntentOptional Attributes Name
type(fmm_tree_type), intent(in) :: t

Tree data structure

public subroutine tree_populate_farnear_lists_safe(t, min_dist_thr)

Just for testing, creates far and near list using a double loop algorithm, it is basically just the application of the following definition: 1. Two nodes are near IF they are both leaves and if the distance is below [min_dist_thr] 2. Two nodes are far IF none of their discendent are near 3. Descendent of two far nodes are not present in any list

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Arguments

Type IntentOptional Attributes Name
type(fmm_tree_type), intent(inout) :: t

Tree data structure to populate
real(kind=rp), intent(in), optional :: min_dist_thr

Minimum threshold for two nodes to be near, every nodes within this threshold are guaranteed to be near

private subroutine aggregative_pass(t, uncompressed_n_far, uncompressed_far)

Aggregates far nodes to upper levels of the tree. Operation are performed on uncompressed list

Arguments

Type IntentOptional Attributes Name
type(fmm_tree_type), intent(in) :: t
integer(kind=ip), intent(inout) :: uncompressed_n_far(t%n_nodes)
integer(kind=ip), intent(inout) :: uncompressed_far(:,:)

public subroutine tree_populate_farnear_lists(t, min_dist_thr)

Now compress in yale sparse format and delete the uncompressed lists

Arguments

Type IntentOptional Attributes Name
type(fmm_tree_type), intent(inout) :: t

Tree data structure to populate
real(kind=rp), intent(in), optional :: min_dist_thr

Minimum threshold for two nodes to be near, every nodes within this threshold are guaranteed to be near

public subroutine populate_leaf_list(t)

Arguments

Type IntentOptional Attributes Name
type(fmm_tree_type), intent(inout) :: t

Tree data structure to populate

public subroutine populate_level_list(t)

Arguments

Type IntentOptional Attributes Name
type(fmm_tree_type), intent(inout) :: t

Tree data structure to populate