Modules

ModuleSource FileDescription
mod_adjacency_matmod_adjacency_mat.f90

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.

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mod_bondedmod_bonded.f90

Module to handle the bonded part of the FF, it closely follows the AMOEBA functional form.

mod_constantsmod_constants.f90

Contains several constants that are usefoul around the code. There are physical constants (there should be no duplicate around!), default force-field parameters that are used when no other input is specified, and internal constants that are used as easy-to-remember names of code constants.

mod_electrostaticsmod_electrostatics.f90

TODO Check the signs in electrostatic elemental functions TODO [OPT] Use Laplace equation to simplify the calculations: TODO 1. Egrd(zz) = -(Egrd(xx) + Egrd(yy)) TODO 2. EHes(zzz) = -(EHes(xxz) + EHes(yyz)) TODO 3. EHes(zzx) = -(EHes(xxx) + EHes(yyx)) TODO 4. EHes(zzy) = -(EHes(xxy) + EHes(yyy)) TODO [OPT] Fundamental electrostatic functions should be pure/elemental TODO [BUG] Handling of flags gg

mod_geomgradmod_geomgrad.f90
mod_inputloadermod_inputloader.f90
mod_iomod_io.f90

Unified Input/Output handling across the code.

mod_jacobian_matmod_jacobian_mat.f90
mod_link_atommod_link_atom.f90
mod_memorymod_memory.f90

This module is used to handle the memory, the variable kinds, the dynamic allocation and the optional soft memory limit of the openMMPol library.

mod_mmpolmod_mmpol.f90

Main module for the control of openMMPol library. It contains all the scalar and vector (allocatable) quantities needed to build up the atomistic polarizable embedding model and perform the calculation required from the quantum chemical software.

mod_neighbor_listmod_neighbors_list.f90
mod_nonbondedmod_nonbonded.f90
mod_ommp_C_interfacemod_c_interface.f90

The interface of the library, basically all the operation performed by an external code should be done through the routines of this module. The interface is conceived to work naturally with C and Fortran; the C interface is also used to build the interface for Python. In a fortran code, this module can be imported and it should expose directly all the vector and scalar quantities needed. In a C code, routines are provided to get the pointer or the values of vector and scalar quantites respectively.

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mod_polarizationmod_polarization.f90

Module to handle the calculation of the induced dipoles; this means find the solution of the polarization problem. The polarization problem is defined by the linear system where is the 'external' (here external means the sum of the electric field generated by QM density and the one generated by the MM sites) electric field at induced dipole sites, are the induced dipoles - the solution of the linear system -, and is the interaction tensor between the induced point dipoles.

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mod_prmmod_prm.f90

This module handles the reading of a parameter file in .prm format and the asignament of parameters based on atom type and connectivity.

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mod_profilingmod_profiling.f90

Unified Input/Output handling across the code.

mod_qm_helpermod_qm_helper.f90

This is an utility module, that is not actually used my openMMpol itself, but can be initialized and used by a QM program interfaced with openMMPol to simplify certain steps of the interface using already well tested code.

mod_solversmod_solvers.f90

Module that contains the routines used to solve the polarization linear system . Currently three methods are implemented:
1. matrix inversion;
2. (preconditioned) conjugate gradients - since polarization equations are symmetric and positive definite, this is the optimal choice;
3. jacobi iterations accelerated with Pulay's direct inversion in the iterative subspace (DIIS): this is a pretty robust solver that can be use for general systems and that is less sensitive to small errors in the symmetry of the matrix.

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mod_topologymod_topology.f90
mod_utilsmod_utils.f90

This module contains some very generic utils for string manipulation, or very basic computational/mathematic operation. It should not depend on any module except from mod_memory.

ommp_interfacemod_interface.f90

The interface of the library, basically all the operation performed by an external code should be done through the routines of this module. The interface is conceived to work naturally with C and Fortran; the C interface is also used to build the interface for Python. In a fortran code, this module can be imported and it should expose directly all the vector and scalar quantities needed. In a C code, routines are provided to get the pointer or the values of vector and scalar quantites respectively.

test_geomgradtest_SI_geomgrad_num.f90
test_geomgradtest_SI_geomgrad.f90
module~~graph~~ModuleGraph module~mod_electrostatics mod_electrostatics module~mod_topology mod_topology module~mod_electrostatics->module~mod_topology module~mod_profiling mod_profiling module~mod_electrostatics->module~mod_profiling module~mod_adjacency_mat mod_adjacency_mat module~mod_electrostatics->module~mod_adjacency_mat module~mod_memory mod_memory module~mod_electrostatics->module~mod_memory module~mod_constants mod_constants module~mod_electrostatics->module~mod_constants module~mod_io mod_io module~mod_electrostatics->module~mod_io module~ommp_interface ommp_interface module~ommp_interface->module~mod_electrostatics module~ommp_interface->module~mod_topology module~ommp_interface->module~mod_profiling module~ommp_interface->module~mod_memory module~ommp_interface->module~mod_constants module~ommp_interface->module~mod_io module~mod_mmpol mod_mmpol module~ommp_interface->module~mod_mmpol module~mod_qm_helper mod_qm_helper module~ommp_interface->module~mod_qm_helper module~mod_topology->module~mod_adjacency_mat module~mod_topology->module~mod_memory module~mod_nonbonded mod_nonbonded module~mod_nonbonded->module~mod_topology module~mod_neighbor_list mod_neighbor_list module~mod_nonbonded->module~mod_neighbor_list module~mod_nonbonded->module~mod_adjacency_mat module~mod_nonbonded->module~mod_memory module~mod_nonbonded->module~mod_constants module~mod_neighbor_list->module~mod_adjacency_mat module~mod_neighbor_list->module~mod_memory module~mod_neighbor_list->module~mod_io module~mod_profiling->module~mod_memory module~mod_profiling->module~mod_constants module~mod_profiling->module~mod_io module~mod_geomgrad mod_geomgrad module~mod_geomgrad->module~mod_topology module~mod_geomgrad->module~mod_memory module~mod_geomgrad->module~mod_io module~mod_geomgrad->module~mod_mmpol module~mod_polarization mod_polarization module~mod_polarization->module~mod_electrostatics module~mod_polarization->module~mod_memory module~mod_polarization->module~mod_io module~mod_polarization->module~mod_mmpol module~mod_link_atom mod_link_atom module~mod_link_atom->module~mod_topology module~mod_link_atom->module~mod_nonbonded module~mod_utils mod_utils module~mod_link_atom->module~mod_utils module~mod_link_atom->module~mod_memory module~mod_bonded mod_bonded module~mod_link_atom->module~mod_bonded module~mod_link_atom->module~mod_constants module~mod_link_atom->module~mod_io module~mod_adjacency_mat->module~mod_memory module~test_geomgrad~2 test_geomgrad module~test_geomgrad~2->module~ommp_interface module~mod_inputloader mod_inputloader module~mod_inputloader->module~mod_profiling module~mod_inputloader->module~mod_constants module~mod_inputloader->module~mod_io module~mod_inputloader->module~mod_mmpol module~mod_utils->module~mod_memory module~mod_utils->module~mod_constants module~mod_memory->module~mod_constants module~mod_memory->module~mod_io iso_c_binding iso_c_binding module~mod_memory->iso_c_binding module~mod_bonded->module~mod_topology module~mod_bonded->module~mod_memory module~mod_bonded->module~mod_io module~mod_ommp_c_interface mod_ommp_C_interface module~mod_ommp_c_interface->module~ommp_interface module~mod_ommp_c_interface->module~mod_constants module~mod_ommp_c_interface->iso_c_binding module~test_geomgrad test_geomgrad module~test_geomgrad->module~ommp_interface module~mod_jacobian_mat mod_jacobian_mat module~mod_jacobian_mat->module~mod_memory module~mod_prm mod_prm module~mod_prm->module~mod_electrostatics module~mod_prm->module~mod_topology module~mod_prm->module~mod_utils module~mod_prm->module~mod_memory module~mod_prm->module~mod_bonded module~mod_prm->module~mod_constants module~mod_prm->module~mod_io module~mod_constants->iso_c_binding module~mod_solvers mod_solvers module~mod_solvers->module~mod_electrostatics module~mod_solvers->module~mod_memory module~mod_solvers->module~mod_constants module~mod_solvers->module~mod_io module~mod_io->module~mod_constants module~mod_mmpol->module~mod_electrostatics module~mod_mmpol->module~mod_topology module~mod_mmpol->module~mod_nonbonded module~mod_mmpol->module~mod_link_atom module~mod_mmpol->module~mod_adjacency_mat module~mod_mmpol->module~mod_memory module~mod_mmpol->module~mod_bonded module~mod_mmpol->module~mod_constants module~mod_mmpol->module~mod_io module~mod_qm_helper->module~mod_topology module~mod_qm_helper->module~mod_nonbonded module~mod_qm_helper->module~mod_memory module~mod_qm_helper->module~mod_mmpol program~test_si_potential test_SI_potential program~test_si_potential->module~ommp_interface program~test_si_potential->iso_c_binding program~test_si_geomgrad test_SI_geomgrad program~test_si_geomgrad->module~ommp_interface program~test_si_geomgrad->module~test_geomgrad program~test_si_geomgrad->iso_c_binding program~test_si_geomgrad_num test_SI_geomgrad_num program~test_si_geomgrad_num->module~ommp_interface program~test_si_geomgrad_num->module~test_geomgrad program~test_si_geomgrad_num->iso_c_binding program~test_si_init test_SI_init program~test_si_init->module~ommp_interface program~test_si_init->iso_c_binding proc~ommp_potential_pol2ext ommp_potential_pol2ext proc~ommp_potential_pol2ext->module~mod_electrostatics proc~tmatvec_otf TMatVec_otf proc~tmatvec_otf->module~mod_electrostatics proc~inplane_angle_jacobian inplane_angle_jacobian proc~inplane_angle_jacobian->module~mod_utils proc~strtor_init strtor_init proc~strtor_init->module~mod_memory proc~ommp_field_mmpol2ext ommp_field_mmpol2ext proc~ommp_field_mmpol2ext->module~mod_electrostatics proc~opb_angle_jacobian opb_angle_jacobian proc~opb_angle_jacobian->module~mod_utils proc~opb_angle_jacobian->module~mod_constants proc~c_ommp_field_pol2ext C_ommp_field_pol2ext proc~c_ommp_field_pol2ext->module~mod_electrostatics proc~ommp_init_hdf5 ommp_init_hdf5 mod_iohdf5 mod_iohdf5 proc~ommp_init_hdf5->mod_iohdf5 proc~torsion_angle_jacobian torsion_angle_jacobian proc~torsion_angle_jacobian->module~mod_utils proc~torsion_angle_jacobian->module~mod_constants proc~mmpol_save_as_mmp mmpol_save_as_mmp proc~mmpol_save_as_mmp->module~mod_constants proc~mmpol_save_as_mmp->module~mod_io proc~assign_pol assign_pol proc~assign_pol->module~mod_electrostatics proc~assign_pol->module~mod_memory proc~assign_pol->module~mod_constants proc~ommp_polelec_geomgrad ommp_polelec_geomgrad proc~ommp_polelec_geomgrad->module~mod_geomgrad 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~assign_mpoles assign_mpoles proc~assign_mpoles->module~mod_electrostatics proc~assign_mpoles->module~mod_memory proc~assign_mpoles->module~mod_constants proc~pitors_geomgrad pitors_geomgrad proc~pitors_geomgrad->module~mod_jacobian_mat proc~pitors_geomgrad->module~mod_constants proc~tmatvec_offdiag TMatVec_offdiag proc~tmatvec_offdiag->module~mod_memory proc~topology_init topology_init proc~topology_init->module~mod_memory proc~pitors_init pitors_init proc~pitors_init->module~mod_memory 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~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~ommp_full_geomgrad ommp_full_geomgrad proc~ommp_full_geomgrad->module~mod_nonbonded proc~ommp_full_geomgrad->module~mod_geomgrad proc~ommp_full_geomgrad->module~mod_memory proc~assign_angtor assign_angtor proc~assign_angtor->module~mod_memory proc~assign_angtor->module~mod_bonded proc~assign_angtor->module~mod_constants proc~screening_rules screening_rules proc~screening_rules->module~mod_constants proc~vdw_init vdw_init proc~vdw_init->module~mod_neighbor_list proc~vdw_init->module~mod_memory proc~vdw_init->module~mod_constants proc~vdw_init->module~mod_io proc~vdw_geomgrad_inter_restricted vdw_geomgrad_inter_restricted proc~vdw_geomgrad_inter_restricted->module~mod_jacobian_mat proc~vdw_geomgrad_inter_restricted->module~mod_constants proc~vdw_geomgrad_inter_restricted->module~mod_io proc~compress_list compress_list proc~compress_list->module~mod_memory proc~ommp_fixedelec_geomgrad ommp_fixedelec_geomgrad proc~ommp_fixedelec_geomgrad->module~mod_geomgrad proc~c_ommp_field_mm2ext C_ommp_field_mm2ext proc~c_ommp_field_mm2ext->module~mod_electrostatics 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~vdw_potential vdw_potential proc~vdw_potential->module~mod_neighbor_list proc~vdw_potential->module~mod_profiling proc~vdw_potential->module~mod_memory proc~vdw_potential->module~mod_constants proc~vdw_potential->module~mod_io proc~bond_geomgrad bond_geomgrad proc~bond_geomgrad->module~mod_jacobian_mat proc~bond_geomgrad->module~mod_constants proc~init_vdw_for_link_atom init_vdw_for_link_atom proc~init_vdw_for_link_atom->module~mod_topology proc~init_vdw_for_link_atom->module~mod_constants proc~init_vdw_for_link_atom->module~mod_io proc~bond_potential bond_potential proc~bond_potential->module~mod_constants 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~rotation_matrix rotation_matrix proc~rotation_matrix->module~mod_memory proc~rotation_matrix->module~mod_constants proc~rotation_matrix->module~mod_io proc~read_atom_cards read_atom_cards proc~read_atom_cards->module~mod_memory proc~read_atom_cards->module~mod_io proc~assign_opb assign_opb proc~assign_opb->module~mod_memory proc~assign_opb->module~mod_bonded proc~assign_opb->module~mod_constants proc~assign_strbnd assign_strbnd proc~assign_strbnd->module~mod_memory proc~assign_strbnd->module~mod_bonded proc~assign_strbnd->module~mod_constants proc~link_atom_angle_geomgrad link_atom_angle_geomgrad proc~link_atom_angle_geomgrad->module~mod_bonded proc~assign_bond assign_bond proc~assign_bond->module~mod_memory proc~assign_bond->module~mod_bonded proc~assign_bond->module~mod_constants proc~assign_bond->module~mod_io proc~torsion_terminate torsion_terminate proc~torsion_terminate->module~mod_memory proc~c_ommp_terminate_qm_helper C_ommp_terminate_qm_helper proc~c_ommp_terminate_qm_helper->module~mod_qm_helper proc~set_def_matv set_def_matv proc~set_def_matv->module~mod_constants proc~imptorsion_terminate imptorsion_terminate proc~imptorsion_terminate->module~mod_memory proc~electrostatics_init electrostatics_init proc~electrostatics_init->module~mod_memory proc~electrostatics_init->module~mod_constants proc~link_atom_bond_geomgrad link_atom_bond_geomgrad proc~link_atom_bond_geomgrad->module~mod_bonded proc~electrostatic_for_grad electrostatic_for_grad proc~electrostatic_for_grad->module~mod_electrostatics proc~electrostatic_for_grad->module~mod_memory proc~tortor_terminate tortor_terminate proc~tortor_terminate->module~mod_memory proc~set_def_solver set_def_solver proc~set_def_solver->module~mod_constants proc~ommp_system_from_qm_helper ommp_system_from_qm_helper proc~ommp_system_from_qm_helper->module~mod_topology proc~ommp_system_from_qm_helper->module~mod_adjacency_mat proc~ommp_system_from_qm_helper->module~mod_utils proc~ommp_system_from_qm_helper->module~mod_prm proc~ommp_system_from_qm_helper->module~mod_constants proc~ommp_system_from_qm_helper->module~mod_io proc~ommp_system_from_qm_helper->module~mod_mmpol proc~vdw_potential_inter_restricted vdw_potential_inter_restricted proc~vdw_potential_inter_restricted->module~mod_constants proc~vdw_potential_inter_restricted->module~mod_io 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~angtor_terminate angtor_terminate proc~angtor_terminate->module~mod_memory proc~electrostatics_terminate electrostatics_terminate proc~electrostatics_terminate->module~mod_adjacency_mat proc~electrostatics_terminate->module~mod_memory proc~create_new_bond create_new_bond proc~create_new_bond->module~mod_adjacency_mat proc~create_new_bond->module~mod_io proc~assign_urey assign_urey proc~assign_urey->module~mod_memory proc~assign_urey->module~mod_bonded proc~assign_urey->module~mod_constants proc~strtor_terminate strtor_terminate proc~strtor_terminate->module~mod_memory proc~mmpol_init mmpol_init proc~mmpol_init->module~mod_electrostatics proc~mmpol_init->module~mod_profiling proc~mmpol_init->module~mod_constants proc~mmpol_init->module~mod_io proc~damped_coulomb_kernel damped_coulomb_kernel proc~damped_coulomb_kernel->module~mod_memory proc~damped_coulomb_kernel->module~mod_constants 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~pitors_angle_jacobian pitors_angle_jacobian proc~pitors_angle_jacobian->module~mod_utils proc~get_eij_inter get_eij_inter proc~get_eij_inter->module~mod_constants proc~urey_potential urey_potential proc~urey_potential->module~mod_constants proc~tokenize_pure tokenize_pure proc~tokenize_pure->module~mod_memory proc~ommp_get_vdw_energy ommp_get_vdw_energy proc~ommp_get_vdw_energy->module~mod_nonbonded 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_set_external_field->module~mod_memory proc~check_keyword~2 check_keyword proc~check_keyword~2->module~mod_utils proc~check_keyword~2->module~mod_memory proc~check_keyword~2->module~mod_constants proc~check_keyword~2->module~mod_io proc~sort_ivec sort_ivec proc~sort_ivec->module~mod_memory proc~ommp_set_vdw_cutoff ommp_set_vdw_cutoff proc~ommp_set_vdw_cutoff->module~mod_nonbonded proc~ommp_set_vdw_cutoff->module~mod_constants proc~ommp_get_imptorsion_energy ommp_get_imptorsion_energy proc~ommp_get_imptorsion_energy->module~mod_bonded proc~ommp_get_tortor_energy ommp_get_tortor_energy proc~ommp_get_tortor_energy->module~mod_bonded proc~update_coordinates update_coordinates proc~update_coordinates->module~mod_link_atom proc~update_coordinates->module~mod_memory proc~urey_init urey_init proc~urey_init->module~mod_memory proc~skip_lines skip_lines proc~skip_lines->module~mod_memory proc~conjugate_gradient_solver conjugate_gradient_solver proc~conjugate_gradient_solver->module~mod_memory proc~conjugate_gradient_solver->module~mod_constants proc~ommp_qm_helper_update_coord ommp_qm_helper_update_coord proc~ommp_qm_helper_update_coord->module~mod_qm_helper proc~ommp_get_pitors_energy ommp_get_pitors_energy proc~ommp_get_pitors_energy->module~mod_bonded proc~versor_der versor_der proc~versor_der->module~mod_memory proc~mmpol_init_from_mmp mmpol_init_from_mmp proc~mmpol_init_from_mmp->module~mod_electrostatics proc~mmpol_init_from_mmp->module~mod_adjacency_mat proc~mmpol_init_from_mmp->module~mod_utils proc~mmpol_init_from_mmp->module~mod_memory proc~mmpol_init_from_mmp->module~mod_constants proc~mmpol_init_from_mmp->module~mod_io proc~mmpol_init_from_mmp->module~mod_mmpol proc~assign_pitors assign_pitors proc~assign_pitors->module~mod_memory proc~assign_pitors->module~mod_bonded proc~assign_pitors->module~mod_constants proc~create_tmat create_tmat proc~create_tmat->module~mod_constants proc~create_tmat->module~mod_io proc~tokenize tokenize proc~tokenize->module~mod_memory proc~qm_helper_terminate qm_helper_terminate proc~qm_helper_terminate->module~mod_topology proc~qm_helper_terminate->module~mod_nonbonded proc~qm_helper_terminate->module~mod_memory proc~init_link_atom init_link_atom proc~init_link_atom->module~mod_topology proc~init_link_atom->module~mod_constants proc~init_link_atom->module~mod_io proc~ommp_get_angtor_energy ommp_get_angtor_energy proc~ommp_get_angtor_energy->module~mod_bonded proc~ommp_init_xyz ommp_init_xyz proc~ommp_init_xyz->module~mod_inputloader proc~large_file_read large_file_read proc~large_file_read->module~mod_constants proc~ommp_terminate_qm_helper ommp_terminate_qm_helper proc~ommp_terminate_qm_helper->module~mod_qm_helper proc~assign_torsion assign_torsion proc~assign_torsion->module~mod_memory proc~assign_torsion->module~mod_bonded proc~assign_torsion->module~mod_constants proc~qm_helper_link_atom_geomgrad qm_helper_link_atom_geomgrad proc~qm_helper_link_atom_geomgrad->module~mod_link_atom proc~qm_helper_link_atom_geomgrad->module~mod_memory proc~qm_helper_link_atom_geomgrad->module~mod_mmpol 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~vdw_set_pair vdw_set_pair proc~vdw_set_pair->module~mod_memory proc~vdw_set_pair->module~mod_constants proc~vdw_set_pair->module~mod_io 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_set_default_solver ommp_set_default_solver proc~ommp_set_default_solver->module~mod_electrostatics proc~ommp_get_strbnd_energy ommp_get_strbnd_energy proc~ommp_get_strbnd_energy->module~mod_bonded proc~ommp_get_strtor_energy ommp_get_strtor_energy proc~ommp_get_strtor_energy->module~mod_bonded proc~ommp_set_default_matv ommp_set_default_matv proc~ommp_set_default_matv->module~mod_electrostatics proc~ommp_terminate ommp_terminate proc~ommp_terminate->module~mod_mmpol proc~ommp_urey_geomgrad ommp_urey_geomgrad proc~ommp_urey_geomgrad->module~mod_bonded proc~tortor_potential tortor_potential proc~tortor_potential->module~mod_utils proc~add_link_atom add_link_atom proc~add_link_atom->module~mod_topology proc~add_link_atom->module~mod_constants proc~add_link_atom->module~mod_io proc~check_conn_matrix check_conn_matrix proc~check_conn_matrix->module~mod_adjacency_mat proc~check_conn_matrix->module~mod_io proc~numerical_geomgrad numerical_geomgrad proc~numerical_geomgrad->module~mod_mmpol proc~vdw_geomgrad_inter vdw_geomgrad_inter proc~vdw_geomgrad_inter->module~mod_jacobian_mat proc~vdw_geomgrad_inter->module~mod_constants proc~vdw_geomgrad_inter->module~mod_io 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_memory proc~init_eel_for_link_atom->module~mod_prm proc~init_eel_for_link_atom->module~mod_constants proc~init_eel_for_link_atom->module~mod_io proc~add_screening_pair add_screening_pair proc~add_screening_pair->module~mod_constants proc~add_screening_pair->module~mod_io proc~ommp_set_frozen_atoms ommp_set_frozen_atoms proc~ommp_set_frozen_atoms->module~mod_topology proc~guess_connectivity guess_connectivity proc~guess_connectivity->module~mod_adjacency_mat proc~guess_connectivity->module~mod_memory proc~guess_connectivity->module~mod_constants proc~guess_connectivity->module~mod_io proc~qm_helper_init qm_helper_init proc~qm_helper_init->module~mod_topology proc~qm_helper_init->module~mod_memory proc~ommp_init_mmp ommp_init_mmp proc~ommp_init_mmp->module~mod_inputloader proc~set_frozen set_frozen proc~set_frozen->module~mod_io proc~reverse_grp_tab reverse_grp_tab proc~reverse_grp_tab->module~mod_memory 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~ommp_strbnd_geomgrad ommp_strbnd_geomgrad proc~ommp_strbnd_geomgrad->module~mod_bonded proc~get_prm_ff_type get_prm_ff_type proc~get_prm_ff_type->module~mod_constants proc~get_prm_ff_type->module~mod_io proc~ommp_pitors_geomgrad ommp_pitors_geomgrad proc~ommp_pitors_geomgrad->module~mod_bonded proc~pitors_terminate pitors_terminate proc~pitors_terminate->module~mod_memory proc~diis diis proc~diis->module~mod_memory proc~ommp_angle_geomgrad ommp_angle_geomgrad proc~ommp_angle_geomgrad->module~mod_link_atom proc~ommp_angle_geomgrad->module~mod_bonded 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_get_opb_energy C_ommp_get_opb_energy proc~c_ommp_get_opb_energy->module~mod_bonded proc~rotate_multipoles rotate_multipoles proc~rotate_multipoles->module~mod_electrostatics proc~rotate_multipoles->module~mod_memory proc~bond_terminate bond_terminate proc~bond_terminate->module~mod_memory proc~strbnd_terminate strbnd_terminate proc~strbnd_terminate->module~mod_memory proc~ommp_strtor_geomgrad ommp_strtor_geomgrad proc~ommp_strtor_geomgrad->module~mod_bonded proc~angle_terminate angle_terminate proc~angle_terminate->module~mod_memory 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~urey_terminate urey_terminate proc~urey_terminate->module~mod_memory proc~opb_terminate opb_terminate proc~opb_terminate->module~mod_memory proc~ommp_tortor_geomgrad ommp_tortor_geomgrad proc~ommp_tortor_geomgrad->module~mod_bonded proc~torsion_potential torsion_potential proc~torsion_potential->module~mod_constants proc~imptorsion_geomgrad imptorsion_geomgrad proc~imptorsion_geomgrad->module~mod_jacobian_mat proc~angtor_init angtor_init proc~angtor_init->module~mod_memory proc~torsion_geomgrad torsion_geomgrad proc~torsion_geomgrad->module~mod_jacobian_mat 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_get_fixedelec_energy ommp_get_fixedelec_energy proc~ommp_get_fixedelec_energy->module~mod_electrostatics proc~opb_init opb_init proc~opb_init->module~mod_memory proc~opb_init->module~mod_constants proc~opb_init->module~mod_io proc~set_iof_mmpol set_iof_mmpol proc~set_iof_mmpol->module~mod_constants proc~assign_strtor assign_strtor proc~assign_strtor->module~mod_memory proc~assign_strtor->module~mod_bonded proc~assign_strtor->module~mod_constants proc~adj_mat_from_conn adj_mat_from_conn proc~adj_mat_from_conn->module~mod_utils proc~adj_mat_from_conn->module~mod_memory proc~strtor_geomgrad strtor_geomgrad proc~strtor_geomgrad->module~mod_jacobian_mat proc~strtor_potential strtor_potential proc~strtor_potential->module~mod_constants proc~ommp_update_link_atoms_position ommp_update_link_atoms_position proc~ommp_update_link_atoms_position->module~mod_link_atom proc~ommp_update_link_atoms_position->module~mod_io proc~ommp_update_link_atoms_position->module~mod_qm_helper proc~tortor_init tortor_init proc~tortor_init->module~mod_memory proc~ommp_smartinput_cpstr ommp_smartinput_cpstr proc~ommp_smartinput_cpstr->iso_c_binding proc~ommp_smartinput ommp_smartinput proc~ommp_smartinput->iso_c_binding 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~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_bonded proc~init_bonded_for_link_atom->module~mod_prm proc~init_bonded_for_link_atom->module~mod_constants proc~init_bonded_for_link_atom->module~mod_io proc~link_atom_torsion_geomgrad link_atom_torsion_geomgrad proc~link_atom_torsion_geomgrad->module~mod_bonded proc~opb_potential opb_potential proc~opb_potential->module~mod_constants 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~angtor_geomgrad angtor_geomgrad proc~angtor_geomgrad->module~mod_jacobian_mat proc~compress_data compress_data proc~compress_data->module~mod_memory proc~energy_mm_pol energy_MM_pol proc~energy_mm_pol->module~mod_memory proc~close_output close_output proc~close_output->module~mod_constants proc~c_ommp_update_coordinates C_ommp_update_coordinates proc~c_ommp_update_coordinates->module~mod_mmpol 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~polgroup11_to_mm2pg polgroup11_to_mm2pg proc~polgroup11_to_mm2pg->module~mod_memory proc~mmpol_init_from_xyz mmpol_init_from_xyz proc~mmpol_init_from_xyz->module~mod_electrostatics proc~mmpol_init_from_xyz->module~mod_topology proc~mmpol_init_from_xyz->module~mod_adjacency_mat proc~mmpol_init_from_xyz->module~mod_utils proc~mmpol_init_from_xyz->module~mod_memory proc~mmpol_init_from_xyz->module~mod_prm proc~mmpol_init_from_xyz->module~mod_constants proc~mmpol_init_from_xyz->module~mod_io proc~mmpol_init_from_xyz->module~mod_mmpol proc~rotation_geomgrad rotation_geomgrad proc~rotation_geomgrad->module~mod_electrostatics proc~rotation_geomgrad->module~mod_memory proc~bond_init bond_init proc~bond_init->module~mod_memory proc~qm_helper_init_vdw_prm qm_helper_init_vdw_prm proc~qm_helper_init_vdw_prm->module~mod_utils proc~qm_helper_init_vdw_prm->module~mod_prm proc~qm_helper_init_vdw_prm->module~mod_constants proc~qm_helper_init_vdw_prm->module~mod_io proc~c_ommp_full_geomgrad C_ommp_full_geomgrad proc~c_ommp_full_geomgrad->module~ommp_interface proc~energy_mm_mm energy_MM_MM proc~energy_mm_mm->module~mod_memory proc~ommp_bond_geomgrad ommp_bond_geomgrad proc~ommp_bond_geomgrad->module~mod_link_atom proc~ommp_bond_geomgrad->module~mod_bonded proc~prepare_fixedelec prepare_fixedelec proc~prepare_fixedelec->module~mod_memory proc~c_ommp_get_polar_mm C_ommp_get_polar_mm proc~c_ommp_get_polar_mm->module~mod_memory proc~assign_imptorsion assign_imptorsion proc~assign_imptorsion->module~mod_memory proc~assign_imptorsion->module~mod_bonded proc~assign_imptorsion->module~mod_constants proc~torsion_init torsion_init proc~torsion_init->module~mod_memory proc~link_atom_project_grd link_atom_project_grd proc~link_atom_project_grd->module~mod_utils proc~qm_helper_vdw_energy qm_helper_vdw_energy proc~qm_helper_vdw_energy->module~mod_nonbonded proc~qm_helper_vdw_energy->module~mod_link_atom proc~qm_helper_vdw_energy->module~mod_mmpol proc~strbnd_geomgrad strbnd_geomgrad proc~strbnd_geomgrad->module~mod_jacobian_mat proc~angle_geomgrad angle_geomgrad proc~angle_geomgrad->module~mod_jacobian_mat proc~angle_geomgrad->module~mod_constants proc~qm_helper_vdw_geomgrad qm_helper_vdw_geomgrad proc~qm_helper_vdw_geomgrad->module~mod_nonbonded proc~qm_helper_vdw_geomgrad->module~mod_link_atom proc~qm_helper_vdw_geomgrad->module~mod_mmpol proc~ommp_vdw_geomgrad ommp_vdw_geomgrad proc~ommp_vdw_geomgrad->module~mod_nonbonded proc~topology_terminate topology_terminate proc~topology_terminate->module~mod_adjacency_mat proc~topology_terminate->module~mod_memory proc~ommp_potential_mm2ext ommp_potential_mm2ext proc~ommp_potential_mm2ext->module~mod_electrostatics proc~ommp_turn_pol_off ommp_turn_pol_off proc~ommp_turn_pol_off->module~mod_electrostatics proc~ommp_turn_pol_off->module~mod_constants proc~ommp_turn_pol_off->module~mod_io proc~vdw_set_cutoff vdw_set_cutoff proc~vdw_set_cutoff->module~mod_neighbor_list proc~check_keyword check_keyword proc~check_keyword->module~mod_utils proc~check_keyword->module~mod_memory proc~check_keyword->module~mod_constants proc~check_keyword->module~mod_io proc~cross_product cross_product proc~cross_product->module~mod_memory proc~vec_skw vec_skw proc~vec_skw->module~mod_memory proc~vdw_terminate vdw_terminate proc~vdw_terminate->module~mod_neighbor_list proc~vdw_terminate->module~mod_adjacency_mat proc~vdw_terminate->module~mod_memory proc~make_screening_lists make_screening_lists proc~make_screening_lists->module~mod_adjacency_mat proc~make_screening_lists->module~mod_memory proc~make_screening_lists->module~mod_constants proc~ommp_potential_mmpol2ext ommp_potential_mmpol2ext proc~ommp_potential_mmpol2ext->module~mod_electrostatics proc~pitors_potential pitors_potential proc~pitors_potential->module~mod_constants proc~strbnd_init strbnd_init proc~strbnd_init->module~mod_memory proc~prepare_polelec prepare_polelec proc~prepare_polelec->module~mod_memory proc~cyclic_spline cyclic_spline proc~cyclic_spline->module~mod_memory proc~get_rij0_inter get_Rij0_inter proc~get_rij0_inter->module~mod_constants proc~ommp_qm_helper_set_frozen_atoms ommp_qm_helper_set_frozen_atoms proc~ommp_qm_helper_set_frozen_atoms->module~mod_topology proc~jacobi_diis_solver jacobi_diis_solver proc~jacobi_diis_solver->module~mod_memory proc~jacobi_diis_solver->module~mod_constants proc~assign_vdw assign_vdw proc~assign_vdw->module~mod_nonbonded proc~assign_vdw->module~mod_memory proc~assign_vdw->module~mod_constants proc~assign_vdw->module~mod_io proc~sort_ivec_inplace sort_ivec_inplace proc~sort_ivec_inplace->module~mod_memory proc~angle_potential angle_potential proc~angle_potential->module~mod_constants proc~angle_init angle_init proc~angle_init->module~mod_memory proc~inversion_solver inversion_solver proc~inversion_solver->module~mod_memory proc~polarization_terminate polarization_terminate proc~polarization_terminate->module~mod_memory proc~qm_helper_init_vdw qm_helper_init_vdw proc~qm_helper_init_vdw->module~mod_nonbonded proc~qm_helper_init_vdw->module~mod_memory proc~qm_helper_init_vdw->module~mod_constants proc~qm_helper_init_vdw->module~mod_io proc~urey_geomgrad urey_geomgrad proc~urey_geomgrad->module~mod_jacobian_mat proc~urey_geomgrad->module~mod_constants 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~assign_angle assign_angle proc~assign_angle->module~mod_memory proc~assign_angle->module~mod_bonded proc~assign_angle->module~mod_constants proc~qm_helper_update_coord qm_helper_update_coord proc~qm_helper_update_coord->module~mod_topology proc~qm_helper_update_coord->module~mod_adjacency_mat proc~qm_helper_update_coord->module~mod_constants proc~qm_helper_update_coord->module~mod_io proc~ommp_save_as_hdf5 ommp_save_as_hdf5 proc~ommp_save_as_hdf5->mod_iohdf5 proc~polarization polarization proc~polarization->module~mod_profiling proc~polarization->module~mod_memory proc~polarization->module~mod_constants proc~polarization->module~mod_solvers proc~polarization->module~mod_io proc~ommp_init_qm_helper ommp_init_qm_helper proc~ommp_init_qm_helper->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~ommp_checkpoint ommp_checkpoint proc~ommp_checkpoint->mod_iohdf5 proc~dipole_t dipole_T proc~dipole_t->module~mod_electrostatics proc~dipole_t->module~mod_constants proc~get_eij get_eij proc~get_eij->module~mod_constants proc~compute_bicubic_interp compute_bicubic_interp proc~compute_bicubic_interp->module~mod_memory 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~polelec_geomgrad polelec_geomgrad proc~polelec_geomgrad->module~mod_electrostatics proc~polelec_geomgrad->module~mod_polarization proc~assign_tortors assign_tortors proc~assign_tortors->module~mod_memory proc~assign_tortors->module~mod_bonded proc~assign_tortors->module~mod_constants proc~mmpol_ommp_print_summary mmpol_ommp_print_summary proc~mmpol_ommp_print_summary->module~mod_utils proc~mmpol_ommp_print_summary->module~mod_memory proc~mmpol_ommp_print_summary->module~mod_io proc~nl_terminate nl_terminate proc~nl_terminate->module~mod_adjacency_mat proc~imptorsion_potential imptorsion_potential proc~imptorsion_potential->module~mod_constants proc~ommp_get_link_atom_coordinates ommp_get_link_atom_coordinates proc~ommp_get_link_atom_coordinates->module~mod_link_atom proc~imptorsion_init imptorsion_init proc~imptorsion_init->module~mod_memory proc~tortor_geomgrad tortor_geomgrad proc~tortor_geomgrad->module~mod_utils proc~tortor_geomgrad->module~mod_jacobian_mat proc~get_rij0 get_Rij0 proc~get_rij0->module~mod_constants proc~thole_init thole_init proc~thole_init->module~mod_constants proc~ommp_qm_helper_vdw_energy ommp_qm_helper_vdw_energy proc~ommp_qm_helper_vdw_energy->module~mod_qm_helper proc~ommp_opb_geomgrad ommp_opb_geomgrad proc~ommp_opb_geomgrad->module~mod_bonded proc~coulomb_kernel coulomb_kernel proc~coulomb_kernel->module~mod_memory proc~coulomb_kernel->module~mod_constants proc~coulomb_kernel->module~mod_io 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~ommp_create_link_atom ommp_create_link_atom proc~ommp_create_link_atom->module~mod_topology proc~ommp_create_link_atom->module~mod_nonbonded proc~ommp_create_link_atom->module~mod_link_atom proc~ommp_create_link_atom->module~mod_memory proc~ommp_create_link_atom->module~mod_mmpol proc~ommp_create_link_atom->module~mod_qm_helper proc~vdw_potential_inter vdw_potential_inter proc~vdw_potential_inter->module~mod_constants proc~vdw_potential_inter->module~mod_io 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~nl_update nl_update proc~nl_update->module~mod_profiling proc~nl_update->module~mod_adjacency_mat proc~nl_update->module~mod_constants proc~nl_update->module~mod_io 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_field_pol2ext ommp_field_pol2ext proc~ommp_field_pol2ext->module~mod_electrostatics proc~ommp_get_urey_energy ommp_get_urey_energy proc~ommp_get_urey_energy->module~mod_bonded proc~fixedelec_geomgrad fixedelec_geomgrad proc~fixedelec_geomgrad->module~mod_electrostatics proc~build_pg_adjacency_matrix build_pg_adjacency_matrix proc~build_pg_adjacency_matrix->module~mod_adjacency_mat proc~ommp_torsion_geomgrad ommp_torsion_geomgrad proc~ommp_torsion_geomgrad->module~mod_link_atom proc~ommp_torsion_geomgrad->module~mod_bonded proc~tortor_newmap tortor_newmap proc~tortor_newmap->module~mod_utils proc~tortor_newmap->module~mod_memory proc~ommp_field_mm2ext ommp_field_mm2ext proc~ommp_field_mm2ext->module~mod_electrostatics proc~ommp_angtor_geomgrad ommp_angtor_geomgrad proc~ommp_angtor_geomgrad->module~mod_bonded proc~mmpol_terminate mmpol_terminate proc~mmpol_terminate->module~mod_electrostatics proc~mmpol_terminate->module~mod_nonbonded proc~mmpol_terminate->module~mod_memory proc~mmpol_terminate->module~mod_bonded proc~opb_geomgrad opb_geomgrad proc~opb_geomgrad->module~mod_jacobian_mat proc~vdw_geomgrad vdw_geomgrad proc~vdw_geomgrad->module~mod_neighbor_list proc~vdw_geomgrad->module~mod_profiling proc~vdw_geomgrad->module~mod_memory proc~vdw_geomgrad->module~mod_jacobian_mat proc~vdw_geomgrad->module~mod_constants proc~vdw_geomgrad->module~mod_io 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~remove_null_pol remove_null_pol proc~remove_null_pol->module~mod_memory proc~remove_null_pol->module~mod_constants proc~ommp_imptorsion_geomgrad ommp_imptorsion_geomgrad proc~ommp_imptorsion_geomgrad->module~mod_bonded proc~ommp_get_opb_energy ommp_get_opb_energy proc~ommp_get_opb_energy->module~mod_bonded proc~ommp_qm_helper_vdw_geomgrad ommp_qm_helper_vdw_geomgrad proc~ommp_qm_helper_vdw_geomgrad->module~mod_qm_helper proc~mmpol_prepare mmpol_prepare proc~mmpol_prepare->module~mod_electrostatics proc~mmpol_prepare->module~mod_profiling proc~mmpol_prepare->module~mod_adjacency_mat proc~mmpol_prepare->module~mod_constants proc~mmpol_prepare->module~mod_io proc~electrostatic_for_ene electrostatic_for_ene proc~electrostatic_for_ene->module~mod_electrostatics proc~electrostatic_for_ene->module~mod_memory
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