Documentation for module topology_types

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source: topology_types.F
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public Types:

constr_list_type
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topology_parameters_type
...
atom_info_type
...
connectivity_info_type
...
constraint_info_type
...

public Subroutines/Functions:

1. Just DEALLOCATE all the stuff
SUBROUTINE
init_topology (topology)
1. Just NULLIFY and zero all the stuff
Deallocate possibly allocated arrays before reading topology

public Types:

TYPE :: atom_info_type

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INTEGER,
DIMENSION(:), POINTER :: id_molname ...
INTEGER,
DIMENSION(:), POINTER :: id_resname ...
INTEGER,
DIMENSION(:), POINTER :: id_atmname ...
INTEGER,
DIMENSION(:), POINTER :: id_atom_names ...
INTEGER,
DIMENSION(:), POINTER :: id_element ...
INTEGER,
POINTER :: resid ...
REAL(dp),
DIMENSION(:,:), POINTER :: r ...
INTEGER,
POINTER :: map_mol_typ ...
INTEGER,
POINTER :: map_mol_num ...
INTEGER,
POINTER :: map_mol_res ...
REAL(dp),
POINTER :: atm_charge ...
REAL(dp),
POINTER :: atm_mass ...
REAL(dp),
POINTER :: occup ...
REAL(dp),
POINTER :: beta ...

TYPE :: connectivity_info_type

...


INTEGER,
POINTER :: bond_a ...
INTEGER,
POINTER :: bond_b ...
INTEGER,
POINTER :: bond_type ...
INTEGER,
POINTER :: ub_a ...
INTEGER,
POINTER :: ub_b ...
INTEGER,
POINTER :: ub_c ...
INTEGER,
POINTER :: theta_a ...
INTEGER,
POINTER :: theta_b ...
INTEGER,
POINTER :: theta_c ...
INTEGER,
POINTER :: theta_type ...
INTEGER,
POINTER :: phi_a ...
INTEGER,
POINTER :: phi_b ...
INTEGER,
POINTER :: phi_c ...
INTEGER,
POINTER :: phi_d ...
INTEGER,
POINTER :: phi_type ...
INTEGER,
POINTER :: impr_a ...
INTEGER,
POINTER :: impr_b ...
INTEGER,
POINTER :: impr_c ...
INTEGER,
POINTER :: impr_d ...
INTEGER,
POINTER :: impr_type ...
INTEGER,
POINTER :: onfo_a ...
INTEGER,
POINTER :: onfo_b ...
INTEGER,
POINTER :: c_bond_a ...
INTEGER,
POINTER :: c_bond_b ...
INTEGER,
POINTER :: c_bond_type ...

TYPE :: constraint_info_type

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LOGICAL
:: hbonds_restraint ...
REAL(dp)
:: hbonds_k0 ...
INTEGER
:: nfixed_atoms ...
INTEGER,
POINTER :: fixed_atoms ...
INTEGER,
POINTER :: fixed_type ...
INTEGER,
POINTER :: fixed_mol_type ...
LOGICAL,
POINTER :: fixed_restraint ...
REAL(dp),
POINTER :: fixed_k0 ...
INTEGER
:: freeze_qm ...
INTEGER
:: freeze_mm ...
INTEGER
:: freeze_qm_type ...
INTEGER
:: freeze_mm_type ...
LOGICAL
:: fixed_mm_restraint ...
LOGICAL
:: fixed_qm_restraint ...
REAL(dp)
:: fixed_mm_k0 ...
REAL(dp)
:: fixed_qm_k0 ...
LOGICAL,
POINTER :: fixed_mol_restraint ...
REAL(dp),
POINTER :: fixed_mol_k0 ...
POINTER :: fixed_molnames ...
LOGICAL,
POINTER, DIMENSION(:) :: fixed_exclude_qm ...
LOGICAL,
POINTER, DIMENSION(:) :: fixed_exclude_mm ...
INTEGER
:: nconst_colv ...
INTEGER,
POINTER :: const_colv_mol ...
POINTER :: const_colv_molname ...
REAL(dp),
POINTER :: const_colv_target ...
REAL(dp),
POINTER :: const_colv_target_growth ...
POINTER, DIMENSION(:) :: colvar_set ...
LOGICAL,
POINTER :: colv_intermolecular ...
LOGICAL,
POINTER :: colv_restraint ...
REAL(dp),
POINTER :: colv_k0 ...
LOGICAL,
POINTER, DIMENSION(:) :: colv_exclude_qm ...
LOGICAL,
POINTER, DIMENSION(:) :: colv_exclude_mm ...
INTEGER
:: nconst_g33 ...
INTEGER,
POINTER :: const_g33_mol ...
POINTER :: const_g33_molname ...
INTEGER,
POINTER :: const_g33_a ...
INTEGER,
POINTER :: const_g33_b ...
INTEGER,
POINTER :: const_g33_c ...
REAL(dp),
POINTER :: const_g33_dab ...
REAL(dp),
POINTER :: const_g33_dac ...
REAL(dp),
POINTER :: const_g33_dbc ...
LOGICAL,
POINTER :: g33_intermolecular ...
LOGICAL,
POINTER :: g33_restraint ...
REAL(dp),
POINTER :: g33_k0 ...
LOGICAL,
POINTER, DIMENSION(:) :: g33_exclude_qm ...
LOGICAL,
POINTER, DIMENSION(:) :: g33_exclude_mm ...
INTEGER
:: nconst_g46 ...
INTEGER,
POINTER :: const_g46_mol ...
POINTER :: const_g46_molname ...
INTEGER,
POINTER :: const_g46_a ...
INTEGER,
POINTER :: const_g46_b ...
INTEGER,
POINTER :: const_g46_c ...
INTEGER,
POINTER :: const_g46_d ...
REAL(dp),
POINTER :: const_g46_dab ...
REAL(dp),
POINTER :: const_g46_dac ...
REAL(dp),
POINTER :: const_g46_dbc ...
REAL(dp),
POINTER :: const_g46_dad ...
REAL(dp),
POINTER :: const_g46_dbd ...
REAL(dp),
POINTER :: const_g46_dcd ...
LOGICAL,
POINTER :: g46_intermolecular ...
LOGICAL,
POINTER :: g46_restraint ...
REAL(dp),
POINTER :: g46_k0 ...
LOGICAL,
POINTER, DIMENSION(:) :: g46_exclude_qm ...
LOGICAL,
POINTER, DIMENSION(:) :: g46_exclude_mm ...
INTEGER
:: nconst_vsite ...
INTEGER,
POINTER :: const_vsite_mol ...
POINTER :: const_vsite_molname ...
INTEGER,
POINTER :: const_vsite_a ...
INTEGER,
POINTER :: const_vsite_b ...
INTEGER,
POINTER :: const_vsite_c ...
INTEGER,
POINTER :: const_vsite_d ...
REAL(dp),
POINTER :: const_vsite_wbc ...
REAL(dp),
POINTER :: const_vsite_wdc ...
LOGICAL,
POINTER :: vsite_intermolecular ...
LOGICAL,
POINTER :: vsite_restraint ...
REAL(dp),
POINTER :: vsite_k0 ...
LOGICAL,
POINTER, DIMENSION(:) :: vsite_exclude_qm ...
LOGICAL,
POINTER, DIMENSION(:) :: vsite_exclude_mm ...

TYPE :: constr_list_type

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INTEGER,
DIMENSION(:), POINTER :: constr ...

TYPE :: topology_parameters_type

...


POINTER :: atom_info ...
POINTER :: conn_info ...
POINTER :: cons_info ...
TYPE(cell_type),
POINTER :: cell ...
TYPE(cell_type),
POINTER :: cell_ref ...
TYPE(cell_type),
POINTER :: cell_muc ...
INTEGER
:: conn_type ...
INTEGER
:: coord_type ...
INTEGER
:: exclude_vdw ...
INTEGER
:: exclude_ei ...
INTEGER
:: bondparm_type ...
INTEGER
:: natoms ...
INTEGER
:: natom_type ...
INTEGER
:: nmol ...
INTEGER
:: nmol_type ...
INTEGER
:: nmol_conn ...
LOGICAL
:: aa_element ...
LOGICAL
:: molname_generated ...
REAL(dp)
:: bondparm_factor ...
LOGICAL
:: create_molecules ...
LOGICAL
:: reorder_atom ...
LOGICAL
:: molecules_check ...
LOGICAL
:: coordinate ...
LOGICAL
:: use_g96_velocity ...
:: coord_file_name ...
:: conn_file_name ...
LOGICAL
:: const_atom ...
LOGICAL
:: const_hydr ...
LOGICAL
:: const_colv ...
LOGICAL
:: const_33 ...
LOGICAL
:: const_46 ...
LOGICAL
:: const_vsite ...
LOGICAL
:: charge_occup ...
LOGICAL
:: charge_beta ...
LOGICAL
:: charge_extended ...
LOGICAL
:: para_res ...

SUBROUTINEdeallocate_topology(topology)

1. Just DEALLOCATE all the stuff

Arguments:
INTENT(inout)
:: topology ...

SUBROUTINEinit_topology(topology)

1. Just NULLIFY and zero all the stuff

Arguments:
INTENT(inout)
:: topology ...

SUBROUTINEpre_read_topology(topology)

Deallocate possibly allocated arrays before reading topology

Arguments:
INTENT(inout)
:: topology ...