molecule_kind_types Namespace Reference

Define the molecule kind structure types and the corresponding functionality. More...

Classes
struct	atom_type
struct	shell_type
struct	bond_type
struct	bend_type
struct	ub_type
struct	torsion_type
struct	impr_type
struct	opbend_type
struct	restraint_type
struct	colvar_constraint_type
struct	g3x3_constraint_type
struct	g4x6_constraint_type
struct	vsite_constraint_type
struct	fixd_constraint_type
struct	local_fixd_constraint_type
struct	molecule_kind_type
Functions
subroutine, public	setup_colvar_counters (colv_list, ncolv, error)
subroutine, public	allocate_molecule_kind_set (molecule_kind_set, nmolecule_kind, error)
	Allocate and initialize a molecule kind set.
subroutine, public	deallocate_molecule_kind_set (molecule_kind_set, error)
	Deallocate a molecule kind set.
subroutine, public	get_molecule_kind (molecule_kind, atom_list, bond_list, bend_list, ub_list, impr_list, opbend_list, colv_list, fixd_list, g3x3_list, g4x6_list, vsite_list, torsion_list, shell_list, name, mass, charge, kind_number, natom, nbend, nbond, nub, nimpr, nopbend, nconstraint, nconstraint_fixd, nfixd, ncolv, ng3x3, ng4x6, nvsite, nfixd_restraint, ng3x3_restraint, ng4x6_restraint, nvsite_restraint, nrestraints, nmolecule, nsgf, nshell, ntorsion, molecule_list, nelectron, bond_kind_set, bend_kind_set, ub_kind_set, impr_kind_set, opbend_kind_set, torsion_kind_set, molname_generated)
	Get informations about a molecule kind.
subroutine, public	get_molecule_kind_set (molecule_kind_set, maxatom, natom, nbond, nbend, nub, ntorsion, nimpr, nopbend, nconstraint, nconstraint_fixd, nmolecule, nrestraints)
	Get informations about a molecule kind set.
subroutine, public	num_ao_el_per_molecule (molecule_kind_set, charge_x_mol)
	Read a molecule kind data set from the input file.
subroutine, public	set_molecule_kind (molecule_kind, name, mass, charge, kind_number, molecule_list, atom_list, nbond, bond_list, nbend, bend_list, nub, ub_list, nimpr, impr_list, nopbend, opbend_list, ntorsion, torsion_list, fixd_list, ncolv, colv_list, ng3x3, g3x3_list, ng4x6, nfixd, g4x6_list, nvsite, vsite_list, ng3x3_restraint, ng4x6_restraint, nfixd_restraint, nshell, shell_list, nvsite_restraint, bond_kind_set, bend_kind_set, ub_kind_set, torsion_kind_set, impr_kind_set, opbend_kind_set, nelectron, nsgf, molname_generated)
	Set the components of a molecule kind.
subroutine, public	write_molecule_kind (molecule_kind, output_unit, error)
	Write a molecule kind data set to the output unit.
subroutine, public	write_molecule_kind_set (molecule_kind_set, subsys_section, error)
	Write a moleculeatomic kind set data set to the output unit.
Variables
CHARACTER(len=*), parameter, private	moduleN = 'molecule_kind_types'

---

Detailed Description

Define the molecule kind structure types and the corresponding functionality.

History

Teodoro Laino [tlaino] 12.2008 - Preparing for VIRTUAL SITE constraints (patch by Marcel Baer)

Author:

MK (22.08.2003)

---

Function Documentation

subroutine,public molecule_kind_types::allocate_molecule_kind_set	(	TYPE(molecule_kind_type),dimension(:),pointer	molecule_kind_set,
		INTEGER,intent(in)	nmolecule_kind,
		TYPE(cp_error_type),intent(inout)	error
	)

Allocate and initialize a molecule kind set.

Author:

MK

Date:

22.08.2003

Version:

1.0

Definition at line 338 of file molecule_kind_types.f90.

References deallocate_molecule_kind_set(), and setup_colvar_counters().

Referenced by topology_connectivity_util::topology_connectivity_pack().

Here is the call graph for this function:

Here is the caller graph for this function:

subroutine,public molecule_kind_types::deallocate_molecule_kind_set	(	TYPE(molecule_kind_type),dimension(:),pointer	molecule_kind_set,
		TYPE(cp_error_type),intent(inout)	error
	)

Deallocate a molecule kind set.

Author:

MK

Date:

22.08.2003

Version:

1.0

Definition at line 413 of file molecule_kind_types.f90.

References force_field_types::impr_kind_dealloc_ref(), termination::stop_program(), force_field_types::torsion_kind_dealloc_ref(), and force_field_types::ub_kind_dealloc_ref().

Referenced by allocate_molecule_kind_set(), and mol_kind_new_list_types::mol_kind_new_list_release().

Here is the call graph for this function:

Here is the caller graph for this function:

subroutine,public molecule_kind_types::get_molecule_kind	(	TYPE(molecule_kind_type),pointer	molecule_kind,
		TYPE(atom_type),dimension(:),optional,pointer	atom_list,
		TYPE(bond_type),dimension(:),optional,pointer	bond_list,
		TYPE(bend_type),dimension(:),optional,pointer	bend_list,
		TYPE(ub_type),dimension(:),optional,pointer	ub_list,
		TYPE(impr_type),dimension(:),optional,pointer	impr_list,
		TYPE(opbend_type),dimension(:),optional,pointer	opbend_list,
		TYPE(colvar_constraint_type),dimension(:),optional,pointer	colv_list,
		TYPE(fixd_constraint_type),dimension(:),optional,pointer	fixd_list,
		TYPE(g3x3_constraint_type),dimension(:),optional,pointer	g3x3_list,
		TYPE(g4x6_constraint_type),dimension(:),optional,pointer	g4x6_list,
		TYPE(vsite_constraint_type),dimension(:),optional,pointer	vsite_list,
		TYPE(torsion_type),dimension(:),optional,pointer	torsion_list,
		TYPE(shell_type),dimension(:),optional,pointer	shell_list,
		CHARACTER(LEN=default_string_length),intent(out),optional	name,
		REAL(KIND=dp),optional	mass,
		REAL(KIND=dp),optional	charge,
		INTEGER,intent(out),optional	kind_number,
		INTEGER,intent(out),optional	natom,
		INTEGER,intent(out),optional	nbend,
		INTEGER,intent(out),optional	nbond,
		INTEGER,intent(out),optional	nub,
		INTEGER,intent(out),optional	nimpr,
		INTEGER,intent(out),optional	nopbend,
		INTEGER,intent(out),optional	nconstraint,
		INTEGER,intent(out),optional	nconstraint_fixd,
		INTEGER,intent(out),optional	nfixd,
		TYPE(colvar_counters),intent(out),optional	ncolv,
		INTEGER,intent(out),optional	ng3x3,
		INTEGER,intent(out),optional	ng4x6,
		INTEGER,intent(out),optional	nvsite,
		INTEGER,intent(out),optional	nfixd_restraint,
		INTEGER,intent(out),optional	ng3x3_restraint,
		INTEGER,intent(out),optional	ng4x6_restraint,
		INTEGER,intent(out),optional	nvsite_restraint,
		INTEGER,intent(out),optional	nrestraints,
		INTEGER,intent(out),optional	nmolecule,
		INTEGER,intent(out),optional	nsgf,
		INTEGER,intent(out),optional	nshell,
		INTEGER,intent(out),optional	ntorsion,
		INTEGER,dimension(:),optional,pointer	molecule_list,
		INTEGER,intent(out),optional	nelectron,
		TYPE(bond_kind_type),dimension(:),optional,pointer	bond_kind_set,
		TYPE(bend_kind_type),dimension(:),optional,pointer	bend_kind_set,
		TYPE(ub_kind_type),dimension(:),optional,pointer	ub_kind_set,
		TYPE(impr_kind_type),dimension(:),optional,pointer	impr_kind_set,
		TYPE(opbend_kind_type),dimension(:),optional,pointer	opbend_kind_set,
		TYPE(torsion_kind_type),dimension(:),optional,pointer	torsion_kind_set,
		LOGICAL,intent(out),optional	molname_generated
	)

Get informations about a molecule kind.

Author:

MK

Date:

27.08.2003

Version:

1.0

Definition at line 539 of file molecule_kind_types.f90.

References termination::stop_program(), and input_constants::use_perd_x.

Referenced by force_fields_util::clean_intra_force_kind(), reftraj_util::compute_msd_reftraj(), distribution_methods::distribute_2d_cost_model(), distribution_methods::distribute_molecules_1d(), distribution_methods::distribute_molecules_2d(), input_cp2k_restarts::dump_coordinates_cp2k(), constraint::dump_lagrange_mult(), force_fields_all::force_field_pack_bend(), force_fields_all::force_field_pack_bond(), force_fields_all::force_field_pack_impr(), force_fields_all::force_field_pack_opbend(), force_fields_all::force_field_pack_shell(), force_fields_all::force_field_pack_tors(), force_fields_all::force_field_pack_ub(), force_fields_util::force_field_qeff_output(), force_fields_all::force_field_unique_bend(), force_fields_all::force_field_unique_bond(), force_fields_all::force_field_unique_impr(), force_fields_all::force_field_unique_opbend(), force_fields_all::force_field_unique_tors(), force_fields_all::force_field_unique_ub(), fist_intra_force::force_intra_control(), constraint_vsite::force_vsite_int(), get_molecule_kind_set(), reftraj_util::initialize_msd_reftraj(), num_ao_el_per_molecule(), constraint::rattle_control(), constraint::rattle_roll_control(), input_cp2k_restarts::section_coord_val_set(), thermostat_utils::setup_adiabatic_thermostat_info(), thermostat_utils::setup_thermostat_info(), constraint::shake_control(), constraint::shake_roll_control(), constraint::shake_update_targets(), constraint_vsite::shake_vsite_int(), topology_connectivity_util::topology_connectivity_pack(), topology_constraint_util::topology_constraint_pack(), constraint_vsite::vsite_force_control(), and qs_loc_molecules::wfc_to_molecule().

Here is the call graph for this function:

Here is the caller graph for this function:

subroutine,public molecule_kind_types::get_molecule_kind_set	(	TYPE(molecule_kind_type),dimension(:),pointer	molecule_kind_set,
		INTEGER,intent(out),optional	maxatom,
		INTEGER,intent(out),optional	natom,
		INTEGER,intent(out),optional	nbond,
		INTEGER,intent(out),optional	nbend,
		INTEGER,intent(out),optional	nub,
		INTEGER,intent(out),optional	ntorsion,
		INTEGER,intent(out),optional	nimpr,
		INTEGER,intent(out),optional	nopbend,
		INTEGER,intent(out),optional	nconstraint,
		INTEGER,intent(out),optional	nconstraint_fixd,
		INTEGER,intent(out),optional	nmolecule,
		INTEGER,intent(out),optional	nrestraints
	)

Get informations about a molecule kind set.

Author:

MK

Date:

27.08.2003

Version:

1.0

Definition at line 699 of file molecule_kind_types.f90.

References get_molecule_kind(), and termination::stop_program().

Referenced by write_molecule_kind_set().

Here is the call graph for this function:

Here is the caller graph for this function:

subroutine,public molecule_kind_types::num_ao_el_per_molecule	(	TYPE(molecule_kind_type),dimension(:),pointer	molecule_kind_set,
		INTEGER,dimension(:),optional,pointer	charge_x_mol
	)

Read a molecule kind data set from the input file.

Author:

MI

Date:

22.11.2004

Version:

1.0

Definition at line 781 of file molecule_kind_types.f90.

References basis_set_types::get_gto_basis_set(), get_molecule_kind(), and set_molecule_kind().

Here is the call graph for this function:

subroutine,public molecule_kind_types::set_molecule_kind	(	TYPE(molecule_kind_type),pointer	molecule_kind,
		CHARACTER(LEN=*),intent(in),optional	name,
		REAL(KIND=dp),optional	mass,
		REAL(KIND=dp),optional	charge,
		INTEGER,intent(in),optional	kind_number,
		INTEGER,dimension(:),optional,pointer	molecule_list,
		TYPE(atom_type),dimension(:),optional,pointer	atom_list,
		INTEGER,intent(in),optional	nbond,
		TYPE(bond_type),dimension(:),optional,pointer	bond_list,
		INTEGER,intent(in),optional	nbend,
		TYPE(bend_type),dimension(:),optional,pointer	bend_list,
		INTEGER,intent(in),optional	nub,
		TYPE(ub_type),dimension(:),optional,pointer	ub_list,
		INTEGER,intent(in),optional	nimpr,
		TYPE(impr_type),dimension(:),optional,pointer	impr_list,
		INTEGER,intent(in),optional	nopbend,
		TYPE(opbend_type),dimension(:),optional,pointer	opbend_list,
		INTEGER,intent(in),optional	ntorsion,
		TYPE(torsion_type),dimension(:),optional,pointer	torsion_list,
		TYPE(fixd_constraint_type),dimension(:),optional,pointer	fixd_list,
		TYPE(colvar_counters),intent(in),optional	ncolv,
		TYPE(colvar_constraint_type),dimension(:),optional,pointer	colv_list,
		INTEGER,intent(in),optional	ng3x3,
		TYPE(g3x3_constraint_type),dimension(:),optional,pointer	g3x3_list,
		INTEGER,intent(in),optional	ng4x6,
		INTEGER,intent(in),optional	nfixd,
		TYPE(g4x6_constraint_type),dimension(:),optional,pointer	g4x6_list,
		INTEGER,intent(in),optional	nvsite,
		TYPE(vsite_constraint_type),dimension(:),optional,pointer	vsite_list,
		INTEGER,intent(in),optional	ng3x3_restraint,
		INTEGER,intent(in),optional	ng4x6_restraint,
		INTEGER,intent(in),optional	nfixd_restraint,
		INTEGER,intent(in),optional	nshell,
		TYPE(shell_type),dimension(:),optional,pointer	shell_list,
		INTEGER,intent(in),optional	nvsite_restraint,
		TYPE(bond_kind_type),dimension(:),optional,pointer	bond_kind_set,
		TYPE(bend_kind_type),dimension(:),optional,pointer	bend_kind_set,
		TYPE(ub_kind_type),dimension(:),optional,pointer	ub_kind_set,
		TYPE(torsion_kind_type),dimension(:),optional,pointer	torsion_kind_set,
		TYPE(impr_kind_type),dimension(:),optional,pointer	impr_kind_set,
		TYPE(opbend_kind_type),dimension(:),optional,pointer	opbend_kind_set,
		INTEGER,intent(in),optional	nelectron,
		INTEGER,intent(in),optional	nsgf,
		LOGICAL,intent(in),optional	molname_generated
	)

Set the components of a molecule kind.

Author:

MK

Date:

27.08.2003

Version:

1.0

Definition at line 855 of file molecule_kind_types.f90.

References termination::stop_program().

Referenced by force_fields_util::clean_intra_force_kind(), force_fields_all::force_field_pack_bend(), force_fields_all::force_field_pack_bond(), force_fields_all::force_field_pack_impr(), force_fields_all::force_field_pack_opbend(), force_fields_all::force_field_pack_shell(), force_fields_all::force_field_pack_tors(), force_fields_all::force_field_pack_ub(), force_fields_util::force_field_qeff_output(), force_fields_all::force_field_unique_bend(), force_fields_all::force_field_unique_bond(), force_fields_all::force_field_unique_impr(), force_fields_all::force_field_unique_opbend(), force_fields_all::force_field_unique_tors(), force_fields_all::force_field_unique_ub(), num_ao_el_per_molecule(), topology_connectivity_util::topology_connectivity_pack(), and topology_constraint_util::topology_constraint_pack().

Here is the call graph for this function:

Here is the caller graph for this function:

subroutine,public molecule_kind_types::setup_colvar_counters	(	TYPE(colvar_constraint_type),dimension(:),pointer	colv_list,
		TYPE(colvar_counters)	ncolv,
		TYPE(cp_error_type),intent(inout)	error
	)

Definition at line 240 of file molecule_kind_types.f90.

References colvar_types::angle_colvar_id, colvar_types::combine_colvar_id, colvar_types::coord_colvar_id, colvar_types::dfunct_colvar_id, colvar_types::dist_colvar_id, colvar_types::gyration_colvar_id, colvar_types::hydronium_colvar_id, colvar_types::plane_distance_colvar_id, colvar_types::plane_plane_angle_colvar_id, colvar_types::population_colvar_id, colvar_types::qparm_colvar_id, colvar_types::reaction_path_colvar_id, colvar_types::rotation_colvar_id, colvar_types::torsion_colvar_id, colvar_types::xyz_diag_colvar_id, and colvar_types::xyz_outerdiag_colvar_id.

Referenced by allocate_molecule_kind_set(), and topology_constraint_util::topology_constraint_pack().

Here is the caller graph for this function:

subroutine,public molecule_kind_types::write_molecule_kind	(	TYPE(molecule_kind_type),pointer	molecule_kind,
		INTEGER,intent(in)	output_unit,
		TYPE(cp_error_type),intent(inout)	error
	)

Write a molecule kind data set to the output unit.

Author:

MK

Date:

24.09.2003

Version:

1.0

Definition at line 1003 of file molecule_kind_types.f90.

Referenced by write_molecule_kind_set().

Here is the caller graph for this function:

subroutine,public molecule_kind_types::write_molecule_kind_set	(	TYPE(molecule_kind_type),dimension(:),pointer	molecule_kind_set,
		TYPE(section_vals_type),pointer	subsys_section,
		TYPE(cp_error_type),intent(inout)	error
	)

Write a moleculeatomic kind set data set to the output unit.

Author:

MK

Date:

24.09.2003

Version:

1.0

Definition at line 1084 of file molecule_kind_types.f90.

References cp_output_handling::cp_print_key_finished_output(), get_molecule_kind_set(), timings::timeset(), and write_molecule_kind().

Here is the call graph for this function:

---

Variable Documentation

CHARACTER(len=*),parameter,private molecule_kind_types::moduleN = 'molecule_kind_types'

Definition at line 56 of file molecule_kind_types.f90.