molecule_types_new Namespace Reference

Define the data structure for the molecule information. More...

Classes
struct	local_colvar_constraint_type
struct	local_g3x3_constraint_type
struct	local_g4x6_constraint_type
struct	local_molecule_type
struct	local_constraint_type
struct	global_constraint_type
struct	molecule_type
Functions
subroutine, public	allocate_molecule_set (molecule_set, nmolecule, error)
	Allocate a molecule set.
subroutine, public	deallocate_molecule_set (molecule_set, error)
	Deallocate a molecule set.
subroutine, public	get_molecule (molecule, molecule_kind, lmi, lg3x3, lg4x6, lcolv, first_atom, last_atom, first_shell, last_shell)
	Get components from a molecule data set.
subroutine, public	set_molecule (molecule, molecule_kind, lmi, lci, lcolv, lg3x3, lg4x6)
	Set a molecule data set.
subroutine, public	set_molecule_set (molecule_set, first_atom, last_atom)
	Set a molecule data set.
subroutine, public	molecule_of_atom (molecule_set, atom_to_mol, error)
	finds for each atom the molecule it belongs to
Variables
CHARACTER(len=*), parameter, private	moduleN = 'molecule_types_new'

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Detailed Description

Define the data structure for the molecule information.

History

JGH (22.05.2004) add last_atom information Teodoro Laino [tlaino] 12.2008 - Preparing for VIRTUAL SITE constraints (patch by Marcel Baer)

Author:

MK (29.08.2003)

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Function Documentation

subroutine,public molecule_types_new::allocate_molecule_set	(	TYPE(molecule_type),dimension(:),pointer	molecule_set,
		INTEGER,intent(in)	nmolecule,
		TYPE(cp_error_type),intent(inout)	error
	)

Allocate a molecule set.

Author:

MK

Date:

29.08.2003

Version:

1.0

Definition at line 141 of file molecule_types_new.f90.

References deallocate_molecule_set().

Referenced by topology_connectivity_util::topology_connectivity_pack().

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subroutine,public molecule_types_new::deallocate_molecule_set	(	TYPE(molecule_type),dimension(:),pointer	molecule_set,
		TYPE(cp_error_type),intent(inout)	error
	)

Deallocate a molecule set.

Author:

MK

Date:

29.08.2003

Version:

1.0

Definition at line 177 of file molecule_types_new.f90.

Referenced by allocate_molecule_set(), and mol_new_list_types::mol_new_list_release().

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subroutine,public molecule_types_new::get_molecule	(	TYPE(molecule_type),pointer	molecule,
		TYPE(molecule_kind_type),optional,pointer	molecule_kind,
		TYPE(local_molecule_type),optional,pointer	lmi,
		TYPE(local_g3x3_constraint_type),dimension( : ),optional,pointer	lg3x3,
		TYPE(local_g4x6_constraint_type),dimension( : ),optional,pointer	lg4x6,
		TYPE(local_colvar_constraint_type),dimension(:),optional,pointer	lcolv,
		INTEGER,optional	first_atom,
		INTEGER,optional	last_atom,
		INTEGER,optional	first_shell,
		INTEGER,optional	last_shell
	)

Get components from a molecule data set.

Author:

MK

Date:

29.08.2003

Version:

1.0

Definition at line 247 of file molecule_types_new.f90.

Referenced by thermostat_mapping::adiabatic_mapping_region_low(), thermostat_mapping::adiabatic_region_evaluate(), al_system_dynamics::al_OU_step(), reftraj_util::compute_msd_reftraj(), integrator_utils::damp_v_particle_set(), integrator_utils::damp_v_velocity(), input_cp2k_restarts::dump_coordinates_cp2k(), al_system_dynamics::dump_vel(), colvar_utils::eval_colv_int(), 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(), thermostat_utils::get_adiabatic_region_info(), thermostat_utils::get_defined_region_info(), constraint_util::getold(), reftraj_util::initialize_msd_reftraj(), thermostat_utils::ke_region_particles(), thermostat_mapping::mapping_region_evaluate(), thermostat_mapping::massive_list_generate(), molecule_of_atom(), thermostat_utils::momentum_region_particles(), constraint_util::pv_constraint(), qmmm_topology_util::qmmm_connectivity_control(), constraint_3x3::rattle_3x3_int(), constraint_4x6::rattle_4x6_int(), constraint_clv::rattle_colv_int(), constraint_3x3::rattle_roll_3x3_int(), constraint_4x6::rattle_roll_4x6_int(), constraint_clv::rattle_roll_colv_int(), restraint::restraint_3x3_int(), restraint::restraint_4x6_int(), restraint::restraint_colv_int(), input_cp2k_restarts::section_coord_val_set(), thermostat_utils::setup_adiabatic_thermostat_info(), thermostat_utils::setup_thermostat_subsys(), constraint_3x3::shake_3x3_int(), constraint_4x6::shake_4x6_int(), constraint_clv::shake_colv_int(), constraint_3x3::shake_roll_3x3_int(), constraint_4x6::shake_roll_4x6_int(), constraint_clv::shake_roll_colv_int(), constraint_vsite::shake_vsite_int(), thermostat_mapping::thermostat_mapping_region_low(), topology_constraint_util::topology_constraint_pack(), topology_coordinate_util::topology_coordinate_pack(), and thermostat_utils::vel_rescale_particles().

subroutine,public molecule_types_new::molecule_of_atom	(	TYPE(molecule_type),dimension(:),pointer	molecule_set,
		INTEGER,dimension(:),intent(out)	atom_to_mol,
		TYPE(cp_error_type),intent(inout)	error
	)

finds for each atom the molecule it belongs to

Definition at line 430 of file molecule_types_new.f90.

References get_molecule().

Referenced by dm_ls_scf::ls_scf_create(), and qs_energy::qs_energies_scf().

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subroutine,public molecule_types_new::set_molecule	(	TYPE(molecule_type),pointer	molecule,
		TYPE(molecule_kind_type),optional,pointer	molecule_kind,
		TYPE(local_molecule_type),optional,pointer	lmi,
		TYPE(local_constraint_type),optional,pointer	lci,
		TYPE(local_colvar_constraint_type),dimension(:),optional,pointer	lcolv,
		TYPE(local_g3x3_constraint_type),dimension( : ),optional,pointer	lg3x3,
		TYPE(local_g4x6_constraint_type),dimension( : ),optional,pointer	lg4x6
	)

Set a molecule data set.

Author:

MK

Date:

29.08.2003

Version:

1.0

Definition at line 315 of file molecule_types_new.f90.

subroutine,public molecule_types_new::set_molecule_set	(	TYPE(molecule_type),dimension(:),pointer	molecule_set,
		INTEGER,dimension(:),intent(in),optional	first_atom,
		INTEGER,dimension(:),intent(in),optional	last_atom
	)

Set a molecule data set.

Author:

MK

Date:

29.08.2003

Version:

1.0

Definition at line 377 of file molecule_types_new.f90.

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Variable Documentation

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

Definition at line 38 of file molecule_types_new.f90.