molecule_types Module Reference

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

Data Types
type	global_constraint_type
type	local_colvar_constraint_type
type	local_constraint_type
type	local_g3x3_constraint_type
type	local_g4x6_constraint_type
type	local_states_type
type	molecule_type

Functions/Subroutines
subroutine, public	deallocate_global_constraint (gci)
	Deallocate a global constraint.
subroutine, public	allocate_molecule_set (molecule_set, nmolecule)
	Allocate a molecule set.
subroutine, public	deallocate_molecule_set (molecule_set)
	Deallocate a molecule set.
subroutine, public	get_molecule (molecule, molecule_kind, lmi, lci, 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)
	finds for each atom the molecule it belongs to
subroutine, public	get_molecule_set_info (molecule_set, atom_to_mol, mol_to_first_atom, mol_to_last_atom, mol_to_nelectrons, mol_to_nbasis, mol_to_charge, mol_to_multiplicity)
	returns information about molecules in the set.

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)

Function/Subroutine Documentation

deallocate_global_constraint()

subroutine, public molecule_types::deallocate_global_constraint

(

type(global_constraint_type), pointer

gci

)

Deallocate a global constraint.

Parameters

gci

...

History

07.2003 created [fawzi] 01.2014 moved from cp_subsys_release() into separate routine.

Author

Ole Schuett

Definition at line 151 of file molecule_types.F.

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allocate_molecule_set()

subroutine, public molecule_types::allocate_molecule_set	(	type(molecule_type), dimension(:), pointer	molecule_set,
		integer, intent(in)	nmolecule
	)

Allocate a molecule set.

Parameters

molecule_set	...
nmolecule	...

Date

29.08.2003

Author

MK

Version

1.0

Definition at line 201 of file molecule_types.F.

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deallocate_molecule_set()

subroutine, public molecule_types::deallocate_molecule_set

(

type(molecule_type), dimension(:), pointer

molecule_set

)

Deallocate a molecule set.

Parameters

molecule_set

...

Date

29.08.2003

Author

MK

Version

1.0

Definition at line 218 of file molecule_types.F.

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get_molecule()

subroutine, public molecule_types::get_molecule	(	type(molecule_type), intent(in)	molecule,
		type(molecule_kind_type), optional, pointer	molecule_kind,
		type(local_states_type), dimension(:), optional, pointer	lmi,
		type(local_constraint_type), optional, pointer	lci,
		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.

Parameters

molecule	...
molecule_kind	...
lmi	...
lci	...
lg3x3	...
lg4x6	...
lcolv	...
first_atom	...
last_atom	...
first_shell	...
last_shell	...

Date

29.08.2003

Author

MK

Version

1.0

Definition at line 275 of file molecule_types.F.

set_molecule()

subroutine, public molecule_types::set_molecule	(	type(molecule_type), intent(inout)	molecule,
		type(molecule_kind_type), optional, pointer	molecule_kind,
		type(local_states_type), dimension(:), 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.

Parameters

molecule	...
molecule_kind	...
lmi	...
lci	...
lcolv	...
lg3x3	...
lg4x6	...

Date

29.08.2003

Author

MK

Version

1.0

Definition at line 336 of file molecule_types.F.

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set_molecule_set()

subroutine, public molecule_types::set_molecule_set	(	type(molecule_type), dimension(:), intent(inout)	molecule_set,
		integer, dimension(:), intent(in), optional	first_atom,
		integer, dimension(:), intent(in), optional	last_atom
	)

Set a molecule data set.

Parameters

molecule_set	...
first_atom	...
last_atom	...

Date

29.08.2003

Author

MK

Version

1.0

Definition at line 385 of file molecule_types.F.

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molecule_of_atom()

subroutine, public molecule_types::molecule_of_atom	(	type(molecule_type), dimension(:), intent(in)	molecule_set,
		integer, dimension(:), intent(out)	atom_to_mol
	)

finds for each atom the molecule it belongs to

Parameters

molecule_set	...
atom_to_mol	...

Definition at line 422 of file molecule_types.F.

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get_molecule_set_info()

subroutine, public molecule_types::get_molecule_set_info	(	type(molecule_type), dimension(:), intent(in)	molecule_set,
		integer, dimension(:), intent(out), optional	atom_to_mol,
		integer, dimension(:), intent(out), optional	mol_to_first_atom,
		integer, dimension(:), intent(out), optional	mol_to_last_atom,
		integer, dimension(:), intent(out), optional	mol_to_nelectrons,
		integer, dimension(:), intent(out), optional	mol_to_nbasis,
		integer, dimension(:), intent(out), optional	mol_to_charge,
		integer, dimension(:), intent(out), optional	mol_to_multiplicity
	)

returns information about molecules in the set.

Parameters

molecule_set	...
atom_to_mol	...
mol_to_first_atom	...
mol_to_last_atom	...
mol_to_nelectrons	...
mol_to_nbasis	...
mol_to_charge	...
mol_to_multiplicity	...

History

2011.06 created [Rustam Z Khaliullin]

Author

Rustam Z Khaliullin

Definition at line 451 of file molecule_types.F.

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