molecule_kind_types Module Reference

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

Data Types
type	atom_type
type	shell_type
type	bond_type
type	bend_type
type	ub_type
type	torsion_type
type	impr_type
type	opbend_type
type	colvar_constraint_type
type	g3x3_constraint_type
type	g4x6_constraint_type
type	vsite_constraint_type
type	fixd_constraint_type
type	local_fixd_constraint_type
type	molecule_kind_type

Functions/Subroutines
subroutine, public	setup_colvar_counters (colv_list, ncolv)
	...
subroutine, public	allocate_molecule_kind_set (molecule_kind_set, nmolecule_kind)
	Allocate and initialize a molecule kind set.
subroutine, public	deallocate_molecule_kind_set (molecule_kind_set)
	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, nelectron_alpha, nelectron_beta, 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	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_set (molecule_kind_set, subsys_section)
	Write a moleculeatomic kind set data set to the output unit.
subroutine, public	write_colvar_constraint (colvar_constraint, icolv, iw)
	Write collective variable constraint information to output unit.
subroutine, public	write_fixd_constraint (fixd_constraint, ifixd, iw)
	Write fix atom constraint information to output unit.
subroutine, public	write_g3x3_constraint (g3x3_constraint, ig3x3, iw)
	Write G3x3 constraint information to output unit.
subroutine, public	write_g4x6_constraint (g4x6_constraint, ig4x6, iw)
	Write G4x6 constraint information to output unit.
subroutine, public	write_vsite_constraint (vsite_constraint, ivsite, iw)
	Write virtual site constraint information to output unit.

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

Matthias Krack (22.08.2003)

Function/Subroutine Documentation

setup_colvar_counters()

subroutine, public molecule_kind_types::setup_colvar_counters	(	type(colvar_constraint_type), dimension(:), pointer	colv_list,
		type(colvar_counters), intent(out)	ncolv )

...

Parameters

colv_list	...
ncolv	...

Definition at line 241 of file molecule_kind_types.F.

Here is the caller graph for this function:

allocate_molecule_kind_set()

subroutine, public molecule_kind_types::allocate_molecule_kind_set	(	type(molecule_kind_type), dimension(:), pointer	molecule_kind_set,
		integer, intent(in)	nmolecule_kind )

Allocate and initialize a molecule kind set.

Parameters

molecule_kind_set	...
nmolecule_kind	...

Date

22.08.2003

Author

Matthias Krack

Version

1.0

Definition at line 328 of file molecule_kind_types.F.

Here is the call graph for this function:

Here is the caller graph for this function:

deallocate_molecule_kind_set()

subroutine, public molecule_kind_types::deallocate_molecule_kind_set

(

type(molecule_kind_type), dimension(:), pointer

molecule_kind_set

)

Deallocate a molecule kind set.

Parameters

molecule_kind_set

...

Date

22.08.2003

Author

Matthias Krack

Version

1.0

Definition at line 355 of file molecule_kind_types.F.

Here is the call graph for this function:

Here is the caller graph for this function:

get_molecule_kind()

subroutine, public molecule_kind_types::get_molecule_kind	(	type(molecule_kind_type), intent(in)	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,
		integer, intent(out), optional	nelectron_alpha,
		integer, intent(out), optional	nelectron_beta,
		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.

Parameters

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	...
nelectron_alpha	...
nelectron_beta	...
bond_kind_set	...
bend_kind_set	...
ub_kind_set	...
impr_kind_set	...
opbend_kind_set	...
torsion_kind_set	...
molname_generated	...

Date

27.08.2003

Author

Matthias Krack

Version

1.0

Definition at line 506 of file molecule_kind_types.F.

get_molecule_kind_set()

subroutine, public molecule_kind_types::get_molecule_kind_set	(	type(molecule_kind_type), dimension(:), intent(in)	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.

Parameters

molecule_kind_set	...
maxatom	...
natom	...
nbond	...
nbend	...
nub	...
ntorsion	...
nimpr	...
nopbend	...
nconstraint	...
nconstraint_fixd	...
nmolecule	...
nrestraints	...

Date

27.08.2003

Author

Matthias Krack

Version

1.0

Definition at line 661 of file molecule_kind_types.F.

Here is the call graph for this function:

Here is the caller graph for this function:

set_molecule_kind()

subroutine, public molecule_kind_types::set_molecule_kind	(	type(molecule_kind_type), intent(inout)	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.

Parameters

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	...

Date

27.08.2003

Author

Matthias Krack

Version

1.0

Definition at line 774 of file molecule_kind_types.F.

Here is the caller graph for this function:

write_molecule_kind_set()

subroutine, public molecule_kind_types::write_molecule_kind_set	(	type(molecule_kind_type), dimension(:), intent(in)	molecule_kind_set,
		type(section_vals_type), intent(in)	subsys_section )

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

Parameters

molecule_kind_set	...
subsys_section	...

Date

24.09.2003

Author

Matthias Krack

Version

1.0

Definition at line 978 of file molecule_kind_types.F.

Here is the call graph for this function:

Here is the caller graph for this function:

write_colvar_constraint()

subroutine, public molecule_kind_types::write_colvar_constraint	(	type(colvar_constraint_type), intent(in), pointer	colvar_constraint,
		integer, intent(in)	icolv,
		integer, intent(in)	iw )

Write collective variable constraint information to output unit.

Parameters

colvar_constraint	Data set of the collective variable constraint
icolv	Collective variable number (index)
iw	Logical unit number of the output unit

Author

Matthias Krack (25.11.2025)

Definition at line 1056 of file molecule_kind_types.F.

Here is the caller graph for this function:

write_fixd_constraint()

subroutine, public molecule_kind_types::write_fixd_constraint	(	type(fixd_constraint_type), intent(in), pointer	fixd_constraint,
		integer, intent(in)	ifixd,
		integer, intent(in)	iw )

Write fix atom constraint information to output unit.

Parameters

fixd_constraint	Data set of the fix atom constraint
ifixd	Fix atom constraint/restraint number (index)
iw	Logical unit number of the output unit

Author

Matthias Krack (26.11.2025)

Definition at line 1155 of file molecule_kind_types.F.

Here is the caller graph for this function:

write_g3x3_constraint()

subroutine, public molecule_kind_types::write_g3x3_constraint	(	type(g3x3_constraint_type), intent(in), pointer	g3x3_constraint,
		integer, intent(in)	ig3x3,
		integer, intent(in)	iw )

Write G3x3 constraint information to output unit.

Parameters

g3x3_constraint	Data set of the g3x3 constraint
ig3x3	G3x3 constraint/restraint number (index)
iw	Logical unit number of the output unit

Author

Matthias Krack (26.11.2025)

Definition at line 1198 of file molecule_kind_types.F.

Here is the caller graph for this function:

write_g4x6_constraint()

subroutine, public molecule_kind_types::write_g4x6_constraint	(	type(g4x6_constraint_type), intent(in), pointer	g4x6_constraint,
		integer, intent(in)	ig4x6,
		integer, intent(in)	iw )

Write G4x6 constraint information to output unit.

Parameters

g4x6_constraint	Data set of the g4x6 constraint
ig4x6	G4x6 constraint/restraint number (index)
iw	Logical unit number of the output unit

Author

Matthias Krack (26.11.2025)

Definition at line 1233 of file molecule_kind_types.F.

Here is the caller graph for this function:

write_vsite_constraint()

subroutine, public molecule_kind_types::write_vsite_constraint	(	type(vsite_constraint_type), intent(in), pointer	vsite_constraint,
		integer, intent(in)	ivsite,
		integer, intent(in)	iw )

Write virtual site constraint information to output unit.

Parameters

vsite_constraint	Data set of the vsite constraint
ivsite	Virtual site constraint/restraint number (index)
iw	Logical unit number of the output unit

Author

Matthias Krack (01.12.2025)

Definition at line 1272 of file molecule_kind_types.F.

Here is the caller graph for this function: