topology_util Module Reference

Collection of subroutine needed for topology related things. More...

Data Types
type	array1_list_type
type	array2_list_type
interface	reorder_structure

Functions/Subroutines
subroutine, public	topology_reorder_atoms (topology, qmmm, qmmm_env_mm, subsys_section, force_env_section)
	...
recursive subroutine, public	reorder_list_array (ilist1, ilist2, ilist3, ilist4, nsize, ndim)
	Order arrays of lists.
recursive subroutine, public	give_back_molecule (icheck, bond_list, i, mol_natom, mol_map, my_mol)
	...
recursive subroutine, public	tag_molecule (icheck, bond_list, i, my_mol)
	gives back a mapping of molecules.. icheck needs to be initialized with -1
subroutine, public	find_molecule (atom_bond_list, mol_info, mol_name)
	each atom will be assigned a molecule number based on bonded fragments The array mol_info should be initialized with -1 before calling the find_molecule routine
subroutine, public	topology_set_atm_mass (topology, subsys_section)
	Use info from periodic table and set atm_mass.
subroutine, public	topology_molecules_check (topology, subsys_section)
	Check and verify that all molecules of the same kind are bonded the same.
subroutine, public	check_subsys_element (element_in, atom_name_in, element_out, subsys_section, use_mm_map_first)
	Check and returns the ELEMENT label.

Detailed Description

Collection of subroutine needed for topology related things.

History

jgh (23-05-2004) Last atom of molecule information added

Function/Subroutine Documentation

topology_reorder_atoms()

subroutine, public topology_util::topology_reorder_atoms	(	type(topology_parameters_type), intent(inout)	topology,
		logical, intent(in), optional	qmmm,
		type(qmmm_env_mm_type), optional, pointer	qmmm_env_mm,
		type(section_vals_type), pointer	subsys_section,
		type(section_vals_type), pointer	force_env_section
	)

...

Parameters

topology	...
qmmm	...
qmmm_env_mm	...
subsys_section	...
force_env_section	...

History

Teodoro Laino 09.2006 - Rewritten with a graph matching algorithm

Definition at line 87 of file topology_util.F.

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reorder_list_array()

recursive subroutine, public topology_util::reorder_list_array	(	integer, dimension(:), pointer	ilist1,
		integer, dimension(:), optional, pointer	ilist2,
		integer, dimension(:), optional, pointer	ilist3,
		integer, dimension(:), optional, pointer	ilist4,
		integer, intent(in)	nsize,
		integer, intent(in)	ndim
	)

Order arrays of lists.

Parameters

Ilist1	...
Ilist2	...
Ilist3	...
Ilist4	...
nsize	...
ndim	...

Author

Teodoro Laino 09.2006

Definition at line 594 of file topology_util.F.

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give_back_molecule()

recursive subroutine, public topology_util::give_back_molecule	(	logical, dimension(:), pointer	icheck,
		type(array1_list_type), dimension(:), pointer	bond_list,
		integer, intent(in)	i,
		integer, intent(inout)	mol_natom,
		integer, dimension(:), pointer	mol_map,
		integer, intent(in)	my_mol
	)

...

Parameters

icheck	...
bond_list	...
i	...
mol_natom	...
mol_map	...
my_mol	...

Author

Teodoro Laino 09.2006

Definition at line 710 of file topology_util.F.

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tag_molecule()

recursive subroutine, public topology_util::tag_molecule	(	integer, dimension(:), pointer	icheck,
		type(array1_list_type), dimension(:), pointer	bond_list,
		integer, intent(in)	i,
		integer, intent(in)	my_mol
	)

gives back a mapping of molecules.. icheck needs to be initialized with -1

Parameters

icheck	...
bond_list	...
i	...
my_mol	...

Author

Teodoro Laino 04.2007 - Zurich University

Definition at line 743 of file topology_util.F.

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find_molecule()

subroutine, public topology_util::find_molecule	(	type(array1_list_type), dimension(:), intent(in)	atom_bond_list,
		integer, dimension(:), pointer	mol_info,
		integer, dimension(:), pointer	mol_name
	)

each atom will be assigned a molecule number based on bonded fragments The array mol_info should be initialized with -1 before calling the find_molecule routine

Parameters

atom_bond_list	...
mol_info	...
mol_name	...

Author

Joost 05.2006

Definition at line 862 of file topology_util.F.

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topology_set_atm_mass()

subroutine, public topology_util::topology_set_atm_mass	(	type(topology_parameters_type), intent(inout)	topology,
		type(section_vals_type), pointer	subsys_section
	)

Use info from periodic table and set atm_mass.

Parameters

topology	...
subsys_section	...

Definition at line 917 of file topology_util.F.

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topology_molecules_check()

subroutine, public topology_util::topology_molecules_check	(	type(topology_parameters_type), intent(inout)	topology,
		type(section_vals_type), pointer	subsys_section
	)

Check and verify that all molecules of the same kind are bonded the same.

Parameters

topology	...
subsys_section	...

Definition at line 995 of file topology_util.F.

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check_subsys_element()

subroutine, public topology_util::check_subsys_element	(	character(len=*), intent(in)	element_in,
		character(len=*), intent(in)	atom_name_in,
		character(len=default_string_length), intent(out)	element_out,
		type(section_vals_type), pointer	subsys_section,
		logical	use_mm_map_first
	)

Check and returns the ELEMENT label.

Parameters

element_in	...
atom_name_in	...
element_out	...
subsys_section	...
use_mm_map_first	...

History

12.2005 created [teo]

Author

Teodoro Laino

Definition at line 1143 of file topology_util.F.

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