topology_generate_util Module Reference

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

Functions/Subroutines
subroutine, public	topology_generate_molname (conn_info, natom, natom_prev, nbond_prev, id_molname)
	Generates molnames: useful when the connectivity on file does not provide them.
subroutine, public	topology_generate_molecule (topology, qmmm, qmmm_env, subsys_section)
	Use information from bond list to generate molecule. (ie clustering)
subroutine, public	topology_generate_bond (topology, para_env, subsys_section)
	Use info from periodic table and assumptions to generate bonds.
subroutine, public	topology_generate_bend (topology, subsys_section)
	Using a list of bonds, generate a list of bends.
subroutine, public	topology_generate_ub (topology, subsys_section)
	The list of Urey-Bradley is equal to the list of bends.
subroutine, public	topology_generate_dihe (topology, subsys_section)
	Generate a list of torsions from bonds.
subroutine, public	topology_generate_impr (topology, subsys_section)
	Using a list of bends, generate a list of impr.
subroutine, public	topology_generate_onfo (topology, subsys_section)
	Using a list of torsion, generate a list of onfo.

Detailed Description

Collection of subroutine needed for topology related things.

History

Teodor Laino 09.2006 - Major rewriting with linear scaling routines

Function/Subroutine Documentation

topology_generate_molname()

subroutine, public topology_generate_util::topology_generate_molname	(	type(connectivity_info_type), pointer	conn_info,
		integer, intent(in)	natom,
		integer, intent(in)	natom_prev,
		integer, intent(in)	nbond_prev,
		integer, dimension(:), intent(inout)	id_molname
	)

Generates molnames: useful when the connectivity on file does not provide them.

Parameters

conn_info	...
natom	...
natom_prev	...
nbond_prev	...
id_molname	...

Author

Teodoro Laino [tlaino] - University of Zurich 10.2008

Definition at line 93 of file topology_generate_util.F.

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topology_generate_molecule()

subroutine, public topology_generate_util::topology_generate_molecule	(	type(topology_parameters_type), intent(inout)	topology,
		logical, intent(in), optional	qmmm,
		type(qmmm_env_mm_type), optional, pointer	qmmm_env,
		type(section_vals_type), pointer	subsys_section
	)

Use information from bond list to generate molecule. (ie clustering)

Parameters

topology	...
qmmm	...
qmmm_env	...
subsys_section	...

Definition at line 182 of file topology_generate_util.F.

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topology_generate_bond()

subroutine, public topology_generate_util::topology_generate_bond	(	type(topology_parameters_type), intent(inout)	topology,
		type(mp_para_env_type), pointer	para_env,
		type(section_vals_type), pointer	subsys_section
	)

Use info from periodic table and assumptions to generate bonds.

Parameters

topology	...
para_env	...
subsys_section	...

Author

Teodoro Laino 09.2006

Definition at line 565 of file topology_generate_util.F.

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topology_generate_bend()

subroutine, public topology_generate_util::topology_generate_bend	(	type(topology_parameters_type), intent(inout)	topology,
		type(section_vals_type), pointer	subsys_section
	)

Using a list of bonds, generate a list of bends.

Parameters

topology	...
subsys_section	...

Author

Teodoro Laino 09.2006

Definition at line 1488 of file topology_generate_util.F.

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topology_generate_ub()

subroutine, public topology_generate_util::topology_generate_ub	(	type(topology_parameters_type), intent(inout)	topology,
		type(section_vals_type), pointer	subsys_section
	)

The list of Urey-Bradley is equal to the list of bends.

Parameters

topology	...
subsys_section	...

Definition at line 1725 of file topology_generate_util.F.

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topology_generate_dihe()

subroutine, public topology_generate_util::topology_generate_dihe	(	type(topology_parameters_type), intent(inout)	topology,
		type(section_vals_type), pointer	subsys_section
	)

Generate a list of torsions from bonds.

Parameters

topology	...
subsys_section	...

Author

Teodoro Laino 09.2006

Definition at line 1768 of file topology_generate_util.F.

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topology_generate_impr()

subroutine, public topology_generate_util::topology_generate_impr	(	type(topology_parameters_type), intent(inout)	topology,
		type(section_vals_type), pointer	subsys_section
	)

Using a list of bends, generate a list of impr.

Parameters

topology	...
subsys_section	...

Author

Teodoro Laino 09.2006

Definition at line 1853 of file topology_generate_util.F.

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topology_generate_onfo()

subroutine, public topology_generate_util::topology_generate_onfo	(	type(topology_parameters_type), intent(inout)	topology,
		type(section_vals_type), pointer	subsys_section
	)

Using a list of torsion, generate a list of onfo.

Parameters

topology	...
subsys_section	...

Definition at line 1960 of file topology_generate_util.F.

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