Documentation for module topology_generate_util

Collection of subroutine needed for topology related things

source: topology_generate_util.F
Loading...

public Subroutines/Functions:

Using a list of bonds, generate a list of bends
Use info from periodic table and assumptions to generate bonds
Generate a list of torsions from bonds
Using a list of bends, generate a list of impr
Use information from bond list to generate molecule. (ie clustering)
Generates molnames: useful when the connectivity on file does not provide them
Using a list of torsion, generate a list of onfo
The list of Urey-Bradley is equal to the list of bends

SUBROUTINEtopology_generate_bend(topology, subsys_section)

Using a list of bonds, generate a list of bends

Arguments:
INTENT(inout)
:: topology ...
POINTER
:: subsys_section ...

SUBROUTINEtopology_generate_bond(topology, para_env, subsys_section)

Use info from periodic table and assumptions to generate bonds

Arguments:
INTENT(inout)
:: topology ...
POINTER
:: para_env ...
POINTER
:: subsys_section ...

SUBROUTINEtopology_generate_dihe(topology, subsys_section)

Generate a list of torsions from bonds

Arguments:
INTENT(inout)
:: topology ...
POINTER
:: subsys_section ...

SUBROUTINEtopology_generate_impr(topology, subsys_section)

Using a list of bends, generate a list of impr

Arguments:
INTENT(inout)
:: topology ...
POINTER
:: subsys_section ...

SUBROUTINEtopology_generate_molecule(topology, qmmm, qmmm_env, subsys_section)

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

Arguments:
INTENT(inout)
:: topology ...
LOGICAL,
INTENT(in),
OPTIONAL
:: qmmm ...
OPTIONAL, POINTER
:: qmmm_env ...
POINTER
:: subsys_section ...

SUBROUTINEtopology_generate_molname(conn_info, natom, natom_prev, nbond_prev, id_molname)

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

Arguments:
POINTER
:: conn_info ...
INTEGER,
INTENT(in)
:: natom ...
INTEGER,
INTENT(in)
:: natom_prev ...
INTEGER,
INTENT(in)
:: nbond_prev ...
INTEGER,
INTENT(inout)
:: id_molname(:) ...

SUBROUTINEtopology_generate_onfo(topology, subsys_section)

Using a list of torsion, generate a list of onfo

Arguments:
INTENT(inout)
:: topology ...
POINTER
:: subsys_section ...

SUBROUTINEtopology_generate_ub(topology, subsys_section)

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

Arguments:
INTENT(inout)
:: topology ...
POINTER
:: subsys_section ...