Documentation for module topology

Control for reading in different topologies and coordinates

source: topology.F
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public Subroutines/Functions:

1. If reading in from external file, make sure its there first 2. Generate the connectivity if no information to be read in
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SUBROUTINEconnectivity_control(topology, para_env, qmmm, qmmm_env, subsys_section, force_env_section)

1. If reading in from external file, make sure its there first 2. Generate the connectivity if no information to be read in

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

SUBROUTINEtopology_control(atomic_kind_set, particle_set, molecule_kind_set, molecule_set, colvar_p, gci, root_section, para_env, qmmm, qmmm_env, force_env_section, subsys_section, use_motion_section, exclusions)

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Arguments:
POINTER
:: atomic_kind_set(:) ...
POINTER
:: particle_set(:) ...
POINTER
:: molecule_kind_set(:) ...
POINTER
:: molecule_set(:) ...
POINTER
:: colvar_p(:) ...
POINTER
:: gci ...
POINTER
:: root_section ...
POINTER
:: para_env ...
LOGICAL,
INTENT(in),
OPTIONAL
:: qmmm ...
OPTIONAL, POINTER
:: qmmm_env ...
POINTER
:: force_env_section ...
POINTER
:: subsys_section ...
LOGICAL,
INTENT(in)
:: use_motion_section ...
OPTIONAL, POINTER
:: exclusions(:) ...