ommp_topology_type Derived Type

type, public :: ommp_topology_type


Inherits

type~~ommp_topology_type~~InheritsGraph type~ommp_topology_type ommp_topology_type type~yale_sparse yale_sparse type~ommp_topology_type->type~yale_sparse conn

Inherited by

type~~ommp_topology_type~~InheritedByGraph type~ommp_topology_type ommp_topology_type type~ommp_system ommp_system type~ommp_system->type~ommp_topology_type top type~ommp_electrostatics_type ommp_electrostatics_type type~ommp_system->type~ommp_electrostatics_type eel type~ommp_bonded_type ommp_bonded_type type~ommp_system->type~ommp_bonded_type bds type~ommp_nonbonded_type ommp_nonbonded_type type~ommp_system->type~ommp_nonbonded_type vdw type~ommp_link_atom_type ommp_link_atom_type type~ommp_system->type~ommp_link_atom_type la type~ommp_electrostatics_type->type~ommp_topology_type top type~ommp_bonded_type->type~ommp_topology_type top type~ommp_nonbonded_type->type~ommp_topology_type top type~ommp_link_atom_type->type~ommp_topology_type mmtop, qmtop, qmmmtop type~ommp_link_atom_type->type~ommp_bonded_type bds type~ommp_qm_helper ommp_qm_helper type~ommp_qm_helper->type~ommp_topology_type qm_top type~ommp_qm_helper->type~ommp_nonbonded_type qm_vdw

Contents

Variables

Source Code

ommp_topology_type

Components

Type Visibility Attributes Name Initial
integer(kind=ip), public :: mm_atoms

number of MM atoms
real(kind=rp), public, allocatable :: cmm(:,:)

Coordinates of MM atoms (3:mm_atoms)
type(yale_sparse), public, allocatable :: conn(:)

connectivity matrices listing atoms separetad by 1, 2, 3 (and 4 -- only for AMOEBA) bonds. 1st element is the adjacency matrix.
logical(kind=lp), public :: use_frozen = .false.

Flag to use the frozen atom feature, if it is set to true frozen array is read/used otherwise all atoms are active
logical(kind=lp), public, allocatable :: frozen(:)

For each atom, if set to true, it will contribute to the total energy but its coordinates are locked to the initial value.
integer(kind=ip), public, allocatable :: atz(:)

The atomic number for each atom of the system, when it is not initialized, it contains only zeros.
logical(kind=lp), public :: atz_initialized = .false.

Initialization flag for atz, when it is filled with actual values it should be set to true
real(kind=rp), public, allocatable :: atmass(:)

The atomic mass for each atom in the system, when it is not initialized it contains only zeros
logical(kind=lp), public :: atmass_initialized = .false.

Initialization flag for atmass, when it is filled with actual values it should be set to true
integer(kind=ip), public, allocatable :: attype(:)

Atom class for each atom in the system. It is only used during certain parameters assignaments; when it is not initialized, it contains only zeros.
logical(kind=lp), public :: attype_initialized = .false.

Initialization flag for attype, when it is filled with actual values it should be set to true
integer(kind=ip), public, allocatable :: atclass(:)

Atom class for each atom in the system. It is only used during certain parameters assignaments; when it is not initialized, it contains only zeros.
logical(kind=lp), public :: atclass_initialized = .false.

Initialization flag for atclass, when it is filled with actual values it should be set to true

Source Code

    type ommp_topology_type
        integer(ip) :: mm_atoms 
        !! number of MM atoms
        real(rp), allocatable :: cmm(:,:)
        !! Coordinates of MM atoms (3:mm_atoms)
        type(yale_sparse), allocatable :: conn(:)
        !! connectivity matrices listing atoms separetad by 1, 2, 3 
        !! (and 4 -- only for AMOEBA) bonds. 1st element is the adjacency 
        !! matrix.
        logical(lp) :: use_frozen = .false.
        !! Flag to use the frozen atom feature, if it is set to true frozen
        !! array is read/used otherwise all atoms are active
        logical(lp), allocatable :: frozen(:)
        !! For each atom, if set to true, it will contribute to the total
        !! energy but its coordinates are locked to the initial value.
        integer(ip), allocatable :: atz(:)
        !! The atomic number for each atom of the system, when it is not 
        !! initialized, it contains only zeros.
        logical(lp) :: atz_initialized = .false.
        !! Initialization flag for atz, when it is filled with actual values
        !! it should be set to true
        real(rp), allocatable :: atmass(:)
        !! The atomic mass for each atom in the system, when it is not initialized
        !! it contains only zeros
        logical(lp) :: atmass_initialized = .false.
        !! Initialization flag for atmass, when it is filled with actual values
        !! it should be set to true
        integer(ip), allocatable :: attype(:)
        !! Atom class for each atom in the system.
        !! It is only used during certain parameters assignaments; when it
        !! is not initialized, it contains only zeros.
        logical(lp) :: attype_initialized = .false.
        !! Initialization flag for attype, when it is filled with actual values
        !! it should be set to true
        integer(ip), allocatable :: atclass(:)
        !! Atom class for each atom in the system.
        !! It is only used during certain parameters assignaments; when it
        !! is not initialized, it contains only zeros.
        logical(lp) :: atclass_initialized = .false.
        !! Initialization flag for atclass, when it is filled with actual values
        !! it should be set to true
    end type ommp_topology_type