Documentation for module molecule_types

Define the data structure for the molecule information.

source: molecule_types.F
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public Types:

local_molecule_type
...
molecule_type
...
local_constraint_type
...
local_colvar_constraint_type
...
local_g4x6_constraint_type
...
local_g3x3_constraint_type
...
global_constraint_type
...

public Subroutines/Functions:

Allocate a molecule set.
Deallocate a global constraint.
Deallocate a molecule set.
Get components from a molecule data set.
returns information about molecules in the set.
finds for each atom the molecule it belongs to
Set a molecule data set.
Set a molecule data set.

public Types:

TYPE :: global_constraint_type

...


:: ncolv ...
INTEGER
:: ntot ...
INTEGER
:: nrestraint ...
INTEGER
:: ng3x3 ...
INTEGER
:: ng3x3_restraint ...
INTEGER
:: ng4x6 ...
INTEGER
:: ng4x6_restraint ...
INTEGER
:: nvsite ...
INTEGER
:: nvsite_restraint ...
DIMENSION(:), POINTER :: fixd_list ...
DIMENSION(:), POINTER :: colv_list ...
DIMENSION(:), POINTER :: g3x3_list ...
DIMENSION(:), POINTER :: g4x6_list ...
DIMENSION(:), POINTER :: vsite_list ...
DIMENSION(:), POINTER :: lcolv ...
DIMENSION(:), POINTER :: lg3x3 ...
DIMENSION(:), POINTER :: lg4x6 ...

TYPE :: local_colvar_constraint_type

...


LOGICAL
:: init ...
POINTER :: colvar ...
POINTER :: colvar_old ...
REAL(dp)
:: lambda ...
REAL(dp)
:: sigma ...

TYPE :: local_constraint_type

...


DIMENSION(:), POINTER :: lcolv ...
DIMENSION(:), POINTER :: lg3x3 ...
DIMENSION(:), POINTER :: lg4x6 ...

TYPE :: local_g3x3_constraint_type

...


LOGICAL
:: init ...
REAL(dp)
:: scale ...
REAL(dp)
:: scale_old ...
REAL(dp)
:: imass1 ...
REAL(dp)
:: imass2 ...
REAL(dp)
:: imass3 ...
REAL(dp),
DIMENSION(3) :: fa ...
REAL(dp),
DIMENSION(3) :: fb ...
REAL(dp),
DIMENSION(3) :: fc ...
REAL(dp),
DIMENSION(3) :: f_roll1 ...
REAL(dp),
DIMENSION(3) :: f_roll2 ...
REAL(dp),
DIMENSION(3) :: f_roll3 ...
REAL(dp),
DIMENSION(3) :: ra_old ...
REAL(dp),
DIMENSION(3) :: rb_old ...
REAL(dp),
DIMENSION(3) :: rc_old ...
REAL(dp),
DIMENSION(3) :: va ...
REAL(dp),
DIMENSION(3) :: vb ...
REAL(dp),
DIMENSION(3) :: vc ...
REAL(dp),
DIMENSION(3) :: lambda ...
REAL(dp),
DIMENSION(3) :: del_lambda ...
REAL(dp),
DIMENSION(3) :: lambda_old ...
REAL(dp),
DIMENSION(3) :: r0_12 ...
REAL(dp),
DIMENSION(3) :: r0_13 ...
REAL(dp),
DIMENSION(3) :: r0_23 ...
REAL(dp),
DIMENSION(3,3) :: amat ...

TYPE :: local_g4x6_constraint_type

...


LOGICAL
:: init ...
REAL(dp)
:: scale ...
REAL(dp)
:: scale_old ...
REAL(dp)
:: imass1 ...
REAL(dp)
:: imass2 ...
REAL(dp)
:: imass3 ...
REAL(dp)
:: imass4 ...
REAL(dp),
DIMENSION(3) :: fa ...
REAL(dp),
DIMENSION(3) :: fb ...
REAL(dp),
DIMENSION(3) :: fc ...
REAL(dp),
DIMENSION(3) :: fd ...
REAL(dp),
DIMENSION(3) :: fe ...
REAL(dp),
DIMENSION(3) :: ff ...
REAL(dp),
DIMENSION(3) :: f_roll1 ...
REAL(dp),
DIMENSION(3) :: f_roll2 ...
REAL(dp),
DIMENSION(3) :: f_roll3 ...
REAL(dp),
DIMENSION(3) :: f_roll4 ...
REAL(dp),
DIMENSION(3) :: f_roll5 ...
REAL(dp),
DIMENSION(3) :: f_roll6 ...
REAL(dp),
DIMENSION(3) :: ra_old ...
REAL(dp),
DIMENSION(3) :: rb_old ...
REAL(dp),
DIMENSION(3) :: rc_old ...
REAL(dp),
DIMENSION(3) :: rd_old ...
REAL(dp),
DIMENSION(3) :: re_old ...
REAL(dp),
DIMENSION(3) :: rf_old ...
REAL(dp),
DIMENSION(3) :: va ...
REAL(dp),
DIMENSION(3) :: vb ...
REAL(dp),
DIMENSION(3) :: vc ...
REAL(dp),
DIMENSION(3) :: vd ...
REAL(dp),
DIMENSION(3) :: ve ...
REAL(dp),
DIMENSION(3) :: vf ...
REAL(dp),
DIMENSION(3) :: r0_12 ...
REAL(dp),
DIMENSION(3) :: r0_13 ...
REAL(dp),
DIMENSION(3) :: r0_14 ...
REAL(dp),
DIMENSION(3) :: r0_23 ...
REAL(dp),
DIMENSION(3) :: r0_24 ...
REAL(dp),
DIMENSION(3) :: r0_34 ...
REAL(dp),
DIMENSION(6) :: lambda ...
REAL(dp),
DIMENSION(6) :: del_lambda ...
REAL(dp),
DIMENSION(6) :: lambda_old ...
REAL(dp),
DIMENSION(6,6) :: amat ...

TYPE :: local_molecule_type

...


INTEGER,
DIMENSION(:), POINTER :: states ...
INTEGER
:: nstates ...

TYPE :: molecule_type

...


POINTER :: molecule_kind ...
POINTER :: lmi ...
POINTER :: lci ...
INTEGER
:: first_atom ...
INTEGER
:: last_atom ...
INTEGER
:: first_shell ...
INTEGER
:: last_shell ...

SUBROUTINEallocate_molecule_set(molecule_set, nmolecule)

Allocate a molecule set.

Arguments:
POINTER
:: molecule_set(:) ...
INTEGER,
INTENT(in)
:: nmolecule ...

SUBROUTINEdeallocate_global_constraint(gci)

Deallocate a global constraint.

Arguments:
POINTER
:: gci ...

SUBROUTINEdeallocate_molecule_set(molecule_set)

Deallocate a molecule set.

Arguments:
POINTER
:: molecule_set(:) ...

SUBROUTINEget_molecule(molecule, molecule_kind, lmi, lci, lg3x3, lg4x6, lcolv, first_atom, last_atom, first_shell, last_shell)

Get components from a molecule data set.

Arguments:
POINTER
:: molecule ...
OPTIONAL, POINTER
:: molecule_kind ...
OPTIONAL, POINTER
:: lmi ...
OPTIONAL, POINTER
:: lci ...
OPTIONAL, POINTER
:: lg3x3(:) ...
OPTIONAL, POINTER
:: lg4x6(:) ...
OPTIONAL, POINTER
:: lcolv(:) ...
INTEGER,
OPTIONAL
:: first_atom ...
INTEGER,
OPTIONAL
:: last_atom ...
INTEGER,
OPTIONAL
:: first_shell ...
INTEGER,
OPTIONAL
:: last_shell ...

SUBROUTINEget_molecule_set_info(molecule_set, atom_to_mol, mol_to_first_atom, mol_to_last_atom, mol_to_nelectrons, mol_to_nbasis, mol_to_charge, mol_to_multiplicity)

returns information about molecules in the set.

Arguments:
POINTER
:: molecule_set(:) ...
INTEGER,
INTENT(out),
OPTIONAL
:: atom_to_mol(:) ...
INTEGER,
INTENT(out),
OPTIONAL
:: mol_to_first_atom(:) ...
INTEGER,
INTENT(out),
OPTIONAL
:: mol_to_last_atom(:) ...
INTEGER,
INTENT(out),
OPTIONAL
:: mol_to_nelectrons(:) ...
INTEGER,
INTENT(out),
OPTIONAL
:: mol_to_nbasis(:) ...
INTEGER,
INTENT(out),
OPTIONAL
:: mol_to_charge(:) ...
INTEGER,
INTENT(out),
OPTIONAL
:: mol_to_multiplicity(:) ...

SUBROUTINEmolecule_of_atom(molecule_set, atom_to_mol)

finds for each atom the molecule it belongs to

Arguments:
POINTER
:: molecule_set(:) ...
INTEGER,
INTENT(out)
:: atom_to_mol(:) ...

SUBROUTINEset_molecule(molecule, molecule_kind, lmi, lci, lcolv, lg3x3, lg4x6)

Set a molecule data set.

Arguments:
POINTER
:: molecule ...
OPTIONAL, POINTER
:: molecule_kind ...
OPTIONAL, POINTER
:: lmi ...
OPTIONAL, POINTER
:: lci ...
OPTIONAL, POINTER
:: lcolv(:) ...
OPTIONAL, POINTER
:: lg3x3(:) ...
OPTIONAL, POINTER
:: lg4x6(:) ...

SUBROUTINEset_molecule_set(molecule_set, first_atom, last_atom)

Set a molecule data set.

Arguments:
POINTER
:: molecule_set(:) ...
INTEGER,
INTENT(in),
OPTIONAL
:: first_atom(:) ...
INTEGER,
INTENT(in),
OPTIONAL
:: last_atom(:) ...