m_globals Module

Maximum length of character string for input line buffer.

Maximum number of MC move types. Type 1: backbone pivot, type 2: side chain crankshaft, type 3: side chain pivot, type 4: backbone restricted pivot, type 5: displacement

Lattice vector of simulation box along x-axis.

Lattice vector of simulation box along y-axis.

Lattice vector of simulation box along z-axis.

Flag specifying boundary condition on the simulation box.

Number of atom_types

(num_atom_types,) array.

(num_atom_types,) array. Population of atoms of each type.

Number of atoms

(num_atoms,) array. For atom i, its type at = atoms(i), charge charge(i), position coordinates(:,i), orientation (if the style requires) orientations(:,i).

(num_atoms,) array.

(3, num_atoms) array

(4, num_atoms) array

Number of bond_types

(num_bond_types,) array

Total number of bonds.

(3, num_bonds) array. Bond i is of type bt = bonds(1,i), directed from atom bonds(2,i) to bonds(3,i).

Number of angle_types

(num_angle_types,) array

Number of angles

(4, num_angles) array. Angle i is of type ant = angles(1,i), incident to atoms angles(2,i), angles(3,i), and angles(4,i).

Number of dihedral_types

(num_dihedral_types,) array

Number of dihedrals

(5, num_dihedrals) array. Dihedral i is of type dt = dihedrals(1,i), incident to atoms dihedrals(2,i), dihedrals(3,i), dihedrals(4,i), and dihedrals(5,i).

Total number of branches (including the backbone)

(3,num_branches) array. Branch i is tethered to atom branches(1,i), contains branches(2,i) atoms, with the beginning atom index branches(3,i).

Number of molecule_types

(num_molecule_types,) array

(num_molecule_types,) array

Number of molecules

(9,num_molecules) array. For molecule i, its type mt = molecules(1,i), containing molecules(2,i) atoms with beginning index molecules(3,i), molecules(4,i) bonds with beginning index molecules(5,i), molecules(6,i) angles with beginning index molecules(7,i), and molecules(8,i) dihedrals with beginning index molecules(9,i).

Number of tethers

(num_tethers,) array

Number of vdw_types

(2, num_vdw_types) array. Stores atom type of interacting pairs, such that at_i >= at_j.

(num_vdw_types,) array.

Number of external fields

(num_externals,) array

Is the system equilibrating? {T, F}

Is this a restart run? {T, F}.

Counter for MC cycles

Counter for MC blocks

Interval for logging (in MC cycles)

Interval for dumping to revive file (in MC cycles)

Number of MC cycles for equilibration

Sampling interval during equilibration (in MC cycles)

Number of MC cycles in each block

Total number of blocks in production run

Use MC pivot moves? {T, F}

Use MC restricted pivot moves? {T, F}

Use MC displacement moves? {T, F}.

Use MC crankshaft moves? {T, F}. If side chains are present, crankshaft moves will operate only on side chain atoms. Otherwise, they will be performed on the backbone atoms.

Use MC pivot (only side chains) moves? {T, F}

Use Verlet neighbor table? {T, F}

Maximum displacement for MC displacement move.

Maximum cutoff for short-ranged forces

Thickness of the skin sphere (same for all)

Name of the file containing the initial configuration

Name of the revive file

Name of the trajectory file

Name of the statistics file

Trajectory object

A tag useful for array jobs, available only as a command line argument

{T, F}

Whether to initialize the random number generator by reading a seed from a file. If read_seed == T, the seed will be read from a file 'random_seed.txt'

{T, F}

Whether to write the random number generator seed. If write_seed == T the seed will be written to a file named 'random_seed.txt'

During equilibration, should the statistics file be written? {T, F}

Should the trajectory be written to file? {T, F}

Bond energy

Angle energy

Dihedral energy

vdw interaction energy

Energetic contribution from tethers

Energetic contribution from external fields

Number of MC moves of each type in an MC cycle.

Number of attempts (first element) & accepts (second element) of MC moves. See above for type details.

Control for excluded atoms in vdw calculation. No exclusion: 0, exclude 1-ring bonded neighbors: 1, exclude 2-ring bonded neighbors: 2, exclude 3-ring bonded neighbors: 3.

Whether to calculate VDW interactions

Whether to calculate electrostatic interactions