Input File

This document describes the input file for the Gibbs program.
Each line of the input file is written out, then the input options are explained.

Gibbs Ensemble type ('NVT' or 'NPT')

The type of ensemble, two options 'NVT' or 'NPT'.

Temperature (K)

The temperature for the simulation.

Pressure (in bar), used only for NPT ensemble

The system pressure, only significant when using the NPT ensemble. However, a value must be given when using either ensemble.

Number of LJ / Exp-6 groups in the simulation

The number of unique Lennard-Jones or exponential-6 groups used to form the molecule(s).

Group_no   Group_name  Mass (amu) Epsilon/k_b(K) Sigma(Angstrom)   C   Alpha

List for each group: the group number, name, mass, energy parameter, size parameter, C value and alpha value. The C parameter is used to differentiate between LJ and exp-6 groups. A value of +1 is used for exp-6 groups and a value of -1 is used for LJ groups. The Alpha value indicates the a parameter for the exp-6 potential and the n parameter for the LJ n-6 potential. If using a value of n=12 for the LJ potential, you may want to change the appropriate lines is the file e6molecule.f90 to make the program more efficient.

Cross parameters:

kappa_ij (correction to Berthelot rule):

k₁₁ k₁₂ … k_1n   k₂₁ k₂₂ … k_2n   …   k_n1 k_n2 … k_nn

lamda_ij (correction to Lorentz rule):

l₁₁ l₁₂ … l_1n   l₂₁ l₂₂ … l_2n   …   l_n1 l_n2 … l_nn

gamma_ij (correction to geometric mean rule):

m₁₁ m₁₂ … m_1n   m₂₁ m₂₂ … m_2n   …   m_n1 m_n2 … m_nn

The deviations to the Lorentz, Berthelot and geometric mean combining rules for s, e and a or n respectively. k_ij, l_ij and m_ij are matrices of size (number of LJ /exp-6 groups) X (number of LJ /exp-6 groups). The matrices are entered row by row on a single line.

Number of Coulombic groups in the the simulation

This is exactly analogous to the number of LJ/exp-6 groups. The number of unique point charge groups.

Group_no   Group_name     Mass (amu)    Charge(e)

List for each group: the group number, name, mass and charge value. Note that a molecule's mass is the sum of the masses of the groups that make it up. Hence, listing a mass for a interaction center that has both a LJ/exp-6 site and point charge will result in double counting that center's mass. If the number of Coulombic groups is zero this line must be removed.

Nspecies

The number of different molecules used.

The following section must be repeated for each different molecule.

Species_name     Growth Steps     LJ length     Ionic length

List the species name, number of configurational-bias (CCB) steps used to create the molecule, number of LJ/exp-6 beads in the molecule and number of Coulombic beads in the molecule.

Bead St        Bead End         Bead Type      Group No.

Identification of the beads used to create the molecule.

Growth Step     Attempts   Start Bead   End Bead

Definition of configurational-bias steps.

Bead   Method      IntegerParams      Real Params

Identification of the growth method used to grow each bead. The methods available to grow beads are described in Configurational Bias Growth Methods. The method name should be entered exactly as written in Configurational Bias Growth Methods including letter case.

Read the distribution of molecules from the disk?

When the program starts it has to either create the system from scratch or read a configuration from a file. To create the system from scratch enter .false., to continue from an existing configuration enter .true..

Species      Molecules( Phase 1 )   Molecules( Phase 2 )

For each species in the simulation, list the molecule's name followed by the starting number of molecules in phase 1 and 2. This is only important when the system is created from scratch.

Random number generator seed

This is the starting seed value for the random number generator. Any integer value will do.

Probability of selecting MC move: TransRot, Volume Change, Transfer, Regrow

The relative weight of each Monte Carlo move is listed here. The first number is for translations and rotations, the second is for volume changes, the third for transfer attempts and the last for internal regrowths.

Ratio of translations to rotations

This entry gives the relative weight of the translations and rotations.

Probability of selecting each species for transfer

This gives the relative weight of selecting a given species for transfer. This is only important in multi-component runs. This line should include Nspecies entries.

Probability of selecting each species for Regrowth

Exactly Analogous to the line above, however these weights are for selecting a species to regrow the internal structure.

Number of attemped MC moves for this simulation (Equilibration, Production)

This line requires two entries, the length of the equalibration phase and that of the production phase in terms of attempted Monte Carlo moves.

Number of blocks in production period for error estimation

This number indicates how many blocks the production phase should be separated into to estimate the uncertainties.

Number of attempted MC moves per cycle

This number indicates how many Monte Carlo steps define a cycle. At the end of a cycle information is written to the screen and to a file.

Number of attempted MC moves for temporary storage of configuration

This number indicates how many Monte Carlo steps progress before the configuration is stored. At this point the energy-particle number histogram is also written to disk.

Number of attempted MC moves for changing max % displacement etc.

This specifies the number of MC steps during the equilibration phase after which the maximum particle displacement, rotation and volume change size are changed to achieve a target fraction of moves.