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'.
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.
kappa_ij (correction to Berthelot rule):
k11 k12 … k1n k21 k22 … k2n … kn1 kn2 … knn
lamda_ij (correction to Lorentz rule):
l11 l12 … l1n l21 l22 … l2n … ln1 ln2 … lnn
gamma_ij (correction to geometric mean rule):
m11 m12 … m1n m21 m22 … m2n … mn1 mn2 … mnn
The deviations to the Lorentz, Berthelot and geometric mean combining rules for s, e and a or n respectively. kij, lij and mij 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.
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.