Input File

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

Number of hamiltonians to be studied

The number of Hamiltonians (potential models) run during the simulation.

Temperature(s) (K)

The temperature that each of the Hamiltonians are run at.

Log of Activity(s)

The activity, defined as exp(-bm)/q(T), that each of the Hamiltonians are run at.

Volume of simulation box ( Cubic Angstroms )

Volume of simulation cell. The same volume is used for all Hamiltonians

Energy Bin Width ( K )

The bin width for the energy histogram.

Number of stages for changing temperature and hamiltonian weights

The number of times during the simulation that the temperature and activity are adjusted to follow the behavior of the first Hamiltonian and/or the weight of each Hamiltonian is adjusted such that each Hamiltonian is sampled with approximately the same frequency. This line of input is coupled to the information at the bottom of the input file. If a single Hamiltonian is being simulated, simply enter a value of 1.

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)

List for each group: the group number, group name and group mass.

Hamiltonian_no     Group_no     Epsilon/k_b(K)     sigma(Angstrom)     C     Alpha

For each Hamiltonian list the properties of each group. The Cparameter is used to differentiate between LJ and exp-6 groups. A value of +1 is us 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 for Hamiltonian i:

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)

List for each group: the group number, group name and group mass. 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.

Hamiltonian     Group_no     Charge (e)

For each Hamiltonian list the properties of each Coulombic group. If the number of Coulombic groups is zero this line must be removed.

Number of Reservoir Structures

The number of unique reservoir structures used. For each reservoir structure a file reserv_?.dat must exist.

Number of structures per reservoir

The number of structures kept in each reservoir.

Nspecies

The number of different molecules used.

The following section must be repeated for each different molecule.

Species_name     ER Steps     EE Steps     Growth Steps     LJ length     Ionic length

List the species name, number of early rejection (ER) steps used to grow the molecule, number of expanded ensemble (EE) steps used to insert the molecule, 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.

ER Step     Start Step     End Step

Definition of early rejection steps.

Expanded Ensemble Alpha values for each bead
Bead       Alpha values for each EE step

Definition of expanded ensemble steps. List the EE step followed by the damping values at each step.

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     Initial Molecules

For each species in the simulation, list the molecule's name followed by the starting number of molecules. 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: Trans/Rot, Creation/Destruction, Regrowth

The relative weight of each Monte Carlo move is listed here. The first number is for translations and rotations, the second is for creations and destructions and the third is 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 Creation/Destruction

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 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 and maximum rotation are changed to achieve a target fraction of moves.

Number of attempted MC moves for changing EE Weights

Number of MC steps after which the expanded ensemble steps are adjusted. Not important if a single EE step is used.

Number of attempted MC moves before updating reservoir

After this many MC steps the reservoir structures are refreshed.

Number of attemped MC moves per histogram collection

The rate at which observations are added to the histogram.

Type of histogram ( 'matrix' or 'list' )

If 'matrix', the histogram is written to disk in a condensed matrix output. If 'list', the histogram is written to disk as a series of individual obserations.

Stages for changing temperature and hamiltonian weights information
Total steps     Before Avg     Stop Ham     Repeat

This is used to tell the program when and how to adjust the temperatures, activities and weights of the Hamiltonians. This information is coupled to the "Number of stages for changing temperature and Hamiltonian weighhts" line above.

Total Steps - The number of steps to progress until the temperatures, activities and/or weights are adjusted.

Before Avg - The number of steps (out of the total number of steps) to wait until the program starts to collect data which is used to adjust the temperatures, activities and/or weights.

Stop Ham - Indicates what to adjust. The absolute value of this number indicates the "critical" Hamiltonian number for adjusting the weights. The weights of each of the Hamiltonians that are sampled with greater frequency then the critical Hamiltonian are adjusted. If the number given is larger than the total number of Hamiltonians, then all of the weights are adjusted. If the number is positive, then just the weights are updated. If the number is negative, then the temperatures, activities and weights are all adjusted. If the number is given as -100, the temperatures and activities are adjusted, however the weights are not.

Repeat - How many times to repeat the sequence. The total number of lines plus the sum of the repeat values must be equal to the "Number of stages for ..." given above. If you want to avoid the repeat just put a zero for each case and list individually each step.

If a single Hamiltonian is being run, enter a single line with a value for "Total Steps" greater than the total number of MC steps.

The best way to get a feel for the input file is to look at example input files.