Code DetailsΒΆ


The GCMC code will perform niter (control_MC file option) Grand Canonical Monte Carlo trial moves, and accept or reject them based on the Energy produced by the ReaxFF minimization step of the trial geometry. The Monte Carlo algorithm will always accept a step if it results in a decrease of the energy, and accept steps that go up in energy with a probability. This section will give some details about how the code works.

MC Moves (Insert/Delete/Move/Volume)

The GCMC code currently supports 4 types of MC Moves: Insert, Delete, Move (displace), Volume change. The first three moves always change a whole “molecule” of the system, as defined in the control_MC file (a molecule can of course contain only a single atom). Every MC iteration selects one MC Molecule Type from the defined molecules in control_MC at random, followed by a random MC Move (unless there are no molecules of the type in the system, in that case it will do an insert move).

The Insert and Displace (move) MC Moves will generate a random rotation and position for the molecule, and then check if the random positions are within the “RminPl” and “RmaxPl” boundaries (this means no atom in the molecule can be closer to any atom currently in the system than “RminPl”, and it should be within “RmaxPl” distance to an atom in the system). If the conditions are not satisfied, a new set of coordinates is generated and the code checks again. This is repeated a maximum number of “nmctry” times before stopping with an error.

The volume change is controlled by the “ivlim” variable in control_MC. The ivlim sets the volume change limit, and it should be a value between between 0 and 1. The new volume will be calculated like this: Vnew = (1+ivlim)*Vold.

Calculating energies

Because the GCMC simulation adds and deletes atoms or molecules during the runtime, it cannot directly compare the ReaxFF energies for the MC acceptance criteria: inserting a molecule will usually lower the total energy of the system, causing the MC to always accept it, and always reject a deletion. To balance this out, the GCMC code calculates a “corrected” MC energy to compare the trial reaxFF energy with, consisting of the previously accepted ReaxFF energy + the chemical potential (cmpot in control)MC) for the inserted molecule, or the ReaxFF energy - the chemical potential for the deleted molecule. The volume change energy is also corrected, using the following formula:

E_MC_Corr = E_reaxff_last_accept - (Pressure * 0.1439 * (newV-oldV)) + ((1.0/beta) * nInsertedMols * log(newVavail/oldVavail))

where newVavail and oldVavail are calculated from the MC available volume (see the section calculating volumes).

Calculating volumes

The GCMC code can calculate the available volume in a couple of different ways, depending on the ivol setting in control_MC:

  • ivol = 0: volume = total volume - occupied volume - specified vacuum volume (vvacu)
  • ivol = 1: volume = total cell volume
  • ivol = 2: volume = specified accessible volume (vacc)
  • ivol = 3: volume = total cell volume - occupied volume
  • ivol = 4: volume = specified accessible volume (vacc) - occupied volume

Where the occupied volume is calculated by summing up the volumes of the atoms in the geo file that are not specified to be part of an MC type molecule. The volume of an atom is calculated using the average of the covalent atomic radius and the vd Waals radius of the atom, which are found in the reaxff forcefield file (ffield).

the vacc and vvacu options can be specified in the control_MC file to get a more accurate available volume.

Acceptance criteria

An MC move is always accepted if the reaxff energy is lower than the corrected MC energy of the last accepted MC move, or if the energy increase is small enough. If the new energy is higher, the code generates a random number between 0 and 1, and accepts the move if the random number is bigger than:

prob = preFactor * exp(-Beta*deltaE)

Where the prefactor is calculated (for insert and delete moves) using the deBroglie wavelength of the inserted molecules, the number of inserted molecules and the available MC volume of the system.