# TUTORIAL 4 : GCMC Lennard-Jones¶

Authors: James Grant (r.j.grant{at}bath.ac.uk), Tom L. Underwood (t.l.underwood{at}bath.ac.uk)

## Introduction¶

Grand Canonical Monte Carlo (GCMC) is so named because it allows sampling from the grand canonical ensemble. In NVT we couple the simulation to a thermostat, with which the system exchanges energy at constant temperature. Similarly with NPT we introduce a barostat which allows volume exchange at constant pressure. GCMC marks a distinction from ensembles that can be modelled with molecular dynamics (MD) because we now allow particles to be added or deleted from the system. This exchange happens at constant chemical potential $$\mu$$ and the ensemble is alternatively known as $$\mu\mathrm{VT}$$ since volume and temperature are also held constant. The total energy, $$E$$ of the system is now defined as

$E=U(\underline{r})+\mu N$

where $$U(\underline{r})$$ is the energy of the configuration and N the number of particles.

## Inputs¶

The CONTROL file needs to be modified as below.

  1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 GCMC Lennard-Jones finish seeds 12 34 56 78 # Seed RNG seeds explicitly to the default temperature 1.4283461511745 # Corresponds to T*=1.1876; # T(in K) = T* / BOLTZMAN steps 10000 # Number of moves to perform in simulation equilibration 0 # Equilibration period: statistics # are gathered after this period print 1000 # Print statistics every 'print' moves stack 1000 # Size of blocks for block averaging to obtain statistics sample coord 10000 # How often to print configurations to ARCHIVE.000 revconformat dlmonte # REVCON file is in DL_MONTE CONFIG format archiveformat dlpoly4 # ARCHIVE.000/HISTORY.000/TRAJECTORY.000 format # In this case: HISTORY.000 in DLPOLY4 style yamldata 1000 move gcinsertmol 1 100 0.7 # Perform insertion/removal moves for lj, a weight 100 # with a min. distance of 0.7 from atoms for inserts lj 0.06177 # Use an activity of 0.06177 # move atom 1 512 # Move atoms with a weight of 512 # LJ core # move volume cubic linear 1 # Move volume, box is cubic, # # linear scaling with a weight of 1 start 

Firstly we need to remove or comment out directives that switch on the neighbour lists nbrlist and maxnonbondnbrs (and verlet). The cost of maintaining the list in GCMC negates the benefits when calculating the energy. In this calculation DL_MONTE is using the activity a rather than the chemical potential $$\mu$$, which are related according to

$a = \exp(\mu/RT)$

where R is the gas constant. Note that the grand-canonical insert/delete moves are performed on the molecule level.

Here we have turned off atom translation moves though there is nothing in principle wrong with allowing these types of moves. However in order to work in the $$\mu\mathrm{VT}$$ ensemble volume moves MUST be switched off. Consider what could happen if both insert/deletes and volume moves were allowed. The acceptance rule for linear displacement using the Metropolis approach for insertions is:

$P_{\mathrm{acc}}([\mathbf{r}_1,N_1] \rightarrow [\mathbf{r}_2,N_2] ) = \min(1, \frac{V\Lambda^{-3}}{N+1} \exp \{- \beta [E(\mathbf{r}_2,N_2) - E(\mathbf{r}_1,N_1)] \} )$

and for deletions is:

$P_{\mathrm{acc}}([\mathbf{r}_1,N_1] \rightarrow [\mathbf{r}_2,N_2] ) = \min(1, \frac{N}{V\Lambda^{-3}}\exp \{- \beta [E(\mathbf{r}_2,N_2) - E(\mathbf{r}_1,N_1)] \} )$

The FIELD and CONFIG files need slight changes in order to work with GCMC in DL_MONTE. First we will consider the FIELD file:

  1 2 3 4 5 6 7 8 9 10 11 12 13 14 Lennard-Jones, 2.5*sigma cut-off, sigma = 1 angstrom, epsilon = 1eV CUTOFF 2.5 UNITS internal NCONFIGS 1 ATOMS 1 LJ core 1.0 0.0 MOLTYPES 1 lj ATOMS 1 1 LJ core 0.0 0.0 0.0 FINISH VDW 1 LJ core LJ core lj 1.0 1.0 CLOSE 

Although the cutoff and units and number of configurations nconfigs remain the same as in NVT and NPT exercises, and there is still 1 atom type and 1 molecule type, the FIELD the block declaring the molecules is different from what was used previously.

In the NVT and NPT cases all the particles were declared to be part of the same molecule. In GCMC each particle should be considered a molecule’ in its own right. To this end, the *maxatom* directive that we used before is now replaced with another directive: *atoms <initial atoms> <max atoms>* which provides a template for the atoms’ coordinates (if there were more atoms in a molecule then the coordinates for all of them would have to be specified).

In principle atoms can be added or removed from a molecule. However in the cases we will consider only molecule will be inserted or deleted, so molecules will have a fixed number of particles, in this case 1. We also define an archetype of the molecule listing the atoms comprising the molecule and their relative coordinates. Again, since we have a single Lennard–Jones particle in each molecule we simply position it at the origin of the reference molecule. The molecule entry is completed with the finish directive and the file is completed with the interactions, in this case a single vdw interaction as before.

Turning to the CONFIG, this is also altered to take account of the changes in the molecule declaration given in the FIELD file:

  1 2 3 4 5 6 7 8 9 10 11 12 13 Lennard-Jones starting configuration rho = 0.125; particles are molecules, not atoms 0 1 10.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 10.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 10.0000000000000000 NUMMOL 8 1000 MOLECULE lj 1 1 LJ core -5.0000000000000000 -5.0000000000000000 -5.0000000000000000 MOLECULE lj 1 1 LJ core 0.0000000000000000 -5.0000000000000000 -5.0000000000000000 etc 

The molecule declaration mirrors that seen in the FIELD file. Each particle must be declared as part of a molecule along with its type and initial and maximum numbers of atoms. The atom/particle declaration and its position then follows as before.

## Exercises¶

The inputs for the GCMC Lennard-Jones tutorial are found in the tutorial_4 directory. Launch DL_MONTE as before. Then run the script:

strip_gcmc.sh


to extract a time sequence of the number of particles in the system. Increase the length of the simulation to establish whether the system has equilibrated. What happens as you systematically vary the temperature and activity (chemical potential)? In OUTPUT.000 the average and fluctuations in the number of particles are printed just before the final energies summary. You can also explore histograms once you have produced the time sequence of adsorbed particles with the script:

hist.sh nmol.dat N
`

where $N$ is the width of each bin used to generate the histogram.