TUTORIAL 9 : Gibbs ensemble Monte Carlo¶

Author: Tom L. Underwood, t.l.underwood@bath.ac.uk

Introduction¶

The liquid-vapour coexistence curve (i.e. the temperatures and pressures corresponding to the boiling phase transition) is one of the key features of a substance’s phase diagram. An important application of Monte Carlo simulation is to calculate this curve for a given fluid. Monte Carlo is regarded as the method par excellence for such calculations. The reason for this is that in Monte Carlo one can add and remove particles from the system. It turns out that this enables liquid-vapour coexistence to be probed extremely efficiently, more efficiently than if one performed a simulation with a fixed number of particles.

Gibbs ensemble Monte Carlo (GEMC) is a popular method for calculating liquid-vapour coexistence curves. In this tutorial you will use GEMC in DL_MONTE to calculate the liquid-vapour coexistence curve for the Lennard-Jones fluid, in which the particles interact via the Lennard-Jones potential:

$\phi(r) = 4\epsilon\biggl[\Bigl(\frac{\sigma}{r}\Bigr)^{12}-\Bigl(\frac{\sigma}{r}\Bigr)^{6}\biggr],$

where we truncate the interactions at a distance $$r_c=2.5\sigma$$. To elaborate, at various temperatures, you will calculate the gas and liquid densities corresponding to coexistence using GEMC.

Prerequisites¶

This tutorial assumes that the reader is familiar with the basics of DL_MONTE, i.e. can perform simple NVT, NPT and GCMC simulations: see TUTORIAL 1 : NVT Lennard-Jones fluid, TUTORIAL 2 : NPT Lennard-Jones fluid and TUTORIAL 4 : GCMC Lennard-Jones.

Solutions¶

Note that example output and input files for all simulations to be performed in this tutorial can be found in the solutions subdirectory within the tutorial9 directory in the archive containing the tutorial files.

Background and methodology¶

In most simulation techniques the system to be simulated is comprised of one ‘box’, which is subject to periodic boundary conditions and which contains particles whose positions are evolved somehow during the course of the simulation. GEMC is somewhat unusual in that the system is comprised of two simulation boxes. Particles in one box do not interact with particles in the other box. Moreover, in GEMC the (two-box) system is evolved using the following Monte Carlo moves (where we are assuming that the particles are molecules with rotational degrees of freedom):

1. Translate a single molecule: a translation move.
2. Rotate a single molecule: a rotation move.
3. Transfer a molecule from one box to a random position in the other box: we refer to this here as a transfer move.
4. Change the volume of one box by an amount $$\Delta V$$, determined stochastically, while simultaneously changing the the other box by an amount $$-\Delta V$$ so that the total volume of the two-box system is preserved in the move. We will refer to this as a volume move here. (Note however that this volume move is not the same as the volume move used in NPT simulations the Gibbs volume move affects two boxes).

Note that moves 1 and 2 above are also employed in NVT and NPT simulations. Moves 3 and 4 are, however, particular to GEMC. For brevity we do not give the formulae for the acceptance probabilities of the above moves here; such details, as well as further information describing GEMC is provided at the end of this tutorial. Moreover, while we mentioned above that the total volume of the two boxes is conserved in GEMC, it is worth emphasising that the total number of molecules in the system is also conserved, though the number in each box can vary during the simulation as a result of molecules being transferred between the two boxes.

Consider how the phase of a single-component fluid changes with density $$\rho$$ at a fixed temperature $$T$$. Clearly at low densities the fluid will be in the gas phase, and at high densities the fluid will be in the liquid phase. At intermediate densities, however, there is a two-phase region demarcated by the gas and liquid densities corresponding to coexistence, which we denote as $$rho_G$$ and $$\rho_L$$, respecively. The two-phase region is illustrated in the figure below. Note that it only exists below the critical temperature.

For $$rho$$ and $$T$$ within the two-phase region the equilibrium state of the fluid is a mixed system, comprised of gas and liquid phases which coexist, where densities of the gas and liquid are given by the $$rho_G$$ and $$\rho_L$$ appropriate to $$T$$ under consideration. The elegance of GEMC is that if the $$T$$ and initial density $$\rho$$ of the system (i.e. the total number of molecules in the system, over both boxes, divided by the total volume of the system) reside within the two-phase region, then the system will ‘find’ this two-phase equilibrium. It does this by exchanging molecules and volume between the two boxes until one box becomes a gas with $$rho_G$$ and the other box corresponds to the liquid with $$\rho_L$$. It finds this equilibrium relatively quickly because, unlike other methods, in the two-box system there is never a liquid-gas interface.

Once the two-phase equilibrium has been found $$rho_G$$ and $$\rho_L$$ can be obtained from the simulation results by simply measuring the densities of the gas and liquid boxes. We will now demonstrate this using DL_MONTE.

We begin with a GEMC simulation at $$T^*\equiv k_BT/\epsilon = 1.0$$ and $$\rho=0.3$$, which happens to be in the middle of the two-phase region of the phase diagram for the LJ fluid.

FIELD¶

We begin by inspecting the FIELD file (note that the line numbers at the start of each line are not actually present in the file):

  1 2 3 4 5 6 7 8 9 10 11 12 13 14 Lennard-Jones, 2.5*sigma cut-off, sigma=1A, epsilon = k; 2 CONFIGS for Gibbs ensemble CUTOFF 2.5 UNITS k NCONFIGS 2 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 

This file is similar to the one you encountered in the grand-canonical Monte Carlo tutorial. Crucially though, NCONFIGS is set to 2 instead of 1, since GEMC uses two simulation boxes. Thus DL_MONTE will expect to find two configurations in the CONFIG file.

CONFIG¶

Inspecting the CONFIG file, we indeed find two configurations:

  1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 Lennard-Jones starting; particles are molecules, not atoms 0 0 7.93700526 0.0000000 0.0000000 0.0000000 7.93700526 0.0000000 0.0000000 0.0000000 7.93700526 NUMMOL 150 1000 MOLECULE lj 1 1 LJ c 0.139682 0.116455 -0.0535593 MOLECULE lj 1 1 LJ c -0.457034 -0.421912 0.313942 MOLECULE lj 1 1 LJ c -0.269838 0.226045 -0.357893 MOLECULE lj 1 1 LJ c -0.417234 0.0306274 0.173153 ... ... ... MOLECULE lj 1 1 LJ c -0.32143 0.170441 0.344404 MOLECULE lj 1 1 LJ c 0.258839 0.218443 -0.290028 MOLECULE lj 1 1 LJ c -0.481594 0.0323228 -0.447171 Lennard-Jones starting; particles are molecules, not atoms 0 0 7.93700526 0.0000000 0.0000000 0.0000000 7.93700526 0.0000000 0.0000000 0.0000000 7.93700526 NUMMOL 150 1000 MOLECULE lj 1 1 LJ c 0.139682 0.116455 -0.0535593 MOLECULE lj 1 1 LJ c -0.457034 -0.421912 0.313942 MOLECULE lj 1 1 LJ c -0.269838 0.226045 -0.357893 ... 

Note that in this case both configurations are identical. This is the case for the sake of convenience: when setting up the initial configurations of the two boxes, it is easier to make them the same, and both corresponding to the density of interest. One could, however, start with boxes with different configurations. Note also that the second number on the lines immediately below the configuration title lines (containing ‘Lennard-Jones starting; particles…’) is 0. This signifies that the positions of atoms in the following configurations are given in fractional coordinates in the CONFIG file, not Cartesian coordinates as would normally be the case. We do this here for convenience; later we will perform GEMC simulations using different initial densities, and the use of fractional coordinates will make it easier to generate the required CONFIG files.

CONTROL¶

Finally, we come to the CONTROL file:

  1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 Gibbs simulation Lennard-Jones fluid # Comment line use ortho # Flag to use 'fast' functionality for orthorhombic boxes finish ranseed # Use a random seed temperature 1.0 steps 1800000 # Simulation length sample coord 300000 # Frequency to store configurations during simulation stat 300000 # Frequency to print to PTFILE print 300000 # Frequency to print to OUTPUT yamldata 1000 # Frequency to output important data to YAMLDATA files noewald all move molecule 1 100 # Translate molecules, followed by frequency (100) lj move gibbstransfmol 1 100 lj move volume gibbs 1 start 

The key features of this file are the move gibbstransfmol and move volume gibbs directives, which along with the use of two simulation boxes, make the DL_MONTE simulation a GEMC simulation. move gibbstransfmol invokes transfer moves betwen the two boxes. Here we apply the moves to the ‘lj’ molecular species, which is why ‘lj’ is specified in the line following move gibbstransfmol above. move volume gibbs invokes Gibbs volume moves where volume is transfered between the two boxes, but the total volume of the whole system is conserved. As with the other move directives, the frequencies of each move is specified; in the above CONTROL file the ratio of translation moves to transfer moves to volume moves is 100:100:1.

Exercise¶

Create a directory called density_0.3, and copy the CONTROL, CONFIG and FIELD files into that directory. Then perform a DL_MONTE simulation in the directory. The simulation should not take long to complete: 1.5-3 minutes.

Output files¶

GEMC simulations in DL_MONTE create two versions of many output files, one for each simulation box; see the DL_MONTE manual for details. Of importance here are the YAMLDATA files: a GEMC simulation will produce two YAMLDATA files: YAMLDATA-1.000 pertains to simulation box 1, while YAMLDATA-2.000 pertains to simulation box 2. Here are the first few lines of YAMLDATA-2.000 output by an instance of the above simulation:

  1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 temperature: 1.00000000000000E+00 gibbsmols: --- - timestamp: 1000 energy: -1.11660465569217E+02 energyvdw: -1.11660465569217E+02 volume: 4.99999778765834E+02 nmol: [ 146 ] - timestamp: 2000 energy: -2.54952759149814E+02 energyvdw: -2.54952759149814E+02 volume: 4.99998945385850E+02 nmol: [ 143 ] - timestamp: 3000 energy: -2.40232294084996E+02 energyvdw: -2.40232294084996E+02 volume: 4.99997535232507E+02 nmol: [ 132 ] - timestamp: 4000 energy: -2.23217638349257E+02 energyvdw: -2.23217638349257E+02 volume: 4.99997053420530E+02 nmol: [ 128 ] 

The meaning of the data should be obvious. Recall that we are interested in using GEMC to determine the liquid and gas densities corresponding to coexistence at this temperature, and that, if the simulation was successful, then the equilibrated density of one box should correspond to a liquid and the equilibrated density of the other box should correspond to a gas. The density at a give timestep in the simulation can be obtained from the number of molecules in the box and the box’s volume at that timestep. This information can be obtained from YAMLDATA-1.000: see the nmol: and volume: tags in the example above.

Exercise¶

Included with the tutorial files is a script, yaml_to_density_gibbs.sh which can be used to extract a time series of densities from a YAMLDATA-1.000 or YAMLDATA-2.000 file obtained from a DL_MONTE GEMC simulation. Apply the following commands to create two files, density_1.dat and density_2.dat which contain such time series for both boxes.

[tutorial_9]$yaml_to_rho_gibbs.sh YAMLDATA-1.000 > density_1.dat [tutorial_9]$ yaml_to_rho_gibbs.sh YAMLDATA-2.000 > density_2.dat


Then plot the files. You should see that one box equilibrates at the gas density (about 0.05) and the other at the liquid density (about 0.65).

Example plots of density_1.dat and density_2.dat are given below.

In this case box 1 becomes the liquid and box 2 becomes the gas. Note that there is an equilibration time at the beginning of the ssimulation, during which the two boxes ‘find’ the two-phase equilibrium of the system.

Exploring different initial conditions¶

Recall that the atomic coordinates in the CONFIG files are fractional. Recall also that the initial density of the system is 0.3: as can be seen from inspection of the CONFIG file the configuration for each box consists of 150 molecules in a cubic cell with dimension 7.93700526, and hence the density is $$150/7.93700526^3=0.3$$. Now, one could change the initial density of the system by altering the dimensions of both cells in CONFIG; denoting the cell dimension by $$L$$, the density is given by $$\rho=150/L^3$$.

Exercise¶

With this in mind, create a new directory density_0.2, and populate it with the CONTROL, CONFIG and FIELD files used for the simulation described above. Then modify the cell dimensions in the CONFIG file so that it corresponds to an initial system density of 0.2. Then run a DL_MONTE simulation in that directory. Then create density_1.dat and density_2.dat data files as described above, and plot them.

Example plots of density_1.dat and density_2.dat at a density of 0.2 are given below.

Note that the system finds the same two-phase equilibrium: a gas and liquid with densities of $$\approx 0.05$$ and 0.65, respectively. However, you should also see that the equilibration period is longer than for $$\rho=0.3$$. This reflects the fact that the further the initial system density is from the centre of the two-phase region, the longer the GEMC simulation will take to find equilibrium - for this system :rho=0.3 is closer to the centre of the two-phase region than $$\rho=0.2$$.

To cement this point, perform another simulation at $$\rho=0.15$$. You should see that the equilibration time is even longer than for $$\rho=0.2$$.

Finally, perform a simulation at $$\rho=0.01$$. You should see that both boxes remain rigidly at their initial densities. Example plots are shown below.

There are two reasons why this might be the case. One is that the equilibration time is so long that we have yet to observe a discernable change in the boxes towards the two-phase equilibrium. The other possibility is that there is no two-phase equilibrium at this density, i.e. the density resides within the one-phase region of the phase diagram. In this case the two boxes will both equilibrate in the equilibrium phase, and thus will both have the same density. In fact $$\rho=0.01$$ resides within the one-phase region of the phase diagram for this model, explaining our observations.

Calculating the phase diagram¶

We have learned above, for a given temperature, if the GEMC simulation is set up with an initial system density close to the centre of the two-phase region, then equilibration to the two-phase equilibrium will be relatively quick. Once the simulation has found equilibrium, the gas and liquid densities corresponding to coexistence, i.e. $$\rho_G$$ and $$\rho_L$$, can be obtained via simple analysis of the simulation results: $$\rho_G$$ is the equilibrium density of the box with the lower density, and $$\rho_L$$ is the equilibrium density of the box with the higher density.

For this system, $$\rho=0.3$$ has proved to be close to the centre of the two-phase region at $$T=1.0$$. We therefore expect it would be a good initial density to use in GEMC simulations to determine $$\rho_G$$ and $$\rho_L$$ at other temperatures. If, with $$\rho=0.3$$, we find that equilibration is slow, then we can always tweak the density to find a better one.

Exercise¶

Using what you have learned above, use GEMC to come up with values for $$\rho_G$$ and $$\rho_L$$ at the following temperatures: $$T^*=0.8$$, 0.9, 1.0, 1.1, 1.15 and 1.2. Recall that $$T^*\equiv k_BT/\epsilon$$. Hence $$T^*$$, which in the above simulations took the value 1, can be changed by altering $$\epsilon$$ in the FIELD file. Noting that the unit of energy in FIELD is $$k_BT$$ (via the k option for units), the Lennard-Jones $$\epsilon$$ in FIELD should be set to $$1/T^*$$ to realise a reduced temperature of $$T^*$$.

You should find that the gap between $$\rho_G$$ and $$\rho_L$$ narrows as the temperature is increased. This is expected: as can be seen from the schematic phase diagram earlier in this tutorial, the difference between $$\rho_G$$ and $$\rho_L$$ decreases as temperature is increased, and tends to zero at the critical temperature. You should see that something interesting happens at $$T^*=1.2$$. This is very close to the critical temperature. You should see that there are massive fluctuations in the density of both boxes, fluctuations which take the system from liquid to gas and vice versa. In fact, when one box is a liquid the other is a gas, and vice versa. Such fluctuations are characteristic of fluids near the critical point, and complicate analysis of the simulation data. However, methods for analysing data near the critical point do exist, though this is beyond the scope of the current tutorial.

An example of what you might see in your simulations is given below.

Further information¶

• An instructive pedagogical article discussing GEMC for the liquid-gas problem can be found here.
• The Sklog wiki page for GEMC has links to the original references for GEMC, as well as some other interesting links.
• This paper contains plots of the phase diagram for the model considered here: see Fig. 2, dotted curve.