Molecular dynamics module

Simulation of argon liquid and gas

Objective: to create a model of argon and study the calculation of thermodynamic properties from a molecular dynamics simulation using DISCOVER

Method: create a box of argon atoms in a face-centered cubic structure. We have done this for you using the program FCC written by Allen and Tildesley. In the face-centered cubic lattice there will be one atom at a vertex (blue) and three located in face-centered positions shown below (violet).

This basic group of four atoms is replicated along the x, y, and z axes N times. Thus, the number of atoms in the unit cell will be NC = 4N3. The f.c.c. lattice for N = 2 is shown to illustrate that there are 8 replications of the basic unit. In early simulations values of N = 3 or N = 4 were used giving NC = 108 or NC = 256. In 1964, Rahman used NC = 6 to give 864 argon atoms.

Step 1. Read in the coordinate file with 864 argon atoms in DISCOVER.

If you use the Molecule/Rendering option and select Ball and Stick the face-centered cubic lattice will have the following appearance on the monitor.

Figure 1. Face-centered cubic lattice of 108 argon atoms.

Note that your file will include 864 atoms.

Use the Molecule/Get command to read in the file rahman_864.car.

The menu choices should default to

Get File Type Archive (this is an MSI file type)

You may either click on the file in the Files value-aid or type in the file name.

File Name will then read [rahman_864.car].

Get Molecule will be automatically selected as RAHMAN_864.

This will be the internal or OBJECT name for the file you have read in.

This file is a collection of 864 argon atoms in a cubic box with periodic boundary conditions applied. The box dimensions are 34.74 Å on a side. This corresponds to a reduced Lennard-Jones density of r* = 0.81 (or a dimensioned density of r = 1.364 g/cm3). Your box dimensions will be different than those here, but the procedure is otherwise the same.

Use the Assembly/Cell command to identify the OBJECT RAHMAN_864 as an assembly.

The menu that appears will have your unit cell parameters.

You may select center in cell in the bottom of the Assembly/Cell menu.

Once you have executed this command your collection of argon atoms should have moved to a new location and should be surrounded by a white box.

You are now ready to set up the calculation.

The arrangement argon in a quasi-solid state is the starting point for molecular dynamics simulations in two stages

  1. equilibration
  2. constant volume dynamics (or constant pressure dynamics)

Use the DISCOVER3 pulldown menu to create a second menu bar below the INSIGHT menu bar. In DISCOVER3 choose the system for study using the Setup/System menu. Under Disco Object Name you should see RAHMAN_864. Make sure that the box is checked (yellow) for PBC On. This turns on periodic boundary conditions in the calculation.

Select Execute.

The Specify/Nonbonds command allows you to specify the cut-off or other treatment of long range interactions. In the Nonbonds menu select the following

PBC Sum Method [Atom_based]

Cutoff Distance [8.0] (the cutoff distance cannot be larger than one half the shortest dimension of the box you have created). The cutoff distance used in the MC and MD calculations should be consistent. The value used in the MC calculations is 5.0 in reduced units. The value used the MD simulation should be appropriately scaled.

Spline width [1.5] (this variable determines the width of the switching function that smoothly switches the potential to zero at the cutoff distance)

Buffer width [0.5] (this determines how far any atom must move before the neighbor list is updated).

Select Execute.

To set up the two stages of dynamics (equilibration and production dynamics) use the Calculate pull-down menu. Under Calculate/Dynamics select the following

Run Time fs [5000.0]

Velocity [Create] (check the box to turn it yellow)

PBC Ensemble [NVT_PBC] (check the box to turn it yellow)

Temperature [desired temperature]

Select execute.

To set up the stages of dynamics use the Calculate pull-down menu. Under Calculate/Dynamics select the following

Run Time fs [20000.0]

Velocity [Current] (check the box to turn it yellow)

PBC Ensemble [NVT_PBC] (check the box to turn it yellow)

Temperature [desired temperature]

Select execute.

To write a history file (e.g. rahman_864.his) that will be used in the data analysis use the Analyze/Output command to generate a menu. Choose the second dynamics stage for analysis (this should be stage 5 dynamics if you have followed everything exactly up to this point).

File type [history] (check the diamond to turn it yellow)

To instruct the INSIGHT program to write an input file that you can modify and run in background mode on the computer go to the Background_Job/Setup_Bkgd_Job menu.

Submission mode [immediate]

Execution mode [cmd_file_only]

Box for

Host [local]

Select Execute

Use the D_run/Run command to write the input file. This file will be called by DISCOVER when you run in background mode.

Once you have written the input file, you will need to include a user-defined force field.

Look at the rahman_864.car file to see a list of the atomic coordinates and the dimensions of the box for periodic boundary conditions. You will also want to check that PBC=ON in this file, meaning that periodic boundary conditions have been activated.

You can examine the file using "more" or the "vi" editor.

In another window (assuming INSIGHT is still running) type

To scroll through the document you hit the space bar. To quit you type q.

Alternatively, you can examine the file using

You will also want to examine the input file rahman_864.inp to see the form of the commands required for DISCOVER. You can modify the temperature or other parameters in the input file using the vi editor.

Note that you can write an input file without using the INSIGHT interface or you can modify the file. You will do this later to change the temperature or density.

In another window, run the job using

It is necessary to run the program in background mode. To do this use the downloadable run_DISCOVER script. The syntax is:

You can write the script to a current directory using the "Save as.." command on you Browser. This script will prompt you for the requested CPU time. This time will typically be less than 3600 seconds, but you can use the default time of 43200 seconds. The default memory is sufficient. We will use one processor for these calculations. The output of the script will be file called rahman_864.job. To submit this job use the command:

To examine the progress of the job observe the *.pek file