3.2. Example: 38 Lennard-Jones Particles

Tip

The sample input and output files can be found in testfiles/atom/1-lj38.

The system here is composed of 38 particles interacting with Lennard-Jones potential. We want to find its global minimum.

Step 1: call abcinp to generate input files:

$ abcinp lj38 1 LennardJones 5.0 30 300 5 30 38 C
Parameters for atom 0: sigma epsilon > 1.4 1.0

This meaning of arguments of abcinp is explained Build atom Input. You will see that three files are generated: lj38.inp, lj38.par, and lj38i.xyz

Step 2: Run the global optimization:

$ atom lj38.inp > lj38.out

After a few seconds, you will find several new files:

  • lj38.out The main output file.

  • lj38.xyz The global minimum in XYZ format. It can be read by for example, VMD, CYLView, or VESTA.

  • lj38.gjf The global minimum in Gaussian input format. It can be read by for example, GaussView.

  • lj38-LM A folder containing all local minima, each one having two files in XYZ and Gaussian input format, respectively. They are sorted in energy-increasing order, for example, 0.xyz is lower in energy than 13.xyz.

  • abcluster*.xyz/gjf The file containing the currently found global minimum during the running of atom. You can check the current stable structure before atom terminates. It it crashes, one can use this abcluster*.xyz to start a new optimization.

Now, you can check the global minimal energy in lj38.out:

lj38.out
    -- Results Report --
    * 30 LMs will be saved in [ lj38-LM ].
        #          Energy      Match-RMSD
        0   -173.92842659      0.00000000
        1   -173.25237842      0.71507423
        2   -173.13431701      0.70945024
        3   -172.95863341      0.76108783
        4   -172.87773641      0.76045325
        5   -172.23492649      0.74732850
        6   -172.23071016      0.73688291
        7   -172.22667896      0.73840467
        8   -171.86939588      0.72369028
        9   -171.85602243      0.69971268
       10   -171.79229098      0.83970678
       11   -171.75808589      0.71170034
       12   -171.69540490      0.69620306
       13   -171.64009388      0.67759186
       14   -171.50996865      0.76198085
       15   -171.44256681      0.69102789
       16   -171.43424502      0.65131617
       17   -171.38576546      0.66268896
       18   -171.35733954      0.76830008
       19   -171.34259018      0.68397072
       20   -171.32073147      0.75987386
       21   -171.29716664      0.67851866
       22   -171.27902087      0.69044599
       23   -171.20726248      0.86629661
       24   -171.18001445      0.78347207
       25   -171.14751710      0.76899129
       26   -171.13754901      0.70110475
       27   -171.11143840      0.77154060
       28   -171.10452382      0.64102747
       29   -171.09481231      0.77978973

    * Final Global Minimal Energy : -173.92842659
    * The Global Minimum is saved as: [ lj38.(gjf/xyz) ]

The energies and RMSDs relative to lj38-LM/0.xyz of 30 local minima are listed. Their geometries are stored in lj38-LM. The geometry of the global minimum is lj38.xyz or lj38-LM/0.xyz. This global minimum is visualized below. It is a face-centred-cubic truncated octahedron cluster.

alternate text