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38 atom Lennard-Jones cluster

TO USE THE FUNCTION LIBRARY (VERSION UP TO DATE) IN THE INTERACTIVE SHELL:

you@eulerX ~$ module load courses mmm vmd

you@eulerX ~$ mmm-init

REMEMBER: this is the command to load the module for the cp2k program:

you@eulerX ~$ module load cp2k

and to submit the job (note: since all the examples of this week are ultrafast, we will run them interactively, and NOT on a compute node. This is not the normal procedure for the next lectures).

you@eulerX ~$ cp2k.popt -i file.inp -o file.out

Download the 1.1 exercise into your $HOME folder and unzip it.

you@eulerX ~$ wget http://www.cp2k.org/_media/exercises:2017_ethz_mmm:exercise_1.1.zip
you@eulerX ~$ unzip exercises:2017_ethz_mmm:exercise_1.1.zip

All files of this exercise (input and scripts are all commented) can be downloaded from the wiki: exercise_1.1.zip

In this exercise you will test the Lennard-Jones potential. In particular, we will focus on the system described in the following paper about the energy landscape of the 38 atom Lennard-Jones cluster:

1999_the_double-funnel_energy_landscape_of_the_38-atom_lennard-jones_cluster.pdf

Login to euler using your nethz credentials. Then go to the directory “exercise_1.1”.

you@eulerX ~$ cd exercise_1.1

Geometry optimization

In this first part you will perform a simple energy optimization, to find the two lowest lying minima in the potential energy surface.

The input file structure of the template is the following:

geo_opt.inp

&GLOBAL
 FLUSH_SHOULD_FLUSH
 PRINT_LEVEL low
 PROJECT geo_opt_bfgs
 RUN_TYPE geo_opt
 WALLTIME 600
&END GLOBAL

&MOTION
 &GEO_OPT
  OPTIMIZER BFGS
  MAX_ITER  200
  MAX_DR    0.001
  RMS_DR    0.0003
  MAX_FORCE 0.0001
  RMS_FORCE 0.00003
  &BFGS
   USE_MODEL_HESSIAN yes
  &END BFGS
 &END GEO_OPT
 &PRINT
  &TRAJECTORY on
   FORMAT xyz
   &EACH
    GEO_OPT 1
   &END EACH
  &END TRAJECTORY
 &END PRINT
&END MOTION

&FORCE_EVAL
 METHOD Fist
 STRESS_TENSOR ANALYTICAL
 &MM
    &FORCEFIELD
      &CHARGE
        ATOM Ar
        CHARGE 0.0
      &END
      &NONBONDED
        &LENNARD-JONES
          atoms Ar Ar
          EPSILON 119.8
          SIGMA 3.405
          RCUT 8.4
        &END LENNARD-JONES
      &END NONBONDED
      &CHARGE
        ATOM Kr
        CHARGE 0.0
      &END CHARGE
    &END FORCEFIELD
  &POISSON
   PERIODIC NONE
   &EWALD
    EWALD_TYPE none
   &END EWALD
  &END POISSON
  &PRINT
   &FF_INFO OFF
    SPLINE_DATA
    SPLINE_INFO
   &END FF_INFO
  &END PRINT
 &END MM
 &PRINT
  &FORCES off
  &END FORCES
  &GRID_INFORMATION
  &END GRID_INFORMATION
  &PROGRAM_RUN_INFO
   &EACH
    GEO_OPT 1
   &END EACH
  &END PROGRAM_RUN_INFO
  &STRESS_TENSOR
   &EACH
    GEO_OPT 1
   &END EACH
  &END STRESS_TENSOR
 &END PRINT
 &SUBSYS
  &CELL
   A      100 0 0
   B      0   100 0
   C      0 0 100
   PERIODIC NONE
  &END CELL
  &TOPOLOGY
      COORD_FILE_NAME in.xyz
      COORDINATE xyz
  &END
  &PRINT
   &CELL
   &END CELL
   &KINDS
   &END KINDS
   &MOLECULES OFF
   &END MOLECULES
   &SYMMETRY
   &END SYMMETRY
  &END PRINT
 &END SUBSYS
&END FORCE_EVAL

NOTE ON THE UNITS: CP2K USES SO CALLED “atomic units”. Meaning that the resulting energies are expressed in Hartree, 1 Hartree=27.2114 eV. In the input file, the epsilon value (depth of the well) is expressed in KT units, namely, in “temperature” units (there is a Boltzmann constant to make units work…). The sigma value is in Angstrom.

Ordered List Item

c2h2.chain

At this point submit the job grid, first loading the module for cp2k entering

you@eulerX c2h2$ module load cp2k
you@eulerX c2h2$ bsub cp2k.popt < c2h2.chain

fit.gnu

Compare the values that you obtain with the ones listed in the “human readable” potential file c2h2-force_field.pot that was generated by cp2k.

Now, perform the same exercise in another directory for the molecule C2H4.

you@eulerX c2h2$ cd ../c2h4

c2h4.chain

Assignment:

Report the energy of the minimum
Report the value of the order parameter of the minumum, and discuss what you see
Plot the energy curve as a function of the homogeneous contraction/expansion of the cluster