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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  =====

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

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