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38 atom Lennard-Jones cluster
you@eulerX ~$ module load courses mmm vmd
you@eulerX ~$ mmm-init
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
In this exercise you will test the Lennard-Jones potential. In particular, we will focus on the system described in the following file 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_1.1/38/”.
you@eulerX ~$ cd exercise_1.1/38/
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
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
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
- 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