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exercises:2018_ethz_mmm:lennard_jones_cluster_2018

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# 38 atom Lennard-Jones cluster

(picture by Luke Abraham)

The command to run cp2k is the following:

max@qmobile:~$cp2k.ssmp -i file.inp -o file.out Download the 1.1 exercise into your$HOME folder and unzip it.

max@qmobile:~$<note tip>wget http://www.cp2k.org/_media/exercises:2018_ethz_mmm:exercise_1.1.zip</note> max@qmobile:~$ unzip exercises:2018_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 paper about the energy landscape of the 38 atom Lennard-Jones cluster:

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

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.
1. randomize the coordinate files fcc.xyz
m_xyzrand 1.0 < fcc.xyz > fcc_rand.xyz

Do the same with ico.xyz. You can look at all files with vmd.

2. extract the q4 order parameter from fcc.xyz and from fcc_rand.xyz and compare the values.
3.  python stein.py file.xyz

You will be asked the cutoff radius for the neighbors, it is 1.391 in sigma units. You should input it in Angstrom.

4. before running the simulation, copy the input coordinate file into in.xyz
cp fcc_rand.xyz in.xyz
5. run cp2k
cp2k.ssmp -i geo_opt.inp -o geo_opt.out
6. in the output file, note the final energy, transform it in the unit of the paper (epsilon units)
7. Open vmd and play with the optimization trajectory
vmd OPT-pos-1.xyz

8. apply the script myq4 to the optimization trajectory: this generates a list of q4 and energies for the whole trajectory.
./myq4 OPT-pos-1.xyz > fcc.ene.q4
9. plot q4 and energies with gnuplot (ask the teacher)
10. have a look at the myq4 script
nano myq4
11. repeat for the ico.xyz starting point, don't forget to first copy/remove the files appropriately. For example:
mkdir FCC ; mv OPT* FCC ; mv geo_opt.out FCC
12. finally, run the bash script
./curve

. Look inside, and try to understand what you get.

Assignment:
1. Report the energy of the minima, compare it with the ones of the initial configurations.
2. Plot q4 vs. energy and q4 vs. optimization steps, for the two cases. Discuss the results. Are the minima in two separate basins?
3. Report the value of the order parameter of the minumum, and discuss what you see
4. Use “gnuplot” to make the output of “./curve” understandable, discuss the results.
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