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exercises:2018_ethz_mmm:lennard_jones_cluster_2018

38 atom Lennard-Jones cluster

(picture by Luke Abraham)

All files of this exercise be downloaded directly from the wiki: exercise_1.1.zip

Download the 1.1 exercise into your EXERCISES folder and unzip it.

max@qmobile:~$cd ; cd EXERCISES max@qmobile:~$ wget http://www.cp2k.org/_media/exercises:2018_ethz_mmm:exercise_1.1.zip
max@qmobile:~$unzip exercises:2018_ethz_mmm:exercise_1.1.zip max@qmobile:~$ cd exercise_1.1

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:

The command to run cp2k is the following (with a generic file.inp input file):

max@qmobile:~\$ cp2k.ssmp -i file.inp -o file.out

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 K_b to make units work…).
1 Kelvin*K_b=3.2E-6 Hartree

. Using this conversion factor you can transform the epsilon value into Hartree, and the total energy can be expressed in units of epsilon. The sigma value is in Angstrom.

1. randomize the coordinate files fcc.xyz (which represents the “cubic” structure)
m_xyzrand 1.0 < fcc.xyz > fcc_rand.xyz

Do the same with ico.xyz which represents the icosahedral structure. 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. You will also be asked “value of l” This means the symmetry of the order parameter, which is l=4 in this case.

4. before running the simulation, copy the input coordinate file into in.xyz
cp fcc_rand.xyz in.xyz
5. Before running cp2k, check if the file OPT-pos-1.xyz is already present from a previous run. In that case remove or delete it accordingly. It contains the trajectory of the optimization.
6. run cp2k
cp2k.ssmp -i geo_opt.inp | tee geo_opt.out

(to see the output on the screen as well), or AS AN ALTERNATIVE

cp2k.ssmp -i geo_opt.inp > geo_opt.out

(to retain the output in the geo_opt.out file only)

7. in the output file, grep the final energy
grep "ENERGY|“ geo_opt.out

and transform it in the unit of the paper (epsilon units)

8. Open vmd and play with the optimization trajectory
vmd OPT-pos-1.xyz

9. 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
10. plot q4 and energies with gnuplot (ask the teacher)
11. have a look at the myq4 script
nano myq4
12. 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
13. Run the bash script
./curve

Look inside, and try to understand what you get.

14. create a FCC_OUT subdirectory (mkdir FCC_OUT ; cd FCC_OUT) and copy there the files you want to keep; then go back one dir (cd ..), delete all the OPT* files (rm OPT* ) and repeat the exercise with ico.xyz
Assignment:
1. Report the energy of the minima, compare it with the ones of the initial configurations.
2. After converting the energy into “epsilon” units, estimate the number of bonds in the cluster, assuming a pairwise interaction.
3. Plot q4 vs. energy and q4 vs. optimization steps, for the two cases. Discuss the results. Are the minima in two separate basins?
4. Report the value of the order parameter of the minumum, and discuss what you see
5. Use “gnuplot” to make the output of “./curve” understandable, discuss the results.
exercises/2018_ethz_mmm/lennard_jones_cluster_2018.txt · Last modified: 2018/04/14 16:50 by oschuett