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--- exercises:2018_ethz_mmm:lennard_jones_cluster_2018 [2018/02/22 14:33] – dpasserone
+++ exercises:2018_ethz_mmm:lennard_jones_cluster_2018 [2018/02/23 08:48] – dpasserone
@@ Line 6: / Line 6: @@
+<note tip>
+All files of this exercise be downloaded directly from the wiki: {{exercise_1.1.zip|}}
+</note>
+Download the 1.1 exercise into your **EXERCISES** folder and unzip it.
+<code>
+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
+</code>
+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:
+<note tip>{{ :exercises:2017_ethz_mmm:1999_the_double-funnel_energy_landscape_of_the_38-atom_lennard-jones_cluster.pdf |}}
+</note>
+The command to run cp2k is the following (with a generic **file.inp** input file):
 <code>
 max@qmobile:~$ cp2k.ssmp -i file.inp -o file.out
 </code>
+===== 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:
+<code - 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
+</code>
+<note important>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...). <code>1 Kelvin*K_b=3.2E-6 Hartree</code>. 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.**
+</note>
+<note tip>
+  - randomize the coordinate files **fcc.xyz** (which represents the "cubic" structure) <code>m_xyzrand 1.0 < fcc.xyz > fcc_rand.xyz</code>Do the same with **ico.xyz** which represents the icosahedral structure. You can look at all files with **vmd**.
+  - extract the q4 order parameter from **fcc.xyz** and from **fcc_rand.xyz** and compare the values.
+  - <code> python stein.py file.xyz </code>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.
+  - before running the simulation, copy the input coordinate file into in.xyz <code>cp fcc_rand.xyz in.xyz</code>
+  - 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.
+  - run cp2k  <code>cp2k.ssmp -i geo_opt.inp | tee geo_opt.out </code> (to see the output on the screen as well), or **AS AN ALTERNATIVE** <code>cp2k.ssmp -i geo_opt.inp > geo_opt.out </code> (to retain the output in the geo_opt.out file only)
+  - in the output file, grep the final energy <code>grep "ENERGY|“ geo_opt.out</code> and transform it in the unit of the paper (epsilon units)
+  - Open vmd and play with the optimization trajectory <code>vmd OPT-pos-1.xyz</code> (ask the teacher)
+  - apply the script **myq4** to the optimization trajectory: this generates a list of q4 and energies for the whole trajectory. <code>./myq4 OPT-pos-1.xyz > fcc.ene.q4</code>
+  - plot q4 and energies with **gnuplot** (ask the teacher)
+  - have a look at the myq4 script <code>nano myq4</code>
+  - repeat for the ico.xyz starting point, don't forget to first copy/remove the files appropriately. For example: <code>mkdir FCC ; mv OPT* FCC ; mv geo_opt.out FCC</code>
+  - Run the bash script <code>./curve</code>Look inside, and try to understand what you get.
+  - 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
+</note>
@@ Line 21: / Line 180: @@
 <note tip>Assignment:
   - Report the energy of the minima, compare it with the ones of the initial configurations.
+  - After converting the energy into "epsilon" units, estimate the number of bonds in the cluster, assuming a pairwise interaction.
   - Plot q4 vs. energy and q4 vs. optimization steps, for the two cases. Discuss the results. Are the minima in two separate basins?
   - Report the value of the order parameter of the minumum, and discuss what you see
   - Use "gnuplot" to make the output of "./curve" understandable, discuss the results.
 </note>
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