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--- exercises:2018_ethz_mmm:index [2018/02/22 14:22] – dpasserone
+++ exercises:2018_ethz_mmm:index [2018/05/25 10:04] – dpasserone
@@ Line 6: / Line 6: @@
   - [[lennard_jones_cluster_2018| 3D 38 Atom Lennard-Jones cluster - optimization ]]
   - [[c2h2_bond_energy_2018|Bond Strength in a molecule]]
-  - [[alanine_dipeptide_2018|Alanine dipeptide: Ramachandran plot]]
-====== m_ bash functions ======
+===== Lecture 2 =====
+  - [[H2O_MD| Molecular dynamics of water ]]
-We have programmed in the virtual machine some useful bash functions. They all start with **m_** and can be called from the command line.
+===== Lecture 3 =====
+  - [[MC2018| Monte Carlo simulations for the estimation of pair interactions ]]
+  - [[KMC2018| Kinetic Monte Carlo simulations for the diffusion of molecules @Ag(111) ]]
+===== Lecture 4 =====
+  - [[BF3| BF3 Hartree Fock calculation and orbitals ]]
+===== Lecture 5 =====
+  - [[Ethanol_2018| Dehydration of ethanol ]]
+===== Lecture 6 =====
+  - [[Adsorption_2018| Adsoprtion of acetylene on PdGa  ]]
+===== Lecture 7 =====
+  - [[Infrared_2018| Infrared spectroscopy with cp2k  ]]
+===== Lecture 8 =====
+  - [[Bands_I_2018| Crystallographic point groups, free electron model  ]]
+===== Lecture 9 =====
+  - [[Bands_II_2018| Bandstructure calculations  ]]
+===== Lecture 10 =====
+  - [[STM_2018| STM and AFM simulations  ]]
+===== Lecture 11 =====
+  - [[RE_2018| Replica Exchange molecular dynamics  ]]
+  - [[QMMM_2018| QM/MM for a slab  ]]
+===== Lecture 12 =====
+  - [[PMF| Potential of mean force  ]]
+<!--  - [[alanine_dipeptide_2018|Alanine dipeptide: Ramachandran plot]]
+-->
+===== note on the Quantum Mobile =====
+Remember that the Quantum Mobile VM is a Linux environment. As such, copy/paste operations are sometimes application-dependent.
+<note tip>
+  * In a browser or other graphical programs: use CTRL+C/CTRL+V
+  * In a terminal: use SHIFT+CTRL+C/SHIFT+CTRL+V
+</note>
+===== m_ bash functions =====
+We have programmed in the virtual machine some useful bash functions. They all start with **m_** and can be called from the command line. To see the usage of one of them, use the -h flag.
 Here the list and usage of all of them:
@@ Line 156: / Line 204: @@
 Usage:
         m_distance x1 y1 z1 x2 y2 z2
-==================================================================
-==================================================================
-m_functions.bash
 ==================================================================
@@ Line 367: / Line 410: @@
-Download the 1.1 exercise into your $HOME folder and unzip it.
-<code>
-you@eulerX ~$ 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
-</code>
-<!--
-<note tip>
-All files of this exercise be downloaded from the wiki: {{exercise_1.1.zip|}}
-</note>
-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>
-Login to euler using your nethz credentials.
-Then go to the directory "exercise_1.1".
-<code>
-you@eulerX ~$ cd exercise_1.1
-</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 to make units work...). **The sigma value is in Angstrom.**
-</note>
-<note tip>
-  - load the module with the special m_* bash functions and initialize the module: <code>module load courses mmm ; mmm-init </code>
-  - randomize the coordinate files **fcc.xyz**  <code>m_xyzrand 1.0 < fcc.xyz > fcc_rand.xyz</code> . Do the same with ico.xyz
-  - extract the q4 order parameter from **fcc.xyz** and from **fcc_rand.xyz** and compare the values.<code>module load new gcc/4.8.2 python/2.7.12
-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**.
-  - before running the simulation, copy the input coordinate file into in.xyz <code>cp fcc_rand.xyz in.xyz</code>
-  - run cp2k <code>module load cp2k</code>(this has only to be done once)<code>cp2k.popt -i geo_opt.inp -o geo_opt.out </code>
-  - in the output file, note the final energy, **transform it in the unit of the paper (epsilon units)**
-  - load vmd module 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>
-  - finally, run the bash script <code>./curve</code>. Look inside, and try to understand what you get.
-</note>
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