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--- exercises:2017_ethz_mmm:t_melting_2017 [2017/03/24 09:25] – created dpasserone
+++ exercises:2017_ethz_mmm:t_melting_2017 [2020/08/21 10:15] (current) – external edit 127.0.0.1
@@ Line 5: / Line 5: @@
 For this job we will use the cluster **HYPATIA** available at Empa. There we have access to parallel facilities with reserved nodes for the lecture.
 How to connect to **HYPATIA**:
+Dear Student,
+In order to be able to run simulations at high priority, today we will work on the Empa Cluster.
+We have created a personal account for you. Since the cluster is behind a firewall, we must connect to a gate machine (jumphost) to be allowed to access to the cluster. For security reasons, there are two temporary passwords that you should change to a personal password (can be the same for the gate and for the cluster.
+Here the instructions to connect. Your username/password  (EMPA-USER, TEMP-PASSW1, TEMP-PASSW2) are listed at the end of this message.
+) Decide a password (we will call it EMPA-PASSW )
+) connect to the jumphost:
+ssh -X EMPA-USER@jump1.empa.ch
+Password: TEMP-PASSW1
+) Accept the contract
+) Set a new password (input old password, TEMP-PASSW1, write new password, EMPA-PASSW)
+) Connect to hypatia:
+ssh -X hypatia
+password: TEMP-PASSW2
+) Accept the contract
+) Change your password as in point 4) using TMP-PASSW2 as old password and set EMPA-PASSW
+============================================
+User-specific information (note: TMP-PASSW1 ist the password for jump1, that is the FIRST one, but is listed as second):
+EMPA-USER:TMP-PASSW2:TMP-PASSW1
 <code bash>
-you@eulerX ~$ module load new cp2k
+[you@hypatia ~]$ mmm-init
+[you@hypatia ~]$ cd exercise_5.1
 </code>
+is then the only thing you need to do in order to initialize the m_* scripts. This time the exercise is already in your home directory, and the cp2k module is already loaded!
-you@eulerX ~$ module load courses mmm vmd
-you@eulerX ~$ mmm-init
 </note>
-<note important> **REMEMBER: this is the command to load the  module for the cp2k program:**
+<note important> **REMEMBER: this is the command to run interactively cp2k:**
 <code bash>
-you@eulerX ~$ module load new cp2k
+[you@hypatia ~]$ cp2k.popt -i file.inp -o file.out
 </code>
@@ Line 27: / Line 58: @@
 <code bash>
-you@eulerX ~$ bsub < jobname
+[stb@hypatia exercise_5.1]$ qsub -v INP=file run
+[stb@hypatia exercise_5.1]$ qstat -u stb # checks if it is running
 </code>
+where **file** is the name of the input file without suffix.
 </note>
 In this exercise, we will use a slab geometry (without vacuum region, so without a surface) with full periodic boundary conditions to study the melting behavior of copper.
+All files of this exercise (**all inputs and scripts are commented**) can be also downloaded from the wiki: {{exercise5.1.zip|exercise5.1.zip}}
-  * Download the 5.1 exercise into your $HOME folder and unzip it:
+  * First of all, we will test the NOSE-HOOVER thermostat
-<code bash>
-you@eulerX ~$ wget http://www.cp2k.org/_media/exercises:2015_ethz_mmm:exercise_5.1.zip
-you@eulerX ~$ unzip exercises:2015_ethz_mmm:exercise_5.1.zip
-you@eulerX ~$ cd exercise_5.1
-</code>
 <note tip>
-All files of this exercise (**all inputs and scripts are commented**) can be also downloaded from the wiki: {{exercise_5.1.zip|exercise_5.1.zip}}
+  - Take a look at the file 111.xyz with vmd.
+  - We will apply a thermostat to half of the cell.
+  - copy the half_TIMECON.inp into half_20.inp
+  - Edit the half_20.inp and change _MYTIMECON_ to 20 (two places in the file). This sets the time constant of the thermostat.
+  - Run the job (interactively): > cp2k.popt -i half_20.inp -o half_20.out
+  - Plot the temperature behavior with gnuplot, file half_20-1.ener
+  - Take a look at the half_20.inp file. How is the temperature controlled? Are all particles moving? Why? Which are the relevant sections for MD? Which kind of MD is it?
+  - Repeat by copying half_TIMECON.inp into half_300.inp (TIMECON 300)
+  - Plot the -growing- half*ener file with gnuplot together with the previous ones. Comment the differences
 </note>
-  * Now, run the first simulation, that should melt your system:
+  * Now, run the  simulation that should melt your system:
 <code bash>
-you@eulerX exercise_5.1$ cp2k.popt -i half.inp -o half.out
+you@hypatia exercise_5.1$ cp2k.popt -i half.inp -o half.out
 </code>
@@ Line 57: / Line 92: @@
 <note tip>
   - Take a look at the file 111.xyz with vmd. Visualize it on the screen, and try to reproduce the figure similar to the one on the last slide of the lectures of today. Include the pbc box, create a representation with vdw, periodic images, rotate the sample, etc. Produce a snapshot and include the file in your assignment.
-  - Take a look at the half.inp file. How is the temperature controlled? Are all particles moving? Why? Which are the relevant sections for MD? Which kind of MD is it?
+    - Plot the -growing- half*ener file with gnuplot. How is temperature changing? Is there a conserved quantity?
-  - Plot the -growing- half*ener file with gnuplot. How is temperature changing? Is there a conserved quantity?
 </note>
@@ Line 64: / Line 98: @@
 <code bash>
-you@eulerX exercise_5.1$ ./doprof half-pos-1.xyz
+you@hypatia exercise_5.1$ ./doprof half-pos-1.xyz
 </code>
@@ Line 72: / Line 106: @@
 <code bash>
-you@eulerX exercise_5.1$ animate -loop 0 -delay 100 movie.half-pos-1.xyz.gif
+you@hypatia exercise_5.1$ animate -alpha off -loop 0 -delay 100 movie.half-pos-1.xyz.gif
 </code>
 or download the file to your local machine and open in your internet browser. It will run the animation.
@@ Line 84: / Line 118: @@
 <code bash>
-you@eulerX exercise_5.1$ bsub cp2k.popt -i 1400nve.inp -o 1400nve.out
+you@hypatia exercise_5.1$ qsub run -v  INP=1400nve
 </code>
@@ Line 103: / Line 137: @@
   * Copy the files TEMPnpe.init.inp and TEMPnpe.inp into 1300npe.init.inp and 1300npe.inp (for T=1300) and then edit them in the appropriate points: PROJECT name, INITIAL temperature and RESTART filename.
-  * Run the first simulation: bsub cp2k.popt -i 1300npe.init.inp > 1300npe.init.out ; This is a very short simulation to set the temperature using the old velocities. Why do you need it?
+  * Run the first simulation: qsub run -v INP=1300npe.init ; This is a very short simulation to set the temperature using the old velocities. Why do you need it?
-  * Run the second simulation: bsub cp2k.popt -i 1300npe.inp > 1300npe.out
+  * Run the second simulation: qsub run -v INP=1300npe
   * Observe the temperature and the z profile. Can you find the melting temperature? How do you choose temperatures?