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exercises:2015_ethz_mmm:c2h2_bond_energy [2015/02/26 14:32] – yakutovichexercises:2015_ethz_mmm:c2h2_bond_energy [2015/03/06 02:40] – dpasserone
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 ====== C2H2 and C2H4 bond energy ====== ====== C2H2 and C2H4 bond energy ======
 <note warning> <note warning>
-Before you start it is **ABSOLUTELY NEСESSARY** to update the function library. So from you $HOME directory please run: +TO USE THE FUNCTION LIBRARY (VERSION UP TO DATE) IN THE INTERACTIVE SHELL: 
-<code> +you@eulerX ~$ module load courses mmm ; mmm-init 
-you@eulerX ~$ ./update_functionlibrary +</note>
-</code> +
-** Pay attention to the output of this program. It may give you some helpful information**+
  
-If you don't have the file "update_functionlibrary" please download it from here {{update_functionlibrary.zip|}} and unzip into your $HOME directory 
-<code> 
-you@eulerX ~$ unzip update_functionlibrary.zip 
-you@eulerX ~$ chmod 755 update_functionlibrary 
-</code> 
-Or if you are working on the remote computer you can also do the following: 
-<code> 
-you@eulerX ~$ wget http://www.cp2k.org/_media/exercises:2015_ethz_mmm:update_functionlibrary.zip 
-you@eulerX ~$ unzip exercises:2015_ethz_mmm:update_functionlibrary.zip 
-you@eulerX ~$ chmod 755 update_functionlibrary 
-</code> 
  
-</note> 
  
-<note important> **REMEMBER** to load the  module for the cp2k program:+<note important> **REMEMBER: this is the command to load the  module for the cp2k program:**
  
 <code> <code>
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 </code> </code>
  
-**and to submit the job chain:**+**and to submit the job:**
  
 <code> <code>
-you@eulerX ~$ bsub < c2h2.a.chain+you@eulerX ~$ bsub < jobname
 </code>  </code> 
 </note>  </note> 
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 In this exercise you will test the general AMBER force field, which is suitable for a large class of molecules. In this example you will compute the classical energy of a simple acetylene molecule and apply small variations to the C-C bond lengths.  In this exercise you will test the general AMBER force field, which is suitable for a large class of molecules. In this example you will compute the classical energy of a simple acetylene molecule and apply small variations to the C-C bond lengths. 
  
-Please go to the directory "exercise_2.1/c2h2/". +Then go to the directory "exercise_2.1/c2h2/". 
 <code> <code>
 you@eulerX ~$ cd exercise_2.1/c2h2/ you@eulerX ~$ cd exercise_2.1/c2h2/
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 <code> <code>
-you@brutusX mmm_exercise_2.1$ module load new cp2k +you@eulerX c2h2$ module load new cp2k 
-you@brutusX mmm_exercise_2.1$ bsub < c2h2.chain+you@eulerX c2h2$ bsub < c2h2.chain
 </code> </code>
  
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 <code> <code>
-you@brutusX mmm_exercise_2.1$ gnuplot fit.gnu+you@eulerX c2h2$ gnuplot fit.gnu
 </code> </code>
  
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 Now, perform the same exercise in another directory for the molecule C2H4. Now, perform the same exercise in another directory for the molecule C2H4.
 <code> <code>
-you@eulerX ~$ cd ../c2h4+you@eulerX c2h2$ cd ../c2h4
 </code> </code>
  
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 <note tip>Assignment:  <note tip>Assignment: 
   - Report the values of the bond length and force constants in all cases.    - Report the values of the bond length and force constants in all cases. 
-  - Discuss these values in view of the kind of molecules we are simulatin+  - Discuss these values in view of the kind of molecules we are simulating.
 </note> </note>
exercises/2015_ethz_mmm/c2h2_bond_energy.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1