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exercises:2015_ethz_mmm:c2h2_bond_energy [2015/02/26 14:19] – yakutovichexercises:2015_ethz_mmm:c2h2_bond_energy [2015/03/06 02:39] – dpasserone
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 ====== C2H2 and C2H4 bond energy ====== ====== C2H2 and C2H4 bond energy ======
 +<note warning>
 +<note warning>
 +TO USE THE FUNCTION LIBRARY (VERSION UP TO DATE) IN THE INTERACTIVE SHELL:
 +you@eulerX ~$ module load courses mmm ; mmm-init
 +</note>
 +
 <note warning> <note warning>
 Before you start it is **ABSOLUTELY NEСESSARY** to update the function library. So from you $HOME directory please run: Before you start it is **ABSOLUTELY NEСESSARY** to update the function library. So from you $HOME directory please run:
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 </note> </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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 The script to modify the C-C distance in the input and generate the curve is the following: The script to modify the C-C distance in the input and generate the curve is the following:
  
-<code bash c2h2.amber.chain>+<code bash c2h2.chain>
 # #
 # task 2.1 C2H2 bond strength # task 2.1 C2H2 bond strength
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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.a.chain+you@eulerX c2h2$ bsub < c2h2.chain
 </code> </code>
  
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 <code> <code>
-you@brutusX mmm_exercise_2.1$ gnuplot fit.triple.gnu+you@eulerX c2h2$ gnuplot fit.gnu
 </code> </code>
  
-<code - fit.triple.gnu>+<code - fit.gnu>
 #!/usr/bin/gnuplot #!/usr/bin/gnuplot
 f(x)=k*(x-x0)*(x-x0)+e0         # definition of the function to be fitted f(x)=k*(x-x0)*(x-x0)+e0         # definition of the function to be fitted
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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>
 +you@eulerX c2h2$ cd ../c2h4
 +</code>
  
-    * The input c2h4.amber.inp.templ is similar to the previous one, only with different project name (C2H4) and coordinates:+    * The new input c2h4.inp.templ is similar to the previous one, only with different project name (C2H4) and coordinates:
  
 <code coo.ch4> <code coo.ch4>
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    * The script to modify the bond lengths changes slightly as well    * The script to modify the bond lengths changes slightly as well
  
-<code bash c2h4.a.chain>+<code bash c2h4.chain>
 # #
 # task 2.2 C2H4 bond strength # task 2.2 C2H4 bond strength
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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 simulating+  - Discuss these values in view of the kind of molecules we are simulating. 
 +</note>
exercises/2015_ethz_mmm/c2h2_bond_energy.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1