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exercises:2015_ethz_mmm:c2h2_bond_energy

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exercises:2015_ethz_mmm:c2h2_bond_energy [2015/02/26 13:28] – yakutovichexercises:2015_ethz_mmm:c2h2_bond_energy [2020/08/21 10:15] (current) – external edit 127.0.0.1
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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 $HOME directory please run: +TO USE THE FUNCTION LIBRARY (VERSION UP TO DATE) IN THE INTERACTIVE SHELL:
-<code> +
-you@eulerX ~$ ./update_functionlibrary +
-</code> +
- +
-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 +
-</code>+
  
 +you@eulerX ~$ module load courses mmm vmd
 + 
 +you@eulerX ~$ mmm-init
 </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> 
  
-Create a new directory for this exercise:+Download the 2.1 exercise into your $HOME folder and unzip it. 
  
 <code> <code>
-you@eulerX ~$ mkdir mmm_exercise_2.1 +you@eulerX ~$ wget http://www.cp2k.org/_media/exercises:2015_ethz_mmm:exercise_2.1.zip 
-you@eulerX ~$ cd mmm_exercise_2.1+you@eulerX ~$ unzip exercises:2015_ethz_mmm:exercise_2.1.zip
 </code> </code>
  
- 
- 
- 
-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.  
 <note tip> <note tip>
 All files of this exercise (**input and scripts are all commented**) can be downloaded from the wiki: {{exercise_2.1.zip|}}  All files of this exercise (**input and scripts are all commented**) can be downloaded from the wiki: {{exercise_2.1.zip|}} 
 </note> </note>
-Please copy them to your directory. The input file structure of the template is the following: 
  
-<code - c2h2.amber.inp.templ>+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.  
 + 
 +Then go to the directory "exercise_2.1/c2h2/".  
 +<code> 
 +you@eulerX ~$ cd exercise_2.1/c2h2/ 
 +</code> 
 +The input file structure of the template is the following: 
 + 
 +<code - c2h2.inp.templ>
 &FORCE_EVAL                     ! This section defines method for calculating energy and forces &FORCE_EVAL                     ! This section defines method for calculating energy and forces
   METHOD FIST                   ! Using Molecular Mechanics   METHOD FIST                   ! Using Molecular Mechanics
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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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 # #
 # loads the functions # loads the functions
-# this script uses the functions: change replace getcolumn add list+# this script uses the functions: m_change m_replace m_getcolumn m_sum m_list
 # #
 module load new cp2k module load new cp2k
-. ~/Scripts/myfunctions.bash+. /cluster/apps/courses/mmm/m_functions.bash
  
  
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 # #
  
-for n in `list -5 5`+for n in `m_list -5 5`
 do do
-  dist_cc=`change $dist_cc0 $n $delta` +  dist_cc=`m_change $dist_cc0 $n $delta` 
-  c2=`add $dist_hc $dist_cc ` +  c2=`m_sum $dist_hc $dist_cc` 
-  h2=`add $c2 $dist_hc `+  h2=`m_sum $c2 $dist_hc `
   #   #
   # replaces coordinates in the input   # replaces coordinates in the input
   #   #
-  replace _C1_ $dist_hc < c2h2.amber.inp.templ | replace _C2_ $c2  | replace _H2_ $h2 > c2h2.$dist_cc.inp+  m_replace _C1_ $dist_hc < c2h2.inp.templ | m_replace _C2_ $c2  | m_replace _H2_ $h2 > c2h2.$dist_cc.inp
   #   #
   # Runs cp2k   # Runs cp2k
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   # gets the energy from the output (in a.u.)   # gets the energy from the output (in a.u.)
   #   #
-  energy=` getcolumn 'ENERGY|' 9 < c2h2.$dist_cc.out `+  energy=` m_getcolumn 'ENERGY|' 9 < c2h2.$dist_cc.out ` 
   echo $dist_cc $energy  >> curve.amber.c2h2   echo $dist_cc $energy  >> curve.amber.c2h2
 # #
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 mv c2h2.*.inp c2h2.*.out Logs mv c2h2.*.inp c2h2.*.out Logs
 rm RUN* *restart* rm RUN* *restart*
 +
 +
  
 </code> </code>
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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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 # #
 # loads the functions # loads the functions
-# this script uses the functions: change replace getcolumn add list+# this script uses the functions: m_change m_replace m_getcolumn m_sum m_list
 # #
 module load new cp2k module load new cp2k
-. ~/Scripts/myfunctions.bash+#. ~/Scripts/myfunctions.bash 
 +. /cluster/apps/courses/mmm/m_functions.bash
  
  
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 # #
  
-for n in `list -5 5`+for n in `m_list -5 5`
 do do
-  dist_cc=`change $dist_cc0 $n $delta` +  dist_cc=`m_change $dist_cc0 $n $delta` 
-  c2=`add $dist_hcx $dist_cc` +  c2=`m_sum $dist_hcx $dist_cc` 
-  h3=`add $c2 $dist_hcx `+  h3=`m_sum $c2 $dist_hcx `
   #   #
   # replaces coordinates in the input   # replaces coordinates in the input
   #   #
-  replace _C1_ $dist_hcx < c2h4.amber.inp.templ | replace _C2_ $c2  | replace _H3_ $h3 > c2h4.$dist_cc.inp+  m_replace _C1_ $dist_hcx < c2h4.inp.templ | m_replace _C2_ $c2  | m_replace _H3_ $h3 > c2h4.$dist_cc.inp
   #   #
   # Runs cp2k   # Runs cp2k
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   # gets the energy from the output (in a.u.)   # gets the energy from the output (in a.u.)
   #   #
-  energy=` getcolumn 'ENERGY|' 9 < c2h4.$dist_cc.out ` +  energy=` m_getcolumn 'ENERGY|' 9 < c2h4.$dist_cc.out `
   echo $dist_cc $energy  >> curve.amber.c2h4   echo $dist_cc $energy  >> curve.amber.c2h4
 # #
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 mv c2h4.*.inp c2h4.*.out Logs mv c2h4.*.inp c2h4.*.out Logs
 rm RUN* *restart* rm RUN* *restart*
-                                                                                                                                                                        + 
 +                                                                                                                                                  
 </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 simulating+  - Discuss these values in view of the kind of molecules we are simulating. 
 +</note>
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