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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 15:33] – 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 +you@eulerX ~$ module load courses mmm vmd 
-</code> +  
-** Pay attention to the output of this program. It may give you some helpful information**+you@eulerX ~$ mmm-init 
 +</note>
  
-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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 # #
 # 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.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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 # #
 # 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 simulatin+  - Discuss these values in view of the kind of molecules we are simulating.
 </note> </note>
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