CP2K Open Source Molecular Dynamics

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exercises:2016_ethz_mmm:t_melting [2016/04/07 23:27] – yakutovichexercises:2016_ethz_mmm:t_melting [2016/04/08 00:44] – yakutovich
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   * What is the physical meaning of the parameter ε in the Lennard-Jones potential?   * What is the physical meaning of the parameter ε in the Lennard-Jones potential?
   * What is the cohesive energy? How it can be related to the ε? Remember in the FCC structure one atom is surrounded by 12 neighbours.    * What is the cohesive energy? How it can be related to the ε? Remember in the FCC structure one atom is surrounded by 12 neighbours. 
-  * Melting temperature of Lennard-Jones system is about 1/12 of cohesive energy. Try to estimate it, because this estimation will be necessary later +  * Melting temperature of Lennard-Jones system is about 1/12 of cohesive energy. Try to estimate it, because this estimation will be used later 
 </note> </note>
  
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 you@eulerX exercise_5.1$ tail -n 98 opt_cell-pos-1.xyz >  ./ELEMENT_opt_unit.xyz you@eulerX exercise_5.1$ tail -n 98 opt_cell-pos-1.xyz >  ./ELEMENT_opt_unit.xyz
 </code> </code>
-Among all the parameters that you should provide there are also the unit cell parameters! They can be found in the file opt_cell-1.restart (section CELL)+For the next simulation you will need the file called half.inp. Open it and again provide all the necessary parameters. Note, that unit cell for this run can be found in the file opt_cell-1.restart (section CELL)
  
  
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-It is a 3000 step molecular dynamics. While it is running you can complete the first assignments.+It is a 5000 step molecular dynamics. While it is running you can complete the folowing assignments:
 <note tip> <note tip>
   - Take a look at the file ELEMENT_opt_unit.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 file ELEMENT_opt_unit.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.
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 </note> </note>
  
-  * Now, starting from the restart of this simulation, we equilibrate the system in nve, and we move all particles:+ 
 +Now, starting from the restart of this simulation, we equilibrate the system in nve, and we move all particles. But again some parameters needs to be specified in the file nve.inp. Use unit cell from the file half-1.restart. Also file with coordinates (X_init_nve.xyz) needs to be created. Use the coordinates from the last frame of the previous run. 
 + 
 +And run the simulations:
  
  
 <code bash> <code bash>
-you@eulerX exercise_5.1$ bsub cp2k.popt -i 1400nve.inp -o 1400nve.out+you@eulerX exercise_5.1$ bsub cp2k.popt -i nve.inp -o nve.out
 </code> </code>
  
 The resulting configuration (check) will be an equilibrated system (which profile?). The resulting configuration (check) will be an equilibrated system (which profile?).
  
-Now we have a file called "1400nve-1.restart". **Do not delete it !!!** It will be used as a restart file for all simulations.+Now we have a file called "nve-1.restart". **Do not delete it !!!** It will be used as a restart file for all simulations.
  
  
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-  * 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. +  * Copy the files TEMPnpe.init.inp and TEMPnpe.inp into 100npe.init.inp and 100npe.inp (for T=100) and then edit them in the appropriate points: PROJECT name, INITIAL temperature and RESTART filename and all other parameters specified as X 
-  * 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: bsub cp2k.popt -i 100npe.init.inp -o 100npe.init.out ; 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: bsub cp2k.popt -i 100npe.inp > 100npe.out
   * Observe the temperature and the z profile. Can you find the melting temperature? How do you choose temperatures?   * Observe the temperature and the z profile. Can you find the melting temperature? How do you choose temperatures?
  
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 <note tip> <note tip>
-  * What is the melting temperature of copper that you have found using this potential?+  * What is the melting temperature of the nobel gas that you have chosen?
 </note> </note>
exercises/2016_ethz_mmm/t_melting.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1