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exercises:2014_ethz_mmm:nudged_elastic_band

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exercise:nudged_elastic_band [2014/02/20 16:38] – scleliaexercise:2014_ethz_mmm:nudged_elastic_band [2014/10/15 13:38] – oschuett
Line 10: Line 10:
 ^  Path 1  ^  Path 2  ^ ^  Path 1  ^  Path 2  ^
 |  Direct exchange with the central atom  |  Coordinated rotation of three atoms  | |  Direct exchange with the central atom  |  Coordinated rotation of three atoms  |
-|  {{:exercise:neb_path1.gif|}}  |  {{:exercise:neb_path2.gif|}}  |+|  {{neb_path1.gif|}}  |  {{neb_path2.gif|}}  |
  
  
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         &LENNARD-JONES         &LENNARD-JONES
           atoms  Ar Ar           atoms  Ar Ar
-          EPSILON 119.8 +          EPSILON    [K_e] 119.8 
-          SIGMA 3.401 +          SIGMA [angstrom]   3.401 
-          RCUT  25.0+          RCUT  [angstrom]  25.0
         &END LENNARD-JONES         &END LENNARD-JONES
       &END NONBONDED       &END NONBONDED
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 For the NEB calcualtions, CP2k produces a few output files. The most important are: For the NEB calcualtions, CP2k produces a few output files. The most important are:
  
-  * neb1.out : standard CP2K output file. It tells you whether that the calculation is completed.\\ (See:[[exercise:single_point_calculation|Computation of the Lennard Jones curve for two Ar atoms]].Part I, Step 3)+  * neb1.out : standard CP2K output file. It tells you whether that the calculation is completed.\\ (See:[[single_point_calculation|Computation of the Lennard Jones curve for two Ar atoms]].Part I, Step 3)
   * neb1-pos-Replica_nr_XXX-1.xyz : those are the replica optimization trajectories. You get a trajectory for each replica.    * neb1-pos-Replica_nr_XXX-1.xyz : those are the replica optimization trajectories. You get a trajectory for each replica. 
   * neb1-BANDXXX.out : geometry optimization output for each replica.   * neb1-BANDXXX.out : geometry optimization output for each replica.
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 Here is a short script to create an energy profile as  a function of the replica number.  Here is a short script to create an energy profile as  a function of the replica number. 
 <code> <code>
-$ for a in 1 2 3 4 5 6 7 8 9 10 ; do grep ENERGY  neb1-BAND${a}.out | tail -n 1 | awk '{print '${a}',$9}' ; done +$ for a in 1 2 3 4 5 6 7 8 9 10 ; do grep ENERGY  neb1-BAND${a}.out | tail -n 1 | awk '{print '${a}',$9}' ; done > neb1_profile 
 +</code> 
 + 
 +The energy profile will be stored in the file ''neb1_profile''. Any plotting program should be able to visualize it, e.g. gnuplot: 
 + 
 +<code> 
 +$ echo "plot 'neb1_profile' w l; pause mouse" |  gnuplot
 </code> </code>
-The energy profile will be printed on screen. Any plotting program should be able to handle it. 
  
 ===== Path 2: Coordinated rotation ===== ===== Path 2: Coordinated rotation =====
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         &LENNARD-JONES         &LENNARD-JONES
           atoms  Ar Ar           atoms  Ar Ar
-          EPSILON 119.8 +          EPSILON    [K_e] 119.8 
-          SIGMA 3.401 +          SIGMA [angstrom]   3.401 
-          RCUT  25.0+          RCUT  [angstrom]  25.0
         &END LENNARD-JONES         &END LENNARD-JONES
       &END NONBONDED       &END NONBONDED
exercises/2014_ethz_mmm/nudged_elastic_band.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1