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exercises:2015_pitt:gga [2015/02/27 08:27] – [4. Task: ab initio molecular dynamics] vondeleexercises:2015_pitt:gga [2020/08/21 10:15] (current) – external edit 127.0.0.1
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   * Use vmd to vizualize the geometries (provided below) named ''mode1.xyz'' and ''mode2.xyz''   * Use vmd to vizualize the geometries (provided below) named ''mode1.xyz'' and ''mode2.xyz''
   * To edit the input files provided below, use an editor such as ''vi'' or ''nano''. While ''nano'' is simple to use, ''vi'' can be [[http://www.cp2k.org/tools| configured to colour-code cp2k inputs]].   * To edit the input files provided below, use an editor such as ''vi'' or ''nano''. While ''nano'' is simple to use, ''vi'' can be [[http://www.cp2k.org/tools| configured to colour-code cp2k inputs]].
-  * You will need files named ''BASIS_MOLOPT'' ''GTH_POTENTIALS'' ''dftd3.dat'' that are provided as part of CP2K in a directory ''cp2k/data'' +  * You will need files named ''BASIS_MOLOPT'' ''GTH_POTENTIALS'' ''dftd3.dat'' that are provided as part of CP2K in a directory ''cp2k/data'', unless the code has been compiled with the proper flag ('' -D__DATA_DIR'') so that these are found automatically. 
-  * Use a job script to submit jobs on the cluster, an example job submission script might look like (TODO: adjust for environment)+  * Use a job script to submit jobs on the cluster, an example job submission script might look like 
  
 <code - job> <code - job>
-#!/bin/bash --login +#PBS -N mode1 
-#SBATCH --job-name=mode1 +#PBS -j oe 
-#SBATCH --nodes=6 +#PBS -q dist_small 
-#SBATCH --time=0:10:00 +#PBS -nodes=4:ppn=16 
-#SBATCH --account=ch5 +#PBS -l walltime=10:00 
-aprun -n 144 -N 24 -d 1 cp2k.popt -i mode1.inp -o mode1.out+#PBS -A cp2k2015 
 + 
 +cd $PBS_O_WORKDIR 
 + 
 +module purge 
 +module load cp2k/2.6 
 + 
 +prun cp2k.popt -i mode1.inp -o mode1.out
 </code> </code>
  
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 In order to compute the relative stability of mode1 and mode2, both configurations need to be geometry optimized.  In order to compute the relative stability of mode1 and mode2, both configurations need to be geometry optimized. 
  
-To do so, turn of the generation of cubes (''&E_DENSITY_CUBE OFF'') in mode1.inp, change to ''RUN_TYPE GEO_OPT'' and adjust the project name. Create and run a similar input file for mode2.+To do so, turn off the generation of cubes (''&E_DENSITY_CUBE OFF'') in mode1.inp, change to ''RUN_TYPE GEO_OPT'' and adjust the project name. Create and run a similar input file for mode2.
  
 input topics: input topics:
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 What can you say about the hydrogen bond to the surface, relative acidity of the two oxygens ?  What can you say about the hydrogen bond to the surface, relative acidity of the two oxygens ? 
 Note that, in order to be statistically relevant, longer trajectories should be employed, and surface slab thickness will play an important role. Also compare to Fig. 7 of the paper referenced. Note that, in order to be statistically relevant, longer trajectories should be employed, and surface slab thickness will play an important role. Also compare to Fig. 7 of the paper referenced.
-===== Required Files =====+====== Required Files =====
 + 
 +(right) click on the filename to download to your local machine. 
 <code - mode1.inp> <code - mode1.inp>
 &GLOBAL &GLOBAL
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     &MGRID     &MGRID
        ! PW cutoff ... depends on the element (basis) too small cutoffs lead to the eggbox effect.        ! PW cutoff ... depends on the element (basis) too small cutoffs lead to the eggbox effect.
-       ! certain calculations (e.g. geometry optimization, vibrational frequencies, NPT and cell optimizations, need higher cutoffs)+       ! certain calculations (e.g. geometry optimization, vibrational frequencies, 
 +       NPT and cell optimizations, need higher cutoffs)
        CUTOFF [Ry] 400         CUTOFF [Ry] 400 
     &END     &END
  
     &QS     &QS
-       METHOD GPW  ! use the GPW method (i.e. pseudopotential based calculations with the Gaussian and Plane Waves scheme). +       ! use the GPW method (i.e. pseudopotential based calculations with the Gaussian and Plane Waves scheme). 
-       EPS_DEFAULT 1.0E-10 ! default threshold for numerics ~ roughly numerical accuracy of the total energy per electron, sets reasonable values for all other thresholds +       METHOD GPW  
-       EXTRAPOLATION ASPC ! used for MD, the method used to generate the initial guess. +       ! default threshold for numerics ~ roughly numerical accuracy of the total energy per electron, 
 +       sets reasonable values for all other thresholds
 +       EPS_DEFAULT 1.0E-10  
 +       ! used for MD, the method used to generate the initial guess. 
 +       EXTRAPOLATION ASPC 
     &END     &END
  
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     &END CELL     &END CELL
  
-    ! atom coordinates can be in the &COORD section, or provided as an external file.+    ! atom coordinates can be in the &COORD section, 
 +    ! or provided as an external file.
     &TOPOLOGY     &TOPOLOGY
       COORD_FILE_NAME mode1.xyz       COORD_FILE_NAME mode1.xyz
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     &END     &END
  
-    ! MOLOPT basis sets are fairly costly, but in the 'DZVP-MOLOPT-SR-GTH' available for all elements +    ! MOLOPT basis sets are fairly costly, 
-    ! their contracted nature makes them suitable for condensed and gas phase systems alike.+    ! but in the 'DZVP-MOLOPT-SR-GTH' available for all elements 
 +    ! their contracted nature makes them suitable 
 +    ! for condensed and gas phase systems alike.
     &KIND H                                   &KIND H                              
       BASIS_SET DZVP-MOLOPT-SR-GTH                BASIS_SET DZVP-MOLOPT-SR-GTH         
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    TEMPERATURE [K] 300    TEMPERATURE [K] 300
    TIMESTEP [fs] 0.5    TIMESTEP [fs] 0.5
-   STEPS 100+   STEPS 1000
    # GLE thermostat as generated at http://epfl-cosmo.github.io/gle4md     # GLE thermostat as generated at http://epfl-cosmo.github.io/gle4md 
    # GLE provides an effective NVT sampling.    # GLE provides an effective NVT sampling.
exercises/2015_pitt/gga.1425025647.txt.gz · Last modified: 2020/08/21 10:15 (external edit)