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exercises:2015_cecam_tutorial:neb [2015/08/20 13:53] – properly set file links tmuellerexercises:2015_cecam_tutorial:neb [2020/08/21 10:15] (current) – external edit 127.0.0.1
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 Problem: compute activation barrier for the last step (6 to 7) of the cyclodehydrogenation reaction CHP@Cu(111) -> TBC Problem: compute activation barrier for the last step (6 to 7) of the cyclodehydrogenation reaction CHP@Cu(111) -> TBC
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   * Original author: Carlo Pignedoli   * Original author: Carlo Pignedoli
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     - Please note that the geometry optimization of the final state is constrained with respect to the position of the final H2 molecule.     - Please note that the geometry optimization of the final state is constrained with respect to the position of the final H2 molecule.
   - Perform a NEB simulation to find a //saddle point// between ''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX2/INI/ini_eq.xyz|ini_eq.xyz]]'' and ''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX2/FIN/fin_eq.xyz|fin_eq.xzy]]''.   - Perform a NEB simulation to find a //saddle point// between ''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX2/INI/ini_eq.xyz|ini_eq.xyz]]'' and ''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX2/FIN/fin_eq.xyz|fin_eq.xzy]]''.
-    - A linear guess for the path is not a good idea in this case; a clever guess can be obtained from a series of constrained geometry optimizations where the H-H distance is forced to vary from its initial value (more than 3 Å) to the H2 equilibrium distance. Such a guess is given, in the directory ''EX2'', with the files ''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX2/ini_eq.xyz|ini_eq.xyz]]'', ''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX2/due.xyz|due.xyz]]'',''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX2/tre.xyz|tre.xyz]]'',…,''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX2/tredici.xyz|tredici.xyz]]'',''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX2/fin_eq.xyz|fin_eq.xyz]]'').\\ Check that the initial step of the NEB calculation is reasonable and determine the activation barrier at the and of the optimization. In the directory ''EX2'' you will find the input for the calculation (''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX2/neb.inp|neb.inp]]''), the output (''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX2/out|out]]'') and the optimization trajectory of each //image// of the system (''NEB-pos-Replica_nr_XX-1.xyz'', 14 images are used in the example)+    - A linear guess for the path is not a good idea in this case; a clever guess can be obtained from a series of constrained geometry optimizations where the H-H distance is forced to vary from its initial value (more than 3 Å) to the H2 equilibrium distance. Such a guess is given, in the directory ''EX2'', with the files ''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX2/ini_eq.xyz|ini_eq.xyz]]'', ''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX2/due.xyz|due.xyz]]'',''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX2/tre.xyz|tre.xyz]]'',…,''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX2/tredici.xyz|tredici.xyz]]'',''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX2/fin_eq.xyz|fin_eq.xyz]]'').\\ Check that the initial step of the NEB calculation is reasonable and determine the activation barrier at the and of the optimization. In the directory ''EX2'' you will find the input for the calculation (''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX2/neb.inp|neb.inp]]''), the output (''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX2/out|out]]'') and the optimization trajectory of each //image// of the system (''NEB-pos-Replica_nr_XX-1.xyz'', 14 images are used in the example)
  
 The last section of the input described above is modified as follows: The last section of the input described above is modified as follows:
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 <note important>''[[inp>FORCE_EVAL/DFT/SCF#SCF_GUESS|SCF_GUESS RESTART]]''  in combination with  ''[[inp>FORCE_EVAL/DFT/QS#EXTRAPOLATION|EXTRAPOLATION USE_GUESS]]'' has to be declared in the ''[[inp>FORCE_EVAL/DFT]]'' section to allow for an efficient guess of the wavefunctions at each step of  the BAND optimization.</note> <note important>''[[inp>FORCE_EVAL/DFT/SCF#SCF_GUESS|SCF_GUESS RESTART]]''  in combination with  ''[[inp>FORCE_EVAL/DFT/QS#EXTRAPOLATION|EXTRAPOLATION USE_GUESS]]'' has to be declared in the ''[[inp>FORCE_EVAL/DFT]]'' section to allow for an efficient guess of the wavefunctions at each step of  the BAND optimization.</note>
  
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 ===== Exercise 2: Metadynamics ===== ===== Exercise 2: Metadynamics =====
  
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 We perform a metadynamics simulation with two collective variables: the sum of C-H distances (CV1) and the  H-H distance (CV2). We perform a metadynamics simulation with two collective variables: the sum of C-H distances (CV1) and the  H-H distance (CV2).
 Walls have to be introduced to limit the range of variability of the two CVs. Walls have to be introduced to limit the range of variability of the two CVs.
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 To define the collective variables introduce a ''[[inp>FORCE_EVAL/SUBSYS/COLVAR|COLVAR]]'' card in the ''[[inp>FORCE_EVAL/SUBSYS|SUBSYS]]'' section of the first ''[[inp>FORCE_EVAL]]'': To define the collective variables introduce a ''[[inp>FORCE_EVAL/SUBSYS/COLVAR|COLVAR]]'' card in the ''[[inp>FORCE_EVAL/SUBSYS|SUBSYS]]'' section of the first ''[[inp>FORCE_EVAL]]'':
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 During execution you can monitor the evolution of the CVs of each walker from the files  During execution you can monitor the evolution of the CVs of each walker from the files 
-''[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX1/WALK1/META-COLVAR.metadynLog|META-COLVAR.metadynLog]]'' and ''[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX1/WALK2/META-COLVAR.metadynLog|META-COLVAR.metadynLog]]''+''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX1/WALK1/META-COLVAR.metadynLog|META-COLVAR.metadynLog]]'' and ''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX1/WALK2/META-COLVAR.metadynLog|META-COLVAR.metadynLog]]''
  
 e.g. e.g.
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 </code> </code>
  
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 ===== References ===== ===== References =====
  
 ~~REFNOTES~~ ~~REFNOTES~~
exercises/2015_cecam_tutorial/neb.1440078822.txt.gz · Last modified: 2020/08/21 10:14 (external edit)