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neb_simulation [2009/12/04 10:53]
prokop
neb_simulation [2009/12/04 11:53]
prokop
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-== Input == + 
-Here we provide brief description how to run Nudged Elastic Band ([http://​theory.cm.utexas.edu/​henkelman/​research/​saddle/​ NEB]) simulations to explore reaction pathways between two known atomic configurations. ​ +===== Input ===== 
-More details about the method including list of references can be found [http://​theory.cm.utexas.edu/​henkelman/​research/​saddle/ ​ here].+ 
 +Here we provide brief description how to run Nudged Elastic Band ([http://​theory.cm.utexas.edu/​henkelman/​research/​saddle/​ NEB]) simulations to explore reaction pathways between two known atomic configurations. More details about the method including list of references can be found [http://​theory.cm.utexas.edu/​henkelman/​research/​saddle/ ​ here]. 
 + 
 To start, we need an initial and final atomic configuration. To start, we need an initial and final atomic configuration.
  
-The initial configuration is defined in input  ''​*.bas''​ file defined in '''​ fireball.in'''​ input file. Final configuration +  * The initial configuration is defined in input  ''​*.bas''​ file defined in ''​ fireball.in''​ input file. Final configuration is defined in other ''​*.bas''​ file, which name is defined in ''​neb.optional''​ file (see bellow). ​
-is defined in other ''​*.bas''​ file, which name is defined in ''​neb.optional''​ file (see bellow). ​+
  
-Next step, we need to activate ''​ineb''​ flag in the section OPTION of the '''​fireball.in'''​ input file: <br \>+  * Next step, we need to activate ''​ineb''​ flag in the section OPTION of the ''​fireball.in''​ input file:
  
 <​code>​ <​code>​
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 </​code>​ </​code>​
  
-In addition, we create an extra input file ''​neb.optional''​ including parameters to control NEB searching process. This file has to be presented in the working directory (This file will probably converted into section format of ''​fireball.in''​ soon, for details please checkout your current version). +  * In addition, we create an extra input file ''​neb.optional''​ including parameters to control NEB searching process. This file has to be presented in the working directory (This file will probably converted into section format of ''​fireball.in''​ soon, for details please checkout your current version). The format of ''​neb.optional''​ file is following:
- +
-The format of '''​neb.optional'''​ file is following:+
  
 <​code>​ <​code>​
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 </​code>​ </​code>​
  
-== Output & Convergence== +===== Output & Convergence ===== 
-Information about the convergence status/​progress can be checked out searching lines with a string ''​NEB''​ in output file; e.g. typing from command line: + 
 +Information about the convergence status/​progress can be checked out searching lines with a string ''​NEB''​ in output file; e.g. typing from command line: 
 + 
 <​code>​ <​code>​
 grep "​NEB"​ $output_name grep "​NEB"​ $output_name
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 you'll get a summary in the following format: you'll get a summary in the following format:
 +
 <​code>​ <​code>​
 ... ...
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 </​code>​ </​code>​
  
-In addition actual optimized position of each NEB image is stored in '''​answer_neb_''​XX''​.bas''' ​ file;  where ''​XX''​ means image no.. File ''​'​answer_neb_''​XX''​.xyz'''​ contains whole optimization history of an individual image. +In addition actual optimized position of each NEB image is stored in ''​answer_neb_**XX**.bas'' ​ file;  where ''​**XX**''​ means image no.. File ''​answer_neb_XX.xyz''​ contains whole optimization history of an individual image. 
-Files '''​answer_image.bas'''​ and '''​answer_image.xyz'''​ contain all, last optimized, NEB images including the initial and final ones.<​br/> ​ +Files ''​answer_image.bas''​ and ''​answer_image.xyz''​ contain all, last optimized, NEB images including the initial and final ones. 
-Note: The files '''​answer_image.bas'''​ can be directly used for a restart of NEB-optimization process.+  
 +**Note**: The files ''​answer_image.bas''​ can be directly used for a restart of NEB-optimization process
 + 
 + 
 +==== Main sources of convergence troubles: ==== 
 + 
 +  * **large time step: ** Initial forces can be pretty large, therefore a small time step is advisable to avoid any numerical instabilities of [http://​en.wikipedia.org/​wiki/​Verlet_integration Verlet] alghorithm used to integrate the equations of motion.  
 +  * **wrong initial guess of NEB images: **  Linear extrapolation is used to build up set of NEB images at begin. In special cases, where the reaction trajectories are complicated,​ can lead to unrealistic configurations with atoms close to each other. Such configurations will suffer large repulsive forces which consequently may lead to numerical instabilities during optimization. 
 +  * **weak spring constant:** If the potential energy surface is complicated,​ the imaginary elastic band can get kinked. On other hand, large spring constant will lead to less precise estimation of the saddle point.
  
--- +===== Restart =====
-Main sources of convergence troubles: +
-# '''​large time step'''<​br/>​initial forces can be pretty large, therefore a small time step is advisable to avoid any numerical instabilities of [http://​en.wikipedia.org/​wiki/​Verlet_integration Verlet] alghorithm used to integrate the equations of motion.  +
-# '''​wrong initial guess of NEB images'''​ <​br/>​Linear extrapolation is used to build up set of NEB images at begin. In special cases, where the reaction trajectories are complicated,​ can lead to unrealistic configurations with atoms close to each other. Such configurations will suffer large repulsive forces which consequently may lead to numerical instabilities during optimization. +
-# '''​weak spring constant'''<​br/>​If the potential energy surface is complicated,​ the imaginary elastic band can get kinked. On other hand, large spring constant will lead to less precise estimation of the saddle point.+
  
-== Restart == +There is possibility to make a restart of previous run on penultimate line in the file ''​neb.optional'':​
-There is possibility to make a restart of previous run on penultimate line in the file '''​neb.optional''':​+
  
 <​code>​ <​code>​
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 </​code>​ </​code>​
  
-In this case, an initial NEB images will be uploaded from a file declared on the next line of '''​neb.optional'''​ file. +In this case, an initial NEB images will be uploaded from a file declared on the next line of ''​neb.optional''​ file. 
-Format of this file has to be indentical to the '''​answer_image.bas'''​ file, where the first line containing total number of NEB images.+Format of this file has to be indentical to the ''​answer_image.bas''​ file, where the first line containing total number of NEB images.
  
neb_simulation.txt · Last modified: 2011/02/18 13:13 (external edit)