neb_simulation
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neb_simulation [2009/11/09 15:17] jelen created |
neb_simulation [2011/02/18 13:13] (current) |
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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 | + | |
| - | is defined in other ''*.bas'' file, which name is defined in ''neb.optional'' file (see bellow). | + | * 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). |
| - | <br \> | + | |
| - | <br \> | + | * Next step, we need to activate ''ineb'' flag in the section OPTION of the ''fireball.in'' input file: |
| - | Next step, we need to activate ''ineb'' flag in the section OPTION of the '''fireball.in''' input file: <br \> | + | |
| - | <br \> | + | <code> |
| - | <pre> | + | |
| &OPTION | &OPTION | ||
| ineb = 1 | ineb = 1 | ||
| &END | &END | ||
| - | </pre> | + | </code> |
| - | <br \> | + | |
| - | 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). <br \> | + | |
| - | The format of '''neb.optional''' file is following: | + | |
| - | <br \> | + | |
| - | <pre> | + | * 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: |
| + | |||
| + | <code> | ||
| 1.0 ! spring strength (k_neb) | 1.0 ! spring strength (k_neb) | ||
| 0.03 ! tolerance of displacement (tol_displ_neb) | 0.03 ! tolerance of displacement (tol_displ_neb) | ||
| Line 29: | Line 29: | ||
| 0 ! restart (irestart) | 0 ! restart (irestart) | ||
| final.bas ! file name including the final configuration (file_neb)) | final.bas ! file name including the final configuration (file_neb)) | ||
| - | </pre> | + | </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: | + | |
| - | <pre> | + | 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> | ||
| grep "NEB" $output_name | grep "NEB" $output_name | ||
| - | </pre> | + | </code> |
| you'll get a summary in the following format: | you'll get a summary in the following format: | ||
| - | <pre> | + | |
| + | <code> | ||
| ... | ... | ||
| NEB_RES no. iter = 52 | NEB_RES no. iter = 52 | ||
| Line 54: | Line 57: | ||
| NEB_RES no. iter = 55 | NEB_RES no. iter = 55 | ||
| ... | ... | ||
| - | </pre> | + | </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. | ||
| + | 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. | ||
| + | |||
| + | |||
| + | ==== Main sources of convergence troubles: ==== | ||
| - | 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. | + | * **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. |
| - | Files '''answer_image.bas''' and '''answer_image.xyz''' contain all, last optimized, NEB images including the initial and final ones.<br/> | + | * **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. |
| - | Note: The files '''answer_image.bas''' can be directly used for a restart of NEB-optimization process.<br/> | + | * **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. |
| - | <br/> | + | |
| - | -- | + | ===== 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''': | + | |
| - | <pre> | + | <code> |
| 1.0 ! spring strength (k_neb) | 1.0 ! spring strength (k_neb) | ||
| 0.03 ! tolerance of displacement (tol_displ_neb) | 0.03 ! tolerance of displacement (tol_displ_neb) | ||
| Line 80: | Line 86: | ||
| 1 ! restart (irestart) | 1 ! restart (irestart) | ||
| final.bas ! file name including the final configuration (file_neb)) | final.bas ! file name including the final configuration (file_neb)) | ||
| - | </pre> | + | </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.1257776245.txt.gz · Last modified: 2011/02/18 13:14 (external edit)
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