neb_simulation
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neb_simulation [2009/12/04 11:19] prokop |
neb_simulation [2011/02/18 13:13] (current) |
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| - | 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. | + | |
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| + | **Note**: The files ''answer_image.bas'' can be directly used for a restart of NEB-optimization process. | ||
| - | -- | ||
| ==== Main sources of convergence troubles: ==== | ==== 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. | + | * **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. | + | * **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. | + | * **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 ===== | ===== Restart ===== | ||
neb_simulation.1259921943.txt.gz · Last modified: 2011/02/18 13:14 (external edit)
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