PENALTYPOT: Difference between revisions
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File that defines the bias potential for a [[:Category:Biased molecular dynamics|biased molecular-dynamics]] run. | |||
< | At the beginning of each metadynamics simulation, VASP attempts to read the file {{TAG|PENALTYPOT}} containing the bias potential acting on the geometric parameters with <code>STATUS=5</code> defined in the {{TAG|ICONST}} file. In analogy to the time-dependent bias potential generated in metadynamics, the bias potential is defined as a superposition of Gaussian hills. Each line in the {{TAG|PENALTYPOT}} file represents one (multidimensional) Gaussian: | ||
where <math>x_1</math> to <math>x_m</math> stand for the position in the space of active coordinates, and <math>h</math> and <math>w</math> are the height and width of the Gaussian, respectively | ::<math>x_1 x_2 ... x_m h w </math>, | ||
where <math>x_1</math> to <math>x_m</math> stand for the position in the space of active coordinates, and <math>h</math> and <math>w</math> are the height and width of the Gaussian, respectively. Note that both positive and negative values are allowed for the parameter <math>h</math>. | |||
For example, if two active coordinates with <code>STATUS=5</code> are defined in the {{TAG|ICONST}} file: | |||
R 1 5 5 | R 1 5 5 | ||
R 1 6 5 | R 1 6 5 | ||
| Line 15: | Line 19: | ||
1.6 2.0 1.0 0.2 | 1.6 2.0 1.0 0.2 | ||
== Related | == Related tags and articles == | ||
{{TAG|MDALGO}},{{TAG|ICONST}} | {{TAG|MDALGO}}, {{TAG|ICONST}} | ||
---- | ---- | ||
[[Category:Files]][[Category:Input | [[Category:Files]][[Category:Input files]][[Category:Molecular dynamics]][[Category:Biased molecular dynamics]] | ||
Latest revision as of 10:52, 18 October 2023
File that defines the bias potential for a biased molecular-dynamics run.
At the beginning of each metadynamics simulation, VASP attempts to read the file PENALTYPOT containing the bias potential acting on the geometric parameters with STATUS=5 defined in the ICONST file. In analogy to the time-dependent bias potential generated in metadynamics, the bias potential is defined as a superposition of Gaussian hills. Each line in the PENALTYPOT file represents one (multidimensional) Gaussian:
- Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://www.vasp.at/wiki/restbase/vasp.at/v1/":): x_{1}x_{2}...x_{m}hw ,
where Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://www.vasp.at/wiki/restbase/vasp.at/v1/":): x_{1} to Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://www.vasp.at/wiki/restbase/vasp.at/v1/":): x_{m} stand for the position in the space of active coordinates, and Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://www.vasp.at/wiki/restbase/vasp.at/v1/":): h and Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://www.vasp.at/wiki/restbase/vasp.at/v1/":): w are the height and width of the Gaussian, respectively. Note that both positive and negative values are allowed for the parameter Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://www.vasp.at/wiki/restbase/vasp.at/v1/":): h .
For example, if two active coordinates with STATUS=5 are defined in the ICONST file:
R 1 5 5 R 1 6 5
then each line in the PENALTYPOT must contain four items. The bias potential is defined in the following lines:
1.6 0.8 1.0 0.2 1.6 1.0 1.0 0.2 1.6 1.2 1.0 0.2 1.6 1.4 1.0 0.2 1.6 1.6 1.0 0.2 1.6 1.8 1.0 0.2 1.6 2.0 1.0 0.2