PENALTYPOT: Difference between revisions

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:

x_{1}x_{2}...x_{m}hw

,

where $x_{1}$ to $x_{m}$ stand for the position in the space of active coordinates, and $h$ and $w$ are the height and width of the Gaussian, respectively. Note that both positive and negative values are allowed for the parameter $h$ .

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

@@ Line 1: / Line 1: @@
+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:
-<math>x_1 x_2 ... x_m  h w </math>
+::<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>.
-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:
+For example, if two active coordinates with <code>STATUS=5</code> are defined in the {{TAG|ICONST}} file:
   R 1 5 5
   R 1 6 5
@@ Line 16: / Line 20: @@
 == Related tags and articles ==
-{{TAG|MDALGO}},{{TAG|ICONST}}
+{{TAG|MDALGO}}, {{TAG|ICONST}}
 ----
-[[The_VASP_Manual|Contents]]
-[[Category:Files]][[Category:Input files]][[Category:Biased molecular dynamics]]
+[[Category:Files]][[Category:Input files]][[Category:Molecular dynamics]][[Category:Biased molecular dynamics]]