Output the function on the grid to a file with the PLUMED grid format.

PLUMED provides a number of actions that calculate the values of functions on grids. For instance, whenever you calculate a free energy as a function of a collective variable using HISTOGRAM and CONVERT_TO_FES you will generally want to output the value of the free energy at a number of points on a discrete grid that covers the CV space uniformly. Alternatively you may want to calculate what value some symmetry function takes at different points inside your simulation cell using MULTICOLVARDENS.

This action allows you to output these functions calculated on a grid using a format that can be read in using gnuplot and other such plotting programs. The file output using this action will have a header that contains some essential information about the function plotted and that looks something like this:

#! FIELDS x y hA1 dhA1_x dhA1_x
#! SET normalisation    2.0000
#! SET min_x 0.0
#! SET max_x 3.0
#! SET nbins_x  100
#! SET periodic_x false
#! SET min_y 0.0
#! SET max_y 3.0
#! SET nbins_y  100
#! SET periodic_y false

The header shown here tells us that we have grid showing the values that a function with two arguments x and y takes at various points in our cell. The lines beneath the first line then tell us a little bit about these two input arguments.

The remaining lines of the file give us information on the positions of our grid points and the value the function and its partial derivatives with respect to x and y. If the header is as above a list of values of the function that have x=0 and 100 values of y between 0.0 and 3.0 will be provided. This block of data will be followed with a blank line. There will then be a second block of values which will all have been evaluated the same value of x and all possible values for y. This block is then followed by a blank line again and this pattern continues until all points of the grid have been covered.

Examples

The following input monitors two torsional angles during a simulation and outputs a continuous histogram as a function of them at the end of the simulation.

Click on the labels of the actions for more information on what each action computes

r1: TORSION ATOMSthe four atoms involved in the torsional angle 
=1,2,3,4 The TORSION action with label r1 calculates a single scalar value
r2: TORSION ATOMSthe four atoms involved in the torsional angle 
=2,3,4,5 The TORSION action with label r2 calculates a single scalar value
hh: HISTOGRAM ...
   ARGthe input for this action is the scalar output from one or more other actions. 
=r1,r2 
   GRID_MINcompulsory keyword 
the lower bounds for the grid =-3.14,-3.14 
   GRID_MAXcompulsory keyword 
the upper bounds for the grid =3.14,3.14 
   GRID_BINthe number of bins for the grid =200,200 
   BANDWIDTHcompulsory keyword 
the bandwidths for kernel density estimation =0.05,0.05 
   
...The HISTOGRAM action with label hh
DUMPGRID GRIDcompulsory keyword 
the action that creates the grid you would like to output 
=hh FILEcompulsory keyword ( default=density )
the file on which to write the grid. 
=histo The DUMPGRID action with label

The following input monitors two torsional angles during a simulation and outputs a discrete histogram as a function of them at the end of the simulation.

Click on the labels of the actions for more information on what each action computes

r1: TORSION ATOMSthe four atoms involved in the torsional angle 
=1,2,3,4 The TORSION action with label r1 calculates a single scalar value
r2: TORSION ATOMSthe four atoms involved in the torsional angle 
=2,3,4,5 The TORSION action with label r2 calculates a single scalar value
hh: HISTOGRAM ...
   ARGthe input for this action is the scalar output from one or more other actions. 
=r1,r2 
   KERNELcompulsory keyword ( default=gaussian )
the kernel function you are using. =DISCRETE 
   GRID_MINcompulsory keyword 
the lower bounds for the grid =-3.14,-3.14 
   GRID_MAXcompulsory keyword 
the upper bounds for the grid =3.14,3.14 
   GRID_BINthe number of bins for the grid =200,200 
   
...The HISTOGRAM action with label hh
DUMPGRID GRIDcompulsory keyword 
the action that creates the grid you would like to output 
=hh FILEcompulsory keyword ( default=density )
the file on which to write the grid. 
=histo The DUMPGRID action with label

The following input monitors two torsional angles during a simulation and outputs the histogram accumulated thus far every 100000 steps.

Click on the labels of the actions for more information on what each action computes

r1: TORSION ATOMSthe four atoms involved in the torsional angle 
=1,2,3,4 The TORSION action with label r1 calculates a single scalar value
r2: TORSION ATOMSthe four atoms involved in the torsional angle 
=2,3,4,5 The TORSION action with label r2 calculates a single scalar value
hh: HISTOGRAM ...
   ARGthe input for this action is the scalar output from one or more other actions. 
=r1,r2 
   GRID_MINcompulsory keyword 
the lower bounds for the grid =-3.14,-3.14 
   GRID_MAXcompulsory keyword 
the upper bounds for the grid =3.14,3.14 
   GRID_BINthe number of bins for the grid =200,200 
   BANDWIDTHcompulsory keyword 
the bandwidths for kernel density estimation =0.05,0.05 
   
...The HISTOGRAM action with label hh
DUMPGRID GRIDcompulsory keyword 
the action that creates the grid you would like to output 
=hh FILEcompulsory keyword ( default=density )
the file on which to write the grid. 
=histo STRIDEcompulsory keyword ( default=0 )
the frequency with which the grid should be output to the file. 
=100000 The DUMPGRID action with label

The following input monitors two torsional angles during a simulation and outputs a separate histogram for each 100000 steps worth of trajectory. Notice how the CLEAR keyword is used here and how it is not used in the previous example.

Click on the labels of the actions for more information on what each action computes

r1: TORSION ATOMSthe four atoms involved in the torsional angle 
=1,2,3,4 The TORSION action with label r1 calculates a single scalar value
r2: TORSION ATOMSthe four atoms involved in the torsional angle 
=2,3,4,5 The TORSION action with label r2 calculates a single scalar value
hh: HISTOGRAM ...
   ARGthe input for this action is the scalar output from one or more other actions. 
=r1,r2 CLEARcompulsory keyword ( default=0 )
the frequency with which to clear all the accumulated data. =100000 
   GRID_MINcompulsory keyword 
the lower bounds for the grid =-3.14,-3.14 
   GRID_MAXcompulsory keyword 
the upper bounds for the grid =3.14,3.14 
   GRID_BINthe number of bins for the grid =200,200 
   BANDWIDTHcompulsory keyword 
the bandwidths for kernel density estimation =0.05,0.05 
   
...The HISTOGRAM action with label hh
DUMPGRID GRIDcompulsory keyword 
the action that creates the grid you would like to output 
=hh FILEcompulsory keyword ( default=density )
the file on which to write the grid. 
=histo STRIDEcompulsory keyword ( default=0 )
the frequency with which the grid should be output to the file. 
=100000 The DUMPGRID action with label

Glossary of keywords and components

Compulsory keywords

GRID	the action that creates the grid you would like to output
STRIDE	( default=0 ) the frequency with which the grid should be output to the file. The default value of 0 ensures that the grid is only output at the end of the trajectory
FILE	( default=density ) the file on which to write the grid.
REPLICA	( default=0 ) the replica for which you would like to output this information

Options

FMT

the format that should be used to output real numbers