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PLUMED manual

Action: DUMPGRID

Action: DUMPGRID

Module	gridtools
Description	Usage
Output the function on the grid to a file with the PLUMED grid format.
This action outputs data to a file. You can read more about how PLUMED manages output files here

Details and examples

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 KDE, 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 or some suitable combination of CUSTOM actions.

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

r1The TORSION action with label r1 calculates the following quantities: Quantity    Type    Description  
r1 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=1,2,3,4
r2The TORSION action with label r2 calculates the following quantities: Quantity    Type    Description  
r2 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=2,3,4,5
hhThe HISTOGRAM action with label hh calculates the following quantities: Quantity    Type    Description  
hh grid the estimate of the histogram as a function of the argument that was obtained: HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details ...
  ARGthe quantities that are being used to construct the histogram=r1,r2
  GRID_MIN the lower bounds for the grid=-3.14,-3.14
  GRID_MAX the upper bounds for the grid=3.14,3.14
  GRID_BINthe number of bins for the grid=200,200
  BANDWIDTHthe bandwidths for kernel density esimtation=0.05,0.05
...
hh: HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details ...
  ARGthe quantities that are being used to construct the histogram=r1,r2
  GRID_MIN the lower bounds for the grid=-3.14,-3.14
  GRID_MAX the upper bounds for the grid=3.14,3.14
  GRID_BINthe number of bins for the grid=200,200
  BANDWIDTHthe bandwidths for kernel density esimtation=0.05,0.05
 NORMALIZATION This controls how the data is normalized it can be set equal to true, false or ndata=ndata STRIDE the frequency with which to store data for averaging=1 CLEAR the frequency with whihc to clear the data that is being averaged=0
...
# PLUMED interprets the command:
# hh: HISTOGRAM ...
#   ARG=r1,r2
#   GRID_MIN=-3.14,-3.14
#   GRID_MAX=3.14,3.14
#   GRID_BIN=200,200
#   BANDWIDTH=0.05,0.05
# ...
# as follows (Click the red comment above to revert to the short version of the input):
hh_weightThe CONSTANT action with label hh_weight calculates the following quantities: Quantity    Type    Description  
hh_weight scalar the constant value that was read from the plumed input: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=1
hh_kdeThe KDE action with label hh_kde calculates the following quantities: Quantity    Type    Description  
hh_kde grid a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: KDECreate a histogram from the input scalar/vector/matrix using KDE More details ARGthe label for the value that should be used to construct the histogram=r1,r2  GRID_MIN the lower bounds for the grid=-3.14,-3.14 GRID_MAX the upper bounds for the grid=3.14,3.14 GRID_BINthe number of bins for the grid=200,200 BANDWIDTHthe bandwidths for kernel density esimtation=0.05,0.05
hh_kdepThe CUSTOM action with label hh_kdep calculates the following quantities: Quantity    Type    Description  
hh_kdep grid the grid obtained by doing an element-wise application of an arbitrary function to the input grid: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=hh_kde,hh_weight FUNCthe function you wish to evaluate=x*y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
hh_uThe ACCUMULATE action with label hh_u calculates the following quantities: Quantity    Type    Description  
hh_u grid a sum calculated from the time series of the input quantity: ACCUMULATESum the elements of this value over the course of the trajectory More details ARGthe label of the argument that is being added to on each timestep=hh_kdep STRIDE the frequency with which the data should be collected and added to the quantity being averaged=1 CLEAR the frequency with which to clear all the accumulated data=0 
hh_nsumThe ACCUMULATE action with label hh_nsum calculates the following quantities: Quantity    Type    Description  
hh_nsum scalar a sum calculated from the time series of the input quantity: ACCUMULATESum the elements of this value over the course of the trajectory More details ARGthe label of the argument that is being added to on each timestep=hh_weight STRIDE the frequency with which the data should be collected and added to the quantity being averaged=1 CLEAR the frequency with which to clear all the accumulated data=0 
hhThe CUSTOM action with label hh calculates the following quantities: Quantity    Type    Description  
hh grid the grid obtained by doing an element-wise application of an arbitrary function to the input grid: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=hh_u,hh_nsum FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- 
DUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details ARGthe label for the grid that you would like to output=hh FILE the file on which to write the grid=histo

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. In this input we have also used the FMT keyword to control the appearance of the numbers in the output file.

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

r1The TORSION action with label r1 calculates the following quantities: Quantity    Type    Description  
r1 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=1,2,3,4
r2The TORSION action with label r2 calculates the following quantities: Quantity    Type    Description  
r2 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=2,3,4,5
hhThe HISTOGRAM action with label hh calculates the following quantities: Quantity    Type    Description  
hh grid the estimate of the histogram as a function of the argument that was obtained: HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details ...
  ARGthe quantities that are being used to construct the histogram=r1,r2
  KERNEL the kernel function you are using=DISCRETE
  GRID_MIN the lower bounds for the grid=-3.14,-3.14
  GRID_MAX the upper bounds for the grid=3.14,3.14
  GRID_BINthe number of bins for the grid=200,200
...
hh: HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details ...
  ARGthe quantities that are being used to construct the histogram=r1,r2
  KERNEL the kernel function you are using=DISCRETE
  GRID_MIN the lower bounds for the grid=-3.14,-3.14
  GRID_MAX the upper bounds for the grid=3.14,3.14
  GRID_BINthe number of bins for the grid=200,200
 NORMALIZATION This controls how the data is normalized it can be set equal to true, false or ndata=ndata STRIDE the frequency with which to store data for averaging=1 CLEAR the frequency with whihc to clear the data that is being averaged=0
...
# PLUMED interprets the command:
# hh: HISTOGRAM ...
#   ARG=r1,r2
#   KERNEL=DISCRETE
#   GRID_MIN=-3.14,-3.14
#   GRID_MAX=3.14,3.14
#   GRID_BIN=200,200
# ...
# as follows (Click the red comment above to revert to the short version of the input):
hh_weightThe CONSTANT action with label hh_weight calculates the following quantities: Quantity    Type    Description  
hh_weight scalar the constant value that was read from the plumed input: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=1
hh_kdeThe KDE action with label hh_kde calculates the following quantities: Quantity    Type    Description  
hh_kde grid a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: KDECreate a histogram from the input scalar/vector/matrix using KDE More details ARGthe label for the value that should be used to construct the histogram=r1,r2  KERNEL the kernel function you are using=DISCRETE GRID_MIN the lower bounds for the grid=-3.14,-3.14 GRID_MAX the upper bounds for the grid=3.14,3.14 GRID_BINthe number of bins for the grid=200,200
hh_kdepThe CUSTOM action with label hh_kdep calculates the following quantities: Quantity    Type    Description  
hh_kdep grid the grid obtained by doing an element-wise application of an arbitrary function to the input grid: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=hh_kde,hh_weight FUNCthe function you wish to evaluate=x*y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
hh_uThe ACCUMULATE action with label hh_u calculates the following quantities: Quantity    Type    Description  
hh_u grid a sum calculated from the time series of the input quantity: ACCUMULATESum the elements of this value over the course of the trajectory More details ARGthe label of the argument that is being added to on each timestep=hh_kdep STRIDE the frequency with which the data should be collected and added to the quantity being averaged=1 CLEAR the frequency with which to clear all the accumulated data=0 
hh_nsumThe ACCUMULATE action with label hh_nsum calculates the following quantities: Quantity    Type    Description  
hh_nsum scalar a sum calculated from the time series of the input quantity: ACCUMULATESum the elements of this value over the course of the trajectory More details ARGthe label of the argument that is being added to on each timestep=hh_weight STRIDE the frequency with which the data should be collected and added to the quantity being averaged=1 CLEAR the frequency with which to clear all the accumulated data=0 
hhThe CUSTOM action with label hh calculates the following quantities: Quantity    Type    Description  
hh grid the grid obtained by doing an element-wise application of an arbitrary function to the input grid: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=hh_u,hh_nsum FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- 
DUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details ARGthe label for the grid that you would like to output=hh FILE the file on which to write the grid=histo FMTthe format that should be used to output real numbers=%10.6f

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

r1The TORSION action with label r1 calculates the following quantities: Quantity    Type    Description  
r1 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=1,2,3,4
r2The TORSION action with label r2 calculates the following quantities: Quantity    Type    Description  
r2 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=2,3,4,5
hhThe HISTOGRAM action with label hh calculates the following quantities: Quantity    Type    Description  
hh grid the estimate of the histogram as a function of the argument that was obtained: HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details ...
  ARGthe quantities that are being used to construct the histogram=r1,r2
  GRID_MIN the lower bounds for the grid=-3.14,-3.14
  GRID_MAX the upper bounds for the grid=3.14,3.14
  GRID_BINthe number of bins for the grid=200,200
  BANDWIDTHthe bandwidths for kernel density esimtation=0.05,0.05
...
hh: HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details ...
  ARGthe quantities that are being used to construct the histogram=r1,r2
  GRID_MIN the lower bounds for the grid=-3.14,-3.14
  GRID_MAX the upper bounds for the grid=3.14,3.14
  GRID_BINthe number of bins for the grid=200,200
  BANDWIDTHthe bandwidths for kernel density esimtation=0.05,0.05
 NORMALIZATION This controls how the data is normalized it can be set equal to true, false or ndata=ndata STRIDE the frequency with which to store data for averaging=1 CLEAR the frequency with whihc to clear the data that is being averaged=0
...
# PLUMED interprets the command:
# hh: HISTOGRAM ...
#   ARG=r1,r2
#   GRID_MIN=-3.14,-3.14
#   GRID_MAX=3.14,3.14
#   GRID_BIN=200,200
#   BANDWIDTH=0.05,0.05
# ...
# as follows (Click the red comment above to revert to the short version of the input):
hh_weightThe CONSTANT action with label hh_weight calculates the following quantities: Quantity    Type    Description  
hh_weight scalar the constant value that was read from the plumed input: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=1
hh_kdeThe KDE action with label hh_kde calculates the following quantities: Quantity    Type    Description  
hh_kde grid a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: KDECreate a histogram from the input scalar/vector/matrix using KDE More details ARGthe label for the value that should be used to construct the histogram=r1,r2  GRID_MIN the lower bounds for the grid=-3.14,-3.14 GRID_MAX the upper bounds for the grid=3.14,3.14 GRID_BINthe number of bins for the grid=200,200 BANDWIDTHthe bandwidths for kernel density esimtation=0.05,0.05
hh_kdepThe CUSTOM action with label hh_kdep calculates the following quantities: Quantity    Type    Description  
hh_kdep grid the grid obtained by doing an element-wise application of an arbitrary function to the input grid: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=hh_kde,hh_weight FUNCthe function you wish to evaluate=x*y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
hh_uThe ACCUMULATE action with label hh_u calculates the following quantities: Quantity    Type    Description  
hh_u grid a sum calculated from the time series of the input quantity: ACCUMULATESum the elements of this value over the course of the trajectory More details ARGthe label of the argument that is being added to on each timestep=hh_kdep STRIDE the frequency with which the data should be collected and added to the quantity being averaged=1 CLEAR the frequency with which to clear all the accumulated data=0 
hh_nsumThe ACCUMULATE action with label hh_nsum calculates the following quantities: Quantity    Type    Description  
hh_nsum scalar a sum calculated from the time series of the input quantity: ACCUMULATESum the elements of this value over the course of the trajectory More details ARGthe label of the argument that is being added to on each timestep=hh_weight STRIDE the frequency with which the data should be collected and added to the quantity being averaged=1 CLEAR the frequency with which to clear all the accumulated data=0 
hhThe CUSTOM action with label hh calculates the following quantities: Quantity    Type    Description  
hh grid the grid obtained by doing an element-wise application of an arbitrary function to the input grid: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=hh_u,hh_nsum FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- 
DUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details ARGthe label for the grid that you would like to output=hh FILE the file on which to write the grid=histo STRIDE the frequency with which the grid should be output to the file=100000

By default each of the histogram estimates are output to separate files. There will thus be one file called analysis.0.histo which contains the histogram that was obtained from the first 100000 steps of the simulation. The file analysis.1.histo contains the histogram that was obtained from the first 200000 steps of the simulation and so on until the final estimate of the histogram is output to a file called histo. If you would like to output all estimates of the histogram to a single file you can use the PRINT_ONE_FILE keyword as shown below:

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

r1The TORSION action with label r1 calculates the following quantities: Quantity    Type    Description  
r1 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=1,2,3,4
r2The TORSION action with label r2 calculates the following quantities: Quantity    Type    Description  
r2 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=2,3,4,5
hhThe HISTOGRAM action with label hh calculates the following quantities: Quantity    Type    Description  
hh grid the estimate of the histogram as a function of the argument that was obtained: HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details ...
  ARGthe quantities that are being used to construct the histogram=r1,r2
  GRID_MIN the lower bounds for the grid=-3.14,-3.14
  GRID_MAX the upper bounds for the grid=3.14,3.14
  GRID_BINthe number of bins for the grid=200,200
  BANDWIDTHthe bandwidths for kernel density esimtation=0.05,0.05
...
hh: HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details ...
  ARGthe quantities that are being used to construct the histogram=r1,r2
  GRID_MIN the lower bounds for the grid=-3.14,-3.14
  GRID_MAX the upper bounds for the grid=3.14,3.14
  GRID_BINthe number of bins for the grid=200,200
  BANDWIDTHthe bandwidths for kernel density esimtation=0.05,0.05
 NORMALIZATION This controls how the data is normalized it can be set equal to true, false or ndata=ndata STRIDE the frequency with which to store data for averaging=1 CLEAR the frequency with whihc to clear the data that is being averaged=0
...
# PLUMED interprets the command:
# hh: HISTOGRAM ...
#   ARG=r1,r2
#   GRID_MIN=-3.14,-3.14
#   GRID_MAX=3.14,3.14
#   GRID_BIN=200,200
#   BANDWIDTH=0.05,0.05
# ...
# as follows (Click the red comment above to revert to the short version of the input):
hh_weightThe CONSTANT action with label hh_weight calculates the following quantities: Quantity    Type    Description  
hh_weight scalar the constant value that was read from the plumed input: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=1
hh_kdeThe KDE action with label hh_kde calculates the following quantities: Quantity    Type    Description  
hh_kde grid a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: KDECreate a histogram from the input scalar/vector/matrix using KDE More details ARGthe label for the value that should be used to construct the histogram=r1,r2  GRID_MIN the lower bounds for the grid=-3.14,-3.14 GRID_MAX the upper bounds for the grid=3.14,3.14 GRID_BINthe number of bins for the grid=200,200 BANDWIDTHthe bandwidths for kernel density esimtation=0.05,0.05
hh_kdepThe CUSTOM action with label hh_kdep calculates the following quantities: Quantity    Type    Description  
hh_kdep grid the grid obtained by doing an element-wise application of an arbitrary function to the input grid: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=hh_kde,hh_weight FUNCthe function you wish to evaluate=x*y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
hh_uThe ACCUMULATE action with label hh_u calculates the following quantities: Quantity    Type    Description  
hh_u grid a sum calculated from the time series of the input quantity: ACCUMULATESum the elements of this value over the course of the trajectory More details ARGthe label of the argument that is being added to on each timestep=hh_kdep STRIDE the frequency with which the data should be collected and added to the quantity being averaged=1 CLEAR the frequency with which to clear all the accumulated data=0 
hh_nsumThe ACCUMULATE action with label hh_nsum calculates the following quantities: Quantity    Type    Description  
hh_nsum scalar a sum calculated from the time series of the input quantity: ACCUMULATESum the elements of this value over the course of the trajectory More details ARGthe label of the argument that is being added to on each timestep=hh_weight STRIDE the frequency with which the data should be collected and added to the quantity being averaged=1 CLEAR the frequency with which to clear all the accumulated data=0 
hhThe CUSTOM action with label hh calculates the following quantities: Quantity    Type    Description  
hh grid the grid obtained by doing an element-wise application of an arbitrary function to the input grid: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=hh_u,hh_nsum FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- 
DUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details ARGthe label for the grid that you would like to output=hh FILE the file on which to write the grid=histo STRIDE the frequency with which the grid should be output to the file=100000 PRINT_ONE_FILE output grids one after the other in a single file

Now all estimates of the histogram are contained in a single file called histo.

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 two examples.

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

r1The TORSION action with label r1 calculates the following quantities: Quantity    Type    Description  
r1 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=1,2,3,4
r2The TORSION action with label r2 calculates the following quantities: Quantity    Type    Description  
r2 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=2,3,4,5
hhThe HISTOGRAM action with label hh calculates the following quantities: Quantity    Type    Description  
hh grid the estimate of the histogram as a function of the argument that was obtained: HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details ...
  ARGthe quantities that are being used to construct the histogram=r1,r2 CLEAR the frequency with whihc to clear the data that is being averaged=100000
  GRID_MIN the lower bounds for the grid=-3.14,-3.14
  GRID_MAX the upper bounds for the grid=3.14,3.14
  GRID_BINthe number of bins for the grid=200,200
  BANDWIDTHthe bandwidths for kernel density esimtation=0.05,0.05
...
hh: HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details ...
  ARGthe quantities that are being used to construct the histogram=r1,r2 CLEAR the frequency with whihc to clear the data that is being averaged=100000
  GRID_MIN the lower bounds for the grid=-3.14,-3.14
  GRID_MAX the upper bounds for the grid=3.14,3.14
  GRID_BINthe number of bins for the grid=200,200
  BANDWIDTHthe bandwidths for kernel density esimtation=0.05,0.05
 NORMALIZATION This controls how the data is normalized it can be set equal to true, false or ndata=ndata STRIDE the frequency with which to store data for averaging=1
...
# PLUMED interprets the command:
# hh: HISTOGRAM ...
#   ARG=r1,r2 CLEAR=100000
#   GRID_MIN=-3.14,-3.14
#   GRID_MAX=3.14,3.14
#   GRID_BIN=200,200
#   BANDWIDTH=0.05,0.05
# ...
# as follows (Click the red comment above to revert to the short version of the input):
hh_weightThe CONSTANT action with label hh_weight calculates the following quantities: Quantity    Type    Description  
hh_weight scalar the constant value that was read from the plumed input: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=1
hh_kdeThe KDE action with label hh_kde calculates the following quantities: Quantity    Type    Description  
hh_kde grid a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: KDECreate a histogram from the input scalar/vector/matrix using KDE More details ARGthe label for the value that should be used to construct the histogram=r1,r2  GRID_MIN the lower bounds for the grid=-3.14,-3.14 GRID_MAX the upper bounds for the grid=3.14,3.14 GRID_BINthe number of bins for the grid=200,200 BANDWIDTHthe bandwidths for kernel density esimtation=0.05,0.05
hh_kdepThe CUSTOM action with label hh_kdep calculates the following quantities: Quantity    Type    Description  
hh_kdep grid the grid obtained by doing an element-wise application of an arbitrary function to the input grid: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=hh_kde,hh_weight FUNCthe function you wish to evaluate=x*y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
hh_uThe ACCUMULATE action with label hh_u calculates the following quantities: Quantity    Type    Description  
hh_u grid a sum calculated from the time series of the input quantity: ACCUMULATESum the elements of this value over the course of the trajectory More details ARGthe label of the argument that is being added to on each timestep=hh_kdep STRIDE the frequency with which the data should be collected and added to the quantity being averaged=1 CLEAR the frequency with which to clear all the accumulated data=100000 
hh_nsumThe ACCUMULATE action with label hh_nsum calculates the following quantities: Quantity    Type    Description  
hh_nsum scalar a sum calculated from the time series of the input quantity: ACCUMULATESum the elements of this value over the course of the trajectory More details ARGthe label of the argument that is being added to on each timestep=hh_weight STRIDE the frequency with which the data should be collected and added to the quantity being averaged=1 CLEAR the frequency with which to clear all the accumulated data=100000 
hhThe CUSTOM action with label hh calculates the following quantities: Quantity    Type    Description  
hh grid the grid obtained by doing an element-wise application of an arbitrary function to the input grid: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=hh_u,hh_nsum FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- 
DUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details ARGthe label for the grid that you would like to output=hh FILE the file on which to write the grid=histo STRIDE the frequency with which the grid should be output to the file=100000

Working with Fibonacci grids

If you have accumulated a histogram using the SPHERICAL_KDE keyword as has been done in the following input, we recommend you use the PRINT_XYZ keyword when using DUMPGRID as shown below:

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

d1The DISTANCE action with label d1 calculates the following quantities: Quantity    Type    Description  
d1 vector the DISTANCE for each set of specified atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=1,2 ATOMS2the pair of atom that we are calculating the distance between=1,3 ATOMS3the pair of atom that we are calculating the distance between=1,4 ATOMS4the pair of atom that we are calculating the distance between=1,5 ATOMS5the pair of atom that we are calculating the distance between=2,3 ATOMS6the pair of atom that we are calculating the distance between=2,4 ATOMS7the pair of atom that we are calculating the distance between=2,5 ATOMS8the pair of atom that we are calculating the distance between=3,4 ATOMS9the pair of atom that we are calculating the distance between=3,5 ATOMS10the pair of atom that we are calculating the distance between=4,5
d1ltThe LESS_THAN action with label d1lt calculates the following quantities: Quantity    Type    Description  
d1lt vector the vector obtained by doing an element-wise application of a function that is one if the input is less than a threshold to the input vectors: LESS_THANUse a switching function to determine how many of the input variables are less than a certain cutoff. More details ARGthe values input to this function=d1 SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL D_0=2.0 R_0=0.5 D_MAX=5.0}
d1ltsThe SUM action with label d1lts calculates the following quantities: Quantity    Type    Description  
d1lts scalar the SUM of the elements in the input value: SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=d1lt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d1cThe DISTANCE action with label d1c calculates the following quantities: Quantity    Type    Description  
d1c.x vector the x-component of the vector connecting the two atoms
d1c.y vector the y-component of the vector connecting the two atoms
d1c.z vector the z-component of the vector connecting the two atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=2,1 ATOMS2the pair of atom that we are calculating the distance between=3,1 ATOMS3the pair of atom that we are calculating the distance between=4,1 ATOMS4the pair of atom that we are calculating the distance between=5,1 ATOMS5the pair of atom that we are calculating the distance between=3,2 ATOMS6the pair of atom that we are calculating the distance between=4,2 ATOMS7the pair of atom that we are calculating the distance between=5,2 ATOMS8the pair of atom that we are calculating the distance between=4,3 ATOMS9the pair of atom that we are calculating the distance between=5,3 ATOMS10the pair of atom that we are calculating the distance between=5,4 COMPONENTS calculate the x, y and z components of the distance separately and store them as label
b1_xThe CUSTOM action with label b1_x calculates the following quantities: Quantity    Type    Description  
b1_x vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=d1c.x,d1 FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
b1_yThe CUSTOM action with label b1_y calculates the following quantities: Quantity    Type    Description  
b1_y vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=d1c.y,d1 FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
b1_zThe CUSTOM action with label b1_z calculates the following quantities: Quantity    Type    Description  
b1_z vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=d1c.z,d1 FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
huThe SPHERICAL_KDE action with label hu calculates the following quantities: Quantity    Type    Description  
hu grid a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: SPHERICAL_KDECreate a histogram from the input scalar/vector/matrix using SPHERICAL_KDE More details HEIGHTSthis keyword takes the label of an action that calculates a vector of values=d1lt ARGthe label for the value that should be used to construct the histogram=b1_x,b1_y,b1_z CONCENTRATIONthe concentration parameter for the Von Mises-Fisher distributions=100 GRID_BINthe number of bins for the grid=144
hThe CUSTOM action with label h calculates the following quantities: Quantity    Type    Description  
h grid the grid obtained by doing an element-wise application of an arbitrary function to the input grid: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=hu,d1lts FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
DUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details PRINT_XYZ output coordinates on fibonacci grid to xyz file ARGthe label for the grid that you would like to output=h PRINT_ONE_FILE output grids one after the other in a single file STRIDE the frequency with which the grid should be output to the file=1 FILE the file on which to write the grid=allkde.xyz

This input outputs an xyz file in which atom represents one of the grid points on your spherical grid. These atoms are shifted in and out radially based on the value of the function at the grid point.

Input

The arguments that serve as the input for this action are specified using one or more of the keywords in the following table.

Keyword	Type	Description
ARG	grid	the label for the grid that you would like to output

Full list of keywords

The following table describes the keywords and options that can be used with this action

Keyword	Type	Default	Description
ARG	input	none	the label for the grid that you would like to output
STRIDE	compulsory	0	the frequency with which the grid should be output to the file
FILE	compulsory	density	the file on which to write the grid
FMT	optional	not used	the format that should be used to output real numbers
PRINT_XYZ	optional	false	output coordinates on fibonacci grid to xyz file
PRINT_ONE_FILE	optional	false	output grids one after the other in a single file

deprecated keywords

The keywords in the following table can still be used with this action but have been deprecated

Keyword	Description
GRID	You should use ARG instead of this keyword which was used in older versions of PLUMED and is provided for back compatibility only