Action: GET_VOLUME_ELEMENT

Module	gridtools
Description	Usage
Get the volume element from the input grid
output value	type
the volume element	scalar

Details and examples

Get the volume element from the input grid

This action is used in the shortcut action that is used within PLUMED to calculate integrals as you can see below

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

c1The COORDINATIONNUMBER action with label c1 calculates the following quantities:
 Quantity   
 Type   
 Description  
c1
vector
the coordination numbers of the specified atoms: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut. More details SPECIESAthe list of atoms for which the symmetry function is being calculated=1-10 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=1-200 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.0}
# PLUMED interprets the command:
# c1: COORDINATIONNUMBER SPECIESA=1-10 SPECIESB=1-200 SWITCH={RATIONAL R_0=1.0}
# as follows (Click the red comment above to revert to the short version of the input):
c1_grpThe GROUP action with label c1_grp calculates the following quantities:
 Quantity   
 Type   
 Description  
c1_grp
atoms
indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1-10
c1_matThe CONTACT_MATRIX action with label c1_mat calculates the following quantities:
 Quantity   
 Type   
 Description  
c1_mat
matrix
a matrix containing the weights for the bonds between each pair of atoms: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPAwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPB=1-10 GROUPBwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPA=1-200 SWITCHthe input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.0}
c1_onesThe CONSTANT action with label c1_ones calculates the following quantities:
 Quantity   
 Type   
 Description  
c1_ones
vector
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=200
c1The MATRIX_VECTOR_PRODUCT action with label c1 calculates the following quantities:
 Quantity   
 Type   
 Description  
c1
vector
the vector that is obtained by taking the product between the matrix and the vector that were input: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details  ARGthe label for the matrix and the vector/scalar that are being multiplied=c1_mat,c1_ones
# --- End of included input --- huThe 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: KDECreate a histogram from the input scalar/vector/matrix using KDE This action has hidden defaults. More details ARGthe label for the value that should be used to construct the histogram=c1 GRID_BINthe number of bins for the grid=200 GRID_MIN the lower bounds for the grid=0 GRID_MAX the upper bounds for the grid=10 BANDWIDTHthe bandwidths for kernel density esimtation=0.1
hu: KDECreate a histogram from the input scalar/vector/matrix using KDE This action uses the defaults shown here. More details ARGthe label for the value that should be used to construct the histogram=c1 GRID_BINthe number of bins for the grid=200 GRID_MIN the lower bounds for the grid=0 GRID_MAX the upper bounds for the grid=10 BANDWIDTHthe bandwidths for kernel density esimtation=0.1  KERNEL the kernel function you are using=GAUSSIAN
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 FUNCthe function you wish to evaluate=x/10 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ivThe INTEGRATE_GRID action with label iv calculates the following quantities:
 Quantity   
 Type   
 Description  
iv
scalar
the numerical integral of the input function over its whole domain: INTEGRATE_GRIDCalculate the numerical integral of the function stored on the grid This action is a shortcut. More details ARGthe label of the function on a grid that is being integrated=h PERIODICif the value of the output integral has a periodid domain then you use this keyword to specify the periodicity=NO
# PLUMED interprets the command:
# iv: INTEGRATE_GRID ARG=h PERIODIC=NO
# as follows (Click the red comment above to revert to the short version of the input):
iv_volelemThe GET_VOLUME_ELEMENT action with label iv_volelem calculates the following quantities:
 Quantity   
 Type   
 Description  
iv_volelem
scalar
the volume element : GET_VOLUME_ELEMENTGet the volume element from the input grid More details ARGthe label for function on the grid that you need the volume element for=h
iv_sumThe SUM action with label iv_sum calculates the following quantities:
 Quantity   
 Type   
 Description  
iv_sum
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=h PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ivThe CUSTOM action with label iv calculates the following quantities:
 Quantity   
 Type   
 Description  
iv
scalar
an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=iv_volelem,iv_sum 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 --- 

As discused in the documentation for INTEGRATE_GRID we compute (approximate) integrals in PLUMED using:

$$y = \frac{b-a}{n} \sum_{i=0}^{n} f\left( a + \frac{i(b-a)}{n} \right)$$

This action gets the the value of $\frac{b-a}{n}$ so that we can multiply by this value by the sum in the expression above, which is computed by a SUM action.

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 function on the grid that you need the volume element for

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 function on the grid that you need the volume element for