Shortcut: TETRA_RADIAL

Module	symfunc
Description	Usage
Calculate the radial tetra CV
output value	type
the value of the radial tetrahedrality parameter for each of the input atoms	vector

Output components

This action can calculate the values in the following table when the associated keyword is included in the input for the action. These values can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the value required from the list below.

Input

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

Further details and examples

Calculate the radial tetra CV

This shortcut calculates a symmetry function. The particular function that is being evaluated for the coordination sphere here is as follows:

$$s_i = 1 - \frac{\sum_{j=1}^4 r_{ij}^2 - z_i\sum_{j=1}^4 r_{ij}}{12 z_i^2} \qquad \textrm{where} \qquad z_i = \frac{1}{4} \sum_{j=1}^4 r_{ij}$$

In this expression the 4 atoms in the sums over $j$ are the four atoms that are nearest to atom $i$ and $r_{ij}$ is the distance between atoms $i$ and $j$. The CV is large if the four atoms nearest atom $i$ are arranged on the vertices of a regular tetrahedron and small otherwise. The following example shows how you can use this action to measure the degree of tetrahedral order in a system.

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

# Calculate a vector that contains 64 values for the symmetry function.
# Sum the elements of the vector and calculate the mean value on the atoms from this sum.
acvThe TETRA_RADIAL action with label acv calculates the following quantities:
 Quantity   
 Type   
 Description  
acv
vector
the value of the radial tetrahedrality parameter for each of the input atoms
acv_sum
scalar
the sum of the colvars
acv_mean
scalar
the mean of the colvars: TETRA_RADIALCalculate the radial tetra CV This action is a shortcut and it has hidden defaults. More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-64 SUM calculate the sum of all the quantities MEAN calculate the mean of all the quantities
acv: TETRA_RADIALCalculate the radial tetra CV This action is a shortcut and uses the defaults shown here. More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-64 SUM calculate the sum of all the quantities MEAN calculate the mean of all the quantities  CUTOFF ignore distances that have a value larger than this cutoff=-1
# PLUMED interprets the command:
# acv: TETRA_RADIAL SPECIES=1-64 SUM MEAN
# as follows (Click the red comment above to revert to the short version of the input):
acv_matThe DISTANCE_MATRIX action with label acv_mat calculates the following quantities:
 Quantity   
 Type   
 Description  
acv_mat
matrix
a matrix containing the weights for the bonds between each pair of atoms: DISTANCE_MATRIXCalculate a matrix of distances between atoms. More details GROUPthe atoms for which you would like to calculate the adjacency matrix=1-64 CUTOFF ignore distances that have a value larger than this cutoff=-1
acv_neighThe NEIGHBORS action with label acv_neigh calculates the following quantities:
 Quantity   
 Type   
 Description  
acv_neigh
matrix
a matrix in which the ij element is one if the ij-element of the input matrix is one of the NLOWEST/NHIGHEST elements on that row of the input matrix and zero otherwise: NEIGHBORSBuild a matrix with ones in for the N nearest neighbours of an atom More details ARGthe label of an adjacency/distance matrix that will be used to find the nearest neighbors=acv_mat NLOWEST in each row of the output matrix set the elements that correspond to the n lowest elements in each row of the input matrix equal to one=4
acv_near4The CUSTOM action with label acv_near4 calculates the following quantities:
 Quantity   
 Type   
 Description  
acv_near4
matrix
the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=acv_mat,acv_neigh 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
acv_onesThe CONSTANT action with label acv_ones calculates the following quantities:
 Quantity   
 Type   
 Description  
acv_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=64
acv_sum4The MATRIX_VECTOR_PRODUCT action with label acv_sum4 calculates the following quantities:
 Quantity   
 Type   
 Description  
acv_sum4
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=acv_near4,acv_ones
acv_near4_2The CUSTOM action with label acv_near4_2 calculates the following quantities:
 Quantity   
 Type   
 Description  
acv_near4_2
matrix
the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=acv_near4 FUNCthe function you wish to evaluate=x*x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
acv_sum4_2The MATRIX_VECTOR_PRODUCT action with label acv_sum4_2 calculates the following quantities:
 Quantity   
 Type   
 Description  
acv_sum4_2
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=acv_near4_2,acv_ones
acv_meanrThe CUSTOM action with label acv_meanr calculates the following quantities:
 Quantity   
 Type   
 Description  
acv_meanr
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=acv_sum4 FUNCthe function you wish to evaluate=0.25*x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
acvThe CUSTOM action with label acv calculates the following quantities:
 Quantity   
 Type   
 Description  
acv
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=acv_sum4,acv_sum4_2,acv_meanr FUNCthe function you wish to evaluate=(1-(y-x*z)/(12*z*z)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
acv_sumThe SUM action with label acv_sum calculates the following quantities:
 Quantity   
 Type   
 Description  
acv_sum
scalar
the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=acv PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
acv_meanThe MEAN action with label acv_mean calculates the following quantities:
 Quantity   
 Type   
 Description  
acv_mean
scalar
the mean of all the elements in the input vector: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=acv PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- # Print out the positions of the 64 atoms for which the symmetry function was calculated
# to an xyz file along with the values of the symmetry function
DUMPATOMSDump selected atoms on a file. More details ATOMSthe atom indices whose positions you would like to print out=1-64 ARGthe labels of vectors that should be output in the xyz file=acv FILEfile on which to output coordinates; extension is automatically detected=mcolv.xyz
# Print out the average value of the symmetry function and the sum of all the symmetry functions
The DUMPATOMS action with label  calculates somethingPRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=acv_sum,acv_mean FILEthe name of the file on which to output these quantities=colvar

References

More information about how this action can be used is available in the following articles: - A. D. White, G. A. Voth, Efficient and Minimal Method to Bias Molecular Simulations with Experimental Data. Journal of Chemical Theory and Computation. 10, 3023–3030 (2014)

Syntax

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