PLUMED-NEST-TEST-SITE

Project ID: plumID:19.049
Source: plumed_GeTe.dat
Originally used with PLUMED version: not specified
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

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

#SETTINGS NATOMS=32768
# Calculate the Steinhardt Q6 vector for each of the atoms in the system
# N.B. Fewer atoms are used here than were used in the paper for technical reasons
q6: Q6Calculate sixth order Steinhardt parameters. More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=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.={GAUSSIAN D_0=5.29 R_0=0.01 D_MAX=5.3} 
# Calculate the local Steinhardt parameter for each of the atoms in the system 
# in the manner described by ten Wolde and Frenkel.
The Q6 action with label q6 calculates the following quantities:
 Quantity   
 Description  
q6.value
the norms of the vectors of spherical harmonic coefficientslq6: LOCAL_Q6Calculate the local degree of order around an atoms by taking the average dot product between the q_6 vector on the central atom and the q_6 vector on the atoms in the first coordination sphere. More details SPECIESthe label of the action that computes the Steinhardt parameters for which you would like to calculate local steinhardt parameters=q6 SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={GAUSSIAN D_0=5.29 R_0=0.01 D_MAX=5.3} 
# Now select only those atoms that have a local q6 parameter that is larger than a certain threshold
The LOCAL_Q6 action with label lq6 calculates the following quantities:
 Quantity   
 Description  
lq6.value
the values of the local steinhardt parameters for the input atomsflq6: MORE_THANUse a switching function to determine how many of the input variables are more than a certain cutoff. More details ARGthe values input to this function=lq6 SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={GAUSSIAN D_0=0.19 R_0=0.01 D_MAX=0.2}
# Calculate the coordination number for those atoms that have a local q6 parameter that is larger than a certain threshold
The MORE_THAN action with label flq6 calculates the following quantities:
 Quantity   
 Description  
flq6.value
a function that is one if the if the input is more than a thresholdcc_cmat: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPspecifies the list of atoms that should be assumed indistinguishable=flq6 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.={GAUSSIAN D_0=3.59 R_0=0.01 D_MAX=3.6}
The CONTACT_MATRIX action with label cc_cmat calculates the following quantities:
 Quantity   
 Description  
cc_cmat.value
a matrix containing the weights for the bonds between each pair of atomsflq6_mat: OUTER_PRODUCTCalculate the outer product matrix of two vectors More details ARGthe labels of the two vectors from which the outer product is being computed=flq6,flq6
The OUTER_PRODUCT action with label flq6_mat calculates the following quantities:
 Quantity   
 Description  
flq6_mat.value
a matrix containing the outer product of the two input vectors that was obtained using the function that was inputcc_mat: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cc_cmat,flq6_mat 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
The CUSTOM action with label cc_mat calculates the following quantities:
 Quantity   
 Description  
cc_mat.value
an arbitrary functionones: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=200
The ONES action with label ones calculates the following quantities:
 Quantity   
 Description  
ones.value
a vector of ones with the required number of elementscc: 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=cc_mat,ones 
# Now select those atoms that are coordinated to six or more atoms that have a value for the local q6 parameter that is larger than 
# a certain threshold
The MATRIX_VECTOR_PRODUCT action with label cc calculates the following quantities:
 Quantity   
 Description  
cc.value
the vector that is obtained by taking the product between the matrix and the vector that were input
cc..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailsfcc: MORE_THANUse a switching function to determine how many of the input variables are more than a certain cutoff. More details ARGthe values input to this function=cc SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={GAUSSIAN D_0=5.99 R_0=0.01 D_MAX=6.0}
# Compute a contact matrix for the atoms that were selected using the previous command
The MORE_THAN action with label fcc calculates the following quantities:
 Quantity   
 Description  
fcc.value
a function that is one if the if the input is more than a thresholdmat_cmat: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPspecifies the list of atoms that should be assumed indistinguishable=q6 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.={GAUSSIAN D_0=3.59 R_0=0.01 D_MAX=3.6}
The CONTACT_MATRIX action with label mat_cmat calculates the following quantities:
 Quantity   
 Description  
mat_cmat.value
a matrix containing the weights for the bonds between each pair of atomsfcc_mat: OUTER_PRODUCTCalculate the outer product matrix of two vectors More details ARGthe labels of the two vectors from which the outer product is being computed=fcc,fcc 
The OUTER_PRODUCT action with label fcc_mat calculates the following quantities:
 Quantity   
 Description  
fcc_mat.value
a matrix containing the outer product of the two input vectors that was obtained using the function that was inputmat: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=mat_cmat,fcc_mat 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
# Perform a depth first search clustering on this matrix
The CUSTOM action with label mat calculates the following quantities:
 Quantity   
 Description  
mat.value
an arbitrary functiondfs: DFSCLUSTERINGFind the connected components of the matrix using the depth first search clustering algorithm. More details MATRIXthe input matrix (can use ARG instead)=mat
# Output the atoms in the largest cluster that was identified
The DFSCLUSTERING action with label dfs calculates the following quantities:
 Quantity   
 Description  
dfs.value
vector with length that is equal to the number of rows in the input matrixOUTPUT_CLUSTEROutput the indices of the atoms in one of the clusters identified by a clustering object More details ATOMSthe atoms for which clustering were performed=1-200 CLUSTERSthe action that performed the clustering=dfs CLUSTER which cluster would you like to look at 1 is the largest cluster, 2 is the second largest, 3 is the the third largest and so on=1 FILEthe name of the file on which to output the details of the cluster=cluster1.xyz
# Calculate the number of clusters that contain 27 or more atoms that have ordered neighbors. 
The OUTPUT_CLUSTER action with label  calculates somethingnclust: CLUSTER_DISTRIBUTIONCalculate functions of the distribution of properties in your connected components. More details ... 
  CLUSTERSthe label of the action that does the clustering=dfs WEIGHTSuse the vector of values calculated by this action as weights rather than giving each atom a unit weight=fcc
  MORE_THANcalculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={GAUSSIAN D_0=26.99 R_0=0.01 D_MAX=27}
... 
# Output the number of clusters to a file
The CLUSTER_DISTRIBUTION action with label nclust calculates the following quantities:
 Quantity   
 Description  
nclust.morethan
the number of colvars that have a value more than a thresholdPRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=nclust.* FILEthe name of the file on which to output these quantities=colvar