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
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#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 detailsSPECIES=1-200this keyword is used for colvars such as coordination numberSWITCH={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. lq6:the switching function that it used in the construction of the contact matrixLOCAL_Q6SPECIES=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 detailsSWITCH={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 flq6:This keyword is used if you want to employ an alternative to the continuous swiching function defined aboveMORE_THANUse a switching function to determine how many of the input variables are more than a certain cutoff. More detailsARG=lq6the input to this functionSWITCH={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 cc_cmat:This keyword is used if you want to employ an alternative to the continuous swiching function defined aboveCONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More detailsGROUP=flq6specifies the list of atoms that should be assumed indistinguishableSWITCH={GAUSSIAN D_0=3.59 R_0=0.01 D_MAX=3.6} flq6_mat:specify the switching function to use between two sets of indistinguishable atomsOUTER_PRODUCTCalculate the outer product matrix of two vectors More detailsARG=flq6,flq6 cc_mat:the input for this action is the scalar output from one or more other actionsCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=cc_cmat,flq6_matthe input to this functionFUNC=x*ythe function you wish to evaluatePERIODIC=NO ones:if the output of your function is periodic then you should specify the periodicity of the functionONESCreate a constant vector with all elements equal to one More detailsSIZE=200 cc:the number of ones that you would like to createMATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More detailsARG=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 fcc:the input for this action is the scalar output from one or more other actionsMORE_THANUse a switching function to determine how many of the input variables are more than a certain cutoff. More detailsARG=ccthe input to this functionSWITCH={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 mat_cmat:This keyword is used if you want to employ an alternative to the continuous swiching function defined aboveCONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More detailsGROUP=q6specifies the list of atoms that should be assumed indistinguishableSWITCH={GAUSSIAN D_0=3.59 R_0=0.01 D_MAX=3.6} fcc_mat:specify the switching function to use between two sets of indistinguishable atomsOUTER_PRODUCTCalculate the outer product matrix of two vectors More detailsARG=fcc,fcc mat:the input for this action is the scalar output from one or more other actionsCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=mat_cmat,fcc_matthe input to this functionFUNC=x*ythe function you wish to evaluatePERIODIC=NO # Perform a depth first search clustering on this matrix dfs:if the output of your function is periodic then you should specify the periodicity of the functionDFSCLUSTERINGFind the connected components of the matrix using the depth first search clustering algorithm. More detailsMATRIX=mat # Output the atoms in the largest cluster that was identifiedthe input matrix (can use ARG instead)OUTPUT_CLUSTEROutput the indices of the atoms in one of the clusters identified by a clustering object More detailsATOMS=1-200the atoms for which clustering were performedCLUSTERS=dfsthe action that performed the clusteringCLUSTER=1which 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 onFILE=cluster1.xyz # Calculate the number of clusters that contain 27 or more atoms that have ordered neighbors. nclust:the name of the file on which to output the details of the clusterCLUSTER_DISTRIBUTION...Calculate functions of the distribution of properties in your connected components. More detailsCLUSTERS=dfsthe label of the action that does the clusteringWEIGHTS=fccuse the vector of values calculated by this action as weights rather than giving each atom a unit weightMORE_THAN={GAUSSIAN D_0=26.99 R_0=0.01 D_MAX=27} ... # Output the number of clusters to a filecalculate the number of variables that are more than a certain target valuePrint quantities to a file. More detailsARG=nclustthe input for this action is the scalar output from one or more other actionsFILE=colvarthe name of the file on which to output these quantities