PLUMED-NEST-TEST-SITE

Project ID: plumID:19.049
Source: plumed_urea.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
# Use the vector connecting the carbon and oxygen atoms of each urea
# molecule in the system to define the orientations of the molecules 
m1: DISTANCESCalculate the distances between multiple piars of atoms More details ...
  ATOMS1the pairs of atoms that you would like to calculate the angles for=1,2 LOCATION1the location at which the CV is assumed to be in space=1
  ATOMS2the pairs of atoms that you would like to calculate the angles for=9,10 LOCATION2the location at which the CV is assumed to be in space=9
  COMPONENTS calculate the x, y and z components of the distance separately and store them as label
...	 

# Calculate the SMAC parameter for each of the molecules.  Essentially
# measures whether or not molecules in the first coordination sphere 
# have a similar orientation to the central molecule.
The DISTANCES action with label m1 calculates the following quantities:
 Quantity   
 Description  
m1.value
the DISTANCES between the each pair of atoms that were specified
m1.x
the x-components of the distance vectors
m1.y
the y-components of the distance vectors
m1.z
the z-components of the distance vectorssmac: SMACCalculate the SMAC order parameter for a set of molecules More details ...
   SPECIESthe label of the DISTANCES or PLANES action that computes the orientations of the molecules for which you would like to compute SMAC=m1 
   SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.639 R_0=0.1 D_MAX=0.64} 
   KERNEL1The kernels used in the function of the angle={TRIANGULAR CENTER=0 SIGMA=0.8}
   KERNEL2The kernels used in the function of the angle={TRIANGULAR CENTER=pi SIGMA=0.7}
   SWITCH_COORDThis keyword is used to define the coordination switching function. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.001}
... 

# Use a filter so as to ignore molecules that are not sat in a solid-like,
# ordered environment.
The SMAC action with label smac calculates the following quantities:
 Quantity   
 Description  
smac.value
the value of the smac parameter for each of the input moleculesff: 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=smac SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={GAUSSIAN D_0=0.49 R_0=0.5 D_MAX=0.5}
# Build a contact matrix for the molecules that are in a part of the simulation 
# box where the structure is ordered
The MORE_THAN action with label ff calculates the following quantities:
 Quantity   
 Description  
ff.value
a function that is one if the if the input is more than a thresholdc1: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details ATOMSthe atoms for which you would like to calculate the adjacency matrix=m1_grp 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 D_0=0.639 R_0=0.01 D_MAX=0.64} 
The CONTACT_MATRIX action with label c1 calculates the following quantities:
 Quantity   
 Description  
c1.value
a matrix containing the weights for the bonds between each pair of atomsffmat: 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=ff,ff  
The OUTER_PRODUCT action with label ffmat calculates the following quantities:
 Quantity   
 Description  
ffmat.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=c1,ffmat 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 depth first search clustering on the contact 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 ARGthe input matrix=c1
# Find the sum of the coordination numbers for the atoms in this largest cluster.
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 matrixcc1: CLUSTER_PROPERTIESCalculate properties of the distribution of some quantities that are part of a connected component More details ...
  CLUSTERSthe label of the action that does 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 ARGcalculate the sum of the arguments calculated by this action for the cluster=smac
  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=0.49 R_0=0.5 D_MAX=0.5}
... 
# Print information on the number of atoms in the cluster to a file.
The CLUSTER_PROPERTIES action with label cc1 calculates the following quantities:
 Quantity   
 Description  
cc1.value
a vector that is one if the atom is part of the cluster or interest and zero otherwise
cc1.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=cc1.* FILEthe name of the file on which to output these quantities=colvar