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: 
DISTANCES
Calculate the distances between multiple piars of atoms More details
 ...
  
ATOMS1
the pairs of atoms that you would like to calculate the angles for
=1,2 
LOCATION1
the location at which the CV is assumed to be in space
=1
  
ATOMS2
the pairs of atoms that you would like to calculate the angles for
=9,10 
LOCATION2
the 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.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: 
SMAC
Calculate the SMAC order parameter for a set of molecules More details
 ...
   SPECIES=m1 
   
SWITCH
This keyword is used if you want to employ an alternative to the continuous swiching function defined above
={RATIONAL D_0=0.639 R_0=0.1 D_MAX=0.64} 
   
KERNEL1
The kernels used in the function of the angle
={TRIANGULAR CENTER=0 SIGMA=0.8}
   
KERNEL2
The kernels used in the function of the angle
={TRIANGULAR CENTER=pi SIGMA=0.7}
   
SWITCH_COORD
This keyword is used to define the coordination switching function
={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  ff: 
MORE_THAN
Use a switching function to determine how many of the input variables are more than a certain cutoff. More details
 
ARG
the input to this function
=smac 
SWITCH
This 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_MATRIX
Adjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details
 
ATOMS
the atoms for which you would like to calculate the adjacency matrix
=m1_grp 
SWITCH
specify the switching function to use between two sets of indistinguishable atoms
={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_PRODUCT
Calculate the outer product matrix of two vectors More details
 
ARG
the input for this action is the scalar output from one or more other actions
=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: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=c1,ffmat 
FUNC
the function you wish to evaluate
=x*y 
PERIODIC
if 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: 
DFSCLUSTERING
Find the connected components of the matrix using the depth first search clustering algorithm. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=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_PROPERTIES
Calculate properties of the distribution of some quantities that are part of a connected component More details
 ...
  
CLUSTERS
the 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 
ARG
calculate the sum of the arguments calculated by this action for the cluster
=smac
  
MORE_THAN
calculate the number of variables that are more than a certain target value
={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.morethan
the number of colvars that have a value more than a threshold
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=cc1 
FILE
the name of the file on which to output these quantities
=colvar