PLUMED-NEST

Project ID: plumID:21.021
Source: atlas_inputs/atlas_2d/pca_2/plumed.dat
Originally used with PLUMED version: 2.7-mod
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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UNITS
This command sets the internal units for the code. More details
 
NATURAL
 use natural units
d1: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1,2 
COMPONENTS
 calculate the x, y and z components of the distance separately and store them as label

The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Description  
d1.x
the x-component of the vector connecting the two atoms
d1.y
the y-component of the vector connecting the two atoms
d1.z
the z-component of the vector connecting the two atomsff: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=d1.x,d1.y 
VAR
the names to give each of the arguments in the function
=x0,x1 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
FUNC
the function you wish to evaluate
=30.0*exp(-4.0*(x0-1)^2-4.0*(x1-1)^2)+30.0*exp(-4.0*(x0-1)^2-4.0*(x1+1)^2)+30.0*exp(-4.0*(x0+1)^2-4.0*(x1+1)^2)+30.0/(1.0/((5.0*x0+5.0)^2+(5.0*x1+5.0)^2+1)+1.0/((5.0*x0-5.0)^2+(5.0*x1+5.0)^2+1)+1.0/((5.0*x0-5.0)^2+(5.0*x1-5.0)^2+1)+1.0/((-3.5355339059*x0+3.5355339059*x1)^2+(0.500000000834386*x0+0.500000000834386*x1)^8)+1.0/(1.0*x1^8+(5.0*x0-5.0)^2)+1.0/(1.0*x0^8+(5.0*x1+5.0)^2

bb: 
BIASVALUE
Takes the value of one variable and use it as a bias More details
 
ARG
the input for this action is the scalar output from one or more other actions
=ff

The BIASVALUE action with label bb calculates the following quantities:
 Quantity   
 Description  
bb.bias
the instantaneous value of the bias potential
bb._bias
one or multiple instances of this quantity can be referenced elsewhere in the input filerr: 
ATLAS
This action is not part of PLUMED and was included by using a LOAD command More details
 ...
ARG=d1.x,d1.y REFERENCE=cluster.dat PACE=500
SIGMA=0.20 BIASFACTOR=10 HEIGHT=2.0
GRID_MAX=6.0 GRID_BIN=600 TEMP=1 TRUNCATE_GRIDS
REGULARISE=0.00000001
STATIC_WALL=0.0
ADAPTIVE_WALL=1.0
... 

PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=rr,rr_wtfact 
FILE
the name of the file on which to output these quantities
=rr.gbias 
STRIDE
 the frequency with which the quantities of interest should be output
=500
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=rr_adaptive_wall 
FILE
the name of the file on which to output these quantities
=rr.wall 
STRIDE
 the frequency with which the quantities of interest should be output
=500
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=d1.x,d1.y,bb.bias 
FILE
the name of the file on which to output these quantities
=TRAJ 
STRIDE
 the frequency with which the quantities of interest should be output
=500