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

#
UNITSThis command sets the internal units for the code. More details NATURAL use natural units
The UNITS action with label  calculates somethingd1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe 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 atoms
d1.value
the DISTANCE between this pair of atomsff: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=d1.x,d1.y VARthe names to give each of the arguments in the function=x0,x1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe 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))

The MATHEVAL action with label ff calculates the following quantities:
 Quantity   
 Description  
ff.value
an arbitrary functionbb: BIASVALUETakes the value of one variable and use it as a bias More details ARGthe labels of the scalar/vector arguments whose values will be used as a bias on the system=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: ATLASThis 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
... 

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=rr,rr_wtfact FILEthe 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
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=rr_adaptive_wall FILEthe 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
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d1.x,d1.y,bb.bias FILEthe name of the file on which to output these quantities=TRAJ STRIDE the frequency with which the quantities of interest should be output=500