Project ID: plumID:21.021
Source: atlas_inputs/atlas_3d/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
tested onv2.10
tested onmaster
#
UNITSThis command sets the internal units for the code. More details NATURAL use natural units
d1: 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

ff: 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,d1.z VARthe names to give each of the arguments in the function=x0,x1,x2 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)^2-4.0*(x2+1)^2)+30.0*exp(-4.0*(x0-1)^2-4.0*(x1+1)^2-4.0*(x2-1)^2)+30.0*exp(-4.0*(x0-1)^2-4.0*(x1+1)^2-4.0*(x2+1)^2)+30.0*exp(-4.0*(x0+1)^2-4.0*(x1-1)^2-4.0*(x2-1)^2)+30.0*exp(-4.0*(x0+1)^2-4.0*(x1+1)^2-4.0*(x2-1)^2)+30.0*exp(-4.0*(x0+1)^2-4.0*(x1+1)^2-4.0*(x2+1)^2)+30.0/(1.0/((5.0*x0+5.0)^2+(5.0*x1+5.0)^2+(5.0*x2+5.0)^2+1)+1.0/((5.0*x0+5.0)^2+(5.0*x1+5.0)^2+(5.0*x2-5.0)^2+1)+1.0/((5.0*x0+5.0)^2+(5.0*x1-5.0)^2+(5.0*x2-5.0)^2+1)+1.0/((5.0*x0-5.0)^2+(5.0*x1+5.0)^2+(5.0*x2+5.0)^2+1)+1.0/((5.0*x0-5.0)^2+(5.0*x1+5.0)^2+(5.0*x2-5.0)^2+1)+1.0/((5.0*x0-5.0)^2+(5.0*x1-5.0)^2+(5.0*x2+5.0)^2+1)+1.0/((10.0*x0-10.0)^2+(0.5*x1-0.5*x2)^8+(7.0710678*x1+7.0710678*x2)^2)+1.0/((0.5*x0-0.5*x2)^8+(7.0710678*x0+7.0710678*x2)^2+(10.0*x1-10.0)^2)+1.0/((-7.0710678*x0-7.0710678*x1)^2+(0.288675134189626*x0-0.288675134189626*x1-0.408248289205788*x2)^8+(5.0*x0-5.0*x1+7.0710678*x2)^2)+1.0/(1.0*x2^8+(10.0*x0+10.0)^2+(10.0*x1+10.0)^2)+1.0/(1.0*x0^8+(10.0*x1+10.0)^2+(10.0*x2+10.0)^2)+1.0/(1.0*x0^8+(10.0*x1+10.0)^2+(10.0*x2-10.0)^2))

bb: 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

rr: ATLASThis action is not part of PLUMED and was included by using a LOAD command More details ...
ARG=d1.x,d1.y,d1.z REFERENCE=cluster.dat PACE=500
SIGMA=0.2   BIASFACTOR=10 HEIGHT=2.0
GRID_MAX=5.0 GRID_BIN=500 TEMP=1 TRUNCATE_GRIDS
REGULARISE=1E-8
ADAPTIVE_WALL=1.0
STATIC_WALL=0.0
...

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
DUMPATOMSDump selected atoms on a file. More details STRIDE the frequency with which the atoms should be output=500 FILEfile on which to output coordinates; extension is automatically detected=traj.xyz ATOMSthe atom indices whose positions you would like to print out=1,2
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,d1.z FILEthe name of the file on which to output these quantities=colvar STRIDE the frequency with which the quantities of interest should be output=500