PLUMED-NEST

Project ID: plumID:21.021
Source: atlas_inputs/atlas_6d/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

#
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 atomsd2: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1,3 
COMPONENTS
 calculate the x, y and z components of the distance separately and store them as label

The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Description  
d2.x
the x-component of the vector connecting the two atoms
d2.y
the y-component of the vector connecting the two atoms
d2.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,d1.z,d2.x,d2.y,d2.z 
VAR
the names to give each of the arguments in the function
=x0,x1,x2,x3,x4,x5 
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
=10.0*exp(-4.0*(x0-1.0)^2-4.0*(x1-1.0)^2-4.0*(x2-1.0)^2-4.0*(x3-1.0)^2-4.0*(x4-1.0)^2-4.0*(x5-1.0)^2)+10.0*exp(-4.0*(x0-1.0)^2-4.0*(x1-1.0)^2-4.0*(x2-1.0)^2-4.0*(x3-1.0)^2-4.0*(x4-1.0)^2-4.0*(x5+1.0)^2)+10.0*exp(-4.0*(x0-1.0)^2-4.0*(x1-1.0)^2-4.0*(x2-1.0)^2-4.0*(x3-1.0)^2-4.0*(x4+1.0)^2-4.0*(x5-1.0)^2)+10.0*exp(-4.0*(x0-1.0)^2-4.0*(x1-1.0)^2-4.0*(x2-1.0)^2-4.0*(x3+1.0)^2-4.0*(x4-1.0)^2-4.0*(x5+1.0)^2)+10.0*exp(-4.0*(x0-1.0)^2-4.0*(x1-1.0)^2-4.0*(x2+1.0)^2-4.0*(x3-1.0)^2-4.0*(x4+1.0)^2-4.0*(x5-1.0)^2)+10.0*exp(-4.0*(x0-1.0)^2-4.0*(x1+1.0)^2-4.0*(x2-1.0)^2-4.0*(x3+1.0)^2-4.0*(x4-1.0)^2-4.0*(x5+1.0)^2)+10.0*exp(-4.0*(x0+1.0)^2-4.0*(x1-1.0)^2-4.0*(x2+1.0)^2-4.0*(x3-1.0)^2-4.0*(x4+1.0)^2-4.0*(x5-1.0)^2)+10.0/(1.0/((5.0*x0+5.0)^2+(5.0*x1-5.0)^2+(5.0*x2+5.0)^2+(5.0*x3-5.0)^2+(5.0*x4+5.0)^2+(5.0*x5-5.0)^2+1)+1.0/((5.0*x0-5.0)^2+(5.0*x1+5.0)^2+(5.0*x2-5.0)^2+(5.0*x3+5.0)^2+(5.0*x4-5.0)^2+(5.0*x5+5.0)^2+1)+1.0/((5.0*x0-5.0)^2+(5.0*x1-5.0)^2+(5.0*x2+5.0)^2+(5.0*x3-5.0)^2+(5.0*x4+5.0)^2+(5.0*x5-5.0)^2+1)+1.0/((5.0*x0-5.0)^2+(5.0*x1-5.0)^2+(5.0*x2-5.0)^2+(5.0*x3+5.0)^2+(5.0*x4-5.0)^2+(5.0*x5+5.0)^2+1)+1.0/((5.0*x0-5.0)^2+(5.0*x1-5.0)^2+(5.0*x2-5.0)^2+(5.0*x3-5.0)^2+(5.0*x4+5.0)^2+(5.0*x5-5.0)^2+1)+1.0/((5.0*x0-5.0)^2+(5.0*x1-5.0)^2+(5.0*x2-5.0)^2+(5.0*x3-5.0)^2+(5.0*x4-5.0)^2+(5.0*x5+5.0)^2+1)+1.0/((5.0*x0-5.0)^2+(5.0*x1-5.0)^2+(5.0*x2-5.0)^2+(5.0*x3-5.0)^2+(5.0*x4-5.0)^2+(5.0*x5-5.0)^2+1)+1.0/((-2.04124145231931*x0-1.40824829046386*x1+1.40824829046386*x2-1.40824829046386*x3+1.40824829046386*x4+3.59175170953614*x5)^2.0+(-2.04124145231931*x0-1.40824829046386*x1+1.40824829046386*x2+3.59175170953614*x3+1.40824829046386*x4-1.40824829046386*x5)^2.0+(-2.04124145231931*x0+3.59175170953614*x1+1.40824829046386*x2-1.40824829046386*x3+1.40824829046386*x4-1.40824829046386*x5)^2.0+(-0.408248290463863*x0+0.408248290463863*x1-0.408248290463863*x2+0.408248290463863*x3-0.408248290463863*x4+0.408248290463863*x5)^8.0+(2.04124145231931*x0+1.40824829046386*x1-1.40824829046386*x2+1.40824829046386*x3+3.59175170953614*x4+1.40824829046386*x5)^2.0+(2.04124145231931*x0+1.40824829046386*x1+3.59175170953614*x2+1.40824829046386*x3-1.40824829046386*x4+1.40824829046386*x5)^2.0)+1.0/((-0.447213595499958*x1+0.447213595499958*x2-0.447213595499958*x3+0.447213595499958*x4-0.447213595499958*x5)^8.0+(-2.23606797749979*x0+1.0*x1-1.0*x2+1.0*x3+4.0*x4+1.0*x5+2.23606797749979)^2.0+(-2.23606797749979*x0+1.0*x1+4.0*x2+1.0*x3-1.0*x4+1.0*x5+2.23606797749979)^2.0+(2.23606797749979*x0-1.0*x1+1.0*x2-1.0*x3+1.0*x4+4.0*x5-2.23606797749979)^2.0+(2.23606797749979*x0-1.0*x1+1.0*x2+4.0*x3+1.0*x4-1.0*x5-2.23606797749979)^2.0+(2.23606797749979*x0+4.0*x1+1.0*x2-1.0*x3+1.0*x4-1.0*x5-2.23606797749979)^2.0)+1.0/((5.0*x1-5.0)^2.0+(-0.5*x2+0.5*x3-0.5*x4+0.5*x5)^8.0+(-2.5*x0+1.25*x2-1.25*x3+1.25*x4+3.75*x5+2.5)^2.0+(-2.5*x0+1.25*x2+3.75*x3+1.25*x4-1.25*x5+2.5)^2.0+(2.5*x0-1.25*x2+1.25*x3+3.75*x4+1.25*x5-2.5)^2.0+(2.5*x0+3.75*x2+1.25*x3-1.25*x4+1.25*x5-2.5)^2.0)+1.0/((5.0*x1-5.0)^2.0+(5.0*x3-5.0)^2.0+(5.0*x5-5.0)^2.0+(-0.577350269189626*x0-0.577350269189626*x2-0.577350269189626*x4)^8.0+(2.88675134594813*x0-3.94337567297407*x2+1.05662432702593*x4)^2.0+(2.88675134594813*x0+1.05662432702593*x2-3.94337567297407*x4)^2.0)+1.0/((5.0*x1-5.0)^2.0+(5.0*x2-5.0)^2.0+(-0.577350269189626*x3+0.577350269189626*x4-0.577350269189626*x5)^8.0+(-2.88675134594813*x0+1.66666666666667*x3+3.33333333333333*x4+1.66666666666667*x5+2.88675134594813)^2.0+(2.88675134594813*x0-1.66666666666667*x3+1.66666666666667*x4+3.33333333333333*x5-2.88675134594813)^2.0+(2.88675134594813*x0+3.33333333333333*x3+1.66666666666667*x4-1.66666666666667*x5-2.88675134594813)^2.0)+1.0/((5.0*x1-5.0)^2.0+(5.0*x2-5.0)^2.0+(5.0*x3-5.0)^2.0+(-0.707106781186548*x4+0.707106781186548*x5)^8.0+(-3.53553390593274*x0+2.5*x4+2.5*x5+3.53553390593274)^2.0+(3.53553390593274*x0+2.5*x4+2.5*x5-3.53553390593274)^2.0)+1.0/(1.0*(-x5)^8.0+(5.0*x0-5.0)^2.0+(5.0*x1-5.0)^2.0+(5.0*x2-5.0)^2.0+(5.0*x3-5.0)^2.0+(5.0*x4-5.0)^2.0


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 fileat: 
ATLAS
This action is not part of PLUMED and was included by using a LOAD command More details
 ...
ARG=d1.x,d1.y,d1.z,d2.x,d2.y,d2.z REFERENCE=cluster.dat PACE=500
SIGMA=0.2 BIASFACTOR=15 HEIGHT=3.0
GRID_MAX=15.0 GRID_BIN=750 TEMP=1.0 TRUNCATE_GRIDS
REGULARISE=1E-11
ADAPTIVE_WALL=1.0
STATIC_WALL=0.0
...

PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=at,at_wtfact 
FILE
the name of the file on which to output these quantities
=at.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
=at_adaptive_wall 
FILE
the name of the file on which to output these quantities
=at.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,d1.z,d2.x,d2.y,d2.z 
FILE
the name of the file on which to output these quantities
=colvar 
STRIDE
 the frequency with which the quantities of interest should be output
=500