Project ID: plumID:19.053
Source: plumed.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
tested onv2.9
tested onmaster
UNITS
This command sets the internal units for the code. More details
 
NATURAL
 use natural units


# These two commands calculate one symmetry function for each atom.  These 
# symmetry functions tell us whether the environment around each atom resembles 
# the environment in the solid or the environment in the liquid.
fcc: 
FCCUBIC
Measure how similar the environment around atoms is to that found in a FCC structure. More details
 
SPECIES
this keyword is used for colvars such as coordination number
=1-20736 
SWITCH
the switching function that it used in the construction of the contact matrix
={CUBIC D_0=1.2 D_MAX=1.5} 
ALPHA
 The alpha parameter of the angular function that is used for FCCUBIC
=27 
smapfcc: 
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
=fcc 
SWITCH
This keyword is used if you want to employ an alternative to the continuous swiching function defined above
={SMAP R_0=0.5 A=8 B=8} 
smapfcc_grp: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=1-20736
# This calculates the position of the center of the solid region of the simulation box.  What we are computing here a weighted average position 
# the weights are the order parameters computed using the two commands above.
center: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
PHASES
 use trigonometric phases when computing position of center
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=fcc 
WEIGHTS
what weights should be used when calculating the center
=smapfcc
# This calculates the phase field that tells us whether the structure in each part of the simulation box is solid-like or liquid like.
dens: 
MULTICOLVARDENS
Evaluate the average value of a multicolvar on a grid. More details
 
DATA
the multicolvar which you would like to calculate the density profile for
=smapfcc 
ORIGIN
we will use the position of this atom as the origin
=center 
DIR
the direction in which to calculate the density profile
=xyz 
NBINS
the number of bins to use in each direction (alternative to GRID_NBIN)
=50,80,80 
BANDWIDTH
the bandwidths for kernel density esimtation
=1.0,1.0,1.0 GRID_MIN=0.0,auto,auto GRID_MAX=20.0,auto,auto 
STRIDE
 the frequency with which to accumulate the densities
=1 
CLEAR
 the frequency with which to clear the density
=1
# This finds the instantaneous location of the interface between the solid and liquid phases
contour: 
FIND_CONTOUR_SURFACE
Find an isocontour by searching along either the x, y or z direction. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=dens 
CONTOUR
the value we would like to draw the contour at in the space
=0.5 
SEARCHDIR
In which directions do you wish to search for the contour
=dens_dist.x 

DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=contour 
FILE
 the file on which to write the grid
=contour.dat
# This does the fourier transform of the location of the interface.  We can extract the interfacial stiffness from the average of this fourier transform
ft: 
FOURIER_TRANSFORM
Compute the Discrete Fourier Transform (DFT) by means of FFTW of data stored on a 2D grid. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=contour 
FT_TYPE
choose what kind of data you want as output on the grid
=norm 
FOURIER_PARAMETERS
 what kind of normalization is applied to the output and if the Fourier transform in FORWARD or BACKWARD
=-1,1

DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=ft 
FILE
 the file on which to write the grid
=fourier.dat 
STRIDE
 the frequency with which the grid should be output to the file
=10