PLUMED-NEST

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

UNITSThis 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.
The UNITS action with label  calculates somethingfcc: FCCUBICMeasure how similar the environment around atoms is to that found in a FCC structure. More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-20736 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={CUBIC D_0=1.2 D_MAX=1.5} ALPHA The alpha parameter of the angular function that is used for FCCUBIC=27 
The FCCUBIC action with label fcc calculates the following quantities:
 Quantity   
 Description  
fcc.value
the symmetry function for each of the specified atomssmapfcc: MORE_THANUse a switching function to determine how many of the input variables are more than a certain cutoff. More details ARGthe values input to this function=fcc SWITCHThis 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} 
The MORE_THAN action with label smapfcc calculates the following quantities:
 Quantity   
 Description  
smapfcc.value
a function that is one if the if the input is more than a thresholdsmapfcc_grp: GROUPDefine 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 ATOMSthe 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.
The GROUP action with label smapfcc_grp calculates somethingcenter: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details PHASES use trigonometric phases when computing position of center ATOMSthe group of atoms that you are calculating the Gyration Tensor for=fcc WEIGHTSwhat 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.
The CENTER action with label center calculates the following quantities:
 Quantity   
 Description  
center.value
the position of the center of massdens: MULTICOLVARDENSEvaluate the average value of a multicolvar on a grid. More details DATAthe multicolvar which you would like to calculate the density profile for=smapfcc ORIGINwe will use the position of this atom as the origin=center DIRthe direction in which to calculate the density profile=xyz NBINSthe number of bins to use in each direction (alternative to GRID_NBIN)=50,80,80 BANDWIDTHthe bandwidths for kernel density esimtation=1.0,1.0,1.0 GRID_MINthe lower bounds for the grid (default boxlengths)=0.0,auto,auto GRID_MAXthe upper bounds for the grid (default boxlengths)=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
The MULTICOLVARDENS action with label dens calculates the following quantities:
 Quantity   
 Description  
dens.value
the average value of the order parameters at each point on the gridcontour: FIND_CONTOUR_SURFACEFind an isocontour by searching along either the x, y or z direction. More details ARGthe labels of the grid in which the contour will be found=dens CONTOURthe value we would like to draw the contour at in the space=0.5 SEARCHDIRIn which directions do you wish to search for the contour=dens_dist.x 
The FIND_CONTOUR_SURFACE action with label contour calculates the following quantities:
 Quantity   
 Description  
contour.value
a grid containing the location of the points in the Willard-Chandler surface along the chosen directionDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details ARGthe label for the grid that you would like to output=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_TRANSFORMCompute the Discrete Fourier Transform (DFT) by means of FFTW of data stored on a 2D grid. More details ARGthe label of the grid that you want to fourer transform=contour FT_TYPEchoose 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
The FOURIER_TRANSFORM action with label ft calculates the following quantities:
 Quantity   
 Description  
ft.real
the real part of the function
ft.imag
the imaginary part of the function
ft.value
the fourier transform of the input gridDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details ARGthe label for the grid that you would like to output=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