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Action: DUMPCONTOUR

Module contour
Description Usage
Print the contour used in 0 tutorialsused in 0 eggs
This action outputs data to a file. You can read more about how PLUMED manages output files here

Details and examples

Print the contour

This is a special action that is used to print the output from a FIND_CONTOUR action. The following example illustrates how this method is used to output a xyz file that contains the set of points that FIND_CONTOUR found on the isocontour of interest.

Click on the labels of the actions for more information on what each action computes
tested on2.11
UNITSThis command sets the internal units for the code. More details NATURAL use natural units

# This calculates the value of a set of symmetry functions for the atoms of interest
fcc: FCCUBICMeasure how similar the environment around atoms is to that found in a FCC structure. This action is a shortcut. More details ...
  SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-96000 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 PHI The Euler rotational angle phi=0.0 THETA The Euler rotational angle theta=-1.5708 PSI The Euler rotational angle psi=-2.35619
...

# Transform the symmetry functions with a switching function
tfcc: LESS_THANUse a switching function to determine how many of the input variables are less 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}

# Now compute the center of the solid like region
center: CENTERCalculate the center for a group of atoms, with arbitrary weights. This action is a shortcut. More details ATOMSthe group of atoms that appear in the definition of this center=1-96000 WEIGHTSwhat weights should be used when calculating the center=tfcc

# This determines the positions of the atoms of interest relative to the center of the solid region
dens_dist: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details ORIGINcalculate the distance of all the atoms specified using the ATOMS keyword from this point=center ATOMSthe pairs of atoms that you would like to calculate the angles for=1-96000 COMPONENTS calculate the x, y and z components of the distance separately and store them as label
# This computes the numerator in the expression above for the phase field
dens_numer: KDECreate a histogram from the input scalar/vector/matrix using KDE This action has hidden defaults. More details ...
  VOLUMESthis keyword take the label of an action that calculates a vector of values=tfcc ARGthe label for the value that should be used to construct the histogram=dens_dist.x,dens_dist.y,dens_dist.z
  GRID_BINthe number of bins for the grid=80,80,80 BANDWIDTHthe bandwidths for kernel density esimtation=1.0,1.0,1.0
...
# This computes the denominator
dens_denom: KDECreate a histogram from the input scalar/vector/matrix using KDE This action has hidden defaults. More details ...
  ARGthe label for the value that should be used to construct the histogram=dens_dist.x,dens_dist.y,dens_dist.z
  GRID_BINthe number of bins for the grid=80,80,80 BANDWIDTHthe bandwidths for kernel density esimtation=1.0,1.0,1.0
...
# This computes the final phase field
dens: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=dens_numer,dens_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

# Find the isocontour
cont: FIND_CONTOURFind an isocontour in a smooth function. This action has hidden defaults. 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
# Use the special method for outputting the contour to a file
DUMPCONTOURPrint the contour More details ARGthe labels of the FIND_CONTOUR action that you would like to output=cont FILE the file on which to write the grid=surface.xyz STRIDE the frequency with which the grid should be output to the file=1 FMT the format that should be used to output real numbers=%8.4f

Input

The arguments that serve as the input for this action are specified using one or more of the keywords in the following table.

Keyword Type Description
ARG vector the labels of the FIND_CONTOUR action that you would like to output

Full list of keywords

The following table describes the keywords and options that can be used with this action

Keyword Type Default Description
ARG input none the labels of the FIND_CONTOUR action that you would like to output
STRIDE compulsory 1 the frequency with which the grid should be output to the file
FILE compulsory density the file on which to write the grid
FMT compulsory %f the format that should be used to output real numbers