This is part of the gridtools module

Find an isocontour in a three dimensional grid by searching over a Fibonacci sphere.

As discussed in the part of the manual on Analysis PLUMED contains a number of tools that allow you to calculate a function on a grid. The function on this grid might be a HISTOGRAM as a function of a few collective variables or it might be a phase field that has been calculated using MULTICOLVARDENS. If this function has one or two input arguments it is relatively straightforward to plot the function. If by contrast the data has a three dimensions it can be difficult to visualize.

This action provides one tool for visualizing these functions. It can be used to search for a set of points on a contour where the function takes a particular value. In other words, for the function \(f(x,y,z)\) this action would find a set of points \(\{x_c,y_c,z_c\}\) that have:

\[ f(x_c,y_c,z_c) - c = 0 \]

where \(c\) is some constant value that is specified by the user. The points on this contour are find by searching along a set of equally spaced radii of a sphere that centered at on particular, user-specified atom or virtual atom. To ensure that these search radii are equally spaced on the surface of the sphere the search directions are generated by using a Fibonacci spiral projected on a sphere. In other words, the search directions are given by:

\[ \mathbf{r}_i = \left( \begin{matrix} \sqrt{1 - y^2} \cos(\phi) \\ \frac{2i}{n} - 1 + \frac{1}{n} \\ \sqrt{1 - y^2} \sin(\phi) \end{matrix} \right) \]

where \(y\) is the quantity second component of the vector defined above, \(n\) is the number of directions to look in and \(\phi\) is

\[ \phi = \mod(i + R, n) \pi ( 3 - \sqrt{5} ) \]

where \(R\) is a random variable between 0 and \(n-1\) that is generated during the read in of the input file and that is fixed during the whole calculation.

It is important to note that this action can only be used to detect contours in three dimensional functions. In addition, this action will fail to find the full set of contour points if the contour does not have the same topology as a sphere. If you are uncertain that the isocontours in your function have a spherical topology you should use FIND_CONTOUR in place of FIND_SPHERICAL_CONTOUR.

Examples

The following input demonstrates how this action can be used. The input here is used to study the shape of a droplet that has been formed during the condensation of Lennard Jones from the vapor. The input below achieves this by calculating the coordination numbers of all the atoms within the gas. Obviously, those atoms within the droplet will have a large value for the coordination number while the isolated atoms in the gas will have a low value. As such we can detect the sizes of the droplets by constructing a CONTACT_MATRIX whose \(ij\) element tells us whether atom \(i\) and atom \(j\) have coordination number that is greater that two. The atoms within the various droplets within the system can then be found by performing a DFSCLUSTERING on this matrix to detect the connected components. We can take the largest of these connected components and find the center of the droplet by exploiting the functionality within CENTER_OF_MULTICOLVAR. We can then construct a phase field based on the positions of the atoms in the largest cluster and the values of the coordination numbers of these atoms. The final line in the input then finds the a set of points on the dividing surface that separates the droplet from the surrounding gas. The value of the phase field on this isocontour is equal to 0.75.

Click on the labels of the actions for more information on what each action computes

# Calculate coordination numbers
c1: COORDINATIONNUMBER SPECIESthis keyword is used for colvars such as coordination number. =1-512 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching
function defined above. ={EXP D_0=4.0 R_0=0.5 D_MAX=6.0}  The COORDINATIONNUMBER action with label c1
# Select coordination numbers that are more than 2.0
cf: MFILTER_MORE DATAcompulsory keyword 
The multicolvar that calculates the set of base quantities that we are interested
in =c1 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching
function defined above. ={RATIONAL D_0=2.0 R_0=0.1}  LOWMEM( default=off ) lower the memory requirements  The MFILTER_MORE action with label cf
# Build a contact matrix
mat: CONTACT_MATRIX ATOMSThe list of atoms for which you would like to calculate the contact matrix. =cf SWITCHThis keyword is used if you want to employ an alternative to the continuous switching
function defined above. ={EXP D_0=4.0 R_0=0.5 D_MAX=6.0}  The CONTACT_MATRIX action with label mat
# Find largest cluster
dfs: DFSCLUSTERING MATRIXcompulsory keyword 
the action that calculates the adjacency matrix vessel we would like to analyze =mat LOWMEM( default=off ) lower the memory requirements  The DFSCLUSTERING action with label dfs
clust1: CLUSTER_PROPERTIES CLUSTERScompulsory keyword 
the label of the action that does the clustering =dfs CLUSTERcompulsory keyword ( default=1 )
which cluster would you like to look at 1 is the largest cluster, 2 is the second
largest, 3 is the the third largest and so on. =1 The CLUSTER_PROPERTIES action with label clust1
# Find center of largest cluster
trans1: MTRANSFORM_MORE DATAcompulsory keyword 
The multicolvar that calculates the set of base quantities that we are interested
in =clust1 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching
function defined above. ={RATIONAL D_0=2.0 R_0=0.1}  LOWMEM( default=off ) lower the memory requirements  The MTRANSFORM_MORE action with label trans1
cent: CENTER_OF_MULTICOLVAR DATAcompulsory keyword 
find the average value for a multicolvar =trans1 The CENTER_OF_MULTICOLVAR action with label cent calculates the position of a virtual atom
# Calculate the phase field of the coordination
dens: MULTICOLVARDENS DATAcompulsory keyword 
the multicolvar which you would like to calculate the density profile for =trans1 ORIGINwe will use the position of this atom as the origin. =cent DIRcompulsory keyword 
the direction in which to calculate the density profile =xyz NBINSthe number of bins to use to represent the density profile =30,30,30 BANDWIDTHcompulsory keyword 
the bandwidths for kernel density estimation =2.0,2.0,2.0 The MULTICOLVARDENS action with label dens
# Find the isocontour around the nucleus
sc: FIND_SPHERICAL_CONTOUR GRIDcompulsory keyword 
the action that creates the input grid you would like to use =dens CONTOURcompulsory keyword 
the value we would like to draw the contour at in the space =0.85 INNER_RADIUScompulsory keyword 
the minimum radius on which to look for the contour =10.0 OUTER_RADIUScompulsory keyword 
the outer radius on which to look for the contour =40.0 NPOINTScompulsory keyword 
the number of points for which we are looking for the contour =100 The FIND_SPHERICAL_CONTOUR action with label sc
# And print the grid to a file
GRID_TO_XYZ GRIDcompulsory keyword 
the action that creates the grid you would like to output =sc FILEcompulsory keyword ( default=density )
the file on which to write the grid. =mysurface.xyz UNITScompulsory keyword ( default=PLUMED )
the units in which to print out the coordinates. =A The GRID_TO_XYZ action with label

Glossary of keywords and components

Compulsory keywords

STRIDE	( default=1 ) the frequency with which the data should be collected and added to the quantity being averaged
CLEAR	( default=0 ) the frequency with which to clear all the accumulated data. The default value of 0 implies that all the data will be used and that the grid will never be cleared
NORMALIZATION	( default=true ) This controls how the data is normalized it can be set equal to true, false or ndata. The differences between these options are explained in the manual page for HISTOGRAM
GRID	the action that creates the input grid you would like to use
CONTOUR	the value we would like to draw the contour at in the space
NPOINTS	the number of points for which we are looking for the contour
INNER_RADIUS	the minimum radius on which to look for the contour
OUTER_RADIUS	the outer radius on which to look for the contour
NBINS	( default=1 ) the number of discrete sections in which to divide the distance between the inner and outer radius when searching for a contour

Options

SERIAL	( default=off ) do the calculation in serial. Do not use MPI
LOWMEM	( default=off ) lower the memory requirements
TIMINGS	( default=off ) output information on the timings of the various parts of the calculation
LOGWEIGHTS	list of actions that calculates log weights that should be used to weight configurations when calculating averages
CONCENTRATION	the concentration parameter for Von Mises-Fisher distributions
COMPONENT	if your input is a vector field use this to specify the component of the input vector field for which you wish to use