Raul P. Pelaez 2017 Radial Distribution Function

NAME

rdf - Computes the Radial Distribution Function (RDF) of a group of positions in a file, averages it for all snapshots in the file.
rdf can compute in 4 modes:
* GPU
- Nbody
- Neighbour list
* CPU
- Nbody
- Neighbour list

rdf will choose a between GPU/CPU according to the number of particles (unless specified with -device) and will choose NBody/Neighbour list according to the number of particles and the factor L/rcut.

COMPILE WITH

$ mkdir build; cd build; cmake ..; make

You can specify some options in CMAKE, (use ccmake). For example, set DONT_USE_CUDA to ON to compile in CPU only mode (does not need nvcc).

You can run some test after compiling with:

$ cd test; make test

This will run several test using random numbers, the resulting rdf will be compared between CPU and GPU implementations. Which should be numerically identical.

SYNOPSYS

rdf [OPTIONS]... [FILE]...

DESCRIPTION

Compute the Radial Distribution Function.

With no FILE, or when file is - or not specified, reads from standard input.

Required options:

-N Number of particles, all snapshots must have the same number of particles

-L, -Lx [lx] -Ly [ly] -Lz[lz]
Box size, positions will be folded to a box of size Lx Ly Lz. -L will make Lx= Ly = Lz = L

-rcut
Maximum distance in the rdf, distances greater than rcut will be ignored.

-nbins
Number of bins in the position pair histogram (binSize = rcut/nbins)

-Nsnapshots
Number of snapshots in the file, a snapshot must be separated from the next with a single line

-dim [=3D]
Dimensionality of the input positions. Affects how the histogram is normalized to compute the rdf.
Can be 3D, 2D or q2D (treat as 3D, but normalize as 2D)

-device [=auto]
Switch between GPU/CPU implementations of the algorithm. By default rdf chooses the best according to N

-outputDecimals [=5]
Number of decimals in the output file, set through cout<<setprecision()
-fixBIAS This will weight the distance of a pair in a bin according to the position inside the bin (instead of weighting all distances as 1).
-useTypes This option will interpret the fourth (third in 2D) column as particle type and will compute and output a RDF for each type pair (Ntype*(Ntype+1)/2 in total). Each RDF will start with "# typei typej"

FILE FORMAT

The file must have at least "dim" columns (the rest will be ignored) and each snapshot (including the first)
must be preceded by a line (no matter the content as long as it is a single line). See example.

EXAMPLES:

---pos.dat----
#
1 2 3 4 5
6 7 8 9
10 11 12 13 14
#
15 16 17 18
19 20 21
22 23 24
------

$ cat pos.dat | rdf -N 3 -Nsnapshots 2 -L 25 -nbins 10 -rcut 2 > rdf.dat

rdf will take the file as 2 snapshots with the positions of 3 particles in 3D.