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lammps/tools/matlab/readrdf.m
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readrdf.m
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function varargout = readrdf(varargin)
% Function to read Radial Distribution Funtion output from LAMMPS
% Input
% 'bin' --> number of bins in rdf histogram
% 'runtime' --> Run length of each of the run commands
% 'step' --> rdf Dump step for each of the run commands
% 'ncol' --> number of columns in the file
% 'final' --> 'YES' indicates that only the average values will be extracted
% If only the averages are needed, you don't need to specify 'runtime',
% 'step' and 'ncol'
%
% Output is in the form of a structure with following variables
%
% if 'final' was given as 'NO'
% .rdf_step_data --> Matrix with RDF for each of the dumped steps
% .rdf_ave_data --> Matrix with average RDF for each RUN
% .rdf_ave_data --> Matrix with average RDF for each RUN
%
% if 'final' was given as 'YES'
% .rdf_ave_data --> Matrix with average RDF for each RUN
%
% Example
% rdf = readrdf('inputfile','bin',100,'runtime',[30000;20000],...
% 'step',[100;100],'ncol',3,'final','no')
%
% Author : Arun K. Subramaniyan
% sarunkarthi@gmail.com
% http://web.ics.purdue.edu/~asubrama/pages/Research_Main.htm
% School of Aeronautics and Astronautics
% Purdue University, West Lafayette, IN - 47907, USA.
rdf_name = varargin{1}; % RDF File name
% Setting all status checks to zero
bin_status = 0;
runtime_status = 0;
step_status = 0;
ncol_status = 0;
final_status = 'no';
for id = 2 : 1 : length(varargin)
if strcmpi(varargin{id},'bin')
rdf_bin = varargin{id+1}; % RDF bins
bin_status = 1;
elseif strcmpi(varargin{id},'runtime')
rdf_runtime = varargin{id+1}; % Runtimes
runtime_status = 1;
elseif strcmpi(varargin{id},'step')
rdf_step = varargin{id+1}; % Runtimes
step_status = 1;
elseif strcmpi(varargin{id},'ncol')
ncol = varargin{id+1}; % Runtimes
ncol_status = 1;
elseif strcmpi(varargin{id},'final')
final_status = varargin{id+1};
end
end
if ncol_status == 0
ncol = 3;
end
% Check for errors in input arguments
if bin_status == 0
error('No bin specified');
elseif step_status == 1 && runtime_status == 0
error('Step size specified without Runtime');
elseif step_status == 0 && runtime_status == 1
error('Runtime specified without Step size');
end
if step_status == 1 && runtime_status == 1
if length(rdf_runtime) ~= length(rdf_step)
error('Runtime and Step size do not match');
end
end
% Preallocating memory if runtime and step size are provided
if step_status == 1 && runtime_status == 1 && strcmpi(final_status,'no')
total_steps = round(sum(rdf_runtime./rdf_step));
rdf_step_data = zeros(rdf_bin,ncol,total_steps);
rdf_ave_data = zeros(rdf_bin,ncol,length(rdf_runtime));
elseif strcmpi(final_status,'yes') && step_status == 1 && runtime_status == 1
rdf_ave_data = zeros(rdf_bin,ncol,length(rdf_runtime));
end
try
rdf_file = fopen(rdf_name,'r');
catch
error('RDF file not found!');
end
if strcmpi(final_status,'yes')
run_id = 1; % Run id..
while feof(rdf_file) ~= 1
rdf_data = fgetl(rdf_file);
if strcmpi(rdf_data(1:11),'RUN AVERAGE')
fgetl(rdf_file); % to skip the title
for id = 1 : 1 : rdf_bin
rdf_ave_data(id,:,run_id) = str2num(fgetl(rdf_file));
end
run_id = run_id + 1;
end
end
else
run_id = 1;
id = 1;
while feof(rdf_file) ~= 1
rdf_data = fgetl(rdf_file);
if strcmpi(rdf_data(1:8),'TIMESTEP')
timestep(id,1) = str2num(rdf_data(10:length(rdf_data)));
fgetl(rdf_file); % to skip the title
for j = 1 : 1 : rdf_bin
rdf_step_data(j,:,id) = str2num(fgetl(rdf_file));
end
id = id+1;
elseif strcmpi(rdf_data(1:11),'RUN AVERAGE')
fgetl(rdf_file); % to skip the title
for j = 1 : 1 : rdf_bin
rdf_ave_data(j,:,run_id) = str2num(fgetl(rdf_file));
end
run_id = run_id + 1;
end
end
end
fclose(rdf_file);
if strcmpi(final_status,'no')
out_data.timestep = timestep;
out_data.rdf_step_data = rdf_step_data;
out_data.rdf_ave_data = rdf_ave_data;
else
out_data.rdf_ave_data = rdf_ave_data;
end
varargout{1} = out_data;
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