forked from lijiext/lammps
143 lines
4.3 KiB
Matlab
143 lines
4.3 KiB
Matlab
function varargout = readrdf(varargin)
|
|
% Function to read Radial Distribution Function 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;
|