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