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lammps/tools/matlab/readdump_one.m
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readdump_one.m
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function [varargout] = readdump_one(varargin)
% Read LAMMPS dump file one timestep at a time
% Input
% Dump file name with path
% Starting file pointer position in dump file
% Number of columns in the dump file
% Output is in the form of a structure with following variables
% .timestep --> Vector containing all time steps
% .Natoms --> Vector containing number of atoms at each time step
% .x_bound --> [t,2] array with xlo,xhi at each time step
% .y_bound --> [t,2] array with ylo,yhi at each time step
% .z_bound --> [t,2] array with zlo,zhi at each time step
% .atom_data --> 2 dimensional array with data
% .position --> file pointer for reading next time
%
% Example
% data = readdump_one('dump.LAMMPS',0,5);
% Reads the first timestep in the file dump.LAMMPS
% Specify position = -1 if only the last dump step in the
% file is needed
%
% See also readdump, scandump
%
% 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.
try
dump = fopen(varargin{1},'r');
catch
error('Dumpfile not found!');
end
position = varargin{2}; % from beg of file
ncol = varargin{3}; %number of columns
i=1;
t=0;
done = 0;
last_status = 0;
if position ~= -1
fseek(dump,position,'bof');
else
last_status = 1;
end
while done == 0 & last_status == 0
id = fgetl(dump);
if (strcmpi(id,'ITEM: TIMESTEP'))
if t == 0
timestep(i) = str2num(fgetl(dump));
t=1;
end
else
if (strcmpi(id,'ITEM: NUMBER OF ATOMS'))
Natoms = str2num(fgetl(dump));
else
if (strcmpi(id,'ITEM: BOX BOUNDS'))
x_bound(1,:) = str2num(fgetl(dump));
y_bound(1,:) = str2num(fgetl(dump));
z_bound(1,:) = str2num(fgetl(dump));
else
if (strcmpi(id(1:11),'ITEM: ATOMS'))
atom_data = zeros(Natoms,ncol);%Allocate memory for atom data
for j = 1 : 1: Natoms
atom_data(j,:) = str2num(fgetl(dump));
end
done = 1;
p = ftell(dump);
end
end
end
end
end
% Getting only the last step
if last_status == 1
% First get the position of the beginning of the last step in the
% dumpfile
while ~feof(dump)
temp = fgetl(dump);
if length(temp) == 14
if strcmpi(temp,'ITEM: TIMESTEP')
p = ftell(dump); % starting position of line next to the header
end
end
end
fclose(dump);
dump = fopen(varargin{1},'r');
fseek(dump,p,'bof');
% getting Timestep
timestep = str2num(fgetl(dump));
while ~feof(dump)
id = fgetl(dump);
if (strcmpi(id,'ITEM: NUMBER OF ATOMS'))
Natoms = str2num(fgetl(dump));
else
if (strcmpi(id,'ITEM: BOX BOUNDS'))
x_bound(1,:) = str2num(fgetl(dump));
y_bound(1,:) = str2num(fgetl(dump));
z_bound(1,:) = str2num(fgetl(dump));
else
if (strcmpi(id(1:11),'ITEM: ATOMS'))
atom_data = zeros(Natoms,ncol);%Allocate memory for atom data
for j = 1 : 1: Natoms
atom_data(j,:) = str2num(fgetl(dump));
end
end
end
end
end
end
%----------Outputs-------------
%OUTPUTS IN SAME VARIABLE STRUCTURE
varargout{1}.timestep = timestep;
varargout{1}.Natoms = Natoms;
varargout{1}.x_bound = x_bound;
varargout{1}.y_bound = y_bound;
varargout{1}.z_bound = z_bound;
varargout{1}.atom_data = atom_data;
varargout{1}.position = p; %gives postion of ITEM: TIMESTEP line
%------------------------------
fclose(dump);
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