Diffusion lammps (efficient_neuronet) Browse

lammps/tools/matlab/readdump_all.m
cb83fd5c2b24efficient_neuronet

readdump_all.m
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			function [varargout] = readdump_all(varargin) % Reads all timesteps from a LAMMPS dump file. % Input is dump file name with path % 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 --> 3 dimensional array with data at each time step stored % as atomdata(:,:,t) % Example % data = readdump_all('dump.LAMMPS'); % % See also readdump_one, 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 i=1; while feof(dump) == 0 id = fgetl(dump); switch id case 'ITEM: TIMESTEP' timestep(i) = str2num(fgetl(dump)); case 'ITEM: NUMBER OF ATOMS' Natoms(i) = str2num(fgetl(dump)); case 'ITEM: BOX BOUNDS' x_bound(i,:) = str2num(fgetl(dump)); y_bound(i,:) = str2num(fgetl(dump)); z_bound(i,:) = str2num(fgetl(dump)); case 'ITEM: ATOMS' for j = 1 : 1: Natoms atom_data(j,:,i) = str2num(fgetl(dump)); end i=i+1; 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; %------------------------------ fclose(dump);