git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1559 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -1,120 +1,120 @@
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function [varargout] = readdump_one(varargin)
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% Read LAMMPS dump file one timestep at a time
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% Input
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% Dump file name with path
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% Starting file pointer position in dump file
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% Number of columns in the dump file
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% Output is in the form of a structure with following variables
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% .timestep --> Vector containing all time steps
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% .Natoms --> Vector containing number of atoms at each time step
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% .x_bound --> [t,2] array with xlo,xhi at each time step
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% .y_bound --> [t,2] array with ylo,yhi at each time step
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% .z_bound --> [t,2] array with zlo,zhi at each time step
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% .atom_data --> 2 dimensional array with data
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% .position --> file pointer for reading next time
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%
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% Example
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% data = readdump_one('dump.LAMMPS',0,5);
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% Reads the first timestep in the file dump.LAMMPS
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% Specify position = -1 if only the last dump step in the
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% file is needed
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%
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% See also readdump, scandump
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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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try
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dump = fopen(varargin{1},'r');
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catch
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error('Dumpfile not found!');
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end
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position = varargin{2}; % from beg of file
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ncol = varargin{3}; %number of columns
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i=1;
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t=0;
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done = 0;
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last_status = 0;
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if position ~= -1
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fseek(dump,position,'bof');
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else
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last_status = 1;
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end
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while done == 0 & last_status == 0
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id = fgetl(dump);
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switch id
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case 'ITEM: TIMESTEP'
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if t == 0
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timestep(i) = str2num(fgetl(dump));
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t=1;
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end
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case 'ITEM: NUMBER OF ATOMS'
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Natoms = str2num(fgetl(dump));
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case 'ITEM: BOX BOUNDS'
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x_bound(1,:) = str2num(fgetl(dump));
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y_bound(1,:) = str2num(fgetl(dump));
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z_bound(1,:) = str2num(fgetl(dump));
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case 'ITEM: ATOMS'
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atom_data = zeros(Natoms,ncol);%Allocate memory for atom data
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for j = 1 : 1: Natoms
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atom_data(j,:) = str2num(fgetl(dump));
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end
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done = 1;
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p = ftell(dump);
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end
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end
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% Getting only the last step
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if last_status == 1
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% First get the position of the beginning of the last step in the
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% dumpfile
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while ~feof(dump)
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temp = fgetl(dump);
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if length(temp) == 14
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if strcmpi(temp,'ITEM: TIMESTEP')
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p = ftell(dump); % starting position of line next to the header
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end
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end
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end
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fclose(dump);
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dump = fopen(varargin{1},'r');
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fseek(dump,p,'bof');
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% getting Timestep
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timestep = str2num(fgetl(dump));
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while ~feof(dump)
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id = fgetl(dump);
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switch id
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case 'ITEM: NUMBER OF ATOMS'
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Natoms = str2num(fgetl(dump));
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case 'ITEM: BOX BOUNDS'
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x_bound(1,:) = str2num(fgetl(dump));
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y_bound(1,:) = str2num(fgetl(dump));
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z_bound(1,:) = str2num(fgetl(dump));
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case 'ITEM: ATOMS'
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atom_data = zeros(Natoms,ncol);%Allocate memory for atom data
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for j = 1 : 1: Natoms
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atom_data(j,:) = str2num(fgetl(dump));
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end
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end
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end
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end
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%----------Outputs-------------
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%OUTPUTS IN SAME VARIABLE STRUCTURE
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varargout{1}.timestep = timestep;
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varargout{1}.Natoms = Natoms;
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varargout{1}.x_bound = x_bound;
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varargout{1}.y_bound = y_bound;
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varargout{1}.z_bound = z_bound;
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varargout{1}.atom_data = atom_data;
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varargout{1}.position = p; %gives postion of ITEM: TIMESTEP line
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%------------------------------
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fclose(dump);
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function [varargout] = readdump_one(varargin)
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% Read LAMMPS dump file one timestep at a time
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% Input
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% Dump file name with path
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% Starting file pointer position in dump file
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% Number of columns in the dump file
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% Output is in the form of a structure with following variables
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% .timestep --> Vector containing all time steps
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% .Natoms --> Vector containing number of atoms at each time step
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% .x_bound --> [t,2] array with xlo,xhi at each time step
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% .y_bound --> [t,2] array with ylo,yhi at each time step
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% .z_bound --> [t,2] array with zlo,zhi at each time step
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% .atom_data --> 2 dimensional array with data
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% .position --> file pointer for reading next time
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%
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% Example
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% data = readdump_one('dump.LAMMPS',0,5);
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% Reads the first timestep in the file dump.LAMMPS
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% Specify position = -1 if only the last dump step in the
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% file is needed
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%
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% See also readdump, scandump
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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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try
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dump = fopen(varargin{1},'r');
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catch
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error('Dumpfile not found!');
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end
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position = varargin{2}; % from beg of file
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ncol = varargin{3}; %number of columns
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i=1;
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t=0;
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done = 0;
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last_status = 0;
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if position ~= -1
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fseek(dump,position,'bof');
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else
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last_status = 1;
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end
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while done == 0 & last_status == 0
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id = fgetl(dump);
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switch id
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case 'ITEM: TIMESTEP'
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if t == 0
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timestep(i) = str2num(fgetl(dump));
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t=1;
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end
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case 'ITEM: NUMBER OF ATOMS'
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Natoms = str2num(fgetl(dump));
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case 'ITEM: BOX BOUNDS'
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x_bound(1,:) = str2num(fgetl(dump));
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y_bound(1,:) = str2num(fgetl(dump));
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z_bound(1,:) = str2num(fgetl(dump));
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case 'ITEM: ATOMS'
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atom_data = zeros(Natoms,ncol);%Allocate memory for atom data
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for j = 1 : 1: Natoms
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atom_data(j,:) = str2num(fgetl(dump));
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end
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done = 1;
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p = ftell(dump);
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end
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end
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% Getting only the last step
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if last_status == 1
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% First get the position of the beginning of the last step in the
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% dumpfile
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while ~feof(dump)
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temp = fgetl(dump);
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if length(temp) == 14
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if strcmpi(temp,'ITEM: TIMESTEP')
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p = ftell(dump); % starting position of line next to the header
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end
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end
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end
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fclose(dump);
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dump = fopen(varargin{1},'r');
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fseek(dump,p,'bof');
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% getting Timestep
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timestep = str2num(fgetl(dump));
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while ~feof(dump)
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id = fgetl(dump);
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switch id
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case 'ITEM: NUMBER OF ATOMS'
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Natoms = str2num(fgetl(dump));
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case 'ITEM: BOX BOUNDS'
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x_bound(1,:) = str2num(fgetl(dump));
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y_bound(1,:) = str2num(fgetl(dump));
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z_bound(1,:) = str2num(fgetl(dump));
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case 'ITEM: ATOMS'
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atom_data = zeros(Natoms,ncol);%Allocate memory for atom data
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for j = 1 : 1: Natoms
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atom_data(j,:) = str2num(fgetl(dump));
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end
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end
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end
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end
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%----------Outputs-------------
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%OUTPUTS IN SAME VARIABLE STRUCTURE
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varargout{1}.timestep = timestep;
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varargout{1}.Natoms = Natoms;
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varargout{1}.x_bound = x_bound;
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varargout{1}.y_bound = y_bound;
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varargout{1}.z_bound = z_bound;
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varargout{1}.atom_data = atom_data;
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varargout{1}.position = p; %gives postion of ITEM: TIMESTEP line
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%------------------------------
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fclose(dump);
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