git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@382 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
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tools/matlab/README.pdf
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tools/matlab/README.pdf
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252
tools/matlab/lmp2cfg.m
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tools/matlab/lmp2cfg.m
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function lmp2cfg(varargin)
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% Converts LAMMPS dump file to Extended CFG Format (No velocity) to be used
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% with AtomEye (http://164.107.79.177/Archive/Graphics/A/)
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% Input :
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% Necessary (in order)
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% timestep,Natoms,x_bound,y_bound,z_bound,H,atom_data,mass,
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% cfg file name, dumpfile name
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% Optional
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% 'vel' --> 'yes' (if velocity data needs to be written)
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% --> Default is 'no'
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% 'atomtype' --> {Atom symbol}
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% 'autonumber' --> 'yes' (default) numbers cfgfiles consecutively based on timestep
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% 'autolog' --> 'on' (default) writes details of conversion to a log file
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% 'rotation' --> To specify rotation (Transform in cfg file) say 'rotation' followed by
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% number of rotations,the axes of rotation ('X' or 'Y' or 'Z')and the
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% angle in degrees. CAUTION : Do remember that rotations are
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% non-commutative and hence the order of rotations must be the same as
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% intended
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% 'aux' --> Auxiliary data must be a two column array with Quantity and Type in each
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% column
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%
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%
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% THE DATA MUST BE SCALED (0 to 1)IN ORDER FOR ATOMEYE TO READ PROPERLY
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% Real coordinates x = s * H, x, s are 1x3 row vectors
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%
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% Example
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% lmp2cfg_all(data.timestep,data.Natoms,data.xbound,data.ybound,...
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% data.zbound,H,data.atom_data,mass,cfgfile,dumpfile,...
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% 'vel','no','aux',{'sxx' 'Lammps O/P'
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% 'syy' 'Lammps O/P'
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% 'szz' 'Lammps O/P'
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% 'sxy' 'Lammps O/P'
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% 'sxz' 'Lammps O/P'
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% 'syz' 'Lammps O/P'},...
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% 'atomtype',{'Ni'
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% 'Al'},...
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% 'autonumber','on',...
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% 'autolog','on',...
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% 'rotation',2,'X',45,'Y',30);
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%
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% See also readdump_all, readdump_one, 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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%------------ Defaults
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vel = 'no';
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auxstatus = 0;
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atom_typestatus = 0;
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rotstatus = 0;
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autonumber_status = 1; % default is ON
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autolog_status = 1;
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%----------------------------------
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%-----Required Input --------------
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timestep = varargin{1}
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Natoms = varargin{2};
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x_bound = varargin{3};
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y_bound = varargin{4};
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z_bound = varargin{5};
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H = varargin{6};
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atom_data = varargin{7};
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mass = varargin{8}; %arrange it in order of atom type , ie 1 - mass1 etc
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filename = varargin{9}; %Just give one file name
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if length(varargin) < 10
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dumpfilename = ['dump.' filename];
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else
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dumpfilename = varargin{10};
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end
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if length(varargin) > 10
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i=11;
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while i<length(varargin)
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id = varargin{i};
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switch id
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case 'vel'
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vel = varargin{i+1};
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i=i+2;
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case 'aux'
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auxiliary = varargin{i+1};
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auxstatus = 1;
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i=i+2;
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case 'atomtype'
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atom_type = varargin{i+1};
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atom_typestatus = 1;
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i=i+2;
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case 'rotation'
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nrot = varargin{i+1}; % number of rotations
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i = i+2;
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if nrot <=0
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error('Number of rotations must be a positive value');
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end
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rotstatus = 1;
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for j = 1 : 1 : nrot
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rotaxes{j} = varargin{i};
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i = i + 1;
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rotangle(j) = varargin{i};
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i = i + 1;
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end
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case 'autonumber'
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numberstate = varargin{i+1};
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i = i +2;
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if strcmpi(numberstate,'ON')
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autonumber_status = 1;
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elseif strcmpi(numberstate,'OFF')
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autonumber_status = 0;
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end
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case 'autolog'
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logstate = varargin{i+1};
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i = i + 2;
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if strcmpi(logstate,'ON')
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autolog_status = 1;
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elseif strcmpi(logstate,'OFF')
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autolog_status = 0;
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end
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end
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end
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end
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% Calculating Transformation matrix [T]
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if rotstatus == 0
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T = eye(3); % Identity matrix
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elseif rotstatus == 1
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T = eye(3);
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for j = 1 : 1 : nrot
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B = beta(rotangle(j)*pi/180,rotaxes{j});
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T = B*T;
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end
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end
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T = T'; % because Transform = [beta]transpose
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%----------------------------------
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nfiles = length(timestep);
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%----Default Atom type names------------
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if atom_typestatus == 0
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atom_type = {'Au'
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'Ni'
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'Zn'
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'H'
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'O'
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'Cu'
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'Al'
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'Ag'
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'C'
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'Si'};
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end
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%--------Sorting atom types ---------
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[s,id] = sort(atom_data(:,2,:));
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%---------Writing CFG files---------------
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for i = 1 : 1 : nfiles
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if autonumber_status == 1
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n = [filename '_' num2str(i) '.cfg'];
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elseif autonumber_status == 0
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n = [filename '.cfg'];
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end
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name{i}=n;
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fid = fopen(name{i},'w+');
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fprintf(fid,'Number of particles = %d\n',Natoms(i));
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fprintf(fid,'A = 1.0000000000 Angstrom \n');
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% Writing [H]
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fprintf(fid,'H0(1,1) = %f A \n',H(1,1));
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fprintf(fid,'H0(1,2) = %f A \n',H(1,2));
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fprintf(fid,'H0(1,3) = %f A \n',H(1,3));
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fprintf(fid,'H0(2,1) = %f A \n',H(2,1));
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fprintf(fid,'H0(2,2) = %f A \n',H(2,2));
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fprintf(fid,'H0(2,3) = %f A \n',H(2,3));
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fprintf(fid,'H0(3,1) = %f A \n',H(3,1));
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fprintf(fid,'H0(3,2) = %f A \n',H(3,2));
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fprintf(fid,'H0(3,3) = %f A \n',H(3,3));
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% Writing [T]
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fprintf(fid,'Transform(1,1) = %f \n',T(1,1));
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fprintf(fid,'Transform(1,2) = %f \n',T(1,2));
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fprintf(fid,'Transform(1,3) = %f \n',T(1,3));
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fprintf(fid,'Transform(2,1) = %f \n',T(2,1));
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fprintf(fid,'Transform(2,2) = %f \n',T(2,2));
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fprintf(fid,'Transform(2,3) = %f \n',T(2,3));
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fprintf(fid,'Transform(3,1) = %f \n',T(3,1));
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fprintf(fid,'Transform(3,2) = %f \n',T(3,2));
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fprintf(fid,'Transform(3,3) = %f \n',T(3,3));
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if strcmpi(vel,'no')
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fprintf(fid,'.NO_VELOCITY. \n');
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end
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fprintf(fid,'entry_count = %d \n',length(atom_data(1,:,i))-2);
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if auxstatus == 1
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for k = 1 : 1 : length(auxiliary(:,1))
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fprintf(fid,'auxiliary[%d] = %s [%s]\n',k-1,auxiliary{k,1},...
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auxiliary{k,2});
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end
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end
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aid = 1;
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atom_change = 1;
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for j = 1 : 1 : Natoms(i)
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if atom_change == 1
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fprintf(fid,'%f\n',mass(aid));
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fprintf(fid,'%s\n',atom_type{aid});
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end
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atom_change = 0;
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fprintf(fid,'%f\t',atom_data(id(j,1,i),3:length(atom_data(1,:,i)),i));
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fprintf(fid,'\n');
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if j ~= Natoms
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if atom_data(id(j,1,i),2,i) ~= atom_data(id(j+1,1,i),2,i)
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atom_change = 1;
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aid = aid+1;
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end
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end
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end
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fclose(fid);
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end
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if autolog_status == 1
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flog = fopen([filename '_lmp2cfg.log'],'w+');
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fprintf(flog,'----------------------------------------------------------\n');
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fprintf(flog,['LAMMPS DUMP to CFG file conversion :\t' datestr(now) '\n']);
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fprintf(flog,'----------------------------------------------------------\n');
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fprintf(flog,'LAMMPS Dump file : \t %s \n\n',dumpfilename);
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for i = 1 : 1 : nfiles
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fprintf(flog,'Timestep : %d --> \t\t %s \n',timestep(i),name{i});
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end
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fclose(flog);
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end
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%---------- Function to calculate beta
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function b = beta(angle,axes)
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switch axes
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case 'X' % X axes
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b = [1 0 0
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0 cos(angle) sin(angle)
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0 -sin(angle) cos(angle)];
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case 'Y' % Y axes
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b = [cos(angle) 0 sin(angle)
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0 1 0
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-sin(angle) 0 cos(angle)];
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case 'Z' % Z axes
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b = [cos(angle) sin(angle) 0
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-sin(angle) cos(angle) 0
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0 0 1];
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end
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end
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% --------------------------------------------------
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end % For main function
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166
tools/matlab/readEAM.m
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166
tools/matlab/readEAM.m
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function varargout = readEAM(varargin)
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% Function to read EAM potential files
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% Input
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% 1: EAM potential file name
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% 2: file type --> 'FUNCFL' for single element file
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% --> 'SETFL' for multiple element file
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% Output : Structure with members
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% .embed : Embedding function
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% .pair : Pair Potential
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% .elecden : Electron Density
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% .nrho : Number of points for electron density
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% .drho : increment of r for electron density
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% .nr : Number of points for pair potential
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% .dr : increment of r for pair potential
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% .rcut : cut-off distance
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% All output is in exactly the same units as in the EAM file. For
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% multielement SETFL files the members are multidimensional arrays with
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% each element data stored in (:,:,ELEM)
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%
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% Example
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% eam = readEAM('cuu3.eam','funcfl');
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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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if length(varargin) < 2
|
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error('Too few input parameters : Need Filename and filetype');
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elseif length(varargin) > 2
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error('Too many input parameters');
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end
|
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filename = varargin{1};
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type = varargin{2};
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try
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fid = fopen(filename,'r');
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catch
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error('EAM file not found!');
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end
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|
|
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if strcmpi(type,'FUNCFL')
|
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t = 1;
|
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elseif strcmpi(type,'SETFL')
|
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t = 2;
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else
|
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error(['Unknown file type : "' type '"']);
|
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end
|
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switch t
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case 1 %FUNCFL
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% Read line 1 : comment line
|
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a = fgetl(fid);
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% read Line 2
|
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rem = fgetl(fid); % ielem amass blat lat
|
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[ielem,rem] = strtok(rem);
|
||||||
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[amass,rem] = strtok(rem);
|
||||||
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[blat,rem] = strtok(rem);
|
||||||
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[lat,rem] = strtok(rem);
|
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|
ielem = str2num(ielem); % Atomic Number
|
||||||
|
amass = str2num(amass); % Atomic Mass
|
||||||
|
blat = str2num(blat); % Lattice Constant
|
||||||
|
|
||||||
|
% Read Line 3
|
||||||
|
a = str2num(fgetl(fid));
|
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nrho = a(1);
|
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|
drho = a(2);
|
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nr = a(3);
|
||||||
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dr = a(4);
|
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rcut = a(5);
|
||||||
|
|
||||||
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% Reading embedding function
|
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for i = 1 : 1 : nrho/5
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embed(i,:) = str2num(fgetl(fid));
|
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end
|
||||||
|
|
||||||
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% Reading pair potential
|
||||||
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for i = 1 : 1 : nr/5
|
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pair(i,:) = str2num(fgetl(fid));
|
||||||
|
end
|
||||||
|
|
||||||
|
% Reading electron density function
|
||||||
|
for i = 1 : 1 : nr/5
|
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|
elecden(i,:) = str2num(fgetl(fid));
|
||||||
|
end
|
||||||
|
|
||||||
|
% Output
|
||||||
|
out.embed = embed;
|
||||||
|
out.pair = pair;
|
||||||
|
out.elecden = elecden;
|
||||||
|
out.nrho = nrho;
|
||||||
|
out.drho = drho;
|
||||||
|
out.nr = nr;
|
||||||
|
out.dr = dr;
|
||||||
|
out.rcut = rcut;
|
||||||
|
|
||||||
|
varargout{1} = out;
|
||||||
|
% --------------------------------------------------------------------
|
||||||
|
|
||||||
|
case 2 % SETFL
|
||||||
|
|
||||||
|
% Read lines 1 - 3 : comment lines
|
||||||
|
a = fgetl(fid);
|
||||||
|
a = fgetl(fid);
|
||||||
|
a = fgetl(fid);
|
||||||
|
|
||||||
|
% Atom types
|
||||||
|
ntypes = str2num(fgetl(fid));
|
||||||
|
|
||||||
|
% Read Global information
|
||||||
|
a = str2num(fgetl(fid));
|
||||||
|
nrho = a(1);
|
||||||
|
drho = a(2);
|
||||||
|
nr = a(3);
|
||||||
|
dr = a(4);
|
||||||
|
rcut = a(5);
|
||||||
|
|
||||||
|
% Read element specific Data
|
||||||
|
% Embedding function and Electron Density
|
||||||
|
for elem = 1 : 1 : ntypes
|
||||||
|
rem = fgetl(fid); % ielem amass blat lat
|
||||||
|
[ielem1,rem] = strtok(rem);
|
||||||
|
[amass1,rem] = strtok(rem);
|
||||||
|
[blat1,rem] = strtok(rem);
|
||||||
|
[lat1,rem] = strtok(rem);
|
||||||
|
ielem(elem) = str2num(ielem1); % Atomic Number
|
||||||
|
amass(elem) = str2num(amass1); % Atomic Mass
|
||||||
|
blat(elem) = str2num(blat1); % Lattice Constant
|
||||||
|
lat(elem,:) = lat1; % Lattice type
|
||||||
|
|
||||||
|
% Reading embedding function
|
||||||
|
for i = 1 : 1 : nrho/5
|
||||||
|
embed(i,:,elem) = str2num(fgetl(fid));
|
||||||
|
end
|
||||||
|
|
||||||
|
% Reading electron density function
|
||||||
|
for i = 1 : 1 : nr/5
|
||||||
|
elecden(i,:,elem) = str2num(fgetl(fid));
|
||||||
|
end
|
||||||
|
end
|
||||||
|
|
||||||
|
% Pair Potentials
|
||||||
|
n_pair = ntypes + (factorial(ntypes)/2);
|
||||||
|
for np = 1 : 1 : n_pair
|
||||||
|
for i = 1 : 1 : nr/5
|
||||||
|
pair(i,:,np) = str2num(fgetl(fid));
|
||||||
|
end
|
||||||
|
end
|
||||||
|
|
||||||
|
% Output
|
||||||
|
out.embed = embed;
|
||||||
|
out.elecden = elecden;
|
||||||
|
out.pair = pair;
|
||||||
|
out.nrho = nrho;
|
||||||
|
out.drho = drho;
|
||||||
|
out.nr = nr;
|
||||||
|
out.dr = dr;
|
||||||
|
out.rcut = rcut;
|
||||||
|
|
||||||
|
varargout{1} = out;
|
||||||
|
|
||||||
|
end
|
||||||
|
|
||||||
1
tools/matlab/readdump_all.m
Normal file
1
tools/matlab/readdump_all.m
Normal file
@ -0,0 +1 @@
|
|||||||
|
function [varargout] = readdump_all(varargin)
|
||||||
120
tools/matlab/readdump_one.m
Normal file
120
tools/matlab/readdump_one.m
Normal file
@ -0,0 +1,120 @@
|
|||||||
|
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);
|
||||||
|
switch id
|
||||||
|
case 'ITEM: TIMESTEP'
|
||||||
|
if t == 0
|
||||||
|
timestep(i) = str2num(fgetl(dump));
|
||||||
|
t=1;
|
||||||
|
end
|
||||||
|
case 'ITEM: NUMBER OF ATOMS'
|
||||||
|
Natoms = str2num(fgetl(dump));
|
||||||
|
case 'ITEM: BOX BOUNDS'
|
||||||
|
x_bound(1,:) = str2num(fgetl(dump));
|
||||||
|
y_bound(1,:) = str2num(fgetl(dump));
|
||||||
|
z_bound(1,:) = str2num(fgetl(dump));
|
||||||
|
case '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
|
||||||
|
|
||||||
|
% 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);
|
||||||
|
switch id
|
||||||
|
case 'ITEM: NUMBER OF ATOMS'
|
||||||
|
Natoms = str2num(fgetl(dump));
|
||||||
|
case 'ITEM: BOX BOUNDS'
|
||||||
|
x_bound(1,:) = str2num(fgetl(dump));
|
||||||
|
y_bound(1,:) = str2num(fgetl(dump));
|
||||||
|
z_bound(1,:) = str2num(fgetl(dump));
|
||||||
|
case '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
|
||||||
|
|
||||||
|
%----------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);
|
||||||
|
|
||||||
92
tools/matlab/readlog.m
Normal file
92
tools/matlab/readlog.m
Normal file
@ -0,0 +1,92 @@
|
|||||||
|
function [varargout] = readlog(varargin)
|
||||||
|
% Read LAMMPS log files
|
||||||
|
% input is log file name with path
|
||||||
|
% output is a structure --> out
|
||||||
|
% out.Chead --> has heading of columns in each run
|
||||||
|
% out.data --> has the data during each run in the form of string
|
||||||
|
% Type str2num(out.data{i}) to get the numeric array
|
||||||
|
%
|
||||||
|
% Example
|
||||||
|
% logdata = readlog('log.LAMMPS');
|
||||||
|
%
|
||||||
|
% Author : sarunkarthi@gmail.com
|
||||||
|
% http://web.ics.purdue.edu/~asubrama/pages/Research_Main.htm
|
||||||
|
% Arun K. Subramaniyan
|
||||||
|
% School of Aeronautics and Astronautics
|
||||||
|
% Purdue University, West Lafayette, IN - 47907, USA.
|
||||||
|
|
||||||
|
logfile = varargin{1};
|
||||||
|
try
|
||||||
|
fid = fopen(logfile,'r');
|
||||||
|
catch
|
||||||
|
error('Log file not found!');
|
||||||
|
end
|
||||||
|
|
||||||
|
loop = 1;
|
||||||
|
while feof(fid) == 0
|
||||||
|
%----------- To get first line of thermo output --------
|
||||||
|
while feof(fid) == 0
|
||||||
|
a = fgetl(fid);
|
||||||
|
if length(a) > 4 && strcmp(a(1:4),'Step')
|
||||||
|
findstep = 1;
|
||||||
|
break;
|
||||||
|
end
|
||||||
|
end
|
||||||
|
%-------------------------------------------------------
|
||||||
|
|
||||||
|
%---------Seperate column headings----------------------
|
||||||
|
j=1;
|
||||||
|
k=1;
|
||||||
|
Ch='';
|
||||||
|
i=1;
|
||||||
|
while i < length(a) && findstep == 1
|
||||||
|
for i = k : 1 : length(a)
|
||||||
|
if strcmp(a(i),' ')
|
||||||
|
Chead{loop,j} = Ch;
|
||||||
|
clear Ch;
|
||||||
|
Ch = '';
|
||||||
|
k=i+1;
|
||||||
|
j=j+1;
|
||||||
|
break;
|
||||||
|
else
|
||||||
|
Ch = [Ch a(i)];
|
||||||
|
end
|
||||||
|
end
|
||||||
|
end
|
||||||
|
if findstep == 1
|
||||||
|
Chead{loop,j} = Ch; % to get the last column heading
|
||||||
|
end
|
||||||
|
%-------------------------------------------------------
|
||||||
|
|
||||||
|
%----------------------Get Data-------------------------
|
||||||
|
id = 1; %row id...
|
||||||
|
while feof(fid) == 0
|
||||||
|
a = fgetl(fid);
|
||||||
|
if strcmp(a(1:4),'Loop')
|
||||||
|
loop = loop + 1;
|
||||||
|
break;
|
||||||
|
else
|
||||||
|
logdata(id,:) = str2num(a);
|
||||||
|
id = id+1;
|
||||||
|
end
|
||||||
|
end
|
||||||
|
%--------------------------------------------------------
|
||||||
|
if feof(fid) == 0
|
||||||
|
b = num2str(logdata);
|
||||||
|
data{loop-1} = b;
|
||||||
|
clear b;
|
||||||
|
clear logdata;
|
||||||
|
findstep = 0;
|
||||||
|
end
|
||||||
|
end
|
||||||
|
fclose(fid);
|
||||||
|
|
||||||
|
%--------OUTPUT-------------------------------------------
|
||||||
|
out.Chead = Chead;
|
||||||
|
out.data = data;
|
||||||
|
|
||||||
|
varargout{1} = out;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
142
tools/matlab/readrdf.m
Normal file
142
tools/matlab/readrdf.m
Normal file
@ -0,0 +1,142 @@
|
|||||||
|
function varargout = readrdf(varargin)
|
||||||
|
% Function to read Radial Distribution Funtion 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;
|
||||||
57
tools/matlab/scandump.m
Normal file
57
tools/matlab/scandump.m
Normal file
@ -0,0 +1,57 @@
|
|||||||
|
function [varargout] = scandump(varargin)
|
||||||
|
% Function to scan LAMMPS dump file
|
||||||
|
% Input is dumpfile name
|
||||||
|
% Output is a structure with the following members
|
||||||
|
% .timestep --> column vector with all the timesteps
|
||||||
|
% .natoms --> column vector with number of atoms in each timestep
|
||||||
|
% .position --> column vector with position (for input into readdump)
|
||||||
|
% .ncol --> column vector with number of columns
|
||||||
|
% .boxbound --> 3 by 3 by N (number of time steps) 3D array with
|
||||||
|
% [xlo xhi
|
||||||
|
% ylo yhi
|
||||||
|
% zlo zhi];
|
||||||
|
% Example
|
||||||
|
% dump = scandump('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;
|
||||||
|
out.position(i,1) = 0;
|
||||||
|
|
||||||
|
while ~feof(dump)
|
||||||
|
id = fgetl(dump);
|
||||||
|
switch id
|
||||||
|
case 'ITEM: TIMESTEP'
|
||||||
|
out.timestep(i,1) = str2num(fgetl(dump));
|
||||||
|
case 'ITEM: NUMBER OF ATOMS'
|
||||||
|
out.Natoms(i,1) = str2num(fgetl(dump));
|
||||||
|
case 'ITEM: BOX BOUNDS'
|
||||||
|
out.boxbound(1,:,i) = str2num(fgetl(dump));
|
||||||
|
out.boxbound(2,:,i) = str2num(fgetl(dump));
|
||||||
|
out.boxbound(3,:,i) = str2num(fgetl(dump));
|
||||||
|
case 'ITEM: ATOMS'
|
||||||
|
t = str2num(fgetl(dump));
|
||||||
|
out.ncol(i,1) = length(t);
|
||||||
|
for j = 2 : 1 : out.Natoms(i,1)
|
||||||
|
fgetl(dump);
|
||||||
|
end
|
||||||
|
out.position(i+1,1) = ftell(dump);
|
||||||
|
i = i+1;
|
||||||
|
end
|
||||||
|
end
|
||||||
|
|
||||||
|
% Output
|
||||||
|
varargout{1} = out;
|
||||||
|
|
||||||
Reference in New Issue
Block a user