Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/tools/matlab/lmp2cfg.m
1aeecfb0cfcflammm-master-deprecated

Last Change
Raw File

lmp2cfg.m
View Options

function lmp2cfg(varargin)
% Converts LAMMPS dump file to Extended CFG Format (No velocity) to be used
% with AtomEye (http://164.107.79.177/Archive/Graphics/A/)
% Input :
% Necessary (in order)
% timestep,Natoms,x_bound,y_bound,z_bound,H,atom_data,mass,
% cfg file name, dumpfile name
% Optional
% 'vel' --> 'yes' (if velocity data needs to be written)
% --> Default is 'no'
% 'atomtype' --> {Atom symbol}
% 'autonumber' --> 'yes' (default) numbers cfgfiles consecutively based on timestep
% 'autolog' --> 'on' (default) writes details of conversion to a log file
% 'rotation' --> To specify rotation (Transform in cfg file) say 'rotation' followed by
% number of rotations,the axes of rotation ('X' or 'Y' or 'Z')and the
% angle in degrees. CAUTION : Do remember that rotations are
% non-commutative and hence the order of rotations must be the same as
% intended
% 'aux' --> Auxiliary data must be a two column array with Quantity and Type in each
% column
%
%
% THE DATA MUST BE SCALED (0 to 1)IN ORDER FOR ATOMEYE TO READ PROPERLY
% Real coordinates x = s * H, x, s are 1x3 row vectors
%
% Example
% lmp2cfg_all(data.timestep,data.Natoms,data.xbound,data.ybound,...
% data.zbound,H,data.atom_data,mass,cfgfile,dumpfile,...
% 'vel','no','aux',{'sxx' 'Lammps O/P'
% 'syy' 'Lammps O/P'
% 'szz' 'Lammps O/P'
% 'sxy' 'Lammps O/P'
% 'sxz' 'Lammps O/P'
% 'syz' 'Lammps O/P'},...
% 'atomtype',{'Ni'
% 'Al'},...
% 'autonumber','on',...
% 'autolog','on',...
% 'rotation',2,'X',45,'Y',30);
%
% See also readdump_all, 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.
%------------ Defaults
vel = 'no';
auxstatus = 0;
atom_typestatus = 0;
rotstatus = 0;
autonumber_status = 1; % default is ON
autolog_status = 1;
%----------------------------------
%-----Required Input --------------
timestep = varargin{1}
Natoms = varargin{2};
x_bound = varargin{3};
y_bound = varargin{4};
z_bound = varargin{5};
H = varargin{6};
atom_data = varargin{7};
mass = varargin{8}; %arrange it in order of atom type , ie 1 - mass1 etc
filename = varargin{9}; %Just give one file name
if length(varargin) < 10
dumpfilename = ['dump.' filename];
else
dumpfilename = varargin{10};
end
if length(varargin) > 10
i=11;
while i<length(varargin)
id = varargin{i};
switch id
case 'vel'
vel = varargin{i+1};
i=i+2;
case 'aux'
auxiliary = varargin{i+1};
auxstatus = 1;
i=i+2;
case 'atomtype'
atom_type = varargin{i+1};
atom_typestatus = 1;
i=i+2;
case 'rotation'
nrot = varargin{i+1}; % number of rotations
i = i+2;
if nrot <=0
error('Number of rotations must be a positive value');
end
rotstatus = 1;
for j = 1 : 1 : nrot
rotaxes{j} = varargin{i};
i = i + 1;
rotangle(j) = varargin{i};
i = i + 1;
end
case 'autonumber'
numberstate = varargin{i+1};
i = i +2;
if strcmpi(numberstate,'ON')
autonumber_status = 1;
elseif strcmpi(numberstate,'OFF')
autonumber_status = 0;
end
case 'autolog'
logstate = varargin{i+1};
i = i + 2;
if strcmpi(logstate,'ON')
autolog_status = 1;
elseif strcmpi(logstate,'OFF')
autolog_status = 0;
end
end
end
end
% Calculating Transformation matrix [T]
if rotstatus == 0
T = eye(3); % Identity matrix
elseif rotstatus == 1
T = eye(3);
for j = 1 : 1 : nrot
B = beta(rotangle(j)*pi/180,rotaxes{j});
T = B*T;
end
end
T = T'; % because Transform = [beta]transpose
%----------------------------------
nfiles = length(timestep);
%----Default Atom type names------------
if atom_typestatus == 0
atom_type = {'Au'
'Ni'
'Zn'
'H'
'O'
'Cu'
'Al'
'Ag'
'C'
'Si'};
end
%--------Sorting atom types ---------
[s,id] = sort(atom_data(:,2,:));
%---------Writing CFG files---------------
for i = 1 : 1 : nfiles
if autonumber_status == 1
n = [filename '_' num2str(i) '.cfg'];
elseif autonumber_status == 0
n = [filename '.cfg'];
end
name{i}=n;
fid = fopen(name{i},'w+');
fprintf(fid,'Number of particles = %d\n',Natoms(i));
fprintf(fid,'A = 1.0000000000 Angstrom \n');
% Writing [H]
fprintf(fid,'H0(1,1) = %f A \n',H(1,1));
fprintf(fid,'H0(1,2) = %f A \n',H(1,2));
fprintf(fid,'H0(1,3) = %f A \n',H(1,3));
fprintf(fid,'H0(2,1) = %f A \n',H(2,1));
fprintf(fid,'H0(2,2) = %f A \n',H(2,2));
fprintf(fid,'H0(2,3) = %f A \n',H(2,3));
fprintf(fid,'H0(3,1) = %f A \n',H(3,1));
fprintf(fid,'H0(3,2) = %f A \n',H(3,2));
fprintf(fid,'H0(3,3) = %f A \n',H(3,3));
% Writing [T]
fprintf(fid,'Transform(1,1) = %f \n',T(1,1));
fprintf(fid,'Transform(1,2) = %f \n',T(1,2));
fprintf(fid,'Transform(1,3) = %f \n',T(1,3));
fprintf(fid,'Transform(2,1) = %f \n',T(2,1));
fprintf(fid,'Transform(2,2) = %f \n',T(2,2));
fprintf(fid,'Transform(2,3) = %f \n',T(2,3));
fprintf(fid,'Transform(3,1) = %f \n',T(3,1));
fprintf(fid,'Transform(3,2) = %f \n',T(3,2));
fprintf(fid,'Transform(3,3) = %f \n',T(3,3));
if strcmpi(vel,'no')
fprintf(fid,'.NO_VELOCITY. \n');
end
fprintf(fid,'entry_count = %d \n',length(atom_data(1,:,i))-2);
if auxstatus == 1
for k = 1 : 1 : length(auxiliary(:,1))
fprintf(fid,'auxiliary[%d] = %s [%s]\n',k-1,auxiliary{k,1},...
auxiliary{k,2});
end
end
aid = atom_data(id(1,1,i),2,i);
% aid = 1;
atom_change = 1;
for j = 1 : 1 : Natoms(i)
if atom_change == 1
fprintf(fid,'%f\n',mass(aid));
fprintf(fid,'%s\n',atom_type{aid});
end
atom_change = 0;
fprintf(fid,'%f\t',atom_data(id(j,1,i),3:length(atom_data(1,:,i)),i));
fprintf(fid,'\n');
if j ~= Natoms
if atom_data(id(j,1,i),2,i) ~= atom_data(id(j+1,1,i),2,i)
atom_change = 1;
aid = atom_data(id(j+1,1,i),2,i);
% aid = aid+1;
end
end
end
fclose(fid);
end
if autolog_status == 1
flog = fopen([filename '_lmp2cfg.log'],'w+');
fprintf(flog,'----------------------------------------------------------\n');
fprintf(flog,['LAMMPS DUMP to CFG file conversion :\t' datestr(now) '\n']);
fprintf(flog,'----------------------------------------------------------\n');
fprintf(flog,'LAMMPS Dump file : \t %s \n\n',dumpfilename);
for i = 1 : 1 : nfiles
fprintf(flog,'Timestep : %d --> \t\t %s \n',timestep(i),name{i});
end
fclose(flog);
end
%---------- Function to calculate beta
function b = beta(angle,axes)
switch axes
case 'X' % X axes
b = [1 0 0
0 cos(angle) sin(angle)
0 -sin(angle) cos(angle)];
case 'Y' % Y axes
b = [cos(angle) 0 sin(angle)
0 1 0
-sin(angle) 0 cos(angle)];
case 'Z' % Z axes
b = [cos(angle) sin(angle) 0
-sin(angle) cos(angle) 0
0 0 1];
end
end
% --------------------------------------------------
end % For main function
c4science · Help