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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1614 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2008-03-18 20:20:01 +00:00
parent d260cccc86
commit 4ca648bb1e
7 changed files with 66 additions and 10 deletions
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2
examples/flow/in.flow.couette
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@ -50,7 +50,7 @@ velocity upper set 3.0 0.0 0.0
fix 3 boundary setforce 0.0 0.0 0.0 fix 3 boundary setforce 0.0 0.0 0.0
fix 4 all enforce2d fix 4 all enforce2d
# Poisseuille flow # Poiseuille flow
#velocity boundary set 0.0 0.0 0.0 #velocity boundary set 0.0 0.0 0.0
#fix 3 lower setforce 0.0 0.0 0.0 #fix 3 lower setforce 0.0 0.0 0.0

2
examples/flow/in.flow.poiss
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@ -50,7 +50,7 @@ fix_modify 2 temp mobile
#fix 3 boundary setforce 0.0 0.0 0.0 #fix 3 boundary setforce 0.0 0.0 0.0
#fix 4 all enforce2d #fix 4 all enforce2d
# Poisseuille flow # Poiseuille flow
velocity boundary set 0.0 0.0 0.0 velocity boundary set 0.0 0.0 0.0
fix 3 lower setforce 0.0 0.0 0.0 fix 3 lower setforce 0.0 0.0 0.0

2
examples/obstacle/in.obstacle
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@ -43,7 +43,7 @@ fix 1 all nve
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0 fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
fix_modify 2 temp mobile fix_modify 2 temp mobile
# Poiselle flow # Poisseuille flow
velocity boundary set 0.0 0.0 0.0 velocity boundary set 0.0 0.0 0.0
fix 3 lower setforce 0.0 0.0 0.0 fix 3 lower setforce 0.0 0.0 0.0

8
src/lattice.cpp
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@ -209,8 +209,8 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
error->all("Lattice orient vectors are not orthogonal"); error->all("Lattice orient vectors are not orthogonal");
if (!right_handed()) if (!right_handed())
error->all("Lattice orient vectors are not right-handed"); error->all("Lattice orient vectors are not right-handed");
if (colinear()) if (collinear())
error->all("Lattice primitive vectors are colinear"); error->all("Lattice primitive vectors are collinear");
if (dimension == 2) { if (dimension == 2) {
if (origin[2] != 0.0) if (origin[2] != 0.0)
@ -321,10 +321,10 @@ int Lattice::right_handed()
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
check colinearity of each pair of primitive vectors check collinearity of each pair of primitive vectors
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
int Lattice::colinear() int Lattice::collinear()
{ {
double vec[3]; double vec[3];
cross(a1,a2,vec); cross(a1,a2,vec);

2
src/lattice.h
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@ -48,7 +48,7 @@ private:
int orthogonal(); int orthogonal();
int right_handed(); int right_handed();
int colinear(); int collinear();
void setup_transform(); void setup_transform();
void add_basis(double, double, double); void add_basis(double, double, double);
double dot(double *, double *); double dot(double *, double *);

58
tools/matlab/readdump_all.m
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@ -1 +1,57 @@
function [varargout] = readdump_all(varargin) 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);