diff --git a/examples/flow/in.flow.couette b/examples/flow/in.flow.couette index 542ce1eb79..6eba1c0b31 100644 --- a/examples/flow/in.flow.couette +++ b/examples/flow/in.flow.couette @@ -50,7 +50,7 @@ velocity upper set 3.0 0.0 0.0 fix 3 boundary setforce 0.0 0.0 0.0 fix 4 all enforce2d -# Poisseuille flow +# Poiseuille flow #velocity boundary set 0.0 0.0 0.0 #fix 3 lower setforce 0.0 0.0 0.0 diff --git a/examples/flow/in.flow.poiss b/examples/flow/in.flow.poiss index 98de729533..2fa4462c22 100644 --- a/examples/flow/in.flow.poiss +++ b/examples/flow/in.flow.poiss @@ -50,7 +50,7 @@ fix_modify 2 temp mobile #fix 3 boundary setforce 0.0 0.0 0.0 #fix 4 all enforce2d -# Poisseuille flow +# Poiseuille flow velocity boundary set 0.0 0.0 0.0 fix 3 lower setforce 0.0 0.0 0.0 diff --git a/examples/obstacle/in.obstacle b/examples/obstacle/in.obstacle index 0c4b4fe5ab..e0c38695d8 100644 --- a/examples/obstacle/in.obstacle +++ b/examples/obstacle/in.obstacle @@ -43,7 +43,7 @@ fix 1 all nve fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0 fix_modify 2 temp mobile -# Poiselle flow +# Poisseuille flow velocity boundary set 0.0 0.0 0.0 fix 3 lower setforce 0.0 0.0 0.0 diff --git a/lib/meam/Makefile b/lib/meam/Makefile index cbf961dd6c..4395dcb8a1 100755 --- a/lib/meam/Makefile +++ b/lib/meam/Makefile @@ -45,4 +45,4 @@ clean: -rm *.o *.mod *~ $(LIB) tar: - -tar -cvf ../MEAM.tar $(FILES) \ No newline at end of file + -tar -cvf ../MEAM.tar $(FILES) diff --git a/src/lattice.cpp b/src/lattice.cpp index 1ce74edfc5..436d20b0c5 100644 --- a/src/lattice.cpp +++ b/src/lattice.cpp @@ -209,8 +209,8 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) error->all("Lattice orient vectors are not orthogonal"); if (!right_handed()) error->all("Lattice orient vectors are not right-handed"); - if (colinear()) - error->all("Lattice primitive vectors are colinear"); + if (collinear()) + error->all("Lattice primitive vectors are collinear"); if (dimension == 2) { 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]; cross(a1,a2,vec); diff --git a/src/lattice.h b/src/lattice.h index 798d41ee36..5010777790 100644 --- a/src/lattice.h +++ b/src/lattice.h @@ -48,7 +48,7 @@ private: int orthogonal(); int right_handed(); - int colinear(); + int collinear(); void setup_transform(); void add_basis(double, double, double); double dot(double *, double *); diff --git a/tools/matlab/readdump_all.m b/tools/matlab/readdump_all.m index 22eb3d9c87..1cb184c3a6 100644 --- a/tools/matlab/readdump_all.m +++ b/tools/matlab/readdump_all.m @@ -1 +1,57 @@ -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); \ No newline at end of file +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);