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sjplimp
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@ -45,4 +45,4 @@ clean:
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-rm *.o *.mod *~ $(LIB)
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tar:
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-tar -cvf ../MEAM.tar $(FILES)
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-tar -cvf ../MEAM.tar $(FILES)
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@ -48,4 +48,4 @@ clean:
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-rm *.o *.mod *~ $(LIB)
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tar:
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-tar -cvf ../MEAM.tar $(FILES)
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-tar -cvf ../MEAM.tar $(FILES)
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@ -45,4 +45,4 @@ clean:
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-rm *.o *.mod *~ $(LIB)
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tar:
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-tar -cvf ../MEAM.tar $(FILES)
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-tar -cvf ../MEAM.tar $(FILES)
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@ -1,10 +1,19 @@
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Copyright (C) 2006
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Authors as indicated in Author List and Rensselaer Polytechnic Institute
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Parallelizable Open source Efficient Multibody Software (POEMS) is written and maintained by the authors as indicated in Author's List as a part of Scientific Computation Research Center (SCOREC) at Rensselaer Polytechnic Intitute, Troy, NY, USA.
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Parallelizable Open source Efficient Multibody Software (POEMS) is
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written and maintained by the authors as indicated in Author's List as
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a part of Scientific Computation Research Center (SCOREC) at
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Rensselaer Polytechnic Intitute, Troy, NY, USA.
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This program is free software; you can redistribute it and/or modify it under the terms of the license as found in POEMS_License.txt distributed with the source code.
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This program is free software; you can redistribute it and/or modify
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it under the terms of the license as found in POEMS_License.txt
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distributed with the source code.
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This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the license text for more details.
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This program is distributed in the hope that it will be useful, but
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WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the license
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text for more details.
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A copy of the license file POEMS_License.txt, Authors List and Grants List files should be distributed along with this program.
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A copy of the license file POEMS_License.txt, Authors List and Grants
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List files should be distributed along with this program.
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@ -98,4 +98,4 @@ clean:
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-rm *.o *.d *~ $(LIB)
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tar:
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-tar -cvf ../POEMS.tar $(FILES)
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-tar -cvf ../POEMS.tar $(FILES)
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@ -98,4 +98,4 @@ clean:
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-rm *.o *.d *~ $(LIB)
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tar:
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-tar -cvf ../POEMS.tar $(FILES)
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-tar -cvf ../POEMS.tar $(FILES)
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@ -98,4 +98,4 @@ clean:
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-rm *.o *.d *~ $(LIB)
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tar:
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-tar -cvf ../POEMS.tar $(FILES)
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-tar -cvf ../POEMS.tar $(FILES)
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@ -1,64 +1,80 @@
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Copyright (C) 2005
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Authors as indicated in Author List and Rensselaer Polytechnic Institute
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Parallelizable Open source Efficient Multibody Software (POEMS) is written and maintained by the
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authors as indicated in Author's List as a part of Scientific Computation Research Center (SCOREC)
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at Rensselaer Polytechnic Intitute, Troy, NY, USA.
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Parallelizable Open source Efficient Multibody Software (POEMS) is
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written and maintained by the authors as indicated in Author's List
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as a part of Scientific Computation Research Center (SCOREC) at
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Rensselaer Polytechnic Intitute, Troy, NY, USA.
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This License Agreement applies to any software library or other program which contains a notice
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placed by the copyright holder saying it may be distributed under the terms of this Rensselaer
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Public License (also called "this License"). Each licensee is addressed as "you".
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This License Agreement applies to any software library or other
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program which contains a notice placed by the copyright holder
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saying it may be distributed under the terms of this Rensselaer
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Public License (also called "this License"). Each licensee is
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addressed as "you".
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A "library" means a collection of software functions and/or data prepared so as to be conveniently
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linked with application programs (which use some of those functions and data) to form executables.
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The "Library", below, refers to any such software library or work which has been distributed under
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these terms. A "work based on the Library" means either the Library/code or any derivative work
|
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under copyright law.
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A "library" means a collection of software functions and/or data
|
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prepared so as to be conveniently linked with application programs
|
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(which use some of those functions and data) to form executables.
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The "Library", below, refers to any such software library or work
|
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which has been distributed under these terms. A "work based on the
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Library" means either the Library/code or any derivative work under
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copyright law.
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"Source code" for a work means the preferred form of the work for making modifications to it including
|
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any associated interface definition files, and scripts used to control compilation and installation
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of the library.
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"Source code" for a work means the preferred form of the work for
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making modifications to it including any associated interface
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definition files, and scripts used to control compilation and
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installation of the library.
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This library is free software; Redistribution and use in source code and binary forms, with or
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without modification, are permitted provided that the following conditions are met:
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This library is free software; Redistribution and use in source
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code and binary forms, with or without modification, are permitted
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provided that the following conditions are met:
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1. Redistributions of source code must retain the above copyright notice, this list of conditions,
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the authors list, the grants list, and the following disclaimer without any modifications and in
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its current form.
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1. Redistributions of source code must retain the above copyright
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notice, this list of conditions, the authors list, the grants list,
|
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and the following disclaimer without any modifications and in its
|
||||
current form.
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2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions,
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the authors list, the grants list, and the following disclaimer in the documentation and/or other
|
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materials provided with the distribution.
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2. Redistributions in binary form must reproduce the above copyright
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||||
notice, this list of conditions, the authors list, the grants list,
|
||||
and the following disclaimer in the documentation and/or other
|
||||
materials provided with the distribution.
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3. You must cause the files modified to carry prominent notices stating that you changed the files
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and dates of the change.
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3. You must cause the files modified to carry prominent notices
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stating that you changed the files and dates of the change.
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4. At your discretion, you may submit the differences between the program and your work based on the
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program for inclusion in the source code repository maintained by Rensselaer Polytechnic Institute.
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The mechanics of the submission are explained in the file named CONTRIBUTE distributed with the
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Library. Should you decide to submit the changes, you agree to provide Rensselaer Polytechnic
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Institute with a joint copyright assignment of the changes, and you agree to sign such a copyright
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||||
assignment form at the request of Rensselaer Polytechnic Institute. Changes will then made as
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appropriate to the authors list at the Resselaer repository.
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||||
4. At your discretion, you may submit the differences between the
|
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program and your work based on the program for inclusion in the
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||||
source code repository maintained by Rensselaer Polytechnic
|
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Institute. The mechanics of the submission are explained in the
|
||||
file named CONTRIBUTE distributed with the Library. Should you
|
||||
decide to submit the changes, you agree to provide Rensselaer
|
||||
Polytechnic Institute with a joint copyright assignment of the
|
||||
changes, and you agree to sign such a copyright assignment form at
|
||||
the request of Rensselaer Polytechnic Institute. Changes will then
|
||||
made as appropriate to the authors list at the Resselaer
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||||
repository.
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5. The authors as listed in "Authors_List" reserve the right to distribute the software or any modified
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||||
work in any other license form if they so choose to without infringing on any previous or concurrent
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license agreement.
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5. The authors as listed in "Authors_List" reserve the right to
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distribute the software or any modified work in any other license
|
||||
form if they so choose to without infringing on any previous or
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||||
concurrent license agreement.
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6. The name of the authors or their employer(s), Rensselaer Polytechnic Institute, the Computational
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Dynamics Laboratory, the Scientific Computation Research Center (SCoReC), nor the names of any
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||||
of the software distributors may not be used to endorse or promote products derived
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from this software without specific prior written permission.
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||||
6. The name of the authors or their employer(s), Rensselaer
|
||||
Polytechnic Institute, the Computational Dynamics Laboratory, the
|
||||
Scientific Computation Research Center (SCoReC), nor the names of
|
||||
any of the software distributors may not be used to endorse or
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promote products derived from this software without specific prior
|
||||
written permission.
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||||
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THIS SOFTWARE IS PROVIDED BY THE AUTHORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING,
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BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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||||
ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHORS OR THE SCIENTIFIC COMPUTATION RESEARCH CENTER BE LIABLE
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||||
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
|
||||
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
|
||||
INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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||||
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN
|
||||
IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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||||
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THIS SOFTWARE IS PROVIDED BY THE AUTHORS "AS IS" AND ANY EXPRESS OR
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||||
IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
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||||
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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DISCLAIMED. IN NO EVENT SHALL THE AUTHORS OR THE SCIENTIFIC
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COMPUTATION RESEARCH CENTER BE LIABLE FOR ANY DIRECT, INDIRECT,
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||||
INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
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||||
BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS
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||||
OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
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ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR
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TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE
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USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
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DAMAGE.
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double erf(double x);
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double erfc(double x);
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double erfc(double x);
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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);
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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);
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