diff --git a/lib/meam/Makefile.g95 b/lib/meam/Makefile.g95 index 338321e4f5..fc6d771716 100644 --- a/lib/meam/Makefile.g95 +++ b/lib/meam/Makefile.g95 @@ -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/lib/meam/Makefile.gfortran b/lib/meam/Makefile.gfortran index afd926ec51..fbd1a4fa6c 100644 --- a/lib/meam/Makefile.gfortran +++ b/lib/meam/Makefile.gfortran @@ -48,4 +48,4 @@ 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/lib/meam/Makefile.ifort b/lib/meam/Makefile.ifort index cbf961dd6c..4395dcb8a1 100644 --- a/lib/meam/Makefile.ifort +++ b/lib/meam/Makefile.ifort @@ -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/lib/poems/Copyright_Notice b/lib/poems/Copyright_Notice index 7c87c7fa35..9c6ac05f88 100644 --- a/lib/poems/Copyright_Notice +++ b/lib/poems/Copyright_Notice @@ -1,10 +1,19 @@ Copyright (C) 2006 Authors as indicated in Author List and Rensselaer Polytechnic Institute -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. +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. -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. +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. -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. +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. -A copy of the license file POEMS_License.txt, Authors List and Grants List files should be distributed along with this program. \ No newline at end of file +A copy of the license file POEMS_License.txt, Authors List and Grants +List files should be distributed along with this program. diff --git a/lib/poems/Makefile b/lib/poems/Makefile index ed50802ffb..ce6de4ea8f 100644 --- a/lib/poems/Makefile +++ b/lib/poems/Makefile @@ -98,4 +98,4 @@ clean: -rm *.o *.d *~ $(LIB) tar: - -tar -cvf ../POEMS.tar $(FILES) \ No newline at end of file + -tar -cvf ../POEMS.tar $(FILES) diff --git a/lib/poems/Makefile.g++ b/lib/poems/Makefile.g++ index ed50802ffb..ce6de4ea8f 100644 --- a/lib/poems/Makefile.g++ +++ b/lib/poems/Makefile.g++ @@ -98,4 +98,4 @@ clean: -rm *.o *.d *~ $(LIB) tar: - -tar -cvf ../POEMS.tar $(FILES) \ No newline at end of file + -tar -cvf ../POEMS.tar $(FILES) diff --git a/lib/poems/Makefile.storm b/lib/poems/Makefile.storm index 8a3e01d36c..d2c112c3ee 100644 --- a/lib/poems/Makefile.storm +++ b/lib/poems/Makefile.storm @@ -98,4 +98,4 @@ clean: -rm *.o *.d *~ $(LIB) tar: - -tar -cvf ../POEMS.tar $(FILES) \ No newline at end of file + -tar -cvf ../POEMS.tar $(FILES) diff --git a/lib/poems/POEMS_License.txt b/lib/poems/POEMS_License.txt index 9b54d23168..7767d54058 100644 --- a/lib/poems/POEMS_License.txt +++ b/lib/poems/POEMS_License.txt @@ -1,64 +1,80 @@ Copyright (C) 2005 Authors as indicated in Author List and Rensselaer Polytechnic Institute - 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. + 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. - This License Agreement applies to any software library or other program which contains a notice - placed by the copyright holder saying it may be distributed under the terms of this Rensselaer - Public License (also called "this License"). Each licensee is addressed as "you". + This License Agreement applies to any software library or other + program which contains a notice placed by the copyright holder + saying it may be distributed under the terms of this Rensselaer + Public License (also called "this License"). Each licensee is + addressed as "you". - A "library" means a collection of software functions and/or data prepared so as to be conveniently - linked with application programs (which use some of those functions and data) to form executables. - The "Library", below, refers to any such software library or work which has been distributed under - these terms. A "work based on the Library" means either the Library/code or any derivative work - under copyright law. + A "library" means a collection of software functions and/or data + prepared so as to be conveniently linked with application programs + (which use some of those functions and data) to form executables. + The "Library", below, refers to any such software library or work + which has been distributed under these terms. A "work based on the + Library" means either the Library/code or any derivative work under + copyright law. - "Source code" for a work means the preferred form of the work for making modifications to it including - any associated interface definition files, and scripts used to control compilation and installation - of the library. + "Source code" for a work means the preferred form of the work for + making modifications to it including any associated interface + definition files, and scripts used to control compilation and + installation of the library. - This library is free software; Redistribution and use in source code and binary forms, with or - without modification, are permitted provided that the following conditions are met: + This library is free software; Redistribution and use in source + code and binary forms, with or without modification, are permitted + provided that the following conditions are met: -1. Redistributions of source code must retain the above copyright notice, this list of conditions, - the authors list, the grants list, and the following disclaimer without any modifications and in - its current form. +1. Redistributions of source code must retain the above copyright + notice, this list of conditions, the authors list, the grants list, + and the following disclaimer without any modifications and in its + current form. -2. Redistributions in binary form must reproduce the above copyright 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. +2. Redistributions in binary form must reproduce the above copyright + 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. -3. You must cause the files modified to carry prominent notices stating that you changed the files - and dates of the change. +3. You must cause the files modified to carry prominent notices + stating that you changed the files and dates of the change. -4. At your discretion, you may submit the differences between the program and your work based on the - program for inclusion in the source code repository maintained by Rensselaer Polytechnic 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 repository. +4. At your discretion, you may submit the differences between the + program and your work based on the program for inclusion in the + source code repository maintained by Rensselaer Polytechnic + 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 + repository. -5. The authors as listed in "Authors_List" reserve the right to distribute the software or any modified - work in any other license form if they so choose to without infringing on any previous or concurrent - license agreement. +5. The authors as listed in "Authors_List" reserve the right to + distribute the software or any modified work in any other license + form if they so choose to without infringing on any previous or + concurrent license agreement. -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 promote products derived - from this software without specific prior written permission. +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 + promote products derived from this software without specific prior + written permission. - - -THIS SOFTWARE IS PROVIDED BY THE AUTHORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, -BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE -ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHORS OR THE SCIENTIFIC COMPUTATION RESEARCH CENTER BE LIABLE -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, -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. - - \ No newline at end of file +THIS SOFTWARE IS PROVIDED BY THE AUTHORS "AS IS" AND ANY EXPRESS OR +IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE AUTHORS OR THE SCIENTIFIC +COMPUTATION RESEARCH CENTER BE LIABLE 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, 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. diff --git a/src/MAKE/Windows/erfc.h b/src/MAKE/Windows/erfc.h index 79727d5541..43338ab926 100644 --- a/src/MAKE/Windows/erfc.h +++ b/src/MAKE/Windows/erfc.h @@ -2,4 +2,4 @@ double erf(double x); -double erfc(double x); \ No newline at end of file +double erfc(double x); diff --git a/tools/matlab/readdump_all.m b/tools/matlab/readdump_all.m index 4f8270b4f0..22eb3d9c87 100644 --- a/tools/matlab/readdump_all.m +++ b/tools/matlab/readdump_all.m @@ -1 +1 @@ -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); \ No newline at end of file