Skip to content

GitLab

Commit 0b4ce03d authored by Mark Friedrichs's avatar Mark Friedrichs
Browse files

License header changes; force duplication factor to 4; fixed potential problem... 

License header changes; force duplication factor to 4; fixed potential problem w/ Shake -- if no constraints, pgm crashes
parent 3ec08ba6
Hide whitespace changes
Inline Side-by-side
Showing with 243 additions and 343 deletions
platforms/brook/src/BrookRemoveCMMotionKernel.cpp
View file @ 0b4ce03d
...@@ -6,27 +6,22 @@ ...@@ -6,27 +6,22 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * Medical Research, grant U54 GM072970. See https://simtk.org. *
* * * *
* Portions copyright (c) 2008 Stanford University and the Authors. * * Portions copyright (c) 2009 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Mark Friedrichs, Mike Houston *
* Contributors: * * Contributors: *
* * * *
* Permission is hereby granted, free of charge, to any person obtaining a * * This program is free software: you can redistribute it and/or modify *
* copy of this software and associated documentation files (the "Software"), * * it under the terms of the GNU Lesser General Public License as published *
* to deal in the Software without restriction, including without limitation * * by the Free Software Foundation, either version 3 of the License, or *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, * * (at your option) any later version. *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* * * *
* The above copyright notice and this permission notice shall be included in * * This program is distributed in the hope that it will be useful, *
* all copies or substantial portions of the Software. * * but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU Lesser General Public License for more details. *
* * * *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * * You should have received a copy of the GNU Lesser General Public License *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * * along with this program. If not, see <http://www.gnu.org/licenses/>. *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */ * -------------------------------------------------------------------------- */
#include "openmm/internal/OpenMMContextImpl.h" #include "openmm/internal/OpenMMContextImpl.h"
......
platforms/brook/src/BrookRemoveCMMotionKernel.h
View file @ 0b4ce03d
...@@ -9,27 +9,22 @@ ...@@ -9,27 +9,22 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * Medical Research, grant U54 GM072970. See https://simtk.org. *
* * * *
* Portions copyright ( c ) 2008 Stanford University and the Authors. * * Portions copyright (c) 2009 Stanford University and the Authors. *
* Authors: Peter Eastman, Mark Friedrichs * * Authors: Mark Friedrichs, Mike Houston *
* Contributors: * * Contributors: *
* * * *
* Permission is hereby granted, free of charge, to any person obtaining a * * This program is free software: you can redistribute it and/or modify *
* copy of this software and associated documentation files ( the "Software" ), * * it under the terms of the GNU Lesser General Public License as published *
* to deal in the Software without restriction, including without limitation * * by the Free Software Foundation, either version 3 of the License, or *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, * * (at your option) any later version. *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* * * *
* The above copyright notice and this permission notice shall be included in * * This program is distributed in the hope that it will be useful, *
* all copies or substantial portions of the Software. * * but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU Lesser General Public License for more details. *
* * * *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * * You should have received a copy of the GNU Lesser General Public License *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * * along with this program. If not, see <http://www.gnu.org/licenses/>. *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */ * -------------------------------------------------------------------------- */
#include "openmm/kernels.h" #include "openmm/kernels.h"
......
platforms/brook/src/BrookShakeAlgorithm.cpp
View file @ 0b4ce03d
...@@ -6,27 +6,22 @@ ...@@ -6,27 +6,22 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * Medical Research, grant U54 GM072970. See https://simtk.org. *
* * * *
* Portions copyright (c) 2008 Stanford University and the Authors. * * Portions copyright (c) 2009 Stanford University and the Authors. *
* Authors: Mark Friedrichs * * Authors: Mark Friedrichs, Mike Houston *
* Contributors: * * Contributors: *
* * * *
* Permission is hereby granted, free of charge, to any person obtaining a * * This program is free software: you can redistribute it and/or modify *
* copy of this software and associated documentation files (the "Software"), * * it under the terms of the GNU Lesser General Public License as published *
* to deal in the Software without restriction, including without limitation * * by the Free Software Foundation, either version 3 of the License, or *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, * * (at your option) any later version. *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* * * *
* The above copyright notice and this permission notice shall be included in * * This program is distributed in the hope that it will be useful, *
* all copies or substantial portions of the Software. * * but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU Lesser General Public License for more details. *
* * * *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * * You should have received a copy of the GNU Lesser General Public License *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * * along with this program. If not, see <http://www.gnu.org/licenses/>. *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */ * -------------------------------------------------------------------------- */
#include "BrookShakeAlgorithm.h" #include "BrookShakeAlgorithm.h"
...@@ -461,12 +456,13 @@ int BrookShakeAlgorithm::_setShakeStreams( const std::vector<double>& masses, ...@@ -461,12 +456,13 @@ int BrookShakeAlgorithm::_setShakeStreams( const std::vector<double>& masses,
particleIterator++; particleIterator++;
} }
_numberOfConstraints = static_cast<int>(constraintIndices.size());
if( _numberOfConstraints < 1 )return DefaultReturnValue;
// Find clusters consisting of a central atom with up to three peripheral atoms. // Find clusters consisting of a central atom with up to three peripheral atoms.
particleIterator = constraintIndices.begin(); particleIterator = constraintIndices.begin();
std::vector<double>::const_iterator distanceIterator = constraintLengths.begin(); std::vector<double>::const_iterator distanceIterator = constraintLengths.begin();
_numberOfConstraints = static_cast<int>(constraintIndices.size());
while( particleIterator != constraintIndices.end() ){ while( particleIterator != constraintIndices.end() ){
float distance = static_cast<float>( *distanceIterator ); float distance = static_cast<float>( *distanceIterator );
......
platforms/brook/src/BrookShakeAlgorithm.h
View file @ 0b4ce03d
...@@ -9,27 +9,22 @@ ...@@ -9,27 +9,22 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * Medical Research, grant U54 GM072970. See https://simtk.org. *
* * * *
* Portions copyright (c) 2008 Stanford University and the Authors. * * Portions copyright (c) 2009 Stanford University and the Authors. *
* Authors: Peter Eastman, Mark Friedrichs * * Authors: Mark Friedrichs, Mike Houston *
* Contributors: * * Contributors: *
* * * *
* Permission is hereby granted, free of charge, to any person obtaining a * * This program is free software: you can redistribute it and/or modify *
* copy of this software and associated documentation files (the "Software"), * * it under the terms of the GNU Lesser General Public License as published *
* to deal in the Software without restriction, including without limitation * * by the Free Software Foundation, either version 3 of the License, or *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, * * (at your option) any later version. *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* * * *
* The above copyright notice and this permission notice shall be included in * * This program is distributed in the hope that it will be useful, *
* all copies or substantial portions of the Software. * * but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU Lesser General Public License for more details. *
* * * *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * * You should have received a copy of the GNU Lesser General Public License *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * * along with this program. If not, see <http://www.gnu.org/licenses/>. *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */ * -------------------------------------------------------------------------- */
#include <vector> #include <vector>
......
platforms/brook/src/BrookStreamFactory.cpp
View file @ 0b4ce03d
...@@ -6,27 +6,22 @@ ...@@ -6,27 +6,22 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * Medical Research, grant U54 GM072970. See https://simtk.org. *
* * * *
* Portions copyright (c) 2008 Stanford University and the Authors. * * Portions copyright (c) 2009 Stanford University and the Authors. *
* Authors: Peter Eastman, Mark Friedrichs * * Authors: Mark Friedrichs, Mike Houston *
* Contributors: * * Contributors: *
* * * *
* Permission is hereby granted, free of charge, to any person obtaining a * * This program is free software: you can redistribute it and/or modify *
* copy of this software and associated documentation files (the "Software"), * * it under the terms of the GNU Lesser General Public License as published *
* to deal in the Software without restriction, including without limitation * * by the Free Software Foundation, either version 3 of the License, or *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, * * (at your option) any later version. *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* * * *
* The above copyright notice and this permission notice shall be included in * * This program is distributed in the hope that it will be useful, *
* all copies or substantial portions of the Software. * * but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU Lesser General Public License for more details. *
* * * *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * * You should have received a copy of the GNU Lesser General Public License *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * * along with this program. If not, see <http://www.gnu.org/licenses/>. *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */ * -------------------------------------------------------------------------- */
#include <sstream> #include <sstream>
......
platforms/brook/src/BrookStreamImpl.cpp
View file @ 0b4ce03d
...@@ -6,27 +6,22 @@ ...@@ -6,27 +6,22 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * Medical Research, grant U54 GM072970. See https://simtk.org. *
* * * *
* Portions copyright (c) 2008 Stanford University and the Authors. * * Portions copyright (c) 2009 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Mark Friedrichs, Mike Houston *
* Contributors: * * Contributors: *
* * * *
* Permission is hereby granted, free of charge, to any person obtaining a * * This program is free software: you can redistribute it and/or modify *
* copy of this software and associated documentation files (the "Software"), * * it under the terms of the GNU Lesser General Public License as published *
* to deal in the Software without restriction, including without limitation * * by the Free Software Foundation, either version 3 of the License, or *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, * * (at your option) any later version. *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* * * *
* The above copyright notice and this permission notice shall be included in * * This program is distributed in the hope that it will be useful, *
* all copies or substantial portions of the Software. * * but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU Lesser General Public License for more details. *
* * * *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * * You should have received a copy of the GNU Lesser General Public License *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * * along with this program. If not, see <http://www.gnu.org/licenses/>. *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */ * -------------------------------------------------------------------------- */
#include <sstream> #include <sstream>
......
platforms/brook/src/BrookStreamImpl.h
View file @ 0b4ce03d
...@@ -9,27 +9,22 @@ ...@@ -9,27 +9,22 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * Medical Research, grant U54 GM072970. See https://simtk.org. *
* * * *
* Portions copyright ( c ) 2008 Stanford University and the Authors. * * Portions copyright (c) 2009 Stanford University and the Authors. *
* Authors: Peter Eastman, Mark Friedrichs * * Authors: Mark Friedrichs, Mike Houston *
* Contributors: * * Contributors: *
* * * *
* Permission is hereby granted, free of charge, to any person obtaining a * * This program is free software: you can redistribute it and/or modify *
* copy of this software and associated documentation files ( the "Software" ), * * it under the terms of the GNU Lesser General Public License as published *
* to deal in the Software without restriction, including without limitation * * by the Free Software Foundation, either version 3 of the License, or *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, * * (at your option) any later version. *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* * * *
* The above copyright notice and this permission notice shall be included in * * This program is distributed in the hope that it will be useful, *
* all copies or substantial portions of the Software. * * but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU Lesser General Public License for more details. *
* * * *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * * You should have received a copy of the GNU Lesser General Public License *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * * along with this program. If not, see <http://www.gnu.org/licenses/>. *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */ * -------------------------------------------------------------------------- */
#include "openmm/StreamImpl.h" #include "openmm/StreamImpl.h"
......
platforms/brook/src/BrookStreamInternal.cpp
View file @ 0b4ce03d
...@@ -6,27 +6,22 @@ ...@@ -6,27 +6,22 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * Medical Research, grant U54 GM072970. See https://simtk.org. *
* * * *
* Portions copyright (c) 2008 Stanford University and the Authors. * * Portions copyright (c) 2009 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Mark Friedrichs, Mike Houston *
* Contributors: * * Contributors: *
* * * *
* Permission is hereby granted, free of charge, to any person obtaining a * * This program is free software: you can redistribute it and/or modify *
* copy of this software and associated documentation files (the "Software"), * * it under the terms of the GNU Lesser General Public License as published *
* to deal in the Software without restriction, including without limitation * * by the Free Software Foundation, either version 3 of the License, or *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, * * (at your option) any later version. *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* * * *
* The above copyright notice and this permission notice shall be included in * * This program is distributed in the hope that it will be useful, *
* all copies or substantial portions of the Software. * * but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU Lesser General Public License for more details. *
* * * *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * * You should have received a copy of the GNU Lesser General Public License *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * * along with this program. If not, see <http://www.gnu.org/licenses/>. *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */ * -------------------------------------------------------------------------- */
#include <sstream> #include <sstream>
......
platforms/brook/src/BrookStreamInternal.h
View file @ 0b4ce03d
...@@ -9,27 +9,22 @@ ...@@ -9,27 +9,22 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * Medical Research, grant U54 GM072970. See https://simtk.org. *
* * * *
* Portions copyright ( c ) 2008 Stanford University and the Authors. * * Portions copyright (c) 2009 Stanford University and the Authors. *
* Authors: Peter Eastman, Mark Friedrichs * * Authors: Mark Friedrichs, Mike Houston *
* Contributors: * * Contributors: *
* * * *
* Permission is hereby granted, free of charge, to any person obtaining a * * This program is free software: you can redistribute it and/or modify *
* copy of this software and associated documentation files ( the "Software" ), * * it under the terms of the GNU Lesser General Public License as published *
* to deal in the Software without restriction, including without limitation * * by the Free Software Foundation, either version 3 of the License, or *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, * * (at your option) any later version. *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* * * *
* The above copyright notice and this permission notice shall be included in * * This program is distributed in the hope that it will be useful, *
* all copies or substantial portions of the Software. * * but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU Lesser General Public License for more details. *
* * * *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * * You should have received a copy of the GNU Lesser General Public License *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * * along with this program. If not, see <http://www.gnu.org/licenses/>. *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */ * -------------------------------------------------------------------------- */
#include <brook/brook.hpp> #include <brook/brook.hpp>
......
platforms/brook/src/BrookVelocityCenterOfMassRemoval.cpp
View file @ 0b4ce03d
...@@ -6,27 +6,22 @@ ...@@ -6,27 +6,22 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * Medical Research, grant U54 GM072970. See https://simtk.org. *
* * * *
* Portions copyright (c) 2008 Stanford University and the Authors. * * Portions copyright (c) 2009 Stanford University and the Authors. *
* Authors: Mark Friedrichs * * Authors: Mark Friedrichs, Mike Houston *
* Contributors: * * Contributors: *
* * * *
* Permission is hereby granted, free of charge, to any person obtaining a * * This program is free software: you can redistribute it and/or modify *
* copy of this software and associated documentation files (the "Software"), * * it under the terms of the GNU Lesser General Public License as published *
* to deal in the Software without restriction, including without limitation * * by the Free Software Foundation, either version 3 of the License, or *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, * * (at your option) any later version. *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* * * *
* The above copyright notice and this permission notice shall be included in * * This program is distributed in the hope that it will be useful, *
* all copies or substantial portions of the Software. * * but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU Lesser General Public License for more details. *
* * * *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * * You should have received a copy of the GNU Lesser General Public License *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * * along with this program. If not, see <http://www.gnu.org/licenses/>. *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */ * -------------------------------------------------------------------------- */
#include <sstream> #include <sstream>
......
platforms/brook/src/BrookVelocityCenterOfMassRemoval.h
View file @ 0b4ce03d
...@@ -9,27 +9,22 @@ ...@@ -9,27 +9,22 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * Medical Research, grant U54 GM072970. See https://simtk.org. *
* * * *
* Portions copyright (c) 2008 Stanford University and the Authors. * * Portions copyright (c) 2009 Stanford University and the Authors. *
* Authors: Peter Eastman, Mark Friedrichs * * Authors: Mark Friedrichs, Mike Houston *
* Contributors: * * Contributors: *
* * * *
* Permission is hereby granted, free of charge, to any person obtaining a * * This program is free software: you can redistribute it and/or modify *
* copy of this software and associated documentation files (the "Software"), * * it under the terms of the GNU Lesser General Public License as published *
* to deal in the Software without restriction, including without limitation * * by the Free Software Foundation, either version 3 of the License, or *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, * * (at your option) any later version. *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* * * *
* The above copyright notice and this permission notice shall be included in * * This program is distributed in the hope that it will be useful, *
* all copies or substantial portions of the Software. * * but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU Lesser General Public License for more details. *
* * * *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * * You should have received a copy of the GNU Lesser General Public License *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * * along with this program. If not, see <http://www.gnu.org/licenses/>. *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */ * -------------------------------------------------------------------------- */
#include <vector> #include <vector>
......
platforms/brook/src/BrookVerletDynamics.cpp
View file @ 0b4ce03d
...@@ -6,27 +6,22 @@ ...@@ -6,27 +6,22 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * Medical Research, grant U54 GM072970. See https://simtk.org. *
* * * *
* Portions copyright (c) 2008 Stanford University and the Authors. * * Portions copyright (c) 2009 Stanford University and the Authors. *
* Authors: Mark Friedrichs * * Authors: Mark Friedrichs, Mike Houston *
* Contributors: * * Contributors: *
* * * *
* Permission is hereby granted, free of charge, to any person obtaining a * * This program is free software: you can redistribute it and/or modify *
* copy of this software and associated documentation files (the "Software"), * * it under the terms of the GNU Lesser General Public License as published *
* to deal in the Software without restriction, including without limitation * * by the Free Software Foundation, either version 3 of the License, or *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, * * (at your option) any later version. *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* * * *
* The above copyright notice and this permission notice shall be included in * * This program is distributed in the hope that it will be useful, *
* all copies or substantial portions of the Software. * * but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU Lesser General Public License for more details. *
* * * *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * * You should have received a copy of the GNU Lesser General Public License *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * * along with this program. If not, see <http://www.gnu.org/licenses/>. *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */ * -------------------------------------------------------------------------- */
#include <sstream> #include <sstream>
......
platforms/brook/src/BrookVerletDynamics.h
View file @ 0b4ce03d
...@@ -9,27 +9,22 @@ ...@@ -9,27 +9,22 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * Medical Research, grant U54 GM072970. See https://simtk.org. *
* * * *
* Portions copyright (c) 2008 Stanford University and the Authors. * * Portions copyright (c) 2009 Stanford University and the Authors. *
* Authors: Peter Eastman, Mark Friedrichs * * Authors: Mark Friedrichs, Mike Houston *
* Contributors: * * Contributors: *
* * * *
* Permission is hereby granted, free of charge, to any person obtaining a * * This program is free software: you can redistribute it and/or modify *
* copy of this software and associated documentation files (the "Software"), * * it under the terms of the GNU Lesser General Public License as published *
* to deal in the Software without restriction, including without limitation * * by the Free Software Foundation, either version 3 of the License, or *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, * * (at your option) any later version. *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* * * *
* The above copyright notice and this permission notice shall be included in * * This program is distributed in the hope that it will be useful, *
* all copies or substantial portions of the Software. * * but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU Lesser General Public License for more details. *
* * * *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * * You should have received a copy of the GNU Lesser General Public License *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * * along with this program. If not, see <http://www.gnu.org/licenses/>. *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */ * -------------------------------------------------------------------------- */
#include <vector> #include <vector>
......
platforms/brook/src/OpenMMBrookInterface.cpp
View file @ 0b4ce03d
...@@ -6,27 +6,22 @@ ...@@ -6,27 +6,22 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * Medical Research, grant U54 GM072970. See https://simtk.org. *
* * * *
* Portions copyright (c) 2008 Stanford University and the Authors. * * Portions copyright (c) 2009 Stanford University and the Authors. *
* Authors: Peter Eastman, Mark Friedrichs * * Authors: Mark Friedrichs, Mike Houston *
* Contributors: * * Contributors: *
* * * *
* Permission is hereby granted, free of charge, to any person obtaining a * * This program is free software: you can redistribute it and/or modify *
* copy of this software and associated documentation files (the "Software"), * * it under the terms of the GNU Lesser General Public License as published *
* to deal in the Software without restriction, including without limitation * * by the Free Software Foundation, either version 3 of the License, or *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, * * (at your option) any later version. *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* * * *
* The above copyright notice and this permission notice shall be included in * * This program is distributed in the hope that it will be useful, *
* all copies or substantial portions of the Software. * * but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU Lesser General Public License for more details. *
* * * *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * * You should have received a copy of the GNU Lesser General Public License *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * * along with this program. If not, see <http://www.gnu.org/licenses/>. *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */ * -------------------------------------------------------------------------- */
#include <cmath> #include <cmath>
...@@ -542,7 +537,7 @@ void OpenMMBrookInterface::computeForces( OpenMMContextImpl& context ){ ...@@ -542,7 +537,7 @@ void OpenMMBrookInterface::computeForces( OpenMMContextImpl& context ){
// info // info
if( printOn > 1 ){ if( printOn > 0 ){
//if( 1 ){ //if( 1 ){
printForcesToFile( context ); printForcesToFile( context );
} }
......
platforms/brook/src/OpenMMBrookInterface.h
View file @ 0b4ce03d
...@@ -9,27 +9,22 @@ ...@@ -9,27 +9,22 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * Medical Research, grant U54 GM072970. See https://simtk.org. *
* * * *
* Portions copyright (c) 2008 Stanford University and the Authors. * * Portions copyright (c) 2009 Stanford University and the Authors. *
* Authors: Peter Eastman, Mark Friedrichs * * Authors: Mark Friedrichs, Mike Houston *
* Contributors: * * Contributors: *
* * * *
* Permission is hereby granted, free of charge, to any person obtaining a * * This program is free software: you can redistribute it and/or modify *
* copy of this software and associated documentation files (the "Software"), * * it under the terms of the GNU Lesser General Public License as published *
* to deal in the Software without restriction, including without limitation * * by the Free Software Foundation, either version 3 of the License, or *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, * * (at your option) any later version. *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* * * *
* The above copyright notice and this permission notice shall be included in * * This program is distributed in the hope that it will be useful, *
* all copies or substantial portions of the Software. * * but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU Lesser General Public License for more details. *
* * * *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * * You should have received a copy of the GNU Lesser General Public License *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * * along with this program. If not, see <http://www.gnu.org/licenses/>. *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */ * -------------------------------------------------------------------------- */
#include "openmm/kernels.h" #include "openmm/kernels.h"
......
platforms/brook/src/kernels/invmap.h
View file @ 0b4ce03d
...@@ -9,27 +9,22 @@ ...@@ -9,27 +9,22 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * Medical Research, grant U54 GM072970. See https://simtk.org. *
* * * *
* Portions copyright (c) 2008 Stanford University and the Authors. * * Portions copyright (c) 2009 Stanford University and the Authors. *
* Authors: Peter Eastman, Mark Friedrichs, Chris Bruns * * Authors: Mark Friedrichs, Mike Houston *
* Contributors: * * Contributors: *
* * * *
* Permission is hereby granted, free of charge, to any person obtaining a * * This program is free software: you can redistribute it and/or modify *
* copy of this software and associated documentation files (the "Software"), * * it under the terms of the GNU Lesser General Public License as published *
* to deal in the Software without restriction, including without limitation * * by the Free Software Foundation, either version 3 of the License, or *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, * * (at your option) any later version. *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* * * *
* The above copyright notice and this permission notice shall be included in * * This program is distributed in the hope that it will be useful, *
* all copies or substantial portions of the Software. * * but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU Lesser General Public License for more details. *
* * * *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * * You should have received a copy of the GNU Lesser General Public License *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * * along with this program. If not, see <http://www.gnu.org/licenses/>. *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */ * -------------------------------------------------------------------------- */
/* /*
......
platforms/brook/src/kernels/kcom.br
View file @ 0b4ce03d
...@@ -7,27 +7,22 @@ ...@@ -7,27 +7,22 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * Medical Research, grant U54 GM072970. See https://simtk.org. *
* * * *
* Portions copyright (c) 2008-2009 Stanford University and the Authors. * * Portions copyright (c) 2009 Stanford University and the Authors. *
* Authors: Peter Eastman, Mark Friedrichs, Chris Bruns, Mike Houston * * Authors: Mark Friedrichs, Mike Houston *
* Contributors: * * Contributors: *
* * * *
* Permission is hereby granted, free of charge, to any person obtaining a * * This program is free software: you can redistribute it and/or modify *
* copy of this software and associated documentation files (the "Software"), * * it under the terms of the GNU Lesser General Public License as published *
* to deal in the Software without restriction, including without limitation * * by the Free Software Foundation, either version 3 of the License, or *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, * * (at your option) any later version. *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* * * *
* The above copyright notice and this permission notice shall be included in * * This program is distributed in the hope that it will be useful, *
* all copies or substantial portions of the Software. * * but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU Lesser General Public License for more details. *
* * * *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * * You should have received a copy of the GNU Lesser General Public License *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * * along with this program. If not, see <http://www.gnu.org/licenses/>. *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */ * -------------------------------------------------------------------------- */
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
......
platforms/brook/src/kernels/kcom.h
View file @ 0b4ce03d
...@@ -6,27 +6,22 @@ ...@@ -6,27 +6,22 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * Medical Research, grant U54 GM072970. See https://simtk.org. *
* * * *
* Portions copyright (c) 2008 Stanford University and the Authors. * * Portions copyright (c) 2009 Stanford University and the Authors. *
* Authors: Peter Eastman, Mark Friedrichs, Chris Bruns * * Authors: Mark Friedrichs, Mike Houston *
* Contributors: * * Contributors: *
* * * *
* Permission is hereby granted, free of charge, to any person obtaining a * * This program is free software: you can redistribute it and/or modify *
* copy of this software and associated documentation files (the "Software"), * * it under the terms of the GNU Lesser General Public License as published *
* to deal in the Software without restriction, including without limitation * * by the Free Software Foundation, either version 3 of the License, or *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, * * (at your option) any later version. *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* * * *
* The above copyright notice and this permission notice shall be included in * * This program is distributed in the hope that it will be useful, *
* all copies or substantial portions of the Software. * * but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU Lesser General Public License for more details. *
* * * *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * * You should have received a copy of the GNU Lesser General Public License *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * * along with this program. If not, see <http://www.gnu.org/licenses/>. *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */ * -------------------------------------------------------------------------- */
void kCalculateLinearMomentum( ::brook::stream mass, ::brook::stream velocities, ::brook::stream linearMomentum ); void kCalculateLinearMomentum( ::brook::stream mass, ::brook::stream velocities, ::brook::stream linearMomentum );
......
platforms/brook/src/kernels/kcommon.br
View file @ 0b4ce03d
...@@ -7,27 +7,22 @@ ...@@ -7,27 +7,22 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * Medical Research, grant U54 GM072970. See https://simtk.org. *
* * * *
* Portions copyright (c) 2008-2009 Stanford University and the Authors. * * Portions copyright (c) 2009 Stanford University and the Authors. *
* Authors: Peter Eastman, Mark Friedrichs, Chris Bruns, Mike Houston * * Authors: Mark Friedrichs, Mike Houston *
* Contributors: * * Contributors: *
* * * *
* Permission is hereby granted, free of charge, to any person obtaining a * * This program is free software: you can redistribute it and/or modify *
* copy of this software and associated documentation files (the "Software"), * * it under the terms of the GNU Lesser General Public License as published *
* to deal in the Software without restriction, including without limitation * * by the Free Software Foundation, either version 3 of the License, or *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, * * (at your option) any later version. *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* * * *
* The above copyright notice and this permission notice shall be included in * * This program is distributed in the hope that it will be useful, *
* all copies or substantial portions of the Software. * * but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU Lesser General Public License for more details. *
* * * *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * * You should have received a copy of the GNU Lesser General Public License *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * * along with this program. If not, see <http://www.gnu.org/licenses/>. *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */ * -------------------------------------------------------------------------- */
kernel void kgetxyz( float4 instr<>, out float3 outstr<> ){ kernel void kgetxyz( float4 instr<>, out float3 outstr<> ){
......
platforms/brook/src/kernels/kcommon.h
View file @ 0b4ce03d
...@@ -9,30 +9,24 @@ ...@@ -9,30 +9,24 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * Medical Research, grant U54 GM072970. See https://simtk.org. *
* * * *
* Portions copyright (c) 2008 Stanford University and the Authors. * * Portions copyright (c) 2009 Stanford University and the Authors. *
* Authors: Peter Eastman, Mark Friedrichs, Chris Bruns * * Authors: Mark Friedrichs, Mike Houston *
* Contributors: * * Contributors: *
* * * *
* Permission is hereby granted, free of charge, to any person obtaining a * * This program is free software: you can redistribute it and/or modify *
* copy of this software and associated documentation files (the "Software"), * * it under the terms of the GNU Lesser General Public License as published *
* to deal in the Software without restriction, including without limitation * * by the Free Software Foundation, either version 3 of the License, or *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, * * (at your option) any later version. *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* * * *
* The above copyright notice and this permission notice shall be included in * * This program is distributed in the hope that it will be useful, *
* all copies or substantial portions of the Software. * * but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU Lesser General Public License for more details. *
* * * *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * * You should have received a copy of the GNU Lesser General Public License *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * * along with this program. If not, see <http://www.gnu.org/licenses/>. *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */ * -------------------------------------------------------------------------- */
void kgetxyz(::brook::stream instr, ::brook::stream outstr); void kgetxyz(::brook::stream instr, ::brook::stream outstr);
void kzerof3(::brook::stream outstr); void kzerof3(::brook::stream outstr);
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment