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 244 additions and 342 deletions
platforms/brook/src/BrookFloatStreamInternal.cpp
View file @ 0b4ce03d
...@@ -6,29 +6,25 @@ ...@@ -6,29 +6,25 @@
* 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>
#include "BrookFloatStreamInternal.h" #include "BrookFloatStreamInternal.h"
#include "BrookPlatform.h" #include "BrookPlatform.h"
......
platforms/brook/src/BrookFloatStreamInternal.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 "BrookPlatform.h" #include "BrookPlatform.h"
......
platforms/brook/src/BrookGbsa.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/BrookGbsa.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/BrookInitializeForcesKernel.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>
......
platforms/brook/src/BrookInitializeForcesKernel.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/BrookIntStreamInternal.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 "BrookIntStreamInternal.h" #include "BrookIntStreamInternal.h"
......
platforms/brook/src/BrookIntStreamInternal.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 "BrookStreamInternal.h" #include "BrookStreamInternal.h"
......
platforms/brook/src/BrookIntegrateLangevinStepKernel.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 "BrookIntegrateLangevinStepKernel.h" #include "BrookIntegrateLangevinStepKernel.h"
......
platforms/brook/src/BrookIntegrateLangevinStepKernel.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/BrookIntegrateVerletStepKernel.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 "BrookIntegrateVerletStepKernel.h" #include "BrookIntegrateVerletStepKernel.h"
......
platforms/brook/src/BrookIntegrateVerletStepKernel.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/BrookKernelFactory.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 "BrookKernelFactory.h" #include "BrookKernelFactory.h"
......
platforms/brook/src/BrookLangevinDynamics.cpp
View file @ 0b4ce03d
/* -------------------------------------------------------------------------- * /* -------------------------------------------------------------------------- *
* OpenMM * * OpenMM *
* -i------------------------------------------------------------------------- * * -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from * * This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of * * Simbios, the NIH National Center for Physics-Based Simulation of *
* 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/BrookLangevinDynamics.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/BrookNonBonded.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/BrookNonBonded.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/BrookPlatform.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 "BrookPlatform.h" #include "BrookPlatform.h"
...@@ -414,6 +409,7 @@ int BrookPlatform::getDuplicationFactor( int numberOfParticles ) const { ...@@ -414,6 +409,7 @@ int BrookPlatform::getDuplicationFactor( int numberOfParticles ) const {
duplicationFactor = static_cast<int>( ceil( factor*0.25f ) ); duplicationFactor = static_cast<int>( ceil( factor*0.25f ) );
duplicationFactor *= 4; duplicationFactor *= 4;
} }
duplicationFactor = 4;
// (void) fprintf( stderr, "getDuplicationFactor %.1f numiP=%.1f factor=%.1f duplicationFactor=%d\n", threads, numP, factor, duplicationFactor ); // (void) fprintf( stderr, "getDuplicationFactor %.1f numiP=%.1f factor=%.1f duplicationFactor=%d\n", threads, numP, factor, duplicationFactor );
} }
...@@ -543,7 +539,7 @@ void BrookPlatform::contextCreated( OpenMMContextImpl& context ) const { ...@@ -543,7 +539,7 @@ void BrookPlatform::contextCreated( OpenMMContextImpl& context ) const {
int particles = context.getSystem().getNumParticles(); int particles = context.getSystem().getNumParticles();
OpenMMBrookInterface* openMMBrookInterface = new OpenMMBrookInterface( getParticleStreamWidth(), getDuplicationFactor( particles ) ); OpenMMBrookInterface* openMMBrookInterface = new OpenMMBrookInterface( getParticleStreamWidth(), getDuplicationFactor( particles ) );
// openMMBrookInterface->setLog( stderr ); //openMMBrookInterface->setLog( stderr );
context.setPlatformData( openMMBrookInterface ); context.setPlatformData( openMMBrookInterface );
} }
......
platforms/brook/src/BrookRandomNumberGenerator.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/BrookRandomNumberGenerator.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 "BrookCommon.h" #include "BrookCommon.h"
......
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