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Commit 0b4ce03d authored by Mark Friedrichs's avatar Mark Friedrichs
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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
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platforms/brook/src/kernels/kforce.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. *
* -------------------------------------------------------------------------- */ * -------------------------------------------------------------------------- */
//Define a generic force kernel prototype //Define a generic force kernel prototype
......
platforms/brook/src/kernels/kforce_CDLJ.br
View file @ 0b4ce03d
/* -------------------------------------------------------------------------- * /* -------------------------------------------------------------------------- *
* OpenMM * * OpenMM *
* -------------------------------------------------------------------------- * * -------------------------------------------------------------------------- *
...@@ -6,27 +7,22 @@ ...@@ -6,27 +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 float4 scalar_force_CDLJ( float4 qq, float epsfac, float4 sig, float4 eps, float4 r2 ) { kernel float4 scalar_force_CDLJ( float4 qq, float epsfac, float4 sig, float4 eps, float4 r2 ) {
......
platforms/brook/src/kernels/kgbsa.br
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...@@ -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. *
* -------------------------------------------------------------------------- */ * -------------------------------------------------------------------------- */
//124 FLOPS [??? total] //124 FLOPS [??? total]
......
platforms/brook/src/kernels/kgbsa.h
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#ifndef __KGBSA_H__ #ifndef __KGBSA_H__
#define __KGBSA_H__ #define __KGBSA_H__
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2009 Stanford University and the Authors. *
* Authors: Mark Friedrichs, Mike Houston *
* Contributors: *
* *
* This program is free software: you can redistribute it and/or modify *
* it under the terms of the GNU Lesser General Public License as published *
* by the Free Software Foundation, either version 3 of the License, or *
* (at your option) any later version. *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU Lesser General Public License for more details. *
* *
* You should have received a copy of the GNU Lesser General Public License *
* along with this program. If not, see <http://www.gnu.org/licenses/>. *
* -------------------------------------------------------------------------- */
void kMergeFloat4( void kMergeFloat4(
const float repfac, const float repfac,
const float atomStrWidth, const float atomStrWidth,
......
platforms/brook/src/kernels/kinvmap_gather.br
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...@@ -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. *
* -------------------------------------------------------------------------- */ * -------------------------------------------------------------------------- */
//Gather kernel for use with diferent angle, dihedral and improper functions //Gather kernel for use with diferent angle, dihedral and improper functions
......
platforms/brook/src/kernels/kinvmap_gather.h
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...@@ -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 kinvmap_gather (const float strwidth, void kinvmap_gather (const float strwidth,
......
platforms/brook/src/kernels/kmerge.br
View file @ 0b4ce03d
/**************************************************************** /* -------------------------------------------------------------------------- *
//Linear index of i particle, divided by 2 because we unroll i by 2 * OpenMM *
* This file is part of the gpu acceleration library for gromacs. * -------------------------------------------------------------------------- *
* Author: Mark Friedrichs, Mike Houston * This is part of the OpenMM molecular simulation toolkit originating from *
* * Simbios, the NIH National Center for Physics-Based Simulation of *
* This kernel was developed in collaboration with * Biological Structures at Stanford, funded under the NIH Roadmap for *
* * Medical Research, grant U54 GM072970. See https://simtk.org. *
* Copyright (C) Pande Group, Stanford, 2006 * *
*****************************************************************/ * Portions copyright (c) 2009 Stanford University and the Authors. *
* Authors: Mark Friedrichs, Mike Houston *
* Contributors: *
* *
* This program is free software: you can redistribute it and/or modify *
* it under the terms of the GNU Lesser General Public License as published *
* by the Free Software Foundation, either version 3 of the License, or *
* (at your option) any later version. *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU Lesser General Public License for more details. *
* *
* You should have received a copy of the GNU Lesser General Public License *
* along with this program. If not, see <http://www.gnu.org/licenses/>. *
* -------------------------------------------------------------------------- */
/* After forces above, we have the forces for even numbered particles /* After forces above, we have the forces for even numbered particles
* in one stream, odd numbered particles in another. * in one stream, odd numbered particles in another.
......
platforms/brook/src/kernels/kmerge_partial_forces.br
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...@@ -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) 2008-2009 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. *
* -------------------------------------------------------------------------- */ * -------------------------------------------------------------------------- */
/* After forces above, we have the forces for even numbered particles /* After forces above, we have the forces for even numbered particles
......
platforms/brook/src/kernels/kshakeh.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/kshakeh.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 kshakeh_fix1 ( void kshakeh_fix1 (
......
platforms/brook/src/kernels/kupdatebd.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/kupdatebd.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. *
* -------------------------------------------------------------------------- */ * -------------------------------------------------------------------------- */
/* /*
......
platforms/brook/src/kernels/kupdatemd.br
View file @ 0b4ce03d
/* -------------------------------------------------------------------------- * /* -------------------------------------------------------------------------- *
* OpenMM * * OpenMM *
* -------------------------------------------------------------------------- * * -------------------------------------------------------------------------- *
...@@ -6,27 +7,22 @@ ...@@ -6,27 +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 kupdate_md1( kernel void kupdate_md1(
......
platforms/brook/src/kernels/kupdatemd.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 kupdate_md1( void kupdate_md1(
......
platforms/brook/src/kernels/kupdatesd.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. *
* -------------------------------------------------------------------------- */ * -------------------------------------------------------------------------- */
//Applies a permutation to the given random vector stream //Applies a permutation to the given random vector stream
......
platforms/brook/src/kernels/kupdatesd.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 kupdate_sd1 ( void kupdate_sd1 (
......
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