mirror of
https://github.com/openmm/openmm
synced 2026-06-03 06:39:48 +09:00
adfd84c273
* Basic LCPO support * Add basic test for LCPO from a prmtop file * API for LCPOForce * Started LCPO reference implementation * Finished reference forces & test cases * Use other test for finite difference since grid might have discontinuous forces * Reference platform formatting * Initial implementation of CPU platform * Bugfixes * More vectorization and improve neighbor list query speed * Parallelize part of neighbor search * Check box size for LCPO with periodic boundary conditions * Fixes for updating parameters in context * GBSAOBCForce doesn't use first & last indices for updates, so no need for this optimization here * Changes to neighbor checking and optimization * Fixes and minor changes * Add global surface tension parameter * Only process half of the pairs in the neighbor list * Remove unnecessary checks * Initial version of common platform implementation * Asynchronously download neighbor list size * Debugging * Do pair precomputation in copyPairsToNeighborList * Recompute interactions instead of scanning neighbor list in inner loop * Condense position array before computations * Also make neighbor count download asynchronous on device * Fixes for kernel launching * Topology-based LCPO parameter assignment * Fixes, and use test system for LCPO with nucleic acids * Always raise instead of warn when LCPO parameters can't be assigned * Use Amber convention for phosphates
93 lines
4.3 KiB
C
93 lines
4.3 KiB
C
#ifndef OPENMM_H_
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#define OPENMM_H_
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/* -------------------------------------------------------------------------- *
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* OpenMM *
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* -------------------------------------------------------------------------- *
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* This is part of the OpenMM molecular simulation toolkit. *
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* See https://openmm.org/development. *
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* *
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* Portions copyright (c) 2009-2025 Stanford University and the Authors. *
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* Authors: Peter Eastman *
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* Contributors: *
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* *
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* Permission is hereby granted, free of charge, to any person obtaining a *
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* copy of this software and associated documentation files (the "Software"), *
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* to deal in the Software without restriction, including without limitation *
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* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
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* and/or sell copies of the Software, and to permit persons to whom the *
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* Software is furnished to do so, subject to the following conditions: *
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* *
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* The above copyright notice and this permission notice shall be included in *
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* all copies or substantial portions of the Software. *
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* *
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
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* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
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* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
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* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
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* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
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* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
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* USE OR OTHER DEALINGS IN THE SOFTWARE. *
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* -------------------------------------------------------------------------- */
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#include "openmm/AndersenThermostat.h"
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#include "openmm/BrownianIntegrator.h"
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#include "openmm/CMAPTorsionForce.h"
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#include "openmm/CMMotionRemover.h"
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#include "openmm/CompoundIntegrator.h"
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#include "openmm/ConstantPotentialForce.h"
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#include "openmm/CustomBondForce.h"
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#include "openmm/CustomCentroidBondForce.h"
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#include "openmm/CustomCompoundBondForce.h"
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#include "openmm/CustomAngleForce.h"
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#include "openmm/CustomTorsionForce.h"
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#include "openmm/CustomExternalForce.h"
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#include "openmm/CustomCVForce.h"
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#include "openmm/CustomGBForce.h"
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#include "openmm/CustomHbondForce.h"
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#include "openmm/CustomIntegrator.h"
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#include "openmm/CustomManyParticleForce.h"
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#include "openmm/CustomNonbondedForce.h"
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#include "openmm/CustomVolumeForce.h"
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#include "openmm/DPDIntegrator.h"
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#include "openmm/Force.h"
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#include "openmm/GayBerneForce.h"
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#include "openmm/GBSAOBCForce.h"
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#include "openmm/HarmonicAngleForce.h"
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#include "openmm/HarmonicBondForce.h"
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#include "openmm/Integrator.h"
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#include "openmm/LangevinIntegrator.h"
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#include "openmm/LangevinMiddleIntegrator.h"
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#include "openmm/LCPOForce.h"
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#include "openmm/LocalEnergyMinimizer.h"
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#include "openmm/MonteCarloAnisotropicBarostat.h"
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#include "openmm/MonteCarloBarostat.h"
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#include "openmm/MonteCarloFlexibleBarostat.h"
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#include "openmm/MonteCarloMembraneBarostat.h"
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#include "openmm/NonbondedForce.h"
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#include "openmm/Context.h"
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#include "openmm/OpenMMException.h"
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#include "openmm/OrientationRestraintForce.h"
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#include "openmm/PeriodicTorsionForce.h"
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#include "openmm/PythonForce.h"
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#include "openmm/QTBIntegrator.h"
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#include "openmm/RBTorsionForce.h"
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#include "openmm/RGForce.h"
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#include "openmm/RMSDForce.h"
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#include "openmm/State.h"
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#include "openmm/System.h"
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#include "openmm/TabulatedFunction.h"
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#include "openmm/Units.h"
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#include "openmm/VariableLangevinIntegrator.h"
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#include "openmm/VariableVerletIntegrator.h"
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#include "openmm/Vec3.h"
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#include "openmm/VerletIntegrator.h"
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#include "openmm/NoseHooverIntegrator.h"
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#include "openmm/NoseHooverChain.h"
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#include "openmm/VirtualSite.h"
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#include "openmm/Platform.h"
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#include "openmm/serialization/XmlSerializer.h"
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#include "openmm/ATMForce.h"
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#endif /*OPENMM_H_*/
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