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
91 lines
4.2 KiB
C++
91 lines
4.2 KiB
C++
/* -------------------------------------------------------------------------- *
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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) 2025 Stanford University and the Authors. *
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* Authors: Peter Eastman, Evan Pretti *
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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/internal/AssertionUtilities.h"
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#include "openmm/LCPOForce.h"
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#include "openmm/serialization/XmlSerializer.h"
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#include <iostream>
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#include <sstream>
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using namespace OpenMM;
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using namespace std;
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void testSerialization() {
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// Create a Force.
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LCPOForce force;
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force.setForceGroup(3);
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force.setName("custom name");
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force.setUsesPeriodicBoundaryConditions(true);
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force.setSurfaceTension(100.0);
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force.addParticle(1.0, 2.0, 3.0, 4.0, 5.0);
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force.addParticle(0.0, 0.0, 0.0, 0.0, 0.0);
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force.addParticle(6.0, 7.0, 8.0, 9.0, 10.0);
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force.addParticle(1.0, 2.0, 3.0, 4.0, 5.0);
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force.addParticle(0.0, 0.0, 0.0, 0.0, 0.0);
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force.addParticle(6.0, 7.0, 8.0, 9.0, 10.0);
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// Serialize and then deserialize it.
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stringstream buffer;
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XmlSerializer::serialize<LCPOForce>(&force, "Force", buffer);
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LCPOForce* copy = XmlSerializer::deserialize<LCPOForce>(buffer);
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// Compare the two forces to see if they are identical.
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LCPOForce& force2 = *copy;
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ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
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ASSERT_EQUAL(force.getName(), force2.getName());
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ASSERT_EQUAL(force.usesPeriodicBoundaryConditions(), force2.usesPeriodicBoundaryConditions());
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ASSERT_EQUAL(force.getSurfaceTension(), force2.getSurfaceTension());
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ASSERT_EQUAL(force.getNumParticles(), force2.getNumParticles());
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for (int i = 0; i < force.getNumParticles(); i++) {
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double radius1, radius2, p11, p12, p21, p22, p31, p32, p41, p42;
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force.getParticleParameters(i, radius1, p11, p21, p31, p41);
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force2.getParticleParameters(i, radius2, p12, p22, p32, p42);
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ASSERT_EQUAL(radius1, radius2);
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ASSERT_EQUAL(p11, p12);
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ASSERT_EQUAL(p21, p22);
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ASSERT_EQUAL(p31, p32);
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ASSERT_EQUAL(p41, p42);
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}
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}
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int main() {
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try {
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testSerialization();
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}
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catch(const exception& e) {
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cout << "exception: " << e.what() << endl;
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return 1;
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}
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cout << "Done" << endl;
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return 0;
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}
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