Skip to content

GitLab

Unverified Commit 1e42b8be authored by Peter Eastman's avatar Peter Eastman Committed by GitHub
Browse files

Replaced several AMOEBA bonded forces with custom forces (#3046) 

* Replaced several AMOEBA bonded forces with custom forces

* Deleted obsolete AMOEBA forces

* Replaced AmoebaPiTorsionForce with custom force
parent 014797f4
Expand all Hide whitespace changes
Inline Side-by-side
Showing with 0 additions and 4380 deletions
plugins/amoeba/platforms/reference/src/AmoebaReferenceKernelFactory.cpp
View file @ 1e42b8be
...@@ -48,12 +48,6 @@ extern "C" OPENMM_EXPORT void registerKernelFactories() { ...@@ -48,12 +48,6 @@ extern "C" OPENMM_EXPORT void registerKernelFactories() {
Platform& platform = Platform::getPlatform(i); Platform& platform = Platform::getPlatform(i);
if (dynamic_cast<ReferencePlatform*>(&platform) != NULL) { if (dynamic_cast<ReferencePlatform*>(&platform) != NULL) {
AmoebaReferenceKernelFactory* factory = new AmoebaReferenceKernelFactory(); AmoebaReferenceKernelFactory* factory = new AmoebaReferenceKernelFactory();
platform.registerKernelFactory(CalcAmoebaBondForceKernel::Name(), factory);
platform.registerKernelFactory(CalcAmoebaAngleForceKernel::Name(), factory);
platform.registerKernelFactory(CalcAmoebaInPlaneAngleForceKernel::Name(), factory);
platform.registerKernelFactory(CalcAmoebaPiTorsionForceKernel::Name(), factory);
platform.registerKernelFactory(CalcAmoebaStretchBendForceKernel::Name(), factory);
platform.registerKernelFactory(CalcAmoebaOutOfPlaneBendForceKernel::Name(), factory);
platform.registerKernelFactory(CalcAmoebaTorsionTorsionForceKernel::Name(), factory); platform.registerKernelFactory(CalcAmoebaTorsionTorsionForceKernel::Name(), factory);
platform.registerKernelFactory(CalcAmoebaVdwForceKernel::Name(), factory); platform.registerKernelFactory(CalcAmoebaVdwForceKernel::Name(), factory);
platform.registerKernelFactory(CalcAmoebaMultipoleForceKernel::Name(), factory); platform.registerKernelFactory(CalcAmoebaMultipoleForceKernel::Name(), factory);
...@@ -69,28 +63,6 @@ extern "C" OPENMM_EXPORT void registerAmoebaReferenceKernelFactories() { ...@@ -69,28 +63,6 @@ extern "C" OPENMM_EXPORT void registerAmoebaReferenceKernelFactories() {
} }
KernelImpl* AmoebaReferenceKernelFactory::createKernelImpl(std::string name, const Platform& platform, ContextImpl& context) const { KernelImpl* AmoebaReferenceKernelFactory::createKernelImpl(std::string name, const Platform& platform, ContextImpl& context) const {
ReferencePlatform::PlatformData& referencePlatformData = *static_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
// create AmoebaReferenceData object if contextToAmoebaDataMap does not contain
// key equal to current context
if (name == CalcAmoebaBondForceKernel::Name())
return new ReferenceCalcAmoebaBondForceKernel(name, platform, context.getSystem());
if (name == CalcAmoebaAngleForceKernel::Name())
return new ReferenceCalcAmoebaAngleForceKernel(name, platform, context.getSystem());
if (name == CalcAmoebaInPlaneAngleForceKernel::Name())
return new ReferenceCalcAmoebaInPlaneAngleForceKernel(name, platform, context.getSystem());
if (name == CalcAmoebaPiTorsionForceKernel::Name())
return new ReferenceCalcAmoebaPiTorsionForceKernel(name, platform, context.getSystem());
if (name == CalcAmoebaStretchBendForceKernel::Name())
return new ReferenceCalcAmoebaStretchBendForceKernel(name, platform, context.getSystem());
if (name == CalcAmoebaOutOfPlaneBendForceKernel::Name())
return new ReferenceCalcAmoebaOutOfPlaneBendForceKernel(name, platform, context.getSystem());
if (name == CalcAmoebaTorsionTorsionForceKernel::Name()) if (name == CalcAmoebaTorsionTorsionForceKernel::Name())
return new ReferenceCalcAmoebaTorsionTorsionForceKernel(name, platform, context.getSystem()); return new ReferenceCalcAmoebaTorsionTorsionForceKernel(name, platform, context.getSystem());
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceBondForce.cpp deleted 100644 → 0
View file @ 014797f4
/* Portions copyright (c) 2006 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
* a copy of this software and associated documentation files (the
* "Software"), to deal in the Software without restriction, including
* without limitation the rights to use, copy, modify, merge, publish,
* distribute, sublicense, 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 all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
* OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
* MERCHANTABILITY, 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 "AmoebaReferenceBondForce.h"
#include "AmoebaReferenceForce.h"
using std::vector;
using namespace OpenMM;
void AmoebaReferenceBondForce::setPeriodic(OpenMM::Vec3* vectors) {
usePeriodic = true;
boxVectors[0] = vectors[0];
boxVectors[1] = vectors[1];
boxVectors[2] = vectors[2];
}
/**---------------------------------------------------------------------------------------
Calculate Amoeba bond ixn (force and energy)
@param positionAtomA Cartesian coordinates of atom A
@param positionAtomB Cartesian coordinates of atom B
@param bondLength bond length
@param bondK bond force
@param bondCubic cubic bond force parameter
@param bondQuartic quartic bond force parameter
@param forces force vector
@return energy
--------------------------------------------------------------------------------------- */
double AmoebaReferenceBondForce::calculateBondIxn(const Vec3& positionAtomA, const Vec3& positionAtomB,
double bondLength, double bondK,
double bondCubic, double bondQuartic,
Vec3* forces) const {
// get deltaR, R2, and R between 2 atoms
std::vector<double> deltaR;
if (usePeriodic)
AmoebaReferenceForce::loadDeltaRPeriodic(positionAtomA, positionAtomB, deltaR, boxVectors);
else
AmoebaReferenceForce::loadDeltaR(positionAtomA, positionAtomB, deltaR);
double r = AmoebaReferenceForce::getNorm3(deltaR);
// deltaIdeal = r - r_0
double deltaIdeal = r - bondLength;
double deltaIdeal2 = deltaIdeal*deltaIdeal;
double dEdR = (1.0 + 1.5*bondCubic*deltaIdeal + 2.0*bondQuartic*deltaIdeal2);
dEdR *= 2.0*bondK*deltaIdeal;
dEdR = r > 0.0 ? (dEdR/r) : 0.0;
forces[0][0] = dEdR*deltaR[0];
forces[0][1] = dEdR*deltaR[1];
forces[0][2] = dEdR*deltaR[2];
dEdR *= -1.0;
forces[1][0] = dEdR*deltaR[0];
forces[1][1] = dEdR*deltaR[1];
forces[1][2] = dEdR*deltaR[2];
double energy = bondK*deltaIdeal2*(1.0 + bondCubic*deltaIdeal + bondQuartic*deltaIdeal2);
return energy;
}
double AmoebaReferenceBondForce::calculateForceAndEnergy(int numBonds,
vector<Vec3>& particlePositions,
const std::vector<int>& particle1,
const std::vector<int>& particle2,
const std::vector<double>& length,
const std::vector<double>& kQuadratic,
double globalBondCubic,
double globalBondQuartic,
vector<Vec3>& forceData) const {
double energy = 0.0;
for (int ii = 0; ii < numBonds; ii++) {
int particle1Index = particle1[ii];
int particle2Index = particle2[ii];
double bondLength = length[ii];
double bondK = kQuadratic[ii];
Vec3 forces[2];
energy += calculateBondIxn(particlePositions[particle1Index], particlePositions[particle2Index],
bondLength, bondK, globalBondCubic, globalBondQuartic,
forces);
for (int jj = 0; jj < 3; jj++) {
forceData[particle1Index][jj] += forces[0][jj];
forceData[particle2Index][jj] += forces[1][jj];
}
}
return energy;
}
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