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Unverified Commit 6c6bc628 authored by Peter Eastman's avatar Peter Eastman Committed by GitHub
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Minor optimization to validating exclusions (#4453) 

* Minor optimization to validating exclusions

* Optimizations to findMoleculeGroups()
parent 4e742529
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Showing with 31 additions and 27 deletions
openmmapi/src/CustomGBForceImpl.cpp
View file @ 6c6bc628
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2012 Stanford University and the Authors. *
* Portions copyright (c) 2008-2024 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -29,20 +29,19 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#ifdef WIN32
#define _USE_MATH_DEFINES // Needed to get M_PI
#endif
#include "openmm/OpenMMException.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/internal/CustomGBForceImpl.h"
#include "openmm/internal/Messages.h"
#include "openmm/kernels.h"
#include <cmath>
#include <sstream>
using namespace OpenMM;
using std::map;
using std::pair;
using std::vector;
using std::set;
using std::string;
using std::stringstream;
using namespace std;
CustomGBForceImpl::CustomGBForceImpl(const CustomGBForce& owner) : owner(owner) {
forceGroup = owner.getForceGroup();
......@@ -74,6 +73,8 @@ void CustomGBForceImpl::initialize(ContextImpl& context) {
for (int i = 0; i < owner.getNumExclusions(); i++) {
int particle1, particle2;
owner.getExclusionParticles(i, particle1, particle2);
int minp = min(particle1, particle2);
int maxp = max(particle1, particle2);
if (particle1 < 0 || particle1 >= owner.getNumParticles()) {
stringstream msg;
msg << "CustomGBForce: Illegal particle index for an exclusion: ";
......@@ -86,7 +87,7 @@ void CustomGBForceImpl::initialize(ContextImpl& context) {
msg << particle2;
throw OpenMMException(msg.str());
}
if (exclusions[particle1].count(particle2) > 0 || exclusions[particle2].count(particle1) > 0) {
if (exclusions[minp].count(maxp) > 0) {
stringstream msg;
msg << "CustomGBForce: Multiple exclusions are specified for particles ";
msg << particle1;
......@@ -94,8 +95,7 @@ void CustomGBForceImpl::initialize(ContextImpl& context) {
msg << particle2;
throw OpenMMException(msg.str());
}
exclusions[particle1].insert(particle2);
exclusions[particle2].insert(particle1);
exclusions[minp].insert(maxp);
}
if (owner.getNonbondedMethod() == CustomGBForce::CutoffPeriodic) {
Vec3 boxVectors[3];
......
openmmapi/src/CustomNonbondedForceImpl.cpp
View file @ 6c6bc628
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2022 Stanford University and the Authors. *
* Portions copyright (c) 2008-2024 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -84,6 +84,8 @@ void CustomNonbondedForceImpl::initialize(ContextImpl& context) {
for (int i = 0; i < owner.getNumExclusions(); i++) {
int particle1, particle2;
owner.getExclusionParticles(i, particle1, particle2);
int minp = min(particle1, particle2);
int maxp = max(particle1, particle2);
if (particle1 < 0 || particle1 >= owner.getNumParticles()) {
stringstream msg;
msg << "CustomNonbondedForce: Illegal particle index for an exclusion: ";
......@@ -96,7 +98,7 @@ void CustomNonbondedForceImpl::initialize(ContextImpl& context) {
msg << particle2;
throw OpenMMException(msg.str());
}
if (exclusions[particle1].count(particle2) > 0 || exclusions[particle2].count(particle1) > 0) {
if (exclusions[minp].count(maxp) > 0) {
stringstream msg;
msg << "CustomNonbondedForce: Multiple exclusions are specified for particles ";
msg << particle1;
......@@ -104,8 +106,7 @@ void CustomNonbondedForceImpl::initialize(ContextImpl& context) {
msg << particle2;
throw OpenMMException(msg.str());
}
exclusions[particle1].insert(particle2);
exclusions[particle2].insert(particle1);
exclusions[minp].insert(maxp);
}
if (owner.getNonbondedMethod() == CustomNonbondedForce::CutoffPeriodic) {
Vec3 boxVectors[3];
......
openmmapi/src/NonbondedForceImpl.cpp
View file @ 6c6bc628
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2021 Stanford University and the Authors. *
* Portions copyright (c) 2008-2024 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -81,6 +81,8 @@ void NonbondedForceImpl::initialize(ContextImpl& context) {
int particle[2];
double chargeProd, sigma, epsilon;
owner.getExceptionParameters(i, particle[0], particle[1], chargeProd, sigma, epsilon);
int minp = min(particle[0], particle[1]);
int maxp = max(particle[0], particle[1]);
for (int j = 0; j < 2; j++) {
if (particle[j] < 0 || particle[j] >= owner.getNumParticles()) {
stringstream msg;
......@@ -89,7 +91,7 @@ void NonbondedForceImpl::initialize(ContextImpl& context) {
throw OpenMMException(msg.str());
}
}
if (exceptions[particle[0]].count(particle[1]) > 0 || exceptions[particle[1]].count(particle[0]) > 0) {
if (exceptions[minp].count(maxp) > 0) {
stringstream msg;
msg << "NonbondedForce: Multiple exceptions are specified for particles ";
msg << particle[0];
......@@ -97,8 +99,7 @@ void NonbondedForceImpl::initialize(ContextImpl& context) {
msg << particle[1];
throw OpenMMException(msg.str());
}
exceptions[particle[0]].insert(particle[1]);
exceptions[particle[1]].insert(particle[0]);
exceptions[minp].insert(maxp);
if (sigma < 0)
throw OpenMMException("NonbondedForce: sigma for an exception cannot be negative");
if (epsilon < 0)
......
platforms/common/src/ComputeContext.cpp
View file @ 6c6bc628
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2019-2022 Stanford University and the Authors. *
* Portions copyright (c) 2019-2024 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -210,13 +210,14 @@ void ComputeContext::findMoleculeGroups() {
atomBonds[particle2].push_back(particle1);
}
for (auto force : forces) {
vector<int> particles;
for (int j = 0; j < force->getNumParticleGroups(); j++) {
vector<int> particles;
force->getParticlesInGroup(j, particles);
for (int k = 0; k < (int) particles.size(); k++)
for (int m = 0; m < (int) particles.size(); m++)
if (k != m)
atomBonds[particles[k]].push_back(particles[m]);
for (int k = 1; k < (int) particles.size(); k++)
for (int m = 0; m < k; m++) {
atomBonds[particles[k]].push_back(particles[m]);
atomBonds[particles[m]].push_back(particles[k]);
}
}
}
......@@ -242,13 +243,14 @@ void ComputeContext::findMoleculeGroups() {
system.getConstraintParameters(i, particle1, particle2, distance);
molecules[atomMolecule[particle1]].constraints.push_back(i);
}
for (int i = 0; i < (int) forces.size(); i++)
for (int i = 0; i < (int) forces.size(); i++) {
vector<int> particles;
for (int j = 0; j < forces[i]->getNumParticleGroups(); j++) {
vector<int> particles;
forces[i]->getParticlesInGroup(j, particles);
if (particles.size() > 0)
molecules[atomMolecule[particles[0]]].groups[i].push_back(j);
}
}
}
// Sort them into groups of identical molecules.
......@@ -293,10 +295,10 @@ void ComputeContext::findMoleculeGroups() {
for (int i = 0; i < (int) forces.size() && identical; i++) {
if (mol.groups[i].size() != mol2.groups[i].size())
identical = false;
vector<int> p1, p2;
for (int k = 0; k < (int) mol.groups[i].size() && identical; k++) {
if (!forces[i]->areGroupsIdentical(mol.groups[i][k], mol2.groups[i][k]))
identical = false;
vector<int> p1, p2;
forces[i]->getParticlesInGroup(mol.groups[i][k], p1);
forces[i]->getParticlesInGroup(mol2.groups[i][k], p2);
for (int m = 0; m < p1.size(); m++)
......
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