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Commit 19d2885a authored by Lee-Ping's avatar Lee-Ping
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Merge github.com:SimTk/openmm

parents 99ef4344 57a6768e
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Showing with 92 additions and 144 deletions
platforms/reference/src/SimTKReference/ReferenceBrownianDynamics.cpp
View file @ 19d2885a
......@@ -125,7 +125,7 @@ RealOpenMM ReferenceBrownianDynamics::getFriction( void ) const {
void ReferenceBrownianDynamics::update(const OpenMM::System& system, vector<RealVec>& atomCoordinates,
vector<RealVec>& velocities,
vector<RealVec>& forces, vector<RealOpenMM>& masses ){
vector<RealVec>& forces, vector<RealOpenMM>& masses, RealOpenMM tolerance) {
// ---------------------------------------------------------------------------------------
......@@ -162,7 +162,7 @@ void ReferenceBrownianDynamics::update(const OpenMM::System& system, vector<Real
}
ReferenceConstraintAlgorithm* referenceConstraintAlgorithm = getReferenceConstraintAlgorithm();
if (referenceConstraintAlgorithm)
referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses);
referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses, tolerance);
// Update the positions and velocities.
......
platforms/reference/src/SimTKReference/ReferenceCCMAAlgorithm.cpp
View file @ 19d2885a
......@@ -48,14 +48,12 @@ ReferenceCCMAAlgorithm::ReferenceCCMAAlgorithm(int numberOfAtoms,
const vector<pair<int, int> >& atomIndices,
const vector<RealOpenMM>& distance,
vector<RealOpenMM>& masses,
vector<AngleInfo>& angles,
RealOpenMM tolerance) {
vector<AngleInfo>& angles) {
_numberOfConstraints = numberOfConstraints;
_atomIndices = atomIndices;
_distance = distance;
_maximumNumberOfIterations = 150;
_tolerance = tolerance;
_hasInitializedMasses = false;
// work arrays
......@@ -201,28 +199,20 @@ void ReferenceCCMAAlgorithm::setMaximumNumberOfIterations(int maximumNumberOfIte
_maximumNumberOfIterations = maximumNumberOfIterations;
}
RealOpenMM ReferenceCCMAAlgorithm::getTolerance() const {
return _tolerance;
}
void ReferenceCCMAAlgorithm::setTolerance(RealOpenMM tolerance) {
_tolerance = tolerance;
}
void ReferenceCCMAAlgorithm::apply(vector<RealVec>& atomCoordinates,
vector<RealVec>& atomCoordinatesP,
vector<RealOpenMM>& inverseMasses) {
applyConstraints(atomCoordinates, atomCoordinatesP, inverseMasses, false);
vector<RealOpenMM>& inverseMasses, RealOpenMM tolerance) {
applyConstraints(atomCoordinates, atomCoordinatesP, inverseMasses, false, tolerance);
}
void ReferenceCCMAAlgorithm::applyToVelocities(std::vector<OpenMM::RealVec>& atomCoordinates,
std::vector<OpenMM::RealVec>& velocities, std::vector<RealOpenMM>& inverseMasses) {
applyConstraints(atomCoordinates, velocities, inverseMasses, true);
std::vector<OpenMM::RealVec>& velocities, std::vector<RealOpenMM>& inverseMasses, RealOpenMM tolerance) {
applyConstraints(atomCoordinates, velocities, inverseMasses, true, tolerance);
}
void ReferenceCCMAAlgorithm::applyConstraints(vector<RealVec>& atomCoordinates,
vector<RealVec>& atomCoordinatesP,
vector<RealOpenMM>& inverseMasses, bool constrainingVelocities) {
vector<RealOpenMM>& inverseMasses, bool constrainingVelocities, RealOpenMM tolerance) {
// temp arrays
vector<RealVec>& r_ij = _r_ij;
......@@ -242,15 +232,14 @@ void ReferenceCCMAAlgorithm::applyConstraints(vector<RealVec>& atomCoordinates,
// setup: r_ij for each (i,j) constraint
RealOpenMM tolerance = getTolerance()*2;
for (int ii = 0; ii < _numberOfConstraints; ii++) {
int atomI = _atomIndices[ii].first;
int atomJ = _atomIndices[ii].second;
r_ij[ii] = atomCoordinates[atomI] - atomCoordinates[atomJ];
d_ij2[ii] = r_ij[ii].dot(r_ij[ii]);
}
RealOpenMM lowerTol = 1-2*getTolerance()+getTolerance()*getTolerance();
RealOpenMM upperTol = 1+2*getTolerance()+getTolerance()*getTolerance();
RealOpenMM lowerTol = 1-2*tolerance+tolerance*tolerance;
RealOpenMM upperTol = 1+2*tolerance+tolerance*tolerance;
// main loop
......@@ -267,7 +256,7 @@ void ReferenceCCMAAlgorithm::applyConstraints(vector<RealVec>& atomCoordinates,
if (constrainingVelocities) {
RealOpenMM rrpr = rp_ij.dot(r_ij[ii]);
constraintDelta[ii] = -2*reducedMasses[ii]*rrpr/d_ij2[ii];
if (fabs(constraintDelta[ii]) <= getTolerance())
if (fabs(constraintDelta[ii]) <= tolerance)
numberConverged++;
}
else {
......
platforms/reference/src/SimTKReference/ReferenceConstraints.cpp
View file @ 19d2885a
......@@ -30,6 +30,8 @@
* -------------------------------------------------------------------------- */
#include "ReferenceConstraints.h"
#include "ReferenceCCMAAlgorithm.h"
#include "ReferenceSETTLEAlgorithm.h"
#include "openmm/HarmonicAngleForce.h"
#include "openmm/OpenMMException.h"
#include <map>
......@@ -39,8 +41,7 @@
using namespace OpenMM;
using namespace std;
ReferenceConstraints::ReferenceConstraints(const System& system, RealOpenMM tolerance) : ccma(NULL), settle(NULL) {
this->tolerance = tolerance;
ReferenceConstraints::ReferenceConstraints(const System& system) : ccma(NULL), settle(NULL) {
int numParticles = system.getNumParticles();
vector<RealOpenMM> masses(numParticles);
for (int i = 0; i < numParticles; ++i)
......@@ -141,7 +142,7 @@ ReferenceConstraints::ReferenceConstraints(const System& system, RealOpenMM tole
isSettleAtom[p2] = true;
isSettleAtom[p3] = true;
}
settle = new ReferenceSETTLEAlgorithm(atom1, atom2, atom3, distance1, distance2, masses, tolerance);
settle = new ReferenceSETTLEAlgorithm(atom1, atom2, atom3, distance1, distance2, masses);
}
// All other constraints are handled with CCMA.
......@@ -179,7 +180,7 @@ ReferenceConstraints::ReferenceConstraints(const System& system, RealOpenMM tole
// Create the CCMA object.
ccma = new ReferenceCCMAAlgorithm(numParticles, numCCMA, ccmaIndices, ccmaDistance, masses, angles, tolerance);
ccma = new ReferenceCCMAAlgorithm(numParticles, numCCMA, ccmaIndices, ccmaDistance, masses, angles);
}
}
......@@ -190,28 +191,16 @@ ReferenceConstraints::~ReferenceConstraints() {
delete settle;
}
RealOpenMM ReferenceConstraints::getTolerance() const {
return tolerance;
}
void ReferenceConstraints::setTolerance(RealOpenMM tolerance) {
this->tolerance = tolerance;
if (ccma != NULL)
ccma->setTolerance(tolerance);
if (settle != NULL)
settle->setTolerance(tolerance);
}
void ReferenceConstraints::apply(vector<OpenMM::RealVec>& atomCoordinates, vector<OpenMM::RealVec>& atomCoordinatesP, vector<RealOpenMM>& inverseMasses) {
void ReferenceConstraints::apply(vector<OpenMM::RealVec>& atomCoordinates, vector<OpenMM::RealVec>& atomCoordinatesP, vector<RealOpenMM>& inverseMasses, RealOpenMM tolerance) {
if (ccma != NULL)
ccma->apply(atomCoordinates, atomCoordinatesP, inverseMasses);
ccma->apply(atomCoordinates, atomCoordinatesP, inverseMasses, tolerance);
if (settle != NULL)
settle->apply(atomCoordinates, atomCoordinatesP, inverseMasses);
settle->apply(atomCoordinates, atomCoordinatesP, inverseMasses, tolerance);
}
void ReferenceConstraints::applyToVelocities(vector<OpenMM::RealVec>& atomCoordinates, vector<OpenMM::RealVec>& velocities, vector<RealOpenMM>& inverseMasses) {
void ReferenceConstraints::applyToVelocities(vector<OpenMM::RealVec>& atomCoordinates, vector<OpenMM::RealVec>& velocities, vector<RealOpenMM>& inverseMasses, RealOpenMM tolerance) {
if (ccma != NULL)
ccma->applyToVelocities(atomCoordinates, velocities, inverseMasses);
ccma->applyToVelocities(atomCoordinates, velocities, inverseMasses, tolerance);
if (settle != NULL)
settle->applyToVelocities(atomCoordinates, velocities, inverseMasses);
settle->applyToVelocities(atomCoordinates, velocities, inverseMasses, tolerance);
}
platforms/reference/src/SimTKReference/ReferenceCustomDynamics.cpp
View file @ 19d2885a
......@@ -97,7 +97,7 @@ ReferenceCustomDynamics::~ReferenceCustomDynamics() {
void ReferenceCustomDynamics::update(ContextImpl& context, int numberOfAtoms, vector<RealVec>& atomCoordinates,
vector<RealVec>& velocities, vector<RealVec>& forces, vector<RealOpenMM>& masses,
map<string, RealOpenMM>& globals, vector<vector<RealVec> >& perDof, bool& forcesAreValid){
map<string, RealOpenMM>& globals, vector<vector<RealVec> >& perDof, bool& forcesAreValid, RealOpenMM tolerance){
int numSteps = stepType.size();
globals.insert(context.getParameters().begin(), context.getParameters().end());
oldPos = atomCoordinates;
......@@ -252,12 +252,12 @@ void ReferenceCustomDynamics::update(ContextImpl& context, int numberOfAtoms, ve
break;
}
case CustomIntegrator::ConstrainPositions: {
getReferenceConstraintAlgorithm()->apply(oldPos, atomCoordinates, inverseMasses);
getReferenceConstraintAlgorithm()->apply(oldPos, atomCoordinates, inverseMasses, tolerance);
oldPos = atomCoordinates;
break;
}
case CustomIntegrator::ConstrainVelocities: {
getReferenceConstraintAlgorithm()->applyToVelocities(oldPos, velocities, inverseMasses);
getReferenceConstraintAlgorithm()->applyToVelocities(oldPos, velocities, inverseMasses, tolerance);
break;
}
case CustomIntegrator::UpdateContextState: {
......
platforms/reference/src/SimTKReference/ReferenceDynamics.cpp
View file @ 19d2885a
......@@ -249,11 +249,12 @@ void ReferenceDynamics::setReferenceConstraintAlgorithm( ReferenceConstraintAlgo
@param velocities velocities
@param forces forces
@param masses atom masses
@param tolerance the constraint tolerance
--------------------------------------------------------------------------------------- */
void ReferenceDynamics::update(const OpenMM::System& system, vector<RealVec>& atomCoordinates,
vector<RealVec>& velocities, vector<RealVec>& forces, vector<RealOpenMM>& masses ){
vector<RealVec>& velocities, vector<RealVec>& forces, vector<RealOpenMM>& masses, RealOpenMM tolerance) {
// ---------------------------------------------------------------------------------------
......
platforms/reference/src/SimTKReference/ReferencePME.cpp
View file @ 19d2885a
......@@ -195,7 +195,7 @@ pme_calculate_bsplines_moduli(pme_t pme)
static void
pme_update_grid_index_and_fraction(pme_t pme,
vector<RealVec>& atomCoordinates,
const vector<RealVec>& atomCoordinates,
const RealOpenMM periodicBoxSize[3])
{
int i;
......@@ -317,7 +317,7 @@ pme_update_bsplines(pme_t pme)
static void
pme_grid_spread_charge(pme_t pme, vector<RealOpenMM>& charges)
pme_grid_spread_charge(pme_t pme, const vector<RealOpenMM>& charges)
{
int order;
int i;
......@@ -519,10 +519,10 @@ pme_reciprocal_convolution(pme_t pme,
static void
pme_grid_interpolate_force(pme_t pme,
const RealOpenMM periodicBoxSize[3],
vector<RealOpenMM>& charges,
vector<RealVec>& forces)
pme_grid_interpolate_force(pme_t pme,
const RealOpenMM periodicBoxSize[3],
const vector<RealOpenMM>& charges,
vector<RealVec>& forces)
{
int i;
int ix,iy,iz;
......@@ -666,12 +666,12 @@ pme_init(pme_t * ppme,
int pme_exec(pme_t pme,
vector<RealVec>& atomCoordinates,
vector<RealVec>& forces,
vector<RealOpenMM>& charges,
const RealOpenMM periodicBoxSize[3],
RealOpenMM * energy,
RealOpenMM pme_virial[3][3])
const vector<RealVec>& atomCoordinates,
vector<RealVec>& forces,
const vector<RealOpenMM>& charges,
const RealOpenMM periodicBoxSize[3],
RealOpenMM* energy,
RealOpenMM pme_virial[3][3])
{
/* Routine is called with coordinates in x, a box, and charges in q */
......
platforms/reference/src/SimTKReference/ReferenceSETTLEAlgorithm.cpp
View file @ 19d2885a
......@@ -35,19 +35,23 @@ using namespace OpenMM;
using namespace std;
ReferenceSETTLEAlgorithm::ReferenceSETTLEAlgorithm(const vector<int>& atom1, const vector<int>& atom2, const vector<int>& atom3,
const vector<RealOpenMM>& distance1, const vector<RealOpenMM>& distance2, vector<RealOpenMM>& masses, RealOpenMM tolerance) :
atom1(atom1), atom2(atom2), atom3(atom3), distance1(distance1), distance2(distance2), masses(masses), tolerance(tolerance) {
const vector<RealOpenMM>& distance1, const vector<RealOpenMM>& distance2, vector<RealOpenMM>& masses) :
atom1(atom1), atom2(atom2), atom3(atom3), distance1(distance1), distance2(distance2), masses(masses) {
}
RealOpenMM ReferenceSETTLEAlgorithm::getTolerance() const {
return tolerance;
int ReferenceSETTLEAlgorithm::getNumClusters() const {
return atom1.size();
}
void ReferenceSETTLEAlgorithm::setTolerance(RealOpenMM tolerance) {
this->tolerance = tolerance;
void ReferenceSETTLEAlgorithm::getClusterParameters(int index, int& atom1, int& atom2, int& atom3, RealOpenMM& distance1, RealOpenMM& distance2) const {
atom1 = this->atom1[index];
atom2 = this->atom2[index];
atom3 = this->atom3[index];
distance1 = this->distance1[index];
distance2 = this->distance2[index];
}
void ReferenceSETTLEAlgorithm::apply(vector<OpenMM::RealVec>& atomCoordinates, vector<OpenMM::RealVec>& atomCoordinatesP, vector<RealOpenMM>& inverseMasses) {
void ReferenceSETTLEAlgorithm::apply(vector<OpenMM::RealVec>& atomCoordinates, vector<OpenMM::RealVec>& atomCoordinatesP, vector<RealOpenMM>& inverseMasses, RealOpenMM tolerance) {
for (int index = 0; index < (int) atom1.size(); ++index) {
RealVec apos0 = atomCoordinates[atom1[index]];
RealVec xp0 = atomCoordinatesP[atom1[index]]-apos0;
......@@ -190,7 +194,7 @@ void ReferenceSETTLEAlgorithm::apply(vector<OpenMM::RealVec>& atomCoordinates, v
}
}
void ReferenceSETTLEAlgorithm::applyToVelocities(vector<OpenMM::RealVec>& atomCoordinates, vector<OpenMM::RealVec>& velocities, vector<RealOpenMM>& inverseMasses) {
void ReferenceSETTLEAlgorithm::applyToVelocities(vector<OpenMM::RealVec>& atomCoordinates, vector<OpenMM::RealVec>& velocities, vector<RealOpenMM>& inverseMasses, RealOpenMM tolerance) {
for (int index = 0; index < (int) atom1.size(); ++index) {
RealVec apos0 = atomCoordinates[atom1[index]];
RealVec apos1 = atomCoordinates[atom2[index]];
......
platforms/reference/src/SimTKReference/ReferenceStochasticDynamics.cpp
View file @ 19d2885a
......@@ -200,7 +200,7 @@ void ReferenceStochasticDynamics::updatePart2( int numberOfAtoms, vector<RealVec
--------------------------------------------------------------------------------------- */
void ReferenceStochasticDynamics::update(const OpenMM::System& system, vector<RealVec>& atomCoordinates,
vector<RealVec>& velocities, vector<RealVec>& forces, vector<RealOpenMM>& masses ){
vector<RealVec>& velocities, vector<RealVec>& forces, vector<RealOpenMM>& masses, RealOpenMM tolerance) {
// ---------------------------------------------------------------------------------------
......@@ -235,7 +235,7 @@ void ReferenceStochasticDynamics::update(const OpenMM::System& system, vector<Re
ReferenceConstraintAlgorithm* referenceConstraintAlgorithm = getReferenceConstraintAlgorithm();
if (referenceConstraintAlgorithm)
referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses);
referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses, tolerance);
// copy xPrime -> atomCoordinates
......
platforms/reference/src/SimTKReference/ReferenceVariableStochasticDynamics.cpp
View file @ 19d2885a
......@@ -260,7 +260,7 @@ void ReferenceVariableStochasticDynamics::updatePart2( int numberOfAtoms, vector
void ReferenceVariableStochasticDynamics::update(const OpenMM::System& system, vector<RealVec>& atomCoordinates,
vector<RealVec>& velocities,
vector<RealVec>& forces, vector<RealOpenMM>& masses, RealOpenMM maxStepSize ){
vector<RealVec>& forces, vector<RealOpenMM>& masses, RealOpenMM maxStepSize, RealOpenMM tolerance) {
// ---------------------------------------------------------------------------------------
......@@ -279,7 +279,7 @@ void ReferenceVariableStochasticDynamics::update(const OpenMM::System& system, v
ReferenceConstraintAlgorithm* referenceConstraintAlgorithm = getReferenceConstraintAlgorithm();
if (referenceConstraintAlgorithm)
referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses);
referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses, tolerance);
// copy xPrime -> atomCoordinates
......
platforms/reference/src/SimTKReference/ReferenceVariableVerletDynamics.cpp
View file @ 19d2885a
......@@ -104,7 +104,7 @@ void ReferenceVariableVerletDynamics::setAccuracy( RealOpenMM accuracy ) {
void ReferenceVariableVerletDynamics::update(const OpenMM::System& system, vector<RealVec>& atomCoordinates,
vector<RealVec>& velocities,
vector<RealVec>& forces, vector<RealOpenMM>& masses, RealOpenMM maxStepSize ){
vector<RealVec>& forces, vector<RealOpenMM>& masses, RealOpenMM maxStepSize, RealOpenMM tolerance) {
// ---------------------------------------------------------------------------------------
......@@ -155,7 +155,7 @@ void ReferenceVariableVerletDynamics::update(const OpenMM::System& system, vecto
}
ReferenceConstraintAlgorithm* referenceConstraintAlgorithm = getReferenceConstraintAlgorithm();
if (referenceConstraintAlgorithm)
referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses);
referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses, tolerance);
// Update the positions and velocities.
......
platforms/reference/src/SimTKReference/ReferenceVerletDynamics.cpp
View file @ 19d2885a
......@@ -95,7 +95,7 @@ ReferenceVerletDynamics::~ReferenceVerletDynamics( ){
void ReferenceVerletDynamics::update(const OpenMM::System& system, vector<RealVec>& atomCoordinates,
vector<RealVec>& velocities,
vector<RealVec>& forces, vector<RealOpenMM>& masses ){
vector<RealVec>& forces, vector<RealOpenMM>& masses, RealOpenMM tolerance) {
// ---------------------------------------------------------------------------------------
......@@ -131,7 +131,7 @@ void ReferenceVerletDynamics::update(const OpenMM::System& system, vector<RealVe
}
ReferenceConstraintAlgorithm* referenceConstraintAlgorithm = getReferenceConstraintAlgorithm();
if (referenceConstraintAlgorithm)
referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses);
referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses, tolerance);
// Update the positions and velocities.
......
platforms/reference/tests/CMakeLists.txt
View file @ 19d2885a
......@@ -12,6 +12,7 @@ FOREACH(TEST_PROG ${TEST_PROGS})
# All tests use shared libraries
ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_TARGET})
SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
ADD_TEST(${TEST_ROOT} ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT})
ENDFOREACH(TEST_PROG ${TEST_PROGS})
......
platforms/reference/tests/TestReferenceCustomGBForce.cpp
View file @ 19d2885a
......@@ -251,7 +251,7 @@ void testMembrane() {
for (int i = 0; i < (int) forces.size(); ++i)
norm += forces[i].dot(forces[i]);
norm = std::sqrt(norm);
const double stepSize = 1e-3;
const double stepSize = 1e-2;
double step = 0.5*stepSize/norm;
vector<Vec3> positions2(numParticles), positions3(numParticles);
for (int i = 0; i < (int) positions.size(); ++i) {
......
platforms/reference/tests/TestReferenceGBSAOBCForce.cpp
View file @ 19d2885a
......@@ -66,7 +66,7 @@ void testSingleParticle() {
double bornRadius = 0.15-0.009; // dielectric offset
double eps0 = EPSILON0;
double bornEnergy = (-0.5*0.5/(8*PI_M*eps0))*(1.0/forceField->getSoluteDielectric()-1.0/forceField->getSolventDielectric())/bornRadius;
double extendedRadius = bornRadius+0.14; // probe radius
double extendedRadius = 0.15+0.14; // probe radius
double nonpolarEnergy = CAL2JOULE*PI_M*0.0216*(10*extendedRadius)*(10*extendedRadius)*std::pow(0.15/bornRadius, 6.0); // Where did this formula come from? Just copied it from CpuImplicitSolvent.cpp
ASSERT_EQUAL_TOL((bornEnergy+nonpolarEnergy), state.getPotentialEnergy(), 0.01);
......@@ -171,7 +171,7 @@ void testForce() {
norm += f[0]*f[0] + f[1]*f[1] + f[2]*f[2];
}
norm = std::sqrt(norm);
const double delta = 1e-3;
const double delta = 1e-2;
double step = 0.5*delta/norm;
vector<Vec3> positions2(numParticles), positions3(numParticles);
for (int i = 0; i < numParticles; ++i) {
......
plugins/amoeba/CMakeLists.txt
View file @ 19d2885a
......@@ -16,15 +16,9 @@
#INCLUDE(Dart)
# ----------------------------------------------------------------------------
#SET(CREATE_SERIALIZABLE_OPENMM_AMOEBA OFF CACHE BOOL "Build verison of OpenMMAmoeba w/ backdoor serialization capability")
#SET(CREATE_SERIALIZABLE_OPENMM_AMOEBA TRUE )
SET(CREATE_SERIALIZABLE_OPENMM_AMOEBA FALSE )
# ----------------------------------------------------------------------------
# The source is organized into subdirectories, but we handle them all from
# this CMakeLists file rather than letting CMake visit them as SUBDIRS.
SET(OPENMM_AMOEBA_PLUGIN_SOURCE_SUBDIRS . openmmapi platforms/reference)
SET(OPENMM_AMOEBA_PLUGIN_SOURCE_SUBDIRS . openmmapi serialization)
# Collect up information about the version of the OpenMM library we're building
# and make it available to the code so it can be built into the binaries.
......@@ -41,17 +35,11 @@ ADD_DEFINITIONS(-DOPENMM_AMOEBA_LIBRARY_NAME=${OPENMM_AMOEBA_LIBRARY_NAME}
SET(SHARED_AMOEBA_TARGET ${OPENMM_AMOEBA_LIBRARY_NAME})
SET(STATIC_AMOEBA_TARGET ${OPENMM_AMOEBA_LIBRARY_NAME}_static)
IF( CREATE_SERIALIZABLE_OPENMM_AMOEBA )
SET(SHARED_AMOEBA_SERIALIZABLE_TARGET ${OPENMM_AMOEBA_LIBRARY_NAME}_serializable)
ENDIF( CREATE_SERIALIZABLE_OPENMM_AMOEBA )
# But on Unix or Cygwin we have to add the suffix manually
IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
SET(SHARED_AMOEBA_TARGET ${SHARED_AMOEBA_TARGET}_d)
SET(STATIC_AMOEBA_TARGET ${STATIC_AMOEBA_TARGET}_d)
IF( CREATE_SERIALIZABLE_OPENMM_AMOEBA )
SET(SHARED_AMOEBA_SERIALIZABLE_TARGET ${SHARED_AMOEBA_SERIALIZABLE_TARGET}_d)
ENDIF( CREATE_SERIALIZABLE_OPENMM_AMOEBA )
ENDIF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
# These are all the places to search for header files which are
......@@ -94,11 +82,6 @@ FOREACH(subdir ${OPENMM_AMOEBA_PLUGIN_SOURCE_SUBDIRS})
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include)
ENDFOREACH(subdir)
INCLUDE_DIRECTORIES(BEFORE ${OPENMM_DIR}/platforms/reference/src)
INCLUDE_DIRECTORIES(BEFORE ${OPENMM_DIR}/platforms/reference/src/SimTKReference)
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/platforms/reference/src)
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/platforms/reference/src/SimTKReference)
# ----------------------------------------------------------------------------
# If API_AMOEBA wrappers are being generated, and add them to the build.
......@@ -111,24 +94,18 @@ ENDIF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/src)
ADD_LIBRARY(${SHARED_AMOEBA_TARGET} SHARED ${SOURCE_AMOEBA_FILES} ${SOURCE_AMOEBA_INCLUDE_FILES} ${API_AMOEBA_ABS_INCLUDE_FILES})
SET_TARGET_PROPERTIES(${SHARED_AMOEBA_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_AMOEBA_BUILDING_SHARED_LIBRARY -DLEPTON_BUILDING_SHARED_LIBRARY")
SET_TARGET_PROPERTIES(${SHARED_AMOEBA_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_AMOEBA_BUILDING_SHARED_LIBRARY -DLEPTON_BUILDING_SHARED_LIBRARY")
IF( CREATE_SERIALIZABLE_OPENMM_AMOEBA )
ADD_LIBRARY(${SHARED_AMOEBA_SERIALIZABLE_TARGET} SHARED ${SOURCE_AMOEBA_FILES} ${SOURCE_AMOEBA_INCLUDE_FILES} ${API_AMOEBA_ABS_INCLUDE_FILES})
SET_TARGET_PROPERTIES(${SHARED_AMOEBA_SERIALIZABLE_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_AMOEBA_BUILDING_SHARED_LIBRARY -DLEPTON_BUILDING_SHARED_LIBRARY -DOPENMM_SERIALIZE")
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/../../serialization/include)
ENDIF( CREATE_SERIALIZABLE_OPENMM_AMOEBA )
FILE(GLOB serialization_files ${CMAKE_CUURENT_SOURCE_DIR}/serialization/src/*.cpp)
SET_SOURCE_FILES_PROPERTIES(${serialization_files} PROPERTIES COMPILE_FLAGS "-DOPENMM_AMOEBA_BUILDING_SHARED_LIBRARY -DTIXML_USE_STL")
IF(OPENMM_BUILD_STATIC_LIB)
ADD_LIBRARY(${STATIC_AMOEBA_TARGET} STATIC ${SOURCE_AMOEBA_FILES} ${SOURCE_AMOEBA_INCLUDE_FILES} ${API_AMOEBA_ABS_INCLUDE_FILES})
SET_TARGET_PROPERTIES(${STATIC_AMOEBA_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_USE_STATIC_LIBRARIES -DOPENMM_BUILDING_STATIC_LIBRARY -DLEPTON_USE_STATIC_LIBRARIES -DLEPTON_BUILDING_STATIC_LIBRARY")
SET_TARGET_PROPERTIES(${STATIC_AMOEBA_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_USE_STATIC_LIBRARIES -DOPENMM_BUILDING_STATIC_LIBRARY -DLEPTON_USE_STATIC_LIBRARIES -DLEPTON_BUILDING_STATIC_LIBRARY")
ENDIF(OPENMM_BUILD_STATIC_LIB)
IF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)
ADD_DEPENDENCIES(${SHARED_AMOEBA_TARGET} AmoebaApiWrappers)
IF( CREATE_SERIALIZABLE_OPENMM_AMOEBA )
ADD_DEPENDENCIES(${SHARED_AMOEBA_SERIALIZABLE_TARGET} AmoebaApiWrappers)
ENDIF( CREATE_SERIALIZABLE_OPENMM_AMOEBA )
IF(OPENMM_BUILD_STATIC_LIB)
ADD_DEPENDENCIES(${STATIC_AMOEBA_TARGET} AmoebaApiWrappers)
ENDIF(OPENMM_BUILD_STATIC_LIB)
......@@ -140,9 +117,6 @@ ENDIF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)
FIND_LIBRARY(DL_LIBRARY dl)
IF(DL_LIBRARY)
TARGET_LINK_LIBRARIES(${SHARED_AMOEBA_TARGET} ${DL_LIBRARY})
IF( CREATE_SERIALIZABLE_OPENMM_AMOEBA )
TARGET_LINK_LIBRARIES(${SHARED_AMOEBA_SERIALIZABLE_TARGET} ${DL_LIBRARY})
ENDIF( CREATE_SERIALIZABLE_OPENMM_AMOEBA )
IF(OPENMM_BUILD_STATIC_LIB)
TARGET_LINK_LIBRARIES(${STATIC_AMOEBA_TARGET} ${DL_LIBRARY})
ENDIF(OPENMM_BUILD_STATIC_LIB)
......@@ -155,16 +129,14 @@ IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
ENDIF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
TARGET_LINK_LIBRARIES( ${SHARED_AMOEBA_TARGET} ${SHARED_TARGET} )
IF( CREATE_SERIALIZABLE_OPENMM_AMOEBA )
TARGET_LINK_LIBRARIES( ${SHARED_AMOEBA_SERIALIZABLE_TARGET} ${SHARED_TARGET} )
ENDIF( CREATE_SERIALIZABLE_OPENMM_AMOEBA )
IF(OPENMM_BUILD_STATIC_LIB)
TARGET_LINK_LIBRARIES( ${STATIC_AMOEBA_TARGET} ${STATIC_TARGET} )
ENDIF(OPENMM_BUILD_STATIC_LIB)
ADD_SUBDIRECTORY(platforms/reference/tests)
# Which hardware platforms to build
ADD_SUBDIRECTORY(platforms/reference)
IF(CUDA_FOUND)
SET(OPENMM_BUILD_AMOEBA_CUDA_LIB ON CACHE BOOL "Build OpenMMAmoebaCuda library for Nvidia GPUs")
ELSE(CUDA_FOUND)
......@@ -175,20 +147,11 @@ SET(OPENMM_BUILD_AMOEBA_PATH)
SET(OPENMM_BUILD_AMOEBA_CUDA_PATH)
IF(OPENMM_BUILD_AMOEBA_CUDA_LIB)
ADD_SUBDIRECTORY(platforms/cuda)
SET(OPENMM_BUILD_AMOEBA_PATH ${CMAKE_CURRENT_SOURCE_DIR}/platforms/cuda)
SET(OPENMM_BUILD_AMOEBA_CUDA_PATH ${CMAKE_CURRENT_SOURCE_DIR}/platforms/cuda)
SET(OPENMM_AMOEBA_CUDA_SOURCE_SUBDIRS . openmmapi olla platforms/cuda)
ENDIF(OPENMM_BUILD_AMOEBA_CUDA_LIB)
#SET(OPENMM_BUILD_OPENCL_LIB OFF CACHE BOOL "Build OpenMMOpenCL library for Nvidia GPUs")
#IF(OPENMM_BUILD_OPENCL_LIB)
# ADD_SUBDIRECTORY(platforms/opencl)
#ENDIF(OPENMM_BUILD_OPENCL_LIB)
INSTALL_TARGETS(/lib RUNTIME_DIRECTORY /lib ${SHARED_AMOEBA_TARGET})
IF( CREATE_SERIALIZABLE_OPENMM_AMOEBA )
INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${SHARED_AMOEBA_SERIALIZABLE_TARGET})
ENDIF( CREATE_SERIALIZABLE_OPENMM_AMOEBA )
IF(OPENMM_BUILD_STATIC_LIB)
INSTALL_TARGETS(/lib RUNTIME_DIRECTORY /lib ${STATIC_AMOEBA_TARGET})
ENDIF(OPENMM_BUILD_STATIC_LIB)
......@@ -199,18 +162,6 @@ INSTALL_FILES(/include FILES ${CORE_HEADERS})
INSTALL_FILES(/include/openmm FILES ${TOP_HEADERS})
INSTALL_FILES(/include/openmm/internal FILES ${INTERNAL_HEADERS})
#
# Allow automated build and dashboard.
#
#INCLUDE (Dart)
#IF (UNIX AND NOT CYGWIN AND NOT APPLE)
# IF (NOT CMAKE_BUILD_TYPE OR CMAKE_BUILD_TYPE MATCHES Debug)
# ADD_DEFINITIONS(-fprofile-arcs -ftest-coverage)
# LINK_LIBRARIES(gcov)
# ENDIF (NOT CMAKE_BUILD_TYPE OR CMAKE_BUILD_TYPE MATCHES Debug)
#ENDIF (UNIX AND NOT CYGWIN AND NOT APPLE)
#
# Testing
#
......@@ -223,11 +174,4 @@ ELSE (EXECUTABLE_OUTPUT_PATH)
SET (TEST_PATH .)
ENDIF (EXECUTABLE_OUTPUT_PATH)
IF (OPENMM_BUILD_SERIALIZATION_SUPPORT)
ADD_SUBDIRECTORY(serialization)
ENDIF (OPENMM_BUILD_SERIALIZATION_SUPPORT)
#INCLUDE(ApiDoxygen.cmake)
#ADD_SUBDIRECTORY(tests)
#ADD_SUBDIRECTORY(examples)
ADD_SUBDIRECTORY(serialization/tests)
plugins/amoeba/openmmapi/include/openmm/AmoebaAngleForce.h
View file @ 19d2885a
......@@ -175,6 +175,10 @@ private:
std::vector<AngleInfo> angles;
};
/**
* This is an internal class used to record information about an angle.
* @private
*/
class AmoebaAngleForce::AngleInfo {
public:
int particle1, particle2, particle3;
......
plugins/amoeba/openmmapi/include/openmm/AmoebaBondForce.h
View file @ 19d2885a
......@@ -147,6 +147,10 @@ private:
std::vector<BondInfo> bonds;
};
/**
* This is an internal class used to record information about a bond.
* @private
*/
class AmoebaBondForce::BondInfo {
public:
int particle1, particle2;
......
plugins/amoeba/openmmapi/include/openmm/AmoebaGeneralizedKirkwoodForce.h
View file @ 19d2885a
......@@ -174,6 +174,10 @@ private:
std::vector<ParticleInfo> particles;
};
/**
* This is an internal class used to record information about a particle.
* @private
*/
class AmoebaGeneralizedKirkwoodForce::ParticleInfo {
public:
double charge, radius, scalingFactor;
......
plugins/amoeba/openmmapi/include/openmm/AmoebaInPlaneAngleForce.h
View file @ 19d2885a
......@@ -180,6 +180,10 @@ private:
std::vector<AngleInfo> angles;
};
/**
* This is an internal class used to record information about an angle.
* @private
*/
class AmoebaInPlaneAngleForce::AngleInfo {
public:
int particle1, particle2, particle3, particle4;
......
plugins/amoeba/openmmapi/include/openmm/AmoebaMultipoleForce.h
View file @ 19d2885a
......@@ -368,6 +368,10 @@ private:
std::vector<MultipoleInfo> multipoles;
};
/**
* This is an internal class used to record information about a multipole.
* @private
*/
class AmoebaMultipoleForce::MultipoleInfo {
public:
......
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