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Commit 5270f858 authored by Charlles Abreu's avatar Charlles Abreu
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resolved PR #2611 merge conflicts

parents 697ab72e eec9cd69
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Showing with 304 additions and 36 deletions
plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.cpp
View file @ 5270f858
......@@ -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) 2008-2018 Stanford University and the Authors. *
* Portions copyright (c) 2008-2020 Stanford University and the Authors. *
* Authors: Peter Eastman, Mark Friedrichs *
* Contributors: *
* *
......@@ -1782,7 +1782,7 @@ void CudaCalcAmoebaMultipoleForceKernel::ensureMultipolesValid(ContextImpl& cont
}
}
if (!multipolesAreValid)
context.calcForcesAndEnergy(false, false, -1);
context.calcForcesAndEnergy(false, false, context.getIntegrator().getIntegrationForceGroups());
}
......@@ -3650,7 +3650,7 @@ void CudaCalcHippoNonbondedForceKernel::ensureMultipolesValid(ContextImpl& conte
}
}
if (!multipolesAreValid)
context.calcForcesAndEnergy(false, false, -1);
context.calcForcesAndEnergy(false, false, context.getIntegrator().getIntegrationForceGroups());
}
void CudaCalcHippoNonbondedForceKernel::getLabFramePermanentDipoles(ContextImpl& context, vector<Vec3>& dipoles) {
......
plugins/drude/platforms/common/src/CommonDrudeKernels.cpp
View file @ 5270f858
......@@ -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) 2013-2019 Stanford University and the Authors. *
* Portions copyright (c) 2013-2020 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -282,7 +282,7 @@ void CommonIntegrateDrudeLangevinStepKernel::execute(ContextImpl& context, const
if (cc.getUseMixedPrecision())
kernel2->addArg(cc.getPosqCorrection());
else
kernel2->addArg(NULL);
kernel2->addArg(nullptr);
kernel2->addArg(integration.getPosDelta());
kernel2->addArg(cc.getVelm());
kernel2->addArg(integration.getStepSize());
......@@ -290,7 +290,7 @@ void CommonIntegrateDrudeLangevinStepKernel::execute(ContextImpl& context, const
if (cc.getUseMixedPrecision())
hardwallKernel->addArg(cc.getPosqCorrection());
else
hardwallKernel->addArg(NULL);
hardwallKernel->addArg(nullptr);
hardwallKernel->addArg(cc.getVelm());
hardwallKernel->addArg(pairParticles);
hardwallKernel->addArg(integration.getStepSize());
......@@ -516,7 +516,7 @@ static lbfgsfloatval_t evaluate(void *instance, const lbfgsfloatval_t *x, lbfgsf
// Compute the forces and energy for this configuration.
double energy = context.calcForcesAndEnergy(true, true);
double energy = context.calcForcesAndEnergy(true, true, context.getIntegrator().getIntegrationForceGroups());
long long* force = (long long*) cc.getPinnedBuffer();
cc.getLongForceBuffer().download(force);
double forceScale = -1.0/0x100000000;
......
plugins/drude/platforms/opencl/tests/CMakeLists.txt
View file @ 5270f858
......@@ -17,10 +17,10 @@ FOREACH(TEST_PROG ${TEST_PROGS})
ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_DRUDE_TARGET} ${SHARED_TARGET})
SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
ADD_TEST(${TEST_ROOT}Single ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT} single)
ADD_TEST(${TEST_ROOT}Single ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT} single ${OPENCL_TEST_PLATFORM_INDEX} ${OPENCL_TEST_DEVICE_INDEX})
IF (OPENMM_BUILD_OPENCL_DOUBLE_PRECISION_TESTS)
ADD_TEST(${TEST_ROOT}Mixed ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT} mixed)
ADD_TEST(${TEST_ROOT}Double ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT} double)
ADD_TEST(${TEST_ROOT}Mixed ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT} mixed ${OPENCL_TEST_PLATFORM_INDEX} ${OPENCL_TEST_DEVICE_INDEX})
ADD_TEST(${TEST_ROOT}Double ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT} double ${OPENCL_TEST_PLATFORM_INDEX} ${OPENCL_TEST_DEVICE_INDEX})
ENDIF(OPENMM_BUILD_OPENCL_DOUBLE_PRECISION_TESTS)
ENDFOREACH(TEST_PROG ${TEST_PROGS})
plugins/drude/platforms/reference/src/ReferenceDrudeKernels.cpp
View file @ 5270f858
......@@ -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) 2011-2014 Stanford University and the Authors. *
* Portions copyright (c) 2011-2020 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -497,7 +497,7 @@ static lbfgsfloatval_t evaluate(void *instance, const lbfgsfloatval_t *x, lbfgsf
vector<Vec3>& force = extractForces(context);
for (int i = 0; i < numDrudeParticles; i++)
pos[drudeParticles[i]] = Vec3(x[3*i], x[3*i+1], x[3*i+2]);
double energy = context.calcForcesAndEnergy(true, true);
double energy = context.calcForcesAndEnergy(true, true, context.getIntegrator().getIntegrationForceGroups());
for (int i = 0; i < numDrudeParticles; i++) {
Vec3 f = force[drudeParticles[i]];
g[3*i] = -f[0];
......
plugins/rpmd/platforms/cuda/src/CudaRpmdKernels.cpp
View file @ 5270f858
......@@ -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) 2011-2018 Stanford University and the Authors. *
* Portions copyright (c) 2011-2020 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -123,6 +123,7 @@ void CudaIntegrateRPMDStepKernel::initialize(const System& system, const RPMDInt
groupsNotContracted -= 1<<group;
}
}
groupsNotContracted &= integrator.getIntegrationForceGroups();
if (maxContractedCopies > 0) {
contractedForces.initialize<long long>(cu, maxContractedCopies*paddedParticles*3, "rpmdContractedForces");
contractedPositions.initialize(cu, maxContractedCopies*paddedParticles, elementSize, "rpmdContractedPositions");
......
plugins/rpmd/platforms/opencl/src/OpenCLRpmdKernels.cpp
View file @ 5270f858
......@@ -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) 2011-2018 Stanford University and the Authors. *
* Portions copyright (c) 2011-2020 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -103,6 +103,7 @@ void OpenCLIntegrateRPMDStepKernel::initialize(const System& system, const RPMDI
groupsNotContracted -= 1<<group;
}
}
groupsNotContracted &= integrator.getIntegrationForceGroups();
if (maxContractedCopies > 0) {
contractedForces.initialize(cl, maxContractedCopies*paddedParticles, forceElementSize, "rpmdContractedForces");
contractedPositions.initialize(cl, maxContractedCopies*paddedParticles, elementSize, "rpmdContractedPositions");
......
plugins/rpmd/platforms/opencl/tests/CMakeLists.txt
View file @ 5270f858
......@@ -15,10 +15,10 @@ FOREACH(TEST_PROG ${TEST_PROGS})
ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_RPMD_TARGET} ${SHARED_TARGET})
SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
ADD_TEST(${TEST_ROOT}Single ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT} single)
ADD_TEST(${TEST_ROOT}Single ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT} single ${OPENCL_TEST_PLATFORM_INDEX} ${OPENCL_TEST_DEVICE_INDEX})
IF (OPENMM_BUILD_OPENCL_DOUBLE_PRECISION_TESTS)
ADD_TEST(${TEST_ROOT}Mixed ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT} mixed)
ADD_TEST(${TEST_ROOT}Double ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT} double)
ADD_TEST(${TEST_ROOT}Mixed ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT} mixed ${OPENCL_TEST_PLATFORM_INDEX} ${OPENCL_TEST_DEVICE_INDEX})
ADD_TEST(${TEST_ROOT}Double ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT} double ${OPENCL_TEST_PLATFORM_INDEX} ${OPENCL_TEST_DEVICE_INDEX})
ENDIF(OPENMM_BUILD_OPENCL_DOUBLE_PRECISION_TESTS)
ENDFOREACH(TEST_PROG ${TEST_PROGS})
plugins/rpmd/platforms/reference/src/ReferenceRpmdKernels.cpp
View file @ 5270f858
......@@ -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) 2011-2013 Stanford University and the Authors. *
* Portions copyright (c) 2011-2020 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -99,6 +99,7 @@ void ReferenceIntegrateRPMDStepKernel::initialize(const System& system, const RP
groupsNotContracted -= 1<<group;
}
}
groupsNotContracted &= integrator.getIntegrationForceGroups();
// Create workspace for doing contractions.
......
tests/CMakeLists.txt
View file @ 5270f858
......@@ -8,7 +8,7 @@ ENABLE_TESTING()
FILE(GLOB TEST_PROGS "*Test*.cpp")
FOREACH(TEST_PROG ${TEST_PROGS})
GET_FILENAME_COMPONENT(TEST_ROOT ${TEST_PROG} NAME_WE)
IF ((${TEST_ROOT} MATCHES TestVectorize8) AND NOT X86)
IF ((${TEST_ROOT} MATCHES TestVectorizeAvx*) AND NOT X86)
CONTINUE()
ENDIF()
ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
......@@ -21,9 +21,12 @@ FOREACH(TEST_PROG ${TEST_PROGS})
IF((${TEST_ROOT} MATCHES TestVectorize) AND X86 AND NOT MSVC)
SET(EXTRA_TEST_FLAGS "${EXTRA_COMPILE_FLAGS} -msse4.1")
ENDIF()
IF((${TEST_ROOT} MATCHES TestVectorize8) AND X86 AND NOT MSVC)
IF((${TEST_ROOT} MATCHES TestVectorizeAvx) AND X86 AND NOT MSVC)
SET(EXTRA_TEST_FLAGS "${EXTRA_COMPILE_FLAGS} -mavx")
ENDIF()
IF((${TEST_ROOT} MATCHES TestVectorizeAvx2) AND X86 AND NOT MSVC)
SET(EXTRA_TEST_FLAGS "${EXTRA_COMPILE_FLAGS} -mfma -mavx2")
ENDIF()
SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_TEST_FLAGS}")
ADD_TEST(${TEST_ROOT} ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT})
ENDFOREACH(TEST_PROG ${TEST_PROGS})
......
tests/TestBrownianIntegrator.h
View file @ 5270f858
......@@ -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) 2008-2015 Stanford University and the Authors. *
* Portions copyright (c) 2008-2020 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -31,6 +31,7 @@
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "openmm/CustomExternalForce.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/NonbondedForce.h"
#include "openmm/System.h"
......@@ -279,6 +280,31 @@ void testInitialTemperature() {
ASSERT_USUALLY_EQUAL_TOL(targetTemperature, temperature, 0.01);
}
void testForceGroups() {
System system;
system.addParticle(1.0);
BrownianIntegrator integrator(0, 1.0, 0.001);
integrator.setIntegrationForceGroups(1<<1);
CustomExternalForce* f1 = new CustomExternalForce("x");
f1->addParticle(0);
f1->setForceGroup(1);
CustomExternalForce* f2 = new CustomExternalForce("y");
f2->addParticle(0);
f2->setForceGroup(2);
system.addForce(f1);
system.addForce(f2);
Context context(system, integrator, platform);
context.setPositions(vector<Vec3>(1));
// Take one step and verify that the position was updated based only on f1.
integrator.step(1);
Vec3 pos = context.getState(State::Positions).getPositions()[0];
ASSERT(pos[0] < 0);
ASSERT(pos[1] == 0);
ASSERT(pos[2] == 0);
}
void runPlatformTests();
int main(int argc, char* argv[]) {
......@@ -290,6 +316,7 @@ int main(int argc, char* argv[]) {
testConstrainedMasslessParticles();
testRandomSeed();
testInitialTemperature();
testForceGroups();
runPlatformTests();
}
catch(const exception& e) {
......
tests/TestCustomIntegrator.h
View file @ 5270f858
......@@ -597,6 +597,7 @@ void testForceGroups() {
integrator.addComputeGlobal("oute", "energy");
integrator.addComputeGlobal("oute1", "energy1");
integrator.addComputeGlobal("oute2", "energy2");
integrator.setIntegrationForceGroups((1<<1) + (1<<2));
HarmonicBondForce* bonds = new HarmonicBondForce();
bonds->addBond(0, 1, 1.5, 1.1);
bonds->setForceGroup(1);
......@@ -606,6 +607,10 @@ void testForceGroups() {
nb->addParticle(0.2, 1, 0);
nb->setForceGroup(2);
system.addForce(nb);
CustomExternalForce* external = new CustomExternalForce("x");
external->addParticle(0);
external->setForceGroup(3);
system.addForce(external);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(-1, 0, 0);
......@@ -633,13 +638,13 @@ void testForceGroups() {
// Make sure they also match the values returned by the Context.
State s = context.getState(State::Forces | State::Energy, false);
State s = context.getState(State::Forces | State::Energy, false, 6);
State s1 = context.getState(State::Forces | State::Energy, false, 2);
State s2 = context.getState(State::Forces | State::Energy, false, 4);
vector<Vec3> c, c1, c2;
c = context.getState(State::Forces, false).getForces();
c1 = context.getState(State::Forces, false, 2).getForces();
c2 = context.getState(State::Forces, false, 4).getForces();
c = s.getForces();
c1 = s1.getForces();
c2 = s2.getForces();
ASSERT_EQUAL_VEC(f[0], c[0], 1e-5);
ASSERT_EQUAL_VEC(f[1], c[1], 1e-5);
ASSERT_EQUAL_VEC(f1[0], c1[0], 1e-5);
......
tests/TestLangevinIntegrator.h
View file @ 5270f858
......@@ -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) 2008-2016 Stanford University and the Authors. *
* Portions copyright (c) 2008-2020 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -31,6 +31,7 @@
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "openmm/CustomExternalForce.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/NonbondedForce.h"
#include "openmm/System.h"
......@@ -286,6 +287,31 @@ void testInitialTemperature() {
ASSERT_USUALLY_EQUAL_TOL(targetTemperature, temperature, 0.01);
}
void testForceGroups() {
System system;
system.addParticle(1.0);
LangevinIntegrator integrator(0.0, 1.0, 0.01);
integrator.setIntegrationForceGroups(1<<1);
CustomExternalForce* f1 = new CustomExternalForce("x");
f1->addParticle(0);
f1->setForceGroup(1);
CustomExternalForce* f2 = new CustomExternalForce("y");
f2->addParticle(0);
f2->setForceGroup(2);
system.addForce(f1);
system.addForce(f2);
Context context(system, integrator, platform);
context.setPositions(vector<Vec3>(1));
// Take one step and verify that the position was updated based only on f1.
integrator.step(1);
Vec3 pos = context.getState(State::Positions).getPositions()[0];
ASSERT(pos[0] < 0);
ASSERT(pos[1] == 0);
ASSERT(pos[2] == 0);
}
void runPlatformTests();
int main(int argc, char* argv[]) {
......@@ -297,6 +323,7 @@ int main(int argc, char* argv[]) {
testConstrainedMasslessParticles();
testRandomSeed();
testInitialTemperature();
testForceGroups();
runPlatformTests();
}
catch(const exception& e) {
......
tests/TestLangevinMiddleIntegrator.h
View file @ 5270f858
......@@ -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) 2008-2019 Stanford University and the Authors. *
* Portions copyright (c) 2008-2020 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -31,6 +31,7 @@
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "openmm/CustomExternalForce.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/NonbondedForce.h"
#include "openmm/System.h"
......@@ -289,6 +290,31 @@ void testInitialTemperature() {
ASSERT_USUALLY_EQUAL_TOL(targetTemperature, temperature, 0.01);
}
void testForceGroups() {
System system;
system.addParticle(1.0);
LangevinMiddleIntegrator integrator(0.0, 1.0, 0.01);
integrator.setIntegrationForceGroups(1<<1);
CustomExternalForce* f1 = new CustomExternalForce("x");
f1->addParticle(0);
f1->setForceGroup(1);
CustomExternalForce* f2 = new CustomExternalForce("y");
f2->addParticle(0);
f2->setForceGroup(2);
system.addForce(f1);
system.addForce(f2);
Context context(system, integrator, platform);
context.setPositions(vector<Vec3>(1));
// Take one step and verify that the position was updated based only on f1.
integrator.step(1);
Vec3 pos = context.getState(State::Positions).getPositions()[0];
ASSERT(pos[0] < 0);
ASSERT(pos[1] == 0);
ASSERT(pos[2] == 0);
}
void runPlatformTests();
int main(int argc, char* argv[]) {
......@@ -300,6 +326,7 @@ int main(int argc, char* argv[]) {
testConstrainedMasslessParticles();
testRandomSeed();
testInitialTemperature();
testForceGroups();
runPlatformTests();
}
catch(const exception& e) {
......
tests/TestLocalEnergyMinimizer.h
View file @ 5270f858
......@@ -7,7 +7,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2010-2018 Stanford University and the Authors. *
* Portions copyright (c) 2010-2020 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -231,6 +231,34 @@ void testLargeForces() {
ASSERT(maxdist < 10.0);
}
void testForceGroups() {
// Create a system with two forces, only one of which is in the standard
// integration force groups.
System system;
system.addParticle(1.0);
system.addParticle(1.0);
HarmonicBondForce* bonds1 = new HarmonicBondForce();
HarmonicBondForce* bonds2 = new HarmonicBondForce();
system.addForce(bonds1);
system.addForce(bonds2);
bonds1->addBond(0, 1, 2.0, 1);
bonds2->addBond(0, 1, 4.0, 1);
bonds1->setForceGroup(1);
bonds2->setForceGroup(2);
// Minimize it and check that the bond has the correct length.
VerletIntegrator integrator(0.01);
integrator.setIntegrationForceGroups(1<<1);
Context context(system, integrator, platform);
context.setPositions({Vec3(0, 0, 0), Vec3(5, 0, 0)});
LocalEnergyMinimizer::minimize(context, 1e-5);
State state = context.getState(State::Positions);
Vec3 delta = state.getPositions()[0]-state.getPositions()[1];
ASSERT_EQUAL_TOL(2.0, sqrt(delta.dot(delta)), 1e-4);
}
void runPlatformTests();
int main(int argc, char* argv[]) {
......@@ -240,6 +268,7 @@ int main(int argc, char* argv[]) {
testLargeSystem();
testVirtualSites();
testLargeForces();
testForceGroups();
runPlatformTests();
}
catch(const exception& e) {
......
tests/TestNoseHooverIntegrator.h
View file @ 5270f858
......@@ -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 Stanford University and the Authors. *
* Portions copyright (c) 2019-2020 Stanford University and the Authors. *
* Authors: Andreas Krämer and Andrew C. Simmonett *
* Contributors: *
* *
......@@ -510,6 +510,31 @@ void testAPIChangeNumParticles() {
}
void testForceGroups() {
System system;
system.addParticle(1.0);
NoseHooverIntegrator integrator(1, 1.0, 0.001);
integrator.setIntegrationForceGroups(1<<1);
CustomExternalForce* f1 = new CustomExternalForce("x");
f1->addParticle(0);
f1->setForceGroup(1);
CustomExternalForce* f2 = new CustomExternalForce("y");
f2->addParticle(0);
f2->setForceGroup(2);
system.addForce(f1);
system.addForce(f2);
Context context(system, integrator, platform);
context.setPositions(vector<Vec3>(1));
// Take one step and verify that the position was updated based only on f1.
integrator.step(1);
Vec3 pos = context.getState(State::Positions).getPositions()[0];
ASSERT(pos[0] < 0);
ASSERT(pos[1] == 0);
ASSERT(pos[2] == 0);
}
void runPlatformTests();
int main(int argc, char* argv[]) {
......@@ -528,6 +553,7 @@ int main(int argc, char* argv[]) {
constrain = false; testDimerBox(constrain);
constrain = true; testDimerBox(constrain);
testCheckpoints();
testForceGroups();
runPlatformTests();
}
catch(const exception& e) {
......
tests/TestVariableLangevinIntegrator.h
View file @ 5270f858
......@@ -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) 2008-2016 Stanford University and the Authors. *
* Portions copyright (c) 2008-2020 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -31,6 +31,7 @@
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "openmm/CustomExternalForce.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/NonbondedForce.h"
#include "openmm/System.h"
......@@ -358,6 +359,31 @@ void testInitialTemperature() {
ASSERT_USUALLY_EQUAL_TOL(targetTemperature, temperature, 0.01);
}
void testForceGroups() {
System system;
system.addParticle(1.0);
VariableLangevinIntegrator integrator(0.0, 1.0, 1e-5);
integrator.setIntegrationForceGroups(1<<1);
CustomExternalForce* f1 = new CustomExternalForce("x");
f1->addParticle(0);
f1->setForceGroup(1);
CustomExternalForce* f2 = new CustomExternalForce("y");
f2->addParticle(0);
f2->setForceGroup(2);
system.addForce(f1);
system.addForce(f2);
Context context(system, integrator, platform);
context.setPositions(vector<Vec3>(1));
// Take one step and verify that the position was updated based only on f1.
integrator.step(1);
Vec3 pos = context.getState(State::Positions).getPositions()[0];
ASSERT(pos[0] < 0);
ASSERT(pos[1] == 0);
ASSERT(pos[2] == 0);
}
void runPlatformTests();
int main(int argc, char* argv[]) {
......@@ -370,6 +396,7 @@ int main(int argc, char* argv[]) {
testRandomSeed();
testArgonBox();
testInitialTemperature();
testForceGroups();
runPlatformTests();
}
catch(const exception& e) {
......
tests/TestVariableVerletIntegrator.h
View file @ 5270f858
......@@ -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) 2008-2015 Stanford University and the Authors. *
* Portions copyright (c) 2008-2020 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -31,6 +31,7 @@
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "openmm/CustomExternalForce.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/NonbondedForce.h"
#include "openmm/System.h"
......@@ -337,6 +338,31 @@ void testInitialTemperature() {
ASSERT_USUALLY_EQUAL_TOL(targetTemperature, temperature, 0.01);
}
void testForceGroups() {
System system;
system.addParticle(1.0);
VariableVerletIntegrator integrator(0.001);
integrator.setIntegrationForceGroups(1<<1);
CustomExternalForce* f1 = new CustomExternalForce("x");
f1->addParticle(0);
f1->setForceGroup(1);
CustomExternalForce* f2 = new CustomExternalForce("y");
f2->addParticle(0);
f2->setForceGroup(2);
system.addForce(f1);
system.addForce(f2);
Context context(system, integrator, platform);
context.setPositions(vector<Vec3>(1));
// Take one step and verify that the position was updated based only on f1.
integrator.step(1);
Vec3 pos = context.getState(State::Positions).getPositions()[0];
ASSERT(pos[0] < 0);
ASSERT(pos[1] == 0);
ASSERT(pos[2] == 0);
}
void runPlatformTests();
int main(int argc, char* argv[]) {
......@@ -348,6 +374,7 @@ int main(int argc, char* argv[]) {
testConstrainedMasslessParticles();
testArgonBox();
testInitialTemperature();
testForceGroups();
runPlatformTests();
}
catch(const exception& e) {
......
tests/TestVectorize8.cpp → tests/TestVectorizeAvx.cpp
View file @ 5270f858
......@@ -34,7 +34,7 @@
*/
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/internal/vectorize8.h"
#include "openmm/internal/vectorizeAvx.h"
#include <iostream>
#include "TestVectorizeGeneric.h"
......
tests/TestVectorizeAvx2.cpp 0 → 100644
View file @ 5270f858
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2014-2015 Stanford University and the Authors. *
* Authors: Daniel Towner *
* Contributors: *
* *
* 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. *
* -------------------------------------------------------------------------- */
/**
* This tests vectorized operations.
*/
#include "openmm/internal/AssertionUtilities.h"
#include <iostream>
#ifndef __AVX2__
int main () {
std::cout << "AVX2 CPU is not supported. Exiting." << std::endl;
return 0;
}
#else
#include "openmm/internal/vectorizeAvx2.h"
#include "TestVectorizeGeneric.h"
using namespace OpenMM;
int main(int argc, char* argv[]) {
try {
if (!isAvx2Supported()) {
std::cout << "CPU is not supported. Exiting." << std::endl;
return 0;
}
TestFvec<fvecAvx2>::testAll();
}
catch(const std::exception& e) {
std::cout << "exception: " << e.what() << std::endl;
return 1;
}
std::cout << "Done" << std::endl;
return 0;
}
#endif
\ No newline at end of file
tests/TestVectorizeGeneric.h
View file @ 5270f858
......@@ -338,12 +338,10 @@ void TestFvec<FVEC>::testBinaryOps() const {
ASSERT_VEC_ALMOST_EQUAL(f / v0, applyBinaryFn(fdup, v0, std::divides<float>()));
// Binary functions.
using std::min;
using std::max;
ASSERT_VEC_EQUAL(min(v0, v1),
applyBinaryFn(v0, v1, [](float x, float y) { return min(x, y); }));
applyBinaryFn(v0, v1, [](float x, float y) { return std::min<float>(x, y); }));
ASSERT_VEC_EQUAL(max(v0, v1),
applyBinaryFn(v0, v1, [](float x, float y) { return max(x, y); }));
applyBinaryFn(v0, v1, [](float x, float y) { return std::max<float>(x, y); }));
}
template<typename FVEC>
......
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