Merge pull request #1557 from andysim/dpme

Dispersion PME

plugins/amoeba/platforms/reference/src/AmoebaReferenceKernels.cpp

@@ -602,7 +602,7 @@ void ReferenceCalcAmoebaMultipoleForceKernel::initialize(const System& system, c
             nb.setEwaldErrorTolerance(force.getEwaldErrorTolerance());
             nb.setCutoffDistance(force.getCutoffDistance());
             int gridSizeX, gridSizeY, gridSizeZ;
-            NonbondedForceImpl::calcPMEParameters(system, nb, alphaEwald, gridSizeX, gridSizeY, gridSizeZ);
+            NonbondedForceImpl::calcPMEParameters(system, nb, alphaEwald, gridSizeX, gridSizeY, gridSizeZ, false);
             pmeGridDimension[0] = gridSizeX;
             pmeGridDimension[1] = gridSizeY;
             pmeGridDimension[2] = gridSizeZ;

plugins/cpupme/src/CpuPmeKernelFactory.cpp

@@ -55,5 +55,7 @@ extern "C" OPENMM_EXPORT_PME void registerPlatforms() {
 KernelImpl* CpuPmeKernelFactory::createKernelImpl(std::string name, const Platform& platform, ContextImpl& context) const {
     if (name == CalcPmeReciprocalForceKernel::Name())
         return new CpuCalcPmeReciprocalForceKernel(name, platform);
+    if (name == CalcDispersionPmeReciprocalForceKernel::Name())
+        return new CpuCalcDispersionPmeReciprocalForceKernel(name, platform);
     throw OpenMMException((std::string("Tried to create kernel with illegal kernel name '")+name+"'").c_str());
 }

plugins/cpupme/src/CpuPmeKernels.h

@@ -133,6 +133,98 @@ private:
     gmx_atomic_t atomicCounter;
 };
 
+
+
+/**
+ * This is an optimized CPU implementation of CalcDispersionPmeReciprocalForceKernel.  It is both
+ * vectorized (requiring SSE 4.1) and multithreaded.  It uses FFTW to perform the FFTs.
+ */
+
+class OPENMM_EXPORT_PME CpuCalcDispersionPmeReciprocalForceKernel : public CalcPmeReciprocalForceKernel {
+public:
+    CpuCalcDispersionPmeReciprocalForceKernel(std::string name, const Platform& platform) : CalcPmeReciprocalForceKernel(name, platform),
+            hasCreatedPlan(false), isDeleted(false), realGrid(NULL), complexGrid(NULL)  {
+    }
+    /**
+     * Initialize the kernel.
+     * 
+     * @param gridx        the x size of the PME grid
+     * @param gridy        the y size of the PME grid
+     * @param gridz        the z size of the PME grid
+     * @param numParticles the number of particles in the system
+     * @param alpha        the Ewald blending parameter
+     */
+    void initialize(int xsize, int ysize, int zsize, int numParticles, double alpha);
+    ~CpuCalcDispersionPmeReciprocalForceKernel();
+    /**
+     * Begin computing the force and energy.
+     * 
+     * @param io                  an object that coordinates data transfer
+     * @param periodicBoxVectors  the vectors defining the periodic box (measured in nm)
+     * @param includeEnergy       true if potential energy should be computed
+     */
+    void beginComputation(IO& io, const Vec3* periodicBoxVectors, bool includeEnergy);
+    /**
+     * Finish computing the force and energy.
+     * 
+     * @param io   an object that coordinates data transfer
+     * @return the potential energy due to the PME reciprocal space interactions
+     */
+    double finishComputation(IO& io);
+    /**
+     * This routine contains the code executed by the main thread.
+     */
+    void runMainThread();
+    /**
+     * This routine contains the code executed by each worker thread.
+     */
+    void runWorkerThread(ThreadPool& threads, int index);
+    /**
+     * Get whether the current CPU supports all features needed by this kernel.
+     */
+    static bool isProcessorSupported();
+    /**
+     * Get the parameters being used for PME.
+     * 
+     * @param alpha   the separation parameter
+     * @param nx      the number of grid points along the X axis
+     * @param ny      the number of grid points along the Y axis
+     * @param nz      the number of grid points along the Z axis
+     */
+    void getPMEParameters(double& alpha, int& nx, int& ny, int& nz) const;
+private:
+    class ComputeTask;
+    /**
+     * Select a size for one grid dimension that FFTW can handle efficiently.
+     */
+    int findFFTDimension(int minimum, bool isZ);
+    static bool hasInitializedThreads;
+    static int numThreads;
+    int gridx, gridy, gridz, numParticles;
+    double alpha;
+    bool hasCreatedPlan, isFinished, isDeleted;
+    std::vector<float> force;
+    std::vector<float> bsplineModuli[3];
+    std::vector<float> recipEterm;
+    Vec3 lastBoxVectors[3];
+    std::vector<float> threadEnergy;
+    std::vector<float*> tempGrid;
+    float* realGrid;
+    fftwf_complex* complexGrid;
+    fftwf_plan forwardFFT, backwardFFT;
+    int waitCount;
+    pthread_cond_t startCondition, endCondition;
+    pthread_mutex_t lock;
+    pthread_t mainThread;
+    // The following variables are used to store information about the calculation currently being performed.
+    IO* io;
+    float energy;
+    float* posq;
+    Vec3 periodicBoxVectors[3], recipBoxVectors[3];
+    bool includeEnergy;
+    gmx_atomic_t atomicCounter;
+};
+
 } // namespace OpenMM
 
 #endif /*OPENMM_CPU_PME_KERNELS_H_*/

serialization/src/NonbondedForceProxy.cpp

@@ -42,7 +42,7 @@ NonbondedForceProxy::NonbondedForceProxy() : SerializationProxy("NonbondedForce"
 }
 
 void NonbondedForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 1);
+    node.setIntProperty("version", 2);
     const NonbondedForce& force = *reinterpret_cast<const NonbondedForce*>(object);
     node.setIntProperty("forceGroup", force.getForceGroup());
     node.setIntProperty("method", (int) force.getNonbondedMethod());
@@ -59,6 +59,11 @@ void NonbondedForceProxy::serialize(const void* object, SerializationNode& node)
     node.setIntProperty("nx", nx);
     node.setIntProperty("ny", ny);
     node.setIntProperty("nz", nz);
+    force.getLJPMEParameters(alpha, nx, ny, nz);
+    node.setDoubleProperty("ljAlpha", alpha);
+    node.setIntProperty("ljnx", nx);
+    node.setIntProperty("ljny", ny);
+    node.setIntProperty("ljnz", nz);
     node.setIntProperty("recipForceGroup", force.getReciprocalSpaceForceGroup());
     SerializationNode& particles = node.createChildNode("Particles");
     for (int i = 0; i < force.getNumParticles(); i++) {
@@ -76,7 +81,8 @@ void NonbondedForceProxy::serialize(const void* object, SerializationNode& node)
 }
 
 void* NonbondedForceProxy::deserialize(const SerializationNode& node) const {
-    if (node.getIntProperty("version") != 1)
+    int version = node.getIntProperty("version");
+    if (version < 1 || version > 2)
         throw OpenMMException("Unsupported version number");
     NonbondedForce* force = new NonbondedForce();
     try {
@@ -93,6 +99,13 @@ void* NonbondedForceProxy::deserialize(const SerializationNode& node) const {
         int ny = node.getIntProperty("ny", 0);
         int nz = node.getIntProperty("nz", 0);
         force->setPMEParameters(alpha, nx, ny, nz);
+        if (version >= 2) {
+            alpha = node.getDoubleProperty("ljAlpha", 0.0);
+            nx = node.getIntProperty("ljnx", 0);
+            ny = node.getIntProperty("ljny", 0);
+            nz = node.getIntProperty("ljnz", 0);
+            force->setLJPMEParameters(alpha, nx, ny, nz);
+        }
         force->setReciprocalSpaceForceGroup(node.getIntProperty("recipForceGroup", -1));
         const SerializationNode& particles = node.getChildNode("Particles");
         for (int i = 0; i < (int) particles.getChildren().size(); i++) {

serialization/tests/TestSerializeNonbondedForce.cpp

@@ -53,6 +53,9 @@ void testSerialization() {
     double alpha = 0.5;
     int nx = 3, ny = 5, nz = 7;
     force.setPMEParameters(alpha, nx, ny, nz);
+    double dalpha = 0.8;
+    int dnx = 4, dny = 6, dnz = 7;
+    force.setLJPMEParameters(dalpha, dnx, dny, dnz);
     force.addParticle(1, 0.1, 0.01);
     force.addParticle(0.5, 0.2, 0.02);
     force.addParticle(-0.5, 0.3, 0.03);
@@ -84,6 +87,13 @@ void testSerialization() {
     ASSERT_EQUAL(nx, nx2);
     ASSERT_EQUAL(ny, ny2);
     ASSERT_EQUAL(nz, nz2);    
+    double dalpha2;
+    int dnx2, dny2, dnz2;
+    force2.getLJPMEParameters(dalpha2, dnx2, dny2, dnz2);
+    ASSERT_EQUAL(dalpha, dalpha2);
+    ASSERT_EQUAL(dnx, dnx2);
+    ASSERT_EQUAL(dny, dny2);
+    ASSERT_EQUAL(dnz, dnz2);    
     for (int i = 0; i < force.getNumParticles(); i++) {
         double charge1, sigma1, epsilon1;
         double charge2, sigma2, epsilon2;

tests/TestEwald.h

@@ -365,7 +365,7 @@ void testErrorTolerance(NonbondedForce::NonbondedMethod method) {
 
                 double expectedAlpha, actualAlpha;
                 int expectedSize[3], actualSize[3];
-                NonbondedForceImpl::calcPMEParameters(system, *force, expectedAlpha, expectedSize[0], expectedSize[1], expectedSize[2]);
+                NonbondedForceImpl::calcPMEParameters(system, *force, expectedAlpha, expectedSize[0], expectedSize[1], expectedSize[2], false);
                 force->getPMEParametersInContext(context, actualAlpha, actualSize[0], actualSize[1], actualSize[2]);
                 ASSERT_EQUAL_TOL(expectedAlpha, actualAlpha, 1e-5);
                 for (int i = 0; i < 3; i++) {

tests/TestNonbondedForce.h

@@ -39,6 +39,7 @@
 #include "SimTKOpenMMRealType.h"
 #include "sfmt/SFMT.h"
 #include <iostream>
+#include <iomanip>
 #include <vector>
 
 using namespace OpenMM;

wrappers/python/simtk/openmm/app/__init__.py

@@ -40,6 +40,7 @@ CutoffNonPeriodic = forcefield.CutoffNonPeriodic
 CutoffPeriodic = forcefield.CutoffPeriodic
 Ewald = forcefield.Ewald
 PME = forcefield.PME
+LJPME = forcefield.LJPME
 
 HBonds = forcefield.HBonds
 AllBonds = forcefield.AllBonds

wrappers/python/simtk/openmm/app/amberprmtopfile.py

@@ -169,7 +169,7 @@ class AmberPrmtopFile(object):
         ----------
         nonbondedMethod : object=NoCutoff
             The method to use for nonbonded interactions.  Allowed values are
-            NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, or PME.
+            NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, PME, or LJPME.
         nonbondedCutoff : distance=1*nanometer
             The cutoff distance to use for nonbonded interactions
         constraints : object=None
@@ -202,7 +202,7 @@ class AmberPrmtopFile(object):
             added to a hydrogen is subtracted from the heavy atom to keep their
             total mass the same.
         ewaldErrorTolerance : float=0.0005
-            The error tolerance to use if nonbondedMethod is Ewald or PME.
+            The error tolerance to use if nonbondedMethod is Ewald, PME, or LJPME.
         switchDistance : float=0*nanometers
             The distance at which the potential energy switching function is
             turned on for Lennard-Jones interactions. If the switchDistance is 0
@@ -222,10 +222,11 @@ class AmberPrmtopFile(object):
                      ff.CutoffNonPeriodic:'CutoffNonPeriodic',
                      ff.CutoffPeriodic:'CutoffPeriodic',
                      ff.Ewald:'Ewald',
-                     ff.PME:'PME'}
+                     ff.PME:'PME',
+                     ff.LJPME:'LJPME'}
         if nonbondedMethod not in methodMap:
             raise ValueError('Illegal value for nonbonded method')
-        if not self._prmtop.getIfBox() and nonbondedMethod in (ff.CutoffPeriodic, ff.Ewald, ff.PME):
+        if not self._prmtop.getIfBox() and nonbondedMethod in (ff.CutoffPeriodic, ff.Ewald, ff.PME, ff.LJPME):
             raise ValueError('Illegal nonbonded method for a non-periodic system')
         constraintMap = {None:None,
                          ff.HBonds:'h-bonds',

wrappers/python/simtk/openmm/app/charmmpsffile.py

@@ -690,7 +690,7 @@ class CharmmPsfFile(object):
             The parameter set to use to parametrize this molecule
         nonbondedMethod : object=NoCutoff
             The method to use for nonbonded interactions. Allowed values are
-            NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, or PME.
+            NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, PME, or LJPME.
         nonbondedCutoff : distance=1*nanometer
             The cutoff distance to use for nonbonded interactions.
         switchDistance : distance=0*nanometer
@@ -728,7 +728,7 @@ class CharmmPsfFile(object):
             added to a hydrogen is subtracted from the heavy atom to keep their
             total mass the same.
         ewaldErrorTolerance : float=0.0005
-            The error tolerance to use if the nonbonded method is Ewald or PME.
+            The error tolerance to use if the nonbonded method is Ewald, PME, or LJPME.
         flexibleConstraints : bool=True
             Are our constraints flexible or not?
         verbose : bool=False
@@ -746,10 +746,10 @@ class CharmmPsfFile(object):
                 cutoff = cutoff.value_in_unit(u.nanometers)
 
         if nonbondedMethod not in (ff.NoCutoff, ff.CutoffNonPeriodic,
-                                   ff.CutoffPeriodic, ff.Ewald, ff.PME):
+                                   ff.CutoffPeriodic, ff.Ewald, ff.PME, ff.LJPME):
             raise ValueError('Illegal value for nonbonded method')
         if not hasbox and nonbondedMethod in (ff.CutoffPeriodic,
-                                              ff.Ewald, ff.PME):
+                                              ff.Ewald, ff.PME, ff.LJPME):
             raise ValueError('Illegal nonbonded method for a '
                              'non-periodic system')
         if implicitSolvent not in (HCT, OBC1, OBC2, GBn, GBn2, None):
@@ -1009,6 +1009,8 @@ class CharmmPsfFile(object):
                 force.setNonbondedMethod(mm.NonbondedForce.Ewald)
             elif nonbondedMethod is ff.PME:
                 force.setNonbondedMethod(mm.NonbondedForce.PME)
+            elif nonbondedMethod is ff.LJPME:
+                force.setNonbondedMethod(mm.NonbondedForce.LJPME)
             else:
                 raise ValueError('Cutoff method is not understood')
 
@@ -1088,8 +1090,7 @@ class CharmmPsfFile(object):
                     mm.Discrete2DFunction(num_lj_types, num_lj_types, bcoef))
             cforce.addPerParticleParameter('type')
             cforce.setForceGroup(self.NONBONDED_FORCE_GROUP)
-            if (nonbondedMethod is ff.PME or nonbondedMethod is ff.Ewald or
-                        nonbondedMethod is ff.CutoffPeriodic):
+            if (nonbondedMethod in (ff.PME, ff.LJPME, ff.Ewald, ff.CutoffPeriodic)):
                 cforce.setNonbondedMethod(cforce.CutoffPeriodic)
                 cforce.setCutoffDistance(nonbondedCutoff)
                 cforce.setUseLongRangeCorrection(True)

wrappers/python/simtk/openmm/app/desmonddmsfile.py

@@ -165,11 +165,11 @@ class DesmondDMSFile(object):
         ----------
         nonbondedMethod : object=NoCutoff
             The method to use for nonbonded interactions.  Allowed values are
-            NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, or PME.
+            NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, PME, or LJPME.
         nonbondedCutoff : distance=1*nanometer
             The cutoff distance to use for nonbonded interactions
         ewaldErrorTolerance : float=0.0005
-            The error tolerance to use if nonbondedMethod is Ewald or PME.
+            The error tolerance to use if nonbondedMethod is Ewald, PME, or LJPME.
         removeCMMotion : boolean=True
             If true, a CMMotionRemover will be added to the System
         hydrogenMass : mass=None
@@ -185,7 +185,7 @@ class DesmondDMSFile(object):
         boxSize = self.topology.getUnitCellDimensions()
         if boxSize is not None:
             sys.setDefaultPeriodicBoxVectors((boxSize[0], 0, 0), (0, boxSize[1], 0), (0, 0, boxSize[2]))
-        elif nonbondedMethod in (ff.CutoffPeriodic, ff.Ewald, ff.PME):
+        elif nonbondedMethod in (ff.CutoffPeriodic, ff.Ewald, ff.PME, ff.LJPME):
             raise ValueError('Illegal nonbonded method for a non-periodic system')
 
         # Create all of the particles
@@ -207,7 +207,8 @@ class DesmondDMSFile(object):
                      ff.CutoffNonPeriodic:mm.NonbondedForce.CutoffNonPeriodic,
                      ff.CutoffPeriodic:mm.NonbondedForce.CutoffPeriodic,
                      ff.Ewald:mm.NonbondedForce.Ewald,
-                     ff.PME:mm.NonbondedForce.PME}
+                     ff.PME:mm.NonbondedForce.PME,
+                     ff.LJPME:mm.NonbondedForce.LJPME}
         nb.setNonbondedMethod(methodMap[nonbondedMethod])
         nb.setCutoffDistance(nonbondedCutoff)
         nb.setEwaldErrorTolerance(ewaldErrorTolerance)

wrappers/python/simtk/openmm/app/forcefield.py

@@ -115,6 +115,11 @@ class PME(Singleton):
         return 'PME'
 PME = PME()
 
+class LJPME(Singleton):
+    def __repr__(self):
+        return 'LJPME'
+LJPME = LJPME()
+
 # Enumerated values for constraint type
 
 class HBonds(Singleton):
@@ -971,7 +976,7 @@ class ForceField(object):
             The Topology for which to create a System
         nonbondedMethod : object=NoCutoff
             The method to use for nonbonded interactions.  Allowed values are
-            NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, or PME.
+            NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, PME, or LJPME.
         nonbondedCutoff : distance=1*nanometer
             The cutoff distance to use for nonbonded interactions
         constraints : object=None
@@ -2195,7 +2200,8 @@ class NonbondedGenerator(object):
                      CutoffNonPeriodic:mm.NonbondedForce.CutoffNonPeriodic,
                      CutoffPeriodic:mm.NonbondedForce.CutoffPeriodic,
                      Ewald:mm.NonbondedForce.Ewald,
-                     PME:mm.NonbondedForce.PME}
+                     PME:mm.NonbondedForce.PME,
+                     LJPME:mm.NonbondedForce.LJPME}
         if nonbondedMethod not in methodMap:
             raise ValueError('Illegal nonbonded method for NonbondedForce')
         force = mm.NonbondedForce()
@@ -2307,7 +2313,7 @@ class LennardJonesGenerator(object):
         self.force.addTabulatedFunction('acoef', mm.Discrete2DFunction(numLjTypes, numLjTypes, acoef))
         self.force.addTabulatedFunction('bcoef', mm.Discrete2DFunction(numLjTypes, numLjTypes, bcoef))
         self.force.addPerParticleParameter('type')
-        if nonbondedMethod in [CutoffPeriodic, Ewald, PME]:
+        if nonbondedMethod in [CutoffPeriodic, Ewald, PME, LJPME]:
             self.force.setNonbondedMethod(mm.CustomNonbondedForce.CutoffPeriodic)
         elif nonbondedMethod is NoCutoff:
             self.force.setNonbondedMethod(mm.CustomNonbondedForce.NoCutoff)

wrappers/python/simtk/openmm/app/gromacstopfile.py

@@ -552,7 +552,7 @@ class GromacsTopFile(object):
         ----------
         nonbondedMethod : object=NoCutoff
             The method to use for nonbonded interactions.  Allowed values are
-            NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, or PME.
+            NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, PME, or LJPME.
         nonbondedCutoff : distance=1*nanometer
             The cutoff distance to use for nonbonded interactions
         constraints : object=None
@@ -570,7 +570,7 @@ class GromacsTopFile(object):
             The solvent dielectric constant to use in the implicit solvent
             model.
         ewaldErrorTolerance : float=0.0005
-            The error tolerance to use if nonbondedMethod is Ewald or PME.
+            The error tolerance to use if nonbondedMethod is Ewald, PME, or LJPME.
         removeCMMotion : boolean=True
             If true, a CMMotionRemover will be added to the System
         hydrogenMass : mass=None
@@ -589,7 +589,7 @@ class GromacsTopFile(object):
         boxVectors = self.topology.getPeriodicBoxVectors()
         if boxVectors is not None:
             sys.setDefaultPeriodicBoxVectors(*boxVectors)
-        elif nonbondedMethod in (ff.CutoffPeriodic, ff.Ewald, ff.PME):
+        elif nonbondedMethod in (ff.CutoffPeriodic, ff.Ewald, ff.PME, ff.LJPME):
             raise ValueError('Illegal nonbonded method for a non-periodic system')
         nb = mm.NonbondedForce()
         sys.addForce(nb)
@@ -877,7 +877,8 @@ class GromacsTopFile(object):
                      ff.CutoffNonPeriodic:mm.NonbondedForce.CutoffNonPeriodic,
                      ff.CutoffPeriodic:mm.NonbondedForce.CutoffPeriodic,
                      ff.Ewald:mm.NonbondedForce.Ewald,
-                     ff.PME:mm.NonbondedForce.PME}
+                     ff.PME:mm.NonbondedForce.PME,
+                     ff.LJPME:mm.NonbondedForce.LJPME}
         nb.setNonbondedMethod(methodMap[nonbondedMethod])
         nb.setCutoffDistance(nonbondedCutoff)
         nb.setEwaldErrorTolerance(ewaldErrorTolerance)

wrappers/python/simtk/openmm/app/internal/amber_file_parser.py

@@ -776,6 +776,8 @@ def readAmberSystem(topology, prmtop_filename=None, prmtop_loader=None, shake=No
             force.setNonbondedMethod(mm.NonbondedForce.Ewald)
         elif nonbondedMethod == 'PME':
             force.setNonbondedMethod(mm.NonbondedForce.PME)
+        elif nonbondedMethod == 'LJPME':
+            force.setNonbondedMethod(mm.NonbondedForce.LJPME)
         else:
             raise Exception("Cutoff method not understood.")
 
@@ -885,7 +887,7 @@ def readAmberSystem(topology, prmtop_filename=None, prmtop_loader=None, shake=No
             ii, jj, chg, sig, eps = force.getExceptionParameters(i)
             cforce.addExclusion(ii, jj)
         # Now set the various properties based on the NonbondedForce object
-        if nonbondedMethod in ('PME', 'Ewald', 'CutoffPeriodic'):
+        if nonbondedMethod in ('PME', 'LJPME', 'Ewald', 'CutoffPeriodic'):
             cforce.setNonbondedMethod(cforce.CutoffPeriodic)
             cforce.setCutoffDistance(nonbondedCutoff)
             cforce.setUseLongRangeCorrection(True)

wrappers/python/tests/TestAPIUnits.py

@@ -186,6 +186,8 @@ class TestAPIUnits(unittest.TestCase):
         self.assertTrue(force.usesPeriodicBoundaryConditions())
         force.setNonbondedMethod(NonbondedForce.PME)
         self.assertTrue(force.usesPeriodicBoundaryConditions())
+        force.setNonbondedMethod(NonbondedForce.LJPME)
+        self.assertTrue(force.usesPeriodicBoundaryConditions())
 
     def testCmapForce(self):
         """ Tests the CMAPTorsionForce API features """

wrappers/python/tests/TestAmberPrmtopFile.py

@@ -21,12 +21,14 @@ class TestAmberPrmtopFile(unittest.TestCase):
     """Test the AmberPrmtopFile.createSystem() method."""
 
     def test_NonbondedMethod(self):
-        """Test all five options for the nonbondedMethod parameter."""
+        """Test all six options for the nonbondedMethod parameter."""
 
         methodMap = {NoCutoff:NonbondedForce.NoCutoff,
                      CutoffNonPeriodic:NonbondedForce.CutoffNonPeriodic,
                      CutoffPeriodic:NonbondedForce.CutoffPeriodic,
-                     Ewald:NonbondedForce.Ewald, PME: NonbondedForce.PME}
+                     Ewald:NonbondedForce.Ewald,
+                     PME:NonbondedForce.PME,
+                     LJPME:NonbondedForce.LJPME}
         for method in methodMap:
             system = prmtop1.createSystem(nonbondedMethod=method)
             forces = system.getForces()
@@ -37,7 +39,7 @@ class TestAmberPrmtopFile(unittest.TestCase):
     def test_Cutoff(self):
         """Test to make sure the nonbondedCutoff parameter is passed correctly."""
 
-        for method in [CutoffNonPeriodic, CutoffPeriodic, Ewald, PME]:
+        for method in [CutoffNonPeriodic, CutoffPeriodic, Ewald, PME, LJPME]:
             system = prmtop1.createSystem(nonbondedMethod=method,
                                           nonbondedCutoff=2*nanometer,
                                           constraints=HBonds)
@@ -51,7 +53,7 @@ class TestAmberPrmtopFile(unittest.TestCase):
     def test_EwaldErrorTolerance(self):
         """Test to make sure the ewaldErrorTolerance parameter is passed correctly."""
 
-        for method in [Ewald, PME]:
+        for method in [Ewald, PME, LJPME]:
             system = prmtop1.createSystem(nonbondedMethod=method,
                                           ewaldErrorTolerance=1e-6,
                                           constraints=HBonds)

wrappers/python/tests/TestDesmondDMSFile.py

@@ -14,12 +14,14 @@ class TestDesmondDMSFile(unittest.TestCase):
         self.dms = DesmondDMSFile(path)
     
     def test_NonbondedMethod(self):
-        """Test all five options for the nonbondedMethod parameter."""
+        """Test all six options for the nonbondedMethod parameter."""
 
         methodMap = {NoCutoff:NonbondedForce.NoCutoff, 
                      CutoffNonPeriodic:NonbondedForce.CutoffNonPeriodic, 
                      CutoffPeriodic:NonbondedForce.CutoffPeriodic, 
-                     Ewald:NonbondedForce.Ewald, PME: NonbondedForce.PME}
+                     Ewald:NonbondedForce.Ewald,
+                     PME:NonbondedForce.PME,
+                     LJPME:NonbondedForce.LJPME}
         for method in methodMap:
             system = self.dms.createSystem(nonbondedMethod=method)
             forces = system.getForces()
@@ -30,7 +32,7 @@ class TestDesmondDMSFile(unittest.TestCase):
     def test_Cutoff(self):
         """Test to make sure the nonbondedCutoff parameter is passed correctly."""
 
-        for method in [CutoffNonPeriodic, CutoffPeriodic, Ewald, PME]:
+        for method in [CutoffNonPeriodic, CutoffPeriodic, Ewald, PME, LJPME]:
             system = self.dms.createSystem(nonbondedMethod=method, 
                                             nonbondedCutoff=2*nanometer)
             cutoff_distance = 0.0*nanometer
@@ -43,7 +45,7 @@ class TestDesmondDMSFile(unittest.TestCase):
     def test_EwaldErrorTolerance(self):
         """Test to make sure the ewaldErrorTolerance parameter is passed correctly."""
 
-        for method in [Ewald, PME]:
+        for method in [Ewald, PME, LJPME]:
             system = self.dms.createSystem(nonbondedMethod=method,
                                             ewaldErrorTolerance=1e-6)
             tolerance = 0