Skip to content

GitLab

Commit c9fcabb5 authored by Peter Eastman's avatar Peter Eastman
Browse files

More updates to dispersion PME

parent c274f08d
Show whitespace changes
Inline Side-by-side
Showing with 89 additions and 42 deletions
openmmapi/include/openmm/NonbondedForce.h
View file @ c9fcabb5
......@@ -412,7 +412,8 @@ public:
bool usesPeriodicBoundaryConditions() const {
return nonbondedMethod == NonbondedForce::CutoffPeriodic ||
nonbondedMethod == NonbondedForce::Ewald ||
nonbondedMethod == NonbondedForce::PME;
nonbondedMethod == NonbondedForce::PME ||
nonbondedMethod == NonbondedForce::LJPME;
}
protected:
ForceImpl* createImpl() const;
......
openmmapi/src/NonbondedForceImpl.cpp
View file @ c9fcabb5
......@@ -90,7 +90,7 @@ void NonbondedForceImpl::initialize(ContextImpl& context) {
exceptions[particle1].insert(particle2);
exceptions[particle2].insert(particle1);
}
if (owner.getNonbondedMethod() != NonbondedForce::NoCutoff) {
if (owner.getNonbondedMethod() != NonbondedForce::NoCutoff && owner.getNonbondedMethod() != NonbondedForce::CutoffNonPeriodic) {
Vec3 boxVectors[3];
system.getDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
double cutoff = owner.getCutoffDistance();
......
serialization/src/NonbondedForceProxy.cpp
View file @ c9fcabb5
......@@ -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
View file @ c9fcabb5
......@@ -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;
......
wrappers/python/simtk/openmm/app/__init__.py
View file @ c9fcabb5
......@@ -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
View file @ c9fcabb5
......@@ -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
View file @ c9fcabb5
......@@ -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
View file @ c9fcabb5
......@@ -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
View file @ c9fcabb5
......@@ -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
View file @ c9fcabb5
......@@ -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
View file @ c9fcabb5
......@@ -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
View file @ c9fcabb5
......@@ -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
View file @ c9fcabb5
......@@ -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
View file @ c9fcabb5
......@@ -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
......
wrappers/python/tests/TestForceField.py
View file @ c9fcabb5
......@@ -33,12 +33,14 @@ class TestForceField(unittest.TestCase):
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.forcefield1.createSystem(self.pdb1.topology,
nonbondedMethod=method)
......@@ -62,7 +64,7 @@ class TestForceField(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.forcefield1.createSystem(self.pdb1.topology,
nonbondedMethod=method,
nonbondedCutoff=2*nanometer,
......@@ -776,7 +778,7 @@ class AmoebaTestForceField(unittest.TestCase):
def test_NonbondedMethod(self):
"""Test all five options for the nonbondedMethod parameter."""
"""Test both options for the nonbondedMethod parameter."""
methodMap = {NoCutoff:AmoebaMultipoleForce.NoCutoff,
PME:AmoebaMultipoleForce.PME}
......
wrappers/python/tests/TestGromacsTopFile.py
View file @ c9fcabb5
......@@ -22,12 +22,14 @@ class TestGromacsTopFile(unittest.TestCase):
self.top2 = GromacsTopFile('systems/implicit.top')
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.top1.createSystem(nonbondedMethod=method)
forces = system.getForces()
......@@ -52,7 +54,7 @@ class TestGromacsTopFile(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.top1.createSystem(nonbondedMethod=method,
nonbondedCutoff=2*nanometer,
constraints=HBonds)
......@@ -66,7 +68,7 @@ class TestGromacsTopFile(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.top1.createSystem(nonbondedMethod=method,
ewaldErrorTolerance=1e-6,
constraints=HBonds)
......
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