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Commit c6ebf6e2 authored by Peter Eastman's avatar Peter Eastman
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Removed the word "harmonic" from lots of places it didn't belong, including class and method names

parent 58b094ce
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Showing with 62 additions and 62 deletions
wrappers/python/simtk/openmm/app/forcefield.py
View file @ c6ebf6e2
......@@ -1419,11 +1419,11 @@ def countConstraint(data):
print "Constraints bond=%d angle=%d total=%d" % (bondCount, angleCount, (bondCount+angleCount))
## @private
class AmoebaHarmonicBondGenerator:
class AmoebaBondGenerator:
#=============================================================================================
"""An AmoebaHarmonicBondGenerator constructs a AmoebaHarmonicBondForce."""
"""An AmoebaBondGenerator constructs a AmoebaBondForce."""
#=============================================================================================
......@@ -1442,10 +1442,10 @@ class AmoebaHarmonicBondGenerator:
@staticmethod
def parseElement(element, forceField):
# <AmoebaHarmonicBondForce bond-cubic="-25.5" bond-quartic="379.3125">
# <AmoebaBondForce bond-cubic="-25.5" bond-quartic="379.3125">
# <Bond class1="1" class2="2" length="0.1437" k="156900.0"/>
generator = AmoebaHarmonicBondGenerator(float(element.attrib['bond-cubic']), float(element.attrib['bond-quartic']))
generator = AmoebaBondGenerator(float(element.attrib['bond-cubic']), float(element.attrib['bond-quartic']))
forceField._forces.append(generator)
for bond in element.findall('Bond'):
types = forceField._findAtomTypes(bond, 2)
......@@ -1455,7 +1455,7 @@ class AmoebaHarmonicBondGenerator:
generator.length.append(float(bond.attrib['length']))
generator.k.append(float(bond.attrib['k']))
else:
outputString = "AmoebaHarmonicBondGenerator: error getting types: %s %s" % (
outputString = "AmoebaBondGenerator: error getting types: %s %s" % (
bond.attrib['class1'],
bond.attrib['class2'])
raise ValueError(outputString)
......@@ -1472,15 +1472,15 @@ class AmoebaHarmonicBondGenerator:
#countConstraint(data)
existing = [sys.getForce(i) for i in range(sys.getNumForces())]
existing = [f for f in existing if type(f) == mm.AmoebaHarmonicBondForce]
existing = [f for f in existing if type(f) == mm.AmoebaBondForce]
if len(existing) == 0:
force = mm.AmoebaHarmonicBondForce()
force = mm.AmoebaBondForce()
sys.addForce(force)
else:
force = existing[0]
force.setAmoebaGlobalHarmonicBondCubic(self.cubic)
force.setAmoebaGlobalHarmonicBondQuartic(self.quartic)
force.setAmoebaGlobalBondCubic(self.cubic)
force.setAmoebaGlobalBondQuartic(self.quartic)
for bond in data.bonds:
type1 = data.atomType[data.atoms[bond.atom1]]
......@@ -1499,10 +1499,10 @@ class AmoebaHarmonicBondGenerator:
break
if (hit == 0):
outputString = "AmoebaHarmonicBondGenerator missing: types=[%5s %5s] atoms=[%6d %6d] " % (type1, type2, bond.atom1, bond.atom2)
outputString = "AmoebaBondGenerator missing: types=[%5s %5s] atoms=[%6d %6d] " % (type1, type2, bond.atom1, bond.atom2)
raise ValueError(outputString)
parsers["AmoebaHarmonicBondForce"] = AmoebaHarmonicBondGenerator.parseElement
parsers["AmoebaBondForce"] = AmoebaBondGenerator.parseElement
#=============================================================================================
# Add angle constraint
......@@ -1534,10 +1534,10 @@ def addAngleConstraint(angle, idealAngle, data, sys):
#=============================================================================================
## @private
class AmoebaHarmonicAngleGenerator:
class AmoebaAngleGenerator:
#=============================================================================================
"""An AmoebaHarmonicAngleGenerator constructs a AmoebaHarmonicAngleForce."""
"""An AmoebaAngleGenerator constructs a AmoebaAngleForce."""
#=============================================================================================
def __init__(self, forceField, cubic, quartic, pentic, sextic):
......@@ -1562,10 +1562,10 @@ class AmoebaHarmonicAngleGenerator:
@staticmethod
def parseElement(element, forceField):
# <AmoebaHarmonicAngleForce angle-cubic="-0.014" angle-quartic="5.6e-05" angle-pentic="-7e-07" angle-sextic="2.2e-08">
# <AmoebaAngleForce angle-cubic="-0.014" angle-quartic="5.6e-05" angle-pentic="-7e-07" angle-sextic="2.2e-08">
# <Angle class1="2" class2="1" class3="3" k="0.0637259642196" angle1="122.00" />
generator = AmoebaHarmonicAngleGenerator(forceField, float(element.attrib['angle-cubic']), float(element.attrib['angle-quartic']), float(element.attrib['angle-pentic']), float(element.attrib['angle-sextic']))
generator = AmoebaAngleGenerator(forceField, float(element.attrib['angle-cubic']), float(element.attrib['angle-quartic']), float(element.attrib['angle-pentic']), float(element.attrib['angle-sextic']))
forceField._forces.append(generator)
for angle in element.findall('Angle'):
types = forceField._findAtomTypes(angle, 3)
......@@ -1589,7 +1589,7 @@ class AmoebaHarmonicAngleGenerator:
generator.angle.append(angleList)
generator.k.append(float(angle.attrib['k']))
else:
outputString = "AmoebaHarmonicAngleGenerator: error getting types: %s %s %s" % (
outputString = "AmoebaAngleGenerator: error getting types: %s %s %s" % (
angle.attrib['class1'],
angle.attrib['class2'],
angle.attrib['class3'])
......@@ -1617,20 +1617,20 @@ class AmoebaHarmonicAngleGenerator:
# get force
existing = [sys.getForce(i) for i in range(sys.getNumForces())]
existing = [f for f in existing if type(f) == mm.AmoebaHarmonicAngleForce]
existing = [f for f in existing if type(f) == mm.AmoebaAngleForce]
if len(existing) == 0:
force = mm.AmoebaHarmonicAngleForce()
force = mm.AmoebaAngleForce()
sys.addForce(force)
else:
force = existing[0]
# set scalars
force.setAmoebaGlobalHarmonicAngleCubic(self.cubic)
force.setAmoebaGlobalHarmonicAngleQuartic(self.quartic)
force.setAmoebaGlobalHarmonicAnglePentic(self.pentic)
force.setAmoebaGlobalHarmonicAngleSextic(self.sextic)
force.setAmoebaGlobalAngleCubic(self.cubic)
force.setAmoebaGlobalAngleQuartic(self.quartic)
force.setAmoebaGlobalAnglePentic(self.pentic)
force.setAmoebaGlobalAngleSextic(self.sextic)
for angleDict in angleList:
angle = angleDict['angle']
......@@ -1665,7 +1665,7 @@ class AmoebaHarmonicAngleGenerator:
if (numberOfHydrogens < lenAngle):
angleValue = self.angle[i][numberOfHydrogens]
else:
outputString = "AmoebaHarmonicAngleGenerator angle index=%d is out of range: [0, %5d] " % (numberOfHydrogens, lenAngle)
outputString = "AmoebaAngleGenerator angle index=%d is out of range: [0, %5d] " % (numberOfHydrogens, lenAngle)
raise ValueError(outputString)
else:
angleValue = self.angle[i][0]
......@@ -1674,7 +1674,7 @@ class AmoebaHarmonicAngleGenerator:
force.addAngle(angle[0], angle[1], angle[2], angleValue, self.k[i])
break
if (hit == 0):
outputString = "AmoebaHarmonicAngleGenerator missing types: [%s %s %s] for atoms: " % (type1, type2, type3)
outputString = "AmoebaAngleGenerator missing types: [%s %s %s] for atoms: " % (type1, type2, type3)
outputString += getAtomPrint( data, angle[0] ) + ' '
outputString += getAtomPrint( data, angle[1] ) + ' '
outputString += getAtomPrint( data, angle[2] )
......@@ -1693,20 +1693,20 @@ class AmoebaHarmonicAngleGenerator:
# get force
existing = [sys.getForce(i) for i in range(sys.getNumForces())]
existing = [f for f in existing if type(f) == mm.AmoebaHarmonicInPlaneAngleForce]
existing = [f for f in existing if type(f) == mm.AmoebaInPlaneAngleForce]
if len(existing) == 0:
force = mm.AmoebaHarmonicInPlaneAngleForce()
force = mm.AmoebaInPlaneAngleForce()
sys.addForce(force)
else:
force = existing[0]
# scalars
force.setAmoebaGlobalHarmonicInPlaneAngleCubic(self.cubic)
force.setAmoebaGlobalHarmonicInPlaneAngleQuartic(self.quartic)
force.setAmoebaGlobalHarmonicInPlaneAnglePentic(self.pentic)
force.setAmoebaGlobalHarmonicInPlaneAngleSextic(self.sextic)
force.setAmoebaGlobalInPlaneAngleCubic(self.cubic)
force.setAmoebaGlobalInPlaneAngleQuartic(self.quartic)
force.setAmoebaGlobalInPlaneAnglePentic(self.pentic)
force.setAmoebaGlobalInPlaneAngleSextic(self.sextic)
for angleDict in angleList:
......@@ -1734,19 +1734,19 @@ class AmoebaHarmonicAngleGenerator:
break
if (hit == 0):
outputString = "AmoebaHarmonicInPlaneAngleGenerator missing types: [%s %s %s] atoms: " % (type1, type2, type3)
outputString = "AmoebaInPlaneAngleGenerator missing types: [%s %s %s] atoms: " % (type1, type2, type3)
outputString += getAtomPrint( data, angle[0] ) + ' '
outputString += getAtomPrint( data, angle[1] ) + ' '
outputString += getAtomPrint( data, angle[2] )
outputString += " indices: [%6d %6d %6d]" % (angle[0], angle[1], angle[2])
raise ValueError(outputString)
parsers["AmoebaHarmonicAngleForce"] = AmoebaHarmonicAngleGenerator.parseElement
parsers["AmoebaAngleForce"] = AmoebaAngleGenerator.parseElement
#=============================================================================================
# Generator for the AmoebaOutOfPlaneBend covalent force; also calls methods in the
# AmoebaHarmonicAngleGenerator to generate the AmoebaHarmonicAngleForce and
# AmoebaHarmonicInPlaneAngleForce
# AmoebaAngleGenerator to generate the AmoebaAngleForce and
# AmoebaInPlaneAngleForce
#=============================================================================================
## @private
......@@ -2011,20 +2011,20 @@ class AmoebaOutOfPlaneBendGenerator:
angleDict['isConstrained'] = isConstrained
nonInPlaneAngles.append(angleDict)
# get AmoebaHarmonicAngleGenerator and add AmoebaHarmonicAngle and AmoebaHarmonicInPlaneAngle forces
# get AmoebaAngleGenerator and add AmoebaAngle and AmoebaInPlaneAngle forces
for force in self.forceField._forces:
if (force.__class__.__name__ == 'AmoebaHarmonicAngleGenerator'):
if (force.__class__.__name__ == 'AmoebaAngleGenerator'):
force.createForcePostOpBendAngle(sys, data, nonbondedMethod, nonbondedCutoff, nonInPlaneAngles, args)
force.createForcePostOpBendInPlaneAngle(sys, data, nonbondedMethod, nonbondedCutoff, inPlaneAngles, args)
if (force.__class__.__name__ == 'AmoebaHarmonicBondGenerator'):
if (force.__class__.__name__ == 'AmoebaBondGenerator'):
force.createForce(sys, data, nonbondedMethod, nonbondedCutoff, args)
for force in self.forceField._forces:
if (force.__class__.__name__ == 'AmoebaStretchBendGenerator'):
for angleDict in inPlaneAngles:
nonInPlaneAngles.append(angleDict)
force.createForcePostAmoebaHarmonicBondForce(sys, data, nonbondedMethod, nonbondedCutoff, nonInPlaneAngles, args)
force.createForcePostAmoebaBondForce(sys, data, nonbondedMethod, nonbondedCutoff, nonInPlaneAngles, args)
parsers["AmoebaOutOfPlaneBendForce"] = AmoebaOutOfPlaneBendGenerator.parseElement
......@@ -2569,12 +2569,12 @@ class AmoebaStretchBendGenerator:
#=============================================================================================
# The setup of this force is dependent on AmoebaHarmonicBondForce and AmoebaHarmonicAngleForce
# The setup of this force is dependent on AmoebaBondForce and AmoebaAngleForce
# having been called since the ideal bond lengths and angle are needed here.
# As a conseqeunce, createForce() is not implemented since it is not guaranteed that the generator for
# AmoebaHarmonicBondForce and AmoebaHarmonicAngleForce have been called prior to AmoebaStretchBendGenerator().
# Instead, createForcePostAmoebaHarmonicBondForce() is called
# after the generators for AmoebaHarmonicBondForce and AmoebaHarmonicAngleForce have been called
# AmoebaBondForce and AmoebaAngleForce have been called prior to AmoebaStretchBendGenerator().
# Instead, createForcePostAmoebaBondForce() is called
# after the generators for AmoebaBondForce and AmoebaAngleForce have been called
#=============================================================================================
......@@ -2587,7 +2587,7 @@ class AmoebaStretchBendGenerator:
#=============================================================================================
def createForcePostAmoebaHarmonicBondForce(self, sys, data, nonbondedMethod, nonbondedCutoff, angleList, args):
def createForcePostAmoebaBondForce(self, sys, data, nonbondedMethod, nonbondedCutoff, angleList, args):
if (self.hasBeenCalled):
return
......
wrappers/python/src/swig_doxygen/swigInputConfig.py
View file @ c6ebf6e2
......@@ -17,9 +17,9 @@ SKIP_METHODS = [('State',),
('Stream',),
('Vec3',),
('AmoebaGeneralizedKirkwoodForceImpl',),
('AmoebaHarmonicAngleForceImpl',),
('AmoebaHarmonicBondForceImpl',),
('AmoebaHarmonicInPlaneAngleForceImpl',),
('AmoebaAngleForceImpl',),
('AmoebaBondForceImpl',),
('AmoebaInPlaneAngleForceImpl',),
('AmoebaMultipoleForceImpl',),
('AmoebaOutOfPlaneBendForceImpl',),
('AmoebaPiTorsionForceImpl',),
......@@ -35,9 +35,9 @@ SKIP_METHODS = [('State',),
('BondInfo',),
('BondParameterInfo',),
('CalcAmoebaGeneralizedKirkwoodForceKernel',),
('CalcAmoebaHarmonicAngleForceKernel',),
('CalcAmoebaHarmonicBondForceKernel',),
('CalcAmoebaHarmonicInPlaneAngleForceKernel',),
('CalcAmoebaAngleForceKernel',),
('CalcAmoebaBondForceKernel',),
('CalcAmoebaInPlaneAngleForceKernel',),
('CalcAmoebaMultipoleForceKernel',),
('CalcAmoebaOutOfPlaneBendForceKernel',),
('CalcAmoebaPiTorsionForceKernel',),
......@@ -234,21 +234,21 @@ UNITS = {
("AmoebaGeneralizedKirkwoodForce", "getProbeRadius") : ( 'unit.nanometer', ()),
("AmoebaGeneralizedKirkwoodForce", "getSurfaceAreaFactor") : ( '(unit.nanometer*unit.nanometer)/unit.kilojoule_per_mole',()),
("AmoebaHarmonicAngleForce", "getAmoebaGlobalHarmonicAngleCubic") : ( None,()),
("AmoebaHarmonicAngleForce", "getAmoebaGlobalHarmonicAngleQuartic") : ( None,()),
("AmoebaHarmonicAngleForce", "getAmoebaGlobalHarmonicAnglePentic") : ( None,()),
("AmoebaHarmonicAngleForce", "getAmoebaGlobalHarmonicAngleSextic") : ( None,()),
("AmoebaHarmonicAngleForce", "getAngleParameters") : ( None, (None, None, None, 'unit.radian', 'unit.kilojoule_per_mole/(unit.radian*unit.radian)')),
("AmoebaAngleForce", "getAmoebaGlobalAngleCubic") : ( None,()),
("AmoebaAngleForce", "getAmoebaGlobalAngleQuartic") : ( None,()),
("AmoebaAngleForce", "getAmoebaGlobalAnglePentic") : ( None,()),
("AmoebaAngleForce", "getAmoebaGlobalAngleSextic") : ( None,()),
("AmoebaAngleForce", "getAngleParameters") : ( None, (None, None, None, 'unit.radian', 'unit.kilojoule_per_mole/(unit.radian*unit.radian)')),
("AmoebaHarmonicBondForce", "getAmoebaGlobalHarmonicBondCubic") : ( None,()),
("AmoebaHarmonicBondForce", "getAmoebaGlobalHarmonicBondQuartic") : ( None,()),
("AmoebaHarmonicBondForce", "getBondParameters") : ( None, (None, None, 'unit.nanometer', 'unit.kilojoule_per_mole/(unit.nanometer*unit.nanometer)')),
("AmoebaBondForce", "getAmoebaGlobalBondCubic") : ( None,()),
("AmoebaBondForce", "getAmoebaGlobalBondQuartic") : ( None,()),
("AmoebaBondForce", "getBondParameters") : ( None, (None, None, 'unit.nanometer', 'unit.kilojoule_per_mole/(unit.nanometer*unit.nanometer)')),
("AmoebaHarmonicInPlaneAngleForce", "getAmoebaGlobalHarmonicInPlaneAngleCubic") : ( None,()),
("AmoebaHarmonicInPlaneAngleForce", "getAmoebaGlobalHarmonicInPlaneAngleQuartic") : ( None,()),
("AmoebaHarmonicInPlaneAngleForce", "getAmoebaGlobalHarmonicInPlaneAnglePentic") : ( None,()),
("AmoebaHarmonicInPlaneAngleForce", "getAmoebaGlobalHarmonicInPlaneAngleSextic") : ( None,()),
("AmoebaHarmonicInPlaneAngleForce", "getAngleParameters") : ( None, (None, None, None, None, 'unit.radian', 'unit.kilojoule_per_mole/(unit.radian*unit.radian)')),
("AmoebaInPlaneAngleForce", "getAmoebaGlobalInPlaneAngleCubic") : ( None,()),
("AmoebaInPlaneAngleForce", "getAmoebaGlobalInPlaneAngleQuartic") : ( None,()),
("AmoebaInPlaneAngleForce", "getAmoebaGlobalInPlaneAnglePentic") : ( None,()),
("AmoebaInPlaneAngleForce", "getAmoebaGlobalInPlaneAngleSextic") : ( None,()),
("AmoebaInPlaneAngleForce", "getAngleParameters") : ( None, (None, None, None, None, 'unit.radian', 'unit.kilojoule_per_mole/(unit.radian*unit.radian)')),
("AmoebaMultipoleForce", "getNumMultipoles") : ( None,()),
("AmoebaMultipoleForce", "getNonbondedMethod") : ( None,()),
......
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