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Commit a955feb1 authored by Mark Friedrichs's avatar Mark Friedrichs
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Cleanup

parent 8217295b
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Showing with 89 additions and 189 deletions
wrappers/python/simtk/openmm/app/forcefield.py
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...@@ -1338,15 +1338,14 @@ class AmoebaHarmonicBondGenerator: ...@@ -1338,15 +1338,14 @@ class AmoebaHarmonicBondGenerator:
def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args): def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
verbose = 0
if (self.hasBeenCalled): if (self.hasBeenCalled):
return return
if (verbose):
countConstraint(data)
self.hasBeenCalled = 1 self.hasBeenCalled = 1
countConstraint(data)
print "In AmoebaHarmonicBondForce generator"
existing = [sys.getForce(i) for i in range(sys.getNumForces())] 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.AmoebaHarmonicBondForce]
if len(existing) == 0: if len(existing) == 0:
...@@ -1358,10 +1357,6 @@ class AmoebaHarmonicBondGenerator: ...@@ -1358,10 +1357,6 @@ class AmoebaHarmonicBondGenerator:
force.setAmoebaGlobalHarmonicBondCubic(self.cubic) force.setAmoebaGlobalHarmonicBondCubic(self.cubic)
force.setAmoebaGlobalHarmonicBondQuartic(self.quartic) force.setAmoebaGlobalHarmonicBondQuartic(self.quartic)
if (verbose):
print "In AmoebaHarmonicBondGenerator bonds=%d " % (len(data.bonds))
count = 0
for bond in data.bonds: for bond in data.bonds:
type1 = data.atomType[data.atoms[bond.atom1]] type1 = data.atomType[data.atoms[bond.atom1]]
type2 = data.atomType[data.atoms[bond.atom2]] type2 = data.atomType[data.atoms[bond.atom2]]
...@@ -1374,21 +1369,13 @@ class AmoebaHarmonicBondGenerator: ...@@ -1374,21 +1369,13 @@ class AmoebaHarmonicBondGenerator:
hit = 1 hit = 1
if bond.isConstrained: if bond.isConstrained:
sys.addConstraint(bond.atom1, bond.atom2, self.length[i]) sys.addConstraint(bond.atom1, bond.atom2, self.length[i])
if (verbose):
atomS1 = getAtomPrint(data, bond.atom1)
atomS2 = getAtomPrint(data, bond.atom2)
print "AmoebaHarmonicBondGenerator %5d %5d %5d [%s %s] [%5s %5s] %15.6f %15.6f Constraint" % (count, bond.atom1, bond.atom2, atomS1, atomS2, type1, type2, self.length[i], self.k[i])
elif self.k[i] != 0: elif self.k[i] != 0:
if (verbose):
atomS1 = getAtomPrint(data, bond.atom1)
atomS2 = getAtomPrint(data, bond.atom2)
print "AmoebaHarmonicBondGenerator %5d %5d %5d [%s %s] [%5s %5s] %15.6f %15.6f" % (count, bond.atom1, bond.atom2, atomS1, atomS2, type1, type2, self.length[i], self.k[i])
force.addBond(bond.atom1, bond.atom2, self.length[i], self.k[i]) force.addBond(bond.atom1, bond.atom2, self.length[i], self.k[i])
break break
if (hit == 0):
print "AmoebaHarmonicBondGenerator missing: %5d types=[%5s %5s] atoms=[%6d %6d] " % (count, type1, type2, bond.atom1, bond.atom2)
count += 1 if (hit == 0):
outputString = "AmoebaHarmonicBondGenerator missing: types=[%5s %5s] atoms=[%6d %6d] " % (type1, type2, bond.atom1, bond.atom2)
raise ValueError(outputString)
parsers["AmoebaHarmonicBondForce"] = AmoebaHarmonicBondGenerator.parseElement parsers["AmoebaHarmonicBondForce"] = AmoebaHarmonicBondGenerator.parseElement
...@@ -1420,7 +1407,6 @@ def addAngleConstraint(angle, idealAngle, data, sys): ...@@ -1420,7 +1407,6 @@ def addAngleConstraint(angle, idealAngle, data, sys):
sys.addConstraint(angle[0], angle[2], length) sys.addConstraint(angle[0], angle[2], length)
return return
#============================================================================================= #=============================================================================================
class AmoebaHarmonicAngleGenerator: class AmoebaHarmonicAngleGenerator:
...@@ -1498,7 +1484,6 @@ class AmoebaHarmonicAngleGenerator: ...@@ -1498,7 +1484,6 @@ class AmoebaHarmonicAngleGenerator:
def createForcePostOpBendAngle(self, sys, data, nonbondedMethod, nonbondedCutoff, angleList, args): def createForcePostOpBendAngle(self, sys, data, nonbondedMethod, nonbondedCutoff, angleList, args):
verbose = 0
if (self.hasBeenCalled): if (self.hasBeenCalled):
return return
self.hasBeenCalled += 1 self.hasBeenCalled += 1
...@@ -1514,17 +1499,13 @@ class AmoebaHarmonicAngleGenerator: ...@@ -1514,17 +1499,13 @@ class AmoebaHarmonicAngleGenerator:
else: else:
force = existing[0] force = existing[0]
# scalars # set scalars
force.setAmoebaGlobalHarmonicAngleCubic(self.cubic) force.setAmoebaGlobalHarmonicAngleCubic(self.cubic)
force.setAmoebaGlobalHarmonicAngleQuartic(self.quartic) force.setAmoebaGlobalHarmonicAngleQuartic(self.quartic)
force.setAmoebaGlobalHarmonicAnglePentic(self.pentic) force.setAmoebaGlobalHarmonicAnglePentic(self.pentic)
force.setAmoebaGlobalHarmonicAngleSextic(self.sextic) force.setAmoebaGlobalHarmonicAngleSextic(self.sextic)
if (verbose):
print "In AmoebaHarmonicAngleGenerator angles=%d " % (len(data.angles))
count = 0
for angleDict in angleList: for angleDict in angleList:
angle = angleDict['angle'] angle = angleDict['angle']
isConstrained = angleDict['isConstrained'] isConstrained = angleDict['isConstrained']
...@@ -1558,8 +1539,8 @@ class AmoebaHarmonicAngleGenerator: ...@@ -1558,8 +1539,8 @@ class AmoebaHarmonicAngleGenerator:
if (numberOfHydrogens < lenAngle): if (numberOfHydrogens < lenAngle):
angleValue = self.angle[i][numberOfHydrogens] angleValue = self.angle[i][numberOfHydrogens]
else: else:
print "Error: AmoebaHarmonicAngleGenerator angle index=%d is out of range: [0, %5d] " % (numberOfHydrogens, lenAngle) outputString = "AmoebaHarmonicAngleGenerator angle index=%d is out of range: [0, %5d] " % (numberOfHydrogens, lenAngle)
sys.exit(-1) raise ValueError(outputString)
else: else:
angleValue = self.angle[i][0] angleValue = self.angle[i][0]
...@@ -1567,9 +1548,12 @@ class AmoebaHarmonicAngleGenerator: ...@@ -1567,9 +1548,12 @@ class AmoebaHarmonicAngleGenerator:
force.addAngle(angle[0], angle[1], angle[2], angleValue, self.k[i]) force.addAngle(angle[0], angle[1], angle[2], angleValue, self.k[i])
break break
if (hit == 0): if (hit == 0):
print "AmoebaHarmonicAngleGenerator missing: %5d %s %s %s " % (count, type1, type2, type3) outputString = "AmoebaHarmonicAngleGenerator missing types: [%s %s %s] for atoms: " % (type1, type2, type3)
outputString += getAtomPrint( data, angle[0] ) + ' '
count += 1 outputString += getAtomPrint( data, angle[1] ) + ' '
outputString += getAtomPrint( data, angle[2] )
outputString += " indices: [%6d %6d %6d]" % (angle[0], angle[1], angle[2])
raise ValueError(outputString)
#============================================================================================= #=============================================================================================
# createForcePostOpBendInPlaneAngle is called by AmoebaOutOfPlaneBendForce with the list of # createForcePostOpBendInPlaneAngle is called by AmoebaOutOfPlaneBendForce with the list of
...@@ -1578,7 +1562,6 @@ class AmoebaHarmonicAngleGenerator: ...@@ -1578,7 +1562,6 @@ class AmoebaHarmonicAngleGenerator:
def createForcePostOpBendInPlaneAngle(self, sys, data, nonbondedMethod, nonbondedCutoff, angleList, args): def createForcePostOpBendInPlaneAngle(self, sys, data, nonbondedMethod, nonbondedCutoff, angleList, args):
verbose = 0
self.hasBeenCalled += 1 self.hasBeenCalled += 1
# get force # get force
...@@ -1599,10 +1582,6 @@ class AmoebaHarmonicAngleGenerator: ...@@ -1599,10 +1582,6 @@ class AmoebaHarmonicAngleGenerator:
force.setAmoebaGlobalHarmonicInPlaneAnglePentic(self.pentic) force.setAmoebaGlobalHarmonicInPlaneAnglePentic(self.pentic)
force.setAmoebaGlobalHarmonicInPlaneAngleSextic(self.sextic) force.setAmoebaGlobalHarmonicInPlaneAngleSextic(self.sextic)
if (verbose):
print "In AmoebaHarmonicAngleGenerator angles=%d " % (len(data.angles))
count = 0
for angleDict in angleList: for angleDict in angleList:
angle = angleDict['angle'] angle = angleDict['angle']
...@@ -1620,8 +1599,6 @@ class AmoebaHarmonicAngleGenerator: ...@@ -1620,8 +1599,6 @@ class AmoebaHarmonicAngleGenerator:
types3 = self.types3[i] types3 = self.types3[i]
if (type1 in types1 and type2 in types2 and type3 in types3) or (type1 in types3 and type2 in types2 and type3 in types1): if (type1 in types1 and type2 in types2 and type3 in types3) or (type1 in types3 and type2 in types2 and type3 in types1):
if (verbose):
print "AmoebaHarmonicInPlaneAngleGenerator %5d %5d %5d %5d len=%d [%5s %5s %5s] %15.6f %15.6f" % (count, angle[0], angle[1], angle[2], len(angle), type1, type2, type3, self.angle[i][0], self.k[i])
hit = 1 hit = 1
angleDict['idealAngle'] = self.angle[i][0] angleDict['idealAngle'] = self.angle[i][0]
if (isConstrained and self.k[i] != 0.0): if (isConstrained and self.k[i] != 0.0):
...@@ -1631,9 +1608,12 @@ class AmoebaHarmonicAngleGenerator: ...@@ -1631,9 +1608,12 @@ class AmoebaHarmonicAngleGenerator:
break break
if (hit == 0): if (hit == 0):
print "AmoebaHarmonicInPlaneAngleGenerator missing: %5d %s %s " % (count, type1, type2, type3) outputString = "AmoebaHarmonicInPlaneAngleGenerator missing types: [%s %s %s] atoms: " % (type1, type2, type3)
outputString += getAtomPrint( data, angle[0] ) + ' '
count += 1 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["AmoebaHarmonicAngleForce"] = AmoebaHarmonicAngleGenerator.parseElement
...@@ -1721,11 +1701,8 @@ class AmoebaOutOfPlaneBendGenerator: ...@@ -1721,11 +1701,8 @@ class AmoebaOutOfPlaneBendGenerator:
generator.ks.append(float(angle.attrib['k'])) generator.ks.append(float(angle.attrib['k']))
else: else:
outputString = "AmoebaOutOfPlaneBendGenerator: error getting types: %s %s %s %s." % ( outputString = "AmoebaOutOfPlaneBendGenerator error getting types: %s %s %s %s." % (
angle.attrib['class1'], angle.attrib['class1'], angle.attrib['class2'], angle.attrib['class3'], angle.attrib['class4'])
angle.attrib['class2'],
angle.attrib['class3'],
angle.attrib['class4'])
raise ValueError(outputString) raise ValueError(outputString)
#============================================================================================= #=============================================================================================
...@@ -1760,7 +1737,6 @@ class AmoebaOutOfPlaneBendGenerator: ...@@ -1760,7 +1737,6 @@ class AmoebaOutOfPlaneBendGenerator:
def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args): def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
verbose = 0
if (self.hasBeenCalled): if (self.hasBeenCalled):
return return
self.hasBeenCalled = 1 self.hasBeenCalled = 1
...@@ -1782,9 +1758,6 @@ class AmoebaOutOfPlaneBendGenerator: ...@@ -1782,9 +1758,6 @@ class AmoebaOutOfPlaneBendGenerator:
force.setAmoebaGlobalOutOfPlaneBendPentic( self.pentic) force.setAmoebaGlobalOutOfPlaneBendPentic( self.pentic)
force.setAmoebaGlobalOutOfPlaneBendSextic( self.sextic) force.setAmoebaGlobalOutOfPlaneBendSextic( self.sextic)
count = 0
opBondCount = 0
# this hash is used to insure the out-of-plane-bend bonds # this hash is used to insure the out-of-plane-bend bonds
# are only added once # are only added once
...@@ -1810,9 +1783,9 @@ class AmoebaOutOfPlaneBendGenerator: ...@@ -1810,9 +1783,9 @@ class AmoebaOutOfPlaneBendGenerator:
# if middle atom has covalency of 3 and # if middle atom has covalency of 3 and
# the types of the middle atom and the partner atom (atom bonded to # the types of the middle atom and the partner atom (atom bonded to
# middle atom, but not in angle) match types2 and types2, then # middle atom, but not in angle) match types1 and types2, then
# three out-of-plane bend angles are generated. Three in-plane angle # three out-of-plane bend angles are generated. Three in-plane angle
# are also generated. If the conditions are not satisfied the angle is generic angle (not a in-plane angle) # are also generated. If the conditions are not satisfied, the angle is marked as 'generic' angle (not a in-plane angle)
if (middleAtom > -1 and middleCovalency == 3 and middleAtom not in skipAtoms): if (middleAtom > -1 and middleCovalency == 3 and middleAtom not in skipAtoms):
...@@ -1841,19 +1814,19 @@ class AmoebaOutOfPlaneBendGenerator: ...@@ -1841,19 +1814,19 @@ class AmoebaOutOfPlaneBendGenerator:
if (len(partners) == 3): if (len(partners) == 3):
opBondCount += 3
if (verbose):
print "%5d Opbend: %d type=%s cov=%d " % (opBondCount, middleAtom, middleType, middleCovalency)
force.addOutOfPlaneBend(partners[0], middleAtom, partners[1], partners[2], partnerK[2]) force.addOutOfPlaneBend(partners[0], middleAtom, partners[1], partners[2], partnerK[2])
force.addOutOfPlaneBend(partners[0], middleAtom, partners[2], partners[1], partnerK[1]) force.addOutOfPlaneBend(partners[0], middleAtom, partners[2], partners[1], partnerK[1])
force.addOutOfPlaneBend(partners[1], middleAtom, partners[2], partners[0], partnerK[0]) force.addOutOfPlaneBend(partners[1], middleAtom, partners[2], partners[0], partnerK[0])
# skipAtoms is used to insure angles are only included once
skipAtoms[middleAtom] = set() skipAtoms[middleAtom] = set()
skipAtoms[middleAtom].add(partners[0]) skipAtoms[middleAtom].add(partners[0])
skipAtoms[middleAtom].add(partners[1]) skipAtoms[middleAtom].add(partners[1])
skipAtoms[middleAtom].add(partners[2]) skipAtoms[middleAtom].add(partners[2])
# in-plane angle
angleDict = {} angleDict = {}
angleList = [] angleList = []
angleList.append(angle[0]) angleList.append(angle[0])
...@@ -1872,15 +1845,9 @@ class AmoebaOutOfPlaneBendGenerator: ...@@ -1872,15 +1845,9 @@ class AmoebaOutOfPlaneBendGenerator:
if (atomIndex not in angleSet): if (atomIndex not in angleSet):
angleList.append(atomIndex) angleList.append(atomIndex)
if (verbose):
print "%5d Opbend: middle=%d inPlane1 %d %s" % (opBondCount, middleAtom, len(angleList), str(angleList))
inPlaneAngles.append(angleDict) inPlaneAngles.append(angleDict)
else: else:
if (verbose):
print "%5d Opbend: %d type=%s cov=%d xxx" % (opBondCount, middleAtom, middleType, middleCovalency)
print "%5d Opbend: middle=%d inPlane1 %d %s" % (opBondCount, middleAtom, len(angleList), str(angleList))
angleDict = {} angleDict = {}
angleDict['angle'] = angle angleDict['angle'] = angle
angleDict['isConstrained'] = isConstrained angleDict['isConstrained'] = isConstrained
...@@ -1909,9 +1876,6 @@ class AmoebaOutOfPlaneBendGenerator: ...@@ -1909,9 +1876,6 @@ class AmoebaOutOfPlaneBendGenerator:
if (atomIndex not in angleSet): if (atomIndex not in angleSet):
angleList.append(atomIndex) angleList.append(atomIndex)
if (verbose):
print "%5d Opbend: middle=%d inPlane2 %d angleList=%s partnerSet=%s" % (opBondCount, middleAtom, len(angleList), str(angleList), str(partnerSet))
inPlaneAngles.append(angleDict) inPlaneAngles.append(angleDict)
else: else:
...@@ -1920,8 +1884,6 @@ class AmoebaOutOfPlaneBendGenerator: ...@@ -1920,8 +1884,6 @@ class AmoebaOutOfPlaneBendGenerator:
angleDict['isConstrained'] = isConstrained angleDict['isConstrained'] = isConstrained
nonInPlaneAngles.append(angleDict) nonInPlaneAngles.append(angleDict)
count += 1
# get AmoebaHarmonicAngleGenerator and add AmoebaHarmonicAngle and AmoebaHarmonicInPlaneAngle forces # get AmoebaHarmonicAngleGenerator and add AmoebaHarmonicAngle and AmoebaHarmonicInPlaneAngle forces
for force in self.forceField._forces: for force in self.forceField._forces:
...@@ -1944,9 +1906,7 @@ parsers["AmoebaOutOfPlaneBendForce"] = AmoebaOutOfPlaneBendGenerator.parseElemen ...@@ -1944,9 +1906,7 @@ parsers["AmoebaOutOfPlaneBendForce"] = AmoebaOutOfPlaneBendGenerator.parseElemen
class AmoebaTorsionGenerator: class AmoebaTorsionGenerator:
#============================================================================================= #=============================================================================================
"""An AmoebaTorsionGenerator constructs a AmoebaTorsionForce.""" """An AmoebaTorsionGenerator constructs a AmoebaTorsionForce."""
#============================================================================================= #=============================================================================================
def __init__(self, torsionUnit): def __init__(self, torsionUnit):
...@@ -2015,7 +1975,6 @@ class AmoebaTorsionGenerator: ...@@ -2015,7 +1975,6 @@ class AmoebaTorsionGenerator:
def createForce(self, sys, data, nontorsionedMethod, nontorsionedCutoff, args): def createForce(self, sys, data, nontorsionedMethod, nontorsionedCutoff, args):
verbose = 0
if (self.hasBeenCalled): if (self.hasBeenCalled):
return return
self.hasBeenCalled = 1 self.hasBeenCalled = 1
...@@ -2027,9 +1986,7 @@ class AmoebaTorsionGenerator: ...@@ -2027,9 +1986,7 @@ class AmoebaTorsionGenerator:
sys.addForce(force) sys.addForce(force)
else: else:
force = existing[0] force = existing[0]
if (verbose):
print "In AmoebaTorsionGenerator torsions=%d " % (len(data.propers))
count = 0
for torsion in data.propers: for torsion in data.propers:
type1 = data.atomType[data.atoms[torsion[0]]] type1 = data.atomType[data.atoms[torsion[0]]]
...@@ -2048,20 +2005,18 @@ class AmoebaTorsionGenerator: ...@@ -2048,20 +2005,18 @@ class AmoebaTorsionGenerator:
# match types in forward or reverse direction # match types in forward or reverse direction
if (type1 in types1 and type2 in types2 and type3 in types3 and type4 in types4) or (type4 in types1 and type3 in types2 and type2 in types3 and type1 in types4): if (type1 in types1 and type2 in types2 and type3 in types3 and type4 in types4) or (type4 in types1 and type3 in types2 and type2 in types3 and type1 in types4):
if (verbose):
print "AmoebaTorsionGenerator %5d [%5d %5d %5d %5d] [%5s %5s %5s %5s]" % (
count, torsion[0], torsion[1], torsion[2], torsion[3],
type1, type2, type3, type4)
hit = 1 hit = 1
force.addTorsion(torsion[0], torsion[1], torsion[2], torsion[3], self.t1[i], self.t2[i], self.t3[i]) force.addTorsion(torsion[0], torsion[1], torsion[2], torsion[3], self.t1[i], self.t2[i], self.t3[i])
break break
if (hit == 0):
print "AmoebaTorsionGenerator missing: %5d %s %s " % (count, type1, type2, type3, type4)
count += 1 if (hit == 0):
outputString = "AmoebaTorsionGenerator missing type: [%s %s %s %s] atoms: " % (type1, type2, type3, type4)
if (verbose): outputString += getAtomPrint( data, torsion[0] ) + ' '
print "AmoebaTorsionGenerator number of torsions added=%d " % (force.getNumTorsions()) outputString += getAtomPrint( data, torsion[1] ) + ' '
outputString += getAtomPrint( data, torsion[2] ) + ' '
outputString += getAtomPrint( data, torsion[3] )
outputString += " indices: [%6d %6d %6d %6d]" % (torsion[0], torsion[1], torsion[2], torsion[3])
raise ValueError(outputString)
parsers["AmoebaTorsionForce"] = AmoebaTorsionGenerator.parseElement parsers["AmoebaTorsionForce"] = AmoebaTorsionGenerator.parseElement
...@@ -2109,7 +2064,6 @@ class AmoebaPiTorsionGenerator: ...@@ -2109,7 +2064,6 @@ class AmoebaPiTorsionGenerator:
def createForce(self, sys, data, nonpiTorsionedMethod, nonpiTorsionedCutoff, args): def createForce(self, sys, data, nonpiTorsionedMethod, nonpiTorsionedCutoff, args):
verbose = 0
if (self.hasBeenCalled): if (self.hasBeenCalled):
return return
self.hasBeenCalled = 1 self.hasBeenCalled = 1
...@@ -2123,7 +2077,6 @@ class AmoebaPiTorsionGenerator: ...@@ -2123,7 +2077,6 @@ class AmoebaPiTorsionGenerator:
else: else:
force = existing[0] force = existing[0]
count = 0
for bond in data.bonds: for bond in data.bonds:
# search for bonds with both atoms in bond having covalency == 3 # search for bonds with both atoms in bond having covalency == 3
...@@ -2142,8 +2095,6 @@ class AmoebaPiTorsionGenerator: ...@@ -2142,8 +2095,6 @@ class AmoebaPiTorsionGenerator:
types2 = self.types2[i] types2 = self.types2[i]
if (type1 in types1 and type2 in types2) or (type1 in types2 and type2 in types1): if (type1 in types1 and type2 in types2) or (type1 in types2 and type2 in types1):
if (verbose):
print "AmoebaPiTorsionGenerator %5d %5d %5d [%5s %5s] %15.6f" % (count, atom1, atom2, type1, type2, self.k[i])
# piTorsionAtom1, piTorsionAtom2 are the atoms bonded to atom1, excluding atom2 # piTorsionAtom1, piTorsionAtom2 are the atoms bonded to atom1, excluding atom2
# piTorsionAtom5, piTorsionAtom6 are the atoms bonded to atom2, excluding atom1 # piTorsionAtom5, piTorsionAtom6 are the atoms bonded to atom2, excluding atom1
...@@ -2185,10 +2136,6 @@ class AmoebaPiTorsionGenerator: ...@@ -2185,10 +2136,6 @@ class AmoebaPiTorsionGenerator:
force.addPiTorsion(piTorsionAtom1, piTorsionAtom2, piTorsionAtom3, piTorsionAtom4, piTorsionAtom5, piTorsionAtom6, self.k[i]) force.addPiTorsion(piTorsionAtom1, piTorsionAtom2, piTorsionAtom3, piTorsionAtom4, piTorsionAtom5, piTorsionAtom6, self.k[i])
count += 1
if (verbose):
print "AmoebaPiTorsionGenerator number of pi-torsions added=%d " % (force.getNumPiTorsions())
parsers["AmoebaPiTorsionForce"] = AmoebaPiTorsionGenerator.parseElement parsers["AmoebaPiTorsionForce"] = AmoebaPiTorsionGenerator.parseElement
#============================================================================================= #=============================================================================================
...@@ -2196,9 +2143,7 @@ parsers["AmoebaPiTorsionForce"] = AmoebaPiTorsionGenerator.parseElement ...@@ -2196,9 +2143,7 @@ parsers["AmoebaPiTorsionForce"] = AmoebaPiTorsionGenerator.parseElement
class AmoebaTorsionTorsionGenerator: class AmoebaTorsionTorsionGenerator:
#============================================================================================= #=============================================================================================
"""An AmoebaTorsionTorsionGenerator constructs a AmoebaTorsionTorsionForce.""" """An AmoebaTorsionTorsionGenerator constructs a AmoebaTorsionTorsionForce."""
#============================================================================================= #=============================================================================================
def __init__(self): def __init__(self):
...@@ -2363,7 +2308,6 @@ class AmoebaTorsionTorsionGenerator: ...@@ -2363,7 +2308,6 @@ class AmoebaTorsionTorsionGenerator:
def createForce(self, sys, data, nonpiTorsionedMethod, nonpiTorsionedCutoff, args): def createForce(self, sys, data, nonpiTorsionedMethod, nonpiTorsionedCutoff, args):
verbose = 0
if (self.hasBeenCalled): if (self.hasBeenCalled):
return return
self.hasBeenCalled = 1 self.hasBeenCalled = 1
...@@ -2377,7 +2321,6 @@ class AmoebaTorsionTorsionGenerator: ...@@ -2377,7 +2321,6 @@ class AmoebaTorsionTorsionGenerator:
else: else:
force = existing[0] force = existing[0]
count = 0
for angle in data.angles: for angle in data.angles:
# search for bitorsions; based on TINKER subroutine bitors() # search for bitorsions; based on TINKER subroutine bitors()
...@@ -2439,18 +2382,15 @@ class AmoebaTorsionTorsionGenerator: ...@@ -2439,18 +2382,15 @@ class AmoebaTorsionTorsionGenerator:
for (index, grid) in enumerate(self.grids): for (index, grid) in enumerate(self.grids):
force.setTorsionTorsionGrid(index, grid) force.setTorsionTorsionGrid(index, grid)
if (verbose):
print "AmoebaTorsionTorsionGenerator number of bitorsions added=%d " % (force.getNumTorsionTorsions())
print "AmoebaTorsionTorsionGenerator number of grids added=%d " % (force.getNumTorsionTorsionGrids())
parsers["AmoebaTorsionTorsionForce"] = AmoebaTorsionTorsionGenerator.parseElement parsers["AmoebaTorsionTorsionForce"] = AmoebaTorsionTorsionGenerator.parseElement
#============================================================================================= #=============================================================================================
class AmoebaStretchBendGenerator: class AmoebaStretchBendGenerator:
"""An AmoebaStretchBendGenerator constructs a AmoebaStretchBendForce."""
#============================================================================================= #=============================================================================================
"""An AmoebaStretchBendGenerator constructs a AmoebaStretchBendForce."""
#=============================================================================================
def __init__(self): def __init__(self):
...@@ -2513,7 +2453,6 @@ class AmoebaStretchBendGenerator: ...@@ -2513,7 +2453,6 @@ class AmoebaStretchBendGenerator:
def createForcePostAmoebaHarmonicBondForce(self, sys, data, nonbondedMethod, nonbondedCutoff, angleList, args): def createForcePostAmoebaHarmonicBondForce(self, sys, data, nonbondedMethod, nonbondedCutoff, angleList, args):
verbose = 0
if (self.hasBeenCalled): if (self.hasBeenCalled):
return return
self.hasBeenCalled = 1 self.hasBeenCalled = 1
...@@ -2526,10 +2465,6 @@ class AmoebaStretchBendGenerator: ...@@ -2526,10 +2465,6 @@ class AmoebaStretchBendGenerator:
else: else:
force = existing[0] force = existing[0]
if (verbose):
print "In AmoebaStretchBendGenerator bonds=%d " % (len(data.bonds))
count = 0
for angleDict in angleList: for angleDict in angleList:
angle = angleDict['angle'] angle = angleDict['angle']
...@@ -2542,7 +2477,6 @@ class AmoebaStretchBendGenerator: ...@@ -2542,7 +2477,6 @@ class AmoebaStretchBendGenerator:
type2 = data.atomType[data.atoms[angle[1]]] type2 = data.atomType[data.atoms[angle[1]]]
type3 = data.atomType[data.atoms[angle[2]]] type3 = data.atomType[data.atoms[angle[2]]]
hit = 0
radian = 57.2957795130 radian = 57.2957795130
for i in range(len(self.types1)): for i in range(len(self.types1)):
...@@ -2555,10 +2489,6 @@ class AmoebaStretchBendGenerator: ...@@ -2555,10 +2489,6 @@ class AmoebaStretchBendGenerator:
# get ideal angle # get ideal angle
if (type2 in types2 and ((type1 in types1 and type3 in types3) or (type3 in types1 and type1 in types3))): if (type2 in types2 and ((type1 in types1 and type3 in types3) or (type3 in types1 and type1 in types3))):
if isConstrained:
hit = 1
else:
hit = 1
bondAB = -1.0 bondAB = -1.0
bondCB = -1.0 bondCB = -1.0
swap = 0 swap = 0
...@@ -2578,25 +2508,27 @@ class AmoebaStretchBendGenerator: ...@@ -2578,25 +2508,27 @@ class AmoebaStretchBendGenerator:
# check that ideal angle and bonds are set # check that ideal angle and bonds are set
if ('idealAngle' not in angleDict): if ('idealAngle' not in angleDict):
outputString = "AmoebaStretchBendGenerator: ideal angle is not set for following entry:\n" outputString = "AmoebaStretchBendGenerator: ideal angle is not set for following entry:\n"
outputString += " %5d [%5d %5d %5d] [%5s %5s %5s]" % (count, angle[0], angle[1], angle[2], type1, type2, type3) outputString += " types: %5s %5s %5s atoms: " % (type1, type2, type3)
outputString += getAtomPrint( data, angle[0] ) + ' '
outputString += getAtomPrint( data, angle[1] ) + ' '
outputString += getAtomPrint( data, angle[2] )
raise ValueError(outputString) raise ValueError(outputString)
elif (bondAB < 0 or bondCB < 0): elif (bondAB < 0 or bondCB < 0):
outputString = "AmoebaStretchBendGenerator: bonds not set: %15.7e %15.7e. for following entry:" % (bondAB, bondCB) outputString = "AmoebaStretchBendGenerator: bonds not set: %15.7e %15.7e. for following entry:" % (bondAB, bondCB)
outputString += " %5d [%5d %5d %5d] [%5s %5s %5s]" % (count, angle[0], angle[1], angle[2], type1, type2, type3) outputString += " types: [%5s %5s %5s] atoms: " % (type1, type2, type3)
outputString += getAtomPrint( data, angle[0] ) + ' '
outputString += getAtomPrint( data, angle[1] ) + ' '
outputString += getAtomPrint( data, angle[2] )
raise ValueError(outputString) raise ValueError(outputString)
else: else:
if (verbose):
print "AmoebaStretchBendGenerator %5d [%5d %5d %5d] [%5s %5s %5s] %15.6f %15.6f %15.6f %15.6f" % (count, angle[0], angle[1], angle[2], type1, type2, type3, bondAB, bondCB, angleDict['idealAngle'], self.k1[i])
force.addStretchBend(angle[0], angle[1], angle[2], bondAB, bondCB, angleDict['idealAngle']/radian, self.k1[i]) force.addStretchBend(angle[0], angle[1], angle[2], bondAB, bondCB, angleDict['idealAngle']/radian, self.k1[i])
break
if (hit == 0 and verbose):
print "AmoebaStretchBendGenerator missing: %5d missing [%5d %5d %5d] [%5s %5s %5s] " % (count, angle[0], angle[1], angle[2], type1, type2, type3)
count += 1 break
parsers["AmoebaStretchBendForce"] = AmoebaStretchBendGenerator.parseElement parsers["AmoebaStretchBendForce"] = AmoebaStretchBendGenerator.parseElement
...@@ -2691,7 +2623,6 @@ class AmoebaVdwGenerator: ...@@ -2691,7 +2623,6 @@ class AmoebaVdwGenerator:
sigmaMap = {'ARITHMETIC':1, 'GEOMETRIC':1, 'CUBIC-MEAN':1} sigmaMap = {'ARITHMETIC':1, 'GEOMETRIC':1, 'CUBIC-MEAN':1}
epsilonMap = {'ARITHMETIC':1, 'GEOMETRIC':1, 'HARMONIC':1, 'HHG':1} epsilonMap = {'ARITHMETIC':1, 'GEOMETRIC':1, 'HARMONIC':1, 'HHG':1}
verbose = 0
# get or create force depending on whether it has already been added to the system # get or create force depending on whether it has already been added to the system
...@@ -2709,7 +2640,7 @@ class AmoebaVdwGenerator: ...@@ -2709,7 +2640,7 @@ class AmoebaVdwGenerator:
force.setSigmaCombiningRule(sigmaRule.upper()) force.setSigmaCombiningRule(sigmaRule.upper())
else: else:
stringList = ' ' . join(str(x) for x in sigmaMap.keys()) stringList = ' ' . join(str(x) for x in sigmaMap.keys())
print "sigma combining rule %s not recognized; valid values are %s; using default." % (sigmaRule, stringList) raise ValueError( "AmoebaVdwGenerator: sigma combining rule %s not recognized; valid values are %s; using default." % (sigmaRule, stringList) )
else: else:
force.setSigmaCombiningRule(self.radiusrule) force.setSigmaCombiningRule(self.radiusrule)
...@@ -2719,7 +2650,7 @@ class AmoebaVdwGenerator: ...@@ -2719,7 +2650,7 @@ class AmoebaVdwGenerator:
force.setEpsilonCombiningRule(epsilonRule.upper()) force.setEpsilonCombiningRule(epsilonRule.upper())
else: else:
stringList = ' ' . join(str(x) for x in epsilonMap.keys()) stringList = ' ' . join(str(x) for x in epsilonMap.keys())
print "epsilon combining rule %s not recognized; valid values are %s; using default." % (epsilonRule, stringList) raise ValueError( "AmoebaVdwGenerator: epsilon combining rule %s not recognized; valid values are %s; using default." % (epsilonRule, stringList) )
else: else:
force.setEpsilonCombiningRule(self.epsilonrule) force.setEpsilonCombiningRule(self.epsilonrule)
...@@ -2729,6 +2660,7 @@ class AmoebaVdwGenerator: ...@@ -2729,6 +2660,7 @@ class AmoebaVdwGenerator:
force.setCutoff(float(args['vdwCutoff'])) force.setCutoff(float(args['vdwCutoff']))
else: else:
force.setCutoff(nonbondedCutoff) force.setCutoff(nonbondedCutoff)
if (nonbondedMethod == PME): if (nonbondedMethod == PME):
force.setPBC(1) force.setPBC(1)
force.setUseNeighborList(1) force.setUseNeighborList(1)
...@@ -2758,8 +2690,6 @@ class AmoebaVdwGenerator: ...@@ -2758,8 +2690,6 @@ class AmoebaVdwGenerator:
ivIndex = data.bonds[bondIndex].atom1 ivIndex = data.bonds[bondIndex].atom1
force.addParticle(ivIndex, classIndex, values[0], values[1], values[2]) force.addParticle(ivIndex, classIndex, values[0], values[1], values[2])
if (verbose):
print "Vdw %5d %5d %2d %15.7e %15.7e %15.7e" % (i, ivIndex, classIndex, values[0], values[1], values[2])
else: else:
raise ValueError('No vdw type for atom %s' % (atom.name)) raise ValueError('No vdw type for atom %s' % (atom.name))
...@@ -2789,13 +2719,6 @@ class AmoebaVdwGenerator: ...@@ -2789,13 +2719,6 @@ class AmoebaVdwGenerator:
exclusionSet.add(i) exclusionSet.add(i)
if (verbose):
print "VdwExcl %5d %s || %s" % (i, str(exclusionSet), str(bondedParticleSets[i]))
for atomIndex in sorted(exclusionSet):
atom = data.atoms[atomIndex]
print " %5d [%s %s %d]" % (atomIndex, atom.name, atom.residue.name, atom.residue.index)
print "\n"
force.setParticleExclusions(i, exclusionSet) force.setParticleExclusions(i, exclusionSet)
parsers["AmoebaVdwForce"] = AmoebaVdwGenerator.parseElement parsers["AmoebaVdwForce"] = AmoebaVdwGenerator.parseElement
...@@ -2927,8 +2850,6 @@ class AmoebaMultipoleGenerator: ...@@ -2927,8 +2850,6 @@ class AmoebaMultipoleGenerator:
types = forceField._findAtomTypes(atom, 1) types = forceField._findAtomTypes(atom, 1)
if types is not None: if types is not None:
# print "Multipole Atom %s types=%s." %(atom.attrib['type'], str(types))
# k-indices not provided default to 0 # k-indices not provided default to 0
kIndices = [int(atom.attrib['type'])] kIndices = [int(atom.attrib['type'])]
...@@ -3016,7 +2937,6 @@ class AmoebaMultipoleGenerator: ...@@ -3016,7 +2937,6 @@ class AmoebaMultipoleGenerator:
typeMap['pgrpMap'] = pgrpMap typeMap['pgrpMap'] = pgrpMap
typeMapList[ii] = typeMap typeMapList[ii] = typeMap
hit = 1 hit = 1
#print "Adding polarize for %s map=%d len=%d keys=%s" % (classIndex, ii, len(typeMapList), str(typeMap.keys()))
if (hit == 0): if (hit == 0):
outputString = "AmoebaMultipoleGenerator: error getting type for polarize: class index=%s not in multipole list?" % (atom.attrib['class']) outputString = "AmoebaMultipoleGenerator: error getting type for polarize: class index=%s not in multipole list?" % (atom.attrib['class'])
...@@ -3156,7 +3076,6 @@ class AmoebaMultipoleGenerator: ...@@ -3156,7 +3076,6 @@ class AmoebaMultipoleGenerator:
methodMap = {NoCutoff:mm.AmoebaMultipoleForce.NoCutoff, methodMap = {NoCutoff:mm.AmoebaMultipoleForce.NoCutoff,
PME:mm.AmoebaMultipoleForce.PME} PME:mm.AmoebaMultipoleForce.PME}
verbose = 0
# get or create force depending on whether it has already been added to the system # get or create force depending on whether it has already been added to the system
...@@ -3166,8 +3085,7 @@ class AmoebaMultipoleGenerator: ...@@ -3166,8 +3085,7 @@ class AmoebaMultipoleGenerator:
force = mm.AmoebaMultipoleForce() force = mm.AmoebaMultipoleForce()
sys.addForce(force) sys.addForce(force)
if (nonbondedMethod not in methodMap): if (nonbondedMethod not in methodMap):
print "Warning: AmoebaMultipoleForce: cutoff method not available using NoCutoff." raise ValueError( "AmoebaMultipoleForce: input cutoff method not available." )
force.setNonbondedMethod(mm.AmoebaMultipoleForce.NoCutoff)
else: else:
force.setNonbondedMethod(methodMap[nonbondedMethod]) force.setNonbondedMethod(methodMap[nonbondedMethod])
force.setCutoffDistance(nonbondedCutoff) force.setCutoffDistance(nonbondedCutoff)
...@@ -3433,9 +3351,6 @@ class AmoebaMultipoleGenerator: ...@@ -3433,9 +3351,6 @@ class AmoebaMultipoleGenerator:
# add particle if there was a hit # add particle if there was a hit
if (hit != 0): if (hit != 0):
if (verbose):
print "Multipole hit for Atom %5d %4s of %4s %4d type=%5s hitBranch=%d axes: %4d %4d %4d axisType=%1d." % (atomIndex,
atom.name, atom.residue.name, atom.residue.index, t, hit, zaxis, xaxis, yaxis, savedMultipoleDict['axisType'])
atom.multipoleDict = savedMultipoleDict atom.multipoleDict = savedMultipoleDict
atom.polarizationGroups = dict() atom.polarizationGroups = dict()
...@@ -3516,8 +3431,6 @@ class AmoebaWcaDispersionGenerator: ...@@ -3516,8 +3431,6 @@ class AmoebaWcaDispersionGenerator:
def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args): def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
verbose = 0
# get or create force depending on whether it has already been added to the system # get or create force depending on whether it has already been added to the system
existing = [sys.getForce(i) for i in range(sys.getNumForces())] existing = [sys.getForce(i) for i in range(sys.getNumForces())]
...@@ -3546,8 +3459,6 @@ class AmoebaWcaDispersionGenerator: ...@@ -3546,8 +3459,6 @@ class AmoebaWcaDispersionGenerator:
values = self.typeMap[t] values = self.typeMap[t]
force.addParticle(values[0], values[1]) force.addParticle(values[0], values[1])
if (verbose):
print "WcaDispersion %5d %15.7e %15.7e" % (i, values[0], values[1])
else: else:
raise ValueError('No WcaDispersion type for atom %s of %s %d' % (atom.name, atom.residue.name, atom.residue.index)) raise ValueError('No WcaDispersion type for atom %s of %s %d' % (atom.name, atom.residue.name, atom.residue.index))
...@@ -3628,8 +3539,7 @@ class AmoebaGeneralizedKirkwoodGenerator: ...@@ -3628,8 +3539,7 @@ class AmoebaGeneralizedKirkwoodGenerator:
shct = 0.88 shct = 0.88
if (shct < 0.0): if (shct < 0.0):
shct = 0.80 raise ValueError( "getObcShct: no GK overlap scale factor for atom %s of %s %d" % (atom.name, atom.residue.name, atom.residue.index) )
print "getObcShct: Warning no GK overlap scale factor for atom %s of %s %d using default value=%f" % (atom.name, atom.residue.name, atom.residue.index, shct)
return shct return shct
...@@ -3646,8 +3556,7 @@ class AmoebaGeneralizedKirkwoodGenerator: ...@@ -3646,8 +3556,7 @@ class AmoebaGeneralizedKirkwoodGenerator:
radius = 0.132 radius = 0.132
if (len(bondedAtomIndices) < 1): if (len(bondedAtomIndices) < 1):
outputString = "AmoebaGeneralizedKirkwoodGenerator: error getting atom bonded to %s of %s %d " % (atom.name, atom.residue.name, atom.residue.index) raise ValueError( "AmoebaGeneralizedKirkwoodGenerator: error getting atom bonded to %s of %s %d " % (atom.name, atom.residue.name, atom.residue.index) )
raise ValueError(outputString)
for bondedAtomIndex in bondedAtomIndices: for bondedAtomIndex in bondedAtomIndices:
bondedAtomAtomicNumber = data.atoms[bondedAtomIndex].element.atomic_number bondedAtomAtomicNumber = data.atoms[bondedAtomIndex].element.atomic_number
...@@ -3715,8 +3624,8 @@ class AmoebaGeneralizedKirkwoodGenerator: ...@@ -3715,8 +3624,8 @@ class AmoebaGeneralizedKirkwoodGenerator:
radius = 0.230 radius = 0.230
if (radius < 0.0): if (radius < 0.0):
radius = 2.0 outputString = "No GK radius for atom %s of %s %d" % (atom.name, atom.residue.name, atom.residue.index)
print "Warning no GK radius for atom %s of %s %d using default value=%f" % (atom.name, atom.residue.name, atom.residue.index, radius) raise ValueError( outputString )
return radius return radius
...@@ -3730,8 +3639,8 @@ class AmoebaGeneralizedKirkwoodGenerator: ...@@ -3730,8 +3639,8 @@ class AmoebaGeneralizedKirkwoodGenerator:
if (atomicNumber in bondiMap): if (atomicNumber in bondiMap):
radius = bondiMap[atomicNumber] radius = bondiMap[atomicNumber]
else: else:
radius = 0.206 outputString = "Warning no Bondi radius for atom %s of %s %d using default value=%f" % (atom.name, atom.residue.name, atom.residue.index, radius)
print "Warning no Bondi radius for atom %s of %s %d using default value=%f" % (atom.name, atom.residue.name, atom.residue.index, radius) raise ValueError( outputString )
return radius return radius
...@@ -3756,7 +3665,8 @@ class AmoebaGeneralizedKirkwoodGenerator: ...@@ -3756,7 +3665,8 @@ class AmoebaGeneralizedKirkwoodGenerator:
if (self.hasBeenCalled ): if (self.hasBeenCalled ):
return return
verbose = 0 if( nonbondedMethod != NoCutoff ):
raise ValueError( "Only the nonbondedMethod=NoCutoff option is available for implicit solvent simulations." )
# check if AmoebaMultipoleForce exists since charges needed # check if AmoebaMultipoleForce exists since charges needed
# if it has not been created, raise an error # if it has not been created, raise an error
...@@ -3796,7 +3706,6 @@ class AmoebaGeneralizedKirkwoodGenerator: ...@@ -3796,7 +3706,6 @@ class AmoebaGeneralizedKirkwoodGenerator:
force.setIncludeCavityTerm( int(self.includeCavityTerm)) force.setIncludeCavityTerm( int(self.includeCavityTerm))
else: else:
print "AmoebaGeneralizedKirkwoodForce exists"
force = existing[0] force = existing[0]
self.hasBeenCalled = 1 self.hasBeenCalled = 1
...@@ -3824,8 +3733,6 @@ class AmoebaGeneralizedKirkwoodGenerator: ...@@ -3824,8 +3733,6 @@ class AmoebaGeneralizedKirkwoodGenerator:
radius = self.getBondiTypeRadius(data, bonded12ParticleSets[atomIndex], atomIndex) radius = self.getBondiTypeRadius(data, bonded12ParticleSets[atomIndex], atomIndex)
shct = self.getObcShct(data, atomIndex) shct = self.getObcShct(data, atomIndex)
force.addParticle(multipoleParameters[0], radius, shct) force.addParticle(multipoleParameters[0], radius, shct)
if (verbose):
print "GeneralizedKirkwood %5d %15.7e %15.7e" % (atomIndex, multipoleParameters[0], radius, shct)
parsers["AmoebaGeneralizedKirkwoodForce"] = AmoebaGeneralizedKirkwoodGenerator.parseElement parsers["AmoebaGeneralizedKirkwoodForce"] = AmoebaGeneralizedKirkwoodGenerator.parseElement
...@@ -3834,9 +3741,7 @@ parsers["AmoebaGeneralizedKirkwoodForce"] = AmoebaGeneralizedKirkwoodGenerator.p ...@@ -3834,9 +3741,7 @@ parsers["AmoebaGeneralizedKirkwoodForce"] = AmoebaGeneralizedKirkwoodGenerator.p
class AmoebaUreyBradleyGenerator: class AmoebaUreyBradleyGenerator:
#============================================================================================= #=============================================================================================
"""An AmoebaUreyBradleyGenerator constructs a AmoebaUreyBradleyForce.""" """An AmoebaUreyBradleyGenerator constructs a AmoebaUreyBradleyForce."""
#============================================================================================= #=============================================================================================
def __init__(self, cubic, quartic): def __init__(self, cubic, quartic):
...@@ -3883,8 +3788,6 @@ class AmoebaUreyBradleyGenerator: ...@@ -3883,8 +3788,6 @@ class AmoebaUreyBradleyGenerator:
def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args): def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
verbose = 0
if (self.hasBeenCalled): if (self.hasBeenCalled):
return return
...@@ -3914,9 +3817,6 @@ class AmoebaUreyBradleyGenerator: ...@@ -3914,9 +3817,6 @@ class AmoebaUreyBradleyGenerator:
types3 = self.types3[i] types3 = self.types3[i]
if ((type1 in types1 and type2 in types2 and type3 in types3) or (type3 in types1 and type2 in types2 and type1 in types3)): if ((type1 in types1 and type2 in types2 and type3 in types3) or (type3 in types1 and type2 in types2 and type1 in types3)):
if (verbose):
print "AmoebaUreyBradleyGenerator %5d %5d %5d [%5s %5s %5s] %15.6f %15.6f" % (angle[0], angle[1], angle[2], type1, type2, type3, self.length[i], self.k[i])
force.addUreyBradley(angle[0], angle[2], self.length[i], self.k[i]) force.addUreyBradley(angle[0], angle[2], self.length[i], self.k[i])
break break
......
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