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Commit dbccc9dc authored by Peter Eastman's avatar Peter Eastman
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Fixed bug that caused ForceField to generate an incorrect System if used multiple times

parent a0977e05
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wrappers/python/simtk/openmm/app/forcefield.py
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...@@ -1435,7 +1435,6 @@ class AmoebaBondGenerator: ...@@ -1435,7 +1435,6 @@ class AmoebaBondGenerator:
self.types2 = [] self.types2 = []
self.length = [] self.length = []
self.k = [] self.k = []
self.hasBeenCalled = 0
#============================================================================================= #=============================================================================================
...@@ -1464,11 +1463,6 @@ class AmoebaBondGenerator: ...@@ -1464,11 +1463,6 @@ class AmoebaBondGenerator:
def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args): def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
if (self.hasBeenCalled):
return
self.hasBeenCalled = 1
#countConstraint(data) #countConstraint(data)
existing = [sys.getForce(i) for i in range(sys.getNumForces())] existing = [sys.getForce(i) for i in range(sys.getNumForces())]
...@@ -1554,8 +1548,6 @@ class AmoebaAngleGenerator: ...@@ -1554,8 +1548,6 @@ class AmoebaAngleGenerator:
self.angle = [] self.angle = []
self.k = [] self.k = []
self.hasBeenCalled = 0
#============================================================================================= #=============================================================================================
...@@ -1610,10 +1602,6 @@ class AmoebaAngleGenerator: ...@@ -1610,10 +1602,6 @@ class AmoebaAngleGenerator:
def createForcePostOpBendAngle(self, sys, data, nonbondedMethod, nonbondedCutoff, angleList, args): def createForcePostOpBendAngle(self, sys, data, nonbondedMethod, nonbondedCutoff, angleList, args):
if (self.hasBeenCalled):
return
self.hasBeenCalled += 1
# get force # get force
existing = [sys.getForce(i) for i in range(sys.getNumForces())] existing = [sys.getForce(i) for i in range(sys.getNumForces())]
...@@ -1688,8 +1676,6 @@ class AmoebaAngleGenerator: ...@@ -1688,8 +1676,6 @@ class AmoebaAngleGenerator:
def createForcePostOpBendInPlaneAngle(self, sys, data, nonbondedMethod, nonbondedCutoff, angleList, args): def createForcePostOpBendInPlaneAngle(self, sys, data, nonbondedMethod, nonbondedCutoff, angleList, args):
self.hasBeenCalled += 1
# get force # get force
existing = [sys.getForce(i) for i in range(sys.getNumForces())] existing = [sys.getForce(i) for i in range(sys.getNumForces())]
...@@ -1773,7 +1759,6 @@ class AmoebaOutOfPlaneBendGenerator: ...@@ -1773,7 +1759,6 @@ class AmoebaOutOfPlaneBendGenerator:
self.types4 = [] self.types4 = []
self.ks = [] self.ks = []
self.hasBeenCalled = 0
#============================================================================================= #=============================================================================================
# Local version of findAtomTypes needed since class indices are 0 (i.e., not recognized) # Local version of findAtomTypes needed since class indices are 0 (i.e., not recognized)
...@@ -1864,10 +1849,6 @@ class AmoebaOutOfPlaneBendGenerator: ...@@ -1864,10 +1849,6 @@ class AmoebaOutOfPlaneBendGenerator:
def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args): def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
if (self.hasBeenCalled):
return
self.hasBeenCalled = 1
# get force # get force
existing = [sys.getForce(i) for i in range(sys.getNumForces())] existing = [sys.getForce(i) for i in range(sys.getNumForces())]
...@@ -2017,8 +1998,6 @@ class AmoebaOutOfPlaneBendGenerator: ...@@ -2017,8 +1998,6 @@ class AmoebaOutOfPlaneBendGenerator:
if (force.__class__.__name__ == 'AmoebaAngleGenerator'): if (force.__class__.__name__ == 'AmoebaAngleGenerator'):
force.createForcePostOpBendAngle(sys, data, nonbondedMethod, nonbondedCutoff, nonInPlaneAngles, args) force.createForcePostOpBendAngle(sys, data, nonbondedMethod, nonbondedCutoff, nonInPlaneAngles, args)
force.createForcePostOpBendInPlaneAngle(sys, data, nonbondedMethod, nonbondedCutoff, inPlaneAngles, args) force.createForcePostOpBendInPlaneAngle(sys, data, nonbondedMethod, nonbondedCutoff, inPlaneAngles, args)
if (force.__class__.__name__ == 'AmoebaBondGenerator'):
force.createForce(sys, data, nonbondedMethod, nonbondedCutoff, args)
for force in self.forceField._forces: for force in self.forceField._forces:
if (force.__class__.__name__ == 'AmoebaStretchBendGenerator'): if (force.__class__.__name__ == 'AmoebaStretchBendGenerator'):
...@@ -2049,7 +2028,6 @@ class AmoebaTorsionGenerator: ...@@ -2049,7 +2028,6 @@ class AmoebaTorsionGenerator:
self.t1 = [] self.t1 = []
self.t2 = [] self.t2 = []
self.t3 = [] self.t3 = []
self.hasBeenCalled = 0
#============================================================================================= #=============================================================================================
...@@ -2103,10 +2081,6 @@ class AmoebaTorsionGenerator: ...@@ -2103,10 +2081,6 @@ class AmoebaTorsionGenerator:
def createForce(self, sys, data, nontorsionedMethod, nontorsionedCutoff, args): def createForce(self, sys, data, nontorsionedMethod, nontorsionedCutoff, args):
if (self.hasBeenCalled):
return
self.hasBeenCalled = 1
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.PeriodicTorsionForce] existing = [f for f in existing if type(f) == mm.PeriodicTorsionForce]
if len(existing) == 0: if len(existing) == 0:
...@@ -2169,7 +2143,6 @@ class AmoebaPiTorsionGenerator: ...@@ -2169,7 +2143,6 @@ class AmoebaPiTorsionGenerator:
self.types1 = [] self.types1 = []
self.types2 = [] self.types2 = []
self.k = [] self.k = []
self.hasBeenCalled = 0
#============================================================================================= #=============================================================================================
...@@ -2198,10 +2171,6 @@ class AmoebaPiTorsionGenerator: ...@@ -2198,10 +2171,6 @@ class AmoebaPiTorsionGenerator:
def createForce(self, sys, data, nonpiTorsionedMethod, nonpiTorsionedCutoff, args): def createForce(self, sys, data, nonpiTorsionedMethod, nonpiTorsionedCutoff, args):
if (self.hasBeenCalled):
return
self.hasBeenCalled = 1
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.AmoebaPiTorsionForce] existing = [f for f in existing if type(f) == mm.AmoebaPiTorsionForce]
...@@ -2292,8 +2261,6 @@ class AmoebaTorsionTorsionGenerator: ...@@ -2292,8 +2261,6 @@ class AmoebaTorsionTorsionGenerator:
self.gridIndex = [] self.gridIndex = []
self.grids = [] self.grids = []
self.hasBeenCalled = 0
#============================================================================================= #=============================================================================================
...@@ -2443,10 +2410,6 @@ class AmoebaTorsionTorsionGenerator: ...@@ -2443,10 +2410,6 @@ class AmoebaTorsionTorsionGenerator:
def createForce(self, sys, data, nonpiTorsionedMethod, nonpiTorsionedCutoff, args): def createForce(self, sys, data, nonpiTorsionedMethod, nonpiTorsionedCutoff, args):
if (self.hasBeenCalled):
return
self.hasBeenCalled = 1
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.AmoebaTorsionTorsionForce] existing = [f for f in existing if type(f) == mm.AmoebaTorsionTorsionForce]
...@@ -2536,7 +2499,6 @@ class AmoebaStretchBendGenerator: ...@@ -2536,7 +2499,6 @@ class AmoebaStretchBendGenerator:
self.k1 = [] self.k1 = []
self.k2 = [] self.k2 = []
self.hasBeenCalled = 0
#============================================================================================= #=============================================================================================
...@@ -2589,10 +2551,6 @@ class AmoebaStretchBendGenerator: ...@@ -2589,10 +2551,6 @@ class AmoebaStretchBendGenerator:
def createForcePostAmoebaBondForce(self, sys, data, nonbondedMethod, nonbondedCutoff, angleList, args): def createForcePostAmoebaBondForce(self, sys, data, nonbondedMethod, nonbondedCutoff, angleList, args):
if (self.hasBeenCalled):
return
self.hasBeenCalled = 1
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.AmoebaStretchBendForce] existing = [f for f in existing if type(f) == mm.AmoebaStretchBendForce]
if len(existing) == 0: if len(existing) == 0:
...@@ -2900,7 +2858,6 @@ class AmoebaMultipoleGenerator: ...@@ -2900,7 +2858,6 @@ class AmoebaMultipoleGenerator:
self.polar15Scale = polar15Scale self.polar15Scale = polar15Scale
self.typeMap = {} self.typeMap = {}
self.hasBeenCalled = 0
#============================================================================================= #=============================================================================================
# Set axis type # Set axis type
...@@ -3208,10 +3165,6 @@ class AmoebaMultipoleGenerator: ...@@ -3208,10 +3165,6 @@ class AmoebaMultipoleGenerator:
def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args): def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
if (self.hasBeenCalled ):
return
self.hasBeenCalled = 1
methodMap = {NoCutoff:mm.AmoebaMultipoleForce.NoCutoff, methodMap = {NoCutoff:mm.AmoebaMultipoleForce.NoCutoff,
PME:mm.AmoebaMultipoleForce.PME} PME:mm.AmoebaMultipoleForce.PME}
...@@ -3638,7 +3591,6 @@ class AmoebaGeneralizedKirkwoodGenerator: ...@@ -3638,7 +3591,6 @@ class AmoebaGeneralizedKirkwoodGenerator:
self.includeCavityTerm = includeCavityTerm self.includeCavityTerm = includeCavityTerm
self.probeRadius = probeRadius self.probeRadius = probeRadius
self.surfaceAreaFactor = surfaceAreaFactor self.surfaceAreaFactor = surfaceAreaFactor
self.hasBeenCalled = 0
self.radiusTypeMap = {} self.radiusTypeMap = {}
self.radiusTypeMap['Bondi'] = {} self.radiusTypeMap['Bondi'] = {}
...@@ -3820,9 +3772,6 @@ class AmoebaGeneralizedKirkwoodGenerator: ...@@ -3820,9 +3772,6 @@ class AmoebaGeneralizedKirkwoodGenerator:
def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args): def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
if (self.hasBeenCalled ):
return
if( nonbondedMethod != NoCutoff ): if( nonbondedMethod != NoCutoff ):
raise ValueError( "Only the nonbondedMethod=NoCutoff option is available for implicit solvent simulations." ) raise ValueError( "Only the nonbondedMethod=NoCutoff option is available for implicit solvent simulations." )
...@@ -3866,8 +3815,6 @@ class AmoebaGeneralizedKirkwoodGenerator: ...@@ -3866,8 +3815,6 @@ class AmoebaGeneralizedKirkwoodGenerator:
else: else:
force = existing[0] force = existing[0]
self.hasBeenCalled = 1
# add particles to force # add particles to force
# throw error if particle type not available # throw error if particle type not available
...@@ -3913,8 +3860,6 @@ class AmoebaUreyBradleyGenerator: ...@@ -3913,8 +3860,6 @@ class AmoebaUreyBradleyGenerator:
self.length = [] self.length = []
self.k = [] self.k = []
self.hasBeenCalled = 0
#============================================================================================= #=============================================================================================
@staticmethod @staticmethod
...@@ -3945,11 +3890,6 @@ class AmoebaUreyBradleyGenerator: ...@@ -3945,11 +3890,6 @@ class AmoebaUreyBradleyGenerator:
def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args): def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
if (self.hasBeenCalled):
return
self.hasBeenCalled = 1
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.HarmonicBondForce] existing = [f for f in existing if type(f) == mm.HarmonicBondForce]
......
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