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- ivm.IVM(publicIVM.PublicIVM)
-
- MC
class MC(ivm.IVM) |
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analog of the ivm.IVM class which performs raw Monte Carlo
instead of dynamics/minimization.
NOTE: untested!
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- Method resolution order:
- MC
- ivm.IVM
- publicIVM.PublicIVM
- __builtin__.object
Methods defined here:
- Ra0(s)
- __del__(s)
- __init__(s, simulation)
- help(s)
- info(s)
- run(s)
- setRa0(s, v)
- setStepsizeA(s, v)
#accessors
- setTau(s, v)
- stepsizeA(s)
- tau(s)
- type(s)
- updateStepSize(s, dof, accepted)
Methods inherited from ivm.IVM:
- autoTorsion(s)
set up hinges for torsion angle dynamics/minimization
- baseAtoms(s)
- breakAllBondsIn(s, sel)
break all bonds between atoms in selection
- breakAllBondsTo(s, sel)
break all bonds to bonded atoms in selection
- breakBond(s, el)
specify selection consisting of two atoms corresponding to a
bond to break (topologically). The BOND potential is not altered.
- calcEnergy(s)
calculate energy in internal coordinates, and return the total
energy. This is a safe wrapper around the underlying calcEnergy
- constrainBond(s, el)
specify selection consisting of two atoms corresponding to a
bond to constrain
- finalTime(s)
- fix(s, sel)
- group(s, sel)
- hinge(s, hingeType, sel=None, *sels)
add a hinge definition of type hingeType for atoms specified by
sel, an atomSel.AtomSel, string or list of indices. Some
hinge types require additional selections specified as addtional
arguments.
- idAtom(s, i)
- init(s)
- numSteps(s)
- outputStepInfo(s, step, stepsize, type, totTime)
- printInterval(s)
- reset(s)
- resetCMInterval(s)
- resetReuse(s)
- reuse(s)
- setBaseAtoms(s, l)
- setBondExclude(s, v)
- setConstraintList(s, v)
- setFinalTime(s, v)
- setGroupList(s, v)
- setHingeList(s, v)
- setNumSteps(s, v)
- setPrintInterval(s, v)
- setResetCMInterval(s, v)
- setStepType(s, v)
- setStepsize(s, v)
- setTrajectory(s, v)
- stepsize(s)
- trajectory(s)
Methods inherited from publicIVM.PublicIVM:
- Ekinetic(*args)
- Epotential(*args)
- Etotal(*args)
- __getattr__ lambda self, name
- __repr__(self)
- __setattr__ lambda self, name, value
- adjustStepsize(*args)
- bathTemp(*args)
- bondExclude(*args)
- cTolerance(*args)
- calcTemperature(*args)
- constrainLengths(*args)
- constraintList(*args)
- currentTemp(*args)
- dEpred(*args)
- dim(*args)
- dof(*args)
- eCount(*args)
- eCountReset(*args)
- eTolerance(*args)
- frictionCoeff(*args)
- gTolerance(*args)
- gradMagnitude(*args)
- groupList(*args)
- groupTorsion(*args)
- hingeList(*args)
- initDynamics(*args)
- kBoltzmann(*args)
- maxCalls(*args)
- maxDeltaE(*args)
- maxTSFactor(*args)
- minStepSize(*args)
- minimization(*args)
- nodeList(*args)
- oldBaseAtoms(*args)
- pos(*args)
- potList(*args)
- printStepDetails(*args)
- recenterLargeDispl(*args)
- resetCM(*args)
- responseTime(*args)
- scaleVel(*args)
- setAdjustStepsize(*args)
- setBathTemp(*args)
- setCTolerance(*args)
- setConstrainLengths(*args)
- setDEpred(*args)
- setETolerance(*args)
- setFrictionCoeff(*args)
- setGTolerance(*args)
- setMaxCalls(*args)
- setMaxDeltaE(*args)
- setMaxTSFactor(*args)
- setMinStepSize(*args)
- setOldBaseAtoms(*args)
- setPos(*args)
- setPotList(*args)
- setRVecProd(*args)
- setRVecSize(*args)
- setRecenterLargeDispl(*args)
- setResponseTime(*args)
- setScaleVel(*args)
- setVecVec3Prod(*args)
- setVecVec3Size(*args)
- setVel(*args)
- setVerbose(*args)
- simulation(*args)
- step(*args)
- stepType(*args)
- vel(*args)
- velFromCartesian(*args)
- verbose(*args)
Data and other attributes inherited from publicIVM.PublicIVM:
- __dict__ = <dictproxy object at 0x2206d70>
dictionary for instance variables (if defined)
- __swig_getmethods__ = {}
- __swig_setmethods__ = {}
- __weakref__ = <attribute '__weakref__' of 'PublicIVM' objects>
list of weak references to the object (if defined)
- printCMVel = 32
- printCoords = 1
- printEnergy = 16
- printLoopDebug = 4096
- printLoopInfo = 8192
- printNodeDef = 2048
- printNodeForce = 64
- printNodeKE = 16384
- printNodePos = 128
- printNodeTheta = 256
- printResetCM = 2
- printStepDebug = 512
- printStepInfo = 1024
- printTemperature = 8
- printVelFromCartCost = 4
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