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- Method resolution order:
- MC
- ivm.IVM
- publicIVM.PublicIVM
- builtins.object
Methods defined here:
- Ra0(s)
- __del__(s)
- __init__(s, simulation)
- Constructor. The optional argument is a simulation.Simulation. By
default, the current simulation is used.
- help(s)
- info(s)
- return a string with info on the IVM settings.
An optional argument specifies information to return:
default
integrate - integration specific info
minimization - minimization specific info
topology - information about the topology settings
- run(s)
- Perform dynamics or minimization. Stop when numSteps have been
taken, or finalTime has been reached (whichever is first).
Returns an integer which is 1 on successfull completion of dynamics or
minimization and negative on failure.
- 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:
- addConfigAction(s, action)
- Add a command to be run before topology configuration via
protocol.torsionTopology or protocol.cartesianTopology.
- 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, *args)
- Argument is either two selections specifying one atom each or
a single selection specifying 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)
- fixedAtoms(s)
- Return an atomSel.AtomSel containing all atoms fixed in space.
- group(s, sel)
- groups(s)
- Return a list of atomSel.AtomSel objects corresponding to
atoms grouped in rigid bodies in this IVM object.
[This method converts the indices from groupList() into AtomSel
objects, discarding negative indices which are used for IVM internal
purposes.]
- 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)
- iters(s)
- Actual number of steps taken during dynamics or minimization. It is
reset and updated by run().
- minStepsize(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)
- setMinStepsize(s, v)
- setNumSteps(s, v)
- setPrintInterval(s, v)
- setResetCMInterval(s, v)
- setStepType(s, v)
- setStepsize(s, v)
- setStepsizeThreshold(s, v)
- setTrajectory(s, v)
- stepsize(s)
- stepsizeThreshold(s)
- time(s)
- Actual time elapsed during dynamics. It is reset and updated by
run().
- trajectory(s)
Methods inherited from publicIVM.PublicIVM:
- Ekinetic(self, *args, **kwargs) -> 'float_type'
- Epotential(self, *args, **kwargs) -> 'float_type'
- Etotal(self, *args, **kwargs) -> 'float_type'
- __repr__ = _swig_repr(self)
- adjustStepsize(self, *args, **kwargs) -> 'bool'
- bathTemp(self, *args, **kwargs) -> 'float_type'
- bondExclude(self, *args, **kwargs) -> 'CDSList< BondIDPair >'
- cTolerance(self, *args, **kwargs) -> 'float_type'
- calcTemperature(self, *args, **kwargs) -> 'void'
- clearRecalc(self, *args, **kwargs) -> 'void'
- constrainLengths(self, *args, **kwargs) -> 'bool'
- constraintList(self, *args, **kwargs) -> 'CDSList< BondIDPair >'
- currentTemp(self, *args, **kwargs) -> 'float_type'
- dEpred(self, *args, **kwargs) -> 'float_type'
- dim(self, *args, **kwargs) -> 'int'
- dof(self, *args, **kwargs) -> 'int'
- eCount(self, *args, **kwargs) -> 'int'
- eCountReset(self, *args, **kwargs) -> 'void'
- eTolerance(self, *args, **kwargs) -> 'float_type'
- forceRecalc(self, *args, **kwargs) -> 'void'
- frictionCoeff(self, *args, **kwargs) -> 'float_type'
- gTolerance(self, *args, **kwargs) -> 'float_type'
- gradMagnitude(self, *args, **kwargs) -> 'float_type'
- groupList(self, *args, **kwargs) -> 'CDSList< CDSList< int > >'
- groupTorsion(self, *args, **kwargs) -> 'void'
- hingeList(self, *args, **kwargs) -> 'CDSList< HingeSpec >'
- initDynamics(self, *args, **kwargs) -> 'void'
- kBoltzmann(self, *args, **kwargs) -> 'float_type'
- maxCalls(self, *args, **kwargs) -> 'int'
- maxDeltaE(self, *args, **kwargs) -> 'float_type'
- maxTSFactor(self, *args, **kwargs) -> 'float_type'
- minStepSize(self, *args, **kwargs) -> 'float_type'
- minimization(self, *args, **kwargs) -> 'bool'
- nodeList(self, *args, **kwargs) -> 'CDSList< PublicNode >'
- oldBaseAtoms(self, *args, **kwargs) -> 'CDSList< int >'
- pos(self, *args, **kwargs) -> 'CDSVector< double >'
- potList(self, *args) -> 'rc_DerivedPot< PotList > &'
- printStepDetails(self, *args, **kwargs) -> 'void'
- recenterLargeDispl(self, *args, **kwargs) -> 'bool const'
- resetCM(self, *args, **kwargs) -> 'void'
- responseTime(self, *args, **kwargs) -> 'float_type'
- restoreState(self, *args, **kwargs) -> 'void'
- saveState(self, *args, **kwargs) -> 'void'
- scaleVel(self, *args, **kwargs) -> 'bool'
- setAdjustStepsize(self, *args, **kwargs) -> 'void'
- setBathTemp(self, *args, **kwargs) -> 'void'
- setCTolerance(self, *args, **kwargs) -> 'void'
- setConstrainLengths(self, *args, **kwargs) -> 'void'
- setDEpred(self, *args, **kwargs) -> 'void'
- setETolerance(self, *args, **kwargs) -> 'void'
- setFrictionCoeff(self, *args, **kwargs) -> 'void'
- setGTolerance(self, *args, **kwargs) -> 'void'
- setMaxCalls(self, *args, **kwargs) -> 'void'
- setMaxDeltaE(self, *args, **kwargs) -> 'void'
- setMaxTSFactor(self, *args, **kwargs) -> 'void'
- setMinStepSize(self, *args, **kwargs) -> 'void'
- setOldBaseAtoms(self, *args, **kwargs) -> 'void'
- setPos(self, *args, **kwargs) -> 'void'
- setPotList(self, *args, **kwargs) -> 'void'
- setRVecProd(self, *args, **kwargs) -> 'void'
- setRVecSize(self, *args, **kwargs) -> 'void'
- setRecenterLargeDispl(self, *args, **kwargs) -> 'void'
- setResponseTime(self, *args, **kwargs) -> 'void'
- setScaleVel(self, *args, **kwargs) -> 'void'
- setVecVec3Prod(self, *args, **kwargs) -> 'void'
- setVecVec3Size(self, *args, **kwargs) -> 'void'
- setVel(self, *args, **kwargs) -> 'void'
- setVerbose(self, *args, **kwargs) -> 'void'
- simulation(self, *args, **kwargs) -> 'Simulation *'
- simulationGroupList(self, *args, **kwargs) -> 'CDSList< CDSList< int > >'
- step(self, *args, **kwargs) -> 'int'
- stepType(self, *args, **kwargs) -> 'char const *'
- vel(self, *args, **kwargs) -> 'CDSVector< double >'
- velFromCartesian(self, *args, **kwargs) -> 'void'
- verbose(self, *args, **kwargs) -> 'int'
Static methods inherited from publicIVM.PublicIVM:
- __swig_destroy__ = delete_PublicIVM(...)
Data descriptors inherited from publicIVM.PublicIVM:
- __dict__
dictionary for instance variables (if defined)
- __weakref__
list of weak references to the object (if defined)
- thisown
The membership flag
Data and other attributes inherited from publicIVM.PublicIVM:
- 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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