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Pydoc: module monteCarlo

monteCarlo

index

perform some Monte-Carlo operations. see randomizeTorsions below.

Classes

ivm.IVM(publicIVM.PublicIVM)

MC

class MC(ivm.IVM)

MC(simulation)

analog of the ivm.IVM class which performs raw Monte Carlo
instead of dynamics/minimization.

NOTE: untested!

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

Functions

randSign()

randomizeTorsions(ivm, sel='all', range=180): Randomize torsion angles in the input ivm (an ivm.IVM instance).
The ivm must be configured with at least one torsion hinge for this
function to modify any coordinates.

Applicable torsion angles are those whose two center atoms are contained in
the sel argument (an XPLOR selection string). Note that the ivm
configuration is respected so that rigid regions are not affected. The
argument range (a number; degrees) specifies the maximum +/- change in value
of each torsion angle.