System

class pymem3dg._core.System

The system

Methods

System.__init__(*args, **kwargs)	Overloaded function.
System.addNonconservativeForcing(self[, ...])	Compute and append all non-conservative forces, update mechanicalForce(Vec) and mechErrorNorm
System.computeConservativeForcing(self)	Compute and update all conservative forces, update mechanicalForce(Vec) with conservativeForce(Vec)
System.computeInPlaneFluxForm(self, ...)	Compute in plane flux form from chemical potential
System.computeIntegratedPower(self, dt)	Intermediate function to integrate the power
System.computeTotalEnergy(self)	compute the total energy, where total energy = kinetic energy + potential energy - external work
System.getEnergy(self)	Get the energy
System.getForces(self)	Get the pointwise forces
System.getGeometry(self)	Get the geometry
System.getProteinDensity(self)	get the protein Density
System.getProteinRateOfChange(self)	get the protein rate of change
System.getSpontaneousCurvature(self)	get the pointwise spontaneous curvature
System.getVelocity(self)	get the vertex velocity matrix
System.initialize(self[, ifMutateMesh])	initialize the system
System.mutateMesh(self[, nMutation])	mutate the mesh
System.prescribeExternalForce(self)	prescribe the External Force
System.saveRichData(self, pathToSave[, ...])	save snapshot data to directory
System.smoothenMesh(self, initStep, target, ...)	smoothen the mesh using spontaneous curvature force
System.testConservativeForcing(self, timeStep)	test conservative force computation by validating energy decrease
System.updateConfigurations(self)	update the system configuration due to changes in state variables (e.g vertex positions or protein density)

Attributes

System.meshProcessor	Get the mesh processor object
System.parameters	Get the Parameters struct
System.time	Get the time