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OpenMichroM 1.0.7
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@junioreif junioreif released this 27 Jun 17:27
· 121 commits to main since this release
v1.0.7
27399e8

Main changes:
ChromDynamics.py:

  • addAdditionalForces() : one can add force objects after the system and context has been initialized
  • addCylindricalConfinement(): method to add confining external potential that is cylindrical
  • addCorrelatedNoise(): active noise can be added to the simulation object
  • addHarmonicBonds(): Harmonic bonds for nearest neighbors
  • addSelfAvoidance(): repulsive softcore without diverging LJ

Optimization.py:

  • modified cutoff into cutoff_low and cutoff_high in getPars
  • added norm in getPars -- normalization of input hic is now optional
  • get_lambdas_IC() def now computes and returns the new lambdas
  • Ideal Chromosome list of beads to be trained now should be informed in the initialization of CustomMiChroMTraining class by the new variable IClist.
  • get_lambdas_IC() and get_lambdas_types() def's now has the boolean variable write_error that computes the tolerance and Pearson correlation of the inversion and write in the output file tolerance_and_pearson.

Integrators.py:

  • added integrator object CustomBrownianIntegrator that uses active noise

Minor changes:

  • added Active Chromosome Dynamics tutorial to run correlated noise simulations
  • CustomMiChroMTraining() had its variable and def names standardized, mainly for the Types and Ideal Chromosome training procedure
  • added a tutorial for the Ideal Chromosome potential term
  • New scripts were included in the tutorial folder for the MiChroM training procedure on GPU-based clusters.
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