RadonPy Versions Save

RadonPy is a Python library to automate physical property calculations for polymer informatics.

v0.2.9

6 months ago

Future expansion: switching QM solvers Future expansion: switching force field Improvement: RESP calculations can be performed for all elements Fix: undefined variable in error messages of radonpy.sim.helper Fix: undefined variable in radonpy.sim.lammps.MolToLAMMPSdataBlock

v0.2.8

11 months ago

Implementation: read and write functions of a JSON file Implementation: IO helper functions for pipe-lining scripts Improvement: update sample scripts Bug fix: efield and dipole LAMMPS commands

v0.2.7

1 year ago

Enhancement: compatible for Python 3.11 Enhancement: compatible for Psi4 1.8 Enhancement: compatible for LAMMPS-23Jun2022 Bug fix: optimization convergence error had occur due to the scratch file of optimization remaining. Bug fix: undefined variable in sim.psi4_wrapper.Psi4w.scan

v0.2.6

1 year ago

Enhancement: convergence of DFT optimization in the molecules having a linear angle. Enhancement: changing behavior of psi4_mp=1 in conformation_search to avoid out of memory during psi4 running. Enhancement: changing behavior of mp=1 in polarizability calculation to avoid out of memory during psi4 running. Bug fix: for sample scripts

v0.3.0-beta.2

1 year ago

Implementation: reverse resolution of the Force Field Descriptors Implementation: MIC computation and visualization for the Force Field Descriptors Implementation: function of extracting side chains from SMILES (poly.extract_sidechain) Improvement: new interface of the Force Field Descriptors Improvement: some improvement are imported from v0.2.3-v0.2.5 Change: default value of polar in Force Field Descriptors is changed to True Change: default value of sigma in the Force Field Descriptor with kernel mean is changed to 1/nk/sqrt(2) Change: default value of stats in the Force Field Descriptor with summary statistics is changed to ['mean', 'std', 'max', 'min'] Bug fix: some bug fixes are imported from v0.2.3-v0.2.5 Bug fix: behavior of poly.terminate_rw when H is entered in mol1

v0.2.5

1 year ago

Improvement: added switching of the append keyword in the LAMMPS log file.

v0.2.4

1 year ago
  • Bug fix: Definition error in radonpy.sim.md.Dynamics

v0.2.3

1 year ago
  • Implementation: calculation of wavelength depended polarizability (radonpy.sim.qm.polarizability_sos)
  • Implementation: calculation of wavelength depended refractive index (radonpy.sim.qm.refractive_index_sos)
  • Implementation: calculation of abbe's number (radonpy.sim.qm.abbe_number_sos)
  • Improvement: charge and multiplicity of molecules are automatically set in radonpy.sim.psi4_wrapper.Psi4w
  • Improvement: add yaml files of the conda enviroment to easily install RadonPy
  • Bug fix: wrong code in the reflactive index calculation of copolymers (radonpy.core.calc.refractive_index)
  • Bug fix: return values of atomic coordinates of radonpy.sim.psi4_wrapper.Psi4w.scan
  • Bug fix: global variables (variables in radonpy.core.const) did not inherit to child processes

v0.2.2

2 years ago
  • Psi4 version 1.6 is now supported.
  • Implemented potential energy surface scan by Psi4.
  • Implemented constrained geometry optimization by Psi4.
  • Added CCSD method for polarizability calculation to psi4_wrapper.Psi4w.cc2_polar.
  • Fixed a bug that caused failure of geometry optimization in Psi4 for certain molecules due to failure of inverse transformation of internal coordinates.
  • Fixed return values when poly.polyinfo_classifier caused an error.
  • Fixed a bug that caused failure of 3D coordinates generation for certain molecules in utils.mol_from_smiles.
  • Fixed a bug that caused an error in poly.substruct_match_smiles_list.
  • Improved availability checks for LAMMPS packages.

v0.2.1

2 years ago
  • Fixed memory leak in the generation of polymer chains and simulation cells.
  • Changed behavior when the OpenMP parallel count setting for LAMMPS is 0 and 1.
  • Fixed to be able to use LAMMPS OPT package.
  • Changed default value of multiprocessing parallel count setting in the conformation search and polarizability calculation.