Releases: leeping/forcebalance
Releases · leeping/forcebalance
Version 1.3.0 Major Release
The code is at a reasonably stable state with many features added since the previous release (version 1.2).
From this point forward I will implement the Thermo target (with pandas as a dependency) and add integration with MDTraj.
Major:
- Engine class is a unified interface to MD simulation codes.
- Added Gromacs, OpenMM, and TINKER engines.
- Thermo target; simple support for general thermodynamic properties. (Erik)
- Lipid target; lipid bilayer properties. (Keri
ForceBalance --continue
option continues an aborted run and loads as much data as possible from the latest iteration.- Parameter filtering allows targets to skip over parameters that are known to be irrelevant, for efficiency of finite difference derivatives.
- (Optimizer / Liquid / Lipid) Increase simulation length as we get closer to convergence.
- (Gromacs) Now supports binding energies, interaction energies, multipole moments and vibrational frequencies.
- (OpenMM) Now supports binding energies, interaction energies, and multipole moments.
- (
nifty.py
)exec_()
reads from stdout and stderr asynchronously, allowing us to split the streams andtail -f
the output at the same time.
Minor:
- (Gromacs) Improved behavior of .mdp file editor
- (OpenMM) Force fields with virtual sites are now working.
- (OpenMM) AMOEBA-style force fields now work with virtual sites.
- (TINKER) Improved behavior of .key file editor
- (
molecule.py
) Read Q-Chem error messages - (
molecule.py
) More decimals in GROMACS output coordinates - (
molecule.py
) Fix to Kabsch alignment - (
molecule.py
) Attempt simple repairs to object instead of crashing - (
molecule.py
) TINKER 6.3 compatibility; reads/writes .arc files with/without periodic boxes - (
molecule.py
) Delete symbolic link when attempting to write to one - (
molecule.py
) Simple function for making water molecules rigid - (
molecule.py
) Rebuild bonds when slicing by atom index - (
molecule.py
) Improved topology building; uses grid search and rectangular MIC for finding contacts. - (
molecule.py
) Methods for finding angles and dihedrals - (
molecule.py
) Pathwise RMSD (i.e. each frame's RMSD from previous) - (
molecule.py
) Try to figure out if .xyz is TINKER format or regular .xyz format - (
molecule.py
) Expand tabs to spaces when reading files - (
molecule.py
) Q-Chem output reader is more robust, reads IRC and FSM output - (
nifty.py
)extract_int
extracts representative integer value from floating point array - (
nifty.py
)monotonic
enforces monotonicity in a floating point array - (
nifty.py
)multiD_statisticalInefficiency
multidimensional wrapper tostatisticalInefficiency
(Keri) - (
nifty.py
) Improved WQ interface and CCTools version 4.1 compatibility - (
nifty.py
)click()
provides simple timing - (
nifty.py
)bak()
provides simple file backup - (
nifty.py
)onefile()
searches for one file with a provided extension - (
nifty.py
)wopen()
deletes symbolic link when attempting to write to one - (
nifty.py
)warn_press_key()
only pauses when running interactively