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 and `tail -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 to `statisticalInefficiency` (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