Version 1.7.4 minor release

This release provides compatibility with the Open Force Field Toolkit (OFFTK) v0.7.0, and breaks compatibility with earlier versions. The README has been updated with conda-forge installation instructions.

Version 1.7.3 minor release

#54 Minor changes

• Fix setup.py to raise an error when numpy and scipy cannot be imported.

Version 1.7.2 minor release

Major changes

• Improved convergence criteria so that step size criterion can be satisfied before actually evaluating the objective function at the next step (see comments in code).

Minor changes

• Updates the evaluator target to use the syntax of the full openff-evaluator release rather than the beta syntax.
• Updated molecular weights and physical constants to most recent recommended values from CODATA and NIST.
• Improved error checking in .xyz parser in molecule.py
• ForceBalance-formatted vibrational data can now be read as input (in addition to being written as output).

Version 1.7.1 minor release

New features

OpenFF evaluator

• propertyestimator interface code has been migrated to new openff-evaluator (Simon Boothroyd)

Minor changes

• Enable saving of MM optimized geometries in optimized geometry targets (Hyesu Jang)
• Start adding reference output files from current and previous versions (Lee-Ping Wang)

Version 1.7.0 Major Release

New features

PyTest framework

• Fully migrated from unittest to pytest, motivated by inscrutable test failures on Travis when the old framework was used
• All tests are now located in <root>/src/tests

MacOS support

• Mac OS is supported for Python 3.5 or greater.
• A small but important fix was added in nifty.py to handle streams from processes on Mac OS

Torsion profile target

• This target allows 1D relaxed torsion profiles to be included in the objective function, with the option to carry out MM relaxations (with torsion atoms frozen).
• Implemented and tested using SMIRNOFF engine but expected to work for OpenMM.
• Support in other engines will require implementing energy minimizations with frozen atoms.

Optimized geometry target

• This target allows (QM-MM) deviations in energy-minimized bonds and angles to be included in the objective function.
• Implemented and tested using SMIRNOFF engine but expected to work for OpenMM and other engines that support energy minimization.

Surface tension target

• This target calculates surface tension and enables the deviation of calculated vs. experimental surface tension to be included in the objective function.
• Implemented and tested using OpenMM engine.
• Implementation is described in publication located at https://doi.org/10.1021/acs.jpcb.9b05455

PropertyEstimator / Evaluator target

• This target includes an interface to the OpenFF Evaluator framework (previously called PropertyEstimator) to include evaluated properties in the objective function.
• Uses Evaluator API to compute parametric gradients.
• SMIRNOFF is the only supported engine.
• PropertyEstimator can be found here: https://github.com/openforcefield/propertyestimator

Fitting vibrational frequencies using OpenMM

• Vibration_OpenMM: OpenMM can now compute vibrational frequencies and normal modes

Minor changes

• Enable optimization of charges in .mol2 files when working with SMIRNOFF-formatted force field
• Cookiecutter, codecov and versioneer integrations
• Sanitizing .offxml force field parsing for SMIRKS strings
• constrain_h option in FB input file for specifying H-bond constraints in OpenMM targets
• Improved tools/install_cctools.sh script for Work Queue installs
• Simplify AtomContact function in molecule.py
• Improvements in performance using SMIRNOFF force fields
• Improved remote target file handling
• Improved stability of Hessian diagonalization
• Keep up to date with SMIRNOFF .offxml formatting
• Improved handling of Work Queue workers
• Fix a bug in radius of gyration calculation in molecule.py

Credits

• Yudong Qiu (Optimized geometry target, surface tension target, OpenMM normal modes, SMIRNOFF performance, and various improvements)
• Jeffrey Wagner (MacOS support, Pytest framework)
• Simon Boothroyd (OpenFF Evaluator / propertyestimator interface)
• Hyesu Jang (Pytest framework)
• Michael Schauperl (H-bond constraint)
• Open Force Field Initiative (financial support)

Version 1.6.0 Major Release

New features:

Preliminary support for SMIRNOFF 0.1

Read and write SMIRNOFF force field format. New targets enable the optimization of QM single-point properties and liquid properties using the SMIRNOFF force field.

New penalty functions

Specify a higher power of the L2 norm using:

penalty_power 12.0

Specify separate constraints for each parameter as mvals[i]^power using:

penalty_type box
penalty_power 12.0

Note that penalty_type box and penalty_type L2 are equivalent if the default value of penalty_power (i.e. 2.0) is used.

Version 1.5.5 Minor Release

New features in molecule.py:

• Rotate a molecule rigidly about a chosen bond and check for close contacts: Molecule.rotate_check_clash()
• Molecule.measure_distance and Molecule.measure_angle functions (John Stoppelman)
• Use a predefined energy_rms_override constant for normalizing the energy errors in energy matching.

Fixes:

• Improve the reading of multi-fold dihedrals in AMBER .frcmod format
• Improves force field formatting matching of tools/MatchFormatting.py. Mainly used when projects are finished and you want to create a parameter file for "publication".

Version 1.5.4 Minor Release

New features:

• Fitting of condensed-phase properties in AMBER

Bug fixes:

• Allow free parameters in text and XML force field files simultaneously
• Fixed bugs in handling of Mol2 input/output
• Remove usage of pending-deprecation numpy.matrix
• Update Work Queue printout for compatibility with CCTools version 6+

Version 1.5.1 Minor Release

Tests pass on Travis; this version is the first Conda-installable version

Version 1.5.0 Major Release

The biggest changes in this release are:

• Python 3 compatibility.
• License changed to BSD 3-clause license.