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Psi 4 integration#170

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Commits on Feb 8, 2017

• Fix nwchem parameter serialization

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• Deal with missing properties in nwchem

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• Build MDT with working version, not repo version

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Commits on Feb 10, 2017

• Handle .smiles and .inchi files; always use direct integrals in NWCHem

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• Correct NWChem image path; better handling of PDB files w/ missing chain IDs

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Commits on Feb 17, 2017

• Correctly update positions after NWChem minimization

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• Expand QM tests, write a ridiculous number of digits for XYZ files

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• Begin adding QM/MM interface for NWChem

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• Add forcefield formatting interface

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Commits on Feb 21, 2017

• Switch forcefield storage to ParmEd, wrap it for easier manipulation

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• Update OpenMM interface with support from ParmEd

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• Add abstract QM/MM classes

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Commits on Feb 22, 2017

• Get mechanical embedding QM/MM working (with orbital visualization!)

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• Fix various typos

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• Get electronic embedding working

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Commits on Feb 26, 2017

• Add integrated NWChem/sander build

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Commits on Apr 4, 2017

• Merge commit '3ea85bff941355ecf50d4aef6a1cbdf2de51d3f9' into nwchem_qmmm

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Commits on Apr 5, 2017

• Parse orbitals in movecs file

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Commits on Apr 10, 2017

• Start getting AO basis functions from NWChem

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Commits on Apr 11, 2017

• More orbital work

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Commits on May 18, 2017

• Merge branch 'widgetcleanup' into nwchem_qmmm

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Commits on May 23, 2017

• Merge branch 'master' into nwchem_qmmm

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Commits on Jun 6, 2017

• Fix merge

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Commits on Jun 8, 2017

• Merge branch 'dev' into nwchem_qmmm

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• NWChem in Python 3, with orbitals

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• Fix XYZ writer

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Commits on Jun 9, 2017

• Add mp2 bindings (although dockerfile doesn't have that?)

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• New-style supers don't appear to work in classes with metaclasses

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• Merge pull request Autodesk#156 from Autodesk/fix_energy_model_instantiation

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• --testall

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• Fixes openmm RPC

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• Merge pull request Autodesk#158 from Autodesk/pickleissues

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Commits on Jun 10, 2017

• pytest-xdist rollback, possibly see pytest-dev/pytest-xdist#157

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• Merge pull request Autodesk#152 from Autodesk/dev

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• Docker registry tokens

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• Prep for beta deployment

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• Option to skip test environments

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• Test example directory deployment

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• Merge pull request Autodesk#160 from Autodesk/deploy0.8beta

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• Gets moldesign intro working in python 3

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• Restore molecule markdown (was accidentally moved to nbmolviz)

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• Update final deployment steps

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• Merge branch 'master' into intro_experience

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Commits on Jun 12, 2017

• More deployment work

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• Fix publish environment

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• Fix filename

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• Correct version string

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• more version string

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• fun with versions (note: not really all that fun)

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Commits on Jun 13, 2017

• Use PEP440 versions, not semver

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• Add push to docker-make

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• Fix yml

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• Trying again to make publishing work

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• oops

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• docker auth key

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• Login to registry thru docker-make

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• Merge pull request Autodesk#162 from Autodesk/deploy

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• Merge master (commit 'f03040a0a321e9f1a36928bb3922fc2987f4e92a') into intro_experience

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• Test coverage related to notebooks

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• Handle more symmetry cases

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• Symmetry tests passing

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• Cleanup and a little bug filing help

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• Get first tutorial running

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• Get tutorial 2 working

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Commits on Jun 14, 2017

• Run tests from repo root (fixes weird coverage issues)

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• Attempt fix for CI docker problems

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• Basic test coverage for minimizers

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• Shameless improve test coverage by remove unused code

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• Speed up a few easy bottlenecks

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• Move unused functions out of scope

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• Adds test coverage for some neglected code paths

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• Test compressed file i/o

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Commits on Jun 15, 2017

• update i/o to accept pathlib objects;

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• mo tests mo problems

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• Quick fixes for new tests

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• Keep persistent references in result objects, even if generated remotely

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• py2 compat fixes

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• Add test coverage for GTO math

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• Scale energy conservation test with system size

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• Get ERI calcs working again + better interface + tests

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• Tests for ao basis, stream io, PDB queries

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• Final test coverage push for 0.8

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• Fix test typos

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• Create README.md

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• Merge pull request Autodesk#161 from Autodesk/intro_experience

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• Strip notebook output from repo

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Commits on Jun 16, 2017

• Bump pyccc to fix a race condition

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• Test SHAKE through minimizers, rather than the previous hacky solution

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• Give minimizers a runremotely method

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Commits on Jun 17, 2017

• Add test for pdbfixer mutation

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• Add residue queries to chains and molecules

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• Gets mutate_residue running

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• Test docstring examples for mutation

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• Get waterbox working

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• Clean up solvent box code

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• Fix get_atoms keywords, ion queries

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• Get minimizers up to snuff

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• Missing test helper

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• Add symmetrizer test

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Commits on Jun 18, 2017

• Prune unused code

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• Minimizations run in the same environment as the model, if possible

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Commits on Jun 19, 2017

• Update pyccc req to fix unicode bug, test tweaks

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• Tell py2 to use uniocde for xyz files

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• Merge pull request Autodesk#165 from Autodesk/deploy

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• Merge master commit '939ed29769f971374982a0663dcd3ab22d5f74a4' into nwchem_qmmm

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Commits on Jun 20, 2017

• More tests passing after merge

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• Remove artifacts from merge

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Commits on Jun 21, 2017

• Add "io", "internal" pytest marks for easier test selection

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• Return a Unit object from units.get_units

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• Fix some units corner cases

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Commits on Jun 22, 2017

• Add prinicipal moment of inertia calc

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• Handle assigning to quantity from a quantities

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Commits on Jun 23, 2017

• Clean up coords, add a better angle calculation

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• Add Bond.align method

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• Fix vectorized angle calc

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Commits on Jun 24, 2017

• Mechanical embedding works

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• Clean up bond alignment

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Commits on Jun 25, 2017

• Clean up mathutils and tests

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  b0ffd4d

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• fixes pmi calculation, tests it

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• Return correct types from constraint gradients

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• Assigning units to a string always raises TypeError

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• Fix quantity exception handling

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Commits on Jun 26, 2017

• Adds constraint type for h-bonds + holonomic decomposition machinery

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• Gets constrained optimization running again

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• Fixes Autodesk#79

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• Constraints starting to respect the requested tolerances

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• H-bond constraint values taken from forcefield equilibrium lengths

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Commits on Jun 27, 2017

• Improved OpenMM constraint handling

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• fix py2-only circular import

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• Set constraints earlier, don't assume parmed list orderings

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• Calculate OpenMM energies even when constraints supported

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• Move alignments to geom subpkg

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• Cleanup CI and docker image docs

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• Remove dead code

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• Add OpenMM parameters for platform and CPU thread count.

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• Output and style tweaks

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Commits on Jun 28, 2017

• Correct OpenMM API call

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• Native string types for OpenMM C++ calls

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• Mark subset of tests for faster screening

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• Stash changes

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• Add spherical harmonics up to f functions

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• Hook up SphericalGaussians, fix real harmonics signs

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• Initial Psi4 interface calculates energies

  

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• Fix some random bugs

  

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• Add cleanup, fix property access

  

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• Actually return the calculated properties

  

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• Allows psi4 energy calculations to be run and "potential_energy" and "'dipole'" to be returned. Syntax for "'dipole'" collection will be changed.

  

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• In the ElectronicWfn object, a gradient attribute was added to help with minimizing molecules using qm packages. The gradient will be assigned to the wavefunction using the constructor.

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• The psi4_interface mdt_to_psi4 function now returns a psi4 molecule instead of a string.

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Commits on Jul 17, 2017

• One electron property management was added for psi4. A minimize function was added to the psi4 model. The molecule class was prepared for addding molecular vibrations.

  

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• Fix pickling for minimizer objects in py2

  

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• Pin some versions

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Commits on Jul 27, 2017

• Add features to one electron properties for molecules following psi4 calculations. These changes consisted of handling of units and data structuring of certain quantities.

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• Add handling of normal mode displacements for vizualization and put in a skeleton for saving normal mode displacements to atoms. The skeletal additions to the atoms will need to be reviewed and ren…

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• adds features for advanced psi4 users whose calculations will create fail cases.

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• clean psi4 model.

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• adds proper handling of psi4 calculations that return matrices.

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• adds testing of the MDT Psi4 Interface.

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