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Psi 4 integration#170

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obrien951 wants to merge 158 commits intoAutodesk:psi4Autodesk/molecular-design-toolkit:psi4from obrien951:psi4obrien951/molecular-design-toolkit:psi4Copy head branch name to clipboard

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Commits

Commits on Feb 8, 2017

• Fix nwchem parameter serialization

  avirshup

  committed
  2bbbe2c

• Deal with missing properties in nwchem

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  d0add2e

• Build MDT with working version, not repo version

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  committed
  0d12510

Commits on Feb 10, 2017

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

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  committed
  ce7d67d

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

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  committed
  7344bfb

Commits on Feb 17, 2017

• Correctly update positions after NWChem minimization

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  committed
  24239af

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

  avirshup

  committed
  b40f669

• Begin adding QM/MM interface for NWChem

  avirshup

  committed
  2c406e5

• Add forcefield formatting interface

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  committed
  d8f75b3

Commits on Feb 21, 2017

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

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  committed
  5e63c6c

• Update OpenMM interface with support from ParmEd

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  committed
  be931df

• Add abstract QM/MM classes

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  committed
  de72f13

Commits on Feb 22, 2017

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

  avirshup

  committed
  c6e19cd

• Fix various typos

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  committed
  a842890

• Get electronic embedding working

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  committed
  6c41b59

Commits on Feb 26, 2017

• Add integrated NWChem/sander build

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  committed
  86b966d

Commits on Apr 4, 2017

• Merge commit '3ea85bff941355ecf50d4aef6a1cbdf2de51d3f9' into nwchem_qmmm

  Show description for 520c458
  avirshup

  committed
  520c458

Commits on Apr 5, 2017

• Parse orbitals in movecs file

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  committed
  8709122

Commits on Apr 10, 2017

• Start getting AO basis functions from NWChem

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  committed
  3476cd3

Commits on Apr 11, 2017

• More orbital work

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  86e230b

Commits on May 18, 2017

• Merge branch 'widgetcleanup' into nwchem_qmmm

  Show description for c475de8
  avirshup

  committed
  c475de8

Commits on May 23, 2017

• Merge branch 'master' into nwchem_qmmm

  avirshup

  committed
  b923aaa

Commits on Jun 6, 2017

• Fix merge

  avirshup

  committed
  2bc5ce9

Commits on Jun 8, 2017

• Merge branch 'dev' into nwchem_qmmm

  Show description for e123651
  avirshup

  committed
  e123651

• NWChem in Python 3, with orbitals

  avirshup

  committed
  75185b4

• Fix XYZ writer

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  committed
  e08e652

Commits on Jun 9, 2017

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

  avirshup

  committed
  eca3ac0

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

  avirshup

  committed
  a6d8a1e

• Merge pull request Autodesk#156 from Autodesk/fix_energy_model_instantiation

  Show description for 88ab304
  avirshup

  authored
  88ab304

• --testall

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  committed
  d30e517

• Fixes openmm RPC

  Show description for 68506cd
  avirshup

  committed
  68506cd

• Merge pull request Autodesk#158 from Autodesk/pickleissues

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  avirshup

  authored
  e53384a

Commits on Jun 10, 2017

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

  avirshup

  committed
  9a6fa3e

• Merge pull request Autodesk#152 from Autodesk/dev

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  avirshup

  authored
  d395439

• Docker registry tokens

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  committed
  701d46c

• Prep for beta deployment

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  3d40029

• Option to skip test environments

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  avirshup

  committed
  aa4aecf

• Test example directory deployment

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  avirshup

  committed
  5566994

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

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  avirshup

  authored
  7352033

• Gets moldesign intro working in python 3

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  committed
  499a5f8

• Restore molecule markdown (was accidentally moved to nbmolviz)

  avirshup

  committed
  effa0cd

• Update final deployment steps

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  avirshup

  committed
  16a8570

• Merge branch 'master' into intro_experience

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  committed
  e82db7c

Commits on Jun 12, 2017

• More deployment work

  Show description for 42ca25e
  avirshup

  committed
  42ca25e

• Fix publish environment

  Show description for 936d3cc
  avirshup

  committed
  936d3cc

• Fix filename

  Show description for a06d948
  avirshup

  committed
  a06d948

• Correct version string

  avirshup

  committed
  16498cf

• more version string

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  committed
  93a2a3b

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

  Show description for 7053a6e
  avirshup

  committed
  7053a6e

Commits on Jun 13, 2017

• Use PEP440 versions, not semver

  avirshup

  committed
  ffac26d

• Add push to docker-make

  avirshup

  committed
  6407854

• Fix yml

  avirshup

  committed
  1868e7c

• Trying again to make publishing work

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  committed
  2a53bd7

• oops

  avirshup

  committed
  fd4d8e2

• docker auth key

  avirshup

  committed
  18b751a

• Login to registry thru docker-make

  avirshup

  committed
  ce9d6ae

• Merge pull request Autodesk#162 from Autodesk/deploy

  Show description for f03040a
  avirshup

  authored
  f03040a

• Merge master (commit 'f03040a0a321e9f1a36928bb3922fc2987f4e92a') into intro_experience

  Show description for ebe2a28
  avirshup

  committed
  ebe2a28

• Test coverage related to notebooks

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  committed
  c964d5c

• Handle more symmetry cases

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  committed
  67d8353

• Symmetry tests passing

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  committed
  5569d2a

• Cleanup and a little bug filing help

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  committed
  2d622a2

• Get first tutorial running

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  committed
  bbbc7f3

• Get tutorial 2 working

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  avirshup

  committed
  6dc522f

Commits on Jun 14, 2017

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

  avirshup

  committed
  311bfd0

• Attempt fix for CI docker problems

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  committed
  e0d7b63

• Basic test coverage for minimizers

  avirshup

  committed
  cf156c6

• Shameless improve test coverage by remove unused code

  avirshup

  committed
  41cd546

• Speed up a few easy bottlenecks

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  committed
  dd2cf5d

• Move unused functions out of scope

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  committed
  657215d

• Adds test coverage for some neglected code paths

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  committed
  e591fc0

• Test compressed file i/o

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  committed
  c0deeac

Commits on Jun 15, 2017

• update i/o to accept pathlib objects;

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  committed
  9942777

• mo tests mo problems

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  committed
  9802eb3

• Quick fixes for new tests

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  committed
  a6cfcd7

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

  Show description for 861422d
  avirshup

  committed
  861422d

• py2 compat fixes

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  committed
  0bf6eb7

• Add test coverage for GTO math

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  committed
  8dbdce6

• Scale energy conservation test with system size

  avirshup

  committed
  48374ef

• Get ERI calcs working again + better interface + tests

  avirshup

  committed
  d50c6e4

• Tests for ao basis, stream io, PDB queries

  avirshup

  committed
  1fc320d

• Final test coverage push for 0.8

  avirshup

  committed
  7bcbbbd

• Fix test typos

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  committed
  adb7f40

• Create README.md

  avirshup

  authored
  424d061

• Merge pull request Autodesk#161 from Autodesk/intro_experience

  Show description for c64d3dc
  avirshup

  authored
  c64d3dc

• Strip notebook output from repo

  avirshup

  committed
  5a2f2a1

Commits on Jun 16, 2017

• Bump pyccc to fix a race condition

  avirshup

  authored
  b15a84e

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

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  committed
  fa3ea27

• Give minimizers a runremotely method

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  committed
  7ac42b9

Commits on Jun 17, 2017

• Add test for pdbfixer mutation

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  committed
  6cade4c

• Add residue queries to chains and molecules

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  committed
  4d33955

• Gets mutate_residue running

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  committed
  97cac04

• Test docstring examples for mutation

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  committed
  e4badeb

• Get waterbox working

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  committed
  fb5ea58

• Clean up solvent box code

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  committed
  26b4b12

• Fix get_atoms keywords, ion queries

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  committed
  55370f4

• Get minimizers up to snuff

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  committed
  ff6f00e

• Missing test helper

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  committed
  4e7ca55

• Add symmetrizer test

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  committed
  d926ebb

Commits on Jun 18, 2017

• Prune unused code

  avirshup

  committed
  ce16ce3

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

  avirshup

  committed
  4939b93

Commits on Jun 19, 2017

• Update pyccc req to fix unicode bug, test tweaks

  avirshup

  committed
  b83faa3

• Tell py2 to use uniocde for xyz files

  avirshup

  committed
  65ba58f

• Merge pull request Autodesk#165 from Autodesk/deploy

  Show description for 939ed29
  avirshup

  authored
  939ed29

• Merge master commit '939ed29769f971374982a0663dcd3ab22d5f74a4' into nwchem_qmmm

  Show description for 0eab030
  avirshup

  committed
  0eab030

Commits on Jun 20, 2017

• More tests passing after merge

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  committed
  7ef3bfa

• Remove artifacts from merge

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  committed
  ae9b680

Commits on Jun 21, 2017

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

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  committed
  c4cb75f

• Return a Unit object from units.get_units

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  committed
  07e7424

• Fix some units corner cases

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  committed
  0aee891

Commits on Jun 22, 2017

• Add prinicipal moment of inertia calc

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  committed
  00da737

• Handle assigning to quantity from a quantities

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  committed
  7a989d1

Commits on Jun 23, 2017

• Clean up coords, add a better angle calculation

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  committed
  f093934

• Add Bond.align method

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  committed
  1a0afe5

• Fix vectorized angle calc

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  committed
  2bb7292

Commits on Jun 24, 2017

• Mechanical embedding works

  avirshup

  committed
  31d95f9

• Clean up bond alignment

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  committed
  8ea2308

Commits on Jun 25, 2017

• Clean up mathutils and tests

  avirshup

  committed
  b0ffd4d

• fixes pmi calculation, tests it

  avirshup

  committed
  767d3f5

• Return correct types from constraint gradients

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  committed
  835b8de

• Assigning units to a string always raises TypeError

  avirshup

  committed
  3f952f5

• Fix quantity exception handling

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  committed
  f0c96df

Commits on Jun 26, 2017

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

  avirshup

  committed
  5da7d2d

• Gets constrained optimization running again

  avirshup

  committed
  62a8491

• Fixes Autodesk#79

  avirshup

  committed
  8d74152

• Constraints starting to respect the requested tolerances

  avirshup

  committed
  f94834c

• H-bond constraint values taken from forcefield equilibrium lengths

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  committed
  e591d46

Commits on Jun 27, 2017

• Improved OpenMM constraint handling

  avirshup

  committed
  55236ac

• fix py2-only circular import

  avirshup

  committed
  6ff0a3a

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

  avirshup

  committed
  ceb3f31

• Calculate OpenMM energies even when constraints supported

  avirshup

  committed
  55fe9d9

• Move alignments to geom subpkg

  avirshup

  committed
  09408d0

• Cleanup CI and docker image docs

  avirshup

  committed
  855f10d

• Remove dead code

  avirshup

  committed
  7385b19

• Add OpenMM parameters for platform and CPU thread count.

  Show description for 7bcc4f6
  avirshup

  committed
  7bcc4f6

• Output and style tweaks

  avirshup

  committed
  68fec25

Commits on Jun 28, 2017

• Correct OpenMM API call

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  committed
  2255ed3

• Native string types for OpenMM C++ calls

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  committed
  68e8885

• Mark subset of tests for faster screening

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  committed
  8085b8a

• Stash changes

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  committed
  8c63e57

• Add spherical harmonics up to f functions

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  committed
  efaa71b

• Hook up SphericalGaussians, fix real harmonics signs

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  committed
  54f29c8

• Initial Psi4 interface calculates energies

  

  avirshup

  authored and

  Joseph O'Brien

  committed
  84ed89c

• Fix some random bugs

  

  avirshup

  authored and

  Joseph O'Brien

  committed
  0bffcd4

• Add cleanup, fix property access

  

  avirshup

  authored and

  Joseph O'Brien

  committed
  d4596e8

• Actually return the calculated properties

  

  avirshup

  authored and

  Joseph O'Brien

  committed
  16fbdc8

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

  

  Joseph O'Brien

  authored and

  Joseph O'Brien

  committed
  10831a1

• 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.

  Show description for 3b3bd27
  

  Joseph O'Brien

  authored and

  Joseph O'Brien

  committed
  3b3bd27

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

  Show description for 4be81a4
  

  Joseph O'Brien

  authored and

  Joseph O'Brien

  committed
  4be81a4

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.

  

  Joseph O'Brien

  authored and

  Joseph O'Brien

  committed
  7791426

• Fix pickling for minimizer objects in py2

  

  avirshup

  authored and

  Joseph O'Brien

  committed
  61958da

• Pin some versions

  Show description for fcc0686
  

  avirshup

  authored and

  Joseph O'Brien

  committed
  fcc0686

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.

  obrien951

  committed
  575e047

• 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…

  Show description for a33cf80
  obrien951

  committed
  a33cf80

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

  obrien951

  committed
  938d2f1

• clean psi4 model.

  obrien951

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  2512d96

• adds proper handling of psi4 calculations that return matrices.

  obrien951

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  13671ad

• adds testing of the MDT Psi4 Interface.

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  committed
  e928a2b