Code

Cassandra gmso#756

Code

Merged

daico007 merged 52 commits intomosdef-hub:mainmosdef-hub/gmso:mainfrom emarinri:cassandra-gmsoemarinri/gmso:cassandra-gmsoCopy head branch name to clipboardSep 22, 2023

+834-234

Commits

Commits on Aug 11, 2023

• Add fixed length bonds and angles to potential templates library.

  

  rsdefever

  authored and

  emarinri

  committed
  665feb6

• Working to make MCF writer feature complete. Tests in progress.

  Show description for bd6ad75
  

  rsdefever

  authored and

  emarinri

  committed
  bd6ad75

• [pre-commit.ci] auto fixes from pre-commit.com hooks

  Show description for a6ce48d
  

  pre-commit-ci[bot]

  authored and

  emarinri

  committed
  a6ce48d

• Add dimensions to Fixed Bond and Angle templates

  emarinri

  committed
  a97826c

• Update keys in OPLS dihedral parameters dict

  Show description for c9bd1d1
  emarinri

  committed
  c9bd1d1

• Fix typed OPLS ethane test for MCF format

  Show description for 014b7ae
  emarinri

  committed
  014b7ae

• [pre-commit.ci] auto fixes from pre-commit.com hooks

  Show description for f41d5a9
  pre-commit-ci[bot]

  committed
  f41d5a9

Commits on Aug 13, 2023

• Add typed ethane test.

  Show description for f8e044c
  emarinri

  committed
  f8e044c

• Fix code style

  emarinri

  committed
  059ee03

• Add fixture to parse mcf into sections

  emarinri

  committed
  48fd600

• Support Pydantic v1 and v2 (mosdef-hub#752)

  Show description for aed4c44
  

  2 peopleauthored and

  emarinri

  committed
  aed4c44

Commits on Aug 15, 2023

• Update MCF with GMSO builtin top site sorting

  emarinri

  committed
  76415a8

• Use PotentialFilters to check for unique atomtypes

  emarinri

  committed
  f093262

• Add test to check charge neutrality

  emarinri

  committed
  44a0928

• Add test for incompatible expressions

  emarinri

  committed
  b9efc1b

Commits on Aug 16, 2023

• Test full MCF for Mie-Xe and LJ-Ar

  emarinri

  committed
  f9f2759

• Check charge neutrality in each molecule test

  emarinri

  committed
  5442297

• Add exception for not neutral system in MCF writer

  emarinri

  committed
  86902e6

Commits on Aug 17, 2023

• Move parsing and neutrality check as utils

  emarinri

  committed
  00cc2bc

Commits on Sep 2, 2023

• Merge branch 'main' into cassandra-gmso

  daico007

  authored
  73d24de

Commits on Sep 6, 2023

• Merge branch 'main' into cassandra-gmso

  daico007

  authored
  6094aba

Commits on Sep 11, 2023

• minor docstring/comment fixes, swap out simplify with symengine expand

  daico007

  committed
  51fdad8

• Merge branch 'main' of https://github.com/mosdef-hub/gmso into cassandra-gmso

  daico007

  committed
  5f4ca3c

Commits on Sep 12, 2023

• [pre-commit.ci] pre-commit autoupdate (mosdef-hub#763)

  Show description for 1dc0a3e
  

  pre-commit-ci[bot]

  authored and

  emarinri

  committed
  1dc0a3e

• Test for 0.5 factor of OPLS dihedral potential

  emarinri

  committed
  a1c3fb5

• Test to account for 0.5 factor in harmonic angles

  emarinri

  committed
  4578812

• Test for rigid angles using the TIP3P model

  emarinri

  committed
  6668363

Commits on Sep 13, 2023

• MCF writer test with topology with 10 argon mols

  emarinri

  committed
  80c9be3

• Tentative output of multiple MCF from one Topology

  emarinri

  committed
  2b0c7ee

• Merge branch 'main' into cassandra-gmso

  daico007

  authored
  8317de4

Commits on Sep 14, 2023

• Change psi to phi and consts for ethylene xml test

  emarinri

  committed
  3951954

• Test for 0.5 factor in OPLS dihedrals

  emarinri

  committed
  9579252

Commits on Sep 18, 2023

• Add cassandra test for gmso

  CalCraven

  committed
  ae69a8c

• [pre-commit.ci] auto fixes from pre-commit.com hooks

  Show description for 750d755
  pre-commit-ci[bot]

  committed
  750d755

Commits on Sep 19, 2023

• Add test for two atom fragment

  emarinri

  committed
  a7df9bc

• Test for molecule with one ring

  emarinri

  committed
  685f8b8

• Change nitrogen test to ethane ua

  emarinri

  committed
  1252d2b

• Add ethane rigid reference xml

  emarinri

  committed
  ec3a5dd

• Use Fourier dihedrals as MCF standard dihedrals.

  emarinri

  committed
  a30d7bd

• Fix dihedral type output fourier to opls

  emarinri

  committed
  64b5b8f

Commits on Sep 20, 2023

• Match MCF GMSO Angle header to mb Angle header

  emarinri

  committed
  ad68575

• Add a test comparing gmso and mbuild mcf writers

  emarinri

  committed
  0759365

• Use the Fourier converter for ethylene dihedrals

  emarinri

  committed
  cf4e0c0

• Write atom type masses instead of atom masses to account for UA beads

  emarinri

  committed
  f462d5b

• Output correct case for dihedral styles in MCFs

  emarinri

  committed
  2a40bbf

• Merge branch 'main' into cassandra-gmso

  daico007

  authored
  c12a120

• Merge branch 'cassandra-gmso' of https://github.com/emarinri/gmso into cassandra-gmso

  emarinri

  committed
  6ff41e2

• Run an energy calculation to compare GMSO and mBuild MCF writers

  emarinri

  committed
  c1b9c19

Commits on Sep 21, 2023

• Merge branch 'main' into cassandra-gmso

  daico007

  authored
  dcdc342

• Update gmso/tests/test_mcf.py

  daico007

  authored
  3c12947

• Update gmso/tests/test_mcf.py

  daico007

  authored
  a1f4853

Commits on Sep 22, 2023

• Merge branch 'main' into cassandra-gmso

  daico007

  authored
  f38cfb6