Code

Aniso CG implementation#54

Code

Merged

RainierBarrett merged 99 commits intocmelab:maincmelab/grits:mainfrom RainierBarrett:Aniso_rebasedRainierBarrett/grits:Aniso_rebasedCopy head branch name to clipboardDec 6, 2023

+422-24

Commits

Commits on Oct 20, 2023

• Added our utility functions for use for aniso mapping

  

  Dani Rojas

  authored and

  RainierBarrett

  committed
  a3b0e9f

• Editted the utility file to match an earlier commit we made when we editted the "get_axis_angle" function to calculate the quaternions directly.

  

  Dani Rojas

  authored and

  RainierBarrett

  committed
  e0331af

• Minor name adjustments

  

  Noah Montrose

  authored and

  RainierBarrett

  committed
  867880e

• Start adding aniso mapping flags

  

  Noah Montrose

  authored and

  RainierBarrett

  committed
  ff1ab01

• Add guard against error from zero bond systems

  

  Noah Montrose

  authored and

  RainierBarrett

  committed
  48e2cf3

• Add logic for aniso mapping

  RainierBarrett

  committed
  e5a4cca

• Add orientation tracking array. Fails to save single frame.

  RainierBarrett

  committed
  b7786c8

• Aniso Mapping works

  

  Noah Montrose

  authored and

  RainierBarrett

  committed
  39b3549

• fixed some orientaiton logic for non-aniso systems

  

  Noah Montrose

  authored and

  RainierBarrett

  committed
  377f969

• Still resolving the off by one issue for the bond list

  

  Noah Montrose

  authored and

  RainierBarrett

  committed
  c687d29

• Change to variables for mapping strings to prevent typos

  RainierBarrett

  committed
  ba82049

• remove debug statements, add guard for single-bead mappings

  RainierBarrett

  committed
  2c18a0b

• Set default quaternion for beads with <3 heavy atoms

  RainierBarrett

  committed
  61a3b75

• Address mass scaling in aniso position calculations

  RainierBarrett

  committed
  2a0e87b

• Remove superfluous(?) re-wrap of bead positions

  RainierBarrett

  committed
  8d7cb39

• merge from upstream

  RainierBarrett

  committed
  fcbc178

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

  Show description for b2a5c68
  pre-commit-ci[bot]

  committed
  b2a5c68

Commits on Oct 23, 2023

• [pre-commit.ci] pre-commit autoupdate

  Show description for 571ef95
  pre-commit-ci[bot]

  authored
  571ef95

• Merge pull request cmelab#55 from cmelab/pre-commit-ci-update-config

  Show description for ea2c3bc
  chrisjonesBSU

  authored
  ea2c3bc

Commits on Oct 24, 2023

• begin aniso coverage tests

  RainierBarrett

  committed
  5a85eaf

• Merge branch 'Aniso_rebased' of github.com:RainierBarrett/grits into Aniso_rebased

  RainierBarrett

  committed
  ec9f230

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

  Show description for e7a5ee4
  pre-commit-ci[bot]

  committed
  e7a5ee4

Commits on Oct 25, 2023

• more aniso unit tests

  RainierBarrett

  committed
  d46e210

• Merge branch 'Aniso_rebased' of github.com:RainierBarrett/grits into Aniso_rebased

  RainierBarrett

  committed
  d7cfe68

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

  Show description for 39b8f99
  pre-commit-ci[bot]

  committed
  39b8f99

• system saving unit test

  RainierBarrett

  committed
  976f73a

• Merge branch 'Aniso_rebased' of github.com:RainierBarrett/grits into Aniso_rebased

  RainierBarrett

  committed
  28cd08c

• remove unused minor axis finder

  RainierBarrett

  committed
  2204a6d

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

  Show description for c5b9191
  pre-commit-ci[bot]

  committed
  c5b9191

• make CI happy

  RainierBarrett

  committed
  6acbbef

• Merge branch 'Aniso_rebased' of github.com:RainierBarrett/grits into Aniso_rebased

  RainierBarrett

  committed
  effb79b

• Add COM test

  RainierBarrett

  committed
  d7f67dc

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

  Show description for 1eaece6
  pre-commit-ci[bot]

  committed
  1eaece6

Commits on Oct 26, 2023

• add check for mass to CG_System

  chrisjonesBSU

  committed
  cb90cc6

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

  Show description for c188c93
  pre-commit-ci[bot]

  committed
  c188c93

• gsd files for testing orientation functionality

  

  Dani Rojas

  committed
  cc3bae3

• Merge branch 'Aniso_rebased' of github.com:RainierBarrett/grits into Aniso_rebased

  

  Dani Rojas

  committed
  614bf3b

• Re-add python and numpy to env yaml

  RainierBarrett

  committed
  e3a6c59

• remove old smiles comment

  RainierBarrett

  committed
  8903718

Commits on Oct 30, 2023

• [pre-commit.ci] pre-commit autoupdate

  Show description for 964d982
  pre-commit-ci[bot]

  authored
  964d982

Commits on Nov 2, 2023

• Condense pps rotation test gsd to one file. new test in progress

  RainierBarrett

  committed
  82dc599

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

  Show description for 6564a27
  pre-commit-ci[bot]

  committed
  6564a27

Commits on Nov 10, 2023

• Add build info

  Show description for 129d4ec
  jennyfothergill

  authored
  129d4ec

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

  Show description for d894976
  pre-commit-ci[bot]

  committed
  d894976

• Add mamba as python version

  jennyfothergill

  committed
  7b1eca6

• Try unpinning versions

  jennyfothergill

  committed
  fff33c1

• Merge pull request cmelab#57 from cmelab/jennyfothergill-fix-docs

  Show description for 839cdcf
  jennyfothergill

  authored
  839cdcf

• Merge pull request cmelab#56 from cmelab/pre-commit-ci-update-config

  Show description for 2b37495
  jennyfothergill

  authored
  2b37495

Commits on Nov 13, 2023

• clean up setup.py file for making conda-forge recipe

  chrisjonesBSU

  committed
  77b485f

• Merge pull request cmelab#58 from chrisjonesBSU/setup-file

  Show description for 48e314f
  chrisjonesBSU

  authored
  48e314f

• change license

  chrisjonesBSU

  committed
  35b6bb1

• Revert "change license"

  Show description for 2851f37
  chrisjonesBSU

  committed
  2851f37

• try diff license

  chrisjonesBSU

  committed
  e485f1b

• Revert "try diff license"

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  chrisjonesBSU

  committed
  d91a1a9

• [pre-commit.ci] pre-commit autoupdate

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  pre-commit-ci[bot]

  authored
  d248197

• Merge pull request cmelab#59 from cmelab/pre-commit-ci-update-config

  Show description for ac2a0c9
  chrisjonesBSU

  authored
  ac2a0c9

Commits on Nov 30, 2023

• Add empty get_quaternion warning

  RainierBarrett

  committed
  70da66c

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

  Show description for 41a4587
  pre-commit-ci[bot]

  committed
  41a4587

Commits on Dec 6, 2023

• Added our utility functions for use for aniso mapping

  

  Dani Rojas

  authored and

  RainierBarrett

  committed
  a28ed2e

• Editted the utility file to match an earlier commit we made when we editted the "get_axis_angle" function to calculate the quaternions directly.

  

  Dani Rojas

  authored and

  RainierBarrett

  committed
  169c491

• Minor name adjustments

  

  Noah Montrose

  authored and

  RainierBarrett

  committed
  5da59d9

• Start adding aniso mapping flags

  

  Noah Montrose

  authored and

  RainierBarrett

  committed
  416d4f7

• Add guard against error from zero bond systems

  

  Noah Montrose

  authored and

  RainierBarrett

  committed
  4a9e5b8

• Add logic for aniso mapping

  RainierBarrett

  committed
  12be8b2

• Add orientation tracking array. Fails to save single frame.

  RainierBarrett

  committed
  da0b55a

• Aniso Mapping works

  

  Noah Montrose

  authored and

  RainierBarrett

  committed
  0b35123

• fixed some orientaiton logic for non-aniso systems

  

  Noah Montrose

  authored and

  RainierBarrett

  committed
  0d33a2e

• Still resolving the off by one issue for the bond list

  

  Noah Montrose

  authored and

  RainierBarrett

  committed
  ee507b4

• Change to variables for mapping strings to prevent typos

  RainierBarrett

  committed
  5282d3f

• remove debug statements, add guard for single-bead mappings

  RainierBarrett

  committed
  5535b3c

• Set default quaternion for beads with <3 heavy atoms

  RainierBarrett

  committed
  a6505f8

• Address mass scaling in aniso position calculations

  RainierBarrett

  committed
  84feb8d

• Remove superfluous(?) re-wrap of bead positions

  RainierBarrett

  committed
  7f405ce

• merge from upstream

  RainierBarrett

  committed
  8fa14a9

• begin aniso coverage tests

  RainierBarrett

  committed
  176ef8c

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

  Show description for 408281d
  

  pre-commit-ci[bot]

  authored and

  RainierBarrett

  committed
  408281d

• more aniso unit tests

  RainierBarrett

  committed
  37eb251

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

  Show description for 3783439
  

  pre-commit-ci[bot]

  authored and

  RainierBarrett

  committed
  3783439

• system saving unit test

  RainierBarrett

  committed
  a1511b6

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

  Show description for c2cf2d3
  

  pre-commit-ci[bot]

  authored and

  RainierBarrett

  committed
  c2cf2d3

• remove unused minor axis finder

  RainierBarrett

  committed
  1019c6d

• make CI happy

  RainierBarrett

  committed
  99b5aa8

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

  Show description for a7bc145
  

  pre-commit-ci[bot]

  authored and

  RainierBarrett

  committed
  a7bc145

• Add COM test

  RainierBarrett

  committed
  470311c

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

  Show description for 4100b7a
  

  pre-commit-ci[bot]

  authored and

  RainierBarrett

  committed
  4100b7a

• gsd files for testing orientation functionality

  

  Dani Rojas

  authored and

  RainierBarrett

  committed
  9e4d319

• add check for mass to CG_System

  

  chrisjonesBSU

  authored and

  RainierBarrett

  committed
  e4d0bce

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

  Show description for 4491877
  

  pre-commit-ci[bot]

  authored and

  RainierBarrett

  committed
  4491877

• Re-add python and numpy to env yaml

  RainierBarrett

  committed
  6db6c35

• remove old smiles comment

  RainierBarrett

  committed
  336ba61

• Condense pps rotation test gsd to one file. new test in progress

  RainierBarrett

  committed
  acb40ec

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

  Show description for 774ecb8
  

  pre-commit-ci[bot]

  authored and

  RainierBarrett

  committed
  774ecb8

• Add empty get_quaternion warning

  RainierBarrett

  committed
  7a4c0e5

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

  Show description for 4d2e180
  

  pre-commit-ci[bot]

  authored and

  RainierBarrett

  committed
  4d2e180

• in-progress on sleuthing atom count mismatch

  RainierBarrett

  committed
  df1924b

• add more flexible SMARTS to noH test

  RainierBarrett

  committed
  34d0e9a

• Fix orientation writing and test

  RainierBarrett

  committed
  fc604c0

• Merge branch 'Aniso_rebased' of github.com:RainierBarrett/grits into Aniso_rebased

  RainierBarrett

  committed
  15989f6

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

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  pre-commit-ci[bot]

  committed
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