MaginnGroup/mosdef_cassandra issues and pull requests

#107 - Fix box size modified if run is within a loop

Pull Request - State: closed - Opened by emarinri about 2 years ago

#106 - Allow the user to specify the number of fragments in a library.

Issue - State: open - Opened by emarinri over 2 years ago
Labels: enhancement

#105 - Utilize networkx for ring fragment identification in mcfgen.py

Issue - State: closed - Opened by emarinri over 2 years ago

#104 - mbuild box is passed by reference to system and then run

Issue - State: closed - Opened by GregorySchwing over 2 years ago - 2 comments

#103 - Remove references to openbabel in docs

Pull Request - State: closed - Opened by rsdefever over 3 years ago

#102 - Account for breaking changes in mbuild 0.11.0

Pull Request - State: closed - Opened by rwsmith7531 over 3 years ago

#101 - Add support for Widom insertions

Pull Request - State: open - Opened by rwsmith7531 over 3 years ago - 1 comment

#100 - Add support for Widom insertions

Issue - State: open - Opened by rwsmith7531 over 3 years ago

#99 - Make `mixing_rule` a required argument for `mc.run`

Issue - State: open - Opened by rsdefever over 3 years ago - 3 comments

#98 - Serialize system/moveset?

Issue - State: open - Opened by rsdefever over 3 years ago - 2 comments

#97 - Add load_final_frame to analysis module to facilitate MC-MD workflows

Issue - State: open - Opened by rsdefever over 3 years ago - 1 comment

#96 - Add/midnight build

Pull Request - State: closed - Opened by rsdefever over 3 years ago

#95 - Pin/mbuild

Pull Request - State: closed - Opened by rsdefever over 3 years ago - 2 comments

#94 - Update AZP and docs now that foyer is on conda-forge

Pull Request - State: closed - Opened by rsdefever almost 4 years ago

#93 - Add error message if "-" is used in run_name.

Pull Request - State: closed - Opened by rsdefever almost 4 years ago

#92 - Fix version dunder in init.py and add to bumpversion.

Pull Request - State: closed - Opened by rsdefever almost 4 years ago

#91 - Modify restart function to not use system or moveset

Pull Request - State: closed - Opened by rsdefever about 4 years ago - 6 comments

#90 - Change filename of restart from -rst ro _rst

Pull Request - State: closed - Opened by rmatsum836 about 4 years ago - 1 comment

#89 - Addition of -rst in restart file names results in Cassandra error

Issue - State: closed - Opened by rmatsum836 about 4 years ago - 2 comments

#88 - Add constrainmol support to meet bond length requirements

Pull Request - State: closed - Opened by rsdefever about 4 years ago - 8 comments

#87 - Address fixed-bond-related challenges of starting simulation from a previously generated configuration

Issue - State: closed - Opened by rsdefever about 4 years ago - 1 comment

#86 - Serialize system and moveset (and input file?) for restarts

Issue - State: closed - Opened by rsdefever about 4 years ago - 1 comment

#85 - Update GCMC adsorption example to CIF + zeolite

Pull Request - State: closed - Opened by rsdefever about 4 years ago - 8 comments

#84 - Remove spacing after each custom nb definintion in input file

Pull Request - State: closed - Opened by rmatsum836 about 4 years ago

#83 - Pull version info from module level definition

Pull Request - State: closed - Opened by rsdefever about 4 years ago

#82 - Add/bumpversion

Pull Request - State: closed - Opened by rsdefever about 4 years ago - 2 comments

#81 - Add back in methane nvt example and Update Docs

Pull Request - State: closed - Opened by rmatsum836 about 4 years ago - 1 comment

#80 - Update doc examples

Pull Request - State: closed - Opened by rsdefever about 4 years ago

#79 - Update adsorption example to use zeolite with CIF file

Issue - State: closed - Opened by rsdefever about 4 years ago

#78 - NVT example in docs fails in production environment

Issue - State: closed - Opened by rsdefever about 4 years ago - 2 comments

#77 - Add unyts to docs in quickstart and runners sections

Pull Request - State: closed - Opened by rsdefever about 4 years ago - 1 comment

#76 - List index out of range error in angle_style

Issue - State: open - Opened by rsdefever over 4 years ago

#75 - Production run won't read .out.chk with '-' within the file name.

Issue - State: closed - Opened by nealeellyson over 4 years ago - 1 comment
Labels: bug

#74 - Bump to 0.2.1

Pull Request - State: closed - Opened by rsdefever over 4 years ago

#73 - Make unyt checking more robust and bug fixes

Pull Request - State: closed - Opened by rsdefever over 4 years ago - 2 comments

#72 - Add kwarg for angle style

Pull Request - State: closed - Opened by rmatsum836 over 4 years ago - 3 comments

#71 - Fix for writing restricted insertions to input file

Pull Request - State: closed - Opened by rmatsum836 over 4 years ago

#70 - Bump to version 0.2.0

Pull Request - State: closed - Opened by rsdefever over 4 years ago - 2 comments

#69 - Add default values to `print_valid_kwargs()`

Issue - State: open - Opened by rmatsum836 over 4 years ago - 1 comment

#68 - Add initial section about restricted insertions

Pull Request - State: open - Opened by rmatsum836 over 4 years ago

#67 - Debug codecov

Pull Request - State: closed - Opened by rsdefever over 4 years ago

#66 - Update toctree to include keyword arguments page

Pull Request - State: closed - Opened by rsdefever over 4 years ago

#65 - Continued doc updates

Pull Request - State: closed - Opened by rsdefever over 4 years ago

#64 - Add ``unyt`` support to custom mixing rules

Issue - State: open - Opened by rsdefever over 4 years ago - 2 comments

#63 - Major additions to documentation

Pull Request - State: closed - Opened by rsdefever over 4 years ago

#62 - Add start of analysis module

Pull Request - State: closed - Opened by rsdefever over 4 years ago

#61 - Rename the Moves class to MoveSet

Pull Request - State: closed - Opened by rsdefever over 4 years ago

#60 - Rename Moves MoveSet

Issue - State: closed - Opened by rsdefever over 4 years ago - 1 comment

#59 - Combine CBMC options into Moves

Pull Request - State: closed - Opened by rsdefever over 4 years ago

#58 - Prevent additional attributes from being added to system/moves

Issue - State: open - Opened by rsdefever over 4 years ago
Labels: enhancement

#57 - Update moves attributes

Pull Request - State: closed - Opened by rsdefever over 4 years ago - 1 comment

#56 - Add overwrite=True flag to xyz input writer

Pull Request - State: closed - Opened by rsdefever over 4 years ago

#55 - Fix moves.print() formatting for multiple boxes

Pull Request - State: closed - Opened by rsdefever over 4 years ago - 1 comment

#54 - Add exception to catch Cassandra errors

Pull Request - State: closed - Opened by rsdefever over 4 years ago - 1 comment

#53 - Add run completion verification

Issue - State: closed - Opened by rsdefever over 4 years ago
Labels: enhancement

#52 - Prevent ensemble property of moves object from being edited

Pull Request - State: closed - Opened by rsdefever over 4 years ago - 1 comment

#51 - Integrate the `unyt` package

Pull Request - State: closed - Opened by rmatsum836 over 4 years ago - 7 comments
Labels: WIP

#50 - Prevent ensemble from being edited in `Moves` object once initialized

Issue - State: closed - Opened by rsdefever over 4 years ago - 1 comment

#49 - Consider changes to System and Moves argument specification

Issue - State: open - Opened by rsdefever over 4 years ago
Labels: discussion

#48 - Fix formatting for moves.print()

Issue - State: closed - Opened by rsdefever over 4 years ago
Labels: enhancement, good first issue

#47 - Add restricted insertions attribute for `moves`

Pull Request - State: closed - Opened by rmatsum836 over 4 years ago - 15 comments

#46 - Finish doc build

Pull Request - State: closed - Opened by rsdefever over 4 years ago

#45 - Try pip install instead

Pull Request - State: closed - Opened by rsdefever over 4 years ago

#44 - Trying metachannel

Pull Request - State: closed - Opened by rsdefever over 4 years ago

#43 - Trying with conda

Pull Request - State: closed - Opened by rsdefever over 4 years ago

#42 - Changes to readthedocs yml file

Pull Request - State: closed - Opened by rsdefever over 4 years ago

#41 - Add RTD configuration files

Pull Request - State: closed - Opened by rsdefever over 4 years ago

#40 - Add conda install to docs

Pull Request - State: closed - Opened by rsdefever over 4 years ago

#39 - Update requirements files to be consistent with conda build

Pull Request - State: closed - Opened by rsdefever over 4 years ago

#38 - Add `overwrite` argument to saving box

Issue - State: closed - Opened by rmatsum836 over 4 years ago - 1 comment
Labels: enhancement

#37 - Switch to github release and conda release for AZP testing

Pull Request - State: closed - Opened by rsdefever over 4 years ago - 1 comment

#36 - Update list of acceptable thermo properties to match Cassandra 1.2.2

Pull Request - State: closed - Opened by rsdefever over 4 years ago

#35 - Convert format strings to fstrings

Issue - State: open - Opened by rsdefever over 4 years ago
Labels: enhancement

#34 - Update readme to reflect change in repo ownership

Pull Request - State: closed - Opened by rsdefever over 4 years ago

#33 - Add conda installation

Issue - State: closed - Opened by rsdefever over 4 years ago - 1 comment
Labels: enhancement

#32 - Update docs to new MaginnGroup location

Pull Request - State: closed - Opened by rsdefever over 4 years ago

#31 - Update ReadtheDocs configuration file

Pull Request - State: closed - Opened by rsdefever over 4 years ago

#30 - Add unyt

Pull Request - State: closed - Opened by rmatsum836 over 4 years ago - 7 comments
Labels: WIP

#29 - Fix mbuild/foyer channel priority in install instructions

Pull Request - State: closed - Opened by rsdefever over 4 years ago

#28 - Remove markdown README

Pull Request - State: closed - Opened by rsdefever over 4 years ago

#27 - Add license

Pull Request - State: closed - Opened by rsdefever over 4 years ago

#26 - Add black

Pull Request - State: closed - Opened by rsdefever over 4 years ago - 1 comment

#25 - Overhaul documentation in preparation for 0.1.0 release

Pull Request - State: closed - Opened by rsdefever over 4 years ago
Labels: documentation

#24 - Update and prettify docs - hosting on RTD

Issue - State: closed - Opened by rsdefever over 4 years ago - 1 comment
Labels: documentation

#23 - Add docs to describe new mc.run() syntax

Issue - State: closed - Opened by rsdefever over 4 years ago
Labels: documentation

#22 - Add function to print moves object

Pull Request - State: closed - Opened by rsdefever over 4 years ago

#21 - Add Unyt to keep track of units.

Issue - State: closed - Opened by rmatsum836 over 4 years ago
Labels: enhancement

#20 - Switch mc.run() to more verbose syntax

Pull Request - State: closed - Opened by rsdefever over 4 years ago

#19 - Add support for gmso.Topology as well as parmed.Structure

Issue - State: open - Opened by rsdefever over 4 years ago
Labels: waiting-for: mosdef

#18 - Update documentation to clarify openbabel soft dependency

Issue - State: closed - Opened by rsdefever over 4 years ago
Labels: documentation

#17 - Add requirements files and change pipelines to non-editable installs

Pull Request - State: closed - Opened by rsdefever over 4 years ago

#12 - Print details of Moves object

Issue - State: closed - Opened by rsdefever almost 5 years ago

#11 - Cleanup function to convert to triclinic box and add unit tests

Pull Request - State: closed - Opened by rsdefever almost 5 years ago

#10 - Add black formatting to CI checks

Issue - State: closed - Opened by rsdefever almost 5 years ago - 2 comments

#9 - Apply `black` formatting to all code

Pull Request - State: closed - Opened by rsdefever almost 5 years ago

#8 - Allow float vars to be specified as ints as well

Pull Request - State: closed - Opened by rsdefever almost 5 years ago

#7 - Fix recursion error when using mbuild.Compound in box list

Pull Request - State: closed - Opened by rsdefever almost 5 years ago

#5 - Search for openMP versions of cassandra first

Pull Request - State: closed - Opened by rsdefever almost 5 years ago

#4 - Add setters for all moves objects

Pull Request - State: closed - Opened by rsdefever almost 5 years ago

#1 - `mc.restart()` may run successfully if `mc.run()` fails part way through simulation

Issue - State: closed - Opened by rsdefever almost 5 years ago - 1 comment
Labels: bug

GitHub / MaginnGroup/mosdef_cassandra issues and pull requests