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Joerg's lammps nodes #33
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38ce4b9
Add files via upload
JNmpi 4f06e58
Merge branch 'branch-source' into JNmpi_lammps_nodes
liamhuber 74487d9
Move file into the workflow module and update workflow import paths
liamhuber 8f2347e
Modified/corrected to address code warnings (PEP8 etc.)
JNmpi 79add2a
formatted Black
JNmpi 9f77a1f
Merge remote-tracking branch 'origin/refactor_run_cycle' into JNmpi_l…
JNmpi 48a0376
merged with refactor_run_cycle
JNmpi 187be01
[dependabot skip] Update env file
pyiron-runner 1710b04
Merge branch 'main' into 0.0.2_hotfix
liamhuber aa59cd3
Give atomistic_codes and lammps node packages direct access
liamhuber 2e93143
Don't register node packages in notebook
liamhuber b3fd13a
Exploit single point of import
liamhuber e31a4b4
Exploit node working_directory code instead of hard-coding path
liamhuber eb9e4f2
Re-execute demo notebook
liamhuber b4ebb1b
Comment out draw calls and re-execute
liamhuber b20f0dc
Add contrib to the notebook envs
liamhuber 21263eb
[dependabot skip] Update env file
pyiron-runner b0ca617
Merge branch 'main' into merge_0.0.3
liamhuber a9ea55b
Use new method name
liamhuber 3e6e331
Hint optional kwargs as Optional
liamhuber c8b942b
Pass a string to the string-hinted channel
liamhuber bd43dcd
Remove string casting
liamhuber afd0718
Re-execute notebook
liamhuber c8b2741
Merge pull request #49 from pyiron/merge_0.0.3
liamhuber b2004e2
Merge pull request #43 from pyiron/0.0.2_hotfix
liamhuber 25dc174
adapted to latest main version
JNmpi 3c11a45
[dependabot skip] Update env file
pyiron-runner 58801d6
adapted to latest main version
JNmpi 04c24ba
Merge remote-tracking branch 'origin/JNmpi_lammps_nodes' into JNmpi_l…
JNmpi ab3b09a
Merge remote-tracking branch 'origin/main' into JNmpi_lammps_nodes
JNmpi cb230e5
Merge branch 'main' into JNmpi_lammps_nodes_patch_0.1.0
liamhuber f2e15ac
Re-order notebooks env
liamhuber 65f9f06
Remove binder maggma pin
liamhuber 4d7ec2b
Conform to type hints
liamhuber 4a29d7c
[dependabot skip] Update env file
pyiron-runner 6c586fa
Add contrib to notebook deps
liamhuber 361726f
[dependabot skip] Update env file
pyiron-runner 9ff5e5c
Merge pull request #91 from pyiron/JNmpi_lammps_nodes_patch_0.1.0
liamhuber 21587b7
prototype example of storing node input and output data in a DataStor…
JNmpi ce5c7de
Merge remote-tracking branch 'origin/JNmpi_lammps_nodes' into JNmpi_l…
JNmpi 23cef90
Merge branch 'macro_interface' into merge_JNmpi_lammps_nodes
liamhuber 9d5d94b
Conform to node decorator signature
liamhuber 0a4dfe5
Rename package nodes in a ClassLike way
liamhuber 01a7783
Make sure nodes belong to their macro parent
liamhuber e6c918d
Modernize macro syntax
liamhuber 92b9fa6
Merge branch 'macro_interface' into merge_JNmpi_lammps_nodes
liamhuber 39cdce7
Add default to macro
liamhuber 7d995f4
Remove incorrect type hint
liamhuber 0c8e33e
Update method name
liamhuber a0d0866
Make sure DataStore always has a directory to work with
liamhuber 5609402
In media res notebook updates
liamhuber 62869b5
Merge branch 'macro_interface' into merge_JNmpi_lammps_nodes
liamhuber 1989e1c
Look for value before _convert_to_dict
liamhuber 7f0aa69
Update the example notebook
liamhuber 41aac40
Remove unused nodes
liamhuber 6ece816
Update and extend type hints
liamhuber 0994caf
Remove unused stuff
liamhuber fef104a
Reexecute notebook
liamhuber 8d63194
[dependabot skip] Update env file
pyiron-runner 015d8c0
Format black
pyiron-runner 10c820d
Merge remote-tracking branch 'origin/main' into JNmpi_lammps_nodes
JNmpi 3ab6e84
Merge branch 'main' into JNmpi_lammps_nodes_patch_0p2p0
liamhuber 795fede
Merge pull request #139 from pyiron/JNmpi_lammps_nodes_patch_0p2p0
liamhuber 042efaf
Merge remote-tracking branch 'origin/JNmpi_lammps_nodes' into JNmpi_l…
JNmpi d5eb20c
Further modularization of the atomistics class for the example of pho…
JNmpi c401b8b
Restructering/modularizyation of the node library
JNmpi 4472a4f
Development and implementation of a wf_data_class that extends the fu…
JNmpi d6c57a9
- Restructered node library with several new nodes
JNmpi b62874a
Remove run prior to wf definition
liamhuber a956958
PEP8 kwarg assignment
liamhuber f1aaa0a
Re-introduce the calc_mode input variable to Collect
liamhuber 2cb075b
Update my lammps script and re-execute the notebook
liamhuber 153f6c8
Don't use `**kwargs` as input
liamhuber 33a3ab7
:bug: calculate kinetic energy
liamhuber 14e81b2
Comment out the DataStore stuff
liamhuber e9b0990
Register Jan's package and rerun notebook
liamhuber 9ea245c
Be more flexible when parsing input
liamhuber 4984094
Refactor: rename
liamhuber 2847981
Refactor: move function
liamhuber 9420833
Refactor: rename signature variable
liamhuber fd461b3
Update docstring
liamhuber c1180bf
Provide explicit channels for each piece of input
liamhuber 5f4f25b
Rerun notebook
liamhuber a0f3846
Add matgl dependency for notebooks
liamhuber 80b27a6
Make the elasticity database file a variable
liamhuber 7ff39c0
Add pandas dep
liamhuber a1f2206
Rerun notebook and remove breaklines
liamhuber 64de8de
[dependabot skip] Update env file
pyiron-runner fcc81ea
Merge branch 'main' into JNmpi_notebook_patch
liamhuber e578f1a
Use new registration syntax
liamhuber fa8d8cd
Merge branch 'main' into JNmpi_notebook_patch
liamhuber 4a52aa3
Update notebooks
liamhuber 254e5a4
Don't print what's not there
liamhuber 545dd73
Update workflow notebook
liamhuber dcc1b92
Format black
pyiron-runner 8659ee2
Bump atomistics and contrib
liamhuber e142c2a
[dependabot skip] Update env file
pyiron-runner b5999d8
Reformat cell
liamhuber 52bb470
Add a flag for matgl-requiring cells
liamhuber 9ffec99
Match signature of called object
liamhuber 9b72361
:bug: test against the right instance
liamhuber b1cf8ab
Raise an error if you'd bypass the type checks
liamhuber e876ea4
Give the collect node a lot of freedom on its mode input
liamhuber 86e733c
Pass around the single value calc throughout the macro
liamhuber f6f4cd4
Adjust and rerun phonopy notebook
liamhuber fce8831
Format black
pyiron-runner d50d3ad
Merge pull request #203 from pyiron/JNmpi_notebook_patch
liamhuber 81ede52
Merge branch 'main' into JNmpi_lammps_nodes
JNmpi 9d33815
- save latest jupyter notebooks
JNmpi 4b3874f
Merge branch 'main' into JNmpi_lammps_nodes
JNmpi b69ca0b
- save latest jupyter notebooks and function_nodes
JNmpi 0426c4c
JNmpi lammps nodes patch version ~0.7.0~ 0.7.1 (#315)
liamhuber 4ab3bc1
Merge branch 'main' into JNmpi_lammps_nodes
liamhuber 044598e
Merge branch 'main' into JNmpi_lammps_nodes
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This is nearly the same object as the
FileObject
that we already have infiles.py