Minor docs cleanup (#1047)

* cleanup docs on vasp / openmm

* typo

* change install command to pypi since OpenMM makers released in v0.0.16

https://github.com/materialsproject/atomate2/releases/tag/v0.0.16

---------

Co-authored-by: Janosh Riebesell <[email protected]>

Author: esoteric-ephemera

docs/user/codes/openmm.md

@@ -6,24 +6,17 @@
 >>> conda activate atomate2
 
 # installing atomate2
->>> pip install git+https://github.com/orionarcher/atomate2
-
-# installing classical_md dependencies
->>> conda install -c conda-forge --file .github/classical_md_requirements.txt
+>>> pip install "atomate2[openmm]"
 ```
 
 Alternatively, if you anticipate regularly updating
-atomate2 from source (which at this point, you should),
-you can clone the repository and install from source.
+atomate2 from source, you can clone the repository and install from source.
 
 ``` bash
 # installing atomate2
->>> git clone https://github.com/orionarcher/atomate2
+>>> git clone https://github.com/materialsproject/atomate2
 >>> cd atomate2
->>> git branch openff
->>> git checkout openff
->>> git pull origin openff
->>> pip install -e .
+>>> pip install -e '.[openmm]'
 ```
 
 To test the openmm installation, you can run the following command. If
@@ -458,6 +451,7 @@ run_locally(flows[rank], ensure_success=True)
 For now, you'll need to make sure you have a particular emmet branch installed.
 Later the builders will be integrated into `main`.
 
+<!-- TODO get emmet@md_builders merged -->
 ```bash
 pip install git+https://github.com/orionarcher/emmet@md_builders
 ```

docs/user/codes/vasp-workflows.csv

@@ -1,22 +1,22 @@
 Name,Type,Maker
-`Static`_,job,:obj:`.StaticMaker`
-`Relax`_,job,:obj:`.RelaxMaker`
-`Tight Relax`_,job,:obj:`.TightRelaxMaker`
-`Dielectric`_,job,:obj:`.DielectricMaker`
-`Transmuter`_,job,:obj:`.TransmuterMaker`
-`HSE06 Static`_,job,:obj:`.HSEStaticMaker`
-`HSE06 Relax`_,job,:obj:`.HSERelaxMaker`
-`HSE06 Tight Relax`_,job,:obj:`.HSETightRelaxMaker`
-`Double Relax`_,flow,:obj:`.DoubleRelaxMaker`
-`Band Structure`_,flow,:obj:`.BandStructureMaker`
-`Uniform Band Structure`_,flow,:obj:`.UniformBandStructureMaker`
-`Line-Mode Band Structure`_,flow,:obj:`.LineModeBandStructureMaker`
-`HSE06 Band Structure`_,flow,:obj:`.HSEBandStructureMaker`
-`HSE06 Uniform Band Structure`_,flow,:obj:`.HSEUniformBandStructureMaker`
-`HSE06 Line-Mode Band Structure`_,flow,:obj:`.HSELineModeBandStructureMaker`
-`Relax and Band Structure`_,flow,:obj:`.RelaxBandStructureMaker`
-`Elastic Constant`_,flow,:obj:`.ElasticMaker`
-`Optics`_,flow,:obj:`.OpticsMaker`
-`HSE06 Optics`_,flow,:obj:`.HSEOpticsMaker`
-`Phonons`_,flow,:obj:`.PhononMaker`
-`Lobster`_,flow,:obj:`.VaspLobsterMaker`
+`Static`_,job,:obj:`~atomate2.vasp.jobs.core.StaticMaker`
+`Relax`_,job,:obj:`~atomate2.vasp.jobs.core.RelaxMaker`
+`Tight Relax`_,job,:obj:`~atomate2.vasp.jobs.core.TightRelaxMaker`
+`Dielectric`_,job,:obj:`~atomate2.vasp.jobs.core.DielectricMaker`
+`Transmuter`_,job,:obj:`~atomate2.vasp.jobs.core.TransmuterMaker`
+`HSE06 Static`_,job,:obj:`~atomate2.vasp.jobs.core.HSEStaticMaker`
+`HSE06 Relax`_,job,:obj:`~atomate2.vasp.jobs.core.HSERelaxMaker`
+`HSE06 Tight Relax`_,job,:obj:`~atomate2.vasp.jobs.core.HSETightRelaxMaker`
+`Double Relax`_,flow,:obj:`~atomate2.vasp.flows.core.DoubleRelaxMaker`
+`Band Structure`_,flow,:obj:`~atomate2.vasp.flows.core.BandStructureMaker`
+`Uniform Band Structure`_,flow,:obj:`~atomate2.vasp.flows.core.UniformBandStructureMaker`
+`Line-Mode Band Structure`_,flow,:obj:`~atomate2.vasp.flows.core.LineModeBandStructureMaker`
+`HSE06 Band Structure`_,flow,:obj:`~atomate2.vasp.flows.core.HSEBandStructureMaker`
+`HSE06 Uniform Band Structure`_,flow,:obj:`~atomate2.vasp.flows.core.HSEUniformBandStructureMaker`
+`HSE06 Line-Mode Band Structure`_,flow,:obj:`~atomate2.vasp.flows.core.HSELineModeBandStructureMaker`
+`Relax and Band Structure`_,flow,:obj:`~atomate2.vasp.flows.core.RelaxBandStructureMaker`
+`Elastic Constant`_,flow,:obj:`~atomate2.vasp.flows.elastic.ElasticMaker`
+`Optics`_,flow,:obj:`~atomate2.vasp.flows.core.OpticsMaker`
+`HSE06 Optics`_,flow,:obj:`~atomate2.vasp.flows.core.HSEOpticsMaker`
+`Phonons`_,flow,:obj:`~atomate2.vasp.flows.phonons.PhononMaker`
+`Lobster`_,flow,:obj:`~atomate2.vasp.flows.lobster.VaspLobsterMaker`

docs/user/codes/vasp.md

@@ -324,7 +324,7 @@ run_locally(lobster, create_folders=True, store=SETTINGS.JOB_STORE)
 ```
 
 It is, however,  computationally very beneficial to define two different types of job scripts for the VASP and Lobster runs, as VASP and Lobster runs are parallelized differently (MPI vs. OpenMP).
-[FireWorks](https://github.com/materialsproject/fireworks) allows to run the VASP and Lobster jobs with different job scripts. Please check out the [jobflow documentation on FireWorks](https://materialsproject.github.io/jobflow/tutorials/8-fireworks.html#setting-the-manager-configs) for more information.
+[FireWorks](https://github.com/materialsproject/fireworks) allows one to run the VASP and Lobster jobs with different job scripts. Please check out the [jobflow documentation on FireWorks](https://materialsproject.github.io/jobflow/tutorials/8-fireworks.html#setting-the-manager-configs) for more information.
 
 Specifically, you might want to change the `_fworker` for the LOBSTER runs and define a separate `lobster` worker within FireWorks:
 
@@ -468,7 +468,8 @@ Finally, sometimes you have a workflow containing many VASP jobs. In this case i
 tedious to update the input sets for each job individually. Atomate2 provides helper
 functions called "powerups" that can apply settings updates to all VASP jobs in a flow.
 These powerups also contain filters for the name of the job and the maker used to
-generate them.
+generate them. These functions will apply updates *only* to VASP jobs, including those
+created dynamically - all other jobs in a flow will not be modified.
 
 ```py
 from atomate2.vasp.powerups import update_user_incar_settings