HOOMD-blue 4.x subproject (#250)

* set up init

* update hoomd4 project.py and rahman_hoomd template

* fix small typo

* remove tau variable

* use mttk for shrink

* add property to logger'

* add fix for hoomd logger (for hoomd4)

* opt out nvt and related steps

* use Bussi thermostat for all steps

* update syntax for signac 2.0

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

for more information, see https://pre-commit.ci

* update yml file

* update to match with latest project.py by Jenny

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

for more information, see https://pre-commit.ci

* Changes needed to run on Delta.

* Additional changes for hoomd4.

* Gitpython is no longer needed.

* Fix NPT error.

* Yet more fixes for hoomd4.

* Adjust dt and electrostatics parameters to match LAMMPS.

* Match PPPM args for water and ethanol.

* Cleanup

* Fix environment.yml.

* Add missing files.

* Use latest mbuild.

* Run pre-commit.

* Support siganc 1.x and 2.x Job class.

* Run pre-commit.

* Fix regex match in test.

---------

Co-authored-by: Co Quach <daico007@gmail.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: 3 people

reproducibility_project/hoomd4_subproject/environment.yml

@@ -0,0 +1,36 @@
+name: mosdef-study38
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - constrainmol
+  - ele
+  - freud
+  - foyer=0.11.2
+  - freud
+  - gmso
+  - gsd=2.6.0
+  - h5py
+  - jupyter
+  - jinja2
+  - lammps
+  - matplotlib
+  - mbuild=0.16.3
+  - mdtraj
+  - numpy
+  - openmm>=7.6
+  - packmol>=18
+  - pandas
+  - panedr
+  - parmed>=3.4.3
+  - pymbar=3.0.5
+  - pytest
+  - python=3.8
+  - rdkit
+  - scipy=1.9.0
+  - seaborn
+  - signac
+  - signac-dashboard
+  - signac-flow
+  - unyt
+  - hoomd=4.0.0=*gpu*