Consolidating HOOMD project and clean up (#261)

* Merge hoomd4 subproject into main project Scrap original hoomd project directory in favor of using hoomd4 * remove irrelevant unit tests * Add comments block explaining HOOMD equil checks Also clean up commented out code. * remove lammps-UD
mosdef-hub · May 16, 2024 · 5d53c91 · 5d53c91
1 parent eb84370
commit 5d53c91
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diff --git a/reproducibility_project/aggregate_summary/aggregate_init.py b/reproducibility_project/aggregate_summary/aggregate_init.py
@@ -31,9 +31,8 @@ def dict_product(dd):
     "gromacs",
     "hoomd",
     "lammps-VU",
-    #    "lammps-UD",
 ]
-md_engines = ["gromacs", "hoomd", "lammps-VU"]  # , "lammps-UD"]
+md_engines = ["gromacs", "hoomd", "lammps-VU"]
 mc_engines = ["cassandra", "mcccs", "gomc"]
 forcefields = {}
 r_cuts = {}

diff --git a/reproducibility_project/bin/clean_by_engine.sh b/reproducibility_project/bin/clean_by_engine.sh
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 echo Removing jobs from all engines but $1
-for ENGINE in cassandra mcccs gomc gromacs hoomd lammps-VU lammps-UD
+for ENGINE in cassandra mcccs gomc gromacs hoomd lammps-VU
 do
     if [[ $ENGINE != $1 ]]
     then

diff --git a/reproducibility_project/hoomd4_subproject/src/README.md b/reproducibility_project/hoomd4_subproject/src/README.md
diff --git a/reproducibility_project/hoomd4_subproject/src/__init__.py b/reproducibility_project/hoomd4_subproject/src/__init__.py
diff --git a/reproducibility_project/hoomd4_subproject/src/analysis/__init__.py b/reproducibility_project/hoomd4_subproject/src/analysis/__init__.py
diff --git a/reproducibility_project/hoomd4_subproject/src/analysis/diffusion.py b/reproducibility_project/hoomd4_subproject/src/analysis/diffusion.py
diff --git a/reproducibility_project/hoomd4_subproject/src/analysis/equilibration.py b/reproducibility_project/hoomd4_subproject/src/analysis/equilibration.py