Merge pull request #33 from chrisjonesBSU/hoomd3

Update to hoomd version 4, improved API
cmelab · Feb 23, 2024 · f082627 · f082627
2 parents 5a2b241 + e684423
commit f082627
Show file tree

Hide file tree

Showing 49 changed files with 1,009 additions and 33,986 deletions.
diff --git a/msibi/tutorials/README → Tutorials/README b/msibi/tutorials/README → Tutorials/README
diff --git a/msibi/tutorials/lj/opt.py → Tutorials/lj/opt.py b/msibi/tutorials/lj/opt.py → Tutorials/lj/opt.py
diff --git a/msibi/tutorials/lj/rdfs/rdftarget0.5 → Tutorials/lj/rdfs/rdftarget0.5 b/msibi/tutorials/lj/rdfs/rdftarget0.5 → Tutorials/lj/rdfs/rdftarget0.5
diff --git a/msibi/tutorials/lj/rdfs/rdftarget1.5 → Tutorials/lj/rdfs/rdftarget1.5 b/msibi/tutorials/lj/rdfs/rdftarget1.5 → Tutorials/lj/rdfs/rdftarget1.5
diff --git a/msibi/tutorials/lj/rdfs/rdftarget2.0 → Tutorials/lj/rdfs/rdftarget2.0 b/msibi/tutorials/lj/rdfs/rdftarget2.0 → Tutorials/lj/rdfs/rdftarget2.0
diff --git a/msibi/tutorials/lj/trajectory0.5.gsd → Tutorials/lj/trajectory0.5.gsd b/msibi/tutorials/lj/trajectory0.5.gsd → Tutorials/lj/trajectory0.5.gsd
diff --git a/msibi/tutorials/lj/trajectory1.5.gsd → Tutorials/lj/trajectory1.5.gsd b/msibi/tutorials/lj/trajectory1.5.gsd → Tutorials/lj/trajectory1.5.gsd
diff --git a/msibi/tutorials/lj/trajectory2.0.gsd → Tutorials/lj/trajectory2.0.gsd b/msibi/tutorials/lj/trajectory2.0.gsd → Tutorials/lj/trajectory2.0.gsd
diff --git a/msibi/tutorials/propane/.gitignore → Tutorials/propane/.gitignore b/msibi/tutorials/propane/.gitignore → Tutorials/propane/.gitignore
diff --git a/msibi/tutorials/propane/opt.py → Tutorials/propane/opt.py b/msibi/tutorials/propane/opt.py → Tutorials/propane/opt.py
diff --git a/msibi/tutorials/propane/plot.py → Tutorials/propane/plot.py b/msibi/tutorials/propane/plot.py → Tutorials/propane/plot.py
diff --git a/.../tutorials/propane/rdfs/C3-C3-state_A.txt → Tutorials/propane/rdfs/C3-C3-state_A.txt b/.../tutorials/propane/rdfs/C3-C3-state_A.txt → Tutorials/propane/rdfs/C3-C3-state_A.txt
diff --git a/.../tutorials/propane/rdfs/C3-C3-state_B.txt → Tutorials/propane/rdfs/C3-C3-state_B.txt b/.../tutorials/propane/rdfs/C3-C3-state_B.txt → Tutorials/propane/rdfs/C3-C3-state_B.txt
diff --git a/.../tutorials/propane/rdfs/C3-C3-state_C.txt → Tutorials/propane/rdfs/C3-C3-state_C.txt b/.../tutorials/propane/rdfs/C3-C3-state_C.txt → Tutorials/propane/rdfs/C3-C3-state_C.txt
diff --git a/...als/propane/state_A/hoomd_run_template.py → ...als/propane/state_A/hoomd_run_template.py b/...als/propane/state_A/hoomd_run_template.py → ...als/propane/state_A/hoomd_run_template.py
diff --git a/.../tutorials/propane/state_A/start.hoomdxml → Tutorials/propane/state_A/start.hoomdxml b/.../tutorials/propane/state_A/start.hoomdxml → Tutorials/propane/state_A/start.hoomdxml
diff --git a/...als/propane/state_B/hoomd_run_template.py → ...als/propane/state_B/hoomd_run_template.py b/...als/propane/state_B/hoomd_run_template.py → ...als/propane/state_B/hoomd_run_template.py
diff --git a/.../tutorials/propane/state_B/start.hoomdxml → Tutorials/propane/state_B/start.hoomdxml b/.../tutorials/propane/state_B/start.hoomdxml → Tutorials/propane/state_B/start.hoomdxml
diff --git a/...als/propane/state_C/hoomd_run_template.py → ...als/propane/state_C/hoomd_run_template.py b/...als/propane/state_C/hoomd_run_template.py → ...als/propane/state_C/hoomd_run_template.py
diff --git a/.../tutorials/propane/state_C/start.hoomdxml → Tutorials/propane/state_C/start.hoomdxml b/.../tutorials/propane/state_C/start.hoomdxml → Tutorials/propane/state_C/start.hoomdxml
diff --git a/environment-cpu.yml b/environment-cpu.yml
diff --git a/environment-gpu.yml b/environment-gpu.yml
diff --git a/environment-nohoomd.yml b/environment-nohoomd.yml
diff --git a/environment.yml b/environment.yml
@@ -0,0 +1,10 @@
+name: msibi
+channels:
+- conda-forge
+dependencies:
+- cuda-version==11.8
+- freud>=2.13
+- gsd>=3.0
+- hoomd>=4.0
+- cmeutils
+- more-itertools
diff --git a/msibi/__init__.py b/msibi/__init__.py
@@ -1,6 +1,5 @@
 from msibi.optimize import MSIBI
-from msibi.pair import Pair
-from msibi.bonds import Bond, Angle
+from msibi.forces import Pair, Bond, Angle, Dihedral
 from msibi.potentials import *
 from msibi.state import State
 from msibi.__version__ import __version__
@@ -13,5 +12,6 @@
     "State",
     "Bond",
     "Angle",
+    "Dihedral",
     "utils"
 ]
diff --git a/msibi/__version__.py b/msibi/__version__.py
@@ -1 +1 @@
-__version__ = "0.4.0"
+__version__ = "1.0.0"