Merge pull request #26 from marjanAlbouye/main

Change hoomd_polymers to hoomd_organics

.github/workflows/pytest.yml

@@ -5,13 +5,13 @@ on:
     # Action will run when any changes to these paths are pushed or pr'ed to master
     branches: [ main ]
     paths:
-      - hoomd_polymers/**
+      - hoomd_organics/**
       - environment-cpu.yml
       - .github/workflows/pytest.yml
   pull_request:
     branches: [ main ]
     paths:
-      - hoomd_polymers/**
+      - hoomd_organics/**
       - environment-cpu.yml
       - .github/workflows/pytest.yml
   # Allows workflow to be manually triggered

.pre-commit-config.yaml

@@ -16,7 +16,7 @@ repos:
     - id: check-yaml
     - id: end-of-file-fixer
     - id: trailing-whitespace
-      exclude: 'hoomd_polymers/tests/assets/.* | hoomd_polymers/assets/.*'
+      exclude: 'hoomd_organics/tests/assets/.* | hoomd_organics/assets/.*'
 - repo: https://github.com/psf/black
   rev: 23.7.0
   hooks:

codecov.yml

@@ -7,8 +7,8 @@ comment:
     branches:               # branch names that can post comment
         - "main"
 ignore:
-    - "hoomd-polymers/tests"
-    - "hoomd-polymers/assets"
-    - "hoomd-polymers/__version__.py"
+    - "hoomd_organics/tests"
+    - "hoomd_organics/assets"
+    - "hoomd_organics/__version__.py"
     - "tutorials"
     - "setup.py"

environment-cpu.yml

@@ -1,4 +1,4 @@
-name: hoomd-polymers
+name: hoomd-organics
 channels:
   - conda-forge
 dependencies:

environment-dev.yml

@@ -1,4 +1,4 @@
-name: hoomd-polymers-dev
+name: hoomd-organics-dev
 channels:
   - conda-forge
 dependencies:

environment-gpu.yml

@@ -1,4 +1,4 @@
-name: hoomd-polymers
+name: hoomd-organics
 channels:
   - conda-forge
 dependencies:

hoomd_polymers/base/molecule.py → hoomd_organics/base/molecule.py

@@ -9,10 +9,10 @@
 from grits import CG_Compound
 from mbuild.lib.recipes import Polymer as mbPolymer
 
-from hoomd_polymers.utils import check_return_iterable
-from hoomd_polymers.utils.base_types import FF_Types
-from hoomd_polymers.utils.exceptions import MoleculeLoadError
-from hoomd_polymers.utils.ff_utils import (
+from hoomd_organics.utils import check_return_iterable
+from hoomd_organics.utils.base_types import FF_Types
+from hoomd_organics.utils.exceptions import MoleculeLoadError
+from hoomd_organics.utils.ff_utils import (
     _validate_hoomd_ff,
     apply_xml_ff,
     find_xml_ff,
@@ -318,9 +318,9 @@ class CoPolymer(Molecule):
 
     Parameters
     ----------
-    monomer_A : hoomd_polymers.molecules.Polymer; required
+    monomer_A : hoomd_organics.molecules.Polymer; required
         Class of the A-type monomer
-    monomer_B : hoomd_polymers.molecules.Polymer: required
+    monomer_B : hoomd_organics.molecules.Polymer: required
         Class of the B-type monomer
     length : int; required
         The total number of monomers in the molecule

hoomd_polymers/base/simulation.py → hoomd_organics/base/simulation.py

@@ -7,8 +7,8 @@
 import numpy as np
 import unyt as u
 
-from hoomd_polymers.utils import StdOutLogger, UpdateWalls
-from hoomd_polymers.utils.exceptions import ReferenceUnitError
+from hoomd_organics.utils import StdOutLogger, UpdateWalls
+from hoomd_organics.utils.exceptions import ReferenceUnitError
 
 
 class Simulation(hoomd.simulation.Simulation):

hoomd_polymers/base/system.py → hoomd_organics/base/system.py

@@ -15,9 +15,9 @@
 )
 from gmso.parameterization import apply
 
-from hoomd_polymers.base.molecule import Molecule
-from hoomd_polymers.utils import FF_Types, check_return_iterable, xml_to_gmso_ff
-from hoomd_polymers.utils.exceptions import (
+from hoomd_organics.base.molecule import Molecule
+from hoomd_organics.utils import FF_Types, check_return_iterable, xml_to_gmso_ff
+from hoomd_organics.utils.exceptions import (
     ForceFieldError,
     MoleculeLoadError,
     ReferenceUnitError,
@@ -29,7 +29,7 @@ class System(ABC):
 
     Parameters
     ----------
-    molecule : hoomd_polymers.molecule; required
+    molecule : hoomd_organics.molecule; required
     n_mols : int; required
         The number of times to replicate molecule in the system
     density : float; optional; default None

hoomd_polymers/library/forcefields.py → hoomd_organics/library/forcefields.py

@@ -4,7 +4,7 @@
 import foyer
 import hoomd
 
-from hoomd_polymers.assets import FF_DIR
+from hoomd_organics.assets import FF_DIR
 
 
 class GAFF(foyer.Forcefield):
@@ -29,7 +29,7 @@ class OPLS_AA_PPS(foyer.Forcefield):
     def __init__(self, forcefield_files=f"{FF_DIR}/pps_opls.xml"):
         super(OPLS_AA_PPS, self).__init__(forcefield_files=forcefield_files)
         self.description = (
-            "Based on hoomd_polymers.forcefields.OPLS_AA. "
+            "Based on hoomd_organics.forcefields.OPLS_AA. "
             "Trimmed down to include only PPS parameters. "
             "One missing parameter was added manually: "
             "<Angle class1=CA class2=S class3=CA angle=1.805 k=627.6/> "
@@ -44,7 +44,7 @@ class OPLS_AA_BENZENE(foyer.Forcefield):
     def __init__(self, forcefield_files=f"{FF_DIR}/benzene_opls.xml"):
         super(OPLS_AA_BENZENE, self).__init__(forcefield_files=forcefield_files)
         self.description = (
-            "Based on hoomd_polymers.forcefields.OPLS_AA. "
+            "Based on hoomd_organics.forcefields.OPLS_AA. "
             "Trimmed down to include only benzene parameters."
         )
         self.gmso_ff = ffutils.FoyerFFs().load(forcefield_files).to_gmso_ff()
@@ -56,7 +56,7 @@ def __init__(self, forcefield_files=f"{FF_DIR}/dimethylether_opls.xml"):
             forcefield_files=forcefield_files
         )
         self.description = (
-            "Based on hoomd_polymers.forcefields.OPLS_AA. "
+            "Based on hoomd_organics.forcefields.OPLS_AA. "
             "Trimmed down to include only dimethyl ether parameters."
         )
         self.gmso_ff = ffutils.FoyerFFs().load(forcefield_files).to_gmso_ff()

hoomd_polymers/library/polymers.py → hoomd_organics/library/polymers.py

@@ -3,8 +3,8 @@
 import mbuild as mb
 from mbuild.coordinate_transform import z_axis_transform
 
-from hoomd_polymers import CoPolymer, Polymer
-from hoomd_polymers.assets import MON_DIR
+from hoomd_organics import CoPolymer, Polymer
+from hoomd_organics.assets import MON_DIR
 
 
 class PolyEthylene(Polymer):

hoomd_polymers/library/simulations/tensile.py → hoomd_organics/library/simulations/tensile.py

@@ -1,8 +1,8 @@
 import hoomd
 import numpy as np
 
-from hoomd_polymers.base.simulation import Simulation
-from hoomd_polymers.utils.actions import PullParticles
+from hoomd_organics.base.simulation import Simulation
+from hoomd_organics.utils.actions import PullParticles
 
 
 class Tensile(Simulation):

hoomd_polymers/modules/welding.py → hoomd_organics/modules/welding.py

@@ -2,7 +2,7 @@
 import hoomd
 import numpy as np
 
-from hoomd_polymers.base.simulation import Simulation
+from hoomd_organics.base.simulation import Simulation
 
 
 class Interface:

hoomd_polymers/tests/base/test_molecule.py → hoomd_organics/tests/base/test_molecule.py

@@ -1,8 +1,8 @@
 import pytest
 
-from hoomd_polymers import CoPolymer, Molecule, Polymer
-from hoomd_polymers.tests import BaseTest
-from hoomd_polymers.utils import FF_Types, exceptions
+from hoomd_organics import CoPolymer, Molecule, Polymer
+from hoomd_organics.tests import BaseTest
+from hoomd_organics.utils import FF_Types, exceptions
 
 
 class TestMolecule(BaseTest):

hoomd_polymers/tests/base/test_simulation.py → hoomd_organics/tests/base/test_simulation.py

@@ -4,8 +4,8 @@
 import hoomd
 import numpy as np
 
-from hoomd_polymers import Simulation
-from hoomd_polymers.tests import BaseTest
+from hoomd_organics import Simulation
+from hoomd_organics.tests import BaseTest
 
 
 class TestSimulate(BaseTest):

hoomd_polymers/tests/base/test_system.py → hoomd_organics/tests/base/test_system.py

@@ -2,14 +2,14 @@
 import numpy as np
 import unyt as u
 
-from hoomd_polymers import Lattice, Pack
-from hoomd_polymers.library import (
+from hoomd_organics import Lattice, Pack
+from hoomd_organics.library import (
     GAFF,
     OPLS_AA,
     OPLS_AA_DIMETHYLETHER,
     OPLS_AA_PPS,
 )
-from hoomd_polymers.tests import BaseTest
+from hoomd_organics.tests import BaseTest
 
 
 class TestSystem(BaseTest):

hoomd_polymers/tests/base_test.py → hoomd_organics/tests/base_test.py

@@ -5,8 +5,8 @@
 import pytest
 from gmso.external.convert_mbuild import from_mbuild
 
-from hoomd_polymers import Molecule, Pack, Polymer
-from hoomd_polymers.library import OPLS_AA
+from hoomd_organics import Molecule, Pack, Polymer
+from hoomd_organics.library import OPLS_AA
 
 ASSETS_DIR = os.path.join(os.path.dirname(__file__), "assets")
 

hoomd_polymers/tests/library/test_forcefields.py → hoomd_organics/tests/library/test_forcefields.py

@@ -2,7 +2,7 @@
 
 import hoomd
 
-from hoomd_polymers.library import (
+from hoomd_organics.library import (
     GAFF,
     OPLS_AA,
     OPLS_AA_BENZENE,
@@ -11,7 +11,7 @@
     BeadSpring,
     FF_from_file,
 )
-from hoomd_polymers.tests.base_test import ASSETS_DIR
+from hoomd_organics.tests.base_test import ASSETS_DIR
 
 
 class TestForceFields:

hoomd_polymers/tests/library/test_polymers.py → hoomd_organics/tests/library/test_polymers.py

@@ -1,7 +1,7 @@
 import mbuild as mb
 import pytest
 
-from hoomd_polymers.library import (
+from hoomd_organics.library import (
     PEEK,
     PPS,
     LJChain,

hoomd_polymers/tests/library/test_tensile.py → hoomd_organics/tests/library/test_tensile.py

@@ -1,4 +1,4 @@
-from hoomd_polymers.tests import BaseTest
+from hoomd_organics.tests import BaseTest
 
 
 class TestTensileSimulation(BaseTest):

hoomd_polymers/tests/modules/test_weld.py → hoomd_organics/tests/modules/test_weld.py

@@ -2,17 +2,17 @@
 
 import gsd.hoomd
 
-from hoomd_polymers import Simulation
-from hoomd_polymers.modules.welding import Interface, SlabSimulation
-from hoomd_polymers.tests.base_test import BaseTest
+from hoomd_organics import Simulation
+from hoomd_organics.modules.welding import Interface, SlabSimulation
+from hoomd_organics.tests.base_test import BaseTest
 
 
 class TestWelding(BaseTest):
     def test_interface(self, polyethylene_system):
         sim = Simulation(
             initial_state=polyethylene_system.hoomd_snapshot,
             forcefield=polyethylene_system.hoomd_forcefield,
-            log_write_freq=2000
+            log_write_freq=2000,
         )
         sim.add_walls(wall_axis=(1, 0, 0), sigma=1, epsilon=1, r_cut=2)
         sim.run_update_volume(
@@ -47,7 +47,7 @@ def test_slab_sim_xaxis(self, polyethylene_system):
         sim = SlabSimulation(
             initial_state=polyethylene_system.hoomd_snapshot,
             forcefield=polyethylene_system.hoomd_forcefield,
-            log_write_freq=2000
+            log_write_freq=2000,
         )
         assert sim._axis_array == (1, 0, 0)
         assert sim._axis_index == 0
@@ -58,7 +58,7 @@ def test_slab_sim_yaxis(self, polyethylene_system):
             initial_state=polyethylene_system.hoomd_snapshot,
             forcefield=polyethylene_system.hoomd_forcefield,
             interface_axis="y",
-            log_write_freq=2000
+            log_write_freq=2000,
         )
         assert sim._axis_array == (0, 1, 0)
         assert sim._axis_index == 1
@@ -69,7 +69,7 @@ def test_slab_sim_zaxis(self, polyethylene_system):
             initial_state=polyethylene_system.hoomd_snapshot,
             forcefield=polyethylene_system.hoomd_forcefield,
             interface_axis="z",
-            log_write_freq=2000
+            log_write_freq=2000,
         )
         assert sim._axis_array == (0, 0, 1)
         assert sim._axis_index == 2
@@ -79,7 +79,7 @@ def test_weld_sim(self, polyethylene_system):
         sim = SlabSimulation(
             initial_state=polyethylene_system.hoomd_snapshot,
             forcefield=polyethylene_system.hoomd_forcefield,
-            log_write_freq=2000
+            log_write_freq=2000,
         )
         sim.run_NVT(kT=1.0, tau_kt=0.01, n_steps=500)
         sim.save_restart_gsd()
@@ -88,8 +88,8 @@ def test_weld_sim(self, polyethylene_system):
             gsd_file="restart.gsd", interface_axis="x", gap=0.1
         )
         sim = SlabSimulation(
-                initial_state=interface.hoomd_snapshot,
-                forcefield=polyethylene_system.hoomd_forcefield,
+            initial_state=interface.hoomd_snapshot,
+            forcefield=polyethylene_system.hoomd_forcefield,
         )
         if os.path.isfile("restart.gsd"):
             os.remove("restart.gsd")

hoomd_polymers/utils/ff_utils.py → hoomd_organics/utils/ff_utils.py

@@ -4,7 +4,7 @@
 import hoomd
 from gmso.parameterization import apply
 
-from hoomd_polymers.assets import FF_DIR
+from hoomd_organics.assets import FF_DIR
 
 from .base_types import FF_Types
 from .exceptions import (

setup.py

@@ -14,13 +14,13 @@
 from setuptools import Command, find_packages, setup
 
 # Package meta-data.
-NAME = "hoomd_polymers"
+NAME = "hoomd_organics"
 DESCRIPTION = (
     "Package making it easier to build and simulate polymers in Hoomd-Blue"
 )
-URL = "https://github.com/chrisjonesBSU/hoomd-polymers"
+URL = "https://github.com/cmelab/hoomd-organics"
 EMAIL = "[email protected]"
-AUTHOR = "Chris Jones"
+AUTHOR = "CME Lab"
 REQUIRES_PYTHON = ">=3.9.0"
 VERSION = None
 
@@ -102,7 +102,7 @@ def run(self):
     #     'console_scripts': ['mycli=mymodule:cli'],
     # },
     package_data={
-        "hoomd_polymers": [
+        "hoomd_organics": [
             "modules/*",
             "sim/*",
             "library/*",