Merge pull request #10 from chrisjonesBSU/refactor

Refactor

.github/workflows/pytest.yml

@@ -24,23 +24,23 @@ jobs:
     steps:
     - name: Check out repository
       uses: actions/checkout@v2
- 
+
     - name: Build environment
       uses: conda-incubator/setup-miniconda@v2
       with:
         environment-file: environment-cpu.yml
         miniforge-variant: Mambaforge
         miniforge-version: 4.9.2-4
         use-mamba: true
-    
+
     - name: Install package
       shell: bash -l {0}
       run: pip install -e .
 
     - name: Run pytest with coverage report
       shell: bash -l {0}
       run: python -m pytest -rs -v --cov=./ --cov-report=xml
-          
+
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v3
       with:

.gitignore

@@ -127,3 +127,6 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+# IDE files
+.idea/

.pre-commit-config.yaml

@@ -0,0 +1,47 @@
+ci:
+    autofix_commit_msg: |
+        [pre-commit.ci] auto fixes from pre-commit.com hooks
+
+        for more information, see https://pre-commit.ci
+    autofix_prs: true
+    autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
+    autoupdate_schedule: weekly
+    skip: []
+    submodules: false
+
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.4.0
+  hooks:
+    - id: check-yaml
+    - id: end-of-file-fixer
+    - id: trailing-whitespace
+      exclude: 'hoomd_polymers/tests/assets/.* | hoomd_polymers/assets/.*'
+- repo: https://github.com/psf/black
+  rev: 23.7.0
+  hooks:
+    - id: black
+      args: [--line-length=80]
+- repo: https://github.com/pycqa/isort
+  rev: 5.12.0
+  hooks:
+    - id: isort
+      name: isort (python)
+      args:
+        [--profile=black, --line-length=80]
+      exclude: 'cmeuitls/tests/assets/.* '
+
+- repo: https://github.com/pycqa/flake8
+  rev: 6.1.0
+  hooks:
+    - id: flake8
+      args:
+        - --max-line-length=80
+      exclude: '__init__.py'
+
+#- repo: https://github.com/pycqa/pydocstyle
+#  rev: '6.3.0'
+#  hooks:
+#    - id: pydocstyle
+#      exclude: ^(cmeuitls/tests/|setup.py)
+#      args: [--convention=numpy]

README.md

@@ -2,25 +2,25 @@
 [![codecov](https://codecov.io/gh/chrisjonesBSU/hoomd-polymers/branch/main/graph/badge.svg?token=86LY9WHSH6)](https://codecov.io/gh/chrisjonesBSU/hoomd-polymers)
 ## About
 
-Wrapper for [MoSDeF](https://github.com/mosdef-hub) packages and [Hoomd-Blue](https://github.com/glotzerlab/hoomd-blue) with 
+Wrapper for [MoSDeF](https://github.com/mosdef-hub) packages and [Hoomd-Blue](https://github.com/glotzerlab/hoomd-blue) with
 a focus on simulating soft matter systems.
 
 ## Installation
 
-### 1. Clone this repository: ###  
+### 1. Clone this repository: ###
 
 ```
-git clone [email protected]:chrisjonesbsu/hoomd-polymers.git  
-cd hoomd-polymers  
+git clone [email protected]:chrisjonesbsu/hoomd-polymers.git
+cd hoomd-polymers
 ```
 
-### 2. Set up and activate environment: ###  
+### 2. Set up and activate environment: ###
 #### a. Using HOOMD-blue from conda:
 ```
-conda env create -f environment-cpu.yml  
-conda activate hoomd-polymers 
+conda env create -f environment-cpu.yml
+conda activate hoomd-polymers
 python -m pip install .
-```  
+```
 
 ## Basic Usage
 #### Using the built in molecules, systems and forcefields:

codecov.yml

@@ -8,7 +8,7 @@ comment:
         - "main"
 ignore:
     - "hoomd-polymers/tests"
-    - "hoomd-polymers/library/*"
-    - "hoomd-polymers/logs"
+    - "hoomd-polymers/assets"
     - "hoomd-polymers/__version__.py"
+    - "tutorials"
     - "setup.py"

environment-cpu.yml

@@ -1,19 +1,26 @@
-name: hoomd-polymers 
+name: hoomd-polymers
 channels:
   - conda-forge
 dependencies:
+  - boltons
   - foyer
   - freud
-  - gsd
-  - hoomd>3.7=*cpu*
+    #  - gmso>=0.11.0
+  - gsd<3.0
+  - hoomd=3.11=*cpu*
   - mbuild
   - numpy
+  - openbabel
   - pip
+  - py3Dmol
+  - pydantic
   - pytest
   - pytest-cov
   - python=3.9
-  - signac=1.7.0
-  - signac-flow=0.18.1
+  - symengine
+  - python-symengine
   - unyt
   - pip:
       - git+https://github.com/cmelab/cmeutils.git@master
+      - git+https://github.com/cmelab/grits.git@main
+      - git+https://github.com/mosdef-hub/gmso@main

environment-dev.yml

@@ -0,0 +1,23 @@
+name: hoomd-polymers-dev
+channels:
+  - conda-forge
+dependencies:
+  - foyer
+  - freud
+    #- gmso >= 0.11.0
+  - gsd<3.0
+  - hoomd=3.11=*gpu*
+  - mbuild
+  - numpy
+  - openbabel
+  - pip
+  - py3Dmol
+  - pytest
+  - pytest-cov
+  - python=3.9
+  - unyt
+  - pre-commit
+  - pip:
+      - git+https://github.com/cmelab/cmeutils.git@master
+      - git+https://github.com/cmelab/grits.git@main
+      - git+https://github.com/mosdef-hub/gmso@main

environment-gpu.yml

@@ -1,19 +1,26 @@
-name: hoomd-polymers 
+name: hoomd-polymers
 channels:
   - conda-forge
 dependencies:
+  - boltons
   - foyer
   - freud
-  - gsd
-  - hoomd>3.0=*gpu*
+    #  - gmso>=0.11.0
+  - gsd<3.0
+  - hoomd=3.11=*gpu*
   - mbuild
   - numpy
+  - openbabel
   - pip
+  - py3Dmol
+  - pydantic
   - pytest
   - pytest-cov
   - python=3.9
-  - signac=1.7.0
-  - signac-flow=0.18.1
+  - symengine
+  - python-symengine
   - unyt
   - pip:
       - git+https://github.com/cmelab/cmeutils.git@master
+      - git+https://github.com/cmelab/grits.git@main
+      - git+https://github.com/mosdef-hub/gmso@main

hoomd_polymers/__init__.py

@@ -1,2 +1,9 @@
-from hoomd_polymers.sim import simulation
-from hoomd_polymers.modules import welding
+from .base import (
+    CoPolymer,
+    Lattice,
+    Molecule,
+    Pack,
+    Polymer,
+    Simulation,
+    System,
+)

hoomd_polymers/assets/__init__.py

@@ -0,0 +1,2 @@
+from .forcefields import FF_DIR
+from .molecule_files import MON_DIR

hoomd_polymers/library/forcefields/__init__.py → hoomd_polymers/assets/forcefields/__init__.py

@@ -1,4 +1,3 @@
 import os
 
-
 FF_DIR = os.path.abspath(os.path.dirname(__file__))

hoomd_polymers/assets/forcefields/benzene_opls.xml

@@ -0,0 +1,23 @@
+<ForceField name="OPLS-AA" version="0.0.3" combining_rule="geometric">
+	<AtomTypes>
+		<Type name="ha" class="HA" element="H" mass="1.008" def="[H][C;%ca]" desc="benzene H" overrides=""/>
+		<Type name="ca" class="CA" element="C" mass="12.011" def="[C;X3;r6]1[C;X3;r6][C;X3;r6][C;X3;r6][C;X3;r6][C;X3;r6]1" desc="" overrides=""/>
+	</AtomTypes>
+	<HarmonicBondForce>
+		<Bond class1="CA" class2="CA" length="0.14" k="392459.2"/>
+		<Bond class1="CA" class2="HA" length="0.108" k="307105.6"/>
+	</HarmonicBondForce>
+	<HarmonicAngleForce>
+		<Angle class1="CA" class2="CA" class3="CA" angle="2.09439510239" k="527.184"/>
+		<Angle class1="CA" class2="CA" class3="HA" angle="2.09439510239" k="292.88"/>
+	</HarmonicAngleForce>
+	<RBTorsionForce>
+		<Proper class1="CA" class2="CA" class3="CA" class4="CA" c0="30.334" c1="0.0" c2="-30.334" c3="0.0" c4="0.0" c5="0.0"/>
+		<Proper class1="CA" class2="CA" class3="CA" class4="HA" c0="30.334" c1="0.0" c2="-30.334" c3="0.0" c4="0.0" c5="0.0"/>
+		<Proper class1="HA" class2="CA" class3="CA" class4="HA" c0="30.334" c1="0.0" c2="-30.334" c3="0.0" c4="0.0" c5="0.0"/>
+	</RBTorsionForce>
+	<NonbondedForce coulomb14scale="0.5" lj14scale="0.5">
+		<Atom type="ha" charge="0.115" sigma="0.242" epsilon="0.12552"/>
+		<Atom type="ca" charge="-0.115" sigma="0.355" epsilon="0.29288"/>
+	</NonbondedForce>
+</ForceField>

hoomd_polymers/assets/forcefields/dimethylether_opls.xml

@@ -0,0 +1,25 @@
+<ForceField name="OPLS-AA" version="0.0.3" combining_rule="geometric">
+<AtomTypes>
+<Type name="ct" class="CT" element="C" mass="12.011" def="[C;X4]([O;%os])(H)(H)H" desc="C(H3OR), methyl ether" overrides=""/>
+<Type name="os" class="OS" element="O" mass="15.999" def="[O;X2](C)C" desc="O, dialkyl ether" overrides=""/>
+<Type name="hc" class="HC" element="C" mass="12.011" def="HC[O;%os]" desc="H(COR), alpha H ether" overrides=""/>
+</AtomTypes>
+<HarmonicBondForce>
+<Bond class1="OS" class2="CT" length="0.141" k="267776.0"/>
+<Bond class1="CT" class2="OS" length="0.141" k="267776.0"/>
+<Bond class1="CT" class2="HC" length="0.109" k="284512.0"/>
+</HarmonicBondForce>
+<HarmonicAngleForce>
+<Angle class1="OS" class2="CT" class3="HC" angle="1.91113553093" k="292.88"/>
+<Angle class1="CT" class2="OS" class3="CT" angle="1.91113553093" k="502.08"/>
+<Angle class1="HC" class2="CT" class3="HC" angle="1.88146493365" k="276.144"/>
+</HarmonicAngleForce>
+<RBTorsionForce>
+<Proper class1="CT" class2="OS" class3="CT" class4="HC" c0="1.58992" c1="4.76976" c2="0.0" c3="-6.35968" c4="0.0" c5="0.0"/>
+</RBTorsionForce>
+<NonbondedForce coulomb14scale="0.5" lj14scale="0.5">
+<Atom type="ct" charge="0.11" sigma="0.35" epsilon="0.276144"/>
+<Atom type="os" charge="-0.4" sigma="0.29" epsilon="0.58576"/>
+<Atom type="hc" charge="0.03" sigma="0.25" epsilon="0.12552"/>
+</NonbondedForce>
+</ForceField>