infretis · andersle · Sep 15, 2023 · Sep 15, 2023 · Sep 18, 2023 · Sep 18, 2023
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,10 +1,23 @@
 repos:
-  - repo: https://github.com/psf/black
-    rev: 23.7.0
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-yaml
+    -   id: check-added-large-files
+-   repo: https://github.com/psf/black
+    rev: 23.9.1
     hooks:
       - id: black-jupyter
         # It is recommended to specify the latest version of Python
         # supported by your project here, or alternatively use
         # pre-commit's default_language_version, see
         # https://pre-commit.com/#top_level-default_language_version
         language_version: python3.11
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.0.292
+  hooks:
+    - id: ruff
+      types_or: [python, pyi, jupyter]
diff --git a/examples/lennard.py b/examples/lennard.py
@@ -23,9 +23,7 @@ def create_system():
     for xyz in pos:
         particles.add_particle(pos=xyz, mass=1.0, ptype=0, name="Ar")
 
-    generate_maxwell_velocities(
-        particles, rgen=default_rng(), temperature=0.8
-    )
+    generate_maxwell_velocities(particles, rgen=default_rng(), temperature=0.8)
 
     lennard = LennardJonesCut(dim=3, shift=True, mixing="geometric")
     parameters = {

diff --git a/examples/movie-doublewell-pair.py b/examples/movie-doublewell-pair.py
@@ -13,7 +13,6 @@
 from turtlemd.tools import generate_lattice
 
 sns.set_context("talk", font_scale=0.8)
-# matplotlib.rcParams.update({'font.size': 10})
 
 
 def create_system() -> System:

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "turtlemd"
-version = "2023.3.1"
+version = "2024.1"
 description = "A slow molecular dynamics library for testing"
 authors = [
     "Daniel Zhang <daniel.t.zhang@ntnu.no>",
@@ -13,6 +13,8 @@ readme = "README.md"
 [tool.poetry.dependencies]
 python = ">=3.10,<3.13"
 numpy = "^1.24.2"
+toml = "^0.10.2"
+pint = "^0.23"
 
 [tool.poetry.group.dev.dependencies]
 ruff = "^0.0.261"
@@ -24,6 +26,7 @@ pytest-randomly = "^3.12.0"
 jupyter-black = "^0.3.4"
 pre-commit = "^3.3.3"
 flake8 = "^6.0.0"
+types-toml = "^0.10.8.7"
 
 [tool.ruff]
 line-length = 79
@@ -39,6 +42,9 @@ warn_unused_ignores = true
 show_error_codes = true
 plugins = "numpy.typing.mypy_plugin"
 
+[tool.poetry.scripts]
+turtlemd = "turtlemd.bin:main"
+
 [build-system]
 requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"
diff --git a/tests/inout/box1.toml b/tests/inout/box1.toml
@@ -0,0 +1,4 @@
+[box]
+low = [10, 11, 12]
+high = [23, 24, 25]
+periodic = [true, true, true]
diff --git a/tests/inout/box2.toml b/tests/inout/box2.toml
@@ -0,0 +1,4 @@
+[box]
+low = [10, 11, 12]
+high = [23, 24, 25]
+periodic = true
diff --git a/tests/inout/box3.toml b/tests/inout/box3.toml
@@ -0,0 +1,6 @@
+[box]
+low = [10, 11, 12]
+high = [23, 24, 25]
+periodic = [true, true, true]
+alpha = 75
+beta = 60
diff --git a/tests/inout/config/start.xyz b/tests/inout/config/start.xyz
@@ -0,0 +1,4 @@
+2
+# Step 2 box: 1.0 2.0 3.0
+A   1.0  1.0  1.0  1.0  1.0  1.0
+B   2.0  2.0  2.0  1.0  1.0  1.0
diff --git a/tests/inout/config/system_one_down.toml b/tests/inout/config/system_one_down.toml
@@ -0,0 +1,7 @@
+[box]
+periodic = [true, true, true]
+low = [0.0, 0.0, 0.0]
+high = [1.0, 1.0, 1.0]
+
+[particles]
+file = "../start2.xyz"
diff --git a/tests/inout/integrators/integrator.toml b/tests/inout/integrators/integrator.toml
@@ -0,0 +1,3 @@
+[integrator]
+class = "this-is-integrator-hello"
+timestep = 1234.5678
diff --git a/tests/inout/integrators/langevin1.toml b/tests/inout/integrators/langevin1.toml
@@ -0,0 +1,6 @@
+[integrator]
+class = "LangevinOverdamped"
+timestep = 1
+gamma = 2
+beta = 3
+seed = 123
diff --git a/tests/inout/integrators/langevin2.toml b/tests/inout/integrators/langevin2.toml
@@ -0,0 +1,6 @@
+[integrator]
+class = "LangevinInertia"
+timestep = 1
+gamma = 2
+beta = 3
+seed = 123
diff --git a/tests/inout/integrators/velocityverlet.toml b/tests/inout/integrators/velocityverlet.toml
@@ -0,0 +1,3 @@
+[integrator]
+class = "VelocityVerlet"
+timestep = 1234.5678
diff --git a/tests/inout/integrators/verlet.toml b/tests/inout/integrators/verlet.toml
@@ -0,0 +1,3 @@
+[integrator]
+class = "Verlet"
+timestep = 1234.5678
diff --git a/tests/inout/md.toml b/tests/inout/md.toml
@@ -0,0 +1,40 @@
+# Molecular Dynamics Configuration
+
+# Basic MD settings
+[md]
+total_steps = 200  # Total simulation steps
+temperature = 298.15  # Kelvin
+
+# Integrator settings
+[integrator]
+class = "VelocityVerlet"
+timestep = 0.005
+
+# Initial structure file:
+[particles]
+file = "config/start.xyz"
+
+[particles.masses]
+Ar = 1.0
+
+[particles.types]
+Ar = 1
+
+# Periodic boundary conditions:
+[box]
+periodic = true
+high = [10.0, 10.0, 10.0]
+
+# Potential/Forcefield settings
+[potential]
+type = "Lennard-Jones"  # Could also be "AMBER", "CHARMM", etc.
+
+  [potential.parameters]
+  epsilon = 1.0  # LJ epsilon parameter (for Lennard-Jones potential)
+  sigma = 3.40  # LJ sigma parameter (for Lennard-Jones potential)
+  cut = 2.5  # Cut-off for the potential
+
+# Output settings:
+[output]
+trajectory_file = "traj.xyz"
+log_file = "md.log"
diff --git a/tests/inout/nesting.toml b/tests/inout/nesting.toml
@@ -0,0 +1,16 @@
+[box]
+periodic = [true, true, true]
+low = [0.0, 0.0, 0.0]
+high = [1.0, 1.0, 1.0]
+
+[system]
+file = "system"
+
+[particles]
+file = "particles"
+
+[system.particles]
+file = "system.particles"
+
+[x.y.z.w]
+file = "x.y.z.w"
diff --git a/tests/inout/particles/masses.txt b/tests/inout/particles/masses.txt
@@ -0,0 +1,2 @@
+123.
+456.
diff --git a/tests/inout/particles/particles1.toml b/tests/inout/particles/particles1.toml
@@ -0,0 +1,15 @@
+[box]
+periodic = [true, true, true]
+low = [0.0, 0.0, 0.0]
+high = [1.0, 1.0, 1.0]
+
+[particles]
+file = "../config/start.xyz"
+
+[particles.masses]
+A = 2.0
+B = 10.0
+
+[particles.types]
+A = 9
+B = 55
diff --git a/tests/inout/particles/particles2.toml b/tests/inout/particles/particles2.toml
@@ -0,0 +1,9 @@
+[box]
+periodic = [true, true, true]
+low = [0.0, 0.0, 0.0]
+high = [1.0, 1.0, 1.0]
+
+[particles]
+file = "../config/start.xyz"
+mass_list = [10.0, 40.0]
+type_list = [99, 101]
diff --git a/tests/inout/particles/particles3.toml b/tests/inout/particles/particles3.toml
@@ -0,0 +1,9 @@
+[box]
+periodic = [true, true, true]
+low = [0.0, 0.0, 0.0]
+high = [1.0, 1.0, 1.0]
+
+[particles]
+file = "../config/start.xyz"
+mass_file = "masses.txt"
+type_file = "types.txt"
diff --git a/tests/inout/particles/types.txt b/tests/inout/particles/types.txt
@@ -0,0 +1,2 @@
+33.
+77.
diff --git a/tests/inout/start.xyz b/tests/inout/start.xyz
@@ -0,0 +1,12 @@
+2
+# Step 2 box: 1.0 2.0 3.0
+A   1.0  1.0  1.0  1.0  1.0  1.0
+B   1.0  1.0  1.0  1.0  1.0  1.0
+2
+# Step 3 box: 1.0 2.0 3.0
+A   4.0  4.0  4.0  4.0  4.0  4.0
+B   4.0  4.0  4.0  4.0  4.0  4.0
+2
+# Step 4 box: 1.0 2.0 3.0
+A   8.0  8.0  8.0  8.0  8.0  8.0
+B   8.0  8.0  8.0  8.0  8.0  8.0
diff --git a/tests/inout/start2.xyz b/tests/inout/start2.xyz
@@ -0,0 +1,4 @@
+2
+# Step 4 box: 1.0 2.0 3.0
+A   8.0  8.0  8.0  8.0  8.0  8.0
+B   8.0  8.0  8.0  8.0  8.0  8.0
diff --git a/tests/inout/system.toml b/tests/inout/system.toml
@@ -0,0 +1,7 @@
+[box]
+periodic = [true, true, true]
+low = [0.0, 0.0, 0.0]
+high = [1.0, 1.0, 1.0]
+
+[particles]
+file = "config/start.xyz"
diff --git a/tests/inout/system_missing_xyz.toml b/tests/inout/system_missing_xyz.toml
@@ -0,0 +1,7 @@
+[box]
+periodic = [true, true, true]
+low = [0.0, 0.0, 0.0]
+high = [1.0, 1.0, 1.0]
+
+[particles]
+file = "config/start_not_present.xyz"
diff --git a/tests/inout/system_units1.toml b/tests/inout/system_units1.toml
@@ -0,0 +1,10 @@
+[system]
+units = "real"
+
+[box]
+periodic = [true, true, true]
+low = [0.0, 0.0, 0.0]
+high = [1.0, 1.0, 1.0]
+
+[particles]
+file = "config/start.xyz"
diff --git a/tests/inout/system_units2.toml b/tests/inout/system_units2.toml
@@ -0,0 +1,10 @@
+[system]
+units = "units-that-does-not-exist"
+
+[box]
+periodic = [true, true, true]
+low = [0.0, 0.0, 0.0]
+high = [1.0, 1.0, 1.0]
+
+[particles]
+file = "config/start.xyz"