add molecular dynamics terminology to Key enum

- with metadata in keys.yml
- breaking: rename previous momentum attr in ML section to optimizer_momentum
- adjust keys-schema.yml to support more complex symbols and units

pymatviz/enums.py

@@ -563,6 +563,56 @@ def __reduce_ex__(self, proto: object) -> tuple[type, tuple[str]]:
     collinear = "collinear"
     non_collinear = "non_collinear"
 
+    # Molecular Dynamics
+    trajectory = "trajectory"
+    frames = "frames"
+    frame = "frame"
+    diffusivity = "diffusivity"
+    diffusion_tensor = "diffusion_tensor"
+    msd = "msd"  # mean squared displacement
+    velocity_autocorr = "velocity_autocorr"  # velocity autocorrelation function
+    ensemble = "ensemble"
+    nvt = "nvt"  # canonical ensemble
+    nve = "nve"  # microcanonical ensemble
+    npt = "npt"  # isothermal-isobaric ensemble
+    nvp = "nvp"  # isoenthalpic-isobaric ensemble
+    micro_canonical = "micro_canonical"
+    canonical = "canonical"
+    grand_canonical = "grand_canonical"
+    isothermal_isobaric = "isothermal_isobaric"
+    time_step = "time_step"
+    time_steps = "time_steps"
+    integration_time = "integration_time"
+    equilibration_time = "equilibration_time"
+    production_time = "production_time"
+    thermostat = "thermostat"
+    barostat = "barostat"
+    langevin_damping = "langevin_damping"
+    nose_hoover = "nose_hoover"
+    berendsen = "berendsen"
+    andersen = "andersen"
+    velocity_verlet = "velocity_verlet"
+    verlet = "verlet"
+    leap_frog = "leap_frog"
+    kinetic_energy = "kinetic_energy"
+    potential_energy = "potential_energy"
+    total_energy = "total_energy"
+    conserved_energy = "conserved_energy"
+    temperature_avg = "temperature_avg"
+    pressure_avg = "pressure_avg"
+    volume_avg = "volume_avg"
+    density_avg = "density_avg"
+    rdf = "rdf"  # radial distribution function
+    velocity = "velocity"
+    acceleration = "acceleration"
+    momentum = "momentum"
+    angular_momentum = "angular_momentum"
+    gyration_radius = "gyration_radius"
+    drift = "drift"
+    flux = "flux"
+    correlation_time = "correlation_time"
+    correlation_length = "correlation_length"
+
     # ML
     train_task = "train_task"
     test_task = "test_task"
@@ -582,7 +632,7 @@ def __reduce_ex__(self, proto: object) -> tuple[type, tuple[str]]:
     epochs = "epochs"
     batch_size = "batch_size"
     learning_rate = "learning_rate"
-    momentum = "momentum"
+    optimizer_momentum = "optimizer_momentum"
     weight_decay = "weight_decay"
     early_stopping = "early_stopping"
     n_folds = "n_folds"

pymatviz/io.py

@@ -37,7 +37,7 @@ class TqdmDownload(tqdm):
     """Progress bar for urllib.request.urlretrieve file download.
 
     Adapted from official TqdmUpTo example.
-    See https://github.com/tqdm/tqdm/blob/4c956c20b83be4312460fc0c4812eeb3fef5e7df/README.rst#hooks-and-callbacks
+    See https://github.com/tqdm/tqdm/blob/4c956c2/README.rst#hooks-and-callbacks
     """
 
     def __init__(self, *args: Any, **kwargs: Any) -> None:

pymatviz/keys.yml

@@ -995,8 +995,8 @@ ml: # Machine Learning
     label: Batch Size
   learning_rate:
     label: Learning Rate
-  momentum:
-    label: Momentum
+  optimizer_momentum:
+    label: Optimizer Momentum
   weight_decay:
     label: Weight Decay
   early_stopping:
@@ -1454,3 +1454,200 @@ environmental_indicators:
   sustainability:
     label: Sustainability Index
     description: Composite score of environmental impact including resource depletion, emissions, etc.
+
+molecular_dynamics:
+  trajectory:
+    label: Trajectory
+    description: Time series of atomic positions and other system properties
+  frames:
+    label: Frames
+    description: Collection of snapshots from a molecular dynamics simulation
+  frame:
+    label: Frame
+    description: Single snapshot from a molecular dynamics simulation
+  diffusivity:
+    label: Diffusivity
+    symbol: D
+    unit: cm²/s
+    description: Rate of atomic/molecular motion through the system
+  diffusion_tensor:
+    label: Diffusion Tensor
+    symbol: D
+    unit: cm²/s
+    description: Anisotropic diffusion rates along different crystallographic directions
+  msd:
+    label: Mean Squared Displacement
+    symbol: ⟨r²⟩
+    unit: Ų
+    description: Average squared distance traveled by atoms over time
+  velocity_autocorr:
+    label: Velocity Autocorrelation Function
+    symbol: C<sub>v</sub>
+    description: Correlation of atomic velocities with their initial values over time, used to analyze atomic dynamics and vibrational properties.
+  ensemble:
+    label: Ensemble
+    description: Statistical ensemble used for the simulation (NVE, NVT, NPT, etc.)
+  nvt:
+    label: NVT Ensemble
+    description: Canonical ensemble with constant number of particles, volume, and temperature
+  nve:
+    label: NVE Ensemble
+    description: Microcanonical ensemble with constant number of particles, volume, and energy
+  npt:
+    label: NPT Ensemble
+    description: Isothermal-isobaric ensemble with constant number of particles, pressure, and temperature
+  nvp:
+    label: NVP Ensemble
+    description: Isoenthalpic-isobaric ensemble with constant number of particles, volume, and pressure
+  micro_canonical:
+    label: Microcanonical Ensemble
+    description: System with constant number of particles, volume, and energy (NVE)
+  canonical:
+    label: Canonical Ensemble
+    description: System with constant number of particles, volume, and temperature (NVT)
+  grand_canonical:
+    label: Grand Canonical Ensemble
+    description: System with constant chemical potential, volume, and temperature (μVT)
+  isothermal_isobaric:
+    label: Isothermal-Isobaric Ensemble
+    description: System with constant number of particles, pressure, and temperature (NPT)
+  time_step:
+    label: Time Step
+    symbol: Δt
+    unit: fs
+    description: Integration time step for equations of motion
+  time_steps:
+    label: Time Steps
+    symbol: N<sub>steps</sub>
+    description: Total number of integration steps
+  integration_time:
+    label: Integration Time
+    symbol: t<sub>int</sub>
+    unit: ps
+    description: Total simulation time
+  equilibration_time:
+    label: Equilibration Time
+    symbol: t<sub>eq</sub>
+    unit: ps
+    description: Time allowed for system to reach equilibrium before data collection
+  production_time:
+    label: Production Time
+    symbol: t<sub>prod</sub>
+    unit: ps
+    description: Time during which data is collected for analysis
+  thermostat:
+    label: Thermostat
+    description: Algorithm used to control system temperature
+  barostat:
+    label: Barostat
+    description: Algorithm used to control system pressure
+  langevin_damping:
+    label: Langevin Damping
+    symbol: γ
+    unit: ps⁻¹
+    description: Friction coefficient in Langevin dynamics
+  nose_hoover:
+    label: Nosé-Hoover Thermostat
+    description: Deterministic thermostat based on extended system dynamics
+  berendsen:
+    label: Berendsen Thermostat/Barostat
+    description: Weak-coupling algorithm for temperature/pressure control
+  andersen:
+    label: Andersen Thermostat
+    description: Stochastic velocity reassignment thermostat
+  velocity_verlet:
+    label: Velocity Verlet
+    description: Symplectic integration algorithm for equations of motion
+  verlet:
+    label: Verlet
+    description: Basic integration algorithm for equations of motion
+  leap_frog:
+    label: Leap-Frog
+    description: Variant of Verlet algorithm with velocities offset by half time step
+  kinetic_energy:
+    label: Kinetic Energy
+    symbol: E<sub>k</sub>
+    unit: eV
+    description: Total kinetic energy of the system
+  potential_energy:
+    label: Potential Energy
+    symbol: E<sub>p</sub>
+    unit: eV
+    description: Total potential energy of the system
+  total_energy:
+    label: Total Energy
+    symbol: E<sub>tot</sub>
+    unit: eV
+    description: Sum of kinetic and potential energies
+  conserved_energy:
+    label: Conserved Energy
+    symbol: E<sub>cons</sub>
+    unit: eV
+    description: Energy quantity that should remain constant (includes thermostat terms)
+  temperature_avg:
+    label: Average Temperature
+    symbol: ⟨T⟩
+    unit: K
+    description: Time-averaged temperature during simulation
+  pressure_avg:
+    label: Average Pressure
+    symbol: ⟨P⟩
+    unit: GPa
+    description: Time-averaged pressure during simulation
+  volume_avg:
+    label: Average Volume
+    symbol: ⟨V⟩
+    unit: ų
+    description: Time-averaged volume during simulation
+  density_avg:
+    label: Average Density
+    symbol: ⟨ρ⟩
+    unit: g/cm³
+    description: Time-averaged density during simulation
+  rdf:
+    label: Radial Distribution Function
+    symbol: g(r)
+    description: Probability of finding atoms at distance r relative to random distribution
+  velocity:
+    label: Velocity
+    symbol: v
+    unit: Å/ps
+    description: Atomic velocities
+  acceleration:
+    label: Acceleration
+    symbol: a
+    unit: Å/ps²
+    description: Atomic accelerations
+  momentum:
+    label: Momentum
+    symbol: p
+    unit: eV⋅ps/Å
+    description: Linear momentum of atoms or system
+  angular_momentum:
+    label: Angular Momentum
+    symbol: L
+    unit: eV⋅ps
+    description: Angular momentum of atoms or system
+  gyration_radius:
+    label: Radius of Gyration
+    symbol: R<sub>g</sub>
+    unit: Å
+    description: Root mean square distance of atoms from their center of mass
+  drift:
+    label: Drift
+    unit: Å/ps
+    description: Systematic motion of center of mass
+  flux:
+    label: Flux
+    symbol: J
+    description: Flow rate of mass, momentum, or energy through system
+  correlation_time:
+    label: Correlation Time
+    symbol: τ<sub>c</sub>
+    unit: ps
+    description: Characteristic time for decay of time correlations
+  correlation_length:
+    label: Correlation Length
+    symbol: ξ
+    unit: Å
+    description: Characteristic length for decay of spatial correlations

tests/keys-schema.yml

@@ -11,12 +11,12 @@ definitions:
         minLength: 1
       symbol:
         type: string
-        # Allow Greek letters, HTML tags, combining marks etc.
-        pattern: '^[A-Za-z0-9<>/_ ,\u0300-\u036F\u0370-\u03FF%\-]+$'
+        # Allow Greek letters, HTML tags, combining marks, angle brackets, parentheses, etc.
+        pattern: '^[A-Za-z0-9<>/_ ,\u0300-\u036F\u0370-\u03FF%\-()⟨⟩²³ξτγ]+$'
       unit:
         type: string
-        # Added <sup> tags and more special characters
-        pattern: '^[A-Za-z0-9²³·/%⁻$°Å·∙⋅\u0370-\u03FF\- /<>sup¹½·⁻¹²³emu]+$'
+        # Added more special characters for units and mathematical notation
+        pattern: '^[A-Za-z0-9²³·/%⁻$°Å·∙⋅\u0370-\u03FF\- /<>sup¹½·⁻¹²³emu⋅⁻]+$'
       description:
         type: string
         minLength: 10 # Ensure meaningful descriptions