feat: add dice input generation and player routines for NVT/NPT simulations

diceplayer/dice/__init__.py

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+"""
+DICE Monte Carlo Simulation Interface
+=====================================
+
+This package provides utilities for configuring and running simulations with
+the DICE Monte Carlo molecular simulation program.
+
+DICE performs statistical sampling of molecular systems using the Metropolis
+Monte Carlo algorithm. Simulations are defined by text input files containing
+keywords that control the thermodynamic ensemble, system composition, and
+simulation parameters.
+
+---------------------------------------------------------------------
+
+Simulation Ensembles
+--------------------
+
+DICE supports multiple statistical ensembles.
+
+NVT
+    Canonical ensemble where the following properties remain constant:
+
+    - N: number of molecules
+    - V: system volume
+    - T: temperature
+
+    The system density is fixed and the simulation box volume does not change
+    during the simulation.
+
+NPT
+    Isothermal–isobaric ensemble where the following properties remain constant:
+
+    - N: number of molecules
+    - P: pressure
+    - T: temperature
+
+    The simulation box volume is allowed to fluctuate in order to maintain the
+    target pressure.
+
+---------------------------------------------------------------------
+
+Simulation Stages
+-----------------
+
+Simulations are typically executed in multiple stages.
+
+Thermalization (TER)
+    Initial phase where the system relaxes to the desired thermodynamic
+    conditions. Molecular configurations stabilize and the system reaches
+    equilibrium.
+
+    During this stage statistical properties are **not accumulated**.
+
+Production / Equilibration (EQ)
+    Main sampling phase after the system has equilibrated.
+
+    Statistical properties such as energies, densities, and radial
+    distribution functions are collected and configurations may be saved
+    for later analysis.
+
+---------------------------------------------------------------------
+
+Typical Simulation Pipeline
+---------------------------
+
+Two common execution workflows are used.
+
+NVT Simulation
+    Used when the system density is known.
+
+    1. NVT.ter  → thermalization at constant density
+    2. NVT.eq   → production sampling
+
+NPT Simulation
+    Used when the equilibrium density is unknown.
+
+    1. NVT.ter  → initial thermalization at approximate density
+    2. NPT.ter  → pressure relaxation (volume adjustment)
+    3. NPT.eq   → production sampling at target pressure
+
+---------------------------------------------------------------------
+
+DICE Input Keywords
+-------------------
+
+The following keywords are used in the generated input files.
+
+title
+    Descriptive title printed in the simulation output.
+
+ncores
+    Number of CPU cores used by the DICE executable.
+
+ljname
+    File containing Lennard-Jones parameters and molecular topology.
+
+outname
+    Prefix used for simulation output files.
+
+nmol
+    Number of molecules of each species in the system.
+
+dens
+    System density (g/cm³). Used only in NVT simulations or for
+    initialization of NPT runs.
+
+press
+    Target pressure used in NPT simulations.
+
+temp
+    Simulation temperature.
+
+nstep
+    Number of Monte Carlo cycles executed in the simulation stage.
+
+init
+    Defines how the simulation initializes molecular coordinates.
+
+    yes
+        Random initial configuration.
+
+    no
+        Continue from a previous configuration.
+
+    yesreadxyz
+        Read coordinates from a previously saved XYZ configuration.
+
+vstep
+    Frequency of volume-change moves in NPT simulations.
+
+mstop
+    Molecule displacement control flag used internally by DICE.
+
+accum
+    Enables or disables accumulation of statistical averages.
+
+iprint
+    Frequency of simulation information printed to the output.
+
+isave
+    Frequency at which configurations are written to trajectory files.
+
+irdf
+    Controls calculation of radial distribution functions.
+
+seed
+    Random number generator seed used by the Monte Carlo algorithm.
+
+upbuf
+    Buffer size parameter used internally by DICE during thermalization.
+
+---------------------------------------------------------------------
+
+Output Files
+------------
+
+Important output files produced during the simulation include:
+
+phb.xyz
+    XYZ trajectory containing sampled molecular configurations.
+
+last.xyz
+    Final configuration of the simulation, often used as the starting
+    configuration for the next simulation cycle.
+
+---------------------------------------------------------------------
+
+References
+----------
+
+DICE is a Monte Carlo molecular simulation program developed primarily
+by researchers at the University of São Paulo (USP) for studying liquids,
+solutions, and solvation phenomena.
+"""