""" 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. """