Developers.Variables.simulation

Variable "simulation" in MolDynSim

This variable characterizes the general setup of our simulations. It is used in all of the MolDynSim programs. It is a structured variable that should initially containing the following fields :

Settable parameters

field	description
n_dim	number of dimensions (integer, default:3). However, MolDynSim should also work in reduced (1 or 2) dimensionality (although that hasn't been tested yet)
periodic	whether to use periodic boundary conditions (logical, default:false)
box	size of (periodic) simulation box (column vector of real numbers, length n_dim). Needed only if periodic=true
verbose	whether to produce (tons of) extra output (logical, default: false)

Internal variables

field	description
title	cell vector of character strings
n_spec	number of molecular species, simply deduced from length(molecule).
n_thaw	total number of thawed atoms in all molecules/species
n_froz	total number of frozen atoms in all molecules/species
mass	mass of all atoms in our system (real matrix of size n_dim x n_thaw)
density	mass per volume in units of g / (mol*nm3). Available only if periodic=true

Internal constants

field	description
k_boltz	see the definition of molecular units
coulomb	see the definition of molecular units
planck	see the definition of molecular units
avogadro	see the definition of molecular units