LUCRETIUS
Lucretius is a general-purpose Molecular Dynamics (MD) simulation program, which is written initially for our own research. The code is sufficiently flexible and is able to simulate a wide range of systems without many arbitrary restrictions. The program is highly portable and has been optimized for most of the platforms. The codes are written in FORTRAN and in order to have a flexibility of dynamic allocation of array sizes, a preprocessor is written in C-shell script. Lucretius can not only handle simple liquids, but also mixtures, isolated molecules, crystals and rigid rods. The systems can be run in micro-canonical, canonical and isobaric ensembles.
Each system can be specified using the following input files.
- fort.11 - A connectivity table for the system
- fort.12 - The force-field parameters for the potential used (LJ,Exp-6, Electrostatic, Polarizable models)
- fort.26 - Input coordinates and velocities for the system
- fort.25 - Control parameters for a MD run
The output files generated by the code are:
- fort.66 - Final coordinates of the system in ascii format
- fort.77 - Coordinates in binary format at a frequency determined by control parameters
- fort.76 - Box dipole and charge flux at a frequency determined by control parameters
- fort.78 - Stress tensor output at a frequency determined by control parameters
- fort.65 - Averaged properties of the system over the run
- fort.59 - Averaged non-bonded energy split ( intramolecular and intermolecular)
The format of input files is quite general. A sample system is also distributed along with the source code (Dimethoxy ethane - water). See below for more sample systems.
Technical aspects:
Lucretius is capable of simulating all three phases - gas, liquid and solid. It has a wide range of time reversible integrators, both multiple and single time step. Bond constraints are implemented using SHAKE. Most common potential functions are supported (Lennard-Jones, Exponential-6). Short-range interactions are handled using link-cell method (for efficiently calculating the neighbors) and and long range electrostatics is treated using the well-known EWALD summation technique or Particle Mesh Ewald (PME) technique. The code implements periodic boundary conditions to replicate box in space to from an infinite lattice. The box is allowed to fluctuate in shape and size using Parrinello-Rahman technique. The combination of all these techniques and algorithms makes Lucretius a powerful and advanced tool to investigate structure and properties of atomic systems.
The current version does not include the capabilities of fully flexible cells. The final version will be put up in the near future. References for the code are given below. A detailed documentation will be available soon. The fortran source code can be downloaded from here (lucretius.tar.Z).*
- Download the source code from the above reference.
- Unzip using the command "uncompress"
- Use " tar -xf " to extract from the archive
- The source code along with the C-shell script (mdinit) and a sample set of input files will be extracted.
- Run "mdinit" in the directory and pick your choices further.
- A fortran executable "mdrun" will be created by the script that can be used to run the system without further compilation.