SENPAI/ONICHaN - Simplified Evolutive N-body Processing and Analytics for Integration

SENPAI is a molecular dynamics (MD) simulation software aimed at simulating organic systems. It handles the following interractions:

Covalence (as undamped Newtonian harmonic oscillators)
Bond angles (by enforcing atomic orbital hybridisation via angular undamped Newtonian harmonic oscillators)
Electrostatics (treating atoms as point charges)
Van der Waals (by analytically differentiating the Lennard-Jones potential function)

The simulation is rendered in a cubic universe of constant size, enforcing periodic boundary conditions via coordinate restriction.

Cool features

Unlimited portability: SENPAI does not require any library, and is 100% compliant with the C99 standard. SENPAI could run on a Roomba.
Efficient computing model: the Optimized Numerical Integration, Classical Harmonics, and N-body (ONICHaN) model was tailored for SENPAI over months of work. Inspired by the AMBER family of force fields, it allows SENPAI to compute forces with unprecedented efficiency.
No potential differentiation: Traditional MD simulators compute a particle's total potential and numerically differentiate it to compute the applied force. SENPAI analytically solves for the force vector, resulting in an extreme speed-up.
Tunable thermodynamics: Efficiently write scripts to run simulations with various thermodynamical settings and analyse the impact of the system's surroundings on its evolution.
Render as XYZ: Keep it simple. Simulations are rendered using the XYZ format, and can be directly visualized with software like VMD.
Integrated potential reduction: SENPAI will reduce the system's potential energy with a user-selectable number of potential reduction cycles before starting the simulation.

Installation

On UNIX systems, compilation is achieved using the provided makefile. No additional software is required.

git clone https://github.com/Garuda1/senpai && cd senpai && make

Usage

senpai --i input_file --o output_file [options]

Options:

--in Required. Specifies the path to the input file (MOLV2000 format)
--out Required. Specifies the output file (XYZ format)
--numerical Configures the simulation to use numerical differentiation of the potential energy (defaults to analytical solving)
--time t Specifies the simulation duration (ns) (defaults to 1ns)
--dt t Specifies the timestep (fs) (defaults to 1 fs)
--temp Specifies the thermodynamic temperature of the system (K) (defaults to 273.15 K)
--pressure Specifies the pressure of the system (mbar) (defaults to 1 atm)
--density Specifies the density of the system (g.cm-3) (defaults to 1 g.cm-3)
--copy Specifies how many copies of the loaded system are to be inserted in the simulation
--frameskip Sets a frameskip to reduce I/O usage. Disabled by default
--reduce_potential Reduces the potential energy to the provided value (pJ) or lower (really time consuming) (defaults to 10 pJ)

Example use

./senpai.bin --in examples/DES.mol --out render.xyz

This will tell SENPAI to simulate the contents of examples/DES.mol at STP for one nanosecond using a one femtosecond timestep. The rendered simulation will be saved in render.xyz for further analysis.

./senpai.bin --in examples/water.mol --out water_render.xyz --copy 5000 --reduce_potential 100 --temp 300

This will have SENPAI load 1000 water molecules from examples/water.mol, arrange them so that the total potential energy is lower than 100 pJ, and finally simulate the system at 300 Kelvin for 1 ns, saving the render in water_render.xyz.

Questions and Answers

Q: Why are you doing this? Go out, the sun's out.

A: The sun can't simulate deep eutectic solvents.

Q: Who are you?

A: Thomas Murgia, 19y old at the time of writing this. I'm a second year undergraduate student of chemistry at the Université Toulouse 3 in France.

I plan to keep going with projects like those and hopefully get involved in purely academic and fundamental research in chemistry until the end of my days.

Q: Are you looking for grad programs? Or even internships?

A: Definitely. E-mail me at thomas.murgia@univ-tlse3.fr (academic email). I'm open to all offers :)

Documentation currently unavailable, as things are constantly suspect to drastic changes