pyBrown

Brownian and Stokesian dynamics simulation software. Copyright ©2021- Tomasz Skóra [email protected]

Features

• Brownian dynamics w/o hydrodynamic interactions
• Brownian dynamics w hydrodynamic interactions
• Stokesian dynamics
• flux through an arbitrary plane
• immobile beads
• bead-bead interactions (inter- and intramolecular)
• bead chemistry
• various propagation schemes (EM, IGT, ...)

Quick start

To compile, type following commands in a terminal:

$ ./configure --prefix=DIR --with-lapack=LAPACK_LIBS

where DIR is the installation directory (/usr/local by default) and LAPACK_LIBS is lapack libraries to use (e.g. --with-lapack="-l lapack").

Then proceed with:

$ make
$ make install

To ensure that all needed python are accessible on your computers, you can run:

$ pip3 install -r requirements.txt

If you want tests, go to directory src/bdsim/tests and type:

$ make test

If you want documentation in html, go to directory docs/ and type:

$ make html

If you want documentation in pdf, go to directory docs/ and type:

$ make latexpdf

Example input

{
	"input_str_filename": "test_{}.str",
	"output_xyz_filename": "test_{}.xyz",
	"output_rst_filename": "test_{}.rst",
	"filename_range": [1, 2],
	"number_of_steps": 100000,
	"xyz_write_freq": 1000,
	"rst_write_freq": 100,
	"dt": 1.0,
	"T": 293.15,
	"viscosity": 0.01005,
	"box_length": 750.0,
	"hydrodynamics": "nohi",
	"seed": 0,
	"progress_bar": false,
	"measure_flux": {
		"normal": [1.0, 0.0, 0.0],
		"plane_point": [0.0, 0.0, 0.0]
	}
}

Units

Physical property	Units
Temperature	kelvin (K)
Viscosity	poise (P)
Time	picosecond (ps)
Distance	angstrom (Å)

You can choose the energy units by "energy_unit" keyword in input .json file. Default is "joule" (J), other options are "kcal/mol" (kilocalorie per mol, kcal/mol) and "eV" (electronvolt, eV). Force unit is then energy unit per angstrom.

Authors

The following people contributed to the development of pyBrown.

• Tomasz Skóra -- creator, lead developer (contact: [email protected])

• Svyatoslav Kondrat aka valiska (contact: [email protected])

  • automake configuration and overall project structure,
  • tools for trajectory analysis (average-me.py, average-mexp.py).

Contribute

License