{ "info": { "author": "Alex Seeholzer", "author_email": "seeholzer@gmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 3 - Alpha", "License :: OSI Approved :: GNU General Public License v2 (GPLv2)", "Programming Language :: Python :: 2.7", "Topic :: Scientific/Engineering :: Medical Science Apps." ], "description": "|Build Status|\n\nCILES: Continuous Interval Langevin Equation Simulator\n======================================================\n\nLangevin integrator for SDEs with constant drift and diffusion on\ncontinuous intervals with circular boundary conditions.\n\nCILES is written in Cython and uses GSL for interpolation of drift &\ndiffusion fields, to be able to simulate continuous variables.\n\nDescription\n-----------\n\nGiven a discretized drift field A(x) and a (position dependent)\ndiffusion coefficient B(x) this tool performs simple time-forward\nintegration of the SDE:\n\n::\n\n dx(t)/dt = A(x(t)) + sqrt(B(x(t))) * eta(t)\n\nwhere eta(t) is a gaussian white noise term and x is a variable on an\ninterval with circular boundaries (commonly 0 <= x < 2PI).\n\nBoth drift field A and diffusion B need to be arrays of the same\ndimension. They are internally interpolated (using\n``gsl_interp_cspline_periodic``) to provide continuous fields, which are\nthen used in the forward integration.\n\nForward integration is performed with the `Euler-Murayama\nscheme `__:\nx(t+dt) = x(t) + dt \\* A(x(t)) + r \\* sqrt(dt \\* B(x(t))), where r is a\nnormally distributed random number with zero mean and unit variance.\n\nDependencies\n------------\n\n- Numpy\n- Cython\n- `Cython-gsl `__\n\nInstallation\n------------\n\n- Clone repository\n- ``python setup.py install``\n- To test (using ``nosetests``): ``nosetests``\n\nExample use\n-----------\n\n.. code:: python\n\n from ciles.integrator import LangevinIntegrator as LI\n import numpy as np\n\n drift = np.zeros(100) # no drift field\n diff = np.ones(100) # constant diffusion with 1 deg^2/s\n\n dt = 1e-3 # 1 ms timestep\n tmax = 1. # simulate until 1s\n\n # initialize the integrator\n li = LI(drift, diff, dt=dt, tmax=tmax)\n\n # simulate a single trajectory\n li.run()\n out = li.out\n\nMore examples\n-------------\n\nBelow are the plot results of the currently available examples from `ciles.examples `__.\n\nFinal distributions after 2s diffusion\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nSee the\n`source `__\n\n|Diffusion for 2 seconds|\n\nTrajectories for drift-field with 2 fixed points\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nSee the\n`source `__\n\n|Plotting trajectories|\n\n.. |Build Status| image:: https://travis-ci.org/flinz/ciles.svg?branch=master\n :target: https://travis-ci.org/flinz/ciles\n.. |Diffusion for 2 seconds| image:: https://user-images.githubusercontent.com/97735/33634816-ce92b380-da15-11e7-944c-e704cbe9cfab.png\n\t:width: 75 %\n.. |Plotting trajectories| image:: https://user-images.githubusercontent.com/97735/33634815-ce790f48-da15-11e7-9cd9-1e08fdab9773.png\n\t:width: 75 %\n\n", "description_content_type": null, "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/flinz/ciles", "keywords": "science,langevin,math", "license": "GPLv2", "maintainer": "", "maintainer_email": "", "name": "ciles", "package_url": "https://pypi.org/project/ciles/", "platform": "", "project_url": "https://pypi.org/project/ciles/", "project_urls": { "Homepage": "https://github.com/flinz/ciles" }, "release_url": "https://pypi.org/project/ciles/0.1.0/", "requires_dist": [ "cython", "cythongsl", "numpy" ], "requires_python": "", "summary": "Langevin integrator for SDEs with constant drift and diffusion on continuous intervals with circular boundary conditions.", "version": "0.1.0" }, "last_serial": 3393592, "releases": { "0.1.0": [ { "comment_text": "", "digests": { "md5": "e540ce430d9b7bf8752542c1d81d549b", "sha256": "6f762e9f76762bf003278b2ff24825bfe239d2667a14a9c20278752229b3247b" }, "downloads": -1, "filename": "ciles-0.1.0-cp27-cp27m-macosx_10_11_x86_64.whl", "has_sig": false, "md5_digest": "e540ce430d9b7bf8752542c1d81d549b", "packagetype": "bdist_wheel", "python_version": "cp27", "requires_python": null, "size": 32479, "upload_time": "2017-12-06T11:09:21", "url": "https://files.pythonhosted.org/packages/35/3d/7970983bdc4acf325458114d8c7345b4364ebf8741d134a0bf5427029dcc/ciles-0.1.0-cp27-cp27m-macosx_10_11_x86_64.whl" }, { "comment_text": "", "digests": { "md5": "dadfae809b0476a272ebc2736ef1380e", "sha256": "f9a8eb5749285cec0542ac083d6331163f05e48138d20bf33f111e216eb58d31" }, "downloads": -1, "filename": "ciles-0.1.0.tar.gz", "has_sig": false, "md5_digest": "dadfae809b0476a272ebc2736ef1380e", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 61416, "upload_time": "2017-12-06T11:09:22", "url": "https://files.pythonhosted.org/packages/4e/32/b95462360f49519064f6487f9e9fff9c99461208402b862c04a6e63449aa/ciles-0.1.0.tar.gz" } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "e540ce430d9b7bf8752542c1d81d549b", "sha256": "6f762e9f76762bf003278b2ff24825bfe239d2667a14a9c20278752229b3247b" }, "downloads": -1, "filename": "ciles-0.1.0-cp27-cp27m-macosx_10_11_x86_64.whl", "has_sig": false, "md5_digest": "e540ce430d9b7bf8752542c1d81d549b", "packagetype": "bdist_wheel", "python_version": "cp27", "requires_python": null, "size": 32479, "upload_time": "2017-12-06T11:09:21", "url": "https://files.pythonhosted.org/packages/35/3d/7970983bdc4acf325458114d8c7345b4364ebf8741d134a0bf5427029dcc/ciles-0.1.0-cp27-cp27m-macosx_10_11_x86_64.whl" }, { "comment_text": "", "digests": { "md5": "dadfae809b0476a272ebc2736ef1380e", "sha256": "f9a8eb5749285cec0542ac083d6331163f05e48138d20bf33f111e216eb58d31" }, "downloads": -1, "filename": "ciles-0.1.0.tar.gz", "has_sig": false, "md5_digest": "dadfae809b0476a272ebc2736ef1380e", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 61416, "upload_time": "2017-12-06T11:09:22", "url": "https://files.pythonhosted.org/packages/4e/32/b95462360f49519064f6487f9e9fff9c99461208402b862c04a6e63449aa/ciles-0.1.0.tar.gz" } ] }