How to use pyodesys - 10 common examples

def plot_reaction_contributions(
        xyp, rsys, rate_exprs_cb, substance_keys=None, varied=None, axes=None,
        total=False, linthreshy=1e-9, relative=False, xscale='log', yscale='symlog',
        xlabel='Time', ylabel=None, combine_equilibria=False, selection=slice(None),
        unit_registry=None):
    """ Plots per reaction contributions to concentration evolution of a substance.

    Parameters
    ----------
    xyp : ``pyodesys.results.Result`` instance or length 3 tuple or xout,yout,params
    result : pyodesys.results.Result
    substance_key : str

    """
    from pyodesys.results import Result
    if isinstance(xyp, Result):
        xyp = xyp.odesys.to_arrays(xyp.xout, xyp.yout, xyp.params, reshape=False)
    if varied is None:
        varied = xyp[0]
    if xyp[1].shape[-2] != varied.size:
        raise ValueError("Size mismatch between varied and yout")
    if substance_keys is None:
        substance_keys = rsys.substances.keys()
    if axes is None:
        _fig, axes = plt.subplots(len(substance_keys))
    rates = rate_exprs_cb(*xyp)
    if unit_registry is not None:
        time_unit = get_derived_unit(unit_registry, 'time')
        conc_unit = get_derived_unit(unit_registry, 'concentration')
        rates = to_unitless(rates*conc_unit/time_unit, u.molar/u.second)

    eqk1, eqk2, eqs = _combine_rxns_to_eq(rsys) if combine_equilibria else ([], [], [])

def main(y0='1,0', mu=1.0, tend=10., nt=50, savefig='None', plot=False,
         savetxt='None', integrator='scipy', dpi=100, kwargs='',
         verbose=False):
    assert nt > 1
    y = sp.symarray('y', 2)
    p = sp.Symbol('p', real=True)
    f = [y[1], -y[0] + p*y[1]*(1 - y[0]**2)]
    odesys = SymbolicSys(zip(y, f), params=[p], names=True)
    tout = np.linspace(0, tend, nt)
    y0 = list(map(float, y0.split(',')))
    kwargs = dict(eval(kwargs) if kwargs else {})
    xout, yout, info = odesys.integrate(
        tout, y0, [mu], integrator=integrator, **kwargs)
    if verbose:
        print(info)
    if savetxt != 'None':
        np.savetxt(stack_1d_on_left(xout, yout), savetxt)
    if plot:
        import matplotlib.pyplot as plt
        odesys.plot_result()
        plt.legend()
        if savefig != 'None':
            plt.savefig(savefig, dpi=dpi)
        else:

# -*- coding: utf-8 -*-
from __future__ import (absolute_import, division, print_function)

import copy
import os
from ..util import import_
from ._base import _NativeCodeBase, _NativeSysBase, _compile_kwargs

_config, get_include = import_('pygslodeiv2', '_config', 'get_include')


class NativeGSLCode(_NativeCodeBase):
    """ Looks for the environment variable: ``PYODESYS_BLAS`` (``gslcblas``) """
    wrapper_name = '_gsl_wrapper'

    def __init__(self, *args, **kwargs):
        self.compile_kwargs = copy.deepcopy(_compile_kwargs)
        self.compile_kwargs['include_dirs'].append(get_include())
        self.compile_kwargs['libraries'].extend(_config.env['GSL_LIBS'].split(','))
        self.compile_kwargs['libraries'].extend(os.environ.get('PYODESYS_BLAS', _config.env['BLAS']).split(','))
        super(NativeGSLCode, self).__init__(*args, **kwargs)


class NativeGSLSys(_NativeSysBase):
    _NativeCode = NativeGSLCode

# -*- coding: utf-8 -*-
from __future__ import (absolute_import, division, print_function)

import copy
import os
from ..util import import_
from ._base import _NativeCodeBase, _NativeSysBase, _compile_kwargs

_config, get_include = import_('pygslodeiv2', '_config', 'get_include')


class NativeGSLCode(_NativeCodeBase):
    """ Looks for the environment variable: ``PYODESYS_BLAS`` (``gslcblas``) """
    wrapper_name = '_gsl_wrapper'

    def __init__(self, *args, **kwargs):
        self.compile_kwargs = copy.deepcopy(_compile_kwargs)
        self.compile_kwargs['include_dirs'].append(get_include())
        self.compile_kwargs['libraries'].extend(_config.env['GSL_LIBS'].split(','))
        self.compile_kwargs['libraries'].extend(os.environ.get('PYODESYS_BLAS', _config.env['BLAS']).split(','))
        super(NativeGSLCode, self).__init__(*args, **kwargs)


class NativeGSLSys(_NativeSysBase):
    _NativeCode = NativeGSLCode
    _native_name = 'gsl'

def __init__(self, *args, **kwargs):
        self.compile_kwargs = copy.deepcopy(_compile_kwargs)
        self.compile_kwargs['define'] = ['PYCVODES_NO_KLU={}'.format("0" if config.get('KLU', True) else "1"),
                                         'PYCVODES_NO_LAPACK={}'.format("0" if config.get('LAPACK', True) else "1"),
                                         'ANYODE_NO_LAPACK={}'.format("0" if config.get('LAPACK', True) else "1")]
        self.compile_kwargs['include_dirs'].append(get_include())
        self.compile_kwargs['libraries'].extend(_libs.get_libs().split(','))
        self.compile_kwargs['libraries'].extend([l for l in os.environ.get(
            'PYODESYS_LAPACK', "lapack,blas" if config["LAPACK"] else "").split(",") if l != ""])
        self.compile_kwargs['flags'] = [f for f in os.environ.get("PYODESYS_CVODE_FLAGS", "").split() if f]
        self.compile_kwargs['ldflags'] = [f for f in os.environ.get("PYODESYS_CVODE_LDFLAGS", "").split() if f]
        super(NativeCvodeCode, self).__init__(*args, **kwargs)


class NativeCvodeSys(_NativeSysBase):
    _NativeCode = NativeCvodeCode
    _native_name = 'cvode'

    def as_standalone(self, out_file=None, compile_kwargs=None):
        from pycompilation.compilation import src2obj, link
        from pycodeexport.util import render_mako_template_to
        compile_kwargs = compile_kwargs or {}
        impl_src = open([f for f in self._native._written_files if f.endswith('.cpp')][0], 'rt').read()
        f = render_mako_template_to(
            os.path.join(os.path.dirname(__file__), 'sources/standalone_template.cpp'),
            '%s.cpp' % out_file, {'p_odesys': self, 'p_odesys_impl': impl_src})
        kw = copy.deepcopy(self._native.compile_kwargs)
        kw.update(compile_kwargs)
        objf = src2obj(f, **kw)
        kw['libraries'].append('boost_program_options')
        return link([objf], out_file, **kw)

_config, get_include = import_('pygslodeiv2', '_config', 'get_include')


class NativeGSLCode(_NativeCodeBase):
    """ Looks for the environment variable: ``PYODESYS_BLAS`` (``gslcblas``) """
    wrapper_name = '_gsl_wrapper'

    def __init__(self, *args, **kwargs):
        self.compile_kwargs = copy.deepcopy(_compile_kwargs)
        self.compile_kwargs['include_dirs'].append(get_include())
        self.compile_kwargs['libraries'].extend(_config.env['GSL_LIBS'].split(','))
        self.compile_kwargs['libraries'].extend(os.environ.get('PYODESYS_BLAS', _config.env['BLAS']).split(','))
        super(NativeGSLCode, self).__init__(*args, **kwargs)


class NativeGSLSys(_NativeSysBase):
    _NativeCode = NativeGSLCode
    _native_name = 'gsl'

savetxt='None', integrator='scipy', dpi=100, kwargs='',
         verbose=False):
    assert nt > 1
    y = sp.symarray('y', 2)
    p = sp.Symbol('p', real=True)
    f = [y[1], -y[0] + p*y[1]*(1 - y[0]**2)]
    odesys = SymbolicSys(zip(y, f), params=[p], names=True)
    tout = np.linspace(0, tend, nt)
    y0 = list(map(float, y0.split(',')))
    kwargs = dict(eval(kwargs) if kwargs else {})
    xout, yout, info = odesys.integrate(
        tout, y0, [mu], integrator=integrator, **kwargs)
    if verbose:
        print(info)
    if savetxt != 'None':
        np.savetxt(stack_1d_on_left(xout, yout), savetxt)
    if plot:
        import matplotlib.pyplot as plt
        odesys.plot_result()
        plt.legend()
        if savefig != 'None':
            plt.savefig(savefig, dpi=dpi)
        else:
            plt.show()

def __init__(self, *args, **kwargs):
        self.compile_kwargs = copy.deepcopy(_compile_kwargs)
        self.compile_kwargs['include_dirs'].append(get_include())
        self.compile_kwargs['libraries'].extend(_config.env['GSL_LIBS'].split(','))
        self.compile_kwargs['libraries'].extend(os.environ.get('PYODESYS_BLAS', _config.env['BLAS']).split(','))
        super(NativeGSLCode, self).__init__(*args, **kwargs)

def __init__(self, *args, **kwargs):
        self.compile_kwargs = copy.deepcopy(_compile_kwargs)
        self.compile_kwargs['define'] = ['PYCVODES_NO_KLU={}'.format("0" if config.get('KLU', True) else "1"),
                                         'PYCVODES_NO_LAPACK={}'.format("0" if config.get('LAPACK', True) else "1"),
                                         'ANYODE_NO_LAPACK={}'.format("0" if config.get('LAPACK', True) else "1")]
        self.compile_kwargs['include_dirs'].append(get_include())
        self.compile_kwargs['libraries'].extend(_libs.get_libs().split(','))
        self.compile_kwargs['libraries'].extend([l for l in os.environ.get(
            'PYODESYS_LAPACK', "lapack,blas" if config["LAPACK"] else "").split(",") if l != ""])
        self.compile_kwargs['flags'] = [f for f in os.environ.get("PYODESYS_CVODE_FLAGS", "").split() if f]
        self.compile_kwargs['ldflags'] = [f for f in os.environ.get("PYODESYS_CVODE_LDFLAGS", "").split() if f]
        super(NativeCvodeCode, self).__init__(*args, **kwargs)

def __init__(self, *args, **kwargs):
        self.compile_kwargs = copy.deepcopy(_compile_kwargs)
        self.compile_kwargs['define'] = ['PYCVODES_NO_KLU={}'.format("0" if config.get('KLU', True) else "1"),
                                         'PYCVODES_NO_LAPACK={}'.format("0" if config.get('LAPACK', True) else "1"),
                                         'ANYODE_NO_LAPACK={}'.format("0" if config.get('LAPACK', True) else "1")]
        self.compile_kwargs['include_dirs'].append(get_include())
        self.compile_kwargs['libraries'].extend(_libs.get_libs().split(','))
        self.compile_kwargs['libraries'].extend([l for l in os.environ.get(
            'PYODESYS_LAPACK', "lapack,blas" if config["LAPACK"] else "").split(",") if l != ""])
        self.compile_kwargs['flags'] = [f for f in os.environ.get("PYODESYS_CVODE_FLAGS", "").split() if f]
        self.compile_kwargs['ldflags'] = [f for f in os.environ.get("PYODESYS_CVODE_LDFLAGS", "").split() if f]
        super(NativeCvodeCode, self).__init__(*args, **kwargs)