pyodesys.native package

pyodesys.native

This module contains a pyodesys.symbolic.SymbolicSys subclass which can be used to generate source code representing the system of equations in a native language.

For some integrators (Sundials and GSL), the compiled objects from the generated code are dynamically linked against respective library. You may need to match the choice of BLAS/LAPACK implementation to link against. This can be modified by setting the environment variables PYODESYS_LBLAS and PYODESYS_LLAPACK respectively.

Submodules

pyodesys.native.cvode module

class pyodesys.native.cvode.NativeCvodeCode(*args, **kwargs)

Bases: pyodesys.native._base._NativeCodeBase

Attributes

binary_path

compile_kwargs

extension_name

mod

Cached compiled binary of the Generic_Code class.

so_file

Methods

clean(self)	Delete temp dir if not save_temp set at __init__
compile_and_import_binary(self)	Returnes a module instance of the extension module.
get_cse_code(self, exprs[, basename, …])	Get arrayified code for common subexpression.
variables(self)	Returns dictionary of variables for substituion suitable for use in the templates (formated according to the syntax of the language)

CompilerRunner
as_arrayified_code
clear_mod_cache
write_code

namespace = {'p_baseclass': 'OdeSysIterativeBase', 'p_includes': ['"odesys_anyode_iterative.hpp"'], 'p_indextype': 'int', 'p_jacobian_set_to_zero_by_solver': True, 'p_realtype': 'double', 'p_support_recoverable_error': True}

wrapper_name = '_cvode_wrapper'

class pyodesys.native.cvode.NativeCvodeSys(*args, **kwargs)

Bases: pyodesys.native._base._NativeSysBase

Attributes

linear_invariants

ny

Number of dependent variables in the system.

Methods

adaptive(self, y0, x0, xend[, params])	Integrate with integrator chosen output.
analytic_stiffness(self[, xyp])	Running stiffness ratio from last integration.
chained_parameter_variation(self, \*args, …)	See chained_parameter_variation().
from_callback(rhs[, ny, nparams, …])	Create an instance from a callback.
from_other(ori, \*\*kwargs)	Creates a new instance with an existing one as a template.
from_other_new_params(ori, par_subs, new_pars)	Creates a new instance with an existing one as a template (with new parameters)
from_other_new_params_by_name(ori, par_subs)	Creates a new instance with an existing one as a template (with new parameters)
get_dfdx(self)	Calculates 2nd derivatives of self.exprs
get_dfdx_callback(self)	Generate a callback for evaluating derivative of self.exprs
get_f_ty_callback(self)	Generates a callback for evaluating self.exprs.
get_j_ty_callback(self)	Generates a callback for evaluating the jacobian.
get_jac(self)	Derives the jacobian from self.exprs and self.dep.
get_jtimes(self)	Derive the jacobian-vector product from self.exprs and self.dep
get_jtimes_callback(self)	Generate a callback fro evaluating the jacobian-vector product.
get_roots_callback(self)	Generate a callback for evaluating self.roots
integrate(self, \*args, \*\*kwargs)	Integrate the system of ordinary differential equations.
jacobian_singular(self)	Returns True if Jacobian is singular, else False.
plot_phase_plane(self[, indices])	Plots a phase portrait from last integration.
plot_result(self, \*\*kwargs)	Plots the integrated dependent variables from last integration.
post_process(self, xout, yout, params)	Transforms internal values to output, used internally.
pre_process(self, xout, y0[, params])	Transforms input to internal values, used internally.
predefined(self, y0, xout[, params])	Integrate with user chosen output.
stiffness(self[, xyp, eigenvals_cb])	[DEPRECATED] Use Result.stiffness(), stiffness ration

all_invariant_names
all_invariants
as_autonomous
as_standalone
get_first_step_callback
get_invariants_callback
to_arrays

as_standalone(self, out_file=None, compile_kwargs=None)

pyodesys.native.gsl module

class pyodesys.native.gsl.NativeGSLCode(*args, **kwargs)

Bases: pyodesys.native._base._NativeCodeBase

Looks for the environment variable: PYODESYS_BLAS (gslcblas)

Attributes

binary_path

compile_kwargs

extension_name

mod

Cached compiled binary of the Generic_Code class.

so_file

Methods

clean(self)	Delete temp dir if not save_temp set at __init__
compile_and_import_binary(self)	Returnes a module instance of the extension module.
get_cse_code(self, exprs[, basename, …])	Get arrayified code for common subexpression.
variables(self)	Returns dictionary of variables for substituion suitable for use in the templates (formated according to the syntax of the language)

CompilerRunner
as_arrayified_code
clear_mod_cache
write_code

wrapper_name = '_gsl_wrapper'

class pyodesys.native.gsl.NativeGSLSys(*args, **kwargs)

Bases: pyodesys.native._base._NativeSysBase

Attributes

linear_invariants

ny

Number of dependent variables in the system.

Methods

adaptive(self, y0, x0, xend[, params])	Integrate with integrator chosen output.
analytic_stiffness(self[, xyp])	Running stiffness ratio from last integration.
chained_parameter_variation(self, \*args, …)	See chained_parameter_variation().
from_callback(rhs[, ny, nparams, …])	Create an instance from a callback.
from_other(ori, \*\*kwargs)	Creates a new instance with an existing one as a template.
from_other_new_params(ori, par_subs, new_pars)	Creates a new instance with an existing one as a template (with new parameters)
from_other_new_params_by_name(ori, par_subs)	Creates a new instance with an existing one as a template (with new parameters)
get_dfdx(self)	Calculates 2nd derivatives of self.exprs
get_dfdx_callback(self)	Generate a callback for evaluating derivative of self.exprs
get_f_ty_callback(self)	Generates a callback for evaluating self.exprs.
get_j_ty_callback(self)	Generates a callback for evaluating the jacobian.
get_jac(self)	Derives the jacobian from self.exprs and self.dep.
get_jtimes(self)	Derive the jacobian-vector product from self.exprs and self.dep
get_jtimes_callback(self)	Generate a callback fro evaluating the jacobian-vector product.
get_roots_callback(self)	Generate a callback for evaluating self.roots
integrate(self, \*args, \*\*kwargs)	Integrate the system of ordinary differential equations.
jacobian_singular(self)	Returns True if Jacobian is singular, else False.
plot_phase_plane(self[, indices])	Plots a phase portrait from last integration.
plot_result(self, \*\*kwargs)	Plots the integrated dependent variables from last integration.
post_process(self, xout, yout, params)	Transforms internal values to output, used internally.
pre_process(self, xout, y0[, params])	Transforms input to internal values, used internally.
predefined(self, y0, xout[, params])	Integrate with user chosen output.
stiffness(self[, xyp, eigenvals_cb])	[DEPRECATED] Use Result.stiffness(), stiffness ration

all_invariant_names
all_invariants
as_autonomous
get_first_step_callback
get_invariants_callback
to_arrays

pyodesys.native.odeint module

class pyodesys.native.odeint.NativeOdeintCode(*args, **kwargs)

Bases: pyodesys.native._base._NativeCodeBase

Attributes

binary_path

compile_kwargs

extension_name

mod

Cached compiled binary of the Generic_Code class.

so_file

Methods

clean(self)	Delete temp dir if not save_temp set at __init__
compile_and_import_binary(self)	Returnes a module instance of the extension module.
get_cse_code(self, exprs[, basename, …])	Get arrayified code for common subexpression.
variables(self)	Returns dictionary of variables for substituion suitable for use in the templates (formated according to the syntax of the language)

CompilerRunner
as_arrayified_code
clear_mod_cache
write_code

wrapper_name = '_odeint_wrapper'

class pyodesys.native.odeint.NativeOdeintSys(*args, **kwargs)

Bases: pyodesys.native._base._NativeSysBase

Attributes

linear_invariants

ny

Number of dependent variables in the system.

Methods

adaptive(self, y0, x0, xend[, params])	Integrate with integrator chosen output.
analytic_stiffness(self[, xyp])	Running stiffness ratio from last integration.
chained_parameter_variation(self, \*args, …)	See chained_parameter_variation().
from_callback(rhs[, ny, nparams, …])	Create an instance from a callback.
from_other(ori, \*\*kwargs)	Creates a new instance with an existing one as a template.
from_other_new_params(ori, par_subs, new_pars)	Creates a new instance with an existing one as a template (with new parameters)
from_other_new_params_by_name(ori, par_subs)	Creates a new instance with an existing one as a template (with new parameters)
get_dfdx(self)	Calculates 2nd derivatives of self.exprs
get_dfdx_callback(self)	Generate a callback for evaluating derivative of self.exprs
get_f_ty_callback(self)	Generates a callback for evaluating self.exprs.
get_j_ty_callback(self)	Generates a callback for evaluating the jacobian.
get_jac(self)	Derives the jacobian from self.exprs and self.dep.
get_jtimes(self)	Derive the jacobian-vector product from self.exprs and self.dep
get_jtimes_callback(self)	Generate a callback fro evaluating the jacobian-vector product.
get_roots_callback(self)	Generate a callback for evaluating self.roots
integrate(self, \*args, \*\*kwargs)	Integrate the system of ordinary differential equations.
jacobian_singular(self)	Returns True if Jacobian is singular, else False.
plot_phase_plane(self[, indices])	Plots a phase portrait from last integration.
plot_result(self, \*\*kwargs)	Plots the integrated dependent variables from last integration.
post_process(self, xout, yout, params)	Transforms internal values to output, used internally.
pre_process(self, xout, y0[, params])	Transforms input to internal values, used internally.
predefined(self, y0, xout[, params])	Integrate with user chosen output.
stiffness(self[, xyp, eigenvals_cb])	[DEPRECATED] Use Result.stiffness(), stiffness ration

all_invariant_names
all_invariants
as_autonomous
get_first_step_callback
get_invariants_callback
to_arrays

pyodesys.native.util module

pyodesys.native.util.parse_standalone_output(lines)

pyodesys.native.util.render_mako(tmpl, \*\*kwargs)