pyjac.functional_tester.test module¶

Module for testing function (accuracy) of pyJac.

class pyjac.functional_tester.test.ReactorConstPres(gas)[source]¶

Bases: object

Object for constant pressure ODE system.

Parameters:	gas (`cantera.Solution`) – `cantera.Solution` object with the kinetic system
Returns:
Return type:	None

class pyjac.functional_tester.test.ReactorConstVol(gas)[source]¶

Bases: object

Object for constant volume ODE system.

Initialize ReactorConstVol

Parameters:	gas (`cantera.Solution`) – `cantera.Solution` object with the kinetic system
Returns:
Return type:	None

pyjac.functional_tester.test.convert_mech(mech_filename, therm_filename=None)[source]¶

Convert a mechanism and return a string with the filename.

Convert a CHEMKIN format mechanism to the Cantera CTI format using the Cantera built-in script ck2cti.

Parameters:	mech_filename (str) – Filename of the input CHEMKIN format mechanism. The converted CTI file will have the same name, but with `.cti` extension. thermo_filename (str) – Filename of the thermodynamic database. Optional, if the thermodynamic database is present in the mechanism input.
Returns:	mech_filename – Filename of converted mechanism in Cantera `.cti` format.
Return type:	str

class pyjac.functional_tester.test.AutodiffJacob(pressure, fwd_spec_map)[source]¶

Bases: object

Class for

Initialize autodifferentation object.

Parameters:	pressure (float) – Pressure in Pascals fwd_spec_map (`numpy.array`) – Map of original species indices to new indices
Returns:
Return type:	None

eval_jacobian(gas)[source]¶

Evaluate finite difference Jacobian using Adept autodifferentiation package.

Parameters:	gas (`cantera.Solution`) – `cantera.Solution` object with the kinetic system
Returns:	jacob – Jacobian matrix evaluated using autodifferentiation
Return type:	`numpy.array`

pyjac.functional_tester.test.is_pdep(rxn)[source]¶

Check if reaction is traditionally pressure dependent

Parameters:	rxn (`ReacInfo`) – Reaction object of interest
Returns:
Return type:	`True` if third-body, falloff, or chemically activated reaction.

pyjac.functional_tester.test.run_pasr(pasr_input_file, mech_filename, pasr_output_file=None)[source]¶

Run PaSR simulation to get thermochemical data for testing.

Parameters:	pasr_input_file (str) – Name of PaSR input file in YAML format mech_filename (str) – Name of Cantera-format mechanism file pasr_output_file (str) – Optional; filename for saving PaSR output data
Returns:	state_data – Array with state data (time, temperature, pressure, mass fractions)
Return type:	`numpy.array`

class pyjac.functional_tester.test.cpyjac_evaluator(build_dir, gas, module_name='pyjacob', filename='mechanism.h')[source]¶

Bases: object

Class for pyJac-based Jacobian matrix evaluator

check_numbers(build_dir, gas, filename='mechanism.h')[source]¶

Ensure numbers of species and forward reaction match.

Parameters:	build_dir (str) – Path of directory for build objects gas (`cantera.Solution`) – Object with kinetic system filename (str) – Optional; filename of header with mechanism information
Returns:
Return type:	None

check_optimized(build_dir, gas, filename='mechanism.h')[source]¶

Check if pyJac files were cache-optimized (and thus rearranged)

Parameters:	build_dir (str) – Path of directory for build objects gas (`cantera.Solution`) – Object with kinetic system filename (str) – Optional; filename of header with mechanism information
Returns:
Return type:	None

eval_conc(temp, pres, mass_frac, conc)[source]¶

Evaluate species concentrations at current state.

Parameters:	temp (float) – Temperature, in Kelvin pres (float) – Pressure, in Pascals mass_frac (`numpy.array`) – Species mass fractions conc (`numpy.array`) – Species concentrations, in kmol/m^3
Returns:
Return type:	None

eval_rxn_rates(temp, pres, conc, fwd_rates, rev_rates)[source]¶

Evaluate reaction rates of progress at current state.

Parameters:	temp (float) – Temperature, in Kelvin pres (float) – Pressure, in Pascals conc (`numpy.array`) – Species concentrations, in kmol/m^3 fwd_rates (`numpy.array`) – Reaction forward rates of progress, in kmol/m^3/s rev_rates (`numpy.array`) – Reaction reverse rates of progress, in kmol/m^3/s
Returns:
Return type:	None

get_rxn_pres_mod(temp, pres, conc, pres_mod)[source]¶

Evaluate reaction rate pressure modifications at current state.

Parameters:	temp (float) – Temperature, in Kelvin pres (float) – Pressure, in Pascals conc (`numpy.array`) – Species concentrations, in kmol/m^3 pres_mod (`numpy.array`) – Reaction rate pressure modification
Returns:
Return type:	None

eval_spec_rates(fwd_rates, rev_rates, pres_mod, spec_rates)[source]¶

Evaluate species overall production rates at current state.

Parameters:	fwd_rates (`numpy.array`) – Reaction forward rates of progress, in kmol/m^3/s rev_rates (`numpy.array`) – Reaction reverse rates of progress, in kmol/m^3/s pres_mod (`numpy.array`) – Reaction rate pressure modification spec_rates (`numpy.array`) – Reaction reverse rates of progress, in kmol/m^3/s
Returns:
Return type:	None

dydt(t, pres, y, dydt)[source]¶

Evaluate derivative

Parameters:	t (float) – Time, in seconds pres (float) – Pressure, in Pascals y (`numpy.array`) – State vector (temperature + species mass fractions) dydt (`numpy.array`) – Derivative of state vector
Returns:
Return type:	None

eval_jacobian(t, pres, y, jacob)[source]¶

Evaluate the Jacobian matrix

Parameters:	t (float) – Time, in seconds pres (float) – Pressure, in Pascals y (`numpy.array`) – State vector (temperature + species mass fractions) jacob (`numpy.array`) – Jacobian matrix
Returns:
Return type:	None

update(index)[source]¶

Updates evaluator index

Parameters:	index (int) – Index of data for evaluating quantities
Returns:
Return type:	None

clean()[source]¶

class pyjac.functional_tester.test.cupyjac_evaluator(build_dir, gas, state_data)[source]¶

Bases: pyjac.functional_tester.test.cpyjac_evaluator

Class for CUDA-based pyJac Jacobian matrix evaluator

clean()[source]¶

update(index)[source]¶

Updates evaluator index

Parameters:	index (int) – Index of data for evaluating quantities
Returns:
Return type:	None

czeros(shape)[source]¶

Return array of zeros in C ordering.

Parameters:	shape (int) – Shape of array
Returns:
Return type:	`numpy.array` of zeros with shape `shape` in C ordering

reshaper(arr, shape, reorder=None)[source]¶

eval_conc(temp, pres, mass_frac, conc)[source]¶

Evaluate species concentrations at current state.

Parameters:	temp (float) – Temperature, in Kelvin pres (float) – Pressure, in Pascals mass_frac (`numpy.array`) – Species mass fractions conc (`numpy.array`) – Species concentrations, in kmol/m^3
Returns:
Return type:	None

eval_rxn_rates(temp, pres, conc, fwd_rates, rev_rates)[source]¶

Evaluate reaction rates of progress at current state.

Parameters:	temp (float) – Temperature, in Kelvin pres (float) – Pressure, in Pascals conc (`numpy.array`) – Species concentrations, in kmol/m^3 fwd_rates (`numpy.array`) – Reaction forward rates of progress, in kmol/m^3/s rev_rates (`numpy.array`) – Reaction reverse rates of progress, in kmol/m^3/s
Returns:
Return type:	None

get_rxn_pres_mod(temp, pres, conc, pres_mod)[source]¶

Evaluate reaction rate pressure modifications at current state.

Parameters:	temp (float) – Temperature, in Kelvin pres (float) – Pressure, in Pascals conc (`numpy.array`) – Species concentrations, in kmol/m^3 pres_mod (`numpy.array`) – Reaction rate pressure modification
Returns:
Return type:	None

eval_spec_rates(fwd_rates, rev_rates, pres_mod, spec_rates)[source]¶

Evaluate species overall production rates at current state.

Parameters:	fwd_rates (`numpy.array`) – Reaction forward rates of progress, in kmol/m^3/s rev_rates (`numpy.array`) – Reaction reverse rates of progress, in kmol/m^3/s pres_mod (`numpy.array`) – Reaction rate pressure modification spec_rates (`numpy.array`) – Reaction reverse rates of progress, in kmol/m^3/s
Returns:
Return type:	None

dydt(t, pres, y, dydt)[source]¶

Evaluate derivative

Parameters:	t (float) – Time, in seconds pres (float) – Pressure, in Pascals y (`numpy.array`) – State vector (temperature + species mass fractions) dydt (`numpy.array`) – Derivative of state vector
Returns:
Return type:	None

eval_jacobian(t, pres, y, jacob)[source]¶

Evaluate the Jacobian matrix

Parameters:	t (float) – Time, in seconds pres (float) – Pressure, in Pascals y (`numpy.array`) – State vector (temperature + species mass fractions) jacob (`numpy.array`) – Jacobian matrix
Returns:
Return type:	None

class pyjac.functional_tester.test.tchem_evaluator(build_dir, gas, state_data, mechfile, thermofile, module_name='py_tchem', filename='mechanism.h')[source]¶

Bases: pyjac.functional_tester.test.cpyjac_evaluator

Class for TChem-based Jacobian matrix evaluator

get_conc(conc)[source]¶

Evaluate species concentrations at current state.

Parameters:	conc (`numpy.array`) – Species concentrations, in kmol/m^3
Returns:
Return type:	None

get_rxn_rates(fwd_rates, rev_rates)[source]¶

Evaluate reaction rates of progress at current state.

Parameters:	fwd_rates (`numpy.array`) – Reaction forward rates of progress, in kmol/m^3/s rev_rates (`numpy.array`) – Reaction reverse rates of progress, in kmol/m^3/s
Returns:
Return type:	None

get_spec_rates(spec_rates)[source]¶

Evaluate species overall production rates at current state.

Parameters:	spec_rates (`numpy.array`) – Reaction reverse rates of progress, in kmol/m^3/s
Returns:
Return type:	None

get_dydt(dydt)[source]¶

Evaluate derivative

Parameters:	dydt (`numpy.array`) – Derivative of state vector
Returns:
Return type:	None

get_jacobian(jacob)[source]¶

Evaluate the Jacobian matrix

Parameters:	jacob (`numpy.array`) – Jacobian matrix
Returns:
Return type:	None

pyjac.functional_tester.test.safe_remove(file)[source]¶

Try to safely remove a file

Parameters:	file (str) – Path for file to be removed
Returns:
Return type:	None

pyjac.functional_tester.test.test(lang, home_dir, build_dir, mech_filename, therm_filename=None, pasr_input_file='pasr_input.yaml', generate_jacob=True, compile_jacob=True, seed=None, pasr_output_file=None, last_spec=None, cache_optimization=False, no_shared=False, tchem_flag=False, only_rxn=None, do_not_remove=False, condition_numbers=None)[source]¶

Compares pyJac results against Cantera (and optionally TChem) using state data from PaSR simulations.

Parameters:	lang ({'c', 'cuda'}) – Programming language home_dir (str) – Path to home directory for testing and data build_dir (str) – Path to directory for building Jacobian files mech_filename (str) – Chemkin- or Cantera-format mechanism file therm_filename (str) – Optional; name of thermodynamic database file (if needed) pasr_input_file (str) – Optional; name of YAML-formatted file with PaSR test input generate_jacob (bool) – Optional; if `True`, generate Jacobian files. Otherwise, use existing files. compile_jacob (bool) – Optional; if `True`, compile Jacobian files. Otherwise, using existing. seed (int) – Optional; random seed for PaSR pasr_output_file (str) – Optional; name of output file for saving PaSR results last_spec (str) – Optional; name of species to move to last position. If not specified, will try searching for N2, Ar, or He. cache_optimization (bool) – If `True`, enable reordering to optimize cache usage no_shared (bool) – If `True`, do not use GPU shared memory tchem_flag (bool) – If `True`, compare with TChem results only_rxn (str) – Optional; string with list of reaction numbers to retain. All other reactions removed. do_not_remove (bool) – If `True`, keep all generated files. condition_numbers (int) – Optional; string with list of conditions numbers to use.
Returns:
Return type:	None