pyjac.core.create_jacobian module

Creates source code for calculating analytical Jacobian matrix.

pyjac.core.create_jacobian.calculate_shared_memory(rxn_ind, rxn, specs, reacs, rev_reacs, pdep_reacs)[source]

Estimates usage of the various variables for a given reaction

Parameters:
  • rxn_ind (into) – Index of reaction of interest.
  • rxn (ReacInfo) – Reaction of interest.
  • specs (list of SpecInfo) – List of species.
  • reacs (list of ReacInfo) – Full list of reactions.
  • rev_reacs (list of ReacInfo) – List of reversible reactions.
  • pdep_reacs (list of ReacInfo) – List of pressure-dependent reactions.
Returns:

  • variable_list
  • usages
pyjac.core.create_jacobian.write_dr_dy(file, lang, rev_reacs, rxn, rxn_ind, pres_rxn_ind, get_array)[source]

Writes evaluation of the (non-pressure dependent part) of the reaction rate R that is independent of species

Parameters:
  • file (File) – The open file object to write to
  • lang (str) – The Programming language
  • rev_reacs (list of ReacInfo) – The list of reverisble reactions
  • rxn (ReacInfo) – The reaction to consider
  • rxn_ind (int) – The index of the reaction in the mechanism
  • pres_rxn_ind (int) – The index of the reaction in the pressure dependent reactions
  • get_array (function) – The SMM binded get_array function (or utils.get_array) as required
Returns:
Return type:

None
pyjac.core.create_jacobian.write_rates(file, lang, rxn)[source]

Write evaluation of the forward/reverse rate constant

Parameters:
  • file (File) – The open file object to write to
  • lang (str) – The Programming language
  • rxn (ReacInfo) – The reaction to consider
Returns:
Return type:

None
pyjac.core.create_jacobian.write_dr_dy_species(lang, specs, rxn, pres_rxn_ind, j_sp, sp_j, rxn_ind, rev_reacs, get_array)[source]

Returns string for evaluation of the (non-pressure dependent part) of the reaction rate R with respect to a species j

Parameters:
  • lang (str) – The Programming language
  • specs (list of SpecInfo) – The species in the mechanism
  • rxn (ReacInfo) – The reaction to consider
  • pres_rxn_ind (int) – The index of the reaction in the pressure dependent reactions
  • j_sp (int) – The species index
  • sp_j (SpecInfo) – The species to consider
  • rxn_ind (int) – The index of the reaction in the mechanism
  • rev_reacs (list of ReacInfo) – The list of reverisble reactions
  • get_array (function) – The SMM binded get_array function (or utils.get_array) as required
Returns:

jline – Jacobian evaluation line with non-pressure-dependent part of species derivative added.
Return type:

str
pyjac.core.create_jacobian.write_kc(file, lang, specs, rxn)[source]

Write evaluation of the reaction rate equilibrium constant

Parameters:
  • file (File) – The open file object to write to
  • lang (str) – The Programming language
  • specs (list of SpecInfo) – The species in the mechanism
  • rxn (ReacInfo) – The reaction to consider
Returns:
Return type:

None
pyjac.core.create_jacobian.get_infs(rxn)[source]

Returns the reaction rate parameters for a pressure-dependent reaction

Parameters:rxn (ReacInfo) – Reaction object for pressure-dependent reaction (falloff or chemically activated bimolecular)
Returns:
  • beta_0minf (float) – Low-pressure limit temperature exponent minus high-pressure value.
  • E_0minf (float) – Low-pressure limit activation energy minus high-pressure value.
  • k0kinf (float) – Low-pressure limit reaction coefficient divided by high-pressure value.
pyjac.core.create_jacobian.write_dt_comment(file, lang, rxn_ind)[source]

Writes comment line for temperature partial derivatives of reactions

Parameters:
  • file (File) – Open file object
  • lang (str) – Programming language
  • rxn_ind (int) – Index of reaction
Returns:
Return type:

None
pyjac.core.create_jacobian.write_dy_comment(file, lang, rxn_ind)[source]

Writes comment line for species mass fraction partial derivatives

Parameters:
  • file (File) – Open file object
  • lang (str) – Programming language
  • rxn_ind (int) – Index of reaction
Returns:
Return type:

None
pyjac.core.create_jacobian.write_dy_y_finish_comment(file, lang)[source]

Writes comment line for finishing species mass fraction derivatives

Parameters:
  • file (File) – Open file object
  • lang (str) – Programming language
Returns:
Return type:

None
pyjac.core.create_jacobian.get_rxn_params_dt(rxn, rev=False)[source]

Write evaluation of the forward/reverse reaction rate constant

Parameters:
  • rxn (ReacInfo) – The reaction to consider
  • rev (bool, optional) – If true, get the reverse constant rate constant derivative
Returns:

jline – String containing evaluation of forward/reverse reaction rate constant
Return type:

str
pyjac.core.create_jacobian.write_db_dt_def(file, lang, specs, reacs, rev_reacs, dBdT_flag, do_unroll)[source]

Write definition of dB/dT terms for each species

Parameters:
  • file (File) – The open file object to write to
  • lang ({'c', 'cuda'}) – The programming language
  • specs (list of SpecInfo) – The species in the mechanism
  • reacs (list of ReacInfo) – The reactions in the mechanism
  • rev_reacs (list of ReacInfo) – The reversible reactions in the mechanism
  • dBdT_flag (list of bool) – Upon completion of this method this list contains True for the index of all species with non-zero dB/dT entries
  • do_unroll (bool) – If True, turn on Jacobian unrolling
Returns:
Return type:

None
pyjac.core.create_jacobian.get_db_dt(lang, specs, rxn, do_unroll)[source]

Write evaluation of dB/dT term

Parameters:
  • lang ({'c', 'cuda'}) – The programming language
  • specs (list of SpecInfo) – The species in the mechanism
  • rxn (ReacInfo) – The reaction to consider
  • do_unroll (bool) – If True, Jacobian unrolling is turned on
Returns:

jline – String containing evaluation of dB/dT term
Return type:

str
pyjac.core.create_jacobian.write_pr(file, lang, specs, reacs, pdep_reacs, rxn, get_array, last_conc_temp=None)[source]

Write the evaluation of the reduced pressure

Parameters:
  • file (File) – The open file object to write to
  • lang (str) – The Programming language
  • specs (list of SpecInfo) – The species in the mechanism
  • reacs (list of ReacInfo) – The reactions in the mechanism
  • pdep_reacs (list of ReacInfo) – The pressure dependent reactions (not including PLOG/Chebyshev) reactions in the mechanism
  • rxn (ReacInfo) – The reactio to consider
  • get_array (function) – The SMM binded get_array function (or utils.get_array) as required
  • last_conc_temp (list of tuples) – If specified, the non-unity third body efficiencies and corresponding species for the last pressure dependent reaction
Returns:

conc_temp_log – List with (species index, efficiency) for third-body efficiencies.
Return type:

list of (int, float)
pyjac.core.create_jacobian.write_troe(file, lang, rxn)[source]

Write the evaluation of the Troe falloff terms

Parameters:
  • file (File) – The open file object to write to
  • lang ({'c', 'cuda'}) – The programming language
  • rxn (ReacInfo) – The reaction to consider
Returns:
Return type:

None
pyjac.core.create_jacobian.write_sri(file, lang)[source]

Write the valuation of the SRI exponent

Parameters:
  • file (File) – The open file object to write to
  • lang (str) – The programming language
Returns:
Return type:

None
pyjac.core.create_jacobian.get_pdep_dt(lang, rxn, rev_reacs, rxn_ind, pres_rxn_ind, get_array)[source]

Write contribution from temperature derivative of reaction rate for a pressure dependent reaction

Parameters:
  • lang (str) – The Programming language
  • rxn (ReacInfo) – The reaction to consider
  • rev_reacs (list of ReacInfo) – The list of reverisble reactions
  • rxn_ind (int) – The index of the reaction in the reaction list
  • pres_rxn_ind (int) – The index of the reaction in the pressure dependent reaction list
  • get_array (function) – The SMM binded get_array function (or utils.get_array) as required
Returns:
Return type:

None
pyjac.core.create_jacobian.write_sri_dt(lang, rxn, beta_0minf, E_0minf, k0kinf)[source]

Writes section of line for temperature partial derivative of Troe falloff.

Parameters:
  • lang (str) – Programming language, {‘c’, ‘cuda’}
  • rxn (ReacInfo) – Reaction of interest; pressure dependence expressed with SRI falloff
  • beta_0minf (float) –
  • E_0minf (float) –
  • k0kinf (float) –
Returns:

jline – Line fragment with SRI temperature derivative
Return type:

str
pyjac.core.create_jacobian.write_troe_dt(lang, rxn, beta_0minf, E_0minf, k0kinf)[source]

Writes section of line for temperature partial derivative of Troe falloff.

Parameters:
  • lang (str) – Programming language, {‘c’, ‘cuda’}
  • rxn (ReacInfo) – Reaction of interest; pressure dependence expressed with Troe falloff.
  • beta_0minf (float) – Low-pressure limit temperature exponent minus high-pressure value.
  • E_0minf (float) – Low-pressure limit activation energy minus high-pressure value.
  • k0kinf (float) – Low-pressure limit reaction coefficient divided by high-pressure value.
Returns:

jline – Line fragment with Troe temperature derivative
Return type:

str
pyjac.core.create_jacobian.write_dcp_dt(file, lang, specs)[source]

Write derivative of cp w.r.t. temperature for each species

Parameters:
  • file (File) – The open file object to write to
  • lang (str) – The Programming language
  • specs (list of SpecInfo) – The species in the mechanism
Returns:
Return type:

None
pyjac.core.create_jacobian.get_elementary_rxn_dt(lang, specs, rxn, rxn_ind, rev_idx, get_array, do_unroll)[source]

Write contribution from temperature derivative of reaction rate for elementary reaction.

Parameters:
  • lang (str) – The programming language
  • rxn (ReacInfo) – The reaction to consider
  • rxn_ind (int) – The reaction index
  • rev_idx (int) – The index of the reaction in the reverse reaction list (if applicable)
  • get_array (function) – The SMM binded get_array function (or utils.get_array) as required
  • do_unroll (bool) – If true, Jacobian unrolling is turned on
Returns:

jline – Jacobian entry substring with temperature derivative contribution.
Return type:

str
pyjac.core.create_jacobian.write_cheb_ut(file, lang, rxn)[source]

Computes the derivative of the chebyshev polynomial recursively w.r.t T

Parameters:
  • file (File) – The open file object to write to
  • lang (str) – The Programming language
  • rxn (ReacInfo) – The reaction to consider
Returns:
Return type:

None
pyjac.core.create_jacobian.write_cheb_rxn_dt(file, lang, jline, rxn, rxn_ind, rev_idx, specs, get_array, do_unroll)[source]

Writes the code for the temperature derivative of Chebyshev reactions

Parameters:
  • file (File) – The open file object to write to
  • lang (str) – The Programming language
  • jline (str) – The current jacobian line (containing the non-Chebyshev part of the derivative)
  • specs (list of SpecInfo) – The species in the mechanism
  • rxn (ReacInfo) – The reaction to consider
  • rxn_ind (int) – The reaction index
  • rev_idx (int) – The index of the reaction in the reverse reaction list (if applicable)
  • get_array (function) – The SMM binded get_array function (or utils.get_array) as required
  • do_unroll (bool) – If true, Jacobian unrolling is turned on
pyjac.core.create_jacobian.write_plog_rxn_dt(file, lang, jline, specs, rxn, rxn_ind, rev_idx, get_array, do_unroll)[source]

Writes the code for the temperature derivative of PLog reactions

Parameters:
  • file (File) – The open file object to write to
  • lang (str) – The Programming language
  • jline (str) – The current jacobian line (containing the non-PLog part of the derivative)
  • specs (list of SpecInfo) – The species in the mechanism
  • rxn (ReacInfo) – The reaction to consider
  • rxn_ind (int) – The reaction index
  • rev_idx (int) – The index of the reaction in the reverse reaction list (if applicable)
  • get_array (function) – The SMM binded get_array function (or utils.get_array) as required
  • do_unroll (bool) – If true, Jacobian unrolling is turned on
pyjac.core.create_jacobian.write_dt_completion(file, lang, specs, J_nplusone_touched, get_array)[source]

Finishes calculation of d(partial T / partial t)/dT

Parameters:
  • file (File) – Open file object to write to
  • lang (str) – The Programming language
  • specs (list of SpecInfo) – The species in this mechanism
  • J_nplusone_touched (bool) – If true, the last species has a non-zero contribution to d(partial T / partial t)
  • get_array (function) – The SMM binded get_array function (or utils.get_array) as required
pyjac.core.create_jacobian.write_sub_intro(path, lang, number, rate_list, this_rev, this_pdep, have_pres_mod_temp, batch_has_m, this_thd, this_troe, this_sri, this_cheb, cheb_dim, this_plog, no_shared, has_nsp)[source]

Writes the header and definitions for the Jacobian reaction update subfiles

Parameters:
  • path (str) – Path to build directory for file.
  • lang (str {'c', 'cuda'}) – Programming language
  • number (int) – Jacobian subfile number
  • rate_list (str) – The required reaction/species rate strings needed for the intro
  • this_rev (bool) – If True, batch contains a reversible reaction
  • this_pdep (bool) – If True, batch contains pressure dependent (falloff/bimolecular) reaction
  • have_pres_mod_temp (bool) – If True, batch requires definition of pres_mod_temp
  • batch_has_m (bool) – If True, batch requires the overall concentration ‘m’
  • this_thd (bool) – If True, batch has a third-body reaction
  • this_troe (bool) – If True, batch contains a Troe reaction
  • this_sri (bool) – If True, batch contains an SRI reaction
  • this_cheb (bool) – If True, batch contains a Chebyshev reaction
  • cheb_dim (int) – If this_cheb is True, the largest Chebyshev dimension required
  • this_plog (bool) – If True, batch contains a PLOG reaction
  • no_shared (bool) – If True, do not use CUDA shared memory
  • has_nsp (bool) – If True, >=1 reaction has nonzero contribution from the last species
Returns:

file – Opened Jacobian file
Return type:

File object
pyjac.core.create_jacobian.write_dy_intros(path, lang, number, have_jnplus_jplus)[source]

Writes the header and definitions for the various Jacobian species update subfiles

Parameters:
  • path (str) – The path to place the file in
  • lang (str {'c', 'cuda'}) – The programming language
  • number (int) – The jacobian subfile index
  • have_jnplus_jplus (bool) – If True, the last species has non-zero contributions to the Jacobian
Returns:

file – Jacobian file object
Return type:

File
pyjac.core.create_jacobian.write_jacobian(path, lang, specs, reacs, seen_sp, smm=None)[source]

Write Jacobian subroutine in desired language.

Parameters:
  • path (str) – Path to build directory for file.
  • lang (str {'c', 'cuda', 'fortran', 'matlab'}) – Programming language.
  • specs (list of SpecInfo) – List of species in the mechanism.
  • reacs (list of ReacInfo) – List of reactions in the mechanism.
  • seen_sp (list of bool) – List of bool; False if species has (identically) zero rate
  • smm (shared_memory_manager, optional) – If not None, use this to manage shared memory optimization
Returns:
Return type:

None
pyjac.core.create_jacobian.write_sparse_multiplier(path, lang, touched, nvars)[source]

Write a subroutine that multiplies the non-zero entries of the Jacobian with a column ‘j’ of another matrix.

Parameters:
  • path (str) – Path to build directory for file.
  • lang ({'c', 'cuda', 'fortran', 'matlab'}) – Programming language.
  • inidicies (list) – A list of indicies where the Jacobian is non-zero
  • nvars (int) – Number of variables in the Jacobian matrix
Returns:
Return type:

None
pyjac.core.create_jacobian.create_jacobian(lang, mech_name=None, therm_name=None, gas=None, optimize_cache=False, initial_state='', num_blocks=8, num_threads=64, no_shared=False, L1_preferred=True, multi_thread=None, force_optimize=False, build_path='./out/', last_spec=None, skip_jac=False, auto_diff=False)[source]

Create Jacobian subroutine from mechanism.

Parameters:
  • lang ({'c', 'cuda', 'fortran', 'matlab'}) – Language type.
  • mech_name (str, optional) – Reaction mechanism filename (e.g. ‘mech.dat’). This or gas must be specified
  • therm_name (str, optional) – Thermodynamic database filename (e.g. ‘therm.dat’) or nothing if info in mechanism file.
  • gas (cantera.Solution, optional) – The mechanism to generate the Jacobian for. This or mech_name must be specified
  • optimize_cache (bool, optional) – If True, use the greedy optimizer to attempt to improve cache hit rates
  • initial_state (str, optional) – A comma separated list of the initial conditions to use in form T,P,X (e.g. ‘800,1,H2=1.0,O2=0.5’). Temperature in K, P in atm
  • num_blocks (int, optional) – The target number of blocks / sm to achieve for cuda
  • num_threads (int, optional) – The target number of threads / block to achieve for cuda
  • no_shared (bool, optional) – If True, do not use the shared_memory_manager to attempt to optimize for CUDA
  • L1_preferred (bool, optional) – If True, prefer a larger L1 cache and a smaller shared memory size for CUDA
  • multi_thread (int, optional) – The number of threads to use during optimization
  • force_optimize (bool, optional) – If True, redo the cache optimization even if the same mechanism
  • build_path (str, optional) – The output directory for the jacobian files
  • last_spec (str, optional) – If specified, the species to assign to the last index. Typically should be N2, Ar, He or another inert bath gas
  • skip_jac (bool, optional) – If True, only the reaction rate subroutines will be generated
  • auto_diff (bool, optional) – If True, generate files for use with the Adept autodifferention library.
Returns:
Return type:

None