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jacobian.py
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jacobian.py
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"""Write jacobian functions."""
import copy
import sys
from collections import Counter, OrderedDict
from math import isclose
import ceptr.constants as cc
import ceptr.utilities as cu
import ceptr.writer as cw
def ajac(
fstream,
mechanism,
species_info,
reaction_info,
jacobian=True,
precond=False,
syms=None,
):
"""Write jacobian for a reaction."""
n_species = species_info.n_species
n_reactions = mechanism.n_reactions
cw.writer(fstream)
if precond:
cw.writer(fstream, cw.comment("compute an approx to the reaction Jacobian"))
else:
cw.writer(fstream, cw.comment("compute the reaction Jacobian"))
cw.writer(fstream, "AMREX_GPU_HOST_DEVICE AMREX_FORCE_INLINE")
if n_reactions > 0:
if precond:
cw.writer(
fstream,
"void aJacobian_precond(amrex::Real * J, const"
" amrex::Real * sc, const amrex::Real T, const int HP)",
)
else:
cw.writer(
fstream,
"void aJacobian(amrex::Real * J, const amrex::Real * sc,"
" const amrex::Real T, const int consP)",
)
else:
if precond:
cw.writer(
fstream,
"void aJacobian_precond(amrex::Real * J, const"
" amrex::Real * /*sc*/, const amrex::Real /*T*/, const"
" int /*HP*/)",
)
else:
cw.writer(
fstream,
"void aJacobian(amrex::Real * J, const amrex::Real *"
" /*sc*/, const amrex::Real /*T*/, const int /*consP*/)",
)
cw.writer(fstream, "{")
cw.writer(fstream)
# Analytical jacobian not ready with QSS
if species_info.n_qssa_species > 0:
cw.writer(
fstream,
cw.comment(
"Analytical Jacobian with QSSA is only supported with symbolic"
" implementation. Re-build in ceptr with -qsj flag."
),
)
cw.writer(fstream, "amrex::Abort();")
cw.writer(fstream)
elif not jacobian:
cw.writer(
fstream,
cw.comment(
"Mechanism was generated without a jacobian."
" Re-build in ceptr without the -nj flag."
),
)
cw.writer(fstream, "amrex::Abort();")
else:
cw.writer(
fstream,
"#if defined(PELE_COMPILE_AJACOBIAN) || !defined(AMREX_USE_HIP)",
)
cw.writer(fstream, f"for (int i=0; i<{(n_species + 1) ** 2}; i++) {{")
cw.writer(fstream, "J[i] = 0.0;")
cw.writer(fstream, "}")
if n_reactions > 0:
cw.writer(fstream)
cw.writer(fstream, f"amrex::Real wdot[{n_species}];")
cw.writer(fstream, "for (auto& val : wdot) {")
cw.writer(fstream, "val = 0.0;")
cw.writer(fstream, "}")
cw.writer(fstream)
cw.writer(
fstream,
"const amrex::Real tc[5] = { log(T), T, T*T, T*T*T, T*T*T*T };"
+ cw.comment("temperature cache"),
)
cw.writer(fstream, "amrex::Real invT = 1.0 / tc[1];")
cw.writer(fstream, "amrex::Real invT2 = invT * invT;")
cw.writer(fstream)
cw.writer(
fstream,
cw.comment("reference concentration: P_atm / (RT) in inverse mol/m^3"),
)
cw.writer(
fstream,
f"amrex::Real refC = {cc.Patm_pa:g} /"
f" {cc.R.to(cc.ureg.joule / (cc.ureg.mole / cc.ureg.kelvin)).m:g} / T;",
)
cw.writer(fstream, "amrex::Real refCinv = 1.0 / refC;")
cw.writer(fstream)
cw.writer(fstream, cw.comment("compute the mixture concentration"))
cw.writer(fstream, "amrex::Real mixture = 0.0;")
cw.writer(fstream, f"for (int k = 0; k < {n_species}; ++k) {{")
cw.writer(fstream, "mixture += sc[k];")
cw.writer(fstream, "}")
cw.writer(fstream)
cw.writer(fstream, cw.comment("compute the Gibbs free energy"))
cw.writer(fstream, f"amrex::Real g_RT[{n_species}];")
cw.writer(fstream, "gibbs(g_RT, tc);")
if species_info.n_qssa_species > 0:
cw.writer(
fstream,
f"amrex::Real g_RT_qss[{species_info.n_qssa_species}];",
)
cw.writer(fstream, "gibbs_qss(g_RT_qss, tc);")
cw.writer(fstream)
cw.writer(fstream, cw.comment("compute the species enthalpy"))
cw.writer(fstream, f"amrex::Real h_RT[{n_species}];")
cw.writer(fstream, "speciesEnthalpy(h_RT, tc);")
if species_info.n_qssa_species > 0:
cw.writer(
fstream,
f"amrex::Real h_RT_qss[{species_info.n_qssa_species}];",
)
cw.writer(fstream, "speciesEnthalpy_qss(h_RT_qss, tc);")
if species_info.n_qssa_species > 0:
cw.writer(fstream)
cw.writer(fstream, cw.comment("Fill sc_qss here"))
cw.writer(
fstream,
f"amrex::Real sc_qss[{species_info.n_qssa_species}];",
)
cw.writer(
fstream,
"amrex::Real"
f" kf_qss[{reaction_info.n_qssa_reactions}],"
f" qf_qss[{reaction_info.n_qssa_reactions}],"
f" qr_qss[{reaction_info.n_qssa_reactions}];",
)
cw.writer(fstream, "comp_k_f_qss(tc, invT, kf_qss);")
cw.writer(
fstream,
"comp_qss_coeff(kf_qss, qf_qss, qr_qss, sc, tc, g_RT, g_RT_qss);",
)
cw.writer(fstream, "comp_sc_qss(sc_qss, qf_qss, qr_qss);")
cw.writer(fstream)
cw.writer(fstream)
cw.writer(
fstream,
"amrex::Real phi_f, k_f, k_r, phi_r, Kc, q, q_nocor, Corr, alpha;",
)
cw.writer(fstream, "amrex::Real dlnkfdT, dlnk0dT, dlnKcdT, dkrdT, dqdT;")
cw.writer(fstream, f"amrex::Real dqdci, dcdc_fac, dqdc[{n_species}];")
cw.writer(fstream, "amrex::Real Pr, fPr, F, k_0, logPr;")
cw.writer(
fstream,
"amrex::Real logFcent, troe_c, troe_n, troePr_den, troePr, troe;",
)
cw.writer(fstream, "amrex::Real Fcent1, Fcent2, Fcent3, Fcent;")
cw.writer(fstream, "amrex::Real dlogFdc, dlogFdn, dlogFdcn_fac;")
cw.writer(
fstream,
"amrex::Real dlogPrdT, dlogfPrdT, dlogFdT, dlogFcentdT,"
" dlogFdlogPr, dlnCorrdT;",
)
cw.writer(fstream, "const amrex::Real ln10 = log(10.0);")
cw.writer(fstream, "const amrex::Real log10e = 1.0/log(10.0);")
for orig_idx, _ in reaction_info.idxmap.items():
# if orig_idx == 35:
# exit()
reaction = mechanism.reaction(orig_idx)
cw.writer(
fstream,
cw.comment(f"reaction {orig_idx}: {reaction.equation}"),
)
ajac_reaction_d(
fstream,
mechanism,
species_info,
reaction_info,
reaction,
orig_idx,
precond=precond,
syms=syms,
)
cw.writer(fstream)
cw.writer(
fstream,
f"amrex::Real c_R[{n_species}], dcRdT[{n_species}], e_RT[{n_species}];",
)
cw.writer(fstream, "amrex::Real * eh_RT;")
if precond:
cw.writer(fstream, "if (HP == 1) {")
else:
cw.writer(fstream, "if (consP == 1) {")
cw.writer(fstream, "cp_R(c_R, tc);")
cw.writer(fstream, "dcvpRdT(dcRdT, tc);")
cw.writer(fstream, "eh_RT = &h_RT[0];")
cw.writer(fstream, "}")
cw.writer(fstream, "else {")
cw.writer(fstream, "cv_R(c_R, tc);")
cw.writer(fstream, "dcvpRdT(dcRdT, tc);")
cw.writer(fstream, "speciesInternalEnergy(e_RT, tc);")
cw.writer(fstream, "eh_RT = &e_RT[0];")
cw.writer(fstream, "}")
cw.writer(fstream)
cw.writer(
fstream,
"amrex::Real cmix = 0.0, ehmix = 0.0, dcmixdT=0.0, dehmixdT=0.0;",
)
cw.writer(fstream, f"for (int k = 0; k < {n_species}; ++k) {{")
cw.writer(fstream, "cmix += c_R[k]*sc[k];")
cw.writer(fstream, "dcmixdT += dcRdT[k]*sc[k];")
cw.writer(fstream, "ehmix += eh_RT[k]*wdot[k];")
cw.writer(
fstream,
"dehmixdT += invT*(c_R[k]-eh_RT[k])*wdot[k] +"
f" eh_RT[k]*J[{n_species * (n_species + 1)}+k];",
)
cw.writer(fstream, "}")
cw.writer(fstream)
cw.writer(fstream, "amrex::Real cmixinv = 1.0/cmix;")
cw.writer(fstream, "amrex::Real tmp1 = ehmix*cmixinv;")
cw.writer(fstream, "amrex::Real tmp3 = cmixinv*T;")
cw.writer(fstream, "amrex::Real tmp2 = tmp1*tmp3;")
cw.writer(fstream, "amrex::Real dehmixdc;")
cw.writer(fstream, cw.comment("dTdot/d[X]"))
cw.writer(fstream, f"for (int k = 0; k < {n_species}; ++k) {{")
cw.writer(fstream, "dehmixdc = 0.0;")
cw.writer(fstream, f"for (int m = 0; m < {n_species}; ++m) {{")
cw.writer(fstream, f"dehmixdc += eh_RT[m]*J[k*{n_species + 1}+m];")
cw.writer(fstream, "}")
cw.writer(
fstream,
f"J[k*{n_species + 1}+{n_species}] = tmp2*c_R[k] - tmp3*dehmixdc;",
)
cw.writer(fstream, "}")
cw.writer(fstream, cw.comment("dTdot/dT"))
cw.writer(
fstream,
f"J[{n_species * (n_species + 1) + n_species}] = -tmp1 +"
" tmp2*dcmixdT - tmp3*dehmixdT;",
)
cw.writer(fstream, "#else")
cw.writer(fstream, "amrex::Abort();")
cw.writer(fstream, "#endif")
cw.writer(fstream, "}")
def ajac_symbolic(
fstream,
mechanism,
species_info,
reaction_info,
jacobian=True,
syms=None,
):
"""Print the Jacobian obtained from symbolic recording."""
n_species = species_info.n_species
n_qssa_species = species_info.n_qssa_species
n_reactions = mechanism.n_reactions
cw.writer(fstream)
# main
cw.writer(
fstream,
"AMREX_GPU_HOST_DEVICE AMREX_FORCE_INLINE void "
" aJacobian(amrex::Real * J, amrex::Real * sc, amrex::Real T,"
" const int consP)",
)
cw.writer(fstream, "{")
if not jacobian:
cw.writer(
fstream,
cw.comment(
"Mechanism was generated without a jacobian."
" Re-build in ceptr without the -nj flag."
),
)
cw.writer(fstream, "amrex::Abort();")
return
cw.writer(
fstream,
"#if defined(PELE_COMPILE_AJACOBIAN) || !defined(AMREX_USE_HIP)",
)
if syms.hformat == "cpu":
cw.writer(
fstream,
f"amrex::Real dscqss_dsc[{n_species * n_qssa_species}];",
)
cw.writer(
fstream,
f"for (int i=0; i<{(n_species * n_qssa_species)}; i++) {{",
)
cw.writer(fstream, "dscqss_dsc[i] = 0.0;")
cw.writer(fstream, "}")
cw.writer(
fstream,
"amrex::Real tc[5] = { log(T), T, T*T, T*T*T, T*T*T*T };"
+ cw.comment("temperature cache"),
)
cw.writer(fstream, "amrex::Real invT = 1.0 / tc[1];")
cw.writer(fstream)
if n_reactions == 0:
cw.writer(fstream)
else:
cw.writer(
fstream,
cw.comment("reference concentration: P_atm / (RT) in inverse mol/m^3"),
)
cw.writer(
fstream,
f"const amrex::Real refC = {cc.Patm_pa:g} /"
f" {cc.R.to(cc.ureg.joule / (cc.ureg.mole / cc.ureg.kelvin)).m:g} *"
" invT;",
)
cw.writer(fstream, "const amrex::Real refCinv = 1 / refC;")
cw.writer(fstream, f"amrex::Real g_RT[{species_info.n_species}];")
cw.writer(fstream, f"amrex::Real h_RT[{n_species}];")
if species_info.n_qssa_species > 0:
cw.writer(
fstream,
f"amrex::Real g_RT_qss[{species_info.n_qssa_species}];",
)
cw.writer(
fstream,
f"amrex::Real h_RT_qss[{species_info.n_qssa_species}];",
)
cw.writer(
fstream,
f"amrex::Real sc_qss[{max(1, species_info.n_qssa_species)}];",
)
if syms.store_in_jacobian:
cw.writer(
fstream,
f"amrex::Real kf_qss[{reaction_info.n_qssa_reactions}];",
)
else:
cw.writer(
fstream,
f"amrex::Real kf_qss[{reaction_info.n_qssa_reactions}],"
f" qf_qss[{reaction_info.n_qssa_reactions}],"
f" qr_qss[{reaction_info.n_qssa_reactions}];",
)
# prepare dwdotdT
cw.writer(fstream, "amrex::Real T_pert1, pertT;")
cw.writer(
fstream,
f"amrex::Real wdot_pert1[{n_species}], wdot[{n_species}];",
)
cw.writer(fstream)
cw.writer(fstream, cw.comment("dwdot/dT by finite difference"))
cw.writer(fstream, "pertT = 1e-2;")
cw.writer(fstream, "T_pert1 = T + pertT;")
cw.writer(fstream)
if syms.store_in_jacobian:
cw.writer(fstream, "tc[0] = log(T_pert1);")
cw.writer(fstream, "tc[1] = T_pert1;")
cw.writer(fstream, "tc[2] = T_pert1*T_pert1;")
cw.writer(fstream, "tc[3] = T_pert1*T_pert1*T_pert1;")
cw.writer(fstream, "tc[4] = T_pert1*T_pert1*T_pert1*T_pert1;")
cw.writer(fstream, "invT = 1.0 / tc[1];")
cw.writer(
fstream,
"productionRate_light(wdot_pert1, sc, g_RT, g_RT_qss, sc_qss,"
f" kf_qss, &J[{0}], &J[{reaction_info.n_qssa_reactions}], tc,"
" invT);",
)
cw.writer(fstream, "tc[0] = log(T);")
cw.writer(fstream, "tc[1] = T;")
cw.writer(fstream, "tc[2] = T*T;")
cw.writer(fstream, "tc[3] = T*T*T;")
cw.writer(fstream, "tc[4] = T*T*T*T;")
cw.writer(fstream, "invT = 1.0 / tc[1];")
cw.writer(
fstream,
"productionRate_light(wdot, sc, g_RT, g_RT_qss, sc_qss,"
f" kf_qss, &J[{0}], &J[{reaction_info.n_qssa_reactions}], tc,"
" invT);",
)
else:
cw.writer(fstream, "productionRate(wdot_pert1, sc, T_pert1);")
cw.writer(fstream, "productionRate(wdot, sc, T);")
cw.writer(fstream)
if n_reactions > 0:
# nclassd = n_reactions - nspecial
# nCorr = n3body + ntroe + nsri + nlindemann
# Kc stuff
if not syms.store_in_jacobian:
cw.writer(fstream, cw.comment("compute the Gibbs free energy"))
cw.writer(fstream, "gibbs(g_RT, tc);")
if species_info.n_qssa_species > 0:
cw.writer(fstream, "gibbs_qss(g_RT_qss, tc);")
cw.writer(fstream)
cw.writer(fstream, cw.comment("compute the species enthalpy"))
cw.writer(fstream, "speciesEnthalpy(h_RT, tc);")
if not syms.store_in_jacobian:
if species_info.n_qssa_species > 0:
cw.writer(fstream, "speciesEnthalpy_qss(h_RT_qss, tc);")
if species_info.n_qssa_species > 0:
if not syms.store_in_jacobian:
cw.writer(fstream, cw.comment("Fill sc_qss here"))
cw.writer(fstream, "comp_k_f_qss(tc, invT, kf_qss);")
cw.writer(
fstream,
"comp_qss_coeff(kf_qss, qf_qss, qr_qss, sc, tc, g_RT, g_RT_qss);",
)
cw.writer(fstream, "comp_sc_qss(sc_qss, qf_qss, qr_qss);")
cw.writer(fstream)
# cw.writer(fstream,"comp_Kc_qss(invT, g_RT, g_RT_qss, Kc_qss);")
# Initialize the big Jacobian array
cw.writer(fstream, f"for (int i=0; i<{(n_species + 1) ** 2}; i++) {{")
cw.writer(fstream, "J[i] = 0.0;")
cw.writer(fstream, "}")
# Now write out the species jacobian terms
cw.writer(fstream, cw.comment("Species terms"))
if syms.hformat == "cpu":
syms.write_symjac_to_cpp_cpu(species_info, cw, fstream)
else:
syms.write_symjac_to_cpp_gpu(species_info, cw, fstream)
cw.writer(fstream)
# dwdotdT
cw.writer(fstream)
cw.writer(fstream, f"for (int k = 0; k < {n_species} ; k++) {{")
cw.writer(
fstream,
f"J[{n_species * (n_species + 1)} + k] = (wdot_pert1[k] - wdot[k])/(pertT);",
)
cw.writer(fstream, "}")
# depends on dwdotdT and dwdotdsc
cw.writer(
fstream,
f"amrex::Real c_R[{n_species}], dcRdT[{n_species}], e_RT[{n_species}];",
)
cw.writer(fstream, "amrex::Real * eh_RT;")
# if precond:
# cw.writer(fstream, "if (HP) {")
# else:
# cw.writer(fstream, "if (consP) {")
cw.writer(fstream, "if (consP == 1) {")
cw.writer(fstream, "cp_R(c_R, tc);")
cw.writer(fstream, "dcvpRdT(dcRdT, tc);")
cw.writer(fstream, "eh_RT = &h_RT[0];")
cw.writer(fstream, "}")
cw.writer(fstream, "else {")
cw.writer(fstream, "cv_R(c_R, tc);")
cw.writer(fstream, "dcvpRdT(dcRdT, tc);")
cw.writer(fstream, "speciesInternalEnergy(e_RT, tc);")
cw.writer(fstream, "eh_RT = &e_RT[0];")
cw.writer(fstream, "}")
cw.writer(fstream)
cw.writer(
fstream,
"amrex::Real cmix = 0.0, ehmix = 0.0, dcmixdT=0.0, dehmixdT=0.0;",
)
cw.writer(fstream, f"for (int k = 0; k < {n_species}; ++k) {{")
cw.writer(fstream, "cmix += c_R[k]*sc[k];")
cw.writer(fstream, "dcmixdT += dcRdT[k]*sc[k];")
cw.writer(fstream, "ehmix += eh_RT[k]*wdot[k];")
cw.writer(
fstream,
"dehmixdT += invT*(c_R[k]-eh_RT[k])*wdot[k] +"
f" eh_RT[k]*J[{n_species * (n_species + 1)}+k];",
)
cw.writer(fstream, "}")
cw.writer(fstream)
cw.writer(fstream, "amrex::Real cmixinv = 1.0/cmix;")
cw.writer(fstream, "amrex::Real tmp1 = ehmix*cmixinv;")
cw.writer(fstream, "amrex::Real tmp3 = cmixinv*T;")
cw.writer(fstream, "amrex::Real tmp2 = tmp1*tmp3;")
cw.writer(fstream, "amrex::Real dehmixdc;")
cw.writer(fstream, cw.comment("dTdot/d[X]"))
cw.writer(fstream, f"for (int k = 0; k < {n_species}; ++k) {{")
cw.writer(fstream, "dehmixdc = 0.0;")
cw.writer(fstream, f"for (int m = 0; m < {n_species}; ++m) {{")
cw.writer(fstream, f"dehmixdc += eh_RT[m]*J[k*{n_species + 1}+m];")
cw.writer(fstream, "}")
cw.writer(
fstream,
f"J[k*{n_species + 1}+{n_species}] = tmp2*c_R[k] - tmp3*dehmixdc;",
)
cw.writer(fstream, "}")
cw.writer(fstream, cw.comment("dTdot/dT"))
cw.writer(
fstream,
f"J[{n_species * (n_species + 1) + n_species}] = -tmp1 +"
" tmp2*dcmixdT - tmp3*dehmixdT;",
)
cw.writer(fstream, "#else")
cw.writer(fstream, "amrex::Abort();")
cw.writer(fstream, "#endif")
cw.writer(fstream, "}")
cw.writer(fstream)
def ajac_reaction_d(
fstream,
mechanism,
species_info,
reaction_info,
reaction,
orig_idx,
precond=False,
syms=None,
):
"""Write jacobian of reaction."""
n_species = species_info.n_species
remove_forward = cu.is_remove_forward(reaction_info, orig_idx)
if bool(reaction.orders):
dim = cu.phase_space_units(reaction.orders)
else:
dim = cu.phase_space_units(reaction.reactants)
third_body = reaction.third_body is not None
falloff = reaction.rate.type == "falloff"
is_troe = reaction.rate.sub_type == "Troe"
is_sri = reaction.rate.sub_type == "Sri"
is_lindemann = reaction.rate.sub_type == "Lindemann"
aeuc = cu.activation_energy_units()
if not third_body and not falloff:
# Case 3 !PD, !TB
cw.writer(
fstream,
cw.comment("a non-third-body and non-pressure-fall-off reaction"),
)
ctuc = cu.prefactor_units(cc.ureg("kmol/m**3"), 1 - dim)
pef = (reaction.rate.pre_exponential_factor * ctuc).to_base_units()
beta = reaction.rate.temperature_exponent
ae = (reaction.rate.activation_energy * cc.ureg.joule / cc.ureg.kmol).to(aeuc)
elif not falloff:
# Case 2 !PD, TB
cw.writer(
fstream,
cw.comment("a third-body and non-pressure-fall-off reaction"),
)
ctuc = cu.prefactor_units(cc.ureg("kmol/m**3"), -dim)
pef = (reaction.rate.pre_exponential_factor * ctuc).to_base_units()
beta = reaction.rate.temperature_exponent
ae = (reaction.rate.activation_energy * cc.ureg.joule / cc.ureg.kmol).to(aeuc)
else:
# Case 1 PD, TB
cw.writer(
fstream,
cw.comment("a third-body and pressure-fall-off reaction"),
)
ctuc = cu.prefactor_units(cc.ureg("kmol/m**3"), 1 - dim)
pef = (reaction.rate.high_rate.pre_exponential_factor * ctuc).to_base_units()
beta = reaction.rate.high_rate.temperature_exponent
ae = (
reaction.rate.high_rate.activation_energy * cc.ureg.joule / cc.ureg.kmol
).to(aeuc)
low_pef = (reaction.rate.low_rate.pre_exponential_factor * ctuc).to_base_units()
low_beta = reaction.rate.low_rate.temperature_exponent
low_ae = (
reaction.rate.low_rate.activation_energy * cc.ureg.joule / cc.ureg.kmol
).to(aeuc)
if is_troe:
troe = reaction.rate.falloff_coeffs
ntroe = len(troe)
elif is_sri:
pass
# sri = reaction.rate.falloff_coeffs
# nsri = len(sri)
elif is_lindemann:
pass
else:
print(
f"Unrecognized reaction rate type {reaction.rate.type},"
f" {reaction.rate.sub_type} for reaction: {reaction.equation}"
)
sys.exit(1)
has_alpha = False
corr_s = ""
if not third_body and not falloff:
pass
elif (
not falloff
and len(reaction.third_body.efficiencies) == 1
and isclose(reaction.third_body.default_efficiency, 0.0)
):
pass
elif not falloff:
corr_s = "alpha *"
has_alpha = True
else:
corr_s = "Corr *"
has_alpha = True
rea_dict = OrderedDict()
pro_dict = OrderedDict()
all_dict = OrderedDict()
all_wqss_dict = OrderedDict()
sum_nuk = 0
all_reactants = copy.deepcopy(reaction.reactants)
all_products = copy.deepcopy(reaction.products)
if reaction.third_body:
if len(reaction.third_body.efficiencies) == 1:
if isclose(reaction.third_body.default_efficiency, 0.0):
all_reactants = dict(
sum(
(
Counter(x)
for x in [
all_reactants,
reaction.third_body.efficiencies,
]
),
Counter(),
)
)
all_products = dict(
sum(
(
Counter(x)
for x in [
all_products,
reaction.third_body.efficiencies,
]
),
Counter(),
)
)
# Build rea_dict containing reaction species
for symbol, coefficient in all_reactants.items():
k = species_info.ordered_idx_map[symbol]
sum_nuk -= coefficient
if k in rea_dict:
coe_old = rea_dict[k][1]
rea_dict[k] = (symbol, coefficient + coe_old)
else:
rea_dict[k] = (symbol, coefficient)
# Build pro_dict containing product species
for symbol, coefficient in all_products.items():
k = species_info.ordered_idx_map[symbol]
sum_nuk += coefficient
if k in pro_dict:
coe_old = pro_dict[k][1]
pro_dict[k] = (symbol, coefficient + coe_old)
else:
pro_dict[k] = (symbol, coefficient)
# Build the dict with species and coefficients
for k in range(n_species):
if k in rea_dict and k in pro_dict:
sr, nur = rea_dict[k]
sp, nup = pro_dict[k]
all_dict[k] = (sr, nup - nur)
elif k in rea_dict:
sr, nur = rea_dict[k]
all_dict[k] = (sr, -nur)
elif k in pro_dict:
sp, nup = pro_dict[k]
all_dict[k] = (sp, nup)
elif species_info.all_species_list[k] in reaction.orders:
sp = species_info.all_species_list[k]
all_dict[k] = (sp, 0)
# Build the dict including qss species
for k in range(len(species_info.all_species_list)):
if k in rea_dict and k in pro_dict:
sr, nur = rea_dict[k]
sp, nup = pro_dict[k]
all_wqss_dict[k] = (sr, nup - nur)
elif k in rea_dict:
sr, nur = rea_dict[k]
all_wqss_dict[k] = (sr, -nur)
elif k in pro_dict:
sp, nup = pro_dict[k]
all_wqss_dict[k] = (sp, nup)
elif species_info.all_species_list[k] in reaction.orders:
sp = species_info.all_species_list[k]
all_wqss_dict[k] = (sp, 0)
sorted_reactants = sorted(rea_dict.values())
sorted_products = sorted(pro_dict.values())
if not reaction.reversible:
if falloff or has_alpha:
print("FIXME: irreversible reaction in _ajac_reaction may not work")
cw.writer(
fstream,
cw.comment(
"Irreversible reaction in _ajac_reaction may not work",
),
)
for k in range(n_species):
if k in sorted_reactants and k in sorted_products:
print("FIXME: irreversible reaction in _ajac_reaction may not work")
cw.writer(
fstream,
cw.comment(
"Irreversible reaction in _ajac_reaction may not work",
),
)
if has_alpha:
cw.writer(fstream, cw.comment("3-body correction factor"))
enhancement_d = cu.enhancement_d(
# mechanism, species_info, reaction, syms
mechanism,
species_info,
reaction,
syms=None,
)
cw.writer(fstream, f"alpha = {enhancement_d};")
# forward
qss_ps = cu.qss_sorted_phase_space(
mechanism, species_info, reaction, reaction.reactants
)
cw.writer(fstream, cw.comment("forward"))
cw.writer(
fstream,
f"phi_f = {qss_ps};",
)
cw.writer(fstream, f"k_f = {pef.m:.15g}")
if (ae.m == 0) and (beta == 0):
cw.writer(fstream, " ;")
elif ae.m == 0:
cw.writer(
fstream,
f" * exp({beta:.15g} * tc[0]);",
)
elif beta == 0:
cw.writer(
fstream,
" * exp(-"
f" ({(1.0 / cc.Rc / cc.ureg.kelvin * ae).m:.15g}) * invT);",
)
else:
cw.writer(
fstream,
f" * exp({beta:.15g} * tc[0] -"
f" ({(1.0 / cc.Rc / cc.ureg.kelvin * ae).m:.15g}) * invT);",
)
if remove_forward:
cw.writer(fstream, cw.comment("Remove forward reaction"))
cw.writer(
fstream,
cw.comment(
f"dlnkfdT = {beta:.15g} * invT +"
f" ({(1.0 / cc.Rc / cc.ureg.kelvin * ae).m:.15g}) * invT2;"
),
)
cw.writer(fstream, "dlnkfdT = 0.0;")
else:
if (beta == 0) and (ae.m == 0):
cw.writer(
fstream,
"dlnkfdT = 0.0;",
)
elif ae.m == 0:
cw.writer(
fstream,
f"dlnkfdT = {beta:.15g} * invT;",
)
elif beta == 0:
cw.writer(
fstream,
f"dlnkfdT = ({(1.0 / cc.Rc / cc.ureg.kelvin * ae).m:.15g}) * invT2;",
)
else:
cw.writer(
fstream,
f"dlnkfdT = {beta:.15g} * invT +"
f" ({(1.0 / cc.Rc / cc.ureg.kelvin * ae).m:.15g}) * invT2;",
)
if falloff:
cw.writer(fstream, cw.comment("pressure-fall-off"))
if low_beta == 0 and low_ae.m == 0:
cw.writer(
fstream,
f"k_0 = {low_pef.m * 10 ** 3 ** dim:.15g};",
)
elif low_ae.m == 0:
cw.writer(
fstream,
f"k_0 = {low_pef.m * 10 ** 3 ** dim:.15g} *"
f" exp({low_beta:.15g} * tc[0]);",
)
elif low_beta == 0:
cw.writer(
fstream,
f"k_0 = {low_pef.m * 10 ** 3 ** dim:.15g} *"
f" exp(-({(1.0 / cc.Rc / cc.ureg.kelvin * low_ae).m:.15g})"
" * invT);",
)
else:
cw.writer(
fstream,
f"k_0 = {low_pef.m * 10 ** 3 ** dim:.15g} *"
f" exp({low_beta:.15g} * tc[0] -"
f" ({(1.0 / cc.Rc / cc.ureg.kelvin * low_ae).m:.15g}) *"
" invT);",
)
cw.writer(fstream, f"Pr = 1e-{int(dim * 6)} * alpha / k_f * k_0;")
cw.writer(fstream, "fPr = Pr / (1.0+Pr);")
if (low_beta == 0) and (low_ae.m == 0):
cw.writer(
fstream,
"dlnk0dT = 0.0;",
)
elif low_ae.m == 0:
cw.writer(
fstream,
f"dlnk0dT = {low_beta:.15g} * invT;",
)
elif low_beta == 0:
cw.writer(
fstream,
"dlnk0dT ="
f" ({(1.0 / cc.Rc / cc.ureg.kelvin * low_ae).m:.15g}) *"
" invT2;",
)
else:
cw.writer(
fstream,
f"dlnk0dT = {low_beta:.15g} * invT +"
f" ({(1.0 / cc.Rc / cc.ureg.kelvin * low_ae).m:.15g}) *"
" invT2;",
)
cw.writer(fstream, "dlogPrdT = log10e*(dlnk0dT - dlnkfdT);")
cw.writer(fstream, "dlogfPrdT = dlogPrdT / (1.0+Pr);")
#
if is_sri:
cw.writer(fstream, cw.comment("SRI form"))
print("FIXME: sri not supported in _ajac_reaction yet")
sys.exit(1)
elif is_troe:
cw.writer(fstream, cw.comment("Troe form"))
troe = reaction.rate.falloff_coeffs
ntroe = len(troe)
cw.writer(fstream, "logPr = log10(Pr);")
if abs(troe[1]) > 1.0e-100:
if troe[0] < 0:
cw.writer(
fstream,
f"Fcent1 = (1.+{-troe[0]:.15g})*exp(-T/{troe[1]:.15g});",
)
else:
cw.writer(
fstream,
f"Fcent1 = (1.-{troe[0]:.15g})*exp(-T/{troe[1]:.15g});",
)
else:
cw.writer(fstream, "Fcent1 = 0.;")
if abs(troe[2]) > 1.0e-100:
cw.writer(
fstream,
f"Fcent2 = {troe[0]:.15g} * exp(-T/{troe[2]:.15g});",
)
else:
cw.writer(fstream, "Fcent2 = 0.;")
if ntroe == 4:
if troe[3] < 0:
cw.writer(fstream, f"Fcent3 = exp({-troe[3]:.15g} * invT);")
else:
cw.writer(fstream, f"Fcent3 = exp(-{troe[3]:.15g} * invT);")
else:
cw.writer(fstream, "Fcent3 = 0.;")
cw.writer(fstream, "Fcent = Fcent1 + Fcent2 + Fcent3;")
cw.writer(fstream, "logFcent = log10(Fcent);")
cw.writer(fstream, "troe_c = -.4 - .67 * logFcent;")
cw.writer(fstream, "troe_n = .75 - 1.27 * logFcent;")
cw.writer(fstream, "troePr_den = 1.0 / (troe_n - .14*(troe_c + logPr));")
cw.writer(fstream, "troePr = (troe_c + logPr) * troePr_den;")
cw.writer(fstream, "troe = 1.0 / (1.0 + troePr*troePr);")
cw.writer(fstream, "F = exp(M_LN10 * logFcent * troe);")
cw.writer(fstream, "dlogFcentdT = log10e/Fcent*( ")
if abs(troe[1]) > 1.0e-100:
cw.writer(fstream, f" -Fcent1/{troe[1]:.15g}")
if abs(troe[2]) > 1.0e-100:
cw.writer(fstream, f" -Fcent2/{troe[2]:.15g}")
if ntroe == 4:
if abs(troe[3]) > 1.0e-100:
cw.writer(fstream, f" + Fcent3*{troe[3]:.15g}*invT2")
cw.writer(fstream, ");")
cw.writer(
fstream,
"dlogFdcn_fac = 2.0 * logFcent * troe*troe * troePr * troePr_den;",
)
cw.writer(fstream, "dlogFdc = -troe_n * dlogFdcn_fac * troePr_den;")
cw.writer(fstream, "dlogFdn = dlogFdcn_fac * troePr;")
cw.writer(fstream, "dlogFdlogPr = dlogFdc;")
cw.writer(
fstream,
"dlogFdT = dlogFcentdT*(troe - 0.67*dlogFdc -"
" 1.27*dlogFdn) + dlogFdlogPr * dlogPrdT;",
)
else:
cw.writer(fstream, cw.comment("Lindemann form"))
cw.writer(fstream, "F = 1.0;")
if precond:
cw.writer(fstream, "// dlogFdlogPr is 0.0 and unused")
else:
cw.writer(fstream, "dlogFdlogPr = 0.0;")
cw.writer(fstream, "dlogFdT = 0.0;")
# reverse
if not reaction.reversible:
cw.writer(fstream, cw.comment("rate of progress"))
if (not has_alpha) and (not falloff):
if remove_forward:
cw.writer(fstream, cw.comment("Remove forward reaction"))
cw.writer(fstream, cw.comment("q = k_f*phi_f;"))
cw.writer(fstream, "q = 0.0;")
else:
cw.writer(fstream, "q = k_f*phi_f;")
else:
if remove_forward:
cw.writer(fstream, cw.comment("Remove forward reaction"))
cw.writer(fstream, cw.comment("q_nocor = k_f*phi_f;"))
cw.writer(fstream, "q_nocor = 0.0;")
else:
cw.writer(fstream, "q_nocor = k_f*phi_f;")
if falloff:
cw.writer(fstream, "Corr = fPr * F;")
cw.writer(fstream, "q = Corr * q_nocor;")
else:
cw.writer(fstream, "q = alpha * q_nocor;")