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Fix for derivative of PLOG w/ zero temperature exponent & activation energy #35

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Fix for derivative of PLOG w/ zero temperature exponent & activation energy #35

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49 changes: 29 additions & 20 deletions pyjac/core/create_jacobian.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1746,7 +1746,9 @@ def write_plog_rxn_dt(file, lang, jline, specs, rxn, rxn_ind,
# log(K2) - log(K1) term differently
raise NotImplementedError
else:
assert b_p1 != 0.0 or E_p1 != 0.0 or b_p2 != 0.0 or E_p2 != 0.0, "PLOG Derivative undefined"
if b_p1 == 0.0 and E_p1 == 0.0 and b_p2 == 0.0 and E_p2 == 0.0:
# derivative is identically zero
jline_p += '0.0'
if b_p1 != 0.0:
jline_p += '{:.16e}'.format(b_p1)
if E_p1 != 0.0:
Expand All @@ -1757,14 +1759,17 @@ def write_plog_rxn_dt(file, lang, jline, specs, rxn, rxn_ind,

jline_p += '('
if b_p2 - b_p1 != 0.0:
jline_p += '{:.16e} + '.format(b_p2 - b_p1)
jline_p += '{:.16e}'.format(b_p2 - b_p1)
if E_p2 - E_p1 != 0.0:
jline_p += '{:.16e} / T) * (log(pres)'.format(E_p2 - E_p1)
if p1 != 1.0:
jline_p += ' - {:.16e}'.format(math.log(p1))
jline_p += ') / '
assert p1 != p2, 'Cannot have equal pressures in PLOG'
jline_p += '{:.16e})'.format(math.log(p2) - math.log(p1))
if jline_p: jline_p += ' + '
jline_p += '{:.16e} / T'.format(E_p2 - E_p1)

jline_p += ') * (log(pres)'
if p1 != 1.0:
jline_p += ' - {:.16e}'.format(math.log(p1))
jline_p += ') / '
assert p1 != p2, 'Cannot have equal pressures in PLOG'
jline_p += '{:.16e})'.format(math.log(p2) - math.log(p1))
else:
jline_p += ')'

Expand Down Expand Up @@ -1833,21 +1838,25 @@ def write_plog_rxn_dt(file, lang, jline, specs, rxn, rxn_ind,
dkdt = get_elementary_rxn_dt(lang, specs, rxn_p, rxn_ind,
rev_idx, get_array, do_unroll
)
if have_prev:
file.write(utils.line_start +
'}} else if (pres > {:.4e}) {{\n'.format(pn)
)
else:
file.write(utils.line_start +
'j_temp = 0' + utils.line_end[lang]
)
file.write(utils.line_start +
'if (pres > {:.4e}) {{\n'.format(pn)
)
if dkdt:
if have_prev:
file.write(utils.line_start +
'}} else if (pres > {:.4e}) {{\n'.format(pn)
)
else:
file.write(utils.line_start +
'j_temp = 0' + utils.line_end[lang]
)
file.write(utils.line_start +
'if (pres > {:.4e}) {{\n'.format(pn)
)
file.write(utils.line_start + jline + dkdt)
else:
file.write(utils.line_start * 2 +
'j_temp = 0' + utils.line_end[lang]
)

file.write(utils.line_start + '}\n')
file.write(utils.line_start + '}\n')


def write_dt_completion(file, lang, specs, J_nplusone_touched, get_array):
Expand Down