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_julia.py
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_julia.py
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from collections import OrderedDict
from chempy import Reaction
from chempy.kinetics.rates import MassAction, RadiolyticBase
from chempy.units import to_unitless, default_units as u
def jl_dict(od):
return "Dict([%s])" % ", ".join(['(:%s, %.4g)' % (k, v) for k, v in od.items()])
def _r(r, p, substmap, parmap, *, unit_conc, unit_time, variables=None):
"""
Parameters
==========
...
variables: dict
e.g. dict(doserate=99.9*u.Gy/u.s, density=998*u.kg/u.m3)
"""
pk, = r.param.unique_keys
if isinstance(r.param, MassAction):
ratcoeff = to_unitless(
p[pk], unit_conc**(1-r.order())/unit_time
)
if not r.inact_reac:
r_str = '{}, {}'.format(parmap[pk], r.string(substances=substmap, with_param=False,
Reaction_arrow='-->', Reaction_coeff_space=''))
else:
all_keys = r.keys()
reac_stoichs = r.all_reac_stoich(all_keys)
act_stoichs = r.active_reac_stoich(all_keys)
rate = '*'.join([parmap[pk]] + [('%s^%d' % (substmap[k], v)) if v > 1 else substmap[k]
for k, v in zip(all_keys, act_stoichs) if v > 0])
r2 = Reaction(dict([(k, v) for k, v in zip(all_keys, reac_stoichs) if v]), r.prod)
r_str = '{}, {}'.format(rate, r2.string(substances=substmap, with_param=False,
Reaction_arrow='\u21D2', Reaction_coeff_space=''))
elif isinstance(r.param, RadiolyticBase):
ratcoeff = to_unitless(
p[pk]*variables['doserate']*variables['density'],
unit_conc/unit_time
)
assert not r.reac and not r.inact_reac and not r.inact_prod
(prod, n), = r.prod.items()
assert n == 1
r_str = ('{}, 0 \u21D2 {}' if ratcoeff > 0 else '{}, {} \u21D2 0').format(
parmap[pk], substmap[prod])
else:
raise NotImplementedError("Whats that?")
return r_str, pk, abs(ratcoeff)
class DiffEqBioJl:
_template_body = """\
{name} = @{crn_macro} begin
{reactions}
end {parameters}
{post}
"""
defaults = dict(unit_conc=u.molar, unit_time=u.second)
def __init__(self, *, rxs, pars, substance_key_map, parmap, **kwargs):
self.rxs = rxs
self.pars = pars
self.substance_key_map = substance_key_map
self.parmap = parmap
self.unit_conc = kwargs.get('unit_conc', self.defaults['unit_conc'])
self.unit_time = kwargs.get('unit_time', self.defaults['unit_time'])
@classmethod
def from_rsystem(cls, rsys, par_vals, *, variables=None, substance_key_map=lambda i, sk: 'y%d' % i, **kwargs):
if not isinstance(substance_key_map, dict):
substance_key_map = {sk: substance_key_map(si, sk) for si, sk in enumerate(rsys.substances)}
parmap = dict([(r.param.unique_keys[0], 'p%d' % i) for i, r in enumerate(rsys.rxns)])
rxs, pars = [], OrderedDict()
for r in rsys.rxns:
rs, pk, pv = _r(r, par_vals, substance_key_map, parmap, variables=variables,
unit_conc=kwargs.get('unit_conc', cls.defaults['unit_conc']),
unit_time=kwargs.get('unit_time', cls.defaults['unit_time']))
rxs.append(rs)
if pk in pars:
raise ValueError("Are you sure (sometimes intentional)?")
pars[parmap[pk]] = pv
return cls(rxs=rxs, pars=pars, substance_key_map=substance_key_map, parmap=parmap, **kwargs)
def render_body(self, sparse_jac=False):
name = 'rn'
return self._template_body.format(
crn_macro='min_reaction_network' if sparse_jac else 'reaction_network',
name=name,
reactions='\n '.join(self.rxs),
parameters=' '.join(self.pars),
post="addodes!({}, sparse_jac=True)".format(name) if sparse_jac else ''
)
def render_setup(self, *, ics, atol, tex=True, tspan=None):
export = ""
export += "p = %s\n" % jl_dict(self.pars)
export += "ics = %s\n" % jl_dict(OrderedDict({self.substance_key_map[k]: v for
k, v in to_unitless(ics, u.molar).items()}))
if atol:
export += "abstol_d = %s\n" % jl_dict({self.substance_key_map[k]: v for
k, v in to_unitless(atol, u.molar).items()})
export += "abstol = Array([get(abstol_d, k, 1e-10) for k=keys(speciesmap(rn))])"
if tex:
export += "subst_tex = Dict([%s])\n" % ", ".join(
'(:%s, ("%s", "%s"))' % (v, k, k.latex_name) for
k, v in self.substance_key_map.items())
if tspan:
export += """\
tspan = (0., %12.5g)
u0 = Array([get(ics, k, 1e-28) for k=keys(speciesmap(rn))])
parr = Array([p[k] for k=keys(paramsmap(rn))])
oprob = ODEProblem(rn, u0, tspan, parr)
"""
return export
def render_solve(self):
return ("sol = solve(oprob, reltol=1e-9, abstol=abstol, Rodas5(),"
" callback=PositiveDomain(ones(length(u0)), abstol=abstol))")