IonMixture

class PlasmaCalcs.mhd.multifluid.mhd_fluids.IonMixture(species, i=None, *, q=UNSET, name=UNSET, m_mean_mode='simple', m_tol=UNSET)

Bases: MhdFluid

Fluid corresponding to multiple ions grouped together, e.g. Mg+Al+Si_II

CAUTION: some code assumes (without checking) that IonMixture objects are immutable.: Changing an IonMixture after creating it could lead to unexpected behavior.

IonMixtures usually have a name. Every IonMixture has a charge (probably charge=1).

Name and charge can be inferred from the species in the mixture.

species: iterable of Specie or dict objects: the list of Species in this mixture. length must be at least 1.

internally stored as SpecieList(species)

dicts –> convert to SpecieList via SpecieList.from_dicts(species).
i: None or int: the index of this mixture (within an IonMixtureList or MhdFluidList)

None –> cannot convert self to int.
q: UNSET or number: charge, in elementary charge units (e.g. +1 for H_II).

all species must have the same charge else raise NotImplementedError.

UNSET –> infer q from species.

number –> assert q > 0, and q == spec.q for spec in species.
name: UNSET, None, or str: name of this mixture. None –> unnamed.

UNSET –> infer from species. E.g. Mg_II, Al_II, Si_II –> Mg+Al+Si_II
m_mean_mode: str in {‘simple’, ‘density’}: how to calculate the mass of this mixture.

‘simple’ –> m = mean(spec.m for spec in species). This is a constant.

‘density’ –> m = density weighted mean of spec.m for spec in species.

this might vary across maindims and snaps…
m_tol: UNSET, None, or number: crash if any |m_s - mean(m)| is more than m_tol * mean(m).

(using simple mean for this test, regardless of m_mean_mode)

(Prevents accidentally creating a mixture of ions with very different masses.)

UNSET –> use self.DEFAULT_M_TOL (default=0.1)

None –> allow any masses.

Methods

`__eq__`(v)	return self==v.
`__init_subclass__`(*[, _serial_typename])	register cls as a subclass of XarrayIoSerializable.
`copy`(**kw_init)	return a copy of self.
`deserialize`(serial)	creates an XarrayIoSerializable object from a serialized representation.
`equal_except_i`(v)	returns whether self == v (another DimensionValue), ignoring i.
`from_dict`(d)	return cls from dict d.
`get_element`([default])	return self.element if it exists and is not None, else crash with FluidKeyError.
`get_elements`([default])	return list of elements in self, i.e. spec.get_element() for spec in self.
`infer_name`()	infer name based on species' names.
`ion`([q])	return ionized Specie of self.get_element()
`is_charged`()	tells whether self is a charged fluid.
`is_electron`()	tells whether self is an electron.
`is_ion`()	tells whether self is an ion.
`is_neutral`()	tells whether self is a neutral fluid.
`lookup_dict`()	return dict for looking up self within a DimensionValueList, given int, str, or self.
`neutral`(**kw_specie)	return neutral Specie of self.get_element().
`register_type`(cls_to_register[, ...])	register cls_to_register as a serializable subclass of XarrayIoSerializable.
`saha_list`(*[, istart])	return SpecieList of neutral & once-ionized ions of self.get_element().
`serialize`()	return dict of info about self, including 'typename' key.
`to_dict`(*[, species_to_dict])	return dictionary of info about self.
`with_i`(i)	return copy of self with i=i, or self if self.i==i already.
`_check_m_tol`()	crash if any \|m_s - mean(m)\| is more than m_tol * mean(m).
`_repr_contents`()	contents used by self.__repr__
`_repr_simple`()	return simple repr for self: Classname(s, i).

Attributes

`DEFAULT_M_TOL_DENSITY`
`DEFAULT_M_TOL_SIMPLE`
`SERIAL_TYPES`
`get`	return self.species.get(key)
`get_I`	alias to neutral
`get_II`	alias to ion
`m_mean`	return mean mass of species in this mixture.
`m_mean_mode`	str telling how to calculate the mass of this mixture.
`name`	alias to s
`ndim`
`size`

__eq__(v): return self==v. Equal if:

- v is an instance of type(self), and

all kw from both self._kw_eq and v._kw_eq have the same values.

(any kw missing attrs will be treated as UNSET.)

For DimensionValue, just compares self.s==v.s and self.i==v.i.

Subclasses may add more kwargs to compare by altering _kw_def.

- or, self.s == v or self.i == v, and v is not another DimensionValue

- or, v is a DimensionSingleValueSpecifier and v.checker(self) gives True.

Not equal if v is a DimensionValue but not an instance of type(self),

e.g. class Fluid(DimensionValue):…; class Snap(DimensionValue):…;

Fluid(‘H’, 0) != Snap(‘H’, 0).

classmethod __init_subclass__(*, _serial_typename=None, **kw)

register cls as a subclass of XarrayIoSerializable.

_serial_typename: None or str: name to use for this type, for serialization purposes.

None –> use cls.__name__.

This method also sets cls._serial_typename = _serial_typename.

_check_m_tol(): crash if any |m_s - mean(m)| is more than m_tol * mean(m).

return max(|m_s - mean(m)| / mean(m)).

_repr_contents(): contents used by self.__repr__

_repr_simple(): return simple repr for self: Classname(s, i).

if s is None, use Classname(i) instead.

if i is None, use Classname(s, i=None) instead.

Called when using PlasmaCalcs.tools.repr_simple.

copy(**kw_init): return a copy of self. Can provide new kwargs here to override old values in result.

E.g. self.copy(i=7) makes a copy of self but with i=7 instead of self.i.

static deserialize(serial)

creates an XarrayIoSerializable object from a serialized representation.

serial: dict or str: str –> convert to dict via ast.literal_eval.

dict must contain ‘typename’ key.

The output here will be an instance of XarrayIoSerializable.SERIAL_TYPES[typename]

element_cls: alias of Element

equal_except_i(v): returns whether self == v (another DimensionValue), ignoring i.

equal if v is an instance of type(self) and

all kw from both self._kw_eq and v._kw_eq have the same values.

(any kw missing attrs will be treated as UNSET.)

For DimensionValue: self.s==v.s and self.i==v.i. Subclasses may add more.

classmethod from_dict(d): return cls from dict d.

If ‘d’ contains ‘typename’, result is like cls.deserialize(d) instead,

however, first require that result is an instance of cls (or subclass of cls).

E.g. Fluid.from_dict(dict(typename=’EppicDist’, …)) returns EppicDist,

but Snap.from_dict(dict(typename=’EppicDist’, …)) crashes with InputError.

Subclasses wishing to alter deserialize behavior will probably override this method instead.

property get: return self.species.get(key)

property get_I: alias to neutral

property get_II: alias to ion

get_element(default=NO_VALUE)

return self.element if it exists and is not None, else crash with FluidKeyError.

default: NO_VALUE or any value.: If provided, when element missing or None, return default instead of crash.

get_elements(default=NO_VALUE): return list of elements in self, i.e. spec.get_element() for spec in self.

infer_name(): infer name based on species’ names.

if all species’ names have the same suffix (starting at underscore),

‘+’.join(names without suffix) + suffix.

else, ‘+’.join(names).

ion(q=1, **kw_specie)

return ionized Specie of self.get_element()

q: charge in elementary charge units. (default: +1)

is_charged(): tells whether self is a charged fluid. i.e. self.q != 0.

if self.q is None, returns None instead of bool.

is_electron(): tells whether self is an electron. i.e. self.q < 0.

if self.q is None, returns None instead of bool.

is_ion(): tells whether self is an ion. i.e. self.q > 0.

if self.q is None, returns None instead of bool.

is_neutral(): tells whether self is a neutral fluid. i.e. self.q == 0.

if self.q is None, returns None instead of bool.

lookup_dict(): return dict for looking up self within a DimensionValueList, given int, str, or self.

(used by DimensionValueList.lookup_dict)

in addition to being able to lookup self,

also allows lookup of any species within self, by name or object (but not index).

E.g. if H_II=Specie(‘H_II’, i=3) in self,

result will include {‘H_II’: H_II, H_II: H_II}, but will not include {3: H_II}

property m_mean: return mean mass of species in this mixture.

(Always using a simple mean: sum(s.m for s in species)/len(species))

property m_mean_mode: str telling how to calculate the mass of this mixture.

‘simple’ –> m = mean(spec.m for spec in species). This is a constant.

‘density’ –> m = density weighted mean of spec.m for spec in species.

this might vary across maindims and snaps…

property name: alias to s

neutral(**kw_specie): return neutral Specie of self.get_element().

static register_type(cls_to_register, _serial_typename=None)

register cls_to_register as a serializable subclass of XarrayIoSerializable.

_serial_typename: str or None: name to use for serialization. if None, use cls_to_register.__name__.

saha_list(*, istart=0, **kw_specie)

return SpecieList of neutral & once-ionized ions of self.get_element().

istart: start index for the SpecieList. Index affects conversion to int.

serialize(): return dict of info about self, including ‘typename’ key.

specie_cls: alias of Specie

specie_list_cls: alias of SpecieList

to_dict(*, species_to_dict=True)

return dictionary of info about self. Attribute values for keys in self._kw_def.

species_to_dict: bool, default True: whether to also convert result[‘species’].to_dict() too.

with_i(i): return copy of self with i=i, or self if self.i==i already.