Specie

class PlasmaCalcs.mhd.multifluid.mhd_fluids.Specie(name=UNSET, i=None, *, q, m=UNSET, element=None)

Bases: ElementHaver

Fluid corresponding to a specie, e.g. H_I, H_II, e, Fe_II.

(code uses ‘specie’ as singular of ‘species’, to clarify singular vs plural.)

CAUTION: some code assumes (without checking) that Specie objects are immutable.

Changing a Specie after creating it could lead to unexpected behavior.

species usually have a name. Every specie has a charge (possibly charge=0)

non-electron species should also have an associated Element.

name: UNSET, None, or str

name of this specie.

UNSET –> infer from element and q; None if no element.

inferred name will be element name + roman numeral based on q,

e.g. H_I for neutral H, H_II for H+.

None –> cannot convert self to str.

i: None or int

the index of this specie (within a SpecieList).

None –> cannot convert self to int.

q: number

charge, in elementary charge units (e.g. -1 for electrons, +1 for H_II)

m: UNSET, None, or number

mass, in atomic mass units (e.g. ~1 for H_I or H_II).
UNSET –> use element.m.
None –> cannot get self.m

element: None, dict, or Element

Element associated with this specie.

dict –> convert to Element via Element.from_dict(element).

Methods

`__eq__`(v)	return self==v.
`__init_subclass__`(*[, _serial_typename])	register cls as a subclass of XarrayIoSerializable.
`array_equals`(other)	return whether self == other (which is assumed to be a numpy array or xarray.DataArray).
`copy`(**kw_init)	return a copy of self.
`deserialize`(serial)	creates an XarrayIoSerializable object from a serialized representation.
`electron`([name, i, m])	create an electron Specie (with q=-1).
`equal_except_i`(v)	returns whether self == v (another DimensionValue), ignoring i.
`from_dict`(d)	return cls from dict d.
`from_element`(element[, i])	create a Specie from this Element (& charge q [elementary charge units]).
`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.
`ion`(element[, i, q])	create an ion Specie from element and q [elementary charge units]
`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.
`is_nonelectron`()	tells whether self is not an electron, i.e. self.q >= 0.
`lookup_dict`()	returns dict for looking up self within a DimensionValueList, given int, str, or self.
`neutral`(element[, i])	create a neutral Specie (with q=0) from 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`(*[, element_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.
`_assert_array_equals`(other)	raise DimensionValueError unless self.array_equals(other).
`_assert_single`(vals, *[, meaning])	assert len(vals)==1.
`_repr_contents`()	contents used by self.__repr__
`_repr_simple`()	return simple repr for self: Classname(s, i).

Attributes

`SERIAL_TYPES`
`get_I`	alias to neutral
`get_II`	alias to ion
`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.

_assert_array_equals(other): raise DimensionValueError unless self.array_equals(other).

classmethod _assert_single(vals, *, meaning='value'): assert len(vals)==1. Raise DimensionKeyError if len==0; DimensionValueError if len>=2.

meaning can be provided to clarify what vals should represent, in case of crash;

error message will be ‘expected exactly 1 {meaning}, but got {len(vals)}’.

This check tends to make more sense coming from a DimensionValueList,

but it is convenient to attach here too in case of using isel from an array.

_dimension_key_error: alias of FluidKeyError

_dimension_value_error: alias of FluidValueError

_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.

array_equals(other): return whether self == other (which is assumed to be a numpy array or xarray.DataArray).

return False if other.size != 1. Else, compare to other.item().

(Extremely convenient if comparing to xarray DataArray or numpy array,

with potentially unknown size / dimensionality.

Also, convenient if “self” might be DimensionValueList instead,

because DimensionValueList also provides an array_equals method.)

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]

classmethod electron(name='e', i=None, *, m=UNSET, **kw_init): create an electron Specie (with q=-1).

m: if UNSET, use physical value: DEFAULTS.PHYSICAL.CONSTANTS_SI[‘me amu-1’]

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.

classmethod from_element(element, i=None, *, q, **kw_init): create a Specie from this Element (& charge q [elementary charge units]).

name and m inferred from element and q, unless provided explicitly here.

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.

The implementation here just returns [self.get_element(default=default)].

classmethod ion(element, i=None, *, q=1, **kw_init): create an ion Specie from element and q [elementary charge units]

element: Element object. Used to infer name and m, by default.

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.

is_nonelectron(): tells whether self is not an electron, i.e. self.q >= 0.

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

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

(used by DimensionValueList.lookup_dict)

property name: alias to s

classmethod neutral(element, i=None, **kw_init): create a neutral Specie (with q=0) from element.

element: Element object. Used to infer name and m, by default.

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(*, element_to_dict=True): return dictionary of info about self. Attribute values for keys in self._kw_def.

e.g. if _kw_def={‘name’, ‘i’, ‘m’}, then result = {‘name’: self.name, ‘i’: self.i, ‘m’: self.m}

element_to_dict: bool, default True

whether to also convert result[‘element’].to_dict() too, if non-None ‘element’ in result.

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