File Format Functions and Classes¶

IONMIX (.cn4)¶

class opacplot2.OpacIonmix(fn, mpi, twot=False, man=False, hassele=False, verbose=False)¶

Class to read in IONMIX EOS and Opacity Files.

The OpacIonmix class is used to read in an IONMIX file and translate its information into object attributes. All energies in this file are in Joules and must be converted to ergs. Unlike other file classes, OpacIonmix does not store its data as a dictionary. Instead, it stores its data in class attributes.

Parameters:	fn (str) – The name of the file to open. mpi (str) – The mass per ion in grams. twot (bool) – Flag for two-temperature data. man (bool) – Flag for manual temperature/density points. hassele (bool) – lag for electron entropy data.

fn¶

str

Filename.

mpi¶

float

Mass per ion.

twot¶

bool

Two-temperature data.

man¶

bool

Manual temp/dens points.

hassele¶

bool

Has electron entropy data.

verb¶

bool

Verbose.

ntemp¶

int

Number of temperature points.

ndens¶

int

Number of density points.

numDens¶

numpy.ndarray

Number densitites.

temps¶

numpy.ndarray

Temperatures.

ngroups¶

numpy.ndarray

Number of groups

data¶

str

Data at the end of the IONMIX file.

dens¶

numpy.ndarray

Densities.

ngroups

int

Number of groups.

zbar¶

numpy.ndarray

Average ionizations.

etot¶

numpy.ndarray

Total energy. Only included in single-temperature data.

cvtot¶

numpy.ndarray

Total C_v. Only included in single-temperature data.

dedn¶

numpy.ndarray

de/dn. Only included in single-temperature data.

dzdt¶

numpy.ndarray

dz/dt. Only included in two-temperature data.

pion¶

numpy.ndarray

Ion pressure. Only included in two-temperature data.

pele¶

numpy.ndarray

Electron pressure. Only included in two-temperature data.

dpidt¶

numpy.ndarray

dp_i/dt. Only included in two-temperature data.

dpedt¶

numpy.ndarray

dp_e/dt. Only included in two-temperature data.

eion¶

numpy.ndarray

Ion energy. Only included in two-temperature data.

eele¶

numpy.ndarray

Electron energy. Only included in two-temperature data.

cvion¶

numpy.ndarray

C_v for ions. Only included in two-temperature data.

cvele¶

numpy.ndarray

C_v for electrons. Only included in two-temperature data.

deidn¶

numpy.ndarray

de_i/dn. Only included in two-temperature data.

deedn¶

numpy.ndarray

de_e/dn. Only included in two-temperature data.

opac_bounds¶

numpy.ndarray

Opacity boundaries.

rosseland¶

numpy.ndarray

Rosseland opacity.

planck_absorb¶

numpy.ndarray

Planck absorption.

planck_emiss¶

numpy.ndarray

Planck emissivity.

Examples

For a directory with the IONMIX file imx.cn4 for Aluminum:

>>> import opacplot2 as opp
>>> op = opp.Opac_Ionmix('imx.cn4', 4.4803895e-23) # Al mass in grams
>>> print(op.zbar)
array([...]) # Array of average ionizations for dens/temp points.

Notes

If you receive a ValueError: invalid literal for int() with base 10 error, setting man=True may help to fix this.

extendToZero()¶: This routine adds another temperature point at zero.

write(fn, zvals, fracs, twot=None, man=None)¶

This method writes to an IONMIX file.

Parameters:	fn (str) – Name of output file. zvals (tuple) – Atomic numbers. fracs (tuple) – Element fractions. twot (bool) – Flag for two-temperature data. man (bool) – Flag for manual temp/dens points.

Examples

In order to extend imx.cn4 for Al to zero:

>>> import opacplot2 as opp
>>> op = opp.OpacIonmix('imx.cn4', (13,), (1,))
>>> op.extendToZero() # Add temperature point at zero.
>>> op.write('imx-0.cn4', (13,), (1,))

opacplot2.writeIonmixFile(fn, zvals, fracs, numDens, temps, zbar=None, dzdt=None, pion=None, pele=None, dpidt=None, dpedt=None, eion=None, eele=None, cvion=None, cvele=None, deidn=None, deedn=None, ngroups=None, opac_bounds=None, rosseland=None, planck_absorb=None, planck_emiss=None, sele=None)¶

opacplot2.writeIonmixFile() provides an explicit and flexible way to write IONMIX files.

Parameters:

fn (str) – Name of the file to write.
zvals (tuple) – Atomic numbers of elements to write to file.
fracs (tuple) – Element fractions.
numdens (numpy.ndarray) – Number densities.
temps (numpy.ndarray) – Temperature array.
zbar=None (numpy.ndarray) – Average ionization. Only used for tabulated EoS in FLASH.
dzdt=None (numpy.ndarray) – Temperature derivative of average ionization. Ignored by FLASH.
pion=None (numpy.ndarray) – Ion pressure Only used for tabulated EoS in FLASH.
pele=None (numpy.ndarray) – Electron pressure. Only used for tabulated EoS in FLASH.
dpidt=None (numpy.ndarray) – Temperature derivative of ion pressure. Ignored by FLASH.
dpedt=None (numpy.ndarray) – Temperature derivative of electron pressure. Ignored by FLASH.
eion=None (numpy.ndarray) – Ion specific internal energy. Only used for tabulated EoS in FLASH.
eele=None (numpy.ndarray) – Electron specific internal energy. Only used for tabulated EoS in FLASH.
cvion=None (numpy.ndarray) – Ion heat capacity at constant volume. Ignored by FLASH.
cvele=None (numpy.ndarray) – Electron heat capacity at constant volume. Ignored by FLASH.
deidn=None (numpy.ndarray) – Number derivative of ion energy. Ignored by FLASH.
deedn=None (numpy.ndarray) – Number derivative of electron energy. Ignored by FLASH.
ngroups=None (int) – Number of energy groups.
opac_bounds=None (numpy.ndarray) – Energy group boundaries.
rosseland=None (numpy.ndarray) – Rosseland opacities. Only used for tabulated EoS in FLASH.
orb=None (planck_abs) – Planck absorption opacity. Only used for tabulated EoS in FLASH.
planck_emiss=None (numpy.ndarray) – Planck emission opacity. Only used for tabulated EoS in FLASH.
sele=None (numpy.ndarray) – Electron entropy.

Examples

Here we open an HDF5 file containing EoS and Opacity data and write it to an IONMIX file:

>>> import opacplot2 as opp
>>> op = opp.OpgHdf5.open_file('/path/to/infile.h5')
>>> opp.writeIonmixFile('outfile.cn4',
                op['Znum'], op['Xnum'],
                numDens=op['idens'][:], temps=op['temp'][:],
                ngroups=op.Ng,
                opac_bounds=op['groups'][:],
                planck_absorb=op['opp_mg'][:],
                rosseland=op['opr_mg'][:],
                planck_emiss=op['emp_mg'][:])

MULTI (.opp, .opr, .eps)¶

class opacplot2.OpgMulti(*cargs, **vargs)¶

Can be used either to parse or to write MULTIv5 tables.

OpgMulti is a subclass of dict. Through open_file(), it can read opacity data (only) from MULTI files. Then, the data can be accessed through the key:value pairs of the OpgMulti instance.

Examples

If we are in a directory with the files He_snp.eps.gz, He_snp.opp.gz, He_snp.opr.gz, and He_snp.opz.gz, then the following would read their data into an OpgMulti object:

>>> import opacplot2 as opp
>>> op = opp.OpgMulti.open_file('/path/to/current/dir', 'He_snp')

classmethod open_file(folder, base_name, verbose=True)¶

Parse MULTI format from a file.

Parameters:	str (folder) – Name of directory containing MULTI files. base_name (str) – Base name of MULTI files. verbose (bool) – Verbose option.
Returns:	Dictionary containing EoS and/or opacity data.
Return type:	OpgMulti

toEosDict(Znum=None, Anum=None, Xnum=None, log=None)¶: This method creates a dictionary with keys that are common among the various EoS table formats.

write(prefix, fmin=None, fmax=None)¶

Write multigroup opacities to files specified by a prefix.

Parameters:	prefix (str) – Prefix to append to files that are written. fmin (float) – Minimum value for opacities to write. fmax (float) – Maximum value for opacities to write.

Examples

After filling an instance of OpgMulti with EoS/opacity data, one could call:

>>> op_multi.write('multi_')

to write data files containing multigroup opacities specified by the ‘multi_’ prefix.

write2hdf(filename, Znum=None, Anum=None, Xnum=None)¶

Convert to HDF5 parameters.

Parameters:	filename (str) – Output filename. Znum (tuple) – Atomic numbers of elements. Anum (tuple) – Atomic masses of elements. Xnum (tuple) – Fractions of elements.

Examples

The atomic number and relative fractions must be given if they are not already parsed into an instance of OpgMulti. If they are not, write2hdf will raise a ValueError.

If we were in the same directory as the previous example, the following would write an HDF5 file with data from our MULTI files:

>>> import opacplot2 as opp
>>> op = opp.OpgMulti.open_file('/path/to/current/dir', 'He_snp')
>>> op.write2hdf('outfile.h5')

opacplot2.get_related_multi_tables(folder, base_name, verbose=False)¶

Get all related multi Tables defined by a folder and a base name.

Parameters:	folder (str) – Folder containing the tables. base_name (str) – Base name of the table. verbose (bool) – Flag for verbose option.

SESAME ASCII (.ses)¶

class opacplot2.OpgSesame(filename, precision, verbose=False)¶

This class is responsible for loading all SESAME formatted data files.

OpgSesame reads in a SESAME file. Each key:value pair of the data attribute corresponds to a table ID and its data from the file, respectively.

Parameters:	fn (str) – Name of file to open. precision (int) – `opacplot2.OpgSesame.SINGLE` for entry lengths of 15 or `opacplot2.OpgSesame.Double` for entry lengths of 22. verbose (bool) – Verbose option.

data¶

dict

Dictionary of material IDs included in the SESAME file.

Examples

The opacplot2.OpgSesame.data dictionary will hold the EoS data for the table referenced by table_id. For example, if we are in a directory with the file sesame.ses:

>>> import opacplot2 as opp
>>> op = opp.OpgSesame('sesame.ses', opp.OpgSesame.SINGLE)
>>> print(op.data.keys())
dict_keys([..., 13719]) # Table ID numbers; Aluminum.
>>> data = op.data[13719]
>>> print(sorted(data.keys()))
dict_keys(['abar',...,'zmax']) # Dictionary containing EoS data.

Note

There are only handling functions for 300 series entries in the SESAME tables.

Data Prefixes¶

From Los Alamos National Laboratory, each SESAME table has five different parts of their EoS tables:

Table # Data Type opacplot2 prefix

Table 301 TotalEOS(304+305+306) total_

Table 303 Ion EOS Plus Cold Curve (305 + 306) ioncc_

Table 304 Electron EOS ele_

Table 305 Ion EOS (Including Zero Point) ion_

Table 306 Cold Curve (No Zero Point) cc_

If we wanted to print out all of the EoS data for the electrons:

>>> import opacplot2 as opp
>>> op = opp.OpgSesame('sesame.ses', opp.OpgSesame.SINGLE)
>>> data = op.data[13719]
>>> for key in data.keys(): # Table ID for aluminum.
...     if 'cc_' == key[:3]:
...         print(key+':')
...         print(data[key])

Data Points¶

There are several top-level data points that are not included in a specific curve of the SESAME tables:

opacplot2 Abbr. Phys. Meaning

abar Mean Atomic Mass

bulkmod Bulk Modulus

excoef Exchange Coefficient

rho0 Normal Density

zmax Mean Atomic number

Furthermore, each table (301, ..., 305) prefixes these data points:

opacplot2 Abbr. Phys. Meaning

dens Density

eint Energy

ndens Number of Densities

ntemp Number of Temperatures

pres Pressures

temps Temperatures

From the example in the previous section, if we wanted to print out the density array of electrons, we would simply type:

>>> print(data['ele_dens'])
array([...]) # Electron density array.

PROPACEOS ASCII (.prp)¶

Warning

Handling for Propaceos EoS tables is not publicly distributed with opacplot2 and so its documentation will not be presented here.

HDF5¶

class opacplot2.OpgHdf5¶

force_eval()¶: Load the whole table into memory.

classmethod open_file(filename, explicit_load=False)¶

Open an HDF5 file containing opacity data.

Parameters:	filename (str) – Name of file to open. explicit_load (bool) – Option to load the whole file to memory.

Examples

To open a file:

>>> import opacplot2 as opp
>>> op = opp.OpgHdf5.open_file('infile.h5')
>>> print(op.keys())
dict_keys(['Anum', ..., 'Znum']) # OpgHdf5 is a dictionary.
>>> print(op['Zf_DT'])
array([...]) # Array for average ionization.

Notes

Loading the entire file into memory can be potentially dangerous. Use explicit_load with caution.

write2file(filename, **args)¶

Write to an HDF5 output file.

Parameters:	filename (str) – Name of output file. args (dict) – Dictionary of data to write.

Data Points¶

Depending on what kind of data has been written to an HDF5 file, each HDF5 file may vary widely. Despite this fact, listed below are the naming conventions opacplot2 uses for HDF5 data points that are relevant to IONMIX. The abbreviations are keys unless otherwise stated to be an attribute to the OpgHdf5 object.

opacplot2 Abbr Physical Meaning

Znum Atomic numbers

Xnum Element fractions

idens Number densities

temp Temperature array

Ng (attr) Number of energy groups

groups Energy group boundaries

opp_mg Planck absorption

opr_mg Rosseland opacities

emp_mg Planck emissivity

For example, if we wanted to open up an HDF5 file named input.h5 and write it to an IONMIX file named output.cn4, we could write:

>>> import opacplot2 as opp
>>> op = OpgHdf5.open_file('input.h5')
>>> opp.writeIonmixFile(outfile,
                 op['Znum'], op['Xnum'],
                 numDens=op['idens'][:], temps=op['temp'][:],
                 ngroups=op.Ng,
                 opac_bounds=op['groups'][:],
                 planck_absorb=op['opp_mg'][:],
                 rosseland=op['opr_mg'][:],
                 planck_emiss=op['emp_mg'][:])