Dependencies¶

opacplot2‘s dependencies include:

• numpy
• six
• tables
• matplotlib
• scipy
• periodictable
• hedp (https://github.com/luli/hedp)

They can be installed as follows:

pip install numpy six tables matplotlib scipy periodictable
pip install git+https://github.com/luli/hedp

Installation¶

This module requires Python 2.7 or 3.5. The latest version can be installed with:

pip install git+https://github.com/flash-center/opacplot2

If you have the Propaceos Python reader, in order to include it in the installation, you must install opacplot2 as follows:

git clone https://github.com/flash-center/opacplot2
cp /path/to/opg_propaceos.py opacplot2/opacplot2/
cd opacplot2
python setup.py install

Configuring Matplotlib for opac-error¶

The plotting capabilities of opacplot2 rely on the matplotlib python module. It can be installed with pip. It can also be installed with conda if you are using Anaconda Python. For information on how to install matplotlib, see their website.

backend: macosx

matplotlib.rcParams['backend'] = 'macosx'

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.

>>> 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])

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

PROPACEOS ASCII (.prp)¶

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.

>>> 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'][:])

opac-convert¶

Command line tool for converting EoS Table formats into the IONMIX format that comes with opacplot2.

Supported input file formats:

• Propaceos (not distributed, contact jtlaune at uchicago dot edu.)
• SESAME (.ses)
• MULTI (.opp, .opr, .opz, .eps)

The only supported output format is IONMIX.

opac-convert [options] myfile.ext

opac-convert --Znum 1, 6 --Xfracs .5, .5 myfile.ses

opac-convert --log emp_mg my-file.ext

ValueError: invalid literal for int() with base 10

opac-error¶

Command line tool for comparing two EoS table data. Unlike opac-convert, this tool will only compare equation of state data (not opacity). It is particularly useful in checking the consistency of opac-convert by comparing the original file with the converted IONMIX output. Supported input file formats:

• Propaceos (not distributed, contact jtlaune at uchicago dot edu.)
• SESAME (.ses)
• IONMIX

The output will consist of an error report with maximum absolute % error RMS % error. All % errors are calculated with respect to the first file listed. The user may also opt to create % error plots for the EoS data stored in the file (ion/electron pressure and energy and average ionization). These consist of three plots with resolutions of 10%, 1%, and .01%.

Interpolation¶

opacplot2.utils.interpDT(arr, dens, temps, bcdmin=0, bctmin=0, lookup=0)¶

Depending on the choice for lookup, this function returns an interpolation function for values in arr, the density derivative of arr, or the temperature derivative of arr.

What interpDT() returns is dependent upon the lookup and bcdmin/bctmin arguments:

INTERP_FUNC will return an interpolation function for any density/temperature point within the range.

INTERP_DFDD will return a function for the density derivative at any density/temperature point within the range.

INTERP_DFDT will return a function for the temperature derivative at any density/temperature point within the range.

BC_BOUND is the default setting. If an input density/temp is smaller than the minimum value in the dens (or temps) array, then it will automatically be set to this minimum value.

BC_EXTRAP_ZERO will insert zero points into the arr and either dens or temps for bcdmin, bctmin respectively.

Parameters:	arr (numpy.ndarray) – Data array. dens (numpy.ndarray) – Density array. temps (numpy.ndarray) – Temperature array. bcdmin (int) – Boundary conditions for density. bctmin (int) – Boundary conditions for temperature. lookup (int) – Type of function to return.

Examples

In order to find a function that interpolates between dens/temp points for an IONMIX file that we had previously opened as imx, we could use:

>>> import opacplot2 as opp
>>> f = opp.utils.interpDT(imx.pion, imx.dens, imx.temps,
...                        bcdmin=BC_EXTRAP_ZERO,
...                        bctmin=BC_EXTRAP_ZERO,
...                        lookup=INTERP_FUNC)
>>> print(f(0,0)) # We added points at zero.
0
>>> print(f(123, 456)) # Density of 123 and temperature of 456.
1234.5678 # Resulting ion pressure at this dens/temp.

opacplot2.utils.intersect_1D_sorted_arr(arr_1, arr_2)¶

Function to return the venn diagram of two sorted 1D arrays.

In other words, this function will return the union of all values from both arrays that are within the intersection of their ranges. This may be used for interpolation schemes.

Parameters:	arr_1 (numpy.ndarray) – 1D sorted array number 1. arr_2 (numpy.ndarray) – 1D sorted array number 2.
Returns:	An array that is the venn diagram of the two input arrays.
Return type:	numpy.ndarray

Examples

>>> import numpy as np
>>> import opacplot2 as opp
>>> a = np.array([1,2,3,4,5])
>>> b = np.array([3.5,4.5,5.5,6])
>>> c = opp.utils.intersect_1D_sorted_arr(a,b)
>>> print(c)
[3.5 4 4.5 5]

Grid Structure¶

class opacplot2.utils.EosMergeGrids(eos_data, filter_dens=<function <lambda>>, filter_temps=<function <lambda>>, intersect=['ele', 'ioncc'], thresh=[], qeos=False)¶

This class provides filtering capabilities for the EoS temperature and density grids.

For instance, SESAME tables may have some additional points in the ion EoS table, compared to the electron EoS table, and as FLASH requires the same density and temperature grid for all species, the simplest solution is to remove those extra points.

Parameters:	eos_data (dict) – Dictionary contraining the EoS data. intersect (list) – The resulting temperature [eV] and density [g/cm^(-3)] grids will be computed as an intersection of grids of all the species given in this list. Default: [‘ele’, ‘ioncc’] filter_dens (function) – A function that takes a grid of densities and returns a mask of points we don’t wont to keep. Defaut: (lamdba x: x>0.) i.e. don’t remove anything. filter_temps (function) – A function that takes a grid of temperatures and returns a mask of points we don’t wont to keep. Defaut: (lamdba x: x>0.) i.e. don’t remove anything. thresh (list) – Zero threshold on following keys
Returns:	out – A dictionary with the same keys as eos_data. The species specified by intersect will have equal temperature and density grids.
Return type:	dict

Examples

>>> eos_sesame = opp.OpgSesame("../sesame/xsesame_ascii",
                               opp.OpgSesame.SINGLE,verbose=False)
>>> eos_data  = eos_sesame.data[3720]  # Aluminum
>>> eos_data_filtered = EosMergeGrids(eos_data,
        intersect=['ele', 'ioncc'],   # Merge ele and ioncc grids
        filter_temps=lamda x: x>1.) # Remove temperatures below 1eV

Miscellaneous¶

opacplot2.utils.randomize_ionmix(filename, outfilename)¶

Randomizes the data from an existing ionmix file and rewrites it to the outfile.

Parameters:	filename (str) – Name of file to randomize. outfilename (str) – Name of output file.