Add example ii.json processing script

## Inventory Interface File

This work has developed a new inventory interface (`ii`) file format for exchanging nuclide inventory data with the MELCOR team. It is a heirarchical description of the inventory in one or more zones, at one or more time points. Currently the `ii` (pronounced aye-aye) data is emitted in standard [JSON](https://www.json.org/json-en.html) format so that one can read the files outside of SCALE. We currently use `ii.json` as the extension for these files. In the future we may provide an [HDF5](https://www.hdfgroup.org/solutions/hdf5/) version as well to save disk space--these would have the extension `.ii.h5`. We made the decision to package relevant nuclear data with the inventory in the `ii` format because typically downstream operations would like to calculate decay heat, mass, activity, and other derived quantities from the number of atoms/moles of each nuclide. Instead of providing number of moles, grams, and activity for each nuclide, we provide the molar mass (grams/mol) and decay constant (1/s) for each nuclide. Including nuclear data also aids us in nuclear data uncertainty studies where we would generate hundreds of `ii.json` files for each realization of the nuclear data. Each one of these realizations is the initial condition for a MELCOR severe accident analysis realization. Although the variation of the inventory in moles has the implicit effect of variations in nuclear data, the direct effect on decay heat and activity requires the perturbed recoverable energy from decay values and the decay constants. Additional details on the format are provided in this copy of the SCALE Quality Assurance (QA) case for this feature: [SCL-2020-003](supplemental/scl-2020-003_inventory-interface.md).

## Example of Processing the Inventory Interface File

An example script `supplemental/example_out.py` shows how to process the `ii.json`

file. It takes the file name and the label for the response. The `case(0)` 

response corresponds to a core total inventory.

```

python3 supplemental/example_out.py INL-A/full_core/depletion/INL-A_core_t6-depl_ce_v7.1.ii.json 'case(0)'

```

The screen output should be:

```

available responses for file INL-A/full_core/depletion/INL-A_core_t6-depl_ce_v7.1.ii.json : case(-1) case(-2) case(0) case(100) case(101) case(102) case(103) case(104) case(105) case(106) case(107) case(108) case(109) case(110) case(111) case(112) case(113) case(114) case(115) case(116) case(117) case(118) case(119) case(120) case(121) case(122) case(123) case(124) case(125) case(126) case(127) case(128) case(129) case(130) case(131) case(132) case(133) case(134) case(135) case(136) case(137) case(138) case(139) case(140) case(141) case(142) case(143) case(144) case(145) case(146) case(147) case(148) case(149) case(150) case(151) case(152) case(153) case(154) case(155) case(156) case(157) case(158) case(159) case(160) case(161) case(162) case(163) case(164) case(165) case(166) case(167) case(168) case(169) case(170) case(171) case(172) case(173) case(174) case(175) case(176) case(177) case(178) case(179) case(180) case(61) case(62) case(71) case(72) case(73) case(74) case(75) case(76) case(81) case(82) case(83) case(84) case(85) case(86) case(87) case(88) case(89) case(90) case(91) case(92) case(93) case(94) case(95) case(96) case(97) case(98) case(99)

   found response case(0) !

   found time list [0.0, 259200.0, 13365490.0, 26471780.0, 39578068.0, 52684360.0, 65790648.0, 78896936.0, 92046424.0, 105195920.0, 118345408.0, 131494896.0, 144644384.0, 157793872.0] in SECONDS !

SYSTEM MASS

     time(s)      mass(g)

 0.00000e+00  2.99799e+06

 2.59200e+05  2.99799e+06

 1.33655e+07  2.99799e+06

 2.64718e+07  2.99799e+06

 3.95781e+07  2.99799e+06

 5.26844e+07  2.99799e+06

 6.57906e+07  2.99799e+06

 7.88969e+07  2.99799e+06

 9.20464e+07  2.99799e+06

 1.05196e+08  2.99799e+06

 1.18345e+08  2.99799e+06

 1.31495e+08  2.99799e+06

 1.44644e+08  2.99799e+06

 1.57794e+08  2.99799e+06

TARGET NUCLIDE Cs137

     time(s)      mass(g) activity(Ci)

 0.00000e+00  1.00450e-14  1.37523e-12

 2.59200e+05  9.02606e-04  1.23573e-01

 1.33655e+07  4.63803e-02  6.34979e+00

 2.64718e+07  9.14244e-02  1.25166e+01

 3.95781e+07  1.36039e-01  1.86247e+01

 5.26844e+07  1.80228e-01  2.46746e+01

 6.57906e+07  2.23996e-01  3.06667e+01

 7.88969e+07  2.67347e-01  3.66017e+01

 9.20464e+07  3.10425e-01  4.24993e+01

 1.05196e+08  3.53090e-01  4.83405e+01

 1.18345e+08  3.95348e-01  5.41259e+01

 1.31495e+08  4.37201e-01  5.98559e+01

 1.44644e+08  4.78653e-01  6.55310e+01

 1.57794e+08  5.19709e-01  7.11519e+01

 ```

The script can be modified to iterate through nuclides and output any desired

quantity.

#import matplotlib.pyplot as plt

import numpy as np

import json

import sys    

import pprint as pp

import os

def canonical_name(izzzaaa,elem):

    a = izzzaaa % 1000

    name = elem+str(a)

    i = izzzaaa // 1000000

    if( i>0 ):

        name+='m'+str(i)

    return name

def read_data_set(file, name):

    # Load JSON file and data set name

    with open(file) as json_file:

        x = json.load(json_file)

    # Pull out data and response definitions first

    nucdb = x['data'].pop('nuclides')

    defines = x['responses'].pop('definitions')

    # Then print available data sets

    print('available responses for file',file,':',*x['responses'])

    # Then extract this response data set

    resp = x['responses'][name]

    vecdef_name = resp['nuclideVector']

    vecdef = defines['nuclideVectors'][vecdef_name]

    print('   found response',name,'!')

    # Initialize dictionary for processed data

    data=dict()

    data['name']=os.path.basename(file)+':'+name

    times = resp['timeList']['list']

    units = resp['timeList']['units']  

    data['seconds']=times

    data['elements']=[]

    data['nuclides']=[]

    print('   found time list',times,'in',units,'!')

    # Store the mass here

    data['grams']=[0] * len(times)

    for inuc in range(0,len(vecdef)):

        id=vecdef[inuc]

        nucdata=nucdb[id]

        # Add unit conversions to nucdata

        na = 6.022e23; #atoms/mole

        lam = nucdata['decayConstant'] #1/seconds

        q = nucdata['decayEnergy'] #Joules/decay

        ci_per_bq = 3.7e10; #Curies/Becquerel

        nucdata['moles_to_watts']=na*lam*q;

        nucdata['moles_to_curies']=lam*na/ci_per_bq;

        nucdata['moles_to_grams']=nucdata['mass'];

        izzzaaa=nucdata['IZZZAAA']

        elem=nucdata['element']  

        name=canonical_name(izzzaaa,elem)

        data['elements'].append(elem)

        data['nuclides'].append(name)

        data[name]=dict()

        data[name]['data']=nucdata

        data[name]['moles']=[0] * len(times)

        for itime in range(0,len(times)):

            amount=resp['amountList'][itime][inuc]

            data[name]['moles'][itime]=amount

            data['grams'][itime] += nucdata['moles_to_grams']*amount

    # Uniquify

    data['elements']=list(set(data['elements']))

    data['nuclides']=list(set(data['nuclides']))

    return data

d = read_data_set(sys.argv[1],sys.argv[2])

# print the whole data structure

# pp.pprint(d)

print('\nSYSTEM MASS\n{:>12s} {:>12s}'.format('time(s)','mass(g)'))

for t,m in zip(d['seconds'],d['grams']):

    print('{:12.5e} {:12.5e}'.format(t,m))

target='Cs137'

print('\nTARGET NUCLIDE {:12s}\n{:>12s} {:>12s} {:>12s}'.format(target,'time(s)','mass(g)','activity(Ci)'))

times=d['seconds']

nucdata = d[target]['data']

for itime in range(0,len(times)):

    moles = d[target]['moles'][itime]

    print('{:12.5e} {:12.5e} {:12.5e}'.format(times[itime],moles,moles*nucdata['moles_to_grams'],moles*nucdata['moles_to_curies']))