CMFGEN
Database from John Hillier’s CMFGEN, a radiative transfer code designed to solve the radiative transfer and statistical equilibrium equations in spherical geometry.
Note:
In this example, the data was downloaded from the CMFGEN website and extracted to the /tmp/atomic folder.
Parsers
The CMFGEN parsers retrieves data from text files preserving its original form (no unit conversions) and stores it in DataFrames. Currently, just osc, col and pho files are supported.
Levels, Lines and Collisions
Energy levels and spectral lines are stored in the osc files, while collisions strengths are provided by the col files.
[1]:
from carsus.io.cmfgen import CMFGENEnergyLevelsParser, CMFGENOscillatorStrengthsParser, CMFGENCollisionalStrengthsParser
ChiantiPy version 0.15.0
found PyQt5 widgets
using PyQt5 widgets
[ py.warnings][WARNING] - /home/runner/micromamba/envs/carsus/lib/python3.12/site-packages/ChiantiPy/tools/data.py:72: UserWarning: klgfb files are not present:
it will not be possible to use the freeBound continuum method
warnings.warn('klgfb files are not present: \n it will not be possible to use the freeBound continuum method')
(warnings.py:112)
[2]:
si2_lvl = CMFGENEnergyLevelsParser('/tmp/atomic/SIL/II/16sep15/si2_osc_kurucz')
[3]:
si2_osc = CMFGENOscillatorStrengthsParser('/tmp/atomic/SIL/II/16sep15/si2_osc_kurucz')
[4]:
si2_col = CMFGENCollisionalStrengthsParser('/tmp/atomic/SIL/II/16sep15/si2_col')
Header information is stored in the header attribute and the DataFrame in the base attribute:
[5]:
si2_col.header
[5]:
{'Number of transitions': '406',
'Number of T values OMEGA tabulated at': '14',
'Scaling factor for OMEGA': '1.0',
'Value for OMEGA if f=0': '0.1'}
[6]:
si2_lvl.base
[6]:
| label | g | E(cm^-1) | 10^15 Hz | eV | Lam(A) | ID | ARAD | C4 | C6 | |
|---|---|---|---|---|---|---|---|---|---|---|
| 0 | 3s2_3p_2Po[1/2] | 2.0 | 0.00 | 3.95241 | 16.346 | 758.505847 | 1 | 0.000000e+00 | -5.290000e-17 | 7.470000e-33 |
| 1 | 3s2_3p_2Po[3/2] | 4.0 | 287.24 | 3.94380 | 16.310 | 760.162036 | 2 | 0.000000e+00 | -5.300000e-17 | 7.460000e-33 |
| 2 | 3s_3p2_4Pe[1/2] | 2.0 | 42824.29 | 2.66857 | 11.036 | 1123.420681 | 3 | 1.222000e+04 | -5.340000e-17 | 7.490000e-33 |
| 3 | 3s_3p2_4Pe[3/2] | 4.0 | 42932.62 | 2.66532 | 11.023 | 1124.789552 | 4 | 2.110000e+03 | -5.340000e-17 | 7.490000e-33 |
| 4 | 3s_3p2_4Pe[5/2] | 6.0 | 43107.91 | 2.66007 | 11.001 | 1127.011617 | 5 | 3.246000e+03 | -5.350000e-17 | 7.490000e-33 |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| 152 | 3s_3p(3Po)4p_4Pe[3/2] | 4.0 | 134079.00 | -0.06718 | -0.278 | -44625.724052 | 153 | 1.159000e+08 | -1.500000e-16 | 3.080000e-32 |
| 153 | 3s_3p(3Po)4p_4Pe[5/2] | 6.0 | 134213.63 | -0.07122 | -0.295 | -42096.577969 | 154 | 1.167000e+08 | -1.500000e-16 | 3.090000e-32 |
| 154 | 3s_3p(3Po)4p_4Se[3/2] | 4.0 | 134905.28 | -0.09195 | -0.380 | -32603.663348 | 155 | 9.275000e+07 | -9.750000e-17 | 2.770000e-32 |
| 155 | 3p3_2Do[5/2] | 6.0 | 135297.30 | -0.10370 | -0.429 | -28908.752414 | 156 | 2.437000e+09 | 4.200000e-17 | 1.450000e-32 |
| 156 | 3p3_2Do[3/2] | 4.0 | 135303.50 | -0.10389 | -0.430 | -28857.030727 | 157 | 2.438000e+09 | 1.390000e-17 | 1.460000e-32 |
157 rows × 10 columns
Photoionization Cross-sections
Photoionization cross-sections are provided by the pho files.
[7]:
from carsus.io.cmfgen import CMFGENPhoCrossSectionsParser
[8]:
si2_cross_sections = CMFGENPhoCrossSectionsParser('/tmp/atomic/SIL/II/16sep15/phot_nahar_A')
[9]:
si2_cross_sections.header
[9]:
{'Date': '05-Sep-2015 16:54:54',
'Number of energy levels': '93',
'Number of photoionization routes': '2',
'Screened nuclear charge': '2.0',
'Final state in ion': '3s2_1Se/3s21Se',
'Excitation energy of final state': '0.0',
'Statistical weight of ion': '1.0',
'Sigma used for Gaussian smoothing': '0.0D0',
'Cross-section unit': 'Megabarns',
'Split J levels': 'False',
'Total number of data pairs': '95107',
'Configuration name': '3s2_3p_2Po',
'Type of cross-section': '20',
'Number of cross-section points': '1487'}
In this case, base is a list containing many DataFrames. Also, each individual DataFrame contains information relative to that specific target under the attribute attr.
[10]:
type(si2_cross_sections.base)
[10]:
list
[11]:
len(si2_cross_sections.base)
[11]:
93
[12]:
si2_cross_sections.base[0]
[12]:
| energy | sigma | |
|---|---|---|
| 0 | 1.000000 | 1.414000 |
| 1 | 1.000333 | 1.405000 |
| 2 | 1.000666 | 1.397000 |
| 3 | 1.000999 | 1.388000 |
| 4 | 1.001332 | 1.379000 |
| ... | ... | ... |
| 1482 | 17.034180 | 0.001255 |
| 1483 | 18.825680 | 0.000929 |
| 1484 | 20.805590 | 0.000689 |
| 1485 | 22.993730 | 0.000510 |
| 1486 | 25.412010 | 0.000378 |
1487 rows × 2 columns
[13]:
si2_cross_sections.base[0].attrs
[13]:
{'Configuration name': '3s2_3p_2Po',
'Type of cross-section': 20,
'Number of cross-section points': 1487}
Batch Convert Files to HDF5
To convert multiple CMFGEN files to the HDF5 format import the hdf_dump function.
Note:
This feature has been temporary disabled.
Required parameters are cmfgen_dir, patterns and parser, while chunk_size and ignore_patterns are optional.
CMFGENReader
The CMFGENReader provides processed levels, lines, ionization_energies, cross_sections and collisions tables to work with. You can provide temperatures for the collisions dataframe using the temperature_grid option.
[14]:
from carsus.io.cmfgen import CMFGENReader
[15]:
cmfgen_reader = CMFGENReader.from_config('Si 0-1', '/tmp/atomic', ionization_energies=True, cross_sections=True, collisions=True, drop_mismatched_labels=True)
[ carsus.io.cmfgen.base][WARNING] - Selecting H 0 from CMFGEN (required to ingest cross-sections). (base.py:557)
[ carsus.io.cmfgen.base][ INFO] - Configuration schema found for H 0. (base.py:571)
[ carsus.io.cmfgen.base][ INFO] - Configuration schema found for Si 0. (base.py:571)
[ carsus.io.cmfgen.base][ INFO] - Configuration schema found for Si 1. (base.py:571)
[ carsus.io.cmfgen.base][ INFO] - Loading atomic data for H 0. (base.py:856)
[ carsus.io.cmfgen.base][ INFO] - Loading atomic data for Si 0. (base.py:856)
[ carsus.io.cmfgen.base][ INFO] - Loading atomic data for Si 1. (base.py:856)
[ carsus.io.cmfgen.base][ INFO] - Dropping collisional ionization data. (base.py:1054)
[ carsus.io.cmfgen.base][ INFO] - Dropping collisional ionization data. (base.py:1054)
[ carsus.io.cmfgen.base][ INFO] - Dropping collisional ionization data. (base.py:1054)
[ carsus.io.cmfgen.base][ INFO] - Dropping collisional ionization data. (base.py:1054)
[ carsus.io.cmfgen.base][ INFO] - Dropping collisional ionization data. (base.py:1054)
[ carsus.io.cmfgen.base][ INFO] - Dropping collisional ionization data. (base.py:1054)
[ carsus.io.cmfgen.base][ INFO] - Dropping collisional ionization data. (base.py:1054)
[ carsus.io.cmfgen.base][ INFO] - Dropping collisional ionization data. (base.py:1054)
[ carsus.io.cmfgen.base][ INFO] - Dropping collisional ionization data. (base.py:1054)
[ carsus.io.cmfgen.base][ INFO] - Dropping collisional ionization data. (base.py:1054)
[ carsus.io.cmfgen.base][ INFO] - Dropping collisional ionization data. (base.py:1054)
[ carsus.io.cmfgen.base][ INFO] - Dropping collisional ionization data. (base.py:1054)
[ carsus.io.cmfgen.base][ INFO] - Dropping collisional ionization data. (base.py:1054)
[ carsus.io.cmfgen.base][ INFO] - Dropping collisional ionization data. (base.py:1054)
[ carsus.io.cmfgen.base][ INFO] - Dropping collisional ionization data. (base.py:1054)
[ carsus.io.cmfgen.base][ INFO] - Dropping collisional ionization data. (base.py:1054)
[ carsus.io.cmfgen.base][ INFO] - Dropping collisional ionization data. (base.py:1054)
[ carsus.io.cmfgen.base][ INFO] - Dropping collisional ionization data. (base.py:1054)
[ carsus.io.cmfgen.base][ INFO] - Dropping collisional ionization data. (base.py:1054)
[ carsus.io.cmfgen.base][ INFO] - Dropping collisional ionization data. (base.py:1054)
[ carsus.io.cmfgen.base][ INFO] - Dropping collisional ionization data. (base.py:1054)
[ carsus.io.cmfgen.base][ INFO] - Dropping collisional ionization data. (base.py:1054)
[ carsus.io.cmfgen.base][ INFO] - Dropping collisional ionization data. (base.py:1054)
[ carsus.io.cmfgen.base][ INFO] - Dropping collisional ionization data. (base.py:1054)
[ carsus.io.cmfgen.base][ INFO] - Dropping collisional ionization data. (base.py:1054)
[ carsus.io.cmfgen.base][ INFO] - Dropping collisional ionization data. (base.py:1054)
[ carsus.io.cmfgen.base][ INFO] - Dropping collisional ionization data. (base.py:1054)
[ carsus.io.cmfgen.base][ INFO] - Dropping collisional ionization data. (base.py:1054)
[ carsus.io.cmfgen.base][ INFO] - Dropping collisional ionization data. (base.py:1054)
[ carsus.io.cmfgen.base][ INFO] - Dropping collisional ionization data. (base.py:1054)
[ carsus.io.cmfgen.base][ INFO] - Entries having label(s): 3s_3p3_5So, 3s2_3p2_3Pe will be dropped for ion: (np.int64(14), 0). (base.py:1059)
[ carsus.io.cmfgen.base][ INFO] - Filling in 1 values for ion (1, 0) that are outside the tabulated temperature range using the last tabulated value. (base.py:1119)
[ carsus.io.cmfgen.base][ INFO] - Filling in 7 values for ion (np.int64(14), 0) that are outside the tabulated temperature range using the last tabulated value. (base.py:1119)
[ carsus.io.cmfgen.base][ INFO] - Filling in 4 values for ion (np.int64(14), 1) that are outside the tabulated temperature range using the last tabulated value. (base.py:1119)
[16]:
cmfgen_reader.levels
[16]:
| energy | j | label | method | priority | |||
|---|---|---|---|---|---|---|---|
| atomic_number | ion_charge | level_index | |||||
| 1 | 0 | 0 | 0.000000 | 0.5 | 1___ | meas | 10 |
| 1 | 82259.096334 | 3.5 | 2___ | meas | 10 | ||
| 2 | 97492.300647 | 8.5 | 3___ | meas | 10 | ||
| 3 | 102823.892736 | 15.5 | 4___ | meas | 10 | ||
| 4 | 105291.651183 | 24.5 | 5___ | meas | 10 | ||
| ... | ... | ... | ... | ... | ... | ... | ... |
| 14 | 1 | 152 | 134079.000000 | 1.5 | 3s_3p(3Po)4p_4Pe[3/2] | meas | 10 |
| 153 | 134213.630000 | 2.5 | 3s_3p(3Po)4p_4Pe[5/2] | meas | 10 | ||
| 154 | 134905.280000 | 1.5 | 3s_3p(3Po)4p_4Se[3/2] | meas | 10 | ||
| 155 | 135297.300000 | 2.5 | 3p3_2Do[5/2] | meas | 10 | ||
| 156 | 135303.500000 | 1.5 | 3p3_2Do[3/2] | meas | 10 |
680 rows × 5 columns
[17]:
cmfgen_reader.lines
[17]:
| energy_lower | energy_upper | gf | j_lower | j_upper | wavelength | ||||
|---|---|---|---|---|---|---|---|---|---|
| atomic_number | ion_charge | level_index_lower | level_index_upper | ||||||
| 1 | 0 | 0 | 1 | 0.00 | 82259.096334 | 8.324000e-01 | 0.5 | 3.5 | 121.5670 |
| 2 | 0.00 | 97492.300647 | 1.582000e-01 | 0.5 | 8.5 | 102.5720 | |||
| 3 | 0.00 | 102823.892736 | 5.798000e-02 | 0.5 | 15.5 | 97.2540 | |||
| 4 | 0.00 | 105291.651183 | 2.788000e-02 | 0.5 | 24.5 | 94.9740 | |||
| 5 | 0.00 | 106632.159810 | 1.559800e-02 | 0.5 | 35.5 | 93.7800 | |||
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| 14 | 1 | 152 | 156 | 134079.00 | 135303.500000 | 1.300000e-05 | 1.5 | 1.5 | 8164.3728 |
| 153 | 155 | 134213.63 | 135297.300000 | 3.963000e-06 | 2.5 | 2.5 | 9225.3865 | ||
| 156 | 134213.63 | 135303.500000 | 2.477400e-07 | 2.5 | 1.5 | 9172.9055 | |||
| 154 | 155 | 134905.28 | 135297.300000 | 3.069200e-05 | 1.5 | 2.5 | 25500.0000 | ||
| 156 | 134905.28 | 135303.500000 | 2.697600e-06 | 1.5 | 1.5 | 25100.0000 |
26422 rows × 6 columns
[18]:
cmfgen_reader.cross_sections
[18]:
| energy | sigma | |||
|---|---|---|---|---|
| atomic_number | ion_charge | level_index | ||
| 1 | 0 | 0 | 0.999466 | 6.310022 |
| 0 | 1.015765 | 6.042398 | ||
| 0 | 1.032328 | 5.786125 | ||
| 0 | 1.049162 | 5.540721 | ||
| 0 | 1.066271 | 5.305726 | ||
| ... | ... | ... | ... | ... |
| 14 | 1 | 154 | -263.073454 | 0.000000 |
| 155 | -0.031522 | 0.000000 | ||
| 155 | -3.152219 | 0.000000 | ||
| 156 | -0.031579 | 0.000000 | ||
| 156 | -3.157868 | 0.000000 |
385466 rows × 2 columns
[19]:
cmfgen_reader.ionization_energies
[19]:
atomic_number ion_charge
1 0 13.598434
14 0 8.151683
1 16.345846
Name: ionization_energy, dtype: float64
The values in the collisions dataframe are thermally-averaged effective collision strengths divided by the statistical weights of the lower levels. Please see Eq. A1 and A2 of [PrzybillaButler04] for definitions. More information about the collisions table is stored inside the collisional_metadata attribute.
[20]:
cmfgen_reader.collisions
[20]:
| 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | ... | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| atomic_number | ion_charge | level_index_lower | level_index_upper | |||||||||||||||||||||
| 1 | 0 | 0 | 1 | 0.331250 | 0.331250 | 0.331250 | 0.331250 | 0.331250 | 0.342092 | 0.372950 | 0.393113 | 0.417929 | 0.450500 | ... | 0.531217 | 0.589667 | 0.659250 | 0.701471 | 0.820400 | 0.820400 | 0.820400 | 0.820400 | 0.820400 | 0.820400 |
| 2 | 0.096550 | 0.096550 | 0.096550 | 0.096550 | 0.096550 | 0.096992 | 0.098250 | 0.100395 | 0.103035 | 0.106500 | ... | 0.125060 | 0.138500 | 0.154500 | 0.164377 | 0.192200 | 0.192200 | 0.192200 | 0.192200 | 0.192200 | 0.192200 | |||
| 3 | 0.008550 | 0.008550 | 0.008550 | 0.008550 | 0.008550 | 0.009850 | 0.013550 | 0.015903 | 0.018799 | 0.022600 | ... | 0.031010 | 0.037100 | 0.044350 | 0.047992 | 0.058250 | 0.058250 | 0.058250 | 0.058250 | 0.058250 | 0.058250 | |||
| 4 | 0.011700 | 0.011700 | 0.011700 | 0.011700 | 0.011700 | 0.012090 | 0.013200 | 0.013980 | 0.014940 | 0.016200 | ... | 0.019583 | 0.022033 | 0.024950 | 0.026535 | 0.031000 | 0.031000 | 0.031000 | 0.031000 | 0.031000 | 0.031000 | |||
| 5 | 0.006550 | 0.006550 | 0.006550 | 0.006550 | 0.006550 | 0.006771 | 0.007400 | 0.007829 | 0.008357 | 0.009050 | ... | 0.010964 | 0.012350 | 0.014000 | 0.014891 | 0.017400 | 0.017400 | 0.017400 | 0.017400 | 0.017400 | 0.017400 | |||
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| 14 | 1 | 25 | 29 | 39.000000 | 39.000000 | 39.000000 | 43.500000 | 46.652174 | 50.750000 | 61.750000 | 68.750000 | 76.000000 | 83.250000 | ... | 97.000000 | 102.500000 | 105.638528 | 109.750000 | 110.750000 | 105.500000 | 100.794276 | 95.000000 | 95.000000 | 95.000000 |
| 30 | 13.950000 | 13.950000 | 13.950000 | 15.300000 | 16.180435 | 17.325000 | 20.175000 | 21.925000 | 23.775000 | 25.750000 | ... | 29.250000 | 30.500000 | 31.257576 | 32.250000 | 32.500000 | 31.000000 | 29.543467 | 27.750000 | 27.750000 | 27.750000 | |||
| 26 | 29 | 3.550000 | 3.550000 | 3.550000 | 3.866667 | 4.011594 | 4.200000 | 4.600000 | 4.816667 | 5.050000 | 5.283333 | ... | 5.716667 | 5.883333 | 5.962698 | 6.066667 | 6.016667 | 5.700000 | 5.460979 | 5.166667 | 5.166667 | 5.166667 | ||
| 30 | 44.833333 | 44.833333 | 44.833333 | 51.333333 | 55.681159 | 61.333333 | 75.666667 | 84.333333 | 93.666667 | 103.000000 | ... | 120.500000 | 127.666667 | 131.707071 | 137.000000 | 138.666667 | 132.333333 | 126.432505 | 119.166667 | 119.166667 | 119.166667 | |||
| 29 | 30 | 17.900000 | 17.900000 | 17.900000 | 19.350000 | 20.241304 | 21.400000 | 24.250000 | 26.100000 | 28.150000 | 30.400000 | ... | 35.250000 | 37.700000 | 39.583117 | 42.050000 | 44.950000 | 45.500000 | 44.626080 | 43.550000 | 43.550000 | 43.550000 |
849 rows × 21 columns
[21]:
cmfgen_reader.collisional_metadata
[21]:
temperatures [100, 2000, 2500, 4000, 5000, 6300, 10000, 126...
dataset [cmfgen]
info The dataframe values are thermally-averaged ef...
dtype: object