This project is closed

we have been combined this project with project spectra

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AtomicQuery

This is an experimental package for the sake of hashing atomic data by (configuration, term, J) level information instead of (idxI, idxJ), so that an Atom object is able to be created by given the information of necessary levels without editing the data file.

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Available Atomic model

Atom & ionization stage	Available Terms	nLevel	Ref : Level & Aji	Ref: electron impact ECS	Ref: proton impact ECS
C III	"1s2.2s2 1S" - "1s2.2p2 1S"	10	NIST	Berrington et al. 1985	not yet
O V	"1s2.2s2 1S" - "1s2.2p2 1S"	10	NIST	Berrington et al. 1985	not yet
Si III (not yet)	"1s2.2s2.2p6.3s2 1S"- "1s2.2s2.2p6.3d.4d 1S"	141	Kanti 2017	Kanti 2017	not yet

Formatting files in database

For instance, we need the information of C^{2+}.

1. Copy Level information and Einstein Aji coefficient from NIST database {: Developer}

Level :

1. open https://physics.nist.gov/PhysRefData/ASD/levels_form.html
2. modified the corresponding parameters in red rectangular shown in Fig 1.
3. The query format looks like Fig 2.
4. copy the whole text to ./atom/NIST_ASCII/C_III/C_III.NistLevel

Fig 1.

Fig 2.

Einstein Aji :

1. open https://physics.nist.gov/PhysRefData/ASD/lines_form.html
2. modified the corresponding parameters in red rectangular shown in Fig 3.
3. The query format looks like Fig 4.
4. copy the whole text to ./atom/NIST_ASCII/C_III/C_III.NistLine

Fig 3.

Fig 4.

2. Format Level data (Config) {: Developer}

in this case, information such as Aji is taken from NIST.

1. check whether we need a _prefix for the inner shell configuration.

for example, in Fig 2., the ground level configuration is '2s2' instead of the full configuration '1s2.2s2', then we need to specify _prefix="1s2."

2. modify the parameter in ./tools/prepare_level_from_nist.py and then execute it. This will output a prototype config file called ./atom/config/C_III.Level looks like Fig 5.
3. modify stage column and add general information into ./atom/config/C_III.Level (Fig 6.). Lines start with '#' is comment line.

Fig 5.

Fig 6.

3. Format Aji and Wavelength data (Database) {: Developer}

in this case, information such as Aji is taken from NIST.

1. check whether we need a _prefix for the inner shell configuration.

for example, in Fig 2., the ground level configuration is '2s2' instead of the full configuration '1s2.2s2', then we need to specify _prefix="1s2."

2. modify the parameter in ./tools/prepare_Aji_from_nist.py and then execute it. This will output a prototype config file called ./atom/C_III/Einstein_A/Nist.Aji looks like Fig 7.
3. add more general information into ./atom/config/C_III.Level as comment line such as "reference" and so on.

Fig 7.

4. Format Effective Collision Strength data for Collisional Excitation (database) {: Developer}

Since for different atom with different ionization stage the data comes from different paper/database/website, there is no definite script to format ECS (Effective Collision Strength) data.

However, like Aji, Effective Collision Strength table should also follow (configuration, term, J) indexing (ctj indexing), like Fig 8.

Fig 8.

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5. Construct Atom() instances (User interface) {: User}

An `AtomCls.Atom()`` instance can be constructed by

import sys
sys.path.append("..")

from src.Structure import AtomCls
file = "../atom/config/C_III.Level"
file_Aji = "../atom/C_III/Einstein_A/Nist.Aji"                                    # optional
file_CEe = "../atom/C_III/Collisional_Excitation/Berrington_et_al_1985.Electron"  # optional
atom = AtomCls.Atom(file, _file_Aji=file_Aji, _file_CEe=file_CEe)

furthermore, Aji and CE data could be read without resetting *.Level config file, like

atom.read_Aji(_file_Aji=file_Aji)
atom.read_CE(_file_CEe=file_CEe)

the available properties of this Class contains

atom.Title, atom.Z, atom.Element, atom.nLevel, atom.nLine, atom.Level, atom.Level_info, atom.Level_info_table, atom.Line_idx_table, atom.Line_ctj_table, atom.Line, atom.CE_Te_table, atom.CE_table, atom.CE_coe, atom.CE_type

6. Generate Grotrian diagram {: User}

Grotrian.Grotrian() to generate Grotrian diagram given a AtomCls.Atom() instance.

import sys
sys.path.append("..")

from src.Structure import AtomCls
from src.Visual import Grotrian

# construct AtomCls.Atom() instance
file = "../atom/config/C_III.Level"
file_Aji = "../atom/C_III/Einstein_A/Nist.Aji"
file_CEe = "../atom/C_III/Collisional_Excitation/Berrington_et_al_1985.Electron"
atom = AtomCls.Atom(file, _file_Aji=file_Aji, _file_CEe=file_CEe)

# construct Grotrian.Grotrian() instance
# _conf_prefix is the configuration prefix that you do not want to plot in grotrian diagram
gro = Grotrian.Grotrian(_atom=atom, _conf_prefix="1s2.")
gro.make_fig(_figsize=(10,6))

# this list defines the transition line you want to plot with between levels.
line_plot = (
    (0, 4, "977", 0.3, 0.5),
    (0, 2, "1909", 0.7, 0.1),
    (4, 9, "1247", 0.3, 0.5),
    (4, 8, "2297", 0.8, 0.5),
    (2, 5, "1175.99", 0.1, 0.1),
    (1, 6, "1175.26", 0.25, 0.25),
    (2, 6, "1175.59", 0.40, 0.40),
    (3, 6, "1176.38", 0.55, 0.55),
    (2, 7, "1174.93", 0.70, 0.70),
    (3, 7, "1175.71", 0.85, 0.85),
)
# plot the transition line listed above
for i, j, wl, _r1, _r2 in line_plot:
    _cfj1 = atom.Level_info_table[i]
    _cfj2 = atom.Level_info_table[j]
    gro.connect_line(_cfj1=_cfj1, _cfj2=_cfj2, _r1=_r1, _r2=_r2, _c="black", _text=wl, _tsize=7, _r=0.4)

gro.show_fig()
# if you want to save the figure
gro.save_fig("../fig/grotrian/" + file.split('/')[-1].replace(".Level",".png"))

the above code will generate the grotrian diagram following the C_III.Level configuration (Fig 9.).

Fig 9.

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Notes

for proton impact collision excitation

• chianti database provides fitting parameters of proton excitation Rate Coefficient and electron excitation Effective Collisional Strength. All of the proton transitions are forbidden transitions taking place between levels within the same configuration (fine structure).

• Copeland et al. 1997 listed a table of references for Be-like to Cl-like ions for elements from C to Ni. Also fine_structure excitation only.