Zenodo package for Y. Wang et al. 2025, A&A --- Warm absorber outflows in radio-loud active galactic nucleus 3C 59

Readme document Yijun Wang Nanjing University, China Homepage: https://yijunyuxuan.github.io/WangYijun.github.io/ Email: w[email protected] Contents 1 Top-level Directory Structure 2 2 XMM-Newton Spectrum and Response File 2 3 Spectral fitting with SPEX (v3.08) 2 3.1 Producing the best-fit results of Table 1 in the paper ............. 2 3.2 Producing the best-fit results of Table A1 in the paper ............ 3 3.3 Other spectral fitting results ........................... 3 4 Python codes to Produce Figures in the Paper 4 4.1 Fig. 1 ....................................... 4 4.2 Fig. 2 ....................................... 5 4.3 Fig. 3 ....................................... 5 4.4 Fig. 4 ....................................... 5 4.5 Fig. 5 ....................................... 6 4.6 Fig. 6 ....................................... 6 4.7 Fig. B1 ...................................... 7 4.8 Fig. B2 ...................................... 7 4.9 Fig. D1 ...................................... 8 4.10 Compare with M19 SED model ......................... 8 1 1 Top-level Directory Structure Table 1: Top-level directory structure of the downloaded folder “./scripts/” File or folder Description or contents ./scripts/readme.pdf This document ./scripts/data/ XMM-Newton spectrum and response file, LAMOST spectrum ./scripts/spectral fitting spex/ SPEX fitting scripts and the best-fit results ./scripts/Figure/ Python codes to produce the figures in the paper 2 XMM-Newton Spectrum and Response File Files in the folder “./scripts/data/” are introduced as follows: •PN.spo: EPIC-pn spectrum of the observation with ID=0205390201 •PN.res: EPIC-pn response matrix of the observation with ID=0205390201 •RGS.spo: combined spectrum of RGS1 and RGS2 of the observation with ID=0205390201 •RGS.res: combined RGS response matrix of the observation with ID=0205390201 •spec-57400-HD021125N313135B01 sp02-107.fits: LAMOST spectrum 3 Spectral fitting with SPEX (v3.08) Detailed spectral analysis processes are shown in the folder “./scripts/spectral fitting spex/”. 3.1 Producing the best-fit results of Table 1 in the paper •Check the required documents in the folder “./scripts/spectral fitting spex/Table1/”: pstep1 data preparation Table1.com pstep2 set up models Table1.com pstep3 import best fit results Table1.com pbest fit parameters Table1.com pbest fit results Table1.out 2 •Run the following SPEX commands in a linux terminal window: user@linux: > cd ./scripts/spectral fitting spex/Table1/ user@linux: > spex SPEX> log exe step1 data preparation Table1 SPEX> log exe step2 set up models Table1 SPEX> log exe step3 import best fit results Table1 SPEX> fit # fit the spectrum SPEX> par show # show the fitting results The output fitting results are also shown in the file “best fit results Table1.out”. 3.2 Producing the best-fit results of Table A1 in the paper •Check the required documents in the folder “./scripts/spectral fitting spex/TableA1/”: pstep1 data preparation TableA1.com pstep2 set up models TableA1.com pstep3 import best fit results TableA1.com pbest fit parameters TableA1.com pbest fit results TableA1.out •Run the following SPEX commands in a linux terminal window: user@linux: > cd ./scripts/spectral fitting spex/TableA1/ user@linux: > spex SPEX> log exe step1 data preparation TableA1 SPEX> log exe step2 set up models TableA1 SPEX> log exe step3 import best fit results TableA1 SPEX> fit # fit the spectrum SPEX> par show # show the fitting results The output fitting results are also shown in the file “best fit results TableA1.out”. 3.3 Other spectral fitting results •Check the required documents in the folder “./scripts/spectral fitting spex/others/”: pbest fit continuum.com pbest fit continuum and one WA.com 3 •Run the following SPEX commands to get the best-fit results without warm absorbers: user@linux: > cd ./scripts/spectral fitting spex/others/ user@linux: > spex SPEX> log exe ../Table1/step1 data preparation Table1 SPEX> log exe ../Table1/step2 set up models Table1 SPEX> log exe best fit continuum SPEX> calculate SPEX> fit # fit the spectrum SPEX> par show # show the fitting results •Run the following SPEX commands to get the best-fit results with only one warm absorber: user@linux: > cd ./scripts/spectral fitting spex/others/ user@linux: > spex SPEX> log exe ../Table1/step1 data preparation Table1 SPEX> log exe ../Table1/step2 set up models Table1 SPEX> log exe best fit continuum and one WA SPEX> calculate SPEX> fit # fit the spectrum SPEX> par show # show the fitting results 4 Python codes to Produce Figures in the Paper Python codes to produce figures in the paper are shown in the folder “./scripts/Figure/”. 4.1 Fig. 1 •Check the required documents in the folder “./scripts/Figure/Fig1/”: pproduce data and model.sh pdata and model.py •Run the following commands in a linux terminal window: user@linux: > cd ./scripts/Figure/Fig1/ user@linux: > sh produce data and model.sh # produce three files: model final.qdp, pn data final.qdp, and RGS data final.qdp user@linux: > python data and model.py # produce Figure1.png 4 4.2 Fig. 2 •Check the required documents in the folder “./scripts/Figure/Fig2/”: pcontinuum model output.sh pcontinuum model.py •Run the following commands in a linux terminal window: user@linux: > cd ./scripts/Figure/Fig2/ user@linux: > sh continuum model output.sh # produce four files: model pow.txt, model comt.txt, model dbb.txt, and model refl.txt user@linux: > python continuum model.py # produce Figure2.png 4.3 Fig. 3 •Check the required documents in the folder “./scripts/Figure/Fig3/”: pRGS spectra with absorption lines.sh pWA absorption line fine.py •Run the following commands in a linux terminal window: user@linux: > cd ./scripts/Figure/Fig3/ user@linux: > sh RGS spectra with absorption lines.sh # produce four files: data rgs absorption.qdp, comp17 WA1 absorb lines.asc, comp18 WA2 absorb lines.asc, and model rgs absorption.qdp user@linux: > python WA absorption line fine.py # produce Figure3.png 4.4 Fig. 4 •Check the required documents in the folder “./scripts/Figure/Fig4/”: presidual all output.sh presidual all output plot.py •Run the following commands in a linux terminal window: user@linux: > cd ./scripts/Figure/Fig4/ user@linux: > sh residual all output.sh # produce six files: residual pn continuum.txt, residual pn 1pion.txt, residual pn 2pion.txt, residual rgs continuum.txt, residual rgs 1pion.txt, and residual rgs 2pion.txt user@linux: > python residual all output plot.py # produce Figure4.png 5 4.5 Fig. 5 •Check the required documents in the folder “./scripts/Figure/Fig5/”: pdistance WA.py •Run the following commands in a linux terminal window: user@linux: > cd ./scripts/Figure/Fig5/ user@linux: > python distance WA.py # produce Figure5.png 4.6 Fig. 6 •Check the required documents in the folder “./scripts/Figure/Fig6/”: pionization vs velocity.py pTest1 fitting process.com pTest1 model.com pTest1 best fit results.com pTest2 fitting process.com pTest2 model.com pTest2 best fit results.com •Run the following commands in a linux terminal window to check the best-fit results for Test1 and Test2: user@linux: > cd ./scripts/Figure/Fig6/ user@linux: > spex SPEX> log exe Test1 fitting process # the best-fit results of Test1 SPEX> quit user@linux: > spex SPEX> log exe Test2 fitting process # the best-fit results of Test2 SPEX> quit •Run the following commands in a linux terminal window: user@linux: > cd ./scripts/Figure/Fig6/ user@linux: > python ionization vs velocity.py # produce Figure6.png 6 4.7 Fig. B1 •Check the required documents in the folder “./scripts/Figure/FigB1/”: pcontours.py ppar 17 zv 17 nh step.stp ppar 17 zv 17 xil step.stp ppar 17 zv 17 v step.stp ppar 18 zv 18 nh step.stp ppar 18 zv 18 xil step.stp ppar 18 zv 18 v step.stp •Run the following commands in a linux terminal window: user@linux: > cd ./scripts/Figure/FigB1/ user@linux: > python contours.py # produce FigureB1.png 4.8 Fig. B2 •Check the required documents in the folder “./scripts/Figure/FigB2/”: pplot velocity flux.py pcomp17 WA1 absorb lines velocity flux 130NeX.qdp pcomp17 WA1 absorb lines velocity flux 123FeXVIII.qdp pcomp17 WA1 absorb lines velocity flux 115OVIII.qdp pcomp18 WA2 absorb lines velocity flux 111NeVIII.qdp pcomp18 WA2 absorb lines velocity flux 134FeX.qdp pcomp18 WA2 absorb lines velocity flux 150FeIX.qdp pcomp17 WA1 absorb lines velocity flux model 130NeX.qdp pcomp17 WA1 absorb lines velocity flux model 123FeXVIII.qdp pcomp17 WA1 absorb lines velocity flux model 115OVIII.qdp pcomp18 WA2 absorb lines velocity flux model 111NeVIII.qdp pcomp18 WA2 absorb lines velocity flux model 134FeX.qdp pcomp18 WA2 absorb lines velocity flux model 150FeIX.qdp •Run the following commands in a linux terminal window: user@linux: > cd ./scripts/Figure/FigB2/ user@linux: > python plot velocity flux.py # produce FigureB2.png 7 4.9 Fig. D1 •Check the required documents in the folder “./scripts/Figure/FigD1/”: pLAMOST spectrum.py •Run the following commands in a linux terminal window: user@linux: > cd ./scripts/Figure/FigD1/ user@linux: > python LAMOST spectrum.py # produce FigureD1.png 4.10 Compare with M19 SED model •Check the required documents in the folder “./scripts/Figure/Compare with M19 SED model/”: pcompare RGS data with M19 SED.py ppreprocessed RGS spectra from XMM website.txt pproduce files.sh pM19 SED model.com •Run the following commands in a linux terminal window: user@linux: > cd ./scripts/Figure/Compare with M19 SED model/ user@linux: > sh produce files.sh # produce two files: RGS data.qdp and M19 SED model.qdp user@linux: > python compare RGS data with M19 SED.py # produce compare RGS data with M19 SED.png 8