European Organisation for Astronomical Research in the Southern Hemisphere Programme: GEN Project/WP: Science Operation Software Department MOLECFIT Pipeline User Manual Document Number: VLT-MAN-ESO-19550-5772 Document Version: 4.1 Document Type: Manual (MAN) Released on: 2021-02-8 Document Classification: Public Prepared by: MOLECFIT Pipeline Team Validated by: Approved by: Name Doc. Number: VLT-MAN-ESO- MOLECFIT Pipeline User Manual 19550-5772 Doc. Version: 4.1 Released on: 2021-02-8 Page: 2 of 119 ESO – Karl-Schwarzschild-Str. 2 – 85748 Garching bei München – Germany www.eso.org Doc. Number: VLT-MAN-ESO- MOLECFIT Pipeline User Manual 19550-5772 Doc. Version: 4.1 Released on: 2021-02-8 Page: 3 of 119 Authors Name Affiliation Nuwanthika Fernando AAO Software Pipelines Team Nuria P. F. Lorente Macquarie University & The Australian National University Michael N. Birchall 105 Delhi Rd, North Ryde, NSW 2113 Brent Miszalski Australia Alain Smette European Southern Observatory, ESO Headquarters Andrea Mehner Karl-Schwarzschild-Str. 2, 85748 Garching bei München Sabine Möhler Germany Gurvan Bazin Jose A. Escartín Stefan Noll Austrian ESO In-Kind Team, Innsbruck Wolfgang Kausch Institute for Astro- and Particle Physics, University of Innsbruck Marco Barden Technikerstr. 25/8, A-6020 Innsbruck Cezary Szyszka Austria Amy M. Jones Stefan Kimeswenger Doc. Number: VLT-MAN-ESO- MOLECFIT Pipeline User Manual 19550-5772 Doc. Version: 4.1 Released on: 2021-02-8 Page: 4 of 119 Change Record Version Date Affected Section Remarks 4.1 08/02/2021 All Major revision of the code (v4.0) 4.0 20/05/2020 All Major revision of the code (v3.0) and overhaul of manual 3.11 31/10/2018 Sect. 4.9 Known issues 3.10 13/04/2018 Sect. 4. Environment variables 3.9 16/01/2018 Sect. 4.9 Known issues 3.8 21/12/2017 All Major revision of the code 3.7 01/04/2014 Sect. 3, 7 Updated installation instructions, documented expert mode 3.6 31/10/2013 Sect. 4.4, 4.5, 5.1, Profiles, FITS keywords, and test updates 6.1, 6.2, and 7.1.4 3.5 26/09/2013 All RIXes for final review considered 3.4 25/07/2013 All Changes related to code-testing workshop, added appendix 3.3 27/05/2013 Sect. 4.5 Changes in parameter description 3.2 30/04/2013 Sect. 5.5.3 Change in input parameter restrictions 3.1 28/03/2013 All Changes related to midterm review and more 3.0 02/12/2012 All Major revision of the code 2.5 17/05/2012 Sect. 4.4, 6.3, and 6.4 Discussing RFM problems and modified output files 2.4 03/05/2012 Sect. 1, 2.2, 4.4.1, 6.5, Discussing telluric absorption correction, and 7 Figure 1 modified 2.3 21/03/2012 Sect. 4 and 5.5.3 Voigt profile approximation added 2.2 16/03/2012 Sect. 5 Updating information concerning GDAS profiles Comment about width zero components (convolution) 2.1 23/11/2011 Sect. 4 and 5.5.3 Adding comments of Alain Smette 2.0 06/04/2011 All Second version 1.0 28/02/2011 All First version Doc. Number: VLT-MAN-ESO- MOLECFIT Pipeline User Manual 19550-5772 Doc. Version: 4.1 Released on: 2021-02-8 Page: 5 of 119 Contents 1 Introduction 9 1.1 Scope . .9 1.2 Acknowledgements . .9 1.3 Stylistic conventions . 10 1.4 Notational Conventions . 10 2 Related Documents 11 2.1 Applicable Documents . 11 2.2 Reference Documents . 11 3 Definitions, Acronyms and Abbreviations 13 4 Overview 15 4.1 The Project . 15 4.2 Algorithm . 16 4.3 Major Changes between MOLECFIT v1.5.9 and v3.x . 20 4.3.1 Driver . 20 4.3.2 Plot Files . 20 4.3.3 ASCII Data Files . 20 4.3.4 OpenMP . 20 4.4 Major Changes between MOLECFIT v3.x and v4.0 . 21 4.4.1 Removed Parameters . 21 4.4.2 Changed Parameters . 21 5 Quick Start 22 5.1 The MOLECFIT Pipeline Recipes . 22 5.2 Running the MOLECFIT Pipeline Recipes . 22 5.2.1 Getting Started with EsoRex ................................. 22 5.3 Running MOLECFIT using EsoRex ................................. 23 5.3.1 Environment Variables . 23 5.3.2 Input spectrum FITS header keywords . 24 Doc. Number: VLT-MAN-ESO- MOLECFIT Pipeline User Manual 19550-5772 Doc. Version: 4.1 Released on: 2021-02-8 Page: 6 of 119 5.3.3 Executing molecfit_model ............................... 24 5.3.4 Executing molecfit_calctrans ............................ 25 5.3.5 Executing molecfit_correct .............................. 26 6 Recipe Reference 27 6.1 The SOF files............................................. 27 6.2 The .rc files............................................. 29 6.2.1 molecfit_model default .rc parameters . 29 6.2.2 molecfit_correct default .rc parameters . 43 6.3 The Parameters . 45 6.3.1 Model Recipe . 45 6.3.2 Calctrans Recipe . 56 6.3.3 Correct Recipe . 59 6.4 Input Spectrum . 60 6.5 Output Products . 61 7 Guide for MOLECFIT 1.5.9 Users 62 7.1 Execution Format . 62 7.2 Parameter Format . 62 7.3 Input Output Filename Specifications . 63 7.4 Plot Files . 64 7.5 Extra LNFL and LBLRTM Control Parameters . 64 7.6 Simple Example . 66 7.7 Old Parameter Renames . 68 7.7.1 Input Data . 68 7.7.2 Results . 68 7.7.3 Fit Precision . 68 7.7.4 Molecular Columns . 69 7.7.5 Background and Continuum . 69 7.7.6 Wavelength Solution . 69 7.7.7 Line Spread Functions . 70 Doc. Number: VLT-MAN-ESO- MOLECFIT Pipeline User Manual 19550-5772 Doc. Version: 4.1 Released on: 2021-02-8 Page: 7 of 119 7.7.8 Ambient Parameters . 71 7.7.9 Instrument Parameters . 71 7.7.10 Atmostpheric Profiles . 72 8 The Model 73 8.1 Atmospheric profiles and meteorological data . 73 8.1.1 MIPAS profiles . 73 8.1.2 GDAS profiles . 78 8.1.3 ESO Meteo Monitor . 78 8.1.4 Processing of ESO Meteor Monitor data, GDAS, and MIPAS profiles . 80 8.2 Radiative transfer code . 82 8.2.1 Line File / Line-By-Line Radiative Transfer Model (LNFL/LBLRTM) . 83 8.2.2 aer line database . 84 8.3 Molecular spectra . 86 8.4 Thermal emission by telescope . 86 8.5 Adaptation of model to input spectrum . 87 8.5.1 The continuum . 87 8.5.2 The wavelength solution . 87 8.5.3 The resolution . 88 9 Installation 90 10 Code Performance 91 11 Tips and tricks 92 A Expert Fitting 94 A.1 Mapping Multiple Extension Data . 94 A.2 Mapping Ranges to Chips . 95 A.3 Expert Range Specific Continuum Modelling . 95 A.4 Expert Chip Specific Wavelength Correcting . 96 A.5 Expert Mode Initial Fitting Values . 96 A.6 Expert Analysis of the BEST_FIT_PARAMETERS.fits FILE . 97 Doc. Number: VLT-MAN-ESO- MOLECFIT Pipeline User Manual 19550-5772 Doc. Version: 4.1 Released on: 2021-02-8 Page: 8 of 119 B Parameters 99 B.1 Molecfit Parameter Name Changes: MOLECFIT_MODEL ..................... 99 B.2 Molecfit Parameter Name Changes: MOLECFIT_CALCTRANS .................. 102 B.3 Molecfit Parameter Name Changes: MOLECFIT_CORRECT .................... 102 B.4 molecfit_model SOF Tag names . 103 B.5 molecfit_calctrans SOF Tag Names . 104 B.6 molecfit_correct SOF Tag Names . 104 B.7 Molecfit Derivative Files . 105 B.7.1 molecfit_model Derived Files . 105 B.7.2 molecfit_calctrans Derived Files . 106 B.7.3 molecfit_correct Derived Files . 106 C Molecular Spectra 107 D Maintenance and License Issues 113 D.1 Maintenance . ..