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USR_MANUAL.txt
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USER MANUAL FOR EXO_TRANSMIT CODE
Authors: Eliza Kempton, Albert Owusu-Asare, Patrick Slough
last edited: Tue May 24 2016
----------------------------------------------------------------------------------------------
The Exo_Transmit code can be obtained from :
https://github.com/elizakempton/Exo_Transmit
When publishing results based on usage of Exo-Transmit please cite:
Kempton, E. M.-R., Lupu, R. E., Owusu-Asare, A., Slough, P., & Cale, B., 2016,
arXiv:1611.03871 (http://adsabs.harvard.edu/abs/2016arXiv161103871K)
If using the opacity data included with Exo-Transmit please additionall cite the following
three papers:
Freedman, R. S., Marley, M. S., & Lodders, K., 2008, ApJS, 174, 504-513
(http://adsabs.harvard.edu/abs/2008ApJS..174..504F)
Freedman, R. S., Lustig-Yaeger, J., Fortney, J. J., et al., 2014, ApJS, 214, 25
(http://adsabs.harvard.edu/abs/2014ApJS..214...25F)
Lupu, R. E., Zahnle, K., Marley, M. S., et al., 2014, ApJ, 784, 27
(http://adsabs.harvard.edu/abs/2014ApJ...784...27L)
==============================================================================================
LICENSE AND LEGAL NOTICE
----------------------------------------------------------------------------------------------
Copyright (C) 2016 Eliza Kempton
Permission is granted to copy, distribute and/or modify this document
under the terms of the GNU Free Documentation License, Version 1.3
or any later version published by the Free Software Foundation;
with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts.
A copy of the license is included the in section entitled "GNU
Free Documentation License".
==============================================================================================
ABOUT THIS MANUAL
----------------------------------------------------------------------------------------------
This manual is intended for persons interested in generating transmission spectra to study
exoplanet atmospheres. The manual includes: instructions on downloading the Exo_Transmit
code, information about the code's functionality, a discussion of the different components of
the code, a tutorial on how to use the code, and a troubleshooting section. The Exo-Transmit
code is described in further detail in E. M.-R. Kempton et al., 2016, arXiv:1611.03871 (http://adsabs.harvard.edu/abs/2016arXiv161103871K).
This manual assumes the code is run on a UNIX, LINUX, or similar platform and references may
be made to certain features of the UNIX or LINUX operating systems.
The manual uses the sign " --> " which serves to troubleshoot some problems that may come up
during the step by step instructions
Every care has been taken to prepare this document however, any input/concerns related to
this document or the Exo_Transmit code are appreciated. Such input/concerns should be emailed
to:
Eliza Kempton
==============================================================================================
CONTENTS
----------------------------------------------------------------------------------------------
* Download instructions
* General Information
* Information on input files
* Sample runs of program
* Troubleshooting: possible errors
* Further help and contact details
* GNU Free Documentation License
==============================================================================================
DOWNLOAD INSTRUCTIONS
----------------------------------------------------------------------------------------------
Please try either option (A) or (B)
---------------------------------
(A) Clone the package from github
***********************************************************************
Prerequisites: git, github account *
*
Move on to 'Steps' if you have both of the above, or else : *
*
Download latest version of git: *
http://git-scm.com/downloads *
Sign up at github: *
https://github.com/join *
For basic help with git: *
http://git-scm.com/doc *
*
OR: *
Try option (B) *
***********************************************************************
Steps:
1. In a terminal window, move to the required directory.
2. Type into the terminal at the required directory:
git clone https://github.com/elizakempton/Exo_Transmit.git
3. Follow given instructions from git about username and password
4. A working directory will be created as 'Exo_Transmit'
--> Downloading of the package may take a while. Check progress percentage.
5. Open Exo_Transmit or move to the directory to have access to the program
EXAMPLE:
1. cd /home/USER/
2. git clone https://github.com/elizakempton/Exo_Transmit.git
3. Username for 'https://github.com': myusername
Password for 'https://[email protected]': ********
4. cd Exo_Transmit
OR
-------------------------------------
(B) Download the package from github website
Steps:
1. Go to: https://github.com/elizakempton/Exo_Transmit
2. Click on "Download ZIP" on the righthand side of the page
3. In a terminal move to the location of the downloaded 'tar' file.
4. Type into the terminal, " tar -zxvf <filename> "
(In the current version of the code, filename = exo_transmit-master.zip)
5. Check if new directory "Exo_Transmit-master" exists
6. Move to new directory to have access to the program
EXAMPLE:
1. I downloaded the package to the location /home/USER/
2. cd /home/USER/
3. unzip exo_transmit-master.zip
4. ls
5. cd Exo_Transmit
==============================================================================================
GENERAL INFORMATION
----------------------------------------------------------------------------------------------
What the code does:
-----------------------
Overview:
Exo-Transmit calculates the transmission spectrum of an exoplanet atmosphere given specified
input information about the planetary and stellar radii, the planet's surface gravity, the
atmospheric temperature-pressure (T-P) profile, the location (in terms of pressure) of any
cloud layers, the composition of the atmosphere, and opacity data for the atoms and molecules
that make up the atmosphere.
The code solves the equation of radiative transfer for absorption of starlight passing
through the planet's atmosphere as it transits, accounting for the oblique path of light
through the planetary atmosphere along an Earth-bound observer's line of sight. The fraction
of light absorbed (or blocked) by the planet plus its atmosphere is calculated as a function
of wavelength to produce the wavelength-dependent transmission spectrum. Funtionality is
provided to simulate the presence of atmospheric aerosols in two ways: (1) an optically
thick (gray) cloud deck can be generated at a user-specified height in the atmosphere, and
(2) the nominal Rayleigh scattering can be increased by a specified factor.
** Unless otherwise noted, the code calculates all quantities in SI units. **
==============================================================================================
Program files and directories:
-----------------------------------
The Exo_Transmit package contains the following files:
----------
header files:
atmos.h include.h opac.h vars.h
constant.h nrutil.h prototypes.h
-----------
source files:
geometry.c -- calculates path lengths and angles associated w/ transmission geometry
getChemSelection.c -- determines which molecules will be included in the opacity calculation
based on user input
getFileArray.c -- reads in file names specified in the input files
getNTau.c -- determines how many layers of the T-P profile lie above a user
specified cloud deck
getVars.c -- reads user inputs from the input files
interpol.c -- interpolation routines
main_transmission.c -- main procedure -- calls a sequence of subroutines to obtain the
transmission spectrum
nrutil.c -- Numerical Recipes routines
planck.c -- calculates the Planck function for a specified temperature
read_t_p.c -- reads in T-P profile files
readchemtable.c -- reads in chemistry table data
readopactable.c -- reads in opacity tables for individual molecules
rt_transmission.c -- radiative transfer driver -- calculates transmission spectrum by
integrating the transfer equation for pure absorption at the
appropriate geometry
totalopac.c -- calculates total opacities
utils.c -- array management routines
------------
other files:
LICENSE.txt -- GNU Lesser General Public License
selectChem.in -- input file for selecting which molecules will be included in opacity
calculations -- details is to have all molecules turned on
otherInput.in -- other input information for Exo_Transmit that typically will not be
altered by the user
Makefile -- makefile for compiling Exo_Transmit
userInput.in -- input file for basic user inputs
README -- basic code information and information on compiling
USR_MANUAL.txt -- this file
-->(NOTE: files ending in ".in" are input files)
----------------------
files in subdirectories:
These are the files in the sub-directories: EOS, Opac, Spectra, T_P
EOS:
EOS/:
eos_0p1Xsolar_cond.dat -- equilibrium chemistry file with metalicity = 0.1
times solar -- condensation and removal via rainout
of molecules out of the gas phase is included -- does
not include condensation and rainout of graphite
eos_0p1Xsolar_gas.dat -- equilibrium chemistry file with metalicity = 0.1
times solar -- only gas phase chemistry is accounted
for
eos_1000Xsolar_cond.dat
eos_1000Xsolar_cond_graphite.dat -- equilibrium chemistry file with metalicity = 1000
times solar -- condensation and removal via rainout
of molecules out of the gas phase (including
graphite) is included
eos_1000Xsolar_gas.dat -- (Same file-naming convention as above)
eos_100Xsolar_cond.dat " "
eos_100Xsolar_cond_graphite.dat " "
eos_100Xsolar_gas.dat
eos_10Xsolar_cond.dat
eos_10Xsolar_cond_graphite.dat
eos_10Xsolar_gas.dat
eos_1Xsolar_cond.dat
eos_1Xsolar_gas.dat
eos_30Xsolar_cond.dat
eos_30Xsolar_cond_graphite.dat
eos_30Xsolar_gas.dat
eos_50Xsolar_cond.dat
eos_50Xsolar_cond_graphite.dat
eos_50Xsolar_gas.dat
eos_5Xsolar_cond.dat
eos_5Xsolar_cond_graphite.dat
eos_5Xsolar_gas.dat
eos_C2H2.dat -- chemistry file for an atmosphere made of 100% C2H2
eos_C2H4.dat -- chemistry file for an atmosphere made of 100% C2H4
eos_C2H6.dat -- chemistry file for an atmosphere made of 100% C2H6
eos_CH4.dat -- chemistry file for an atmosphere made of 100% CH4
eos_CO.dat -- (Same file-naming convention as above)
eos_CO2.dat " "
eos_H2CO.dat " "
eos_H2O.dat
eos_H2S.dat
eos_HCN.dat
eos_HCl.dat
eos_HF.dat
eos_MgH.dat
eos_N2.dat
eos_NH3.dat
eos_NO.dat
eos_NO2.dat
eos_O2.dat
eos_O3.dat
eos_OCS.dat
eos_OH.dat
eos_PH3.dat
eos_SH.dat
eos_SO2.dat
eos_SiH.dat
eos_SiO.dat
eos_TiO.dat
eos_VO.dat
eos_solar_0p2_CtoO_cond.dat -- equilibrium chemistry file for solar metalicity and
a C:O ratio of 0.2 -- condensation and removal via
rainout of molecules out of the gas phase is included
-- does not include condensation and rainout of
graphite
eos_solar_0p2_CtoO_gas.dat -- equilibrium chemistry file for solar metalicity and
a C:O ratio of 0.2 -- only gas phase chemistry is
accounted for
eos_solar_0p4_CtoO_cond.dat
eos_solar_0p4_CtoO_gas.dat
eos_solar_0p6_CtoO_cond.dat
eos_solar_0p6_CtoO_gas.dat
eos_solar_0p8_CtoO_cond.dat
eos_solar_0p8_CtoO_gas.dat
eos_solar_1p0_CtoO_cond.dat
eos_solar_1p0_CtoO_cond_graphite.dat -- equilibrium chemistry file for solar metalicity and
a C:O ratio of 1.0 -- condensation and removal via
rainout of molecules out of the gas phase (including
graphite) is included
eos_solar_1p0_CtoO_gas.dat
eos_solar_1p2_CtoO_cond.dat
eos_solar_1p2_CtoO_cond_graphite.dat
eos_solar_1p2_CtoO_gas.dat
-->(NOTE: The above are the chemistry files supplied with the program. Note that you can
add your own chemistry files provided you maintain the format used in our chemistry files.
Open any of the files above to see format.)
Opac/:
opacC2H2.dat opacCO2.dat opacHF.dat opacNO2.dat opacPH3.dat opacVO.dat
opacC2H4.dat opacH2CO.dat opacK.dat opacNa.dat opacSH.dat
opacC2H6.dat opacH2O.dat opacMgH.dat opacO2.dat opacSO2.dat
opacCH4.dat opacH2S.dat opacN2.dat opacO3.dat opacSiH.dat
opacCIA.dat opacHCN.dat opacNH3.dat opacOCS.dat opacSiO.dat
opacCO.dat opacHCl.dat opacNO.dat opacOH.dat opacTiO.dat
-- Files containing single-molecule opacities (absorption cross sections in m^2)
+ collision-induced opacities
Spectra/:
default.dat
T_P/:
t_p_300K.dat t_p_800K.dat t_p_1300K.dat
t_p_400K.dat t_p_900K.dat t_p_1400K.dat
t_p_500K.dat t_p_1000K.dat t_p_1500K.dat
t_p_600K.dat t_p_1100K.dat
t_p_700K.dat t_p_1200K.dat
-->(NOTE: The above are the isothermal T-P profile files supplied with the program. Note
that you can add your own T-P files provided you maintain the format used in our files. Open
any of the files above to see format.)
Please make sure all the above files and directories are included in your
package.
Information on Compilation (Also available in README)
-----------------------------------------------------------
To compile and run the program:
1. In a terminal, move to the directory where the program files are found
2. Type 'make clean'
3. Type 'make'
--> ( There might be some warnings upon compilation of the
program. Please ignore those warnings. We appreciate feedback on
errors or warnings. please see the 'contact us' section.)
4. Type './Exo_Transmit'
** Before your first run of Exo-Transmit, you must configure your input file. For
details, read the following section. **
--> (An error message of the form:
Error opening file: /YOUR_PATH/EOS/eos_1Xsolar_cond.dat
No such file or directory.
Make sure you have the appropriate file path and name specified in userInput.in
This means you have not configured your input.in file yet. Please
move to the section below this one for help and try again.)
EXAMPLE:
1. cd ~/home/Exo_Transmit/
2. $ make clean
result:
rm -f *.o *~ core*
3. $ make
results:
cc -Wall -g -c main_transmission.c
cc -Wall -g -c readopactable.c
cc -Wall -g -c totalopac.c
cc -Wall -g -c readchemtable.c
cc -Wall -g -c read_t_p.c
cc -Wall -g -c rt_transmission.c
cc -Wall -g -c nrutil.c
cc -Wall -g -c utils.c
cc -Wall -g -c interpol.c
cc -Wall -g -c planck.c
cc -Wall -g -c geometry.c
cc -Wall -g -c getFileArray.c
cc -Wall -g -c getVars.c
cc -Wall -g -c getNTau.c
cc -Wall -g -c getChemSelection.c
cc -lm -o Exo_Transmit main_transmission.o readopactable.o totalopac.o
readchemtable.o read_t_p.o rt_transmission.o nrutil.o utils.o interpol.o planck.o
geometry.o getFileArray.o getVars.o getNTau.o getChemSelection.o
4. $ ./Exo_Transmit
results:
NTEMP: 30, NPRESSURE: 13
Chemistry:
P_0 1.000000e+08
T_0 3.000000e+03
total 1.000000e-04
C 1.840702e-90
CH4 4.884950e-04
CO 1.991248e-75
CO2 1.195601e-63
C2H2 1.840702e-90
C2H4 1.840702e-90
H 1.840702e-90
HCN 1.840702e-90
HCl 0.000000e+00
HF 5.803795e-08
H2 8.367688e-01
H2CO 1.840702e-90
H2O 7.470776e-04
H2S 3.070205e-05
He 1.616752e-01
MgH 0.000000e+00
N 1.840702e-90
N2 3.264241e-23
NO2 1.840702e-90
NH3 1.344474e-04
NO 1.840702e-90
O 1.840702e-90
O2 1.840702e-90
OCS 1.535118e-82
OH 1.840702e-90
PH3 0.000000e+00
SH 0.000000e+00
SO2 1.840702e-90
SiH 0.000000e+00
SiO 0.000000e+00
TiO 0.000000e+00
VO 0.000000e+00
O3 1.840702e-90
C2H6 0.000000e+00
Na 0.000000e+00
K 0.000000e+00
ReadChemTable done
opac 1.700000e-04 1.000000e-04 1.000000e+02
Read CH4 Opacity done
opac 1.700000e-04 1.000000e-04 1.000000e+02
Read CO2 Opacity done
opac 1.700000e-04 1.000000e-04 1.000000e+02
Read CO Opacity done
opac 1.700000e-04 1.000000e-04 1.000000e+02
Read H2O Opacity done
opac 1.700000e-04 1.000000e-04 1.000000e+02
Read NH3 Opacity done
opac 1.700000e-04 1.000000e-04 1.000000e+02
Read O2 Opacity done
opac 1.700000e-04 1.000000e-04 1.000000e+02
Read O3 Opacity done
opac 1.700000e-04 1.000000e-04 1.000000e+02
Read C2H2 Opacity done
opac 1.700000e-04 1.000000e-04 1.000000e+02
Read C2H4 Opacity done
opac 1.700000e-04 1.000000e-04 1.000000e+02
Read C2H6 Opacity done
opac 1.700000e-04 1.000000e-04 1.000000e+02
Read H2CO Opacity done
opac 1.700000e-04 1.000000e-04 1.000000e+02
Read H2S Opacity done
opac 1.700000e-04 1.000000e-04 1.000000e+02
Read HCl Opacity done
opac 1.700000e-04 1.000000e-04 1.000000e+02
Read HCN Opacity done
opac 1.700000e-04 1.000000e-04 1.000000e+02
Read HF Opacity done
opac 1.700000e-04 1.000000e-04 1.000000e+02
Read MgH Opacity done
opac 1.700000e-04 1.000000e-04 1.000000e+02
Read N2 Opacity done
opac 1.700000e-04 1.000000e-04 1.000000e+02
Read NO Opacity done
opac 1.700000e-04 1.000000e-04 1.000000e+02
Read NO2 Opacity done
opac 1.700000e-04 1.000000e-04 1.000000e+02
Read OCS Opacity done
opac 1.700000e-04 1.000000e-04 1.000000e+02
Read OH Opacity done
opac 1.700000e-04 1.000000e-04 1.000000e+02
Read PH3 Opacity done
opac 1.700000e-04 1.000000e-04 1.000000e+02
Read SH Opacity done
opac 1.700000e-04 1.000000e-04 1.000000e+02
Read SiH Opacity done
opac 1.700000e-04 1.000000e-04 1.000000e+02
Read SiO Opacity done
opac 1.700000e-04 1.000000e-04 1.000000e+02
Read SO2 Opacity done
opac 1.700000e-04 1.000000e-04 1.000000e+02
Read TiO Opacity done
opac 1.700000e-04 1.000000e-04 1.000000e+02
Read VO Opacity done
opac 1.700000e-04 1.000000e-04 1.000000e+02
Read Na Opacity done
opac 1.700000e-04 1.000000e-04 1.000000e+02
Read K Opacity done
TotalOpac done
No Cloud layer will be calculated
333 1.013784e+05 8.000000e+02
ReadTP done
No Cloud layer will be calculated
R_atmosphere 3.771415e+06
R (planet & atmosphere) 1.142141e+07
R 0.997178
Exo_Transmit done
--> (Note that you may not get the exact same result as posted here, however do look out
to make sure the program has achieved successful completion by looking for the last
output line indicating 'Exo_Transmit done'. The completed transmission spectrum
should now be found at the path specified in 'userInput.in' under 'Output file'. )
==============================================================================================
INPUT FILE INFORMATION:
----------------------------------------------------------------------------------------------
User-provided input (userInput.in)
----------------------------------------------------------------------------------------------
The program allows users to change specific input data about the system to be modeled such as
the radius of the planet and host star, and the planet's surface gravity.
The following describes what lines in userInput.in represent the parameters you may wish to
modify:
Exo-Transmit home directory line 4
Temperature-pressure data file line 6
Chemistry (gas abundance) data file line 8
Output spectrum file line 10
Planet surface gravity line 12
Planet radius line 14
Steller radius line 16
Pressure of cloud layer line 18
Rayleigh scattering augmentation factor line 25
----------------------------------------------------------------------------------------------
** File selection for userInput.in **
----------------------------------------------------------------------------------------------
*** Update Working directory
Successful running of the program requires that some changes are made in
the input file 'input.in'
Steps:
1. Move to the directory that contains the code if not there already
2. Type 'pwd' in terminal
3. Copy the results of the terminal command 'pwd'.
4. open 'userInput.in'
5. On line 4 in 'input.in' delete the existing directory and paste the result of step 3
-->( It is extremely important that you paste the 'pwd' in line 4 exactly
and make no other changes to input.in, eg. do not hit enter after you
paste. Formating of 'input.in is to be maintained otherwise)
EXAMPLE:
1.$ cd ~/home/Exo_Transmit/
2.$ pwd
Results:
/home/Exo_Transmit
4.$ emacs input.in &
5. line 4 in 'input.in' before paste:
/YOUR_PATH
line 4 in 'input.in' after paste:
/home/Exo_Transmit
-------------------------
Chemistry file input (equation of state)
There are many chemistry files that are included in the package for this program: see the
section 'General Information: Program files and directories: files in sub-directories: EOS/
for the list of the available chemistry files.
On line 8 of 'userInput.in' you can indicate the chemistry file you want to use for the
transmission calculation. Make sure to either specify the full path of the chemistry file
or the path starting from the working directory of Exo_Transmit. You may choose any of the
files included in the 'EOS' sub-directory, or you may create your own chemistry file
following the exact format of the existing files in the 'EOS' sub-directory.
-------------------------
Temperature-pressure profile file input
The Exo_Transmit package contains a number of temperature-pressure (T-P) profile files,
allowing the user to specify the vertical temperature structure of the atmosphere. These
files are contained in the subdirectory 'T_P'. Most of the T-P profiles that are provided
with the code are for isothermal atmospheres with a single temperature expressed as a
function of pressure. Note that transmission spectra are not highly sensitive to temperature
gradients in an exoplanet atmosphere (i.e. temperature inversions vs. isothermal vs.
decreasing temperature as a function or altitude). Transmission spectra do however carry a
sensitivity to the absolute atmospheric temperature, which is seen in both the scale height
dependence of the depth of spectral features and the temperature-dependence of atmospheric
composition and absorption cross-sections.
On line 6 of 'userInput.in' you can indicate the T-P profile file you want to use for the
transmission calculation. Make sure to either specify the full path of the T-P file or the
path starting from the working directory of Exo_Transmit. You may choose any of the files
included in the 'T_P' sub-directory, or you may create your own T-P file following the exact
format of the existing files in the 'T_P' sub-directory.
** Note that the current version of Exo-Transmit only reads in the first 334 lines of the T-P
profile files, corresponding to atmospheric pressures less than 1 bar. If you would like to
read in a different number of data points from the T-P profile that you have specified, you
must edit line 48 of the file 'otherInput.in'.
---------------------
Output file name
On line 10 of 'userInput.in', specify the name of the output file where you will store the
transmission spectrum. The sub-directory 'Spectra/' has been provided for storing output
files, or you may choose another path for storing these files.
The two columns of the spectrum are wavelength (in units of meters) and the transmission
spectrum (given as transit depth in percent).
-->( If you decide not to change the output file name, your output data for
the transmission spectrum will be in default.dat in the Spectra sub-directory.
*** If you do not change the name of the output file, you will overwrite the existing
file. The code will not warn you that this is occurring. ***)
----------------------------------------------------------------------------------------------
** Selection of exoplanet parameters for userInput.in **
----------------------------------------------------------------------------------------------
Surface gravity
The planet's surface gravity should be specified in units of m/s^2. In the current version
of Exo-Transmit, the surface gravity is treated as a constant throughout the vertical extent
of the atmosphere. For transiting planets with measured masses, the surface gravity, g, is
calculated according to g = GM/R^2, where M is the planet's mass in kilograms, and R is the
transit radius in meters.
-------------------------
Planet radius
The planet's radius measured in meters.
** Note the radius specified in the input file corresponds in Exo-Transmit to the planet's
radius at the base of the atmosphere, which is located at a pressure of 1 bar for cloud-free
calculations (using the T-P profiles provided) and at the cloud top for calculations with
clouds.
-------------------------
Star radius
The host star radius measured in meters.
-------------------------
Cloud-top pressure
Pressure (in units of Pa) of the top of an optically thick cloud deck. If a non-zero number
is entered on this line, Exo-Transmit will prevent starlight from propagating through the
atmosphere at pressures in excess of the value entered. In effect, this simulates an
optically thick fully gray cloud deck.
-------------------------
Rayleigh scattering augmentation factor
The nomical Rayleigh scattering off of the gas molecules in the atmosphere can be augmented
(or reduced) here by a factor selected by the user. Increasing the nominal Rayleigh
scattering approximates the effect of Rayleigh scattering aerosols (e.g. hazes) in the
exoplanet atmosphere. A value of 1 entered on this line keeps the nominal Rayleigh
scattering intact. A value of zero turns off Rayleigh scattering in the code.
============================================================================================
EXAMPLE:
To change the surface gravity of the planet
1.Open 'userInput.in'
$ emacs userInput.in
2. In userInput.in move to line 12
3. delete old value and replace with new value
line 12 old value: 9.8
line 12 new value: 14.07
4. Save 'userInput.in'
5. Run program with new parameters:
./Exo_Transmit
-->(Note: you do not have to recompile each time you make changes to
'userInput.in'. The compilation proccess ('make') does not include
'userInput.in' so after saving, you can just re-run the program to see
your changes)
==============================================================================================
INPUT FILE INFORMATION:
CHEMISTRY FILE SELECTOR SYSTEM (selectChem.in)
----------------------------------------------------------------------------------------------
This is our switch system that enables the user to select and de-select which absorption
and/or scattering processes you may or may or may not want to include in the transmission
spectrum calculations. De-selecting any of these molecules or processes will remove its
associated opacity from the transmission spectrum calculation. This will occur regardless of
whether the molecule has a non-zero abundance in the chemistry file that you have selected,
so some care must be taken when turning off opacity sources.
On opening selectChem.in, you will see the gases and processes available to you in the
form below:
CH4 = 1
CO2 = 1
CO = 1
H2O = 1
NH3 = 1
O2 = 1
O3 = 1
C2H2 = 1
C2H4 = 1
C2H6 = 1
H2CO = 1
H2S = 1
HCl = 1
HCN = 1
HF = 1
MgH = 1
N2 = 1
NO = 1
NO2 = 1
OCS = 1
OH = 1
PH3 = 1
SH = 1
SiH = 1
SiO = 1
SO2 = 1
TiO = 1
VO = 1
Na = 1
K = 1
Scattering = 1
Collision Induced Absorption = 1
IMPORTANT NOTE:
"0" indicates that that gas/process is EXCLUDED from the transmission
calcualtions
"1" indicates that that gas/process is INCLUDED in the transmission
calcualtions.
Do not choose a character other than "0" or "1". The default is to have all of the
absorption and scattering processes turned on.
=============================================================================================
SAMPLE RUN OF PROGRAM
--------------------------------------------------------------------------------------------
The demonstration uses all the tips given from the manual to perform a
sample run of the program. It assumes you are running the program for the
first time.
In this demo we will make the following changes:
cloud pressure changed to 1000 in 'userInput.in'
gravity of planet changed to 18.0 in 'userInput.in'
CH4 turned on in 'selectChem.in', all other gases turned off.
Collision induced absorption turned off in 'selectChem.in'
scattering turned on in 'selectChem.in'
Exo-Transmit home directory modified in 'input.in'
EOS, chemistry file modified to show /EOS/eosCH4.dat
output filename changed to /Spectra/transmission_CH4.dat
Process:
--------
1.Move to the directory that contains the program files if not there already
$ cd /home/USER/Exo_Transmit
$ ls -->(this step was done just to see all the available files in the package)
2. Make sure all the files are included in the package
--> (Step 2 is only done when you are using the program package for the
first, time; For subsequent runs skip step 2)
--> (After each 'ls' command, make sure the given list matches the list
provided in the section:General Information)
$ ls *.h -->(To view all header files)
$ ls *.c -->(To view all source files)
$ ls --ignore*.c --ignore *.h -->(To view all other files)
$ ls EOS -->(To view all the files under the 'EOS' sub-directory)
$ ls Opac -->(To view all the files under the 'Opac' sub-directory)
$ ls Spectra
$ ls T_P
3. Open 'userInput.in'
$ emacs userInput.in &
4. Make necessary modifications
**********************************************************************************************
--> ( before modifications:)
userInput.in -
Formatting here is very important, please put the instructed content on the instructed line!
Exo_Transmit home directory:
/YOUR_PATH
Temperature-Pressure data file:
/T_P/t_p_800K.dat
Equation of State file:
/EOS/eos_1Xsolar_cond.dat
Output file:
/Spectra/default.dat
Planet surface gravity (in m/s^-2):
9.8
Planet radius (in m): -- This is the planet's radius at the base of the atmosphere (or at the cloud top for cloudy calculations)
6.40e+06
Star radius (in m):
7.00e+08
Pressure of cloud top (in Pa), -- or leave at 0.0 if you want no cloud calculations.
0.0
Rayleigh scattering augmentation factor -- default is 1.0. Can be increased to simulate additional sources of scattering. 0.0 turns off Rayleigh scattering.
1.0
End of userInput.in (Do not change this line!)
-->(after modifications)
userInput.in -
Formatting here is very important, please put the instructed content on the instructed line!
Exo_Transmit home directory:
/home/USER/Exo_Transmit
Temperature-Pressure data file:
/T_P/t_p_800K.dat
Equation of State file:
/EOS/eosCH4.dat
Output file:
/Spectra/transmission_CH4.dat
Planet surface gravity (in m/s^-2):
18.0
Planet radius (in m): -- This is the planet's radius at the base of the atmosphere (or at the cloud top for cloudy calculations)
6.40e+06
Star radius (in m):
7.00e+08
Pressure of cloud top (in Pa), -- or leave at 0.0 if you want no cloud calculations.
1000.0
Rayleigh scattering augmentation factor -- default is 1.0. Can be increased to simulate additional sources of scattering. 0.0 turns off Rayleigh scattering.
1.0
End of userInput.in (Do not change this line!)
**********************************************************************************************
5. Open 'selectChem.in'
$ emacs
6. Make neccessary modifications
**********************************************************************************************
-->(Before modifications)
For each gas, place a 1 after the equals sign if the gas opacity will be present in your transmission calculations, and 0 if not. Do not change the order of the gases in this file!
CH4 = 1
CO2 = 1
CO = 1
H2O = 1
NH3 = 1
O2 = 1
O3 = 1
C2H2 = 1
C2H4 = 1
C2H6 = 1
H2CO = 1
H2S = 1
HCl = 1
HCN = 1
HF = 1
MgH = 1
N2 = 1
NO = 1
NO2 = 1
OCS = 1
OH = 1
PH3 = 1
SH = 1
SiH = 1
SiO = 1
SO2 = 1
TiO = 1
VO = 1
Na = 1
K = 1
Scattering = 1
Collision Induced Absorption = 1
Do not delete this line!
-->(After modifications)
For each gas, place a 1 after the equals sign if the gas opacity will be present in your transmission calculations, and 0 if not. Do not change the order of the gases in this file!
CH4 = 1
CO2 = 0
CO = 0
H2O = 0
NH3 = 0
O2 = 0
O3 = 0
C2H2 = 0
C2H4 = 0
C2H6 = 0
H2CO = 0
H2S = 0
HCl = 0
HCN = 0
HF = 0
MgH = 0
N2 = 0
NO = 0
NO2 = 0
OCS = 0
OH = 0
PH3 = 0
SH = 0
SiH = 0
SiO = 0
SO2 = 0
TiO = 0
VO = 0
Na = 0
K = 0
Scattering = 1
Collision Induced Absorption = 0
Do not delete this line!
**********************************************************************************************
7. Compile the code (if you haven't done this already)
$ make
8. Run the code:
$ ./Exo_Transmit
==============================================================================================
FURTHER HELP AND CONTACT INFORMATION
----------------------------------------------------------------------------------------------
Citation: