Task 2: SO2 Super lines - Trovemaster/exocross GitHub Wiki

See /scratch/dp114/dc-yurc1/exocross/SO2

In /scratch/dp114/ create a directory SO2 and navigate there

cd /scratch/dp114/<user-name>

mkdir SO2

cd SO2

The SO2 line list can be found at http://exomol.com/data/molecules/SO2/32S-16O2/ExoAmes/. It can be partially also accessed locally at /scratch/dp114/shared/ExoMol/SO2.

Create an input text file (e.g. SO2_T_300K_step1_binning.inp) as follows, e.g. using vim, gedit or nano. This input file is to generate absorption intensities (cm/molecule) and bin then to the non-uniform grid of R=1,000,000 for T = 300 K. Each bin will then be used as super-lines at the next step. The keywords are not sensitive to the case or exact positions.

 mem 190.0 gb
 NRAM 1000000
 NPROCS 4
 
 Temperature  300
 Range 1 1000.0
 
 R 1000000
 
 absorption
 bin
 
 output SO2_T_300_bin_R1M
 
 States "/scratch/dp114/shared/ExoMol/SO2/32S-16O2__ExoAmes.states"
 
 Transitions
 "/scratch/dp114/shared/ExoMol/SO2/32S-16O2__ExoAmes__00000-00100.trans"
 "/scratch/dp114/shared/ExoMol/SO2/32S-16O2__ExoAmes__00100-00200.trans"
 "/scratch/dp114/shared/ExoMol/SO2/32S-16O2__ExoAmes__00200-00300.trans"
 "/scratch/dp114/shared/ExoMol/SO2/32S-16O2__ExoAmes__00300-00400.trans"
 "/scratch/dp114/shared/ExoMol/SO2/32S-16O2__ExoAmes__00400-00500.trans"
 "/scratch/dp114/shared/ExoMol/SO2/32S-16O2__ExoAmes__00500-00600.trans"
 "/scratch/dp114/shared/ExoMol/SO2/32S-16O2__ExoAmes__00600-00700.trans"
 "/scratch/dp114/shared/ExoMol/SO2/32S-16O2__ExoAmes__00700-00800.trans"
 "/scratch/dp114/shared/ExoMol/SO2/32S-16O2__ExoAmes__00800-00900.trans"
 "/scratch/dp114/shared/ExoMol/SO2/32S-16O2__ExoAmes__00900-01000.trans"
 end

Note that the partition function will be computed using the energies from the.states file.

The exocross can be either run from the command line (slow)

exocross.exe <SO2_T_300K_step1_binning.inp >SO2_T_300K_step1_binning.out

or submitted to the DiRAC scheduler to be run on a high memory (1.4 Tb) machine with exclusive access using the submission command (for 4 cores)

start_xcross.sh SO2_T_300K_step1_binning.inp 4

The submission scripts can be found in /scratch/dp114/shared/bin The job status can be checked using

qstat -u <user-name>

showq -u <user-name>

It can be cancelled with

canceljob <jobid>

This calculation will produce a text file SO2_T_300_bin_R1M.xsec with the following two-column format, which will be used as a set of super-lines with the positions (cm-1) defined in the first column and the combined absorption coefficient from the second column (cm/molecule)

    position        combined intensity 
    .....
    9.99967267E+02   6.11769194E-27
    9.99968267E+02   1.93994072E-30
    9.99969267E+02   4.56042180E-27
    9.99970267E+02   1.26052726E-28
    9.99971267E+02   2.16884343E-26
    9.99972267E+02   5.20186653E-29
    9.99973267E+02   8.87992144E-30
    9.99974267E+02   1.43981057E-30

The next step is to prepare an input (e.g. SO2_T_300K_step2.inp) where the superlines SO2_T_300_bin_R1M.xsec are used to generate absorption cross sections on a regular wavenumber grid of 0.1 cm-1 using the Gaussian line profile with HWHM (lalf-width-at-half-maximum) of 0.5 cm-1. To this end SO2_T_300_bin_R1M.xsec is now used as a .trans file in combination with the the keyword super-lines as follows
```
 Temperature  300
 Range 1 1000.0
 
 Npoints  10001
 
 super-lines
 
 absorption
 gaussian
 hwhm 0.5
 
 output SO2_T_300_gauss_0.5
 
 States "/scratch/dp114/shared/ExoMol/SO2/32S-16O2__ExoAmes.states"
 Transitions SO2_T_300_bin_R1M.xsec
```
This is a relatively simple calculation and hence can be run from the command line

exocross.exe < SO2_T_300K_step2.inp > SO2_T_300K_step2.out

This run will produce a cross sections file SO2_T_300_gauss_0.5.xsec, which can be visualised with xmgrace or gnuplot

gnuplot -persist -e "plot 'SO2_T_300_gauss_0.5.xsec' using 1:2 notitle w l"

A complete super-lines set for T=300 K (0-8000 cm-1) can be found in

 Temperature  300
 Range 0 8000.0
 Npoints  80001
 
 super-lines
 
 absorption
 gaussian
 hwhm 0.1
 
 output SO2_T_300_gauss_0.1
 
 States "/scratch/dp114/shared/ExoMol/SO2/32S-16O2__ExoAmes.states"
 
 Transitions "/scratch/dp114/shared/ExoMol/SO2/SO2_T_300_bin_R1M.xsec"

Last task: compute SO2 cross sections using super-lines for the range 0-8000 cm-1.

See also the ExoMol cross-sections App http://exomol.com/data/molecules/SO2/32S-16O2/xsec-ExoAmes/ and the ExoMol Atlas https://arxiv.org/pdf/1805.03711.pdf

This exercise can be found in /scratch/dp114/dc-yurc1/exocross/SO2.

Task 2: SO2 Super lines - Trovemaster/exocross GitHub Wiki

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