Task 3: New water line list POKAZATEL and super lines - Trovemaster/exocross GitHub Wiki

See /scratch/dp114/dc-yurc1/exocross/H2O

  1. In /scratch/dp114/ create a directory H2O and navigate there

cd /scratch/dp114/<use-name>/H2O

  1. The new H2O line list can be found at http://exomol.com/data/molecules/H2O/1H2-16O/POKAZATEL/, e.g. using

It can be partially also accessed locally at /scratch/dp114/shared/ExoMol/H2O.

  1. Download the broadening files for He and H2 from ExoMol at http://exomol.com/data/molecules/H2O/:

wget http://exomol.com/db/H2O/1H2-16O/1H2-16O__H2.broad

wget http://exomol.com/db/H2O/1H2-16O/1H2-16O__He.broad

as well as the partition function file from http://exomol.com/data/molecules/H2O/1H2-16O/POKAZATEL/

wget http://exomol.com/db//H2O/1H2-16O/POKAZATEL/1H2-16O__POKAZATEL.pf

  1. Create symbolic Links to the line lists in /scratch/dp114/shared/ExoMol/H2O/

link /scratch/dp114/shared/ExoMol/H2O/1H2-16O__POKAZATEL__04200-04300.states 1H2-16O__POKAZATEL__04200-04300.states

link /scratch/dp114/shared/ExoMol/H2O/1H2-16O__POKAZATEL.states 1H2-16O__POKAZATEL.states

  1. Create an input text file (e.g.H2O_Voigt_T1000K.inp) to compute absorption cross sections of water for T=1000 K and P=10 atm using the Voigt profile with He and H2 as broadeners (15/85%) in the range 4200-4300 cm-1 on a grid of 0.1 cm-1.

     mem 190.0 gb
 Ncache 10000000
 NPROCS 18
 
 Temperature  1000
 Range 4200 4300
 Npoints 1001
 
 Absorption
 Voigt
 pressure  10.0 (atm)
 species
      H2 file 1H2-16O__H2.broad  ratio 0.85
      he file 1H2-16O__He.broad  ratio 0.15
 end
 
 output H2O_4200_1000_Voigt
 
 States 1H2-16O__POKAZATEL.states
 pffile  1H2-16O__POKAZATEL.pf
 Transitions
   1H2-16O__POKAZATEL__04200-04300.trans
 end

Note that the partition function is taken from the the file 1H2-16O__POKAZATEL.pf.

  1. This is a relatively heavy calculation, which we will run using the high memory 1.4 Tb machine by submitting the a job to the DiRAC scheduler on 18 cores (see the line NPROCS 18):

start_xcross.sh H2O_Voigt_T1000K.inp 18

The calculation should take about a minute. The job status can be checked using

qstat -u <user-name>

or

showq -u <user-name>

It can be cancelled with

canceljob <jobid>

This calculation will produce a text output H2O_4200_1000_Voigt.xsec the following two-column format: cross section (cm2/molecule) vs wavenumber (cm-1).

  1. Now increase the resolution to 0.01 cm-1 by changing the Npoints value to 10001 and rerun the calculation (don't forget to change the name of the output file to something different). This calculation will take more than 3 min.

  2. Super lines. POKAZATEL super-lines for H2O can be found in /scratch/dp114/shared/ExoMol/H2O for a set of temperatures and resolution of 1,000,000. Using this set, compute absorption cross sections of water for T = 1000 K, P=2 atm for the spectroscopic range 0-30000 cm-1 and the resolution of 0.1 cm-1 and the Voigt profile assuming the H2/He as broadeners (85%/15%).

  3. To convert the exomol line list into the HITRAN format, use the following template (1H2-16O__POKAZATEL_HITRAN_4200.inp):

     Temperature  296
 Range 4200 4400
 
 absorption
 stick

 pffile  1H2-16O__POKAZATEL.pf
 
 HITRAN write
 
 mass 18
 
 threshold -1e-40
 
 hitran write
    error-E  qn 4 ierr 2   vmax  100
    error-S  qn 4 ierr 5   vmax  100
    error-Air   ierr 0
    error-self  ierr 0
    error-n     ierr 0
    error-delta ierr 0
 end
 
 absorption
 
 iso 11
 
 abundance 0.99734
 
 pressure  1.0
 species
      air   gamma 0.075  n 0.40 t0 296.0 file 1H2-16O__air_a0.broad  ratio 1.00 delta 0.000000
      self  gamma 0.670  n 1.00 t0 296.0 file 1H2-16O__self_a0.broad ratio 1.00 delta 0.000000
 end
 
 
 output 1H2-16O__POKAZATEL_4200
 
 NRAM 100000000
 
 NCache 4

 States 1H2-16O__POKAZATEL.states
 
 Transitions 1H2-16O__POKAZATEL__04200-04300.trans

The air and self-broadening parameters should be downloaded from http://exomol.com/data/molecules/H2O/:

wget http://exomol.com/db/H2O/1H2-16O/1H2-16O__self_a0.broad

wget http://exomol.com/db/H2O/1H2-16O/1H2-16O__air_a0.broad

Running exocross.exe

exocross.exe <1H2-16O__POKAZATEL_HITRAN_4200.inp

will produce a .par file (1H2-16O__POKAZATEL_4200) in the HITRAN format:

    11 4200.034597 0.539E-37 0.308E-03.03900.287 6531.47700.470.000000  1  1  1 A1  1  0  0 A2                    12 3 1   13 7 7 250000 0 0 0 0 0 0    25.0   27.0
    11 4200.035804 0.200E-38 0.836E-03.07700.412 7279.72400.650.000000  0  2  2 A2  0  2  1 A1                     6 5 1    5 1 4 250000 0 0 0 0 0 0    13.0   11.0
    11 4200.249226 0.209E-39 0.699E+00.02400.240 9365.35670.310.000000  0  3  1 A2  0  2  0 A1                    20 4 1   21 6 1 250000 0 0 0 0 0 0    41.0   43.0
    11 4200.513452 0.635E-39 0.177E+01.02400.240 9532.51320.380.000000  1  1  1 B2  1  1  0 B1                    18 8 1   17 6 1 250000 0 0 0 0 0 0   111.0  105.0

  1. A larger set of pre-computed absorption super-lines for H2O (POKAZATEL) on a grid of temperatures can be found in /scratch/dp114/shared/ExoMol/H2O/ locally as well as at http://exomol.com/data/molecules/H2O/1H2-16O/POKAZATEL/ Below is an example of using this set for generating absorption cross-sections of water for T=1200 K and P=1 atm on the wavenumber grid of 0-41000 cm-1 with the resolution of 1 cm-1 using the Voigt lin profile.

     Temperature  1200
 pressure  1.0 (atm)
 
 Range 0 41000
 Npoints 41001
 
 super-lines
 
 absorption
 Voigt
 
 species
      H2 gamma 0.065 n 0.5  t0 296.0   ratio 0.85
      he gamma 0.03  n 0.3  t0 296.0   ratio 0.15
 end
 
 output H2O_Voigt_SL_T1200K

 Ncache 100000000
 NPROCS 18
 
 States "/scratch/dp114/shared/ExoMol/H2O/1H2-16O__POKAZATEL.states"
 Transitions
   "/scratch/dp114/shared/ExoMol/H2O/1H2-16O__POKAZATEL__0-41200__1200K.super"
 end

  2. Plot the cross sections (H2O_Voigt_SL_T1200K) using, e.g., xmgrace, which can be compareed to the cross sections of water generated using the exomol cross-sections app at http://exomol.com/data/molecules/H2O/1H2-16O/xsec-POKAZATEL/

This exercise can be found in /scratch/dp114/dc-yurc1/exocross/H2O.

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