Task 5: Cross sections of C2H4 using super lines - Trovemaster/exocross GitHub Wiki

Cross sections of C2H4 using super-lines, see /scratch/dp114/dc-yurc1/C2H4

1. The ExoMol super-lines for C2H4 can be found at http://exomol.com/data/molecules/C2H4/12C2-1H4/MaYTY/ and locally at /scratch/dp114/shared/ExoMol/C2H4 (see https://arxiv.org/abs/1806.03469)

2. Create a directory C2H4 inside your project folder /scratch/dp114/:

mkdir /scratch/dp114/<user-name>/C2H4

and navigate there

cd /scratch/dp114/<user-name>/C2H4

3. Create an ExoCross input file to generate absorption cross sections for C2H4 at T=500 K for 0-7000 cm-1 on a wavenumber grid of 0.1 cm- using the Gaussian line profile (HWHM=0.1 cm-1). Here is an example:

    Temperature  500 (K)
    
    Range 0 7000
    Npoints 70001
    
    super-lines
    
    absorption
    gaussian
    hwhm 0.1
    
    output C2H4_Gaussian_SL_T1200K
    
    States "/scratch/dp114/shared/ExoMol/C2H4/12C2-1H4__MaYTY.states"
    Transitions "/scratch/dp114/shared/ExoMol/C2H4/12C2-1H4__MaYTY__0-7100__500K.super"
   

4. One could run this calculation directly from the command line:

exocross.exe <C2H4_Gaussian_SL_T500K.inp >C2H4_Gaussian_SL_T500K.out

however it is more efficient and less destructive for other users to submit it to the designated high memory machine, say, for 4 cores:

start_xcross.sh C2H4_Gaussian_SL_T500K.inp 4

The job will take less than 10 min.

5. Now we generate the same cross-sections using the line list directly (i.e. from a .trans file) for a smaller region 3000-3100 cm-1. This calculation will take longer, therefore it will be submitted to the high memory (1.4 Tb). In the following example we also specify the number of cores and the number of lines to cache, necessary to use the parallelisaion and vectorisation of ExoCross more efficiently.

    mem 140.0 gb
    Ncache 1000000000
    NPROCS 36
    
    Temperature  500 (K)
    
    Range 0 7000
    Npoints 70001
    
    pffile "/scratch/dp114/shared/ExoMol/C2H4/12C2-1H4__MaYTY.pf"
    
    absorption
    gaussian
    hwhm 0.1
    
    output C2H4_Gaussian_T1200K
    States "/scratch/dp114/shared/ExoMol/C2H4/12C2-1H4__MaYTY.states"
    Transitions "/scratch/dp114/shared/ExoMol/C2H4/12C2-1H4__MaYTY__03000-03100.trans"
   

   .

6. Submit this exocross calculation as "a job" to he high memory machine for 36 cores via the command

start_xcross.sh C2H4_Gaussian_T500K.inp 36

The job for a much smaller rage will take significantly longer, about 15 min. You can check the status of your job(s) using

showq -u <user-name>

7. Compare the calculation time and cross section from the super-lines calculations