steps

Before create inp directory (have reference geometry ready):
Step1: Generate ref.int file as in example. Make sure the charge and multiplicity is 0 and 1!
Step2: Run "python3 ~/git/astrophychem/bin/g16-angs-to-bohr.py"
Step3: Copy geomtry from ref.out-bohr into intder.in and make sure the alignment of the geomtry
Step4: Run "Intder2005 < intder.in > intder.out" to generate the file07
       Double check the geomtry in the section "VALUES OF SIMPLE INTERNAL COORDINATES (ANG. OR DEG.) FOR REFERENCE GEOMETRY" in the intder.out file
Step5: Modify molpro.py file to create the inp directory and 1.inp in each displacement sub-directory
       MAKE SURE to change proper molecule name, number of atoms, basis, charge, spin, etc!!!
       


After finish getting the energy points from each of the displacement calculation:

Step1: Generate energy files
       Make a energy directory, (if you have different corrections then make different directory for them and get energy files for different corrections).
       In the composite energy and different energy correction directories:
       You can run a for loop as "for i in {001..625}; do grep "UCCSD(T)/aug-cc-pVDZ energy=" /home/dagbaglo/chem/mgccc/qff/qff-1-linear-triplet/avdz/inp/mgccc$i/1.out >> energy-old.dat"
       Make sure you change the theory/basis-set, directory name (here is for mgccc)
       Then run python3 ~/git/astrophychem/bin/gen-refe.py to get a file "energy.dat" for relative energy
       FOR displacement 743, need to move energy.dat to energy1.dat, then run "python3 ~/git/astrophychem/bin/treat-743energy.py" to get energy for 805 points

Step2: 
       In the energy dirs, make sure you have ref.int, intder_template, intder.in, energy.dat, 
       also need to change files content:
       ref.int (need to change to the correct reference geom)
       intder_template, need to change according to intder.in

       #If need to use relative energies, then need to move absolute energy to energy-old.dat, use gen-refe.py to generate energy.dat 
       cp run.py run.sh run1.sh from ~/git/astrophychem/scripts/ to your working directory, modify those scripts accordingly.

Step3: Generate anpass files
       Run "python3 ~/git/astrophychem/bin/write_anpass_input.py anpass.in ./ ./  "
       It will pop up "What is the run titile: " you just type "anpass" then press enter
       if molecule has c2v symmetry then run "python3 ~/git/astrophychem/bin/write_anpass_input.py anpass.in ./ ./ c2v" (same apply to anpass2.in)

       Then run "anpass.x < anpass.in > anpass.out"
       
       Then run "python3 ~/git/astrophychem/bin/write_anpass_input.py anpass2.in ./ ./"
       It will pop up again "What is the run titile: " you just type "anpass2" then press enter
       Then run "anpass.x < anpass2.in > anpass2.out"
       Then run "python3 ./run.py", Make sure the angle term is corrected if there is angle terms


Step4: Generate intder_freqs.in
       Run "python3 ~/git/astrophychem/bin/write_intder_input.py intder_freqs.in ./"
       It will pop up several questions:
       Is this molecule linear?
       Number of dummy atoms:
       Input atoms with math, put space between two atoms: 
       Input the directory where file fort.9903
       Your answers to these questions will depend on molecules. For example as MGCCC, the answers will be
        Yes
        2
        MG24 C12 C12 C12
        ./

       May need to change certain parts in intder_freqs.in (double check) as for 3344 force constants and other things
       Then Run "Intder2005 < intder_freqs.in > intder_freqs.out"
  
Step5: Run "./run.sh"  
       to cp file15 to fort.15, file20 to fort.30, and file24 to fort.40
       Then cp proper spectro.in to current directory, and change geom with 1.inp-cart.bohr
       Then run "spec3jm.ifort-O0.static.x < spectro.in > spectro.out"
       Change Cu in coord
       Check if there is any reasonance from spectro.out, if yes, then cp spectro.in spectro2.in, and change certain things and run spectro again
       "spec3jm.ifort-O0.static.x < spectro2.in > spectro2.out"

for cucch, need to change order of internal coord in inter_freqs.in
When there is Fermi resonance, get the new fundamental frequency from spectro2.out