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He+CO2, Fermi resonance, CC and CS
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Coupled channels calculation for He+CO\ :sub:`2`, where CO\ :sub:`2` bend (v2) and
symmetric stretch (v1) are included.

Software versions (git commits)::

  gsci_lib6:   30015e4 - Sun, 7 Apr 2024 12:33:42 +0200 
  HeCO2_fermi: 95b56c6 - Sun, 7 Apr 2024 13:39:58 +0000
  gb_sql:      6251f2d - Wed, 3 Apr 2024 00:19:37 +0200 

***********
Quick start
***********

First, pick a `NAMESPACE`. Here, we use the name of the directory
with the jobs as the namespace: `HeCO2fm_v16`::

  git clone lilo.science.ru.nl:/vol/thchem/git/HeCO2_fermi HeCO2fm_v16
  cd HeCO2fm_v16/run1       # here are the jobs

A json file with input paramters is required. We start from `par15.json`::

  cp par15.json par16.json
  # vi par16.json                       # edit parameter file

Next, edit `par16.json` to set the required parameters. To run::

  ./bat1.sh par16.json NS:HeCO2fm_v16
  # The script echos the input
  # You will get some questions - simply press <enter> for the default:

  Reset journal HeCO2fm_v16_JOURNAL [Y/n] ?

  Fd: Re-initialize table "files" [Y/n]

  # job2.sh and job3.sh will be run by bat1.sh, should take about a minute

Three files will have been defined, to check enter::

  Fd ls
  Fd ls -l              # gives more detail

One of the files is the `.SETTINGS` file, which defines some bash variables::

  cat .SETTINGS
  # this shout give
  TERM_TITLE=HeCO2fm_v16
  export TODO=HeCO2fm_v16_TODO
  export FILES=HeCO2fm_v16_FILES
  export JOURNAL=HeCO2fm_v16_JOURNAL

If you use `gi_prompt.sh`, then the title of your terminal should
change to `$TERM_TITLE` when you enter the directory with the `.SETTINGS` file.

Define more files and setup table with jobs::

  bat2.sh
  bat3.sh               # press enter to this question:

  Fd: Re-initialize table "HeCO2fm_v16_TODO" [Y/n]?
  #
  Jb ls                 # show table with jobs
  Jb ls -l              # with more details
  Jb stat               # count number of jobs for each value of status

Next, we run a single job to test::

  ./bat4.sh |& tee bat4.out     # output appears on screen and is written to bat4.otu

In another terminal go to the same directory, and monitor progress::

  # (other terminal)
  cd HeCO2fm_v16/run1
  # To monitor progress use any of these
  ./w.sh                        # uses watch to update, shows status
  ./started.sh                  # shows started jobs
  Jb stat                       # shows status (once)
  Jb ls -w status = started +c Jtot,parity,iE
  Fd ls                         # show files
  Log ls                        # show log files
  cd scratch                    # this links is created by bat1.sh
  ls -l                         # shows directories with output
  cd  48even                    # If first job has Jtot=48 and parity=-1
  ls -l
  # job4_331.out                # should be there

If the status of the jobs turns into `done` then submit the other jobs
using `slurm`::

  ./sbat4.sh                    # will submit one job for each Jtop and parity
                                # and loop over energies
  squeue -u me                  # show slurm jobs

Use the above commands to monitor progress. Use the `Mb` command
to check use of cluster. To start extra jobs, use::

  ./sbat4.sh njob:100            # start hundred extra jobs

Other settings can be passed to this script::

  ./sbat4.sh mem:4G loop:4 njob:10 w:cn21

Files with cross sections can be seen with::

  Fd ls %CS_%.dat               # "%" is SQL wildcard

The underscore `_` is also a SQL wildcard, it may be escaped with a
backslash::

  Fd ls %CS\_%.dat

When all jobs are done the script `alldone.sh` is started. This
script will runs `sbat6.sh`, which will start a `bat6.sh` on each
host that has output. This job collects all cross sections computed
on that host into a spec. They can be seen with::

  Fd ls %Call%

When all jobs are done, output is written to `alldone.log`.

To collect all cross sections in a single file on the current
host::

  ./bat7.sh
  ./csall.sh            # this shows where on /scratch Call is written

Instructions for plotting will be added soon.