IR Spectra Calculation

This tutorial provides detailed, step-by-step instructions for calculating IR spectra using h-CMD simulations.

Steps to Calculate Spectra for h-CMD

1. Setup Sampling Simulations

   • Update the variable i in the sample-setup.sh script to the specific iteration you want to calculate the spectra for. Running the script will setup a sample directory in the iteration directory and submit the job.

2. Generate Dynamics Configurations

   • Once the sampling is done, update the i variable in the config-setup.sh script to the desired iteration and run the script. This will create the dynamics trajectory as well as the config directory and copy the sampling HISTORY file into it. Use the config program to generate the CONFIG files from the HISTORY file.

3. Run Dynamics Trajectories

   • Update the i variable in the dyn-setup.sh script and run it to setup all the dynamics trajectories and run the jobs.

4. Calculate the Spectra

   • Once all the trajectories are finished, navigate into the dynamics directory and use the correlation program to calculate the spectra.

     $ cd iter<i>/dynamics
     
     $ mpirun -n 1 correlation
     

   Tip

   A typical CONTROL file for IR calculation:

   50000 5000
   1
   50
   0.001
   dipole
   1.0
   .t.
   
   !number of time steps to read in, number of time steps to skip
   !number of molecules (use 1 if total dipole was used in DL_POLY)
   !number of trajectories
   !time (ps) between configurations
   !type of correlation function
   !tau value for Hann window (in ps)
   !bool for trimming beginning of trajectory