gaidaiigor / spectrumsdt

A parallel Fortran program for calculation of ro-vibrational energy levels and lifetimes of ABA-molecules.

A parallel Fortran program for calculation of ro-vibrational energy levels and lifetimes of ABA-molecules. Note that the current version is limited to wave functions that do not extend into linear and equilateral triangle configurations (see manual for details).

Building

0. Prerequisites

   1. Make sure the following software is installed: Python 3, CMake (v3.5+), Fortan compiler (gfortran (v9.3.0+) or ifort (v19.0.3+)), MPICH, BLAS and LAPACK libraries. The following example is also going to assume that mpiexec wrapper is availble. Other implementations of Fortran compilers or MPI libraries may work, but have not been tested.
      
      The build files have been configured to work with gfortran by default, but with the appropriate modifications the code should also work with ifort. In our experience, ifort generates much faster code than gfortran, therefore we recommend to change the default settings to build with ifort on system where it is available.
      

   2. Make sure you machine has at least 2GB of RAM (for compilation).

1. Clone the repo git clone https://github.com/IgorGayday/SpectrumSDT
   This example assumes the repo is cloned into ~/SpectrumSDT

2. Build the libraries

   1. fdict

   cd ~/SpectrumSDT/libs/fdict
   

   Edit setup.make to change compiler options as necessary. Then run:

   make
   

   2. PETSc

   cd ~/SpectrumSDT/libs/petsc
   export PETSC_DIR=$PWD
   export PETSC_ARCH=debug_64
   ./configure --with-scalar-type=complex --with-64-bit-indices
   make all
   

   3. SLEPc

   cd ~/SpectrumSDT/libs/slepc
   export SLEPC_DIR=$PWD
   ./configure
   make all
   

3. Build the main program
   cd ~/SpectrumSDT

   1. Edit CMakeLists.txt to specify custom compiler options as necessary

   2. Build the executable
      Note: do not move the executable to another folder since some paths are resolved relative to its location.

   mkdir build && cd build
   cmake ..
   make spectrumsdt
   

Basic example of running (ozone)

1. Generate the grids

mkdir -p ~/SpectrumSDT_runs/o3/ && cd ~/SpectrumSDT_runs/o3/
cp ~/SpectrumSDT/config_examples/o3/1.simple/grids.config spectrumsdt.config
~/SpectrumSDT/build/spectrumsdt

After this, 3 files will be generated: grid_rho.dat, grid_theta.dat and grid_phi.dat. Each file stores values of grid points in each dimension, given in Bohr (for rho) and radians (for theta and phi). Before proceeding to the next stage, user should provide file pes.out with the values of potential at all combinations of these points in atomic units of energy (Hartree). See the potential section in manual for more details.

2. Calculate the values of PES. Here we will use an example program that reads grid files and uses the PES of ozone calculated by Dawes et al. to generate pes.out file. First, compile the program:

cd ~/SpectrumSDT/PES_examples/ozone/
mkdir build && cd build
../compile.sh

Now run:

cd ~/SpectrumSDT_runs/o3/
mpiexec -n <n_procs> ~/SpectrumSDT/PES_examples/ozone/build/ozone_pes 686

Replace <n_procs> with however many MPI tasks you want to use. After this, pes.out file with the values of PES at all grid points will be written.

3. Setup SpectrumSDT directory structure

mkdir J_0 && cd J_0
cp ~/SpectrumSDT/config_examples/o3/1.simple/spectrumsdt.config .

Edit spectrumsdt.config and replace username in the paths. Then execute:
~/SpectrumSDT/scripts/init_spectrum_folders.py -K 0

4. Calculate basis

cd K_0/symmetry_0/basis
mpiexec -n <n_procs> spectrumsdt

5. Calculate basis cross terms (overlaps)

cd ../overlaps
mpiexec -n <n_procs> spectrumsdt

6. Calculate eigenpairs

cd ../eigensolve
mpiexec -n <n_procs> spectrumsdt

Lowest 50 rovibrational energy levels of ozone-686 J=0 will be printed into states.fwc file.

7. Calculate wave function properties (optional)

cd ../properties
mpiexec -n <n_procs> spectrumsdt

The requested properties will be printed into states.fwc file.

References

1. Gayday, I.; Grushnikova, E.; Babikov, D. Influence of the Coriolis Effect on the Properties of Scattering Resonances in Symmetric and Asymmetric Isotopomers of Ozone. Phys. Chem. Chem. Phys. 2020, 22, 27560–27571.

2. Gayday, I.; Teplukhin, A.; Kendrick, B. K.; Babikov, D. The Role of Rotation–Vibration Coupling in Symmetric and Asymmetric Isotopomers of Ozone. J. Chem. Phys. 2020, 152, 144104.

3. Gayday, I.; Teplukhin, A.; Kendrick, B. K.; Babikov, D. Theoretical Treatment of the Coriolis Effect Using Hyperspherical Coordinates, with Application to the Ro-Vibrational Spectrum of Ozone. J. Phys. Chem. A 2020, 124, 2808–2819.

4. Teplukhin, A.; Babikov, D. Efficient Method for Calculations of Ro-Vibrational States in Triatomic Molecules near Dissociation Threshold: Application to Ozone. J. Chem. Phys. 2016, 145, 114106.