hRotor

About

hRotor is a program to compute the rotational partition function for a molecular system at a temperature T or a range of temperatures.

Platforms

hRotor has been tested on the following platforms:

• Ubuntu 20.04 LTS (Focal Fossa)

Additional Linux requirements

• g++ 9.3.0 or later
• cmake 3.8 or later
• Lapack 3.9.0 or later

Citation

The hRotor.x program is based on the following article:

• "The 1-D hindered rotor approximation", J. Pfaendtner, X. Yu and L. J. Broadbelt, Theor Chem Account, 118, 881 (2007)

The solution of Schödinger equation is based on the article (FGH):

• "The Fourier grid Hamiltonian method for bound state eigenvalues and eigenfunctions", C. C. Marston and G. G. Balint-Kurti, J. Chem. Phys., 91, 3571 (1989)

Installation

Let's start by copying or cloning the project in your system. Move or create a build directory. The file tree should look like the following:

-> hrotor/$ tree
.
├── bin
│   └── hRotor.x
├── build
├── example
│   ├── methanol-opt.wfn
│   ├── methanolScanT.txt
│   └── topsFile.txt
├── include
│   ├── Atom.h
│   ├── FourierH.h
│   ├── HPot.h
│   ├── Inertia.h
│   ├── Matrix.h
│   ├── Molecule.h
│   ├── runCommands.h
│   ├── Rvector.h
│   ├── screen.h
│   ├── thermo.h
│   └── version.h.in
├── README.md
└── src
    ├── Atom.cpp
    ├── CMakeLists.txt
    ├── FourierH.cpp
    ├── HPot.cpp
    ├── Inertia.cpp
    ├── main.cpp
    ├── Makefile
    ├── Matrix.cpp
    ├── Molecule.cpp
    ├── runCommands.cpp
    ├── Rvector.cpp
    └── thermo.cpp

Go to the build directory and run the following commands:

 -> hrotor/build/$ cmake ../src

And then run

-> hrotor/build/$ cmake --build .

The executable hRotor.x will be created and moved to the hrotor/bin directory, you can run by typing.

$./hRotor.x -g GEOMETRY -p POTENTIAL -t ROTATING_TOPS -o OutputName

There are mandatory flags such as:

Flag	Type	Description
-g	string	Assign a file with the geometry
-p	string	Indicate a file with the potential
-t	string	Contain the information of rotation tops

There are also optional flags such as:

flag	Type	Description
-o	string	Asign a name for the outpu
-T	float	Indicate a Temperature T different to 298.15 K
-r	float float int	Indicate a range of temperature: Ti, Tf and nT
-s	int	Indicate the symmetry number
-I	int	Indicate the n in I(2,n) for the Inertia moment
-m	float	Assign a numerical value for the Inertia moment
-n	int	Indicate the size in FGH method
-l		Display LAPACK version
-v o -V		Display the code version, compilation date, and git info
-h o -H		Display help

Outputs

The output from the terminal is as follows:

$./hRotor.x -g ../example/methanol-opt.wfn -p ../example/methanolScanT.txt -o output_ -t ../example/topsFile.txt  -T 1500. -s 3
[ INFO  ]  Geometry  name : ../example/methanol-opt.wfn
[ INFO  ]  Potential name : ../example/methanolScanT.txt
[ INFO  ]  Tops      name : ../example/topsFile.txt
[ INFO  ]  Output    name : output_
[ INFO  ]  Single    Temp :  true
[ INFO  ]  Range     Temp :  false
[WARNING]  No Inertia moment assigned
           The Inertia moment will be taken by default I (2,1)
[WARNING]  No Hamiltonian size assigned
           The Hamiltonian size will be taken by default H size = 501
[ INFO  ]   Hamilton size : 501
[ INFO  ]    Kinetic size : 250
[ INFO  ]     delta   x   : 0.0125413
[ INFO  ]     delta   k   : 1
[ INFO  ]     Data in pot : 35
=================================================================
 Print the values of thermo chemical properties
      Temperature  :    1500.00000000  K
          kB T     :      12.47169393  kJ / mol
 Highest potential :       5.57918738  kJ / mol
      I_red(2,1)   :       0.67176249  Da A^2
=================================================================
                  Free Rotor    Hindered Rotor
=================================================================
    Qr :          3.80813558      3.08477950
    S  :          0.01527483      0.01518053   kJ / (mol K )
    E  :          6.23584696      8.72168005   kJ / mol
    Cv :          0.00415723      0.00433721   kJ / (mol K )
=================================================================

The internal energy (E), entropy (S), head capacity at constant volume (Cv), and the partition function are reported at the end ofthe run.

On the other hand, the following files are also generated:

File	Data it contains
output_Energy.dat	eigenvalues of FGH
output_Pot.dat	Potential using in the FGH evaluate in te grid
outPut_Rho.dat	Desity for each eigenstate evaluate in the grid
outPut_Wf.dat	Wavefunction for each eigenstate evaluated in the grid
outPut_chem.dat	The information when range Temperature has been activated

Code contributors

• Raymundo Hernandez-Esparza (rayhe88@gmail.com)
• Julio Manuel Hernandez-Perez
• Sebastian García Pineda