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hRotor

rotorCompleto

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 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

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Project in C++ for hindered Rotors

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