Sindo 4.0

SINDO 4.0

SINDO is a suite of programs to carry out anharmonic vibrational structure calculations. It consists of programs for generating the anharmonic potential energy surface (MakePES), vibrational self-consistent field (VSCF) and post-VSCF solver (FSindo), and a visualizer (JSindo). SINDO is licensed under GNU General Public License v3.0, and is available free of charge.

JSindo is a program to visualize and to manipulate molecular vibrational modes. The program is distributed as an executable JAR file, which runs on multiplatform (Windows, MacOSX, and Linux) using Java. JSindo uses JAMA and JogAmp/Java3D as an external library.

Download

Program, Ver. 4.0, 2022, (41 MB) [sindo-4.0_220319.zip ]
Document and Samples, Ver. 4.0, 2022, (15 MB) [doc-4.0_220319.zip ]

GitHub

Documentation

JSindo
  • Install note (PDF 5 MB) [ PDF ]
  • Users’ guide (1.5 MB) [ PDF ]
MakePES
  • Install note (PDF 150 KB) [ PDF ]
  • Users’ guide (3.5 MB) [ PDF ]
FSindo
  • Install note (200 KB) [ PDF ]
  • Users’ guide (2.5 MB) [ PDF ]
Sindo-GENESIS
  • Anharmonic vibrational calculations based on QM/MM (1.5 MB) [ PDF ]

Lecture notes

  • Lecture 1 (Japanese) : Basics of Vibrational Theory [ PDF ]
  • Lecture 2 : PES generation. QFF, Grid, Multiresolution [ PDF ]
  • Lecture 3 : VSCF, integrals, VCI [ PDF ]
  • Lecture 4 : VMP, VQDPT [ PDF ]
  • Lecture 5 : Optimized coordinate VSCF [ PDF ]

Contact author

Kiyoshi Yagi
Senior Research Scientist
kiyoshi.yagi [*] riken.jp (change [*] to at mark)

References

  • Review
    • (Japanese) Development of Molecular Vibrational Structure Theory with an Explicit Account of Anharmonicity,
      K. Yagi, Mol. Sci. 10, A0085 (2016). [PDF]
  • Vibrational Theories
    • Vibrational quasi-degenerate perturbation theory with optimized coordinates: Applications to ethylene and trans-1,3-butadiene,
      K. Yagi and H. Otaki, J. Chem. Phys. 140, 084113 (2014). [13 pages]
    • Vibrational quasi-degenerate perturbation theory: Applications to Fermi resonance in CO2, H2CO, and C6H6,
      K. Yagi, S. Hirata, and K. Hirao, Phys. Chem. Chem. Phys. 10, 1781-1788 (2008).
  • PES Generation
    • Multiresolution potential energy surfaces for vibrational state calculations,
      K. Yagi, S. Hirata, and K. Hirao, Theor. Chem. Acc. 118, 681-691 (2007).
    • Ab initio vibrational state calculations with a quartic force field: Applications to H2CO, C2H4, CH3OH, CH3CCH, and C6H6,
      K. Yagi, K. Hirao, T. Taketsugu, M. W. Schmidt, and M. S. Gordon, J. Chem. Phys. 121, 1383-1389 (2004).
    • Direct vibrational self-consistent field method: Application to H2O and H2CO,
      K. Yagi, T. Taketsugu, K. Hirao, and M. S. Gordon, J. Chem. Phys. 113, 1005-1017 (2000).
  • Coordinates
    • Optimized coordinates for anharmonic vibrational structure theories,
      K. Yagi, M. Keçeli, and S. Hirata, J. Chem. Phys. 137, 204118 (2012). [16 pages]
    • Anharmonic Vibrational Calculations Based on Group-Localized Coordinates: Applications to Internal Water Molecules in Bacteriorhodopsin,
      K. Yagi and Y. Sugita, J. Chem. Theory Comput. 17, 5007-5020 (2021).
  • Applications
    • Anharmonic Vibrational Analysis of Biomolecules and Solvated Molecules Using Hybrid QM/MM Computations,
      K. Yagi, K. Yamada, C. Kobayashi, and Y. Sugita, J. Chem. Theory Comput. 15, 1924 (2019).
    • Towards complete assignment of the infrared spectrum of the protonated water cluster H+(H2O)21,
      J. Liu, J. Yang, X. C. Zeng, S. S. Xantheas, K. Yagi, and X. He, Nat. Comm. 12, 6141 (2021).