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Some ideas for common input/output formats for the MS codes

Some ideas for common input/output formats for the MS codes. Keisuke Hatada Dipartimento di Fisica, Universit à Camerino. Construction of general interface/platform. Output. Input. MSNano outputs. MSNano codes Inputs. MSNano inputs. MSNano GUI. Electronic structure codes outputs.

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Some ideas for common input/output formats for the MS codes

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  1. Some ideas for common input/output formats for the MS codes Keisuke Hatada Dipartimento di Fisica, UniversitàCamerino

  2. Construction of general interface/platform Output Input MSNano outputs MSNano codes Inputs MSNano inputs MSNano GUI Electronic structure codes outputs Original outputs Chose and run a code

  3. The interface translates inputs of MSNano codes and output of electronic structure codes. The output will be, original, common and input for other codes.

  4. Ideas around

  5. Input files

  6. Coordinate 1) Coordinate of atomic position k-space <=> real space Cartesian x,y,z (PDB)<=> radial coordinates (OpenBabel can handle it in the interface) 2) for movement of atoms, MXAN uses tag for atoms. Ex.) fixed atom “0”, moving atom “1”, moving with the atom “1” as group “-1” 3) displacement parameters, ex. Debye-Waller factor 4) MT radius and overlapping

  7. More specialized inputs • T-matrix/phase shift Phagen (MsSpec,GNXAS,MSPHD) FPMS (MsSpec) : future Phagen, T-matrix and radial integral generator with full potential required info : definition of T-matrix, spherical harmonics order of array for l,m ingoing or outgoing boundary condition kinetic energy with channel (future) • Transition dipole, quadruple, Coulomb matrix • Free propagator (KKR factor) definition of G_LL’ (phase factor is important for NMT) basis of G_LL’, screened one, by Wanier, Hydrogenic, anything else

  8. Interface for extracting data from electronic structure codes • Charge density (mesh radial around core of atom) • radial wave functions of initial state • coefficients and basis functions (plane wave, atomic orbital, slater,) • Potential (Coulomb potential, static xc pot) • Mean square displacement (Abinit,PWSCF) • Total energy (chemical shift )

  9. Input interface for output of electronic structure codes • Molecular Dynamics (DFT, QM/MM) : reading structure done for MXAN • LMTO done for MCMS, Phagen (MsSpec), FPMS • VASP done for FPMS • Abinit done by Sipr and Vackar • Gaussian by Chiba

  10. Which kind of codes (for round table) • KKR : SPR-KKR • Pseudo potential: VASP, Abinit,.. • FLAPW : WIEN2k • LCAO: siesta • Quantum Chemistry : Gaussian, ADF • Molecular dynamics : Important points are, number of users and physical quantity.

  11. Output files • Name of files and format inside should be exported to the interface. Maybe some graphic generator can be coded inside the interface. => xband (one candidate) • molecular view => xcrysden (one candidate) programs should be public, easy to install for any OS

  12. Some remarks • Interface or all programs should keep at least important parameters of calculation in the header or companion file. • Normalization of experiment • How to organize development of interface by many people

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