User's manual of OpenMX Ver. 3.8

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Contributors

T. Ozaki (Univ. of Tokyo)        Y. Shiihara (Toyota Tech. Inst.)

H. Kino (NIMS)        M. Toyoda (Tokyo Inst. Tech.)

J. Yu (SNU)        Y. Okuno (FUJIFILM)

M.J. Han (KAIST)        R. Perez (UAM)

M. Ohfuchi (Fujitsu Labs.)        P.P. Bell (UAM)

F. Ishii (Kanazawa Univ.)        M. Ellner (UAM)

K. Sawada (RIKEN)        Yang Xiao (NUAA)

Y. Kubota (Kanazawa Univ.)        A.M. Ito (NIFS)

Y.P. Mizuta (Kanazawa Univ.)        M. Kawamura (Univ. of Tokyo)

T. Ohwaki (NISSAN ARC)        K. Yoshimi (Univ. of Tokyo)

T.V.T Duy (NISSAN ARC)        C.-C. Lee (Univ. of Tokyo)

H. Weng (CAS)        K. Terakura (NIMS)

Download (PDF)
Tutorial (PDF)
Installation (PDF)
Contents
About OpenMX
Related papers
Installation
- Including libraries
- Serial version
- MPI version
- MPI/OpenMP version
- ScaLAPACK version
- FFTW3
- Other options
- Platforms
- Tips for installation
- Options for make
Test calculation
Automatic running test
Automatic running test with large-scale systems
Input file
- An example: methane molecule
- Keywords
Output files
Functional
Basis sets
- General
- Primitive basis functions
- Optimized basis functions provided by the database Ver. 2013
- Optimization of PAO by yourself
- Empty atom scheme
- Specification of a directory storing PAO and VPS files
Pseudopotentials
- Conventional pseudopotentials
- Open core pseudopotentials
Cutoff energy: grid fineness for numerical integrations
- Convergence
- A tip for calculating the energy curve for bulks
- Fixing the relative position of regular grid
SCF convergence
- General
- Automatic determination of Kerker's factor
- On-the-fly control of SCF mixing parameters
Restarting
- General
- Extrapolation scheme during MD and geometry optimization
- Input file for the restart calculation
Geometry optimization
- Steepest decent optimization
- EF, BFGS, RF, and DIIS optimizations
- Initial Hessian for the RF and EF optimizers
- Constrained relaxation
- Restart of geometry optimization
Variable cell optimization
- Examples
- Stress tensor
- Constraint for cell vectors
Molecular dynamics
- NVE molecular dynamics
- NVT molecular dynamics by a velocity scaling
- NVT molecular dynamics by the Nose-Hoover method
- Multi-heat bath molecular dynamics
- Constraint molecular dynamics
- Initial velocity
- User definition of atomic mass
- Converting the file format: md2axsf
Visualization
Band dispersion
Density of states
- Conventional scheme
- For calculations with lots of k-points
Orbitally decomposed total energy
Orbital optimization
Order() method
- Divide-conquer method
- Krylov subspace method
- User definition of FNAN+SNAN
MPI parallelization
- O() calculation
- Cluster calculation
- Band calculation
- Fully three dimensional parallelization
- Maximum number of processors
MPI/OpenMP hybrid parallelization
Large-scale calculations
- Conventional scheme
- Performance enhancement with ScaLAPACK
- Combination of the O(N) and conventional schemes
Electric field
Charge doping
Virtual atom with fractional nuclear charge
LCAO coefficients
Charge analysis
- Mulliken charge
- Voronoi charge
- Electro-static potential fitting
Natural population analysis
Non-collinear DFT
Relativistic effects
- Fully relativistic
- Controling of spin-orbit coupling strength
- Scalar relativistic treatment
Orbital magnetic moment
LDA+U
Constraint DFT for non-collinear spin orientation
Zeeman terms
- Zeeman term for spin magnetic moment
- Zeeman term for orbital magnetic moment
Macroscopic polarization by Berry's phase
Exchange coupling parameter
Optical conductivity
Electric transport calculations
- General
- Step 1: The calculations for leads
- Step 2: The NEGF calculation
- Step 3: The transmission, current (density, and eigenchannel)
- Running again the step 3 only
- Periodic system under zero bias
- Interpolation of the effect by the bias voltage
- Parallelization of NEGF
- NEGF method for the non-collinear DFT
- Examples
- Automatic running test of NEGF
Maximally Localized Wannier Function
- General
- Analysis
- Monitoring Optimization of Spread Function
- Examples for generating MLWFs
- Output files
- Automatic running test of MLWF
Interface with Wannier90
Numerically exact low-order scaling method for diagonalization
Effective screening medium method
- General
- Example of test calculation
Nudged elastic band (NEB) method
- General
- How to perform
- Examples and keywords
- Restarting the NEB calculation
- User defined initial path
- Monitoring the NEB calculation
- Parallel calculation
- Other tips
STM image by the Tersoff-Hamann scheme
DFT-D2 and DFT-D3 for vdW interaction
- DFT-D2 method
- DFT-D3 method
Unfolding method for band structures
- Analysis of band structures
- Unfolding of band structures
- The origin of the reference unit cell
- Intensity map of unfolded spectral weight
- In case of non-collinear DFT calculations
- Examples
Calculation of Energy vs. lattice constant
- Energy vs. lattice constant
- Delta factor
Fermi surface
Analysis of difference in two Gaussian cube files
Analysis of difference in two geometrical structures
Analysis of difference charge density induced by the interaction
Automatic determination of the cell size
Interface for developers
Automatic force tester
Automatic memory leak tester
Analysis of memory usage
Output of large-sized files in binary mode
Converting of Gaussian cube format to periodic XSF format
Examples of the input files
Known problems
OpenMX Forum
Linkage to other tools
Others
Bibliography
Index

2016-04-03

T. Ozaki (Univ. of Tokyo)		Y. Shiihara (Toyota Tech. Inst.)
H. Kino (NIMS)		M. Toyoda (Tokyo Inst. Tech.)
J. Yu (SNU)		Y. Okuno (FUJIFILM)
M.J. Han (KAIST)		R. Perez (UAM)
M. Ohfuchi (Fujitsu Labs.)		P.P. Bell (UAM)
F. Ishii (Kanazawa Univ.)		M. Ellner (UAM)
K. Sawada (RIKEN)		Yang Xiao (NUAA)
Y. Kubota (Kanazawa Univ.)		A.M. Ito (NIFS)
Y.P. Mizuta (Kanazawa Univ.)		M. Kawamura (Univ. of Tokyo)
T. Ohwaki (NISSAN ARC)		K. Yoshimi (Univ. of Tokyo)
T.V.T Duy (NISSAN ARC)		C.-C. Lee (Univ. of Tokyo)
H. Weng (CAS)		K. Terakura (NIMS)