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1   NMAG User Manual (0.2.1)

Authors:Hans Fangohr, Thomas Fischbacher, Matteo Franchin, Giuliano Bordignon, Jacek Generowicz, Andreas Knittel, Michael Walter, Maximilian Albert Licence:GNU General Public License (GPL) version 2 Version:0.2.1 Date:Manual generated on 2012-01-14 at 23:58. Home page:http://nmag.soton.ac.uk

• 1. Introduction
  • 1.1. Nmag Philosophy
  • 1.2. How to read this document
  • 1.3. Development status
  • 1.4. Mailing list
    • 1.4.1. nmag-announce
    • 1.4.2. nmag-users
  • 1.5. Support
  • 1.6. License and Disclaimer
• 2. Guided Tour
  • 2.1. Example: Demag field in uniformly magnetised sphere
    • 2.1.1. Importing nmag
    • 2.1.2. Creating the simulation object
    • 2.1.3. Defining (magnetic) materials
    • 2.1.4. Loading the mesh
    • 2.1.5. Setting the initial magnetisation
    • 2.1.6. Setting the external field
    • 2.1.7. Extracting and saving data
  • 2.2. Example 2: Computing the time development of a system
    • 2.2.1. Mesh generation
    • 2.2.2. The simulation
    • 2.2.3. Analysing the data
    • 2.2.4. Higher level functions
    • 2.2.5. “Relaxing” the system
    • 2.2.6. “Relaxing” the system faster
    • 2.2.7. Decreasing execution time
  • 2.3. Example: Simple hysteresis loop
    • 2.3.1. Hysteresis simulation script
    • 2.3.2. Hysteresis loop computation
    • 2.3.3. Obtaining the hysteresis loop data
    • 2.3.4. Plotting the hysteresis loop with Gnuplot
  • 2.4. Example: Hysteresis loop for Stoner-Wohlfarth particle
    • 2.4.1. Plotting the hysteresis loop
  • 2.5. Example: Hysteresis loop for thin disk
    • 2.5.1. Thin disk hysteresis loop
  • 2.6. Example: Vortex formation and propagation in disk
  • 2.7. Example: Manipulating magnetisation
    • 2.7.1. Modifying the magnetisation
  • 2.8. Example: IPython
  • 2.9. Example: Pinning Magnetisation
    • 2.9.1. Pinning simulation script
    • 2.9.2. Pinning magnetisation
    • 2.9.3. Visualisation
  • 2.10. Example: Uniaxial anisotropy
    • 2.10.1. Uniaxial anisotropy simulation script
    • 2.10.2. Visualization
    • 2.10.3. Comparison
  • 2.11. Example: Cubic Anisotropy
    • 2.11.1. Cubic anisotropy simulation script
    • 2.11.2. Analyzing the result
  • 2.12. Example: Arbitrary Anisotropy
    • 2.12.1. Arbitrary anisotropy simulation script
    • 2.12.2. The result
  • 2.13. Restart example
    • 2.13.1. Saving the state of the simulation
    • 2.13.2. Starting and restarting the simulation
  • 2.14. Applying a field that changes both in time and in space
    • 2.14.1. Idea: pass simulation object to field-setting function
    • 2.14.2. Complete example: simple moving write-head example
  • 2.15. Example: two different magnetic materials
  • 2.16. Example: Larmor precession
  • 2.17. Example: 1D periodicity
    • 2.17.1. Introduction periodic boundary conditions (“macro geometry”)
    • 2.17.2. 1d example
  • 2.18. Example: 2D periodicity
  • 2.19. Example: Spin-waves in periodic system
    • 2.19.1. Relaxation script
    • 2.19.2. Visualising the magnetisation evolution
  • 2.20. Example: post processing of saved field data
  • 2.21. Example: Spin transfer torque (Zhang-Li model)
    • 2.21.1. Current-driven motion of a vortex in a thin film
    • 2.21.2. Part I: Relaxation
    • 2.21.3. Part II: Current driven dynamics
    • 2.21.4. Standard problem
  • 2.22. Example: Current-driven magnetisation precession in nanopillars
    • 2.22.1. Two simulations in one single script
    • 2.22.2. Results: precession of the magnetisation
  • 2.23. Mesh distortion for edge roughness simulation
    • 2.23.1. Example
    • 2.23.2. Details and command line options
  • 2.24. Compression of the Boundary Element Matrix using HLib
    • 2.24.1. Hierarchical Matrices in Micromagnetism
    • 2.24.2. Installation of HLib
    • 2.24.3. Testing the HLib BEM Matrix compression
    • 2.24.4. Using HLib example 1: Demagnetisation Field of a Sphere
    • 2.24.5. Using HLib Example 2: Thin Films
    • 2.24.6. HLib and MPI
  • 2.25. Example: Calculation of dispersion curves
    • 2.25.1. The system: thesystem.py
    • 2.25.2. Part I: relaxation.py
    • 2.25.3. Part II: dynamics.py
    • 2.25.4. Postprocessing the data
  • 2.26. Example: Timestepper tolerances
    • 2.26.1. Hysteris loop calculation not converging? A word of warning ...
  • 2.27. Example: Parallel execution (MPI)
    • 2.27.1. Using mpich2
    • 2.27.2. Using mpich1
    • 2.27.3. Visualising the partition of the mesh
    • 2.27.4. Performance
  • 2.28. Restarting MPI runs
  • 2.29. More than one magnetic material, exchange coupled
• 3. Background
  • 3.1. Architecture overview
  • 3.2. The nsim library
  • 3.3. Fields and subfields
    • 3.3.1. Field
    • 3.3.2. Subfield
  • 3.4. Fields and Subfields in Nmag
    • 3.4.1. Example: one magnetic material
    • 3.4.2. Example: two magnetic materials
    • 3.4.3. Obtaining and setting subfield data
    • 3.4.4. Primary and secondary fields
  • 3.5. Mesh
    • 3.5.1. Node
    • 3.5.2. node id
    • 3.5.3. node position
  • 3.6. Site
  • 3.7. SI object
    • 3.7.1. Library of useful si constants
  • 3.8. Terms
    • 3.8.1. Stage, Step, iteration, time, etc.
    • 3.8.2. Some geek-talk deciphered
  • 3.9. Solvers and tolerance settings
  • 3.10. The equation of motion: the Landau-Lifshitz-Gilbert equation
• 4. Command reference
  • 4.1. MagMaterial
    • 4.1.1. uniaxial_anisotropy
    • 4.1.2. cubic_anisotropy
  • 4.2. Simulation
    • 4.2.1. advance_time
    • 4.2.2. get_subfield
    • 4.2.3. get_subfield_positions
    • 4.2.4. get_subfield_sites
    • 4.2.5. get_subfield_average
    • 4.2.6. get_subfield_average_siv
    • 4.2.7. probe_subfield
    • 4.2.8. probe_subfield_siv
    • 4.2.9. probe_H_demag_siv
    • 4.2.10. hysteresis
    • 4.2.11. load_mesh
    • 4.2.12. load_m_from_h5file
    • 4.2.13. save_restart_file
    • 4.2.14. relax
    • 4.2.15. save_data
    • 4.2.16. set_m
    • 4.2.17. set_H_ext
    • 4.2.18. set_pinning
    • 4.2.19. set_params
  • 4.3. get_subfield_from_h5file
  • 4.4. get_subfield_positions_from_h5file
  • 4.5. get_subfield_sites_from_h5file
  • 4.6. HMatrixSetup
  • 4.7. SI
    • 4.7.1. value
    • 4.7.2. units
    • 4.7.3. in_units_of
    • 4.7.4. is_compatible_with
  • 4.8. ipython
  • 4.9. Command line options
• 5. Finite element mesh generation
  • 5.1. Nmesh file format
    • 5.1.1. Ascii nmesh
    • 5.1.2. Hdf5 nmesh
  • 5.2. mesh file size
• 6. Executables
  • 6.1. ncol
  • 6.2. nmagpp
    • 6.2.1. Inspecting the content
    • 6.2.2. Dumping data
    • 6.2.3. Range of data to be processed
    • 6.2.4. Conversion to vtk file
    • 6.2.5. Other features
  • 6.3. nmeshpp
    • 6.3.1. General information (--info)
    • 6.3.2. Memory requirements of boundary element matrix
    • 6.3.3. Inspecting the quality of a mesh
    • 6.3.4. Histogram of edge lengths
  • 6.4. Convert nmesh.h5 to nmesh file (and back)
    • 6.4.1. nmeshmirror
    • 6.4.2. nmeshsort
  • 6.5. nmeshimport
  • 6.6. nsim
  • 6.7. nsimversion
• 7. Files and file names
  • 7.1. mesh files (.nmesh, .nmesh.h5)
  • 7.2. Simulation scripts (.py)
  • 7.3. Data files (.ndt)
  • 7.4. Data files (.h5)
  • 7.5. File names for data files
  • 7.6. File names for log files
• 8. Frequently Asked Questions
  • 8.1. What is the difference between the OOMMF and nmag approach?
  • 8.2. ... So, this means the major difference is “cubes” vs. “tetrahedra”?
  • 8.3. Why do you have your own Python interpreter (=nsim)?
  • 8.4. What is nsim - I thought the package is called nmag?
  • 8.5. How fast is nmag in comparison to magpar?
  • 8.6. How do I start a time-consuming nmag run in the background?
  • 8.7. nmag claims to support MPI. So, can I run simulation jobs on multiple processors?
  • 8.8. How should I cite nmag?
  • 8.9. Why can you not use the step as a unique identifier?
  • 8.10. How to generate a mesh with more than one region using GMSH?
  • 8.11. Can I run more than one simulation in one directory?
  • 8.12. Can I save data to an arbitrary directory?
    • 8.12.1. Do you really need to do so?
    • 8.12.2. How to save data to a different directory
  • 8.13. How to check the convergence of a simulation
  • 8.14. What to do in case of convergence problems
  • 8.15. How to visualise the difference between two fields defined over the same mesh
  • 8.16. How to re-sample data from a saved h5 file
  • 8.17. Notes on using GMSH to create a family of related meshes
• 9. Useful tools
  • 9.1. vtk
  • 9.2. MayaVi
  • 9.3. NumPy
• 10. Contact
• 11. Mini tutorial micromagnetic modelling
  • 11.1. Introduction micromagnetic modelling
  • 11.2. What is better: finite differences or finite elements?
  • 11.3. What size of the cells (FD) and tetrahedra (FE) should I choose?
    • 11.3.1. Exchange length
    • 11.3.2. Further reading
  • 11.4. Micromagnetic packages
  • 11.5. Summary
• 12. Acknowledgements