Horace Manual

• 1. Planning a Horace scan
  • 1.1. horace_planner: a simple scan planner
  • 1.2. More detailed planning of scans
• 2. Generating SQW files
  • 2.1. accumulate_sqw
  • 2.2. gen_sqw
  • 2.3. Applying symmetry operations to an entire dataset
• 3. Data diagnostics
  • 3.1. run_inspector
  • 3.2. split
  • 3.3. join
• 4. Correcting for sample misalignment
  • 4.1. Step 1 - determining the true Bragg peak positions
    • 4.1.1. Bragg Positions
    • 4.1.2. Step 2 - check the Bragg positions fits worked properly
    • 4.1.3. Step 3 - calculate the misalignment correction
    • 4.1.4. Step 4 - apply the correction to the data
  • 4.2. Option 1 : apply the correction to an existing sqw file
  • 4.3. Option 2 : calculate goniometer offsets for regeneration of sqw file(s)
  • 4.4. Option 2a (for use with e.g. Mslice): calculate the true u and v for your misaligned crystal
    • 4.4.1. List of alignment correction routines
  • 4.5. bragg_positions
  • 4.6. bragg_positions_view
  • 4.7. crystal_pars_correct
  • 4.8. refine_crystal
  • 4.9. ubmatrix
  • 4.10. uv_correct
  • 4.11. rlu_corr_to_lattice
• 5. Cutting data of interest from SQW files and objects
  • 5.1. cut
    • 5.1.1. Data Source
    • 5.1.2. Projection (proj)
    • 5.1.3. Binning arguments
    • 5.1.4. File- and memory-backed cuts
    • 5.1.5. Projection in more detail
    • 5.1.6. Additional notes
    • 5.1.7. Legacy calls to cut: cut_sqw and cut_dnd
  • 5.2. section
• 6. Special SQW information from sqw objects and files
  • 6.1. head
    • 6.1.1. legacy equivalents of head
  • 6.2. xye
  • 6.3. save_xye
• 7. Loading sqw and dnd objects to memory
  • 7.1. read_horace
  • 7.2. read_sqw
  • 7.3. read_dnd
• 8. Saving sqw objects from memory and creating filebacked objects
  • 8.1. save
• 9. Other shape functions
  • 9.1. replicate
  • 9.2. compact
  • 9.3. permute
  • 9.4. cut
  • 9.5. section
  • 9.6. smooth
  • 9.7. mask
  • 9.8. mask_points
  • 9.9. mask_runs
• 10. Symmetry Operations
  • 10.1. Symmetry Operators
    • 10.1.1. Reflections
    • 10.1.2. Rotations
    • 10.1.3. General Transformations
    • 10.1.4. Groups of symmetry operators
    • 10.1.5. Irreducible region
  • 10.2. Symop Methods
    • 10.2.1. transform_vec
    • 10.2.2. transform_pix
    • 10.2.3. transform_proj
  • 10.3. Commands for cuts and slices
  • 10.4. Symmetrising
    • 10.4.1. symmetrise_sqw
    • 10.4.2. gen_sqw
  • 10.5. Cutting
  • 10.6. Combining
  • 10.7. Rebinning
  • 10.8. Symmetrise data, then unfold back to original range
  • 10.9. Limitations
• 11. Unary operations
  • 11.1. unary plus
  • 11.2. unary minus
  • 11.3. Trigonometric and hyperbolic functions
  • 11.4. Other mathematical functions
• 12. Binary operations
  • 12.1. Introduction
  • 12.2. sqw objects
    • 12.2.1. Single sqw object
    • 12.2.2. Array of sqw objects
  • 12.3. dnd objects
    • 12.3.1. Single dnd object
    • 12.3.2. Array of dnd objects
  • 12.4. Tips and Tricks
    • 12.4.1. List of operations and their equivalent code
    • 12.4.2. Binary operations manager
• 13. Plotting
  • 13.1. plot
  • 13.2. smooth
    • 13.2.1. Altering plot characteristics and other useful commands
  • 13.3. Colour of lines and markers
  • 13.4. Line style
  • 13.5. Marker style
  • 13.6. Axes Limits
  • 13.7. Cursor
  • 13.8. Keeping plots
    • 13.8.1. One dimensional plots
  • 13.9. dd (draw data)
  • 13.10. dl (draw line)
  • 13.11. dm (draw markers)
  • 13.12. dp (draw points)
  • 13.13. de (draw errors)
  • 13.14. dh (draw histogram)
  • 13.15. pd (plot data)
  • 13.16. pl (plot line)
  • 13.17. pm (plot markers)
  • 13.18. pp (plot points)
  • 13.19. pe (plot errors)
  • 13.20. ph (plot histogram)
  • 13.21. ploc (plot line over current)
  • 13.22. pdoc (plot data over current)
  • 13.23. pmoc (plot markers over current)
  • 13.24. ppoc (plot points over current)
  • 13.25. peoc (plot errors over current)
  • 13.26. phoc
    • 13.26.1. Two dimensional plots
  • 13.27. da (draw area)
  • 13.28. ds (draw surface)
  • 13.29. ds2 (draw surface from 2 sources)
  • 13.30. pa (plot area)
  • 13.31. ps (plot surface)
  • 13.32. ps2 (plot surface from 2 objects)
  • 13.33. spaghetti_plot
    • 13.33.1. Three dimensional plots
  • 13.34. sliceomatic
  • 13.35. sliceomatic_overview
    • 13.35.1. Miscellaneous functions
• 14. Simulation
  • 14.1. func_eval
  • 14.2. sqw_eval
  • 14.3. dispersion
  • 14.4. disp2sqw_eval
  • 14.5. dispersion_plot
  • 14.6. disp2sqw_plot
• 15. Multifit
  • 15.1. Overview
  • 15.2. Introduction to setting up and performing a fit
    • 15.2.1. Simple fitting
    • 15.2.2. Background functions
    • 15.2.3. Binding parameters
    • 15.2.4. Semi-global fits
  • 15.3. Summary of commands with multifit
  • 15.4. Fitting functions
    • 15.4.1. multifit function
    • 15.4.2. multifit_func
    • 15.4.3. multifit_sqw
    • 15.4.4. multifit_sqw_sqw
  • 15.5. Parallel fitting
• 16. Tobyfit
  • 16.1. Introduction
  • 16.2. Performing resolution convolution
    • 16.2.1. Setting the sample and instrument information
    • 16.2.2. Fitting data
• 17. Running Horace in Parallel
  • 17.1. Controlling MPI
    • 17.1.1. Enabling Locally
    • 17.1.2. Enabling Globally
  • 17.2. MPI Schemes
  • 17.3. Managing parallel jobs
  • 17.4. Slurm Jobs
• 18. Changing Horace settings
  • 18.1. Horace Config
  • 18.2. HPC Config
  • 18.3. Parallel Config

Horace Manual Appendix

• List of functions
• Input file formats
• FAQ