Diffcalc - A Diffraction Condition Calculator for Diffractometer Control ======================================================================== Diffcalc is a python/jython based diffraction condition calculator used for controlling diffractometers within reciprocal lattice space. It performs the same task as the fourc, sixc, twoc, kappa, psic and surf macros from SPEC. There is a `user guide `_ and `developer guide `_, both at `diffcalc.readthedocs.io `_ |Travis| |Read the docs| .. |Travis| image:: https://travis-ci.org/DiamondLightSource/diffcalc.svg?branch=master :target: https://travis-ci.org/DiamondLightSource/diffcalc :alt: Build Status .. |Read the docs| image:: https://readthedocs.org/projects/diffcalc/badge/?version=latest :target: http://diffcalc.readthedocs.io/en/latest/?badge=latest :alt: Documentation Status .. contents:: .. section-numbering:: Software compatibility ---------------------- - Written in Python using numpy - Works in Jython using Jama - Runs directly in `OpenGDA` - Runs in in Python or IPython using minimal OpenGda emulation (included) - Contact us for help running in your environment Diffractometer compatibility ---------------------------- Diffcalc’s standard calculation engine is an implementation of [You1999]_ and [Busing1967]_. Diffcalc works with any diffractometer which is a subset of: .. image:: https://raw.githubusercontent.com/DiamondLightSource/diffcalc/master/doc/source/youmanual_images/4s_2d_diffractometer.png :alt: 4s + 2d six-circle diffractometer, from H.You (1999) :width: 50% :align: center Diffcalc can be configured to work with any diffractometer geometry which is a subset of this. For example, a five-circle diffractometer might be missing the nu circle above. Note that the first versions of Diffcalc were based on [Vlieg1993]_ and [Vlieg1998]_ and a ‘Vlieg’ engine is still available. There is also an engine based on [Willmott2011]_. The ‘You’ engine is more generic and the plan is to remove the old ‘Vlieg’ engine once beamlines have been migrated. If we choose the x axis parallel to b, the yaxis intheplaneofblandb2,andthezaxis perpendicular to that plane, Installation ------------ Check it out:: $ git clone https://github.com/DiamondLightSource/diffcalc.git Cloning into 'diffcalc'... At Diamond Diffcalc may be installed within an OpenGDA deployment and is available via the 'module' system from bash. Starting -------- Start diffcalc in ipython using a sixcircle dummy diffractometer:: $ cd diffcalc $ ./diffcalc.py --help ... $ ./diffcalc.py sixcircle Running: "ipython --no-banner --HistoryManager.hist_file=/tmp/ipython_hist_zrb13439.sqlite -i -m diffcmd.start sixcircle False" ---------------------------------- DIFFCALC ----------------------------------- Startup script: '/Users/zrb13439/git/diffcalc/startup/sixcircle.py' Loading ub calculation: 'test' ------------------------------------ Help ------------------------------------- Quick: https://github.com/DiamondLightSource/diffcalc/blob/master/README.rst Manual: https://diffcalc.readthedocs.io Type: > help ub > help hkl ------------------------------------------------------------------------------- In [1]: Within Diamond use:: $ module load diffcalc $ diffcalc --help ... $ diffcalc sixcircle Trying it out ------------- Type ``demo.all()`` to see it working and then move try the following quick start guide:: >>> demo.all() ... Getting help ------------ To view help with orientation and then moving in hkl space:: >>> help ub ... >>> help hkl ... Configuring a UB calculation ---------------------------- See the full `user manual for many more options and an explanation of what this all means. To load the last used UB-calculation:: >>> lastub Loading ub calculation: 'mono-Si' To load a previous UB-calculation:: >>> listub UB calculations in: /Users/walton/.diffcalc/i16 0) mono-Si 15 Feb 2017 (22:32) 1) i16-32 13 Feb 2017 (18:32) >>> loadub 0 To create a new UB-calculation:: ==> newub 'example' ==> setlat '1Acube' 1 1 1 90 90 90 where the basis is defined by Busing & Levy: "...we choose the x axis parallel to b, the y axis in the plane of bl and b2, and the zaxis perpendicular to that plane." Find U matrix from two reflections:: ==> pos wl 1 ==> c2th [0 0 1] 59.99999999999999 ==> pos sixc [0 60 0 30 90 0] ==> addref [0 0 1] ==> pos sixc [0 90 0 45 45 90] ==> addref [0 1 1] Check that it looks good:: ==> checkub To see the resulting UB-calculation:: ==> ub Setting the reference vector ---------------------------- See the full `user manual for many more options and an explanation of what this all means. By default the reference vector is set parallel to the phi axis. That is, along the z-axis of the phi coordinate frame. The `ub` command shows the current reference vector, along with any inferred miscut, at the top its report (or it can be shown by calling ``setnphi`` or ``setnhkl'`` with no args):: >>> ub ... n_phi: 0.00000 0.00000 1.00000 <- set n_hkl: -0.00000 0.00000 1.00000 miscut: None ... Constraining solutions for moving in hkl space ---------------------------------------------- See the full `user manual for many more options and an explanation of what this all means. To get help and see current constraints:: >>> help con ... ==> con Three constraints can be given: zero or one from the DET and REF columns and the remainder from the SAMP column. Not all combinations are currently available. Use ``help con`` to see a summary if you run into troubles. To configure four-circle vertical scattering:: ==> con gam 0 mu 0 a_eq_b Moving in hkl space ------------------- Simulate moving to a reflection:: ==> sim hkl [0 1 1] Move to reflection:: ==> pos hkl [0 1 1] ==> pos sixc Scanning in hkl space --------------------- Scan an hkl axis (and read back settings):: ==> scan l 0 1 .2 sixc Scan a constraint (and read back virtual angles and eta):: ==> con psi ==> scan psi 70 110 10 hklverbose [0 1 1] eta Orientation Commands -------------------- ==> UB_HELP_TABLE Motion Commands --------------- ==> HKL_HELP_TABLE References ---------- .. [You1999] H. You. *Angle calculations for a '4S+2D' six-circle diffractometer.* J. Appl. Cryst. (1999). **32**, 614-623. `(pdf link) `__. .. [Busing1967] W. R. Busing and H. A. Levy. *Angle calculations for 3- and 4-circle X-ray and neutron diffractometers.* Acta Cryst. (1967). **22**, 457-464. `(pdf link) `__. .. [Vlieg1993] Martin Lohmeier and Elias Vlieg. *Angle calculations for a six-circle surface x-ray diffractometer.* J. Appl. Cryst. (1993). **26**, 706-716. `(pdf link) `__. .. [Vlieg1998] Elias Vlieg. *A (2+3)-type surface diffractometer: mergence of the z-axis and (2+2)-type geometries.* J. Appl. Cryst. (1998). **31**, 198-203. `(pdf link) `__. .. [Willmott2011] C. M. Schlepütz, S. O. Mariager, S. A. Pauli, R. Feidenhans'l and P. R. Willmott. *Angle calculations for a (2+3)-type diffractometer: focus on area detectors.* J. Appl. Cryst. (2011). **44**, 73-83. `(pdf link) `__.