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 <https://diffcalc.readthedocs.io/en/latest/youmanual.html>_ and developer guide <https://diffcalc.readthedocs.io/en/latest/developer/contents.html>, both at diffcalc.readthedocs.io <https://diffcalc.readthedocs.io>

IMPORTANT: Python 3 version of diffcalc calculator code is available as diffcalc-core project https://github.com/DiamondLightSource/diffcalc-core/

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Software compatibility

• Written in Python using numpy
• Works in Jython using Jama
• Runs directly in OpenGDA<http://www.opengda.org>
• 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.

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<https://diffcalc.readthedocs.io> 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

Find U matrix from two reflections::

pos wl 1 wl: 1.0000 c2th [0 0 1] 59.99999999999999

pos sixc [0 60 0 30 90 0] sixc: mu: 0.0000 delta: 60.0000 gam: 0.0000 eta: 30.0000 chi: 90.0000 phi: 0.0000 addref [0 0 1]

pos sixc [0 90 0 45 45 90] sixc: mu: 0.0000 delta: 90.0000 gam: 0.0000 eta: 45.0000 chi: 45.0000 phi: 90.0000 addref [0 1 1] Calculating UB matrix.

Check that it looks good::

checkub

    ENERGY     H     K     L    H_COMP   K_COMP   L_COMP     TAG
1  12.3984  0.00  0.00  1.00    0.0000   0.0000   1.0000        
2  12.3984  0.00  1.00  1.00    0.0000   1.0000   1.0000        

To see the resulting UB-calculation::

ub UBCALC

  name:       example

  n_phi:      0.00000   0.00000   1.00000 <- set
  n_hkl:     -0.00000   0.00000   1.00000
  miscut:     None

CRYSTAL

  name:        1Acube

  a, b, c:    1.00000   1.00000   1.00000
             90.00000  90.00000  90.00000

  B matrix:   6.28319   0.00000   0.00000
              0.00000   6.28319   0.00000
              0.00000   0.00000   6.28319

UB MATRIX

  U matrix:   1.00000   0.00000   0.00000
              0.00000   1.00000   0.00000
              0.00000   0.00000   1.00000

  U angle:    0

  UB matrix:  6.28319   0.00000   0.00000
              0.00000   6.28319   0.00000
              0.00000   0.00000   6.28319

REFLECTIONS

    ENERGY     H     K     L        MU    DELTA      GAM      ETA      CHI      PHI  TAG
  1 12.398  0.00  0.00  1.00    0.0000  60.0000   0.0000  30.0000  90.0000   0.0000  
  2 12.398  0.00  1.00  1.00    0.0000  90.0000   0.0000  45.0000  45.0000  90.0000  

Setting the reference vector

See the full user manual<https://diffcalc.readthedocs.io> 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<https://diffcalc.readthedocs.io> for many more options and an explanation of what this all means.

To get help and see current constraints::

help con ...

con DET REF SAMP ------ ------ ------ delta --> a_eq_b --> mu --> gam alpha eta qaz beta chi naz psi phi mu_is_gam

   gam  : 0.0000
   a_eq_b
   mu   : 0.0000

   Type 'help con' for instructions

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 gam : 0.0000 a_eq_b mu : 0.0000

Moving in hkl space

Simulate moving to a reflection::

sim hkl [0 1 1] sixc would move to: mu : 0.0000 delta : 90.0000 gam : 0.0000 eta : 45.0000 chi : 45.0000 phi : 90.0000

 alpha :   30.0000
  beta :   30.0000
   naz :   35.2644
   psi :   90.0000
   qaz :   90.0000
   tau :   45.0000
 theta :   45.0000

Move to reflection::

pos hkl [0 1 1] hkl: h: 0.00000 k: 1.00000 l: 1.00000

pos sixc sixc: mu: 0.0000 delta: 90.0000 gam: 0.0000 eta: 45.0000 chi: 45.0000 phi: 90.0000

Scanning in hkl space

Scan an hkl axis (and read back settings)::

scan l 0 1 .2 sixc l mu delta gam eta chi phi

0.00000 0.0000 60.0000 0.0000 30.0000 0.0000 90.0000 0.20000 0.0000 61.3146 0.0000 30.6573 11.3099 90.0000 0.40000 0.0000 65.1654 0.0000 32.5827 21.8014 90.0000 0.60000 0.0000 71.3371 0.0000 35.6685 30.9638 90.0000 0.80000 0.0000 79.6302 0.0000 39.8151 38.6598 90.0000 1.00000 0.0000 90.0000 0.0000 45.0000 45.0000 90.0000

Scan a constraint (and read back virtual angles and eta)::

con psi gam : 0.0000 ! psi : --- mu : 0.0000 scan psi 70 110 10 hklverbose [0 1 1] eta psi eta h k l theta qaz alpha naz tau psi beta

70.00000 26.1183 0.00000 1.00000 1.00000 45.00000 90.00000 19.20748 45.28089 45.00000 70.00000 42.14507 80.00000 35.1489 -0.00000 1.00000 1.00000 45.00000 90.00000 24.40450 40.12074 45.00000 80.00000 35.93196 90.00000 45.0000 0.00000 1.00000 1.00000 45.00000 90.00000 30.00000 35.26439 45.00000 90.00000 30.00000 100.00000 54.8511 -0.00000 1.00000 1.00000 45.00000 90.00000 35.93196 30.68206 45.00000 100.00000 24.40450 110.00000 63.8817 -0.00000 1.00000 1.00000 45.00000 90.00000 42.14507 26.34100 45.00000 110.00000 19.20748

Orientation Commands

+-----------------------------+---------------------------------------------------+ | STATE | +-----------------------------+---------------------------------------------------+ | -- newub {'name'} | start a new ub calculation name | +-----------------------------+---------------------------------------------------+ | -- loadub 'name' | num | load an existing ub calculation | +-----------------------------+---------------------------------------------------+ | -- lastub | load the last used ub calculation | +-----------------------------+---------------------------------------------------+ | -- listub | list the ub calculations available to load | +-----------------------------+---------------------------------------------------+ | -- rmub 'name'|num | remove existing ub calculation | +-----------------------------+---------------------------------------------------+ | -- saveubas 'name' | save the ub calculation with a new name | +-----------------------------+---------------------------------------------------+ | LATTICE | +-----------------------------+---------------------------------------------------+ | -- setlat | interactively enter lattice parameters (Angstroms | | | and Deg) | +-----------------------------+---------------------------------------------------+ | -- setlat name a | assumes cubic | +-----------------------------+---------------------------------------------------+ | -- setlat name a b | assumes tetragonal | +-----------------------------+---------------------------------------------------+ | -- setlat name a b c | assumes ortho | +-----------------------------+---------------------------------------------------+ | -- setlat name a b c | assumes mon/hex with gam not equal to 90 | | gamma | | +-----------------------------+---------------------------------------------------+ | -- setlat name a b c | arbitrary | | alpha beta gamma | | +-----------------------------+---------------------------------------------------+ | -- c2th [h k l] | calculate two-theta angle for reflection | +-----------------------------+---------------------------------------------------+ | -- hklangle [h1 k1 l1] | calculate angle between [h1 k1 l1] and [h2 k2 l2] | | [h2 k2 l2] | crystal planes | +-----------------------------+---------------------------------------------------+ | REFERENCE (SURFACE) | +-----------------------------+---------------------------------------------------+ | -- setnphi {[x y z]} | sets or displays n_phi reference | +-----------------------------+---------------------------------------------------+ | -- setnhkl {[h k l]} | sets or displays n_hkl reference | +-----------------------------+---------------------------------------------------+ | REFLECTIONS | +-----------------------------+---------------------------------------------------+ | -- showref | shows full reflection list | +-----------------------------+---------------------------------------------------+ | -- addref | add reflection interactively | +-----------------------------+---------------------------------------------------+ | -- addref [h k l] | add reflection with current position and energy | | {'tag'} | | +-----------------------------+---------------------------------------------------+ | -- addref [h k l] (p1, | add arbitrary reflection | | .., pN) energy {'tag'} | | +-----------------------------+---------------------------------------------------+ | -- editref num | interactively edit a reflection | +-----------------------------+---------------------------------------------------+ | -- delref num | deletes a reflection (numbered from 1) | +-----------------------------+---------------------------------------------------+ | -- clearref | deletes all the reflections | +-----------------------------+---------------------------------------------------+ | -- swapref | swaps first two reflections used for calculating | | | U matrix | +-----------------------------+---------------------------------------------------+ | -- swapref num1 num2 | swaps two reflections (numbered from 1) | +-----------------------------+---------------------------------------------------+ | CRYSTAL ORIENTATIONS | +-----------------------------+---------------------------------------------------+ | -- showorient | shows full list of crystal orientations | +-----------------------------+---------------------------------------------------+ | -- addorient | add crystal orientation interactively | +-----------------------------+---------------------------------------------------+ | -- addorient [h k l] | add crystal orientation in laboratory frame | | [x y z] {'tag'} | | +-----------------------------+---------------------------------------------------+ | -- editorient num | interactively edit a crystal orientation | +-----------------------------+---------------------------------------------------+ | -- delorient num | deletes a crystal orientation (numbered from 1) | +-----------------------------+---------------------------------------------------+ | -- clearorient | deletes all the crystal orientations | +-----------------------------+---------------------------------------------------+ | -- swaporient | swaps first two crystal orientations used for | | | calculating U matrix | +-----------------------------+---------------------------------------------------+ | -- swaporient num1 num2 | swaps two crystal orientations (numbered from 1) | +-----------------------------+---------------------------------------------------+ | UB MATRIX | +-----------------------------+---------------------------------------------------+ | -- checkub | show calculated and entered hkl values for | | | reflections | +-----------------------------+---------------------------------------------------+ | -- setu | manually set u matrix | | {[[..][..][..]]} | | +-----------------------------+---------------------------------------------------+ | -- setub | manually set ub matrix | | {[[..][..][..]]} | | +-----------------------------+---------------------------------------------------+ | -- calcub | (re)calculate u matrix from ref1 and ref2 | +-----------------------------+---------------------------------------------------+ | -- trialub | (re)calculate u matrix from ref1 only (check | | | carefully) | +-----------------------------+---------------------------------------------------+ | -- refineub {[h k l]} | refine unit cell dimensions and U matrix to match | | {pos} | diffractometer angles for a given hkl value | +-----------------------------+---------------------------------------------------+ | -- addmiscut angle | apply miscut to U matrix using a specified miscut | | {[x y z]} | angle in degrees and a rotation axis | | | (default: [0 1 0]) | +-----------------------------+---------------------------------------------------+ | -- setmiscut angle | manually set U matrix using a specified miscut | | {[x y z]} | angle in degrees and a rotation axis | | | (default: [0 1 0]) | +-----------------------------+---------------------------------------------------+

Motion Commands

+-----------------------------+---------------------------------------------------+ | CONSTRAINTS | +-----------------------------+---------------------------------------------------+ | -- con | list available constraints and values | +-----------------------------+---------------------------------------------------+ | -- con {val} | constrains and optionally sets one constraint | +-----------------------------+---------------------------------------------------+ | -- con {val} | clears and then fully constrains | | {val} {val} | | +-----------------------------+---------------------------------------------------+ | -- uncon | remove constraint | +-----------------------------+---------------------------------------------------+ | HKL | +-----------------------------+---------------------------------------------------+ | -- allhkl [h k l] | print all hkl solutions ignoring limits | +-----------------------------+---------------------------------------------------+ | HARDWARE | +-----------------------------+---------------------------------------------------+ | -- hardware | show diffcalc limits and cuts | +-----------------------------+---------------------------------------------------+ | -- setcut {name {val}} | sets cut angle | +-----------------------------+---------------------------------------------------+ | -- setmin {axis {val}} | set lower limits used by auto sector code (None | | | to clear) | +-----------------------------+---------------------------------------------------+ | -- setmax {name {val}} | sets upper limits used by auto sector code (None | | | to clear) | +-----------------------------+---------------------------------------------------+ | MOTION | +-----------------------------+---------------------------------------------------+ | -- sim hkl scn | simulates moving scannable (not all) | +-----------------------------+---------------------------------------------------+ | -- sixc | show Eularian position | +-----------------------------+---------------------------------------------------+ | -- pos sixc [mu, delta, | move to Eularian position(None holds an axis | | gam, eta, chi, phi] | still) | +-----------------------------+---------------------------------------------------+ | -- sim sixc [mu, delta, | simulate move to Eulerian positionsixc | | gam, eta, chi, phi] | | +-----------------------------+---------------------------------------------------+ | -- hkl | show hkl position | +-----------------------------+---------------------------------------------------+ | -- pos hkl [h k l] | move to hkl position | +-----------------------------+---------------------------------------------------+ | -- pos {h | k | l} val | move h, k or l to val | +-----------------------------+---------------------------------------------------+ | -- sim hkl [h k l] | simulate move to hkl position | +-----------------------------+---------------------------------------------------+

References

.. [You1999] H. You. Angle calculations for a '4S+2D' six-circle diffractometer. J. Appl. Cryst. (1999). 32, 614-623. (pdf link) <http://journals.iucr.org/j/issues/1999/04/00/hn0093/hn0093.pdf>__.

.. [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) <http://journals.iucr.org/q/issues/1967/04/00/a05492/a05492.pdf>__.

.. [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) <http://journals.iucr.org/j/issues/1993/05/00/la0044/la0044.pdf>__.

.. [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) <http://journals.iucr.org/j/issues/1998/02/00/pe0028/pe0028.pdf>__.

.. [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) <http://journals.iucr.org/j/issues/2011/01/00/db5088/db5088.pdf>__.