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

• 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

Diffcalc’s standard calculation engine is an implementation of [You1999] and [Busing1967]. Diffcalc works with any diffractometer which is a subset of:

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.

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.

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

Type demo.all() to see it working and then move try the following quick start guide:

>>> demo.all()
...

To view help with orientation and then moving in hkl space:

>>> help ub
...
>>> help hkl
...

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

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
...

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

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

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