https://github.com/diamondlightsource/diffcalc
Diffcalc: a diffraction condition calculator for X-ray or neutron diffractometer control
https://github.com/diamondlightsource/diffcalc
diffraction numpy python science synchrotron
Last synced: 10 months ago
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Diffcalc: a diffraction condition calculator for X-ray or neutron diffractometer control
- Host: GitHub
- URL: https://github.com/diamondlightsource/diffcalc
- Owner: DiamondLightSource
- License: gpl-3.0
- Created: 2012-03-22T15:23:03.000Z (almost 14 years ago)
- Default Branch: master
- Last Pushed: 2023-04-26T15:35:58.000Z (over 2 years ago)
- Last Synced: 2023-10-20T19:19:08.694Z (about 2 years ago)
- Topics: diffraction, numpy, python, science, synchrotron
- Language: Python
- Homepage:
- Size: 4.6 MB
- Stars: 17
- Watchers: 9
- Forks: 14
- Open Issues: 7
-
Metadata Files:
- Readme: README.rst
- License: COPYING
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README
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 `_
**IMPORTANT**: Python 3 version of diffcalc calculator code is available as ``diffcalc-core`` project https://github.com/DiamondLightSource/diffcalc-core/
|GH Actions| |Read the docs|
.. |GH Actions| image:: https://github.com/DiamondLightSource/diffcalc/actions/workflows/main.yml/badge.svg?branch=master
:target: https://github.com/DiamondLightSource/diffcalc/actions
: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.
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
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 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
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)
`__.
.. [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)
`__.