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release_notes.txt
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6.18.03 DRAFT
GENERAL
HDF Catching a NaN in the input data
KUPLOT Load HDF5
DISCUS Write HDF5
Improved the transformation to a new coordinate system
KUPLOT Load HDF5 improved error message in case increment vectors are of length zero
DISCUS
export Added a 'force:yes' option to 'export shelx' to force writing even if the
structure extends over more than one unit cell. Might happen for long molecules.
mmc Changed the correlation parameter to Warren-Cowley, this has no effect for
binary materials, is much better for ternary searches
Added a new 'pref' energy that relies on the AB correlation only and is unidirectional
'calc' command gives more output
import 'import shelx' can now set up a DISCUS single crystal and/or powder refinement
6.18.02 RELEASE 2025_01_18
GENERAL
'cd' The command accepts special directory names:
$HOME, $HOMEPATH, $WSL_DOC, $WSL
'fget' Improved the 'form:a' parameter
set Added a 'set author:names' command
macros Upon a error driven abort, the macro returns to the inital
directory from which the macro was started
DISCUS
import Added a flag:refine:yes", which will write the DISCUS refinement macros
read Improved reading of molecules, did not work in some space groups
6.18.01 RELEASE 2024_12_04
GENERAL
improved conversion of shelx LIST 4/2 files
variables Added system variables OPERATING, LINUX, MACOSX WINWSL to test operating system
DISCUS
import Improved handling of SHELX import, added a form:waas form:table flag
to fix form factor look up
REFINE
run BUG FIX, the "refine_new.res" file contained an erroneous "exit"
6.18.00 RELEASE 2024_12_01
DISCUS
GENERAL Added guess work to interpret atom names like "O22", "H1N" etc to
extract pure chemical element. If successful this can replace the
'scat H1N, H' instruction
import SHELX: The "LATT" and "SYMM" instructions are interpreted to yield
the corresponding space group symbol
Anisotropic ADP are interpreted
The extrinction parameter is interpreted
optional "refine:yes" creates macros needed for refine
export SHELX: Improved Atom names, Fixed export of rhombohedral systems
with non-heagonal axes
CIF: Impoved Symmetry information in header, includes list of 'x, y, z'
Included anisotropic ADP
powder The asymmetry parameters 3 and 4 have become obsolete, since the
parameters 'asym_1', asym_2' and 'asym_i1' take care of the
2Theta / Q dependence. Side effect is that values of the
asymmetry parameters has changed to achieve an asymmetry.
Added an option to define the origin for a background polynomial
read 'free' and 'spcgr' within unit cell file can now use the
optional "origin:2" parameter
the space group name in the cell file or on the 'free' command
may contain blanks like 'P 21 21 21'
spacegroup can now use the optional "origin:2" parameter
KUPLOT
load Added option to "csv": "separator:[4,4,4,8,8]" will read files with
fixed column widths.
hlin optional 'abs' parameter did not work.
REFINE
run Improved internal R-value calculation for HKL lists.
Missing Bragg reflections are now properly omitted
Improved mixed lists of fixed and refined parameters,
Improved load to do proper KUPLOT reset
Improved default values of 'shift:' parameters to 0.001
6.17.02 RELEASE 2024_08_29
DISCUS
fourier BUG FIX NUFFT did not work properly for large DELTA(hkl) steps
fourier Improved lanczos filter to work in slices along small dimensions == large DELTA(hkl) steps
mmc BUG FIX, site restrictions on atom types at different sites did not work
REFINE
convergence Added a fourth convergence criterion that stops if lambda becomes too large
Improved output of "refine_best.mac and "refine_new.res"
6.17.01 RELEASE 2024_06_30
GENERAL
general on Windows, a parallel process might have crashed due to timing issues
general added a timer command to the command language
DISCUS
mmc The mmc initial reported wrong values for angles.
powder/output The periodic boundary treatment for PDF did not work.
powder/output Added option for partial PDFs via Debye-Scattering-Equation
pdf The partial pdf calculation in the old pdf menu did not work.
rmc RMC needed fixes.
super Ongoing development
REFINE
refine BUG FIX Failed for differing "points:" number.
6.17.00 RELEASE 2024_06_02
GENERAL
DISCUS
KUPLOT
kpar_par Extremely narrow parameter distribution messed up x/y scales.
REFINE
Added parallel refinement
6.16.03 RELEASE 2024_04_22
GENERAL
general The welcome screen shows more clearly if an "autorun.mac"
Macro is used
DISCUS
Many updates are going on for major new release this summer,
hopefully no effect on user yet.
chem BUG FIX env command
fourier Added "extinction" correction as in SHELXL
Added calculation mode for single crystal HKL intensity files
mmc Added option to suppress output, streamlined final output
Added option to calculate all correlations outside a run
powder BUG FIX related to PDF correlated motion correction and
multi phase PDFs
read BUG FIX "unique:name" parameter mistook similar atom names like "Ni, N"
show Added long and short output options for "show atom"
stack BUG FIX corrected weight for multi phase powder pattern
structure Added better check for unusual "generators" in input file
REFINE
refine Bug fixes related to hkl input files
Added a "refine_new.res" macro as output of current status
6.16.02 RELEASE 2023_12_09
DISCUS
fourier BUG FIX for icalculations starting with large negative
lower left corners, point in reciprocal space were
often shifted a pixel or so.
6.16.01 RELEASE 2023_11_27
DISCUS
chem Added output on crystal dimensions/number of unit cells
export BUG FIX corrected output into RMCprofile format;
atom coordinates are mapped into [1,1]; 1 exclusive
6.16.00 RELEASE 2023_11_01
GENERAL
Windows10 BUG FIX update command crashed if WindowsTerminal was not installed
Macro Macros that terminated in a (different) sub level would leave
wrong prompt
DISCUS
general All fourier and related menues received a major internal update
As a side effect, this corrected several bugs in reciprocal
layers that are not the standard HK0 layers.
0KL layers might have an odd shift of pixels
the convolution did not work properly for layers other than HK0
side effects on stacking with non [001] stacking
direction were corrected
chem Added an optional parameter "site:" to homo
export Added occupancies to a CIF file export
import CIF import: Added a check if a centrosymmetric structure
uses origin choice 2 i.e. inversion center at 0,0,0
powder Improved handling of corrlin and corrquad for a powder PDF
plot BUG FIX, Avoiding crash if jmol had never been used before
KUPLOT
load Added option to load SHELX:hklf4 files
rvalue Added optional logfile output
kuplot2global Full 3D, added option to define refine output by parameter name
REFINE
Extensive changes, made full 3D ready
6.15.01 RELEASE 2023_07_20
GENERAL
Improved the handling and transformation of 3D intensities/PDF
DISCUS
surface The names for optional placement of the ellipdois/cylinder axes
were not ideal. The parameter names have been changed to
"first:" and "third".
mmc The molecule modification part will now use internal
parallel processing as well.
6.15.00 RELEASE 2023_06_27
GENERAL
WINDOWS For Windows 11 and wsl version 2 the VcXsrv is no longer needed
Improvement of installation scripts, added option to place
a terminal icon and a startup script
DISCUS/KUPLOT BUG FIX, Improved storage/interpretation in HDF5 files, relevant
for oblique layers
DISCUS
plot Added options to place Jmol window
output Added better scaling options to "shelx", "hklf4", "list5" files
export Improved storage of original space group into CIF file
read/cell BUG FIX, multiple molecule were not properly recognized after
a save
show/symm Added a flag to indicated generator matrices
DIFFEV
run_mpi Improved error message transfer from slaves
6.14.02 RELEASE 2023_05_16
GENERAL
Removed a few unnecessary debug output lines
DISCUS
mmc BUG FIX Very long lines on 'set vec' did not work
export Added output options for scatty
O6.14.01 RELEASE 2023_03_21
GENERAL
Removed a few unnecessary debug output lines
The macro on the command line has been added to the command history
DISCUS
fourier Set symm:apply was not fully active
BUG FIX The absence of "sigtop" caused trouble
mmc BUG FIX Corrected the "all" atom types parameters on 'set target'
powder Added missing output on hkl steps for complete mode
show Added a flag to indicate which symmetry elements are part of the point group
surface Surfaces closer then 0.5 A to the origin cut off all atoms.
Modified to a much smaller tolerance of 10^-9A.
6.14.00 RELEASE 2023_02_15
GENERAL
Moved all FFT's to the FFTW library which is much faster
DISCUS
save/read Added a format specifier. Files with this format can be read much faster
fourier BUG FIX for grid that did not include 0,0,0 in reciprocal space, the phase
of data points was off by half a grid point.
fourier Preparation for major update
mmc Added an option to display initial status
output Added an option to transform data upon write
read Added an option to fine-tune which atoms are considered individual unique atom types
stack BUG FIX, Layers with many different atom types could cause a crash
KUPLOT
save Added a tolerance test to avoid rounding errors
6.13.00 RELEASE 2022_12_19
DISCUS
mmc Added an option to control amount of output during / after mmc loop
powder Added a Pearson Type VII profile function
stack BUG FIX: Improved atom modulo function.
Corrected possible crash if 2nd layer had more atoms than previous.
General
Added a Pearson Type VII profile function
KUPLOT
match Extended 'match mix' to xyz files
help Corrected entry for 'match' command
6.12.07 RELEASE 2022_11_29
General Improved installation scripts on resolve issue of github.com
6.12.06 RELEASE 2022_11_27
DISCUS
GENERAL Corrected wave length CuKa1, 2 to 1.54092 and 1.544343 accroding to
Mendenhal et al. J.Physics B (2017), 50, 115004
DOI 10.1088/1361-6455/aa6c4a
powder BUG FIX Corrected calculation of S(Q), F(Q), PDF for complete mode
powder BUG FIX Asymmetry correction was permanently off.
powder BUG FIX Kalpha 1/2 correction was slightly off.
export Enforced updatas of crystal dimensions
KUPLOT
fit BUX FIX Corrected maxima search for Gauss and Lorentz
6.12.05 RELEASE 2022_10_10
DISCUS
powder The combination of Debye-Scattering-Equation with periodic boundary
conditions and multiple phases did not work well.
6.12.04 RELEASE 2022_10_10
General
Continued move of KUPLOT data to global storage; no effect on user yet.
DISCUS
stack BUG FIX Layers with differing chemical composition were not recognized
6.12.03 RELEASE 2022_09_16
General
Continued move of KUPLOT data to global storage; no effect on user yet.
DISCUS
stack BUG FIX Stacking faults with 'create' and no 'run' caused crash, FIXED
stack BUG FIX if modulus was off, yet modulo vector were set, these were
erroneously added to the layers. FIXED
stack Added option to apply the modulo function to atoms as well, creating a
smoother surface
plot BUG FIX Modifies cif file output to adhere to CIF standard, unique atom labels
This caused Jmol versions 14.32.59 and later to make faulty plot.
export BUG FIX Corrected super cell dimensions
Corrected file name for version 7
Corrected internal BUG that prevented multiple use.
purge Improved estimation of crystal size
perioditize BUG FIX Correctes estimate of unit cell numbers (y dimension was wrong)
6.12.02 RELEASE 2022_07_23
General
Starting to move KUPLOT data into a global data structure format
Moved HDF5 read/write into lib_f90; no effect on user
Windows Version Modified the check for Ubuntu update
KUPLOT Added 1d and 2D to 'fft' command
DISCUS
mmc BUG FIX, "set disallow, all" did not work
Added a new modification mode "swneig" to exchange neighbors
still under development
Improved on "coordination number" energy, added this to help
still under development
6.12.01 RELEASE 2022_07_05
General
BUG FIX Internal test for internet connection was language dependent.
BUG FIX Search for newer DISCUS version did not work after curl adaptations
KUPLOT Started HDF5 write
BUX FIX corrected load of 1D HDF5 files
6.12.00 RELEASE 2022_06_30
General
Revised WSL installation scrips to reduce admin needs as much as possible
Added a new installation script
bbb_install_suite_WINDOWS10_WSL.bat
to avoid powershell execution policy issues
DISCUS
powder Added an empirical uvw form as polynomial on Q
Started to add TOF profile functions
6.11.01 RELEASE 2022_05_24
6.11.00 RELEASE 2022_05_24
DISCUS
bragg New command to convert between parameters in Braggs law
6.10.00 RELEASE 2022_05_06
General
installation scripts BUG FIX fixed issues with 'curl' commands
the 'update' command crashed the program, FIXED
At WSL the Ubuntu update did not work, FIXED
DISCUS
mmc BUG FIX, A 'reset' did not set all shifts to zero
deco BUG FIX, added a 'mmc reset' to avoid unexpected siide effects to mmc
powder Modified the profile parameters uvw to give the same FWHM irrespective
of the axis used in the calculation. Values correspond to FHWM with respect
to a 2Theta scale.
Added FWHM function for powder diffraction with an area detectors
as in Chernyshov et al. ActaCryst A77, 497-505,
doi 10.1107/S2053273321007506
powder BUG FIX corrected Lorentz correction for complete mode
6.09.04 RELEASE 2022_04_21
Superseeds 03
General
Improved handling of missing internet connection
DISCUS
perioditize BUG FIX, help did not work
export BUG FIX, command could not be reached
BUG FIX, Added error messege to 'shelxl' if crystal > 1 unit cell
Modified unit cell size to avoid atoms at coordinates == 1.0
import BUG FIX, increased flexibility for RMC6f formats
BUG FIX, shelxl import did not recognize SYMM
transform BUG FIX, did not run if new lattice parameters were given
6.09.03 RELEASE 2022_04_20
DISCUS
perioditize BUG FIX, help did not work
export BUG FIX, command could not be reached
BUG FIX, Added error messege to 'shelxl' if crystal > 1 unit cell
Modified unit cell size to avoid atoms at coordinates == 1.0
import BUG FIX, increased flexibility for RMC6f formats
BUG FIX, shelxl import did not recognize SYMM
transform BUG FIX, did not run if new lattice parameters were given
6.09.02 RELEASED 2022_03_23
DISCUS
EXP2PDF Continued development, improved limit selection,
fine tuned graphics
KUPLOT
ccal Added a further parameter "sig", which will add a
Gaussian distributed nois to the data set.
fft Added a FastFourier transform
6.09.01 RELEASED 2022_03_10
Minor BUG FIX compared to v.6.09.01
DISCUS
EXP2PDF improved handling of data and background of various lengths
Corrected error related to qscale
6.09.00 RELEASED 2022_03_08
General
'stop' Enabled execution of macros in stopped mode.
DISCUS
PERIODITIZE New menu to transforma structure into a periodic
array, possibly with inclusions of voids
EXP2PDF New menu to transform an experimental powder diffraction
pattern into a powder PDF.
DOMAIN enabled "orient' and 'shape' to handle format specifiers
PLOT enabled a 'run kill:yes' line, just to kill all previous JMOLs
POWDER FIXED BUG Corrected corrlin, corrquad action in powder menue
FIND enabled format specifier for atom names
FOURIER FIXED BUG, in some circumstances the average intensity output
was missing the Friedel pairs.
FOURIER Introduced an automatic scaling between Bragg and diffuse
intensities that applies to a full 3D-PDF only. Not relevant
for 3D-Delta-PDF or plain intensities.
MMC FIXED BUG, Feedback algorithm was always on, even for
target "corr" with last parameter set to "ENER".
MOLECULARIZE Improved the command by adding optional parameters.
READ Improved input speed for larger structures
SURRFACE FIXED BUG, orientation of ellipsoids did not follow instructions
Atomic Form factors
Corrected values for the Elements:, International Tables Table 1.1.1.3
Gd xray a4
Sm xray b4
Cr electron a5
Mo electron a2
H1- xray b3 was wrong in ITC
D1- xray b3 was wrong in ITC
Ru4+ xray b3 was wrong in ITC
Bi5+ xray b2 was wrong in ITC
Implemented Waasmaier & Kirfel Parameters
KUPLOT
load enabled the type parameter to be given as a formatted string
load "%c",'xy'
fit Improved handling of stagnant parameters
color Added option to set the line colors to a color map
REFINE
Thorough improvements to handle parameters with zero derivative,
better default settings
6.08.02 RELEASED 2021_18
General
Modified update command for WSL, avoids powershell.
Modified Windows installation script to handle blanks in User names.
DISCUS
SURFACE FIXED BUG Orientation of ellipsoids was erroneously turned around
long axis.
KUPLOT
FIXED BUG some routines were missing in kuplot_load_hdf5_no
6.08.01 RELEASED 2021_October_11
DISCUS
SURFACE Augmented the boundary command with a center:<value> parameter
and the option to use "com" == "center of mass" for the value.
POWDER FIXED BUG Corrected the calculation of a periodic boundaary PDF
using the Debye-Scattering-Equation
6.08.00 RELEASED 2021_October_08
General
Expanded the internal tests to see if the program runs on a computer
that is online/offline.
DISCUS
MMC Added an optional parameter "log" to 'run' command
READ Structure fiules may no consist of "name x, y, z" only
SURFACE FIXED BUG, optional command 'long' did not work
SYMM FIXED BUG, User 'uvw' was not handeled properly
KUPLOT
All graphics output is written as Postscipt file. ImageMagick is used to
process these into the desired graphics format.
As default the background is no longer transparent.An optional
parameter allows transparent images.
For 'png' and 'pdf' output, the resolution can be specified.
6.07.00 RELEASED 2021_Jul_26
General
Added an option "prepare=libraries" or "prepare=none" to update command
Added a new variable type "EXPR" that is to be evaluated in a menu at 'run' time
DISCUS
FIXED BUG in mmc regarding the sorting of targets with atom groups
like "...(Al), (Be,Cs)..."
FIXED BUG related to symmetry average of 3D diffraction pattern
FIXED BUG Corrected atom names in export to JMol this improved polygon plotting
FIXED BUG Corrected internal handling of user defined anomalous scattering parameters
FIXED BUG Recognition of molecules in domain/read from internal storage
FIXED BUG Internal counting of additional generators
FIXED BUG Included avarage intensity in convolution for single crystal pattern
MMC added a 'group' correlation
MMC extensive revision with regards to molecules
MMC improved convergence
MMC replaced 'neig, add' by 'set neig, ..., number:'
DOMAIN added irregular domains
PLOT Improved handling of atoms with charges
PLOT Changed default atom size (except with polyhedra)
PLOT Added options to draw lines into JMOL plot
PLOT Added export option to JMOL plots
CONN added a new mode to create connectivities from a group
of vectors
FIND Added the option to find an environment that corresponds
to a neighborhood as defined in MMC
FIND Added an option to find a neighborhood that consists of the
recursively searched connectivity.
SYMM and DOMAIN added use of 'EXPR' variables
OUTPUT added an option to add the data into an existing kuplot
data set
added an output of the averaged Intensities
Added 'vesta' output
PERIOD Created a new menu to rearrange the sequence into a
periodic structure
KUPLOT
Added option to plot a line as (filled) polygon
Changed the 'png' output to go through a postscript file. This works
better for multiple color maps.
6.06.00 RELEASED 2021_Feb_16
SUITE
FIXED BUG parallel command did not work for Windows WSL
DISCUS
Added option to accumulate several diffraction pattern
Added option to apply symmetry averaging to diffraction pattern
FIXED BUG in powder, Linear and square parameters were not read correctly.
FIXED BUG Corrected output format for neutron energies at short wave lengths
KUPLOT
Added a FFT for 1D, 2D, 3D
FIXED BUG fit: the old "urf" was transscribed into the lambda start for the new fit.
FIXED BUG fit: The background polynomial indicated wrong parameter number.
FIXED BUG parallel mode at windows did not work.
General
FIXED BUG for update command. Unfortunately the 'update' command had
a bug that rendered it faulty on Linux and MAC.
FIXED BUG change directory was faulty for WSL
6.05.00 RELEASED 2021_Jan_20
DIFFEV
FIXED BUG constraint rules were not working
DISCUS
Added "xplor" file format for 3-D maps (intensity, 3DPDF etc.)
Added 'range' command to output to limit extend of maps for "xplor"
Fixed use of "set vec" into neighborhoods with vectors starting
at several (symmetrically equivalent) sites.
KUPLOT
Added a double peak Pseudo-Voigt function for Kalpha1,2 radiation
as general function and as fit function.
REFINE, KUPLOT
Added a global storage to exchange data, especially calculated derivatives
General
Added a (double-peak) Pseduo-Voigt function
Added a function to determine the number associated to a Refine
parameter name. Used for the calculated derivatives
The Linux installation scripts include a check for the "curl" program
The MacOS installation has a minor update related to the changed brew syntax
6.04.00 RELEASED
FIXED bug in calculations involving matrices. These could not be at a
lower alphabetical order than scalar variables.
DISCUS
Added an optional parameter to the 'value' command in 'output'.
This allows to set a maximum radius in reciprocal space to be
applied prior to the 3D-PDF calculation.
import Adapted RMCf6 import to more flexible file formats
6.03.01 RELEASED