Dear all,
I presently try to get the sequence refinement working. I was partially
successful but I am also plagued by a number of bugs. I had a hard time
to pinpoint most of them but two of them are very persistent and seem to
screws GSASII to the point where nothing works any more, including
previous successful refinements. I will be very grateful for some
insight how to avoid at least the two frequent errors listed below.
Here is some more info:
- The first error appeared after I have removed the third phase from the
refinement and I think the program did not really realise this fact. I
had to start the whole experimental form the beginning and it helped.
- Second issue appeared after adding excluded regions to the sequential
refinement. Restarts of the whole program and a creation of new
experimental files from scratch do not help.
Other potential improvements:
- Perhaps it is only me but a constant resizing of the window containing
the phase/PWD options (while flipping between options) is really
annoying. Please add a possibility to fix the window size.
- While importing structures from existing experimental files please
allow for more than one phase to be imported at the same time
- Removing excluded regions seems to be impossible at the moment and it
would be very handy option.
- Allow in Phase->Data to automatically show settings for the first
histogram
best wishes
Andrzej
========================================================================
General Structure Analysis System-II
by Robert B. Von Dreele and Brian H. Toby
Argonne National Laboratory(C), 2010
This product includes software developed by the UChicago Argonne, LLC,
as Operator of Argonne National Laboratory.
Please cite:
B.H. Toby and R.B. Von Dreele, J. Appl. Cryst. 46, 544-549 (2013)
========================================================================
C:\GSASII>python "C:\GSASII\\GSASII.py" ""
GSAS-II binary directory: C:\GSASII\binwin2.7
Python module versions loaded:
python: 2.7.3
wxpython: 2.8.10.1
matplotlib: 1.1.0
numpy: 1.6.1
scipy: 0.10.1
OpenGL: 3.0.2a5
pillow: 1.1.7
Platform info: win32 32bit AMD64
This is GSAS-II version: 0.2.0 revision 1562
Read powder data PWDR CO2D2O_2bar-to-210Kexp_620176.gsa Bank 1 from file
D:\03_Post-Doc (Goettingen)\Exp\ILL\2008_Expansivity-DecC
H4-hydr\1_CO2D2O_2bar-to-210Kexp\CO2D2O_2bar-to-210Kexp_620176.gsa with
parameters from D:\03_Post-Doc (Goettingen)\Exp\ILL\2008_E
xpansivity-DecCH4-hydr\D20.prm bank 1
No covariance matrix available
no phases found in GetPhaseNames
no phases found in GetPhaseData
Read phase from C:/Users/Andre/Desktop/Al2O3_2101052_edt.cif from file
D:\03_Post-Doc (Goettingen)\Exp\ILL\2012_sep_Exchange_CH4-C
O2_Exp_Ne Hydrate\GSAS - two
phases\4_CH4D2OHydrPowdExch277K60bar3nd\CH4D2OHYDEXCH277K60BAR.EXP
FillMenus
Read phase CO2_D2O_Alice_neutron_low_S from file D:\03_Post-Doc
(Goettingen)\Paper-Expansivities\CO2_D2O_10-130K_may_2011\GSA\CO2D
2OHYD_10-220K.EXP
FillMenus
Traceback (most recent call last):
File "C:\GSASII\\GSASII.py", line 122, in MenuBinding
log.InvokeMenuCommand(event.GetId(),self,event)
File "C:\GSASII\GSASIIlog.py", line 458, in InvokeMenuCommand
handler(event)
File "C:\GSASII\\GSASII.py", line 2734, in OnDeletePhase
del(refList[item])
KeyError: u'New phase'
FillMenus
Read phase Ih_D2O_ICE from file D:\03_Post-Doc
(Goettingen)\Paper-Expansivities\CO2_D2O_10-130K_may_2011\GSA\CO2D2OHYD_10-220K.EXP
FillMenus
No covariance matrix available
No covariance matrix available
FillMenus
FillMenus
save to file: D:\03_Post-Doc
(Goettingen)\Exp\ILL\2008_Expansivity-DecCH4-hydr\1_CO2D2O_2bar-to-210Kexp\1_CO2D2O_2bar-to-210Kexp.
gpx
project save successful
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
First error
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Hessian refinement on 12 variables:
Traceback (most recent call last):
File "C:\GSASII\\GSASII.py", line 122, in MenuBinding
log.InvokeMenuCommand(event.GetId(),self,event)
File "C:\GSASII\GSASIIlog.py", line 458, in InvokeMenuCommand
handler(event)
File "C:\GSASII\\GSASII.py", line 3438, in OnRefine
Rw = G2stMn.Refine(self.GSASprojectfile,dlg)
File "C:\GSASII\GSASIIstrMain.py", line 181, in Refine
rigidbodyDict,parmDict,varyList,calcControls,pawleyLookup,ifPrint,printFile,dlg)
File "C:\GSASII\GSASIIstrMain.py", line 66, in RefineCore
args=([Histograms,Phases,restraintDict,rigidbodyDict],parmDict,varyList,calcControls,pawleyLookup,dlg))
File "C:\GSASII\GSASIImath.py", line 111, in HessianLSQ
M = func(x0,*args)
File "C:\GSASII\GSASIIstrMath.py", line 2231, in errRefine
varylist,Histogram,Phases,calcControls,pawleyLookup)
File "C:\GSASII\GSASIIstrMath.py", line 1621, in getPowderProfile
Phase = Phases[phase]
KeyError: u'from C:/Users/Andre/Desktop/Al2O3_2101052_edt.cif'
save to file: D:\03_Post-Doc
(Goettingen)\Exp\ILL\2008_Expansivity-DecCH4-hydr\1_CO2D2O_2bar-to-210Kexp\1_CO2D2O_2bar-to-210Kexp.
gpx
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Second error
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Traceback (most recent call last):
File "C:\GSASII\\GSASII.py", line 122, in MenuBinding
log.InvokeMenuCommand(event.GetId(),self,event)
File "C:\GSASII\GSASIIlog.py", line 458, in InvokeMenuCommand
handler(event)
File "C:\GSASII\\GSASII.py", line 3438, in OnRefine
Rw = G2stMn.Refine(self.GSASprojectfile,dlg)
File "C:\GSASII\GSASIIstrMain.py", line 181, in Refine
rigidbodyDict,parmDict,varyList,calcControls,pawleyLookup,ifPrint,printFile,dlg)
File "C:\GSASII\GSASIIstrMain.py", line 61, in RefineCore
args=([Histograms,Phases,restraintDict,rigidbodyDict],parmDict,varyList,calcControls,pawleyLookup,dlg))
File "C:\Python27\lib\site-packages\scipy\optimize\minpack.py", line
276, in leastsq
m = _check_func('leastsq', 'func', func, x0, args, n)[0]
File "C:\Python27\lib\site-packages\scipy\optimize\minpack.py", line
13, in _check_func
res = atleast_1d(thefunc(*((x0[:numinputs],) + args)))
File "C:\GSASII\GSASIIstrMath.py", line 2231, in errRefine
varylist,Histogram,Phases,calcControls,pawleyLookup)
File "C:\GSASII\GSASIIstrMath.py", line 1604, in getPowderProfile
yb =
G2pwd.getBackground(hfx,parmDict,bakType,calcControls[hfx+'histType'],x)
File "C:\GSASII\GSASIIpwd.py", line 570, in getBackground
q = 4.0*np.pi*npsind(xdata/2.0)/wave
File "C:\Python27\lib\site-packages\numpy\ma\core.py", line 3650, in
__div__
return divide(self, other)
File "C:\Python27\lib\site-packages\numpy\ma\core.py", line 1079, in
__call__
m |= filled(domain(da, db), True)
File "C:\Python27\lib\site-packages\numpy\ma\core.py", line 772, in
__call__
return umath.absolute(a) * self.tolerance >= umath.absolute(b)
FloatingPointError: underflow encountered in multiply
save to file: D:\03_Post-Doc
(Goettingen)\Exp\ILL\2008_Expansivity-DecCH4-hydr\1_CO2D2O_2bar-to-210Kexp\1_CO2D2O_2bar-to-210Kexp.
gpx
project save successful
--
--
Dr. Andrzej Falenty <afal...@gwdg.de>
Abt. Kristallographie
GZG, Georg-August-Universität
Goldschmidtstraße 1
D-37077 Göttingen
Tel. 0049 551 3912150
http://kristall.uni-mki.gwdg.de/
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