"Exception Caught" error for sequential refinement

jobe

Hello everyone,

I'm doing sequential refinements of variable temperature PXRD data sets. I've set up my refinement according to http://topas.dur.ac.uk/topaswiki/doku.php?id=sequential_refinements, where I essentially use the "num_runs" keyword to define a macro that takes a list of data files.

The problem is that I get the "Exception Caugt" error message in TOPAS at data set no. 1024. (This happens for several data sets across different experiments). I think the value of 1024 is quite suspicious as it is the maximum value that can be represented by 10 bits. I'm thinking that maybe the value of "Run_Number" is somehow restricted by this?

Have anyone had similar problems, and if I'm right, is it then possible to change the limits on "Run_Number"?

Cheers,
Jonas

alancoelho

Run_Number is a double precision number, not 10 bits.

The exception caught could be anything such as no min/max limits on lattice parameters for example.

If the exception-caught always happen at Run_Number 1024 then that INP file is causing the crash. Post a stripped down version of that INP file and I will have a closer look. Or, e-mail to me the simplified INP file with the data file in question.

cheers
alan

jobe

Hello Alan,

I've stripped down the INP file as much as possible:

'------------------------------------------------------------------------------------------------------------------------
'GENERAL REFINEMENT INFORMATION
iters 100
chi2_convergence_criteria 0.00001
do_errors
no_LIMIT_warnings
continue_after_convergence 'Used to try and find the global minimum. ´
conserve_memory 'Makes it run slightly faster in GUI mode, can be commented out.

r_wp 10.0765324 r_exp 2.03919031 r_p 5.18542518 r_wp_dash 13.1924485 r_p_dash 7.42458153 r_exp_dash 2.669759 weighted_Durbin_Watson 0.024812141 gof 4.94143797

macro jiggle {0.20}
macro wiggle { val_on_continue = Val + Rand(-jiggle*Val, jiggle*Val) }

'-------------------------------------------------------------------------------------------------------------------------
'SETTING UP THE SEQUENTIAL REFINEMENT
'Link: http://topas.dur.ac.uk/topaswiki/doku.php?id=sequential_refinements

macro Sequential_Refinement(numruns, ident) { Sequential_Refinement(numruns, ident, , INP_File, Run_Number) }
macro Sequential_Refinement(numruns, ident, output) { Sequential_Refinement(numruns, ident, output, INP_File, Run_Number) }
macro Sequential_Refinement(numruns, ident, output, INPFILE, RUNNUMBER) 'This one would almost never be called directly'
{
num_runs numruns

'saves a backup of the original input file'
#if Run_Number == 0;
system_before_save_OUT { copy INPFILE##.inp INPFILE##.backup }
#endif

'Save each input file with the run number and some other identifier'
system_before_save_OUT { copy INPFILE##.inp INPFILE##_##RUNNUMBER##_##ident##.inp }

'copy the output of the nth file and use it as the input for the (n+1)th file'
out_file = Concat(String(INPFILE), ".INP");

'copies the backup back over the final input file at the end of the run so you can restart from where you started'
#if Run_Number == numruns-1;
system_after_save_OUT { copy INPFILE##.backup INPFILE##.inp }
#endif

'output every refined parameter with the in-built TOPAS keyword'
'This currently doesn't work for multi-file refinement
#m_ifarg output "" #m_else
out_prm_vals_on_convergence output
#m_endif
}

'-------------------------------------------------------------------------------------------------------------------------
'LIST OF FILES TO BE REFINED

#list File_Name 'Identifier
{
Data\BGG_MS_600cvac_-00001.xy
Data\BGG_MS_600cvac_-00002.xy
'...... all of the data files
}

macro data_file { File_Name(Run_Number) }
macro ident { Run_Number }
Sequential_Refinement(1022, Run_Number)
macro ResFileName { RefinementResults.txt }

'-------------------------------------------------------------------------------------------------------------------------
'SETTING UP THE OUTPUT FILES
'Link: http://topas.dur.ac.uk/topaswiki/doku.php?id=sequential_refinements

macro FileNameGenerator(folder, file_name_prefix, suffix, extension)
{
folder##\##file_name_prefix##suffix##extension
}

macro FitFileName { FileNameGenerator(Results, Fit_, Run_Number, .xy) }
macro DifFileName { FileNameGenerator(Results, Dif_, Run_Number, .xy) }

macro Out_Results(ResFileName) { Out_Results(ResFileName, file, seqno, Get(phase_name)) }
macro Out_Results(ResFileName, phasename) { Out_Results(ResFileName, file, seqno, phasename) }
macro Out_Results(ResFileName, file, seqno) { Out_Results(ResFileName, file, seqno, Get(phase_name)) }
macro Out_Results(ResFileName, file, seqno, phasename) {
out ResFileName append
Out_String("\n")
Out_String(data_file)
Out_String("\t")
Out_String(ident)
Out_String("\t")
load out_record out_fmt out_eqn
{
"%s" = phasename;
}
load out_record out_fmt out_fmt_err out_eqn
}

macro O_R(& value) {
"\t%10.9f" "\t%10.9f"
#m_ifarg value #m_code
= If(Prm_There(value),value,-1);
#m_else 'it must be a numeral, an eqn, or a Get(), and therefore, should exist'
=value;
#m_endif
}

macro Out_Header(ResFileName) {
out ResFileName append
Out_String("@file\t")
Out_String("ident\t")
Out_String("phase")
}

macro O_H(head) {
Out_String("\t") Out_String(head)
Out_String("\t") Out_String(head##_err)
}

#define OUTPUT
'This single output macro encapsulate all of the desired outputs, allowing it '
' to be easily turned on and off with the above #define'
' The Output macro is referred to at the end of the input file '
macro Output {
'Only write the header the first time the file is run'
#if Run_Number == 0;
Out_Header(ResFileName)
O_H(Rwp)
'.... header for reported parameters
#endif

'output the following parameters for each str '
for strs 1 to 1 {
Out_Results(ResFileName) {
O_R(Get (r_wp))
'.... values for the reported parameters
}
}
}

'-------------------------------------------------------------------------------------------------------------------------
'DATA FILE AND INSTRUMENTAL PARAMETRES

xdd data_file

continue_after_convergence
x_calculation_step = Yobs_dx_at(Xo); convolution_step 8

start_X 2.0
finish_X 6.8

lam ymin_on_ymax 0.001 la 1.0 lo 0.1261 lh 0.1
LP_Factor(0)

Specimen_Displacement(disp,-0.00262`_0.00010)

bkg bg 723.111301`_5.23849217 269.741011`_8.16461682 -9.50724438`_6.43772228 -40.1591874`_6.41377331 -34.3449549`_5.77645379 -30.53635`_5.98240559

'------------------------------------------------------------------------------------------------------------------------
'PHASE INFORMATION

str
phase_name Ba8Ga16Ge30
scale scale_bgg 5.10341209e-008`_2.87e-010
weight_percent w_bgg 100.000`_0.000

a a_bgg 10.805720`_0.000209
b a_bgg 10.805720`_0.000209
c a_bgg 10.805720`_0.000209
al 90.
be 90.
ga 90.

space_group "Pm-3n"
site Ba1 x 0 y 0 z 0 occ Ba 1.000 beq B_Ba1 1.19854`_0.09019 wiggle;
site Ba2 x 0.25 y 0.5000 z 0 occ Ba 1.000 ADPs { u_11 0.01974`_0.00194 = Get(u33); u_33 0.06232`_0.00154 = 0; = 0; = 0; }
site Ge1 x 0.25 y 0 z 0.5 occ Ge 1.000 beq B_Ge1 1.22365`_0.04069
site Ge2 x 0.18473 y 0.18473 z 0.18473 occ Ge 1.000 beq B_Ge1 1.22365`_0.04069
site Ge3 x 0 y 0.30833 z 0.11829 occ Ge 1.000 beq B_Ge1 1.22365`_0.04069

r_bragg 100

TCHZ_Peak_Type(pku,-0.04707`_0.00693, pkv, 0.01000`_0.00027,!pkw, 0.00000,!pkz, 0.0000,!pky, 0.0000,pkx, 0.00492`_0.00009)

'-------------------------------------------------------------------------------------------------------------------------

#ifdef OUTPUT
Output
Out_X_Ycalc(FitFileName)
Out_X_Difference(DifFileName)
#endif

Thanks for the help!

- Jonas

alancoelho

Its not possible to determine why the INP file crashes at run number 1024 by simply looking at the INP file. Can you e-mail me the INP file with 100 data files in the list and include the file that is run number 1024.

Apart from that the above the parameter with out hard limits are the parameters in the following macros:

TCHZ_Peak_Type
Specimen_Displacement

and the a_bgg lattice parameter. The parameters have "moving window limits" ie.

If_Prm_Eqn_Rpt(u, uv, min = Max(-1, Val-.1); max = Min(2, Val+.1); del 1.0e-4)
etc...

Does the parameter output file show any parameters going astray.

alancoelho

An update on the crash.

Jonas sent me 100 data files and all worked on my computer using TA.EXE and TC.EXE.

I then asked Jonas to use TC.EXE on the more than 1000 files and that worked on his computer.

I then changed the INP file to work with 1200 data files (loading the same 100 twelve times) and all worked with TA.EXE and TC.EXE.

I can only speculated that the text display of the Fit Windows is running out of Windows memory on his computer.

Thus in cases of 1000s of data files and a similar crash - its best to run the INP file using TC.EXE.

cheers
alan

jobe

Thank you for all the help, Alan!

To run an .inp file without the GUI using tc.exe, simply
- open the Windows Command Prompt
- find your way to the Topas folder (e.g. C:\Topas-6) using the "cd" command to change directory
- type "tc some_input_file.inp" into the command line
- let Topas do its magic on your .inp file!

Best,
Jonas