[RMCProfile-users] Two questions: EXAFS weight question AND syntax error message during simulation
Zhang, Yuanpeng
zyroc1990 at gmail.com
Wed Oct 28 16:16:48 GMT 2020
Hi Lisa,
1. 'WEIGHT' is a parameter assigned to each dataset in RMC fitting which will be combined with the accordingly calculated chi square. The purpose of this is, as its name suggests, to give different weight for multiple datasets involved in the fitting to determine their impact on chi square (thus further upon driving the fitting). So there is probably not a golden rule to follow for using a 'reasonable' weight. However two things to mention, one is that since you only have EXAFS data, probably weight parameter won't take that much effect at all. Second, if you refer to the manual, we have an automatic weight adjustment routine in RMCProfile available. You may want to check that out and let me know if any questions.
2. Concerning your issue with running RMC, I checked your input and found the line '> TYPE(S)_OF_ABSORBING_ATOMS :: O Pd' is wrong. Following '::', it should be provided an integer (or integers) representing atom type. In your case, you may want to put '> TYPE(S)_OF_ABSORBING_ATOMS :: 1 2' instead.
Cheers
Yuanpeng
--
Dr. Yuanpeng Zhang
Computational Instrument Scientist
Spallation Neutron Source
Oak Ridge National Laboratory
1 bethel valley road, Oak Ridge, TN 37830, US
Mobile: +1(865)-335-4818
Email: zhangy3 at ornl.gov | Web: https://www.iris2020.net <https://www.iris2020.net/>
On 10/28/20, 11:01 AM, "rmcprofile-users on behalf of Allen, Lisa via rmcprofile-users" <rmcprofile-users-bounces at shadow.nd.rl.ac.uk on behalf of rmcprofile-users at shadow.nd.rl.ac.uk> wrote:
Hi all,
This is a dual question email as one of my questions is quite simple.
1. EXAFS weight question
I am using RMCProfile with only my EXAFS data and am following along with Exercise 7 in the tutorial to generate my own simulation. When creating the snao.dat file, how is the value of WEIGHT obtained (see below)? I have read the description in the tutorial and manual, but I am still unsure. Is this value calculated by Artemis, if that is what you are using for the fitting before RMCProfile?
EXAFS ::
> FILENAME ::
> TYPE(S)_OF_ABSORBING_ATOMS ::
> NUMBER_OF_TYPES_OF_ABSORBING_ATOMS::
> START_POINT_(k_space) ::
> END_POINT_(k_space) ::
> FIT_space ::
> START_POINT_(r_space) ::
> END_POINT_(r_space) ::
> R_SPACING ::
> K_POWER ::
> ENERGY_OFFSET ::
> WEIGHT ::
1. Syntax error message during simulation
I believe this problem might have been posted before in January 2019 ("Initiating a RMCProfile calculation"), however the solution did not follow (likely to have been solved privately).
When I begin my simulation, using the "rmcprofile snao" command, I receive this information and an error message at the bottom:
C:\ RMCProfile\Working_Directory\Sample_A\First_Run>rmcprofile snao
Use CUDA version
----------------------------------------------------------------------------
RMCProfile version 6.7.8
==========================
Version type: Version with molecular constraints and EXAFS
Version date: Sep-12-2020
Release notes: Robust XRAY implementation; automatic weights adjustment
Using files: snao
----------------------------------------------------------------------------
THREADS_numbr = 8
THREADS_id = 4
THREADS_id = 2
THREADS_id = 0
THREADS_id = 6
THREADS_id = 5
THREADS_id = 1
THREADS_id = 3
THREADS_id = 7
No XML/CML output requested
Info> Read history file if present
Reading configuration file snao.rmc6f
Info> ntypes,ni: 2
8192 8192
Info> Elements in configuration:
O
Pd
Info> ntypes,ni: 2
8192 8192
Info> Number of atom types = 2
Info> Number of partials = 3
Message> Check the 'MINIMUM_DISTANCES' section
Message> in the '.dat' file if program stops here.
Message> Check the 'MAXIMUM_MOVES' section
Message> in the '.dat' file if program stops here.
Sorry, no GPU_ACCELERATOR line in file
Material: Sample_A_Pd_Al_2_O_3
Sample temperature: 300 K
Investigator: LA
+++ MOVEOUT option specified. Histogram will be recalculated.
Info> d,d/dr,int(d/dr),nr: 24.7676080000000 2476.76080000000 2476 2476
Info> Numbers of data sets (ngr, nsq, nfq) = 0 0 0
Info> Number of coordination constraints assumed to be zero
Info> Number of average coordination number constraints assumed to be zero
Info> No polyhedral constraints to be used
Bragg Dummy Info> No Bragg dummy data to be generated.
Bragg Info> No Bragg profile data to be used
Info> No magnetic scattering included
No atom swap moves will be generated,
atoms will only be translated.
Since there is no ZMOVESCALE line ZMOVESCALE=1.0
SCALE_FACTOR in 1 spectrum is set to 1
forrtl: severe (59): list-directed I/O syntax error, unit -5, file Internal List-Directed Read
Image PC Routine Line Source
rmcprofile.exe 00007FF6EF0CF4E8 Unknown Unknown Unknown
rmcprofile.exe 00007FF6EF0F48B5 Unknown Unknown Unknown
rmcprofile.exe 00007FF6EEDDEF11 Unknown Unknown Unknown
rmcprofile.exe 00007FF6EED7963E Unknown Unknown Unknown
rmcprofile.exe 00007FF6EF1F67C2 Unknown Unknown Unknown
rmcprofile.exe 00007FF6EF202708 Unknown Unknown Unknown
KERNEL32.DLL 00007FFB18167C24 Unknown Unknown Unknown
ntdll.dll 00007FFB18A0CEA1 Unknown Unknown Unknown
I am unsure where this error is coming from and I think that all of the files I have created are working, but I'm not 100 % confident in my snao.dat file (especially the WEIGHT value as mentioned).
I have also attached a text file of the above information/error message and a zip folder of the files I am using for the simulation.
Many thanks,
Lisa
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