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WarwickMicroscopy / Felix

Felix: Bloch wave method diffraction pattern simulation software
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reenabling felxsim #125

Closed RudoRoemer closed 7 years ago

RudoRoemer commented 8 years ago

when recompiling felixsim in the new master branch and running for GaAs as in samples, I get

phsht@ThinkPad-X1:~/Projects/D-LACBED/Felix/samples/GaAs$ ../../src/felixsim

felixsim: Version :RB_input:, Build :1: Date :5 October 2016:
Status :in test:, Author :Richard+Alex: on rank= 0 of 1 in total.

At line 57 of file inputmodules.f90 Fortran runtime error: End of file

Why?

rbeanland commented 8 years ago

This is because the input file has changed. The version below should work.

Richard

Input file for Felix version :VERSION: Build :BUILD:

------------------------------------

------------------------------------

control flags

IWriteFLAG = 4 IImageFLAG = 10 IScatterFactorMethodFLAG = 0 IMaskFLAG = 1 IHolzFLAG = 0 IAbsorbFLAG = 2 IAnisoDebyeWallerFlag = 0 IByteSize = 8

radius of the beam in pixels

IPixelCount = 64

beam selection criteria

IMinReflectionPool = 160 IMinStrongBeams = 30 IMinWeakBeams = 30

crystal settings

RDebyeWallerConstant = 0.54 RAbsorptionPer = 7.8

microscope settings

ROuterConvergenceAngle = 3.35 IIncidentBeamDirection = [0,0,1] IXDirection = [1,1,0] INormalDirection = [0,0,1] RAcceleratingVoltage (kV) = 200.0 RAcceptanceAngle = 0.0

Image Output Options

RInitialThickness = 1400.0 RFinalThickness = 1500.0 RDeltaThickness = 10.0 IReflectOut = 1

Refinement Specific Flags

IRefineModeFLAG = D IWeightingFLAG = 0 IContinueFLAG = 0 ICorrelationFLAG = 3 IImageProcessingFLAG = 4 RBlurRadius = 0.01 INoofUgs = 1 IAtomicSites = (1,2) IPrint = 4 RSimplexLengthScale = 5.0 RExitCriteria = 0.00001

On 7 Oct 2016, at 19:59, Rudolf A Roemer notifications@github.com<mailto:notifications@github.com> wrote:

when recompiling felixsim in the new master branch and running for GaAs as in samples, I get

phsht@ThinkPad-X1:~/Projects/D-LACBED/Felix/samples/GaAs$ ../../src/felixsim

felixsim: Version :RB_input:, Build :1: Date :5 October 2016:

Status :in test:, Author :Richard+Alex: on rank= 0 of 1 in total.

At line 57 of file inputmodules.f90 Fortran runtime error: End of file

Why?

You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/RudoRoemer/Felix/issues/125, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AHzOuSxJS4PEjJV4EaTyvhJb80Nwok5Xks5qxpaXgaJpZM4KRWgz.

AJMHubert commented 8 years ago

"IRefineModeFLAG = S" - I've been updating the User guide too (still a work in progress)

run ../../src/felixrefine

felixrefine and felixsim have been combined now

RudoRoemer commented 8 years ago

new branch "cleanup", with felix.inp in GaAs. Output shows error. So felixsim does not work nor does felixrefine with "IRefineModeFLAG = S".

felixrefine: Version: VERSION / BUILD / RLS Date: DATE / TIME
Status: AUTHOR
on rank= 0 of 1 in total.

MeanInnerPotential= 15.32 Volts 90 unique structure factors Absorption completed in 0 hrs 0 mins 6 sec Bloch wave calculation... Simulation completed in 0 hrs 1 mins 52 sec Writing simulations for 11 thicknesses Exiting and writing output; At line 75 of file RefineWriteOut.f90 Fortran runtime error: Index '1' of dimension 1 of array 'ioutputreflections' above upper bound of 0 phsht@ThinkPad-X1:~/Projects/D-LACBED/Felix/samples/GaAs$

rbeanland commented 8 years ago

I don't know the source of the error, but is there a Felix.hkl file that lists the output reflections? I can imagine this could give a bug like this.

Richard

On 7 Oct 2016, at 21:40, Rudolf A Roemer notifications@github.com<mailto:notifications@github.com> wrote:

new branch "cleanup", with felix.inp in GaAs. Output shows error. So felixsim does not work nor does felixrefine with "IRefineModeFLAG = S".

felixrefine: Version: VERSION / BUILD / RLS Date: DATE / TIME

Status: AUTHOR

on rank= 0 of 1 in total.

MeanInnerPotential= 15.32 Volts 90 unique structure factors Absorption completed in 0 hrs 0 mins 6 sec Bloch wave calculation... Simulation completed in 0 hrs 1 mins 52 sec Writing simulations for 11 thicknesses Exiting and writing output; At line 75 of file RefineWriteOut.f90 Fortran runtime error: Index '1' of dimension 1 of array 'ioutputreflections' above upper bound of 0 phsht@ThinkPad-X1:~/Projects/D-LACBED/Felix/samples/GaAs$

You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/RudoRoemer/Felix/issues/125#issuecomment-252355758, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AHzOuZIdPYOL9gP1ksrOKagJLdMlRr9-ks5qxq5AgaJpZM4KRWgz.

kidwhizz commented 8 years ago

unless you're changed it, FelixRefine assumes Felix.hkl exists because said file simultaneously tells Felix what reflections are being input and what to output, if IOutputReflections is of 0 size, then its either empty or not being read correctly (or at all)