Enhanced EM transport #211

victorMalkov · 2017-01-13T17:47:52Z

These changes are to include the electric and magnetic field transport that is based on a higher numerical integration algorithm for the condensed history algorithm, analytical transport in a magnetic field for the single scatter, and specialized boundary crossing for the EM-field.

This code is accompanied by a report that describes how to implement and use the EEMF macros (EMFMacrosInEGSnrcReport.pdf](https://github.com/nrc-cnrc/EGSnrc/files/704931/EMFMacrosInEGSnrcReport.pdf).

mchamberland · 2017-01-13T18:28:50Z

Perfect timing! Tony Popescu was just asking me about this code yesterday. People will be very happy to try it out. Awesome work, Victor!

ftessier · 2017-01-17T15:34:14Z

Thank you @victorMalkov! We will merge this into the develop after the 2017 release. It is now tagged to be pushed to master in January 2018.

Cukhen · 2017-01-17T16:14:56Z

Hi, great to hear! I'm not so firm with github, but I fetched your pull request to my local rep and when I tried to compile with EEMF I had some errors.

In short: I think there are some "_" missing in egsnrc.mortan for:

EMFIELD INITIATE SET TUSTEP
EM FIELD SS
ADD WORK EM FIELD
EMFIELD PII
EMFIELD PI
EMFIELD INITIATE SET TUSTEP

Cukhen · 2018-02-22T10:14:15Z

Is this still compatible with the current develop branch? Some things changed in egsnrc.macros and egsnrc.mortan about the way variables are declared (maybe in 3b6b16c) and I think this makes it impossible to compile this in current state? Maybe someone can fix it? :)

mainegra · 2019-03-07T15:27:25Z

@ftessier are we not adding this for the 2019 release?

ftessier · 2019-03-07T16:17:17Z

@mainegra Indeed, it is the last pull request remaining for the Release 2019 milestone. I am working on it, and post review requests when I am done. For the time being, the alternate egsnrc.mortran and egsnrc.macros files will be available as an option, by changing the make file of applications. Later, we can make these the default, and allow selecting the B field transport algorithm from the input file.

ftessier · 2019-03-07T16:28:17Z

@victorMalkov I am currently working to integrate your branch into develop for the 2019 release. I will therefore be pushing (and force pushing to your PR branch) to bring it up to date etc. Let me know if you have any concern.

ftessier · 2019-03-08T17:05:01Z

@victorMalkov to my own amazement, I am not able to massage this pull request to merge cleanly into develop, because the merge base is too old. I will close this pull request and create a new one with your changes apply cleanly on develop, setting the commit authorship to you. For this release, your egsnrc.mortran will be called egsnrc_eemf.mortran, and egsnrc.macros will become egsnrc_eemf.macros.

victorMalkov · 2019-03-08T21:59:23Z

@ftessier Hi there. These are the latest version of the macros. Following the initial merger hopefully subsequent contributions will go more smoothly. Is there anything that was incorrectly done on my end to cause the difficulties in merging?

ftessier · 2019-03-19T18:05:05Z

@victorMalkov you have not done anything wrong. It is just that the merge base is old, so there are conflicts with more recent changes in egsnrc.mortran. I was trying to resolve the conflict so as to keep you as the author of the commit... but then I found I can edit the commit author directly (!), so I will rebuild the pull request while preserving your authorship!

ftessier · 2019-03-19T20:26:10Z

@victorMalkov please review if possible. I was able to "clean" your eemf pull request, which I uploaded to your pull request branch. I have formatted the egsnrc.mortran modifications to better reveal the changes in the diff. You mention in the commit message that there is documentation, but there is none; should I include your CLRP Report in the commit?

rtownson · 2019-03-20T13:58:37Z

HEN_HOUSE/src/EEMF_macros.mortran

+"******************************** CONSTANTS ***********************************"
+REPLACE{$EM_MACROS_ACTIVE}WITH{.true.};
+REPLACE{$SL}WITH{299792458.0}; "speed of light"
+REPLACE{$ERM}WITH{0.510998910}; "electron rest energy in MeV"


Why a different value than PRM from egsnrc.macros?

I think we can address these constants after we have merged into master for the release. The main question is - if we update them for consistency with the rest of the code, will it affect the EMF algorithm? E.g. are there any functional fits that should be recalculated with the new values?

Ok, let's leave the hard-coded values in for now, but please post an issue to remind ourselves to update with the EGSnrc-wide constants.

HEN_HOUSE/src/EEMF_macros.mortran

victorMalkov · 2019-03-20T19:15:26Z

Hello, thank you for correcting the variable conflicts. As for the constants, these are unfortunately a relic from when the code was initially being developed and prior to all of the work that went into producing a consistent notation for the rest mass etc. There are no functional fits which are based on these values. The variable are explicitly used as is in the transport equations. The variables can be updated with the existing ones in egs.

…

On Wed, Mar 20, 2019 at 2:26 PM Reid Townson ***@***.***> wrote: ***@***.**** commented on this pull request. ------------------------------ In HEN_HOUSE/src/EEMF_macros.mortran <#211 (comment)>: > + + +" ****************** BOOLEANS *****************" +REPLACE{$orderBoundary}WITH{.true.}; "selecting 1PI v 3PI so no boundary errors" +REPLACE{$orderAdaptive}WITH{.true.}; "Selecting 1PI v 3PI for B for efficiency" +REPLACE{$duAdaptive}WITH{.true.}; "for B, scaling the step size to a 1.5 T" +REPLACE{$energyLossViaPotential}WITH{.false.};"Boolean for using potential" + "for energy loss. " +" Determine if output at the begining of the simulation is needed: " +REPLACE{$EMInternalOutput}WITH{.true.}; + + +"******************************** CONSTANTS ***********************************" +REPLACE{$EM_MACROS_ACTIVE}WITH{.true.}; +REPLACE{$SL}WITH{299792458.0}; "speed of light" +REPLACE{$ERM}WITH{0.510998910}; "electron rest energy in MeV" I think we can address these constants after we have merged into master for the release. The main question is - if we update them for consistency with the rest of the code, will it affect the EMF algorithm? E.g. are there any functional fits that should be recalculated with the new values? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#211 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ASvkybYSsBsy8nacHeDoNDfnzfCy9I-dks5vYn1vgaJpZM4LjILI> .

ftessier · 2019-03-20T20:17:26Z

@victorMalkov can you confirm: I just noticed pull request #422... which according to the conversation was meant to supersede this one. So #422 is the right one to merge in, no? I will look at diffs with 211 now!

ftessier · 2019-04-01T18:59:34Z

I worked the commits to match this branch to pull request #422: In particular, I checked that EEMF_macros.mortran and EEMF_macros_beamrc.mortran match the corresponding files labeled release_02122018 in #422. These four EEMF: commits should be squashed into d620510 before merging in develop, creating a single commit. Review with whitespace changes hidden to reveal true changes.

ftessier · 2019-04-01T20:40:14Z

I removed the example file HEN_HOUSE/user_codes/dosrznrc/examples/BFieldTestCase.egsinp from this pull request, since it is no longer in #422.

ftessier · 2019-04-01T20:52:31Z

To be perfectly clear, there are 4 files changed between develop and this branch, as of 0e68a0f:

> git diff develop victor/EEMF --name-only

HEN_HOUSE/src/EEMF_macros.mortran
HEN_HOUSE/src/EEMF_macros_beamrc.mortran
HEN_HOUSE/src/egsnrc.macros
HEN_HOUSE/src/egsnrc.mortran

These correspond to the four files changed between pull request #422 and its merge base d0b1ec9:


> git diff  $(git merge-base develop victor/enhancedElectricMagneticMacros) victor/enhancedElectricMagneticMacros --name-only

HEN_HOUSE/src/EEMF_macros_beamrc_release_02122018.mortran
HEN_HOUSE/src/EEMF_macros_release_02122018.mortran
HEN_HOUSE/src/egsnrc.macros
HEN_HOUSE/src/egsnrc.mortran

I checked that these files match between the current tip of #211 and #422.

HEN_HOUSE/src/EEMF_macros.mortran

mainegra

Approving this as it needs to make it into the development branch. But I have not checked thoroughly. Needs more testing!

rtownson · 2019-04-02T13:53:24Z

Tested again - works as expected. This is safe to merge into master because it is disabled by default. You have to add $(EGS_SOURCEDIR)EEMF_macros.mortran to the SOURCES list in the *.make file to enable.

ftessier · 2019-04-02T15:53:30Z

Squashed the top commits on the main one to be rebased in develop.

This code implements charged particle transport in electric and magnetic (EM) fields as described by Malkov and Rogers (Med. Phys. 43, 4447–4458, 2016 doi:10.1118/1.4954318). This code includes: - Three-point numerical integration of the Lorentz force for PRESTA-II - Two-point numerical integration for PRESTA-I - Specialized magnetic field analytical transport in single scatter mode - Boundary crossing adapted for EM fields - Vacuum transport in EM fields EEMF macros are provided as two files: one for general simulations, and one specific to BEAMnrc simulations (required due to the way howfar and hownear are defined in BEAMnrc). Note that electric field transport has not been thoroughly tested and verified at this point. Spatially varying fields are not explicitly supported, however in principle small step sizes would admit spatial variations. A detailed report covering the implementation and use of these macros is provided by the authors via the Carleton Laboratory for Radiotherapy Physics: http://bit.ly/egsnrc-eemf

HEN_HOUSE/src/egsnrc.mortran

ftessier · 2019-04-02T18:34:55Z

Just fixed the EOL whitespace and line lengths in the EEMF BEAMnrc macros file (again!).

blakewalters

Superficially, coding looks okay.

rtownson added the improvement label Jan 15, 2017

ftessier added this to the Release 2018 milestone Jan 17, 2017

ftessier force-pushed the develop branch from acb2365 to 0012606 Compare January 19, 2017 17:31

ftessier assigned mainegra Feb 3, 2017

ftessier force-pushed the develop branch from ed832df to 1c1cdb2 Compare March 1, 2017 18:27

ftessier modified the milestones: Release 2018, Release 2019 Mar 1, 2018

ftessier mentioned this pull request Sep 26, 2018

Enhanced electric and magnetic field transport #422

Closed

ftessier force-pushed the EEMF branch from 94a3617 to 09d7af0 Compare March 7, 2019 16:27

ftessier force-pushed the EEMF branch from 09d7af0 to 24aacdc Compare March 19, 2019 20:20

ftessier requested review from rtownson, blakewalters and mainegra March 19, 2019 20:22

ftessier force-pushed the EEMF branch from 24aacdc to d620510 Compare March 19, 2019 20:28

rtownson reviewed Mar 20, 2019

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ftessier force-pushed the EEMF branch from 77f11e0 to d620510 Compare March 20, 2019 18:08

rtownson approved these changes Mar 20, 2019

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ftessier force-pushed the EEMF branch from fb753fd to eb64e4d Compare April 1, 2019 18:57

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ftessier force-pushed the EEMF branch from 09fa266 to ba716e7 Compare April 2, 2019 15:52

ftessier self-requested a review April 2, 2019 18:24

ftessier force-pushed the EEMF branch from ba716e7 to 61e4504 Compare April 2, 2019 18:33

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ftessier merged commit cfbb245 into nrc-cnrc:develop Apr 11, 2019

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Enhanced EM transport #211

Enhanced EM transport #211

victorMalkov commented Jan 13, 2017

mchamberland commented Jan 13, 2017

ftessier commented Jan 17, 2017

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Enhanced EM transport #211

Enhanced EM transport #211

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victorMalkov commented Jan 13, 2017

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