Add EGS_DynamicSource class #308

blakewalters · 2017-06-23T14:37:39Z

An EGS_DynamicSource allows the user to simulate dynamic (time-varying)
motion of any source during a single calculation. Continuous motion
of the source is simulated between user-defined control points, where
each control point defines a set of incident polar coordinates and an
associated fractional monitor unit (mu) index.

If the source is an IAEA-format phase space file or a BEAM simulation
source, then, provided the source stores the value of mu for each
particle, the user has the option to use these when setting incident
source coordinates, thus synchronizing the motion of EGS_DynamicSource
with jaw and MLC opening coordinates in the upstream BEAM simulation.

For phase space and BEAM simulation sources, EGS_DynamicSource
essentially provides the same functionality as sources 20 and 21
in DOSXYZnrc, as documented by Lobo & Popescu, Phys. Med. Biol.,
55:4431-4443 (2010).

Note that implementation of this source required the implementation
of a new method, EGS_Float getMu(), in egs_base_source. As
reimplemented in iaea_phsp_source and egs_beam_source, getMu returns
the value of mu associated with a particle.

See the source documentation for more info and an example input.

ftessier · 2017-06-27T18:26:18Z

@blakewalters this branch does not pass the travis compilation test, it fails while building the egs++ library. Can you take a look at that?

blakewalters · 2017-06-27T19:36:41Z

Okay, @ftessier, I'll take a look!

rtownson · 2017-07-31T15:11:27Z

HEN_HOUSE/egs++/sources/egs_dynamic_source/egs_dynamic_source.cpp

+
+/*! \file egs_dynamic_source.cpp
+ *  \brief A dynamic source
+ *  \IK


Typo here, should be \BW.

rtownson · 2017-07-31T15:14:12Z

HEN_HOUSE/egs++/sources/egs_dynamic_source/egs_dynamic_source.cpp

+    }
+}
+
+//actually select the rotation coordinats for the incident particle


Typo in comment.

rtownson · 2017-07-31T15:15:06Z

HEN_HOUSE/egs++/sources/egs_dynamic_source/egs_dynamic_source.h

+/*
+###############################################################################
+#
+#  EGSnrc egs++ transformed source headers


File title and authors are wrong.

rtownson

Needs an astyle run.

rtownson · 2017-07-31T15:32:01Z

HEN_HOUSE/egs++/sources/egs_dynamic_source/egs_dynamic_source.h

+                          const string &Name="", EGS_ObjectFactory *f=0) :
+        EGS_BaseSource(Name,f), source(Source) {
+    };
+    /*! \brief Construct a dynamic source from the input \a inp */


There is no inp.

Okay, let me clean these up before this gets merged....

PS. What's an astyle run and can I do it in the safety and comfort of my own home?

Why yes, you can! Check out the handy-dandy wiki docs on coding style:

https://github.com/nrc-cnrc/EGSnrc/wiki/Coding-style

Eeehaa! Thanks!

ftessier · 2017-12-21T20:35:39Z

Cleaned up this branch, put everything in a single commit and rebased on develop. @blakewalters this is awesome! Is it ready for merging into develop?

blakewalters · 2017-12-21T20:42:40Z

Should be ready to merge, @ftessier. It's all part of the effort of stealthily supplanting dosxyznrc.

ftessier · 2017-12-21T20:53:44Z

Updated the Makefile which still referred to the transformed source.

ftessier · 2018-04-11T18:51:53Z

Rebased on develop tip and applied astyle.

blakewalters · 2018-08-23T18:37:14Z

The setSimulationChunk method--essential if you're going to use a dynamic phase space source in parallel runs--was omitted from this source and from EGS_TransformedSource. I've implemented this method in both sources in the latest commit. Thanks @vahx129 for doing all the heavy debugging!

Add an EGS_DynamicSource class to allow simulation of dynamic (time-varying) motion of any source during a single calculation. Continuous motion of the source is simulated between user-defined control points, where each control point defines a set of incident polar coordinates and an associated fractional monitor unit (mu) index. If the source is an IAEA format phase space file or a BEAMnrc simulation source which stores the value of mu for each particle, this mu value can be used to set incident source coordinates, thus synchronizing the motion of EGS_DynamicSource with jaw and MLC opening coordinates in the upstream BEAMnrc simulation. For phase space and BEAMnrc simulation sources, EGS_DynamicSource essentially provides the same functionality as sources 20 and 21 in DOSXYZnrc, as documented by Lobo & Popescu, Phys. Med. Biol., 55:4431-4443 (2010). Note that implementation of this source requires the implementation of a new method, EGS_Float getMu(), in egs_base_source. As reimplemented in iaea_phsp_source and egs_beam_source, getMu returns the value of mu associated with a particle. See the source documentation for more info and sample input. Note: replaced to_string(), which is not a member of std on all g++ compilers, with another method of converting integers to strings during the source input loop.

Implement a getMu method so that egs_dynamic_source can pass on the dynamic indexing parameter mu (monitor unit). Also, fix a bug in the iaea_phsp_source when determining whether mu is stored in the phase space source or not.

Add setSimulationChunk method to dynamic and transformed sources in order to set the portion of the phase space source to use during parallel runs.

ftessier

Brought up to date with develop.

blakewalters added the improvement label Jun 23, 2017

blakewalters self-assigned this Jun 23, 2017

blakewalters requested review from ftessier, mainegra and rtownson June 23, 2017 14:37

rtownson reviewed Jul 31, 2017

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rtownson approved these changes Jul 31, 2017

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rtownson reviewed Jul 31, 2017

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mainegra approved these changes Aug 8, 2017

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ftessier force-pushed the feature-dynamic_source branch from 725fa5f to 655bc7f Compare December 21, 2017 20:34

blakewalters force-pushed the feature-dynamic_source branch from 8f7508d to aa894eb Compare March 26, 2018 18:18

ftessier force-pushed the feature-dynamic_source branch 2 times, most recently from a163c3c to ca22273 Compare April 11, 2018 18:50

ftessier force-pushed the feature-dynamic_source branch from 64f22b7 to a8dbe2b Compare September 21, 2018 22:28

blakewalters added 3 commits October 3, 2018 14:40

Add getMu method to synchronize dynamic sources

522566b

Implement a getMu method so that egs_dynamic_source can pass on the dynamic indexing parameter mu (monitor unit). Also, fix a bug in the iaea_phsp_source when determining whether mu is stored in the phase space source or not.

Set phsp chunks in dynamic and transformed sources

fa382d7

Add setSimulationChunk method to dynamic and transformed sources in order to set the portion of the phase space source to use during parallel runs.

ftessier force-pushed the feature-dynamic_source branch from a8dbe2b to fa382d7 Compare October 3, 2018 18:45

ftessier approved these changes Oct 3, 2018

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ftessier merged commit ca21597 into develop Oct 3, 2018

ftessier deleted the feature-dynamic_source branch October 3, 2018 19:51

ftessier added a commit that referenced this pull request Oct 3, 2018

Merge #308: add an egs++ dynamic source

faaf550

blakewalters mentioned this pull request Oct 4, 2018

Transformed phase space is incorrectly sampled in parallel environment #467

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Add EGS_DynamicSource class #308

Add EGS_DynamicSource class #308

blakewalters commented Jun 23, 2017

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Add EGS_DynamicSource class #308

Add EGS_DynamicSource class #308

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ftessier commented Dec 21, 2017

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