Modified MonteCarloAbsorptionTest.h to add more unit tests, add
integration tests that are based on scenarios with an analytic result
and remove a couple of integration tests where good system test cover
already in place
Add one more test to SpareInstrumentTest to check the inverse square
weighting

Giovanni Di Siena authored Mar 31, 2020 and Gigg, Martyn Anthony committed Apr 07, 2020

In places other substitutions have been made, e.g
Clang does not yet specialize std::shared_ptr for T[]. Vector
has been used instead. The operator[] methods were incorrectly
marked const but returning a non-const reference - this has been fixed.
Refs #25842

Runs clang-tidy pass by ref across the codebase to fix-up various
warnings we are seeing in cppcheck

Also updated class_maker.py

This PR replaces all header guards in Geometry with #pragma once

Main change is change IObject::generatePointInObject to return boost::optional<V3D>
instead of using an out parameter combined with a boolean return value

The sampling is now performed according to the volume of each part of
the sample\environment that intersects the beam profile

Following changes have been made:

a) the function IObject::generatePointInObject has been modified so that it returns
false rather than raising an exception if it fails to generate a point inside
the object that is also in the active region. This is more efficient when it is
being called with a maxAttempts value of 1 in an attempt to fairly sample the
scatter points among the sample + environment components. This involved a change
in IObject and various child classes (MeshObject, CSGObject, MeshObject2D, Container)

b) the code that calls IObject::generatePointInObject and cycles through the
various parts of the environment\sample has been moved from SampleEnvironment into
MCInteractionVolume so that the sample can be included. There is a new function
MCInteractionVolume::generatePoint that randomly generates a scatter point across the
sample and environment components. Possible the SampleEnvironment class could be retired
entirely and just replaced by a vector of IObject items attached to the sample.

c) change CSGObject::generatePointInObject to stop calling the fallback method when the
maxAttempts parameter equals 1. The fallback method always returns a point if the object's
bounding box is inside the active area which doesn't produce the required sampling across
the env components. This change has modified the random number sequences used in various
tests - including the "sample only" tests

d) added some logging to the simulation to show where the scatter points
occurred. These show that for Pearl around 6% of the scatter points are
in the sample which is less than the 50% assumption previously in the code

e) Several changes to the unit tests (MCInteractionVolumeTest.h, MonteCarloAbsorptionTest.h,
DirectILLSelfShieldingTest.py). The updated sampling means that the absorption corrections
are slightly different than before for cases with a sample + environment.

For DirectILLSelfShieldingTest, an extra parameter has been added to underlying algorithm
(DirectILLSelfShielding) so that this test can continue to use 300 events per point while
the ILLDirectGeometryReductionTest can use 5000 events per point

f) some changes to system tests (ILLDirectGeometryReductionTest, complexShapeAbsorptions)

The calculation used in ILLDirectGeometryReductionTest wasn't converged (changing the seed
gave a ~25% change in the output) so have increased the number of events per point from 300
to 5000. I didn't increase the number of events further because I didn't want to make the
runtime of the system test (esp in debug mode) too large

re #27319

Computes the distance to the first intersection point
on a object regardless if it is entry/exit/glancing
track.
Refs #26690

Most issues stemmed from trying to normalize a zero length V3D in the
unit tests. We now throw in a few places where an illegal vector
operation is tried out.

Re #24898

Implemented random point generation within cuboids, spheres and
cylinders. The method always finds a point in these shapes unlike the
generic one and is sometimes faster (depends on how the bounding box is
filled). This should make MonteCarloAbsorption more robust.

Re #24636

Update copyright headers in all files

Squashed commit of the following:

* First version of a script to manage copyright statements

re #23468

* Neatened up script, added comments

re #23488

* move script to tools directory

re #23488

* small script changes and a couple of manual file changes

re #23488

* Minor chnage to whitespace detection in regex

re #23488

* Add an excluded directory

re #23488

* remove a repeasted copyright statement in a file

re #23488

* Don't comsume the comment end if it is on the same line

re #23488

* fix error in new copright parsing

re #23488

* remove double copyrifght entry

re #23488

* Improve handling of old copyrights at the start of comments

re #23488

* remove empty comments re #23488

* exclude gsoapgenerated directories

re #23488

* Sort out greedy line matching re #23488

* improve empty comment removal

re #23488

* improve false positives

re #23488

* impressive speedup by limiting regex matching length

re #23488

* remove evil invisible non ascii character

Also upadte the copyright at the same time

re #23488

* resolve multiple copyrights in a single file

re #23488

* resolve an issue with new statement detection

re #23488

* another unprintable unicode character

re #23488

* pep updates and cmake the new copyright fit clang format

re #23488

* update already done new format headers

re #23488

* wrong type of bracket

re #23488

* Update class_maker and friends

re #23488

* Update all copyright statements

re #23488

* clang format re #23488

* flake8 warnings re #23488

* Flake8 warnings re #23488

* Exclude .cmake.in and rb.in files

re #23488

* replace missing line re #23488

* exclude .py.in files as they are flasely recognized as C++

re #23488

* another setp.py.in re #23488

* another .py.in correction re #23488

* Hopefully the last of the .py.in files re #23488

* resolve utf-8 encoding of python files and changed ABINS checksum

re #23488

* updates to unit tests that reference line numbers

re #23488

* remaining unit test files and other fixes

re #23488

Update to clang-format-5 and reformat the codebase 

# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.

Merge done to enable documentation be be fixed, because of removal of
alias directive and addition of related algorithms directive.

Signed-off-by: Karl Palmen <karl.palmen@stfc.ac.uk>

# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.

Signed-off-by: Karl Palmen <karl.palmen@stfc.ac.uk>