Refactor iterator [1/N]

[t-young31]

Works towards closing #63 . This PR:

• Adds a couple of simple classes for electric E and magnetic H fields
• Adds a Timer class suitable for printing intervals and recording the time between starts and ends. Maximises code reuse and more clearly expresses intention
• Adds a test of the phasor_norm functions (equiv. to extractPhasorENorm and extractPhasorHNorm)
• Adds namespace prefixes to header files removing the requirement for using namespace std before including headers
• Starts a SimulationParameters class to hold the full set of parameters required for the simulation
• Removes the unused matlabio_globals.h header
• Moves numeric.h to the correct directory
• Adds some comments for the simulation dimensionality
• Starts to replace 0 -> false and 1 -> true, for readability
• Implements some clang-tidy suggestions in numerical_derivative.cpp
• Uses the built in pi constant from cmath
• Deletes some dead code in mesh_base.cpp

With a view to have a modest diff this will be continued in other PRs

---

Timings

On an M1 Pro Macbook. Note that there is a few % margin of error between reruns.

Initial

$ export OMP_NUM_THREADS=1
$ time py.test ../tests/system/test_arc01.py 
real	1m57.158s
user	1m55.738s
sys	0m0.496s

Final

real	1m57.463s
user	1m56.250s
sys	0m0.565s

---

Dependencies

• [CI] Run on Windows #48

[t-young31]

this class will be expanded significantly in later PRs

[giordano]

The reason why M_PI couldn't be found on Windows is because having to define the macro _USE_MATH_DEFINES before including cmath (or math.h) introduces an ordering problem: globals.h has to be included before cmath (or math.h) or any other header file which includes them (like complex), because when it gets to globals.h the math.h header file wouldn't be loaded again a second time, and the first time the definition of the math constants was skipped because _USE_MATH_DEFINES wasn't defined.

This patch should do the trick:

diff --git a/tdms/src/electric_field.cpp b/tdms/src/electric_field.cpp
index 0e02b64..f338606 100644
--- a/tdms/src/electric_field.cpp
+++ b/tdms/src/electric_field.cpp
@@ -1,5 +1,5 @@
-#include <complex>
 #include "globals.h"
+#include <complex>
 #include "field.h"
 
 using namespace std;
diff --git a/tdms/src/iterator.cpp b/tdms/src/iterator.cpp
index 01a6aff..f47e67e 100644
--- a/tdms/src/iterator.cpp
+++ b/tdms/src/iterator.cpp
@@ -4,6 +4,7 @@
  *                 such as phasor extraction etc. Works in both pulsed 
  *                 and steady state mode.
  ******************************************************************/
+#include "globals.h"
 #include <complex>
 #include <algorithm>
 #include <cstring>
@@ -15,7 +16,6 @@
 #include "numeric.h"
 #include "mesh_base.h"
 #include "numerical_derivative.h"
-#include "globals.h"
 #include "matlabio.h"
 #include "mesh_base.h"
 #include "timer.h"
diff --git a/tdms/src/magnetic_field.cpp b/tdms/src/magnetic_field.cpp
index 3c8a7e6..6f585d4 100644
--- a/tdms/src/magnetic_field.cpp
+++ b/tdms/src/magnetic_field.cpp
@@ -1,5 +1,5 @@
-#include <complex>
 #include "globals.h"
+#include <complex>
 #include "field.h"
 
 using namespace std;
diff --git a/tdms/src/numerical_derivative.cpp b/tdms/src/numerical_derivative.cpp
index 78e888c..85df4f2 100644
--- a/tdms/src/numerical_derivative.cpp
+++ b/tdms/src/numerical_derivative.cpp
@@ -1,7 +1,7 @@
+#include "globals.h"
 #include <cmath>
 #include <cstdlib>
 #include <fftw3.h>
-#include "globals.h"
 #include "numerical_derivative.h"
 #include "matlabio.h"

[t-young31]

thanks for investigating! I'd be rather inclined to leave the it as is, because adding in a constraint on ordering header files is a little annoying, imo

[prmunro]

These changes all look reasonable