Arrayslice (#96)

* trying mkdocs stuff on master branch as readthedocs seems to have trouble with other branches

* synced with stevengj/master

* sync with stevenj master

* updates

* added src/array_slice.cpp and tests/array_slice_test.cpp

* added src/array_slice.cpp and tests/array_slice_test.cpp

* updates

* updates

* added real_valued and complex_valued array_slice entry points and added sum_to_all processing

* revamped tests/array_slice_test to eliminate reference to h5 files

* updates

* updates

* added libmeepgeom/cavity-arrayslice_ll.cpp

* added libmeepgeom/cavity-arrayslice_ll.cpp

* updates to libmeepgeom/cavity-arrayslice.cpp

* updates to libmeepgeom/array_slice_test.cpp

* added python/examples/cavity_arrayslice.py

* finalized python/examples/cavity_arrayslice.py and typemaps in python/meep.i

* updates to tests/array_slice_test.cpp

* added libmeepgeom/array-slice-ll.cpp test

* updates to libmeepgeom/cavity-arrayslice.cpp

* updates to Makefile.am

* updates to libmeepgeom/array-slice-ll.cpp test code

* added libmeepgeom/array-slice-ll.h5 binary reference data file for array-slice-ll unit test

* update .travis.yml

* try revising .travis.yml to avoid annoying link error that has reappeared

* fixed missing file

* fixed missing file

* update .travis.yml in attempt to decipher inscrutable travis test failures

* added array-slice-ll test to libmeepgeom tests

* removed array-slice-ll test from libmeepgeom

* removed array-slice-ll from libmeepgeom tests

* deleted .travis.yml and replaced it with version from master branch

* added support for derived_components in array_slice

* rebased; restored array-slice-ll test in libmeepgeom

* added array-slice-ll to CHECKS in libmeepgeom/Makefile.am

* pulled updated .travis.yml

* updated libmeepgeom/array-slice-ll to find data file correctly in out-of-tree builds

libmeepgeom/Makefile.am

@@ -11,9 +11,9 @@ AM_CPPFLAGS = -I$(top_srcdir)/src -DDATADIR=\"$(srcdir)/\"
 libmeepgeom_la_SOURCES = \
  meepgeom.cpp meepgeom.hpp material_data.hpp
 
-libmeepgeom_la_LDFLAGS = -version-info @SHARED_VERSION_INFO@ 
+libmeepgeom_la_LDFLAGS = -version-info @SHARED_VERSION_INFO@
 
-check_PROGRAMS      = pw-source-ll ring-ll cyl-ellipsoid-ll absorber-1d-ll
+check_PROGRAMS      = pw-source-ll ring-ll cyl-ellipsoid-ll absorber-1d-ll array-slice-ll
 
 absorber_1d_ll_SOURCES = absorber-1d-ll.cpp
 absorber_1d_ll_LDADD   = libmeepgeom.la $(MEEPLIBS)
@@ -27,10 +27,14 @@ pw_source_ll_LDADD   = libmeepgeom.la $(MEEPLIBS)
 ring_ll_SOURCES = ring-ll.cpp
 ring_ll_LDADD   = libmeepgeom.la $(MEEPLIBS)
 
-TESTS           = cyl-ellipsoid-ll
+array_slice_ll_SOURCES = array-slice-ll.cpp
+array_slice_ll_LDADD   = libmeepgeom.la $(MEEPLIBS)
+
+TESTS           = cyl-ellipsoid-ll array-slice-ll
 
 noinst_PROGRAMS = bend-flux-ll
+
 bend_flux_ll_SOURCES = bend-flux-ll.cpp
 bend_flux_ll_LDADD   = libmeepgeom.la $(MEEPLIBS)
 
-noinst_DATA = cyl-ellipsoid-eps-ref.h5
+noinst_DATA = cyl-ellipsoid-eps-ref.h5 array-slice-ll.h5

libmeepgeom/array-slice-ll.cpp

@@ -0,0 +1,249 @@
+/***************************************************************/
+/***************************************************************/
+/***************************************************************/
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <complex>
+
+#include "meep.hpp"
+
+#include "ctl-math.h"
+#include "ctlgeom.h"
+
+#include "meepgeom.hpp"
+
+#ifndef DATADIR
+  #define DATADIR "./"
+#endif
+
+using namespace meep;
+
+typedef std::complex<double> cdouble;
+
+vector3 v3(double x, double y=0.0, double z=0.0)
+{
+  vector3 v;
+  v.x=x; v.y=y; v.z=z;
+  return v;
+}
+
+// passthrough field function
+cdouble default_field_function(const cdouble *fields,
+			const vec &loc, void *data_)
+{
+  (void) loc; // unused
+  (void) data_; // unused
+  return fields[0];
+}
+
+/***************************************************************/
+/***************************************************************/
+/***************************************************************/
+#define RELTOL 1.0e-6
+double Compare(double *d1, double *d2, int N, const char *Name)
+{
+  double Norm1=0.0, Norm2=0.0, NormDelta=0.0;
+  for(int n=0; n<N; n++)
+   { Norm1     += d1[n]*d1[n];
+     Norm2     += d2[n]*d2[n];
+     NormDelta += (d1[n]-d2[n])*(d1[n]-d2[n]);
+   };
+  Norm1=sqrt(Norm1);
+  Norm2=sqrt(Norm2);
+  NormDelta=sqrt(NormDelta);
+  double RelErr = NormDelta / (0.5*(Norm1+Norm2));
+  if (RelErr > RELTOL)
+   abort("fail: rel error in %s data = %e\n",Name,RelErr);
+  return RelErr;
+}
+
+double Compare(cdouble *d1, cdouble *d2, int N, const char *Name)
+{
+  double Norm1=0.0, Norm2=0.0, NormDelta=0.0;
+  for(int n=0; n<N; n++)
+   { Norm1     += norm(d1[n]);
+     Norm2     += norm(d2[n]);
+     NormDelta += norm(d1[n]-d2[n]);
+   };
+  Norm1=sqrt(Norm1);
+  Norm2=sqrt(Norm2);
+  NormDelta=sqrt(NormDelta);
+  double RelErr = NormDelta / (0.5*(Norm1+Norm2));
+  if (RelErr > RELTOL)
+   abort("fail: rel error in %s data = %e\n",Name,RelErr);
+  return RelErr;
+}
+
+/***************************************************************/
+/* dummy material function needed to pass to structure( )      */
+/* constructor as a placeholder before we can call             */
+/* set_materials_from_geometry                                 */
+/***************************************************************/
+double dummy_eps(const vec &) { return 1.0; }
+
+/***************************************************************/
+/***************************************************************/
+/***************************************************************/
+void usage(char *progname)
+{ master_printf("usage: %s [options]\n",progname);
+  master_printf("options: \n");
+  master_printf(" --use-symmetry    use geometric symmetries\n");
+  master_printf(" --write-files     write reference data files\n");
+  abort();
+}
+
+/***************************************************************/
+/***************************************************************/
+/***************************************************************/
+int main(int argc, char *argv[], char **envp)
+{
+  initialize mpi(argc, argv);
+
+  /***************************************************************/
+  /* parse command-line options **********************************/
+  /***************************************************************/
+  bool use_symmetry=false;
+  bool write_files=false;
+  for(int narg=1; narg<argc; narg++)
+   { if ( argv[narg]==0 )
+      continue;
+     if (!strcasecmp(argv[narg],"--use-symmetry") )
+      { use_symmetry=true;
+        master_printf("Using symmetry.\n");
+      }
+     else if (!strcasecmp(argv[narg],"--write-files") )
+      { write_files=true;
+        master_printf("writing HDF5 data files");
+      }
+     else
+      { master_printf("unknown command-line option %s (aborting)",argv[narg]);
+        usage(argv[0]);
+      }; 
+   };
+
+  /***************************************************************/
+  /* initialize geometry, similar to holey_wvg_cavity   **********/
+  /***************************************************************/
+  double eps=13.0;   // dielectric constant of waveguide
+  double w=1.2;      // width of waveguide
+  double r=0.36;     // radius of holes
+  double d=1.4;      // defect spacing (ordinary spacing = 1)
+  int N=3;           // number of holes on either side of defect
+  double sy=6.0;     // size of cell in y direction (perpendicular to wvg.)
+  double pad=2.0;    // padding between last hole and PML edge
+  double dpml=1.0;   // PML thickness
+  double sx = 2.0*(pad + dpml + N) + d -1.0; // size of cell in x dir
+  double resolution=20.0;
+  geometry_lattice.size.x=sx;
+  geometry_lattice.size.y=sy;
+  geometry_lattice.size.z=0.0;
+  grid_volume gv = voltwo(sx, sy, resolution);
+  gv.center_origin();
+  symmetry sym = use_symmetry ? -mirror(Y,gv) : identity();
+  structure the_structure(gv, dummy_eps, pml(dpml), sym);
+  material_type vacuum     = meep_geom::vacuum;
+  material_type dielectric = meep_geom::make_dielectric(eps);
+  geometric_object objects[7];
+  vector3 origin = v3(0.0,   0.0,  0.0);
+  vector3 xhat   = v3(1.0,   0.0,  0.0);
+  vector3 yhat   = v3(0.0,   1.0,  0.0);
+  vector3 zhat   = v3(0.0,   0.0,  1.0);
+  vector3 size   = v3(ENORMOUS, w, ENORMOUS);
+  double x0      = 0.5*d;
+  double deltax  = 1.0;
+  double height  = ENORMOUS;
+  objects[0] = make_block(dielectric, origin, xhat, yhat, zhat, size);
+  int no=1;
+  for(int n=0; n<N; n++)
+   { vector3 center=v3(x0 + n*deltax,  0.0, 0.0);
+     objects[no++] = make_cylinder(vacuum, center, r, height, zhat);
+   };
+  for(int n=0; n<N; n++)
+   { vector3 center=v3(-x0 - n*deltax,  0.0, 0.0);
+     objects[no++] = make_cylinder(vacuum, center, r, height, zhat);
+   };
+  geometric_object_list g={ no, objects };
+  meep_geom::set_materials_from_geometry(&the_structure, g);
+  fields f(&the_structure);
+
+  /***************************************************************/
+  /* add source and timestep until source has finished (no later)*/
+  /***************************************************************/
+  double fcen = 0.25;  // pulse center frequency
+  double df   = 0.2;   // pulse width (in frequency)
+  gaussian_src_time src(fcen, df);
+  component src_cmpt = Hz;
+  f.add_point_source(src_cmpt, src, vec(0.0, 0.0));
+  while( f.round_time() < f.last_source_time())
+   f.step();
+
+  /***************************************************************/
+  /***************************************************************/
+  /***************************************************************/
+  double xMin = -0.25*sx, xMax=+0.25*sx;
+  double yMin = -0.15*sy, yMax=+0.15*sy;
+  volume v1d( vec(xMin, 0.0),  vec(xMax, 0.0) );
+  volume v2d( vec(xMin, yMin), vec(xMax, yMax) );
+
+  int rank, dims1D[1], dims2D[2];
+  cdouble *file_slice1d=0;
+  double *file_slice2d=0;
+
+#define H5FILENAME DATADIR"array-slice-ll"
+#define NX 126
+#define NY 38
+  if (write_files)
+   { 
+     h5file *file = f.open_h5file(H5FILENAME);
+     f.output_hdf5(Hz, v1d, file);
+     f.output_hdf5(Sy, v2d, file);
+     master_printf("Wrote binary data to file %s.h5\n",H5FILENAME);
+     delete file;
+     exit(0);
+   }
+  else
+   { 
+     //
+     // read 1D and 2D array-slice data from HDF5 file
+     //
+     h5file *file = f.open_h5file(H5FILENAME, h5file::READONLY);
+     double *rdata = file->read("hz.r", &rank, dims1D, 1);
+     if (rank!=1 || dims1D[0]!=NX)
+      abort("failed to read 1D data(hz.r) from file %s.h5",H5FILENAME);
+     double *idata = file->read("hz.i", &rank, dims1D, 1);
+     if (rank!=1 || dims1D[0]!=NX)
+      abort("failed to read 1D data(hz.i) from file %s.h5",H5FILENAME);
+     file_slice1d = new cdouble[dims1D[0]];
+     for(int n=0; n<dims1D[0]; n++)
+      file_slice1d[n] = cdouble(rdata[n], idata[n]);
+     delete[] rdata;
+     delete[] idata;
+
+     file_slice2d = file->read("sy", &rank, dims2D, 2);
+     if (rank!=2 || dims2D[0]!=NX || dims2D[1]!=NY)
+      abort("failed to read 2D reference data from file %s.h5",H5FILENAME);
+     delete file;
+
+     //
+     // generate 1D and 2D array slices and compare to 
+     // data read from file
+     //
+     rank=f.get_array_slice_dimensions(v1d, dims1D);
+     if (rank!=1 || dims1D[0]!=NX)
+      abort("incorrect dimensions for 1D slice");
+     cdouble *slice1d=f.get_complex_array_slice(v1d, Hz);
+     double RelErr1D=Compare(slice1d, file_slice1d, NX, "Hz_1d");
+     master_printf("1D: rel error %e\n",RelErr1D);
+
+     rank=f.get_array_slice_dimensions(v2d, dims2D);
+     if (rank!=2 || dims2D[0]!=NX || dims2D[1]!=NY)
+      abort("incorrect dimensions for 2D slice");
+     double *slice2d=f.get_array_slice(v2d, Sy);
+     double RelErr2D=Compare(slice2d, file_slice2d, NX*NY, "Sy_2d");
+     master_printf("2D: rel error %e\n",RelErr2D);
+
+   }; // if (write_files) ... else ...
+
+  return 0;
+}

python/examples/cavity_arrayslice.py

@@ -0,0 +1,92 @@
+import unittest
+import meep as mp
+import numpy as np
+import matplotlib.pyplot as plt
+
+##################################################
+# set up the geometry
+##################################################
+eps = 13
+w = 1.2
+r = 0.36
+d = 1.4
+N = 3
+sy = 6
+pad = 2
+dpml = 1
+sx = (2 * (pad + dpml + N)) + d - 1
+fcen = 0.25
+df = 0.2
+nfreq = 500
+
+cell = mp.Vector3(sx, sy, 0)
+
+blk = mp.Block(size=mp.Vector3(1e20, w, 1e20),
+               material=mp.Medium(epsilon=eps))
+
+geometry = [blk]
+
+for i in range(3):
+    geometry.append(mp.Cylinder(r, center=mp.Vector3(d / 2 + i)))
+
+for i in range(3):
+    geometry.append(mp.Cylinder(r, center=mp.Vector3(d / -2 - i)))
+
+sim = mp.Simulation(cell_size=cell,
+                         geometry=geometry,
+                         sources=[],
+                         boundary_layers=[mp.pml(dpml)],
+                         resolution=20)
+
+##################################################
+# add sources 
+##################################################
+sim.sources = [mp.Source(mp.GaussianSource(fcen, fwidth=df),
+                    mp.Hz, mp.Vector3())]
+
+#sim.symmetries = [mp.Mirror(mp.Y, phase=-1), mp.Mirror(mp.X, phase=-1)]
+
+##################################################
+# run until sources are finished (and no later)
+##################################################
+sim._run_sources_until(0,[])
+
+##################################################
+# get 1D and 2D array slices
+##################################################
+xMin = -0.25*sx;
+xMax = +0.25*sx;
+yMin = -0.15*sy;
+yMax = +0.15*sy;
+
+# 1D slice of Hz data
+dims1d=np.zeros(3,dtype=np.int32)
+v1d=mp.volume( mp.vec(xMin, 0.0), mp.vec(xMax, 0.0) )
+rank1d  = sim.fields.get_array_slice_dimensions(v1d, dims1d);
+NX1 = dims1d[0];
+slice1d = np.zeros(NX1, dtype=np.double);
+sim.fields.get_array_slice(v1d, mp.Hz, slice1d);
+
+# 2D slice of Hz data
+dims2d=np.zeros(3,dtype=np.int32)
+v2d=mp.volume( mp.vec(xMin, yMin), mp.vec(xMax, yMax) )
+rank2d  = sim.fields.get_array_slice_dimensions(v2d, dims2d);
+NX2 = dims2d[0];
+NY2 = dims2d[1];
+N2 = NX2*NY2;
+slice2d = np.zeros(N2, dtype=np.double);
+sim.fields.get_array_slice(v2d, mp.Hz, slice2d);
+
+# plot 1D slice
+plt.subplot(1,2,1);
+x1d=np.linspace(xMin, xMax, dims1d[0]);
+plt.plot(x1d, slice1d);
+
+# plot 2D slice
+plt.subplot(1,2,2);
+dy = (yMax-yMin) / dims2d[1];
+dx = (xMax-xMin) / dims2d[0];
+(x2d,y2d)=np.mgrid[ slice(xMin, xMax, dx), slice(yMin, yMax, dy)];
+plt.contourf( x2d, y2d, np.reshape(slice2d, (dims2d[0], dims2d[1])) )
+plt.colorbar();
+plt.show()

python/meep.i

@@ -261,6 +261,7 @@ PyObject *py_do_harminv(PyObject *vals, double dt, double f_min, double f_max, i
         SWIG_exception_fail(SWIG_ArgError(tmp_res), "Couldn't convert Python object to meep::src_time");
     }
     $1 = reinterpret_cast<meep::src_time *>(tmp_ptr);
+
 }
 
 // Typemap suite for boundary_region
@@ -295,6 +296,11 @@ PyObject *py_do_harminv(PyObject *vals, double dt, double f_min, double f_max, i
     }
 }
 
+// Typemap suite for array_slice
+// TODO: add (cdouble *, int) version
+%apply (double* INPLACE_ARRAY1, int DIM1) {(double *slice, int slice_length)};
+%apply int INPLACE_ARRAY1[ANY] { int [3] };
+
 // Rename python builtins
 %rename(br_apply) meep::boundary_region::apply;
 %rename(_is) meep::dft_chunk::is;