Preparing files for release 1.2: Windows binaries, sample output, and…

… docs

doc/history

@@ -381,4 +381,69 @@ Changes to the manual:
 + Section "Geometry files": added warning about shown box size.
 
 ------------------------------------------------------------------------------------------------------------------------
-Ver. 1.2 - XX.XX.2013
+Ver. 1.2 - 08.06.2013
+
++ Sparse mode is now fully integrated into ADDA and significantly improved (issue 98, SparseMode). It is designed for
+  very porous particles. New file sparse_ops.h.
++ Linked to new OpenCL FFT library from AMD (clAmdFft), it is now the default one in OpenCL mode (issue 144,
+  InstallingclAmdFft). Speed improvement is a few times depending on the GPU. A few minor improvements of handling FFTs.
++ New iterative solver BCGS2 - an improved version of BICGSTAB (issue 24).
++ New command line option argument -init_field read <filenameY> [<filenameX>]' to initialize an iterative solver by the
+  field read from file (issue 2).
+* Function to read field was moved from GenerateB.c to comm.c, now it is called ReadFields(). It was also optimized in
+  MPI mode.
+* Behavior of WKB initial field was slightly improved. Before WKB result was assigned to E_exc, now it is assigned to E
+ (similar to the behavior of '-init_field read').
++ Subversion revision number was added to the output of -V command line option (issue 125). New files svnrev.h and
+  updsvnrev.sh. 
++ Several improvements of tests/2exec to accomodate OpenCL and sparse modes, as well as comparison of different FFT
+  implementations (r1192, r1200, r1203).
++ Added tests/2exec/README with basic description of using this test suite.
+* Window width is now 120 throughout the code.
++ New files interaction.c/h, which hold all code concerning the calculation of Green's tensor.
+* Intermediate vector DipoleCoord_tmp is no more used in make_particle.c. This somewhat decreases memory usage during
+  prognosis. Overall, the code in MakeParticle() was significantly changed (a lot of moving parts around).
+* Finally removed deprecated options -Cpr_mat and '-sg_format ddscat'.
+* Outdated INLINE macro removed throughout the code.
+* Many if-else-if sequences in the code were changed to switch.
+* The code for CalcField and SaveGeometry, has been simplified by moving conditions (if and switch) inside the loops.
++ Added test for duplicate dipoles in input shape files.
++ Added function FinalizeSymmetry(), which is called immediately after InitShape().
++ Timing for generation of incident beam was added.
+- Fixed inaccuracy in input/scat_params.dat (r1159).
+- A few minor bugs fixed (issues 83, 159, 162).
++ Added wiki pages: SparseMode, InstallingclAmdFft, CodeDesign (issue 75), and CodeStyleGuide (issue 74, includes code
+  style scheme for Eclipse CDT).
+* Replaced most png images with svg ones in ComparisonOtherCodes.
++ Added new folder devtools. It contains a couple of text files, bash scripts for preparing files for release and other
+  tasks, and default set of svn-properties for new files (to be used with TortoiseSVN).
++ Added doxygen config file (doc/doxy/Doxyfile) for automatic generation of extensive docs and GraphViz files (doc/gv/)
+  with schemes describing ADDA design (for svg files in CodeDesign).
+
+Changes to Makefiles:
++ Full support for compilation in 32-bit mode on 64-bit OS, using 'EXTRA_FLAGS=-m32' (see also 
+  InstallingMinGW#Multilib_configuration_on_Windows).
++ Added comment on possible use of 'CC=...' to specify a different compiler.
+* Improved the automatic dependency generation in Makefile. Now it happens during the compilation (in one go) and also
+  works for C++ sources. It should be faster and produce immediate break if, e.g., header file is missing.
++ Added new targets to Makefile - cleanfull, cleanruns, cleanrunsseq, cleanrunsmpi, cleanrunsocl. They enable cleaning
+  output from ADDA runs (in addition to the output of ADDA compilation, which is cleaned by clean).
+* debug.c and prec_time.c are now only compiled when needed.
++ Makefiles in misc/*/ were improved to allow compilation from another folder (path) and with extra flags (e.g. -m32).
+
+Changes to the manual:
++ Changed "authors" to "developers" throughout the manual. Added link to developer list in Section "Introduction".
++ Section "OpenCL (GPU) mode": added link to wiki page OpenCL.
+* Colors in Fig.1a were adjusted because they caused problems during conversion to pdf. 
++ Added figure with examples of predefined shapes (issue 140).
++ Section "Beam type": added note that '-beam read' cancels symmetry.
++ Section "How to calculate scattering quantities": added discussion of symmetry-based tests of DDA results (issue 143).
++ Section "Integral scattering quantities": added note that the result for unpolarized incident light is equal to that
+  for full-range averaging over alpha.
++ Section "Iterative solver": added description of new iterative solver bcgs2 and new option '-init_field read'. Also
+  the intercomparison of iterative solvers was rewritten in terms of matrix-vector products, and a summary table was
+  added. Section "System Requirements" was updated to refer to this table.
++ Section "Fast Fourier transform": added description of a clAmdFft library.
++ Added section "Sparse mode", a few other sections were also updated.
++ Section "Miscellanea": added link to wrapper script in R language by Baptiste Auguie.
++ Section "References": DOIs and URLs were made into hyperlinks.

sample/run000_sphere_g16_m1.5/CrossSec-Y

@@ -1,4 +1,4 @@
-Cext	= 135.0449046
-Qext	= 3.79114961
-Cabs	= -1.937494758e-016
-Qabs	= -5.439177817e-018
+Cext	= 135.0449041
+Qext	= 3.791149597
+Cabs	= -0
+Qabs	= -0

sample/run000_sphere_g16_m1.5/log

@@ -1,6 +1,6 @@
-Generated by ADDA v.1.1
+Generated by ADDA v.1.2
 The program was run on: YURKIN
-command: 'D:\Maxim\Current\adda\win32\adda.exe '
+command: 'd:\Maxim\Current\adda\win64\adda.exe '
 lambda: 6.283185307
 shape: sphere; diameter:6.734551818
 box dimensions: 16x16x16
@@ -42,21 +42,21 @@ RE_004 = 3.0639031825E-001  +   progress = 0.281433
 RE_005 = 2.2448283848E-001  +   progress = 0.267331
 RE_006 = 2.2740255145E-001  -   progress =-0.013006
 RE_007 = 1.5952149116E-001  +   progress = 0.298506
-RE_008 = 6.1602401378E-002  +   progress = 0.613830
-RE_009 = 3.5443250605E-002  +   progress = 0.424645
+RE_008 = 6.1602401377E-002  +   progress = 0.613830
+RE_009 = 3.5443250606E-002  +   progress = 0.424645
 RE_010 = 2.9898244022E-002  +   progress = 0.156447
 RE_011 = 2.4111231314E-002  +   progress = 0.193557
-RE_012 = 3.8307716444E-003  +   progress = 0.841121
-RE_013 = 3.0434605426E-003  +   progress = 0.205523
-RE_014 = 1.3101400517E-003  +   progress = 0.569523
-RE_015 = 8.2588869908E-004  +   progress = 0.369618
-RE_016 = 5.0452779293E-004  +   progress = 0.389109
-RE_017 = 1.1339755208E-004  +   progress = 0.775240
-RE_018 = 9.3640503183E-005  +   progress = 0.174228
-RE_019 = 6.8748638988E-005  +   progress = 0.265824
-RE_020 = 2.2386133356E-005  +   progress = 0.674377
-RE_021 = 1.5169783868E-005  +   progress = 0.322358
-RE_022 = 3.1681489046E-006  +   progress = 0.791154
+RE_012 = 3.8307716443E-003  +   progress = 0.841121
+RE_013 = 3.0434605425E-003  +   progress = 0.205523
+RE_014 = 1.3101400521E-003  +   progress = 0.569523
+RE_015 = 8.2588869759E-004  +   progress = 0.369618
+RE_016 = 5.0452779442E-004  +   progress = 0.389109
+RE_017 = 1.1339754906E-004  +   progress = 0.775240
+RE_018 = 9.3640480043E-005  +   progress = 0.174228
+RE_019 = 6.8748670242E-005  +   progress = 0.265823
+RE_020 = 2.2386393363E-005  +   progress = 0.674373
+RE_021 = 1.5170006983E-005  +   progress = 0.322356
+RE_022 = 3.1673391134E-006  +   progress = 0.791210
 
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 Timing Results             
@@ -67,17 +67,18 @@ Total planes of E field calculation (each 181 points): 2
 
 Total wall time:     0
 --Everything below is processor times--
-Total time:          0.4550
-  Initialization time: 0.1380
-    init Dmatrix         0.0120
-    FFT setup:           0.1230
+Total time:          0.1000
+  Initialization time: 0.0400
+    init Dmatrix         0.0100
+    FFT setup:           0.0300
     make particle:       0.0000
-  Internal fields:     0.2740
-    one solution:        0.2740
-      init solver:         0.0110
-      one iteration:       0.0130
-  Scattered fields:    0.0220
-    one plane:           0.0110
-  Other sc.quantities: 0.0010
-File I/O:            0.0200
+  Internal fields:     0.0500
+    one solution:        0.0500
+      incident beam:       0.0000
+      init solver:         0.0000
+      one iteration:       0.0000
+  Scattered fields:    0.0100
+    one plane:           0.0100
+  Other sc.quantities: 0.0000
+File I/O:            0.0000
 Integration:         0.0000