Preparing files for release 0.79: Win32 binaries, sample output, and …

…docs

doc/history

@@ -149,7 +149,7 @@ Ver. 0.76 - 14.10.06
   reference frame. Thanks to Michiel Min for fruitful discussions.
 
 ----------------------------------
-Ver. 0.77 - (05.06.07)
+Ver. 0.77 - 05.06.07
 
 - Calculation of radiation forces gave segmentation fault. The bug was
   introduced in version 0.76. Fixed.
@@ -185,7 +185,7 @@ Ver. 0.77 - (05.06.07)
   discussion. Thanks to Vitezslav Karasek and Liviu Clime for their feedback.
 
 ----------------------------------
-Ver. 0.78 - (19.03.08)
+Ver. 0.78 - 19.03.08
 
 * Makefiles were improved to enable automatic compilation of both sequential and
   MPI versions from the same source folder. Name of MPI executable is now
@@ -274,3 +274,69 @@ Ver. 0.78.2 - 11.04.08
 - An implementation of a new FCD polarization prescription (-pol fcd) was
   somewhat faulty. Correction terms of orders (kd)^2 and ln(...)(kd)^3 were
   interchanged. Fixed.
+
+----------------------------------
+Ver. 0.79 - 29.05.09
+
++ Added using SLURM job ID, when available.
+- Corrected inaccuracies in passing grid... to FFTW planning functions by making
+  explicit conversion from size_t to int *.
+- Warnings were produced about anisotropic refractive index in the input file
+  for any file in DDSCAT format. Fixed.
++ Saving of granule coordinates to a file was implemented.
++ Discussion of difference between two ways to calculate Csca, possibilities to
+  improve the accuracy of these calculations, and connection between
+  differential cross section and the Mueller matrix has been added to the
+  manual.
++ Tested for 64bit, implementing a number of corrections/improvements.
++ Support for new compiler (IBM XLC/XLF) added to the makefiles.
+- Warnings for grid adjustments (e.g. from odd to even) were extended to cover
+  all possible ambiguities, including combination with specified '-size' command
+  line option. A discussion of these issues is added to the manual.
+* Affiliation of one of the author (Maxim Yurkin) has changed to Institute of
+  Chemical Kinetics & Combustion (Novosibirsk, Russia). This does not change the
+  global strategy of ADDA development.
++ New shape 'axisymmetric' was added. The internals of shape generation routines
+  were adjusted so that shape can now define the absolute size of the particle.
+* Full name of the package was changed from 'Amsterdam DDA' to 'ADDA'.
+* Code for calculating and saving different variants of Mueller matrix
+  integrated over phi was shortened by implementing repeated blocks as inline
+  function.
+* Code repository has been moved to Google Code: http://a-dda.googlecode.com
++ Google groups adda-announce, adda-discuss and adda-develop were created to
+  facilitate interaction with users. This replaces the previous mailing list.
+* Heads of source and a few other files were changed using subversion keywords.
+* Copyright was updated to GPL 3.
+* Exit codes inside the code were changed to standard ones (EXIT_FAILURE,
+  EXIT_SUCCESS).
+* The special code in exit sequence for Borland compiler was removed (no more
+  relevant).
++ Short history of earlier ADDA development was added to the manual.
+* To-do list was replaced by issue tracker http://code.google.com/p/a-dda/issues
+- avg_inc_pol was not initialized in param.c, which could potentially lead to
+  undetermined behavior of LDR polarizability prescription (whether it is
+  averaged over incident polaeization or not). Fixed.
+- MakeParticle() was referenced as int instead of void in ADDAmain.c. This
+  should not cause any problems, but was fixed anyway.
++ A description how to add new beam type and new command line options were added
+  to the code and manual.
+* All 'intel...' compilation options in makefiles were combined into one. Tested
+  with icc 10.1 and 11.0.
++ Information on how to cite the manual was added to its first page. It includes
+  a direct link to the particular version of the manual on Google code.
+* PBS script was updated according to recent changes of module structure and
+  64-bit OS on LISA . An extensive description of this script was removed from
+  the manual.
++ Manual license is now explicitly set to Creative Commons Attribution 3.0
+  license.
++ A small summary of the comparison of the DDA with the FDTD was added to the
+  manual.
+* '-prognose' command line option was replaced by '-prognosis' (correct
+  spelling). The former is still operational but marked as deprecated.
++ A new option '-scat fin' was implemented, which uses finite dipole correction
+  for calculation of Cabs and Cext.
++ Breakdown detection of iterative solvers was improved.
+* The code was transformed to C99 standard without using its parts, which are
+  not yet widely supported by compilers (such as inline and complex). Explicit
+  support of this standard is required during compilation. Some style changes
+  were done, and some work in this direction is still due.

sample/run000_sphere_g16m1_5/CrossSec-Y

@@ -1,4 +1,4 @@
 Cext	= 135.0449046
 Qext	= 3.79114961
-Cabs	= 0
-Qabs	= 0
+Cabs	= -1.937494758e-016
+Qabs	= -5.439177818e-018

sample/run000_sphere_g16m1_5/log

@@ -1,13 +1,13 @@
-Generated by ADDA v.0.78.2
-The program was run on: dda
-command: './adda '
+Generated by ADDA v.0.79
+The program was run on: YURKIN
+command: 'd:\Maxim\Current\adda\win32\adda.exe '
 lambda: 6.283185307
 shape: sphere; diameter:6.734551818
 box dimensions: 16x16x16
 refractive index: 1.5+0i
 Dipoles/lambda: 15
 	(Volume correction used)
-Required relative residual norm: 1e-05
+Required relative residual norm: 1e-005
 Total number of occupied dipoles: 2176
 Volume-equivalent size parameter: 3.367275909
 
@@ -31,51 +31,51 @@ Total memory usage: 2.2 Mb
 
 here we go, calc Y
 
-CoupleConstant:0.005259037197+1.843854148e-05i
+CoupleConstant:0.005259037197+1.843854148e-005i
 x_0 = 0
-RE_000 = 1.0000000000E+00
-RE_001 = 8.4752662637E-01  +   progress = 0.152473
-RE_002 = 8.2113292044E-01  +   progress = 0.031142
-RE_003 = 4.2639057157E-01  +   progress = 0.480729
-RE_004 = 3.0639031825E-01  +   progress = 0.281433
-RE_005 = 2.2448283848E-01  +   progress = 0.267331
-RE_006 = 2.2740255145E-01  -   progress = -0.013006
-RE_007 = 1.5952149116E-01  +   progress = 0.298506
-RE_008 = 6.1602401378E-02  +   progress = 0.613830
-RE_009 = 3.5443250605E-02  +   progress = 0.424645
-RE_010 = 2.9898244022E-02  +   progress = 0.156447
-RE_011 = 2.4111231314E-02  +   progress = 0.193557
-RE_012 = 3.8307716444E-03  +   progress = 0.841121
-RE_013 = 3.0434605426E-03  +   progress = 0.205523
-RE_014 = 1.3101400518E-03  +   progress = 0.569523
-RE_015 = 8.2588869902E-04  +   progress = 0.369618
-RE_016 = 5.0452779281E-04  +   progress = 0.389109
-RE_017 = 1.1339755335E-04  +   progress = 0.775240
-RE_018 = 9.3640503439E-05  +   progress = 0.174228
-RE_019 = 6.8748633527E-05  +   progress = 0.265824
-RE_020 = 2.2386152530E-05  +   progress = 0.674377
-RE_021 = 1.5169835168E-05  +   progress = 0.322356
-RE_022 = 3.1682277704E-06  +   progress = 0.791149
+RE_000 = 1.0000000000E+000
+RE_001 = 8.4752662637E-001  +   progress = 0.152473
+RE_002 = 8.2113292044E-001  +   progress = 0.031142
+RE_003 = 4.2639057157E-001  +   progress = 0.480729
+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_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 = 8.2588869912E-004  +   progress = 0.369618
+RE_016 = 5.0452779292E-004  +   progress = 0.389109
+RE_017 = 1.1339755199E-004  +   progress = 0.775240
+RE_018 = 9.3640503664E-005  +   progress = 0.174228
+RE_019 = 6.8748638938E-005  +   progress = 0.265824
+RE_020 = 2.2386125355E-005  +   progress = 0.674377
+RE_021 = 1.5169773128E-005  +   progress = 0.322358
+RE_022 = 3.1681577504E-006  +   progress = 0.791153
 
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 Timing Results             
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 Total number of iterations: 22
 Total planes of E field calculation (each 181 points): 2
 
-Total wall time:     1
+Total wall time:     0
 --Everything below is processor times--
-Total time:          0.6300
-  Initialization time: 0.2100
-    init Dmatrix         0.0100
-    FFT setup:           0.2000
+Total time:          0.3160
+  Initialization time: 0.1190
+    init Dmatrix         0.0140
+    FFT setup:           0.1020
     make particle:       0.0000
-  Internal fields:     0.3700
-    one solution:        0.3700
-      init solver:         0.0200
-      one iteration:       0.0200
-  Scattered fields:    0.0300
-    one plane:           0.0200
-  Other sc.quantities: 0.0100
-  File I/O:            0.0100
+  Internal fields:     0.1710
+    one solution:        0.1710
+      init solver:         0.0080
+      one iteration:       0.0080
+  Scattered fields:    0.0200
+    one plane:           0.0100
+  Other sc.quantities: 0.0010
+  File I/O:            0.0050
 Integration:         0.0000