76171eec15
added possibility for factors---indicated by "x" at the end---and left-alone condition now comprises "0" as well as "negative numbers. understands packed structures, too.
2013-06-27 12:58:12 +00:00
8b5ba9f8f0
now understands packed geom-files (much faster processing...)
2013-06-21 21:19:14 +00:00
4cf2e75dc1
justification of numbers done with space instead of "0"s
2013-06-21 21:18:10 +00:00
e53c67f0e0
added black list for immutable microstructures.
...
now able to parse packed geom-files.
2013-06-21 21:17:03 +00:00
3b4573301c
removed now obsolete Moore neighborhood array
2013-06-21 19:10:10 +00:00
5d15f68914
added help description.
...
fixed bug for grain index (+1).
renamed some variables and added a few comments.
2013-06-21 19:08:20 +00:00
2e8756b724
faster version of smoother using the scipy gaussian filter to get the diffused microstructure and vectorized sharpening of the diffused microstructure
2013-06-21 16:59:49 +00:00
45951e27c5
script to smooth out interface roughness in a (polycrystal) geom
2013-06-20 19:45:25 +00:00
920195809c
fixed bug in auto determination of size and grid
2013-06-11 10:11:14 +00:00
e635b06270
last polishing on preprocessing scripts, documentation and scripts are all up to date.
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added addSchmidfactors to post processing scripts
2013-06-04 12:56:57 +00:00
a21dd816c7
init reporting of constitutive_*.f90 had less/to much spaces, renamed label to LABEL because it is a parameter.
...
removed debug output of geom_fromEuclideanDistance.py
2013-05-28 17:31:55 +00:00
b3a90a8a3b
last changes on preprocessing tools, only documentation needs to be done
2013-05-17 16:44:03 +00:00
17b81fda7c
still improving preprocessing scripts
2013-05-15 17:23:21 +00:00
53348db000
tested the modified scripts, all scripts generating geometry now named geom_from...
2013-05-15 16:02:38 +00:00
0b4a5cfa9b
geom_check is now using vtk class, other scripts stop execution in case of invalid grid or size
2013-05-14 21:09:37 +00:00
9093cf2072
polishing, unifying,simplifying
2013-05-14 17:51:53 +00:00
2acd737859
polishing, unifying,simplifying
2013-05-14 17:19:36 +00:00
563e74c832
now also using numpy
2013-05-14 17:00:41 +00:00
b2c50124b5
more improvements on structure, comments and header generation of pre processing tools
2013-05-13 13:10:31 +00:00
52af9aaabf
made spectral preprocessing more verbose (now reporting changes on header) and aware of new keywords, added coding information below shebang
2013-05-13 11:27:59 +00:00
a003d14824
grid and size for vicinityOffset, small changes for other scripts
2013-04-25 16:51:32 +00:00
5d8664e230
updated to new keywords + more verbosity
2013-04-25 15:53:41 +00:00
7cbf107751
removed misplaced new line statement
2013-04-24 11:07:05 +00:00
aa07656a90
exchanged final two occurrences of "grains" to "microstructures"
2013-04-18 13:53:13 +00:00
d971a32516
changed keywords, now also printing out altered size/grid/microstructures information
2013-04-16 18:00:14 +00:00
2ff0f1b93e
keywords update from resolution/dimension to grid/size
2013-04-12 14:13:32 +00:00
b4f67248a5
deleted two simple scripts used for debugging but with almost no use any more
2013-04-12 13:22:15 +00:00
7bcf1d6072
added ID information of creator script to header, changed keywords (resolution->grid, dimension->size)
2013-04-12 12:48:39 +00:00
4314ab236e
added ID information of creator script to header
2013-04-12 11:15:17 +00:00
6f0308844f
geom packing/unpacking won't throw away unknown header information any more (might contain comments)
2013-04-12 10:47:44 +00:00
0b1033d63a
switched to new keywords "grid" and "size", still reads the old "resolution" and "dimension" but writes the new ones
2013-04-12 10:27:05 +00:00
010d4c6e26
added script to make 27 periodic copies (3 in each dimension)
2013-03-11 13:40:30 +00:00
8a66693001
added script to convert data used by R.A. Lebensohn to spectral solver (geom, material.config) format
2013-03-05 16:31:17 +00:00
0d7f1e8623
killed "margin" option, now same as all others: resolution and dimension in x and y.
...
can be non-square grid.
2013-02-27 18:43:53 +00:00
565c532546
fixed bugs (grain index start, alpha orientation for elliptic osteons).
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added option to rotate osteon relative to periodic box.
2013-02-27 10:56:30 +00:00
1cc990c7ac
osteon geom and config generator
2013-02-25 17:12:13 +00:00
831ad6d9c8
added leading zeros to names of microstructures and phases, spaces caused problems during initialization
2013-02-20 14:50:01 +00:00
a90f15a3d3
corrected usage of "append" (which does not copy list items but only creates references)
2013-02-13 16:00:02 +00:00
e74b5da19a
changed all remaining routines to fortran-fast arrays (geometry reconstruction etc.)
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changed all remaining routines in f2py to more clever determination of array size (requires f2py >= 2.0)
enabled 3D visualize to work with odd resolution by switching to linear reconstruction
PLEASE NOTE: Redefinition of routines for f2py might cause trouble -> DELETE DAMASK_ROOT/lib/damask/core.so in this case
further changes: added pure statement where possible, polished, unified use of "Q" for "Quaternion" and reordered math to have similar routines together
2013-01-31 16:28:08 +00:00
c8aaf8f6d4
added $id flags and specified line ending types when missing.
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setup script missed ".py" extension for geom_euclideanDistance.
2013-01-18 12:59:26 +00:00
0e93d51fed
adopted same algorithm as in addEuclideanDistance
2013-01-18 11:42:27 +00:00
096204cd79
corrected missing file renaming of output
2013-01-18 11:39:53 +00:00
f63bb747c1
script to calculate the euclidean distance map (shortest distance to a grain boundary) of a given geom description using fast marching method (O(N logN) ops). grain boundary extracted using FD stencil.
2012-11-29 21:53:57 +00:00
05507a6240
removed opening of unused _tmp file
2012-11-27 17:59:56 +00:00
b5945ced5e
changed counting of rows from pythonic (starting at 0) to human way (starting at 1)
2012-11-20 10:27:09 +00:00
1df9be233d
changed default threshold to 0.0
2012-11-08 17:08:41 +00:00
025d6c9048
renamed script to new convention
...
aligned output behavior to that of fromVoronoiTessellation, i.e., standard output is geom, --config gives associated material.config stud
2012-11-08 15:44:51 +00:00
af2aa8500d
added option to specify crystallite index
2012-11-08 15:43:38 +00:00
c4c27860b2
renamed script
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updated to recent standard in io processing
introduced "primitive" bicontinuous structure in addition to "diamond" and "gyroid"
2012-11-07 16:52:10 +00:00
7cf2024be3
fixed buggy parameter checking
2012-11-07 16:51:17 +00:00
e11d107956
fixed reporting to STDOUT/STDERR
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fixed buggy parameter checking
2012-11-07 16:49:47 +00:00
cfc8823328
missed those three in former commit...
2012-11-05 21:28:01 +00:00
1bd4262cfb
renaming of (loosely related) "spectral" scripts to (more tightly related) "geom" versions.
2012-11-05 21:19:12 +00:00
afaf1f4e8c
made errors report to STDERR.
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maxMicrostructure remains silent if not present.
2012-10-30 16:32:00 +00:00
f2229883b5
exchanged "maxGrainCount" for "maxMicrostructure", since this is what it really means...
2012-10-30 16:15:10 +00:00
ff164c9209
changed packing syntax from "N copies of x" to "N of x" (now consistent with IO.f90)
2012-10-30 15:53:46 +00:00
2d36d52cf7
changed packing syntax from "N copies of x" to "N of x" (now consistent with geomPack and IO.f90)
2012-10-30 15:47:11 +00:00
17bfc3b284
added explanation of script purpose to its usage output (-h)
2012-10-18 07:24:44 +00:00
124451ac1a
added missing comment sign #
2012-10-04 08:42:13 +00:00
0a961bef55
made test for spectral packing/unpacking working again, small fixes in the 2 scripts
2012-09-28 14:49:07 +00:00
5dbbb56460
fixed bug in 2D output format alignment.
2012-09-13 12:28:21 +00:00
77b2eef269
corrected wrong compiler option for gfortran in setup and updated naming scheme
2012-09-13 12:20:00 +00:00
b76fee325b
script to shift (physical) origin of geometry file and/or shift microstructure indices by fixed amount and substitute individual indices by other ones.
2012-09-13 10:12:00 +00:00
66e38606f0
syntax errors in one file terminated the script. now continues with next input...
2012-09-13 10:09:54 +00:00
1c0649e17a
syntax errors in one file terminated the script. now continues with next input...
2012-09-13 10:08:57 +00:00
8078585ce8
removed two left-over debug statements
2012-09-13 08:46:18 +00:00
3d14c5b234
functionality now subsumed into geomCanvas
2012-09-13 07:58:29 +00:00
4263191423
functionality now subsumed into geomCanvas
2012-09-13 07:57:57 +00:00
1fe202fd90
added $ID and line endings.
2012-09-13 07:56:45 +00:00
4f6e0eda32
splitter geom-file un/packing into two separate scripts.
2012-09-05 15:15:11 +00:00
a94b089aaa
removed old fortran brute force based tessellation
2012-07-26 09:07:24 +00:00
783e1b50e2
condensed info parsing.
...
added info to report new origin of grid (based on --offset).
2012-06-26 18:08:50 +00:00
fd3d592333
added capability to respect "origin" information in header
2012-06-26 18:07:38 +00:00
cd04f990c5
added $id$ property and LF ending
2012-06-26 17:20:16 +00:00
9041c5de39
fixed help texts
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killed full number range output option (use spectral_geomPack if needed)
2012-06-26 14:41:25 +00:00
2b5ff6a456
2 small corrections for header of geom file
2012-06-26 10:41:22 +00:00
77ee33ec1f
script to changes the (three-dimensional) canvas of a spectral geometry description
2012-06-21 12:57:14 +00:00
01a9290567
deleted old incarnation...
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new script follows established option parsing.
can rescale (increase only) the number of grid points in any dimension (with or without concurrent dimension scaling).
2012-06-20 16:00:48 +00:00
1105824562
new option to not rescale patch (set size = 0)
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added "3 header" to file output
will now extrude for spectral grids
2012-06-20 15:58:43 +00:00
dfc8606207
boundary conditions now consider patch dimension along pulling direction (used to be orthogonal to that..!)
2012-06-13 09:28:59 +00:00
1c427e8642
loop corrected
2012-05-14 07:58:21 +00:00
542768d712
bug fixed
2012-05-11 08:36:42 +00:00
c962452cda
python version of voronoi_tessellation.f90 generating geom file and material_config file (using kd_tree nearest neighbor search)
2012-05-10 16:42:07 +00:00
0cb983606f
spectral_geomPack is now formatting depending on necessary digits (via additional header information)
2012-05-02 13:44:12 +00:00
b87b2160e7
fixed bug occurring for one item lines.
...
shortened logic here and there.
2012-04-25 13:53:56 +00:00
99f2b8603a
new script for reconstruction of elements from F/IP(spectral_buildElements.py), corrected spectral_randomSeeding.py, made post/postResults.py aware of additional header/footer for file positions larger than 2**31-1
2012-04-24 15:09:20 +00:00
f74b16051b
autodetection of line length for geomPack, updated description for both files
2012-04-24 11:31:18 +00:00
14356bf35e
new pre processing script for interpretation of "copies of" and "to" in geom files
2012-04-23 12:46:38 +00:00
31753be16f
updated setup/setup_processing.py with new files
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added data_readLine(LINE) and data_skipLines(LINES) for ascii table
2012-04-18 11:42:57 +00:00
17f644b261
new scripts to add deformed configuration to ASCII table and for generation of layered 2D geometries (EBSD)
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addCompatibilityMismatch.py is now using functions from ASCII table library
2012-04-18 09:58:59 +00:00
a3b37356be
added svn flags
2012-03-31 12:42:49 +00:00
c29ae95af7
new version of AL spectral solver (seems to work, but still experimental)
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new concept of DAMASK for Python: Now using also IO.f90, debug.f90 etc. instead of mimicing their necessary function. This needs DAMASK_python.f90 and DAMASK_python_interface.f90 (At the moment more or less copies of respective spectral files).
polished and renamed the scripts for converging ang files
renamed voronoi_randomSeeding.py to spectral_randomSeeding.py
2012-03-29 19:54:31 +00:00
30d38436c7
switched voronoi seeding to python
2012-03-29 16:41:23 +00:00
4a6cdcc2e2
moved and renamed tools for generating geom file from ang files. using python instead of c++ for hex2cub conversion
2012-03-27 17:47:39 +00:00
3816adac27
removed batch processing (easier done on command line) and changed interactive question for filename to cmd argument
2012-03-21 17:58:11 +00:00
d2051e54a5
PBC meshing can work on 2D models
2012-03-14 13:40:22 +00:00
95a2ed3443
added ability to add "damask option" to input file
2012-03-13 14:08:09 +00:00
d68a3d1869
added LF=UNIX to a bunch of files
2012-02-22 13:30:00 +00:00
ae6abedee7
set makefile line endings.
...
small output polish in patchFrom...
2012-01-16 16:06:41 +00:00
447e181f55
fixed rounding problems with nodal coordinates
2012-01-16 16:05:02 +00:00
7ed2c19d0f
switched importing from "msc_tools" to "damask"
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patchFrom... now skips blank lines, has more commenting, treats (artificial) bi-crystal (somewhat) gracefully.
2012-01-16 09:32:36 +00:00
8d5dcc97bd
added geomCrop to crop a box out of a geom file
2011-12-20 13:33:16 +00:00
ea0fe7b406
corrected 3D visualize (math.f90 part was not working)
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small polishing of voronoi_tessellation.f90
2011-12-06 17:46:33 +00:00
5ebeb96e85
made DAMASK to work with gfortran:
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-removed to long lines
-restructured f2py modules and merged make_DAMASK2Python into setup processing
-setup_code.py now sets library path in makefile and asks for compile switches for spectral code
-substituted \ in format strings with $
restructured DAMASK_spectral:
-more logical output and structure of code
-better input for spectral debug parameters
2011-12-06 16:58:17 +00:00
f685bbba0e
exchanged location of "graincount" in user block.
...
now matches wiki entry:
1. homogenization block
2. grain block
(grain count
sub-block[s] of crystallite and constitutive)
2011-11-23 09:09:00 +00:00
e8f5996a96
renamed MSC_TOOLS.library_paths to libraryPath, since only single string is returned
2011-11-23 08:25:52 +00:00
06176873e4
after a somewhat lengthy discussion with Philip about usability and developability and general file-naming philosophy we think that we found a compromise on the "to-dot-py or not-to-dot-py" issue:
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symlinks in DAMASK_ROOT/bin do not carry the extension, but the source files do.
Hope that results in the maximum number of happy developers and users.
2011-11-09 15:37:45 +00:00
9e3d7d7d6c
made $DAMASK_ROOT definition optional
2011-11-03 13:51:54 +00:00
aba7937845
now uses msc_tools method to figure out Mentat path
2011-11-03 13:16:00 +00:00
db12869c16
shifted back to main folder. small polish.
2011-11-03 12:18:07 +00:00
b847db969a
changed "texture" to more correct "structure"
2011-11-03 12:07:41 +00:00
680ba9082f
removed deadlock when calling IO_warning(33)
...
polished IO_error and IO_warning
checked OpenMP critical statements in DAMASK_spectral.f90
corrected writing of headed in DAMASK_spectral.f90
2011-11-02 14:38:42 +00:00
96223ddf39
corrected for-loop index bug. two-dim output is now optional.
2011-10-14 23:43:45 +00:00
708b4d2eca
seed-file header format corrected, setup script now contains minimalSurface and vicinityOffset. removed .exe from compile output
2011-10-14 22:39:58 +00:00
ba0488638b
alter a spectral geom file such that any voxel that sees within a given vicinity a different microstructure than itself gets offset by a given value. this allows to identify/isolate grain boundary regions...
2011-10-11 17:35:53 +00:00
98c9bf9c15
generates spectral geom file for (currently) gyroid or diamond minimal surfaces. Inside and outside of a given threshold value are distinguished by microstructure 1 and 2.
2011-10-11 17:30:55 +00:00
ffc6442098
can now deal with arbitrarily long lines for microstructure definition. useful for 2D ASCII representation of grain morphology in the geom file.
...
additional internal code reworking.
2011-10-11 17:25:22 +00:00
d235de1aa5
added two small (quick and dirty) tools to convert data from EBSD to input files for spectral method, put them together with patchFromReconstructedBoundaries into new folder.
2011-09-13 15:46:44 +00:00
48ac3956ce
added '\n' escaping of ID string in VTK header
2011-09-05 13:38:10 +00:00
f458f026db
forgot to include string module, too
2011-09-05 08:54:29 +00:00
0ac5109c94
forgot to include string module
2011-09-05 08:50:36 +00:00
272f7cc655
added auto scaling of dimension to voronoi_tessellation.f90. If dimension(i) == 0, it will get the smallest step of the remaining dimensions in that direction. Same is now done by patchFromReconstructedBoundaries
...
setup_processing.py now gives executables the extension *.exe and removes the old executables before compiling
2011-08-25 12:16:06 +00:00
483234047c
renamed to be consistent with other file names
2011-08-19 07:53:35 +00:00
589666d19e
added python script to simply (without antialising) scale a given *.geom file
2011-08-19 07:29:50 +00:00
10493ea8b0
added $Id$ login name escaping
2011-08-18 07:53:07 +00:00
164da22730
added some warnings if Mentat or PIL cabability missing
2011-08-18 07:52:07 +00:00
ff3bac2496
does not double size of 2D data for spectral method any more
2011-08-17 16:06:50 +00:00
bedce496a8
deleted unused option "dimension" since this is figured out by parsing the respective spectral or geom input files anyway.
2011-08-15 08:34:55 +00:00
4d2f6782e7
removed "error" msg about missing /msc directory. if not present, now silently ignored (together with any requests for Mentat interaction).
2011-06-09 12:52:54 +00:00
f2c41aac83
do not use pwd library as it is unix only
...
due to the above path to subroutine is no longer set in mentat
spectral output uses different "grain numbers" for x-margin, y-margin, and margin edge
2011-06-08 15:06:37 +00:00
7aed307bfc
removed obsolet option --frame
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renamed texture component frame to margin
2011-06-08 06:47:23 +00:00
8921f29dce
merged imaging, Mentat, and spectral versions of generating a patch of grains from a reconstructed boundary file into one script.
2011-06-07 19:15:34 +00:00
9f5c9142e5
generate ParaView mesh from spectral geometry (*.geom) description file to check for correct grain assignment
2011-06-01 08:44:14 +00:00
ac3a2ee4e1
alll grain have the same phase now
...
corrected small bug when Image library is not available
2011-05-28 09:48:39 +00:00
fffff202b0
2D mesh option now also alters corresponding job option
2011-04-04 15:47:09 +00:00
73accf79b6
added option for 2D mesh (3D extrusion step is skipped)
2011-04-04 12:12:01 +00:00
a546f8dbd2
changed wording of input queries to (hopefully) clearer statements
2011-03-30 15:48:18 +00:00
874d5067c7
switches drawing of servo links temporarily off to speed up processing.
2011-02-11 11:29:58 +00:00
0cf1404db0
changed from element 117 (hexahedral with reduced integration) to element 7 (hexahedral with full integration). one-IP elements give trouble in the ping-pong scheme by being frequently/always outdated. this is likely connected to their finite element technology such that even high stiffness values do not prevent the solver from altering displacements in subsequent cycles. remedy is to go for full integration combined with /elementhomogeneous/ phase...
2011-01-27 14:32:29 +00:00
ee7a8ad52a
general speed up
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spectral format records physical coordinates
tessellation now based on phys coords instead of discretization.
2011-01-24 16:21:17 +00:00
e721f2b654
sight restructuring of algorithm -- same functionality
2011-01-20 19:22:22 +00:00
52f06009be
rewrote voronoi tessellation. the VE generation is now divided into two parts:
...
-generation of random positions (in a 1x1x1 parameter space) and random angels
-actual voronoi tessellation
for the generation of the positions, a resolution can be specified to ensure that the tessellation works at that resolution. The tessellation will always work on larger resolutions but not necessarily at smaller ones.
2011-01-20 17:21:38 +00:00
5990d94ca3
added description and $ID$
2011-01-19 15:14:05 +00:00
322cbd2597
changed tools for voronoi tessellation to match new specification (file extension and resolution). Also renamed the files, because the space characters cause trouble
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improved reconstruct.f90 and spectral_post.py, both files work now under linux
added make_reconstruct.py, small shell script for using f2py
2011-01-07 14:37:05 +00:00
9d32bc7ae6
added output of complete mesh to voronoi fast.f90
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first version of post processing for spectral method: spectral_post.py
2010-11-29 10:08:53 +00:00
e80e055c75
added three small programs useful for spectral method (fortran sourececode)
...
voronoi fast.f90 and voronoi small memory.f90 are two variants to do a voronoi tessellation and write the result to a mesh file that can be interpreted by mpie_spectral.f90. Difference is the memory management resulting in one faster and one memory saving version. voronoi fast.f90 has also the ability to write out a file for Ricardo Lebensohns spectral code.
colormap.f90 is a simple code that can be used to generate colormaps for gmsh.
2010-10-31 16:06:10 +00:00
74743c0856
little typo fixed...
2010-10-26 18:26:04 +00:00
487466dd88
scripts are now aware of symbolic links to themselves...
2010-10-26 16:26:55 +00:00
5be6604fd6
included definitions of "material" and "geometry" properties after mesh generation...
2010-10-26 13:45:23 +00:00
d965f14f90
generate hexahedral mesh in Mentat based on a data file of Ricardo Lebensohn's "txfft" format (phi1, Phi, phi2, x, y, z, grainId, phaseId)
...
Only grainId is used, physical dimension and subdivisions need to be provided on command line.
improvement possible by parsing x, y, z columns to get those directly.
2010-10-25 17:57:57 +00:00
3a4743f1d3
fixed bug in grain naming scheme. occurred for gaps in consecutive numberings...
2010-09-28 16:56:49 +00:00
23746e7e78
chopped line beginnings
...
introduced check for PIL, if this fails, no image will be output
2010-09-23 07:59:52 +00:00
4a31b175da
1) introduced default colors
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2) complaints are more verbose
2010-09-06 16:51:11 +00:00
3b671faae7
added some flexibility (and bug-fixing) to the pre/post processing. the file 'MSCpath' contains the LOCAL path to the MSC installation (/msc in our case)
2010-08-17 18:21:22 +00:00
94efd57663
started to put Marc/Mentat related scripts to corresponding post/pre processing folders. We should move development from my Code folder to here (sorry, lost history then...)
2010-08-16 20:47:27 +00:00
Harsha Phukan