Commit Graph

1954 Commits

Author SHA1 Message Date
Martin Diehl 73df615ff3 numpy meshgrid can do this now 2019-05-30 09:45:30 +02:00
Martin Diehl 4e0e5a2329 new python formatting style 2019-05-30 09:41:22 +02:00
Martin Diehl f30eda0267 no need to loop over files
will procude the same file over and over again
2019-05-30 09:32:37 +02:00
Philip Eisenlohr cdc8338347 full (not periodic) mirroring is geom_mirror default behavior 2019-05-29 20:22:29 -06:00
Philip Eisenlohr d79f0c6290 replace geom_canvas --blank with geom_fromScratch 2019-05-29 20:02:06 -06:00
Martin Diehl fd9801ba09 StringIO not needed 2019-05-29 19:44:38 +02:00
Martin Diehl d7e8a66746 polishing 2019-05-29 14:18:11 +02:00
Martin Diehl 16bd5294aa loop order as intented 2019-05-29 14:06:39 +02:00
Martin Diehl 78f30684f8 moderized
needs some polishing with respect to array orders
2019-05-29 09:40:56 +02:00
Martin Diehl 6836a2eae8 better readable 2019-05-29 08:04:01 +02:00
Martin Diehl dfc2b47abc better readable 2019-05-29 08:01:00 +02:00
Martin Diehl 8ee23b37b2 should not be part of the repo 2019-05-29 07:52:44 +02:00
Martin Diehl bb6f54963a save some memory (avoid copies if not needed) 2019-05-29 07:49:43 +02:00
Martin Diehl 9f68923038 restored old behavior
save some ressources by avoiding copies.
much slower than old version, better cast formula into meshgrid again
2019-05-29 07:38:11 +02:00
Martin Diehl 2eb964b1ea simplified
needs some manual checking and proper test
2019-05-28 23:49:11 +02:00
Martin Diehl 100a2031d3 [skip ci] no white space needed 2019-05-28 07:55:24 +02:00
Philip Eisenlohr 1f56ac6a4a streamlining and bugfixing of geom-class 2019-05-27 22:45:34 -06:00
Martin Diehl b69f0efbbc improved and simplified reporting 2019-05-27 22:00:26 +02:00
Vitesh Shah 5abcca50ee Merge branch 'more-HDF5-postprocessing-cleaned' into development 2019-05-27 12:17:12 +02:00
Martin Diehl 59c6c5cfe4 not needed anymore
essentially, (gauss) is an Euler angle triplet
2019-05-27 10:49:50 +02:00
Martin Diehl 6e06764e2d using (enhanced) central functionality 2019-05-27 08:38:02 +02:00
Martin Diehl d9ab87cfde crystallite will be removed soon, error handling is done by geom class 2019-05-27 08:35:24 +02:00
Martin Diehl 5cf63bbbc3 vtk 7 is out for more than 3 years 2019-05-27 08:34:36 +02:00
Martin Diehl b5cec797c0 cleaned 2019-05-26 23:03:31 +02:00
Martin Diehl c8dfba89e5 using class
still a very complex script
2019-05-26 22:49:05 +02:00
Martin Diehl 15d5a7ae28 don't access attributes directly 2019-05-26 22:08:14 +02:00
Martin Diehl f251cdb746 simplified 2019-05-26 22:07:50 +02:00
Martin Diehl af493cf9fd using class
needs more memory, but should be faster and is better readable
2019-05-26 21:32:08 +02:00
Martin Diehl 99da46fda8 polished 2019-05-26 20:36:41 +02:00
Martin Diehl 657a30c2f5 using new functionality 2019-05-26 18:51:27 +02:00
Martin Diehl feb2340935 self-reporting functionality for updating 2019-05-26 17:58:54 +02:00
Martin Diehl 34f7bbe2a0 'blank' option does not fit to flow of script
seeds_fromRandom -N 1 | geom_fromVoronoiTessellation -g 30 30 30 -s 1 1 1 > file.geom
or a few lines of python code give the same results
2019-05-26 13:06:22 +02:00
Martin Diehl e7b8ae08d0 polishing 2019-05-26 12:14:48 +02:00
Martin Diehl 974f67ffdc no frills 2019-05-26 12:06:51 +02:00
Martin Diehl be3513d1e0 polishing.
python imports follow PEP8
2019-05-26 09:49:56 +02:00
Martin Diehl a242382bed Merge branch 'geometry-class' of magit1.mpie.de:/damask/DAMASK into geometry-class 2019-05-26 09:19:29 +02:00
Philip Eisenlohr b13aa799c3 updated error message 2019-05-25 17:00:41 +02:00
Martin Diehl c89d344236 polishing 2019-05-25 13:51:05 +02:00
Martin Diehl 2b7d95f800 was accidently commited
gives different results due to interpolation from scipy
2019-05-25 12:09:09 +02:00
Martin Diehl c92969787a geom Class was updated 2019-05-25 11:56:06 +02:00
Martin Diehl 94f85b7f33 better readable 2019-05-25 10:45:58 +02:00
Martin Diehl fc1f65c34e works for dtype='float' 2019-05-25 10:36:46 +02:00
Martin Diehl 875643c363 same style 2019-05-25 10:24:45 +02:00
Martin Diehl 17eb0d1b20 using new class 2019-05-25 08:48:44 +02:00
Martin Diehl 4788fc6046 making use of new class
@philip: 1D arrangement needed?
2019-05-25 08:37:02 +02:00
Martin Diehl 6c7f7c77da specifying non-existing or invalid files is an user error
this is the standard behavior for common unix tools, no need to make an
exception here
2019-05-25 08:24:32 +02:00
Martin Diehl cf374a04dc using new class 2019-05-25 08:21:00 +02:00
Martin Diehl 420abfa162 use new class 2019-05-24 22:34:27 +02:00
Philip Eisenlohr eb13fbc0ce streamlined geom-info reporting; added --float option to some scripts; hardened against NaN; "microstructures" now reports uniques not max 2019-05-23 13:03:24 -04:00
Philip Eisenlohr e6cec6ecbe added option to reverse inside/outside of primitive body 2019-05-23 12:49:03 -04:00
Martin Diehl 339b86f784 bugfix + more verbose reporting 2019-05-16 11:44:03 +02:00
Martin Diehl 9f7fa5393a fix for scalar datasets 2019-05-16 09:31:13 +02:00
Martin Diehl 4599d1c34e does not match
node does not make sense, is weirdly numbered
2019-05-16 00:42:22 +02:00
Martin Diehl 3c0c0a2cd1 more flexible in selecting data 2019-05-16 00:27:06 +02:00
Franz Roters 998789528c Merge branch 'HDF5-out-homog-2' into 'development'
Hdf5 out homog 2

See merge request damask/DAMASK!78
2019-05-13 17:34:59 +02:00
Vitesh Shah feb1465803 Better to have actual increment num in output file 2019-05-08 17:31:18 +02:00
Martin Diehl 0cc2b1214d store requested data in ASCII file 2019-05-07 15:18:12 +02:00
Martin Diehl 1eaf67ad82 store results in subdirectory
defaults to postProc
2019-05-07 13:30:05 +02:00
Martin Diehl f65423fe9f rudimentary postResults for HDF5 output
only meant for compatibility during transition
2019-05-05 10:09:23 +02:00
Martin Diehl 8a9baf6d78 preparing output of mech_homog to HDF5 2019-04-30 18:45:38 +02:00
Philip Eisenlohr d74599d39a Merge branch 'HDF5-postprocessing' into 'development'
Hdf5 postprocessing

See merge request damask/DAMASK!72
2019-04-29 23:24:42 +02:00
Martin Diehl 6b7fd6b7ea visualizing data from DADF5: first prototype 2019-04-18 11:58:17 +02:00
Martin Diehl 7177813710 adding data to geometry 2019-04-17 19:57:16 +02:00
Martin Diehl 8eb1a35dfb first version of a library to parse HDF5
- preliminarly called DADF5 (DAMASK HDF5)
- script to write (empty undeformed) geometries is also added
2019-04-13 11:25:53 +02:00
Martin Diehl 0c6fde97f9 wrong positions for point visualization
- now the cell centers are at the centers of the cells for cell
visualization
2019-04-13 00:42:05 +02:00
Martin Diehl ed7423a3d6 bug fixes 2019-03-10 08:16:01 +01:00
Martin Diehl 67619fa92a consistent definition of axis angle 2019-03-09 20:18:28 +01:00
Martin Diehl 433281f71d following Rowenhorst convention 2019-03-09 19:58:17 +01:00
Martin Diehl 0d08659b2a general cleaning 2019-03-09 11:11:40 +01:00
Martin Diehl 60feb96afd let vtk decide on the file extension 2019-03-09 11:11:40 +01:00
Martin Diehl 5ab8e50d09 consistent with reference paper 2019-03-08 19:07:19 +01:00
Martin Diehl b84d4f1b6a improved error handling/clearer messages 2019-03-05 10:58:57 +01:00
Philip Eisenlohr e030038b73 [skip ci] added --blank option to create fresh canvas (from nothing) 2019-02-27 19:37:38 -05:00
Philip Eisenlohr c706ca5ba3 no progress bars in quite mode 2019-02-26 21:22:49 -05:00
Eureka Pai f3d2803443 addMises failed for single run of either --stress or --strain 2019-02-25 19:29:12 -05:00
Eureka Pai 2089726800 corrected output extension of vtk files to reflect binary format 2019-02-25 18:48:40 -05:00
Eureka Pai e401c21266 dropped obsolete option --inplace from geom_check 2019-02-25 18:30:45 -05:00
Martin Diehl e88182b007 improved converte, now with test
still needs to figure out how +P is handled
2019-02-24 14:39:34 +01:00
Martin Diehl 0d7fd587e3 direct translation from DREAM.3D to DAMASK geom
needs test
2019-02-24 12:59:10 +01:00
Martin Diehl 95be7ef938 directly convert to geom file + material config 2019-02-24 10:33:30 +01:00
Martin Diehl 903edcd429 do not patronize the user, rather give hints 2019-02-24 10:31:08 +01:00
Martin Diehl d3ac3cc0f5 using new Orientation class 2019-02-24 08:34:20 +01:00
Martin Diehl 9dc8dff4b1 cleaning and adding compatibility layer 2019-02-23 22:35:04 +01:00
Martin Diehl 9fa2553af4 task for DREAM.3D if needed
pointwise takeover should not be a problem anymore as reading in takes
no time (at least in comparison to addGrainID)
2019-02-23 22:14:55 +01:00
Martin Diehl a8e8b75cc0 use new rotation class 2019-02-23 22:13:24 +01:00
Martin Diehl fff377de7f initial simplification.
Should be able to generate from table containing either <microstructure>
or <texture> and <phase>
2019-02-23 22:06:31 +01:00
Martin Diehl b3455c825e transition to new orientation class
forward-backward conversion quite stable
2019-02-23 21:49:05 +01:00
Martin Diehl e4bb61c9d9 transition to new orientation class/DREAM.3D 2019-02-23 11:37:09 +01:00
Martin Diehl 93ae5cbd07 Merge remote-tracking branch 'origin/development' into 10-consistent-orientation-conversions-3 2019-02-22 23:05:36 +01:00
Satyapriya Gupta 3bec76e781 can now deal with 1x1x1 geoms 2019-02-19 12:06:46 -05:00
Martin Diehl 25727bfa52 using CamelCase 2019-02-19 10:32:18 +01:00
Martin Diehl 43a451b2e1 inplace not useful
use shell script if you want to keep an backup of your old data
2019-02-18 14:36:04 +01:00
Martin Diehl 27ebe1f665 improved documentation 2019-02-17 08:17:40 +01:00
Martin Diehl 5c20609e81 more verbose help, drop support for really old vtk 2019-02-16 22:20:44 +01:00
Martin Diehl 802ef6fe5c more precise help 2019-02-16 18:25:41 +01:00
Martin Diehl c6781e415a using default notation for vector access 2019-02-16 18:23:00 +01:00
Martin Diehl 0b1bfdfd4e was only working with python2 2019-02-16 18:17:05 +01:00
Martin Diehl 29fc53fdcb more specific about invocation 2019-02-16 17:41:56 +01:00
Martin Diehl fa003e8077 small adjustments for autodoc 2019-02-16 15:26:21 +01:00
Martin Diehl 4ce151c967 camel casing (easer for foswiki) 2019-02-15 23:22:51 +01:00
Martin Diehl 0cc4e582e4 Merge branch 'development' into 26_autodoc-2 2019-02-15 20:47:14 +01:00
Martin Diehl 566099ad81 automatic documentation for some post processing scripts 2019-02-15 18:52:47 +01:00
Philip Eisenlohr dc133344b6 [skip ci] migrated to python3 compatibility 2019-02-14 18:44:06 -05:00
Philip Eisenlohr d58c3008ae fixed too long line in addLinked 2019-02-14 18:31:22 -05:00
Philip Eisenlohr 742d58cfce added ASCIItable tests to CI pipelining 2019-02-14 18:24:09 -05:00
Martin Diehl c4cb35891c all fine with python3 2019-02-14 22:56:39 +01:00
Martin Diehl 889cfc8ba0 vtk script only work with python3 on new testing 2019-02-14 01:39:54 +01:00
Martin Diehl 217024667b forgotten comma 2019-02-12 11:30:43 +01:00
Martin Diehl 608852df83 rotation paper has angle as last component 2019-02-12 10:58:38 +01:00
Martin Diehl 7da8980cc0 bugfixes: wrong shape, wrong conversion 2019-02-12 09:04:35 +01:00
Martin Diehl 336a80091f rodrigues is 4-vector with rotation being the last component
established a single source of truth for length
2019-02-12 08:59:26 +01:00
Martin Diehl 97ac437686 more user friendly constructors 2019-02-12 08:14:27 +01:00
Martin Diehl ef3fc0b58a bugfix: wrong array indexing
rotation of meshgrid tuple implemented
2019-02-12 07:42:46 +01:00
Martin Diehl 48b0307fab using new rotation class
cannot rotate matrices (3,3) and (3,3,3,3) at the moment
2019-02-12 00:27:13 +01:00
Philip Eisenlohr 74956c0290 avoid error for empty "name" 2019-01-23 20:59:07 -05:00
Martin Diehl da115ca9d4 probably never used and outdated (python2.7)
doing the same conversion via DREAM.3D will be available soon
2019-01-16 17:51:37 +01:00
Martin Diehl c5dabbb68f correct comment sign
the # indicates the end of a list
2019-01-09 16:31:00 +01:00
Martin Diehl 0dca8d2740 compatible to python 3 and mentat >= 2017 2019-01-09 16:28:21 +01:00
Martin Diehl 1192f16582 Merge remote-tracking branch 'origin/development' into 56-parallel-hdf5 2019-01-06 20:56:36 +01:00
Martin Diehl 7768c5874b simpler interface for progress bar 2019-01-05 10:41:49 +01:00
Martin Diehl c00d00c219 Merge remote-tracking branch 'origin/development' into misc-improvements 2019-01-05 09:22:41 +01:00
Philip Eisenlohr 3c5df0a4a4 [skip ci] viewTable acknowledges requested output type(s) 2019-01-04 16:34:21 -05:00
Philip Eisenlohr bcd4288f1e [skip ci] groupTable according to unique values in more than one column 2019-01-03 18:25:28 -05:00
Philip Eisenlohr b5d62c8e29 [skip ci] print estimated remaining processing time for postResults 2019-01-03 11:31:04 -05:00
Martin Diehl 835e3f95a5 [skip ci] was not used 2018-12-31 08:05:56 +01:00
Martin Diehl 6f40989465 order was randomized when creating dict 2018-12-31 07:18:45 +01:00
Martin Diehl a992b8b1f5 random order caused test to fail
rather a workaround, but since HDF5 is coming...
2018-12-30 11:41:22 +01:00
Philip Eisenlohr 9bdd4d1d68 added <!skip> line to stop config parser from trying to interpret rest of geom description---huge speedup!! 2018-12-20 17:22:29 -05:00
Philip Eisenlohr 25a80723c0 numpy interface changed to be strict about 2D array shape in histogram 2018-12-20 17:14:55 -05:00
Martin Diehl 1ef82e351b Merge branch 'orientationClass_with_negative_P' into development 2018-12-20 20:43:00 +01:00
Philip Eisenlohr 7df6dfbf3f renamed "showTable" to "viewTable" to avoid clashing with astropy.table module 2018-12-18 15:10:26 -05:00
Martin Diehl 5d7f930592 math.isclose does not exist for older versions
np.isclose does the same
2018-12-17 20:04:16 +01:00
Martin Diehl 3bab08fdeb Merge branch 'development' into 56-parallel-hdf5 2018-12-12 07:46:02 +01:00
Martin Diehl 1f2fbbee21 consistent name 2018-12-10 09:38:57 +01:00
Martin Diehl 767650e002 more general option + improved descriptions
hopefully more user friendly
2018-12-10 09:27:39 +01:00
Martin Diehl d219842ad8 [skip ci] consistent tolerances 2018-12-09 20:19:33 +01:00
Martin Diehl 60686fb72c [skip ci] improved reporting 2018-12-09 18:05:37 +01:00
Martin Diehl bc04b83d8a no reason for using python2.7 2018-12-09 14:09:26 +01:00
Martin Diehl 08ac49fac0 line too long 2018-12-09 13:21:56 +01:00
Martin Diehl 130fac21c6 cleaning 2018-12-09 13:15:59 +01:00
Martin Diehl d43dfa569b lines too long 2018-12-09 12:37:27 +01:00
Martin Diehl 65165ffc5e assumed wrong type
quaternion should have lenght one
2018-12-09 12:35:32 +01:00
Martin Diehl 697d97cd38 cleaned
legacy format was for pre-MPI output where the extra bytes at start and
end of a chunk (Fortran out) had to be handled manually
2018-12-09 12:30:07 +01:00
Martin Diehl 5054291557 python3 compatible status message 2018-12-09 12:25:31 +01:00
Martin Diehl 741032339e time/math/datatype are not used/defined any more 2018-12-09 11:05:35 +01:00
Martin Diehl aefa006d09 simplified
assume quaternions as input
2018-12-09 10:53:53 +01:00
Martin Diehl 213e31ff87 string was split into letters 2018-12-09 10:53:25 +01:00
Martin Diehl d9b47f09bc modernized
split arguments logically, assume 3-vector for coordinates
2018-12-09 10:52:37 +01:00
Martin Diehl 7eaea64d09 python3 compatible
hope that the new bar causes less trouble than the background message
2018-12-09 09:08:33 +01:00
Martin Diehl 6b73840853 works with python3 2018-12-09 08:07:40 +01:00
Martin Diehl 83a3628765 bug fixes 2018-12-09 07:58:42 +01:00
Martin Diehl d145b257aa new version of numpy complain about overlong range argument 2018-12-09 07:57:05 +01:00
Martin Diehl 4130cbcffa simplified
- always use quaternion as input for orientation
- addAPS34IDEstrainCoords uses table functionality
- rotateData can figure out whether input is vector or tensor
2018-12-09 07:10:31 +01:00
Philip Eisenlohr 3f8726464d addOrientations now checks its input for convention conformity 2018-12-08 13:22:22 -05:00
Philip Eisenlohr eaf2c77903 Merge branch 'orientationClass_with_negative_P' of magit1.mpie.de:damask/DAMASK into orientationClass_with_negative_P 2018-12-07 22:07:22 -05:00
Philip Eisenlohr ac45a9e2d3 more output options, frame input changed to "lab expressed in crystal" 2018-12-07 22:03:14 -05:00
Martin Diehl e8f4dc4c9f Merge branch 'orientationClass_with_negative_P' into development 2018-12-06 07:26:08 +01:00
Martin Diehl ee7e4ee0d9 python3 has different encoding syntax 2018-12-06 06:27:07 +01:00
Philip Eisenlohr a6d4c73de0 added list of map and introduced "quat" keyword in quaternion init 2018-12-05 10:20:05 -05:00
Philip Eisenlohr c0f7ae2798 updated scripts that still used formerly valid object properties of quaternions 2018-12-05 09:07:29 -05:00
Philip Eisenlohr 1d7172c971 adopted more intutitive alternative of P=-1 from Rowenhorst_etal2015 2018-12-04 17:05:35 -05:00
Martin Diehl 8f26fc9358 Merge remote-tracking branch 'origin/development' into 56-parallel-hdf5 2018-12-04 22:34:29 +01:00
Martin Diehl 7c1e2e256c os.urandom returns byte, not string in python3 2018-11-24 10:07:47 +01:00
Martin Diehl c0ad496764 eigenvalue solver seems to depent on python version 2018-11-22 23:13:49 +01:00
Martin Diehl 76accdeaf2 all orientations are passive now
.conjugated() not needed anymore.
Rest is polishing
2018-11-22 18:45:01 +01:00
Philip Eisenlohr 9b82b7fadd removed obsolete keyword "Bunge" from asEulers() method 2018-11-22 11:51:53 -05:00
Martin Diehl ba5b623f14 Merge branch 'development' into improved-HDF5 2018-11-18 19:44:36 +01:00
Martin Diehl fcb14f6099 was never used 2018-11-18 12:04:08 +01:00
Martin Diehl d53b01ab56 also works for python3 2018-11-18 08:04:52 +01:00
Martin Diehl 8ee2de61ea map returns no list any more 2018-11-17 12:12:20 +01:00
Martin Diehl 257d9d5350 needs to be list 2018-11-17 12:12:20 +01:00
Martin Diehl 44bd85a041 not working for python3, trying 2018-11-17 12:12:20 +01:00
Martin Diehl e1a730e96b python3 compatible integer division and argument sequence in agreement with documentation 2018-11-17 09:58:54 +01:00
Martin Diehl 015e819d4c python3 does not allow to compare tuple/list with int 2018-11-17 09:29:05 +01:00
Martin Diehl 82861e80bc more python3 related changes 2018-11-17 08:46:58 +01:00
Martin Diehl 558745b548 explicitly require python3
on older systems, python3 tpyically exists but python2 is the defaul
2018-11-17 08:12:12 +01:00
Martin Diehl 50f880afd1 more scripts working with python3 2018-11-16 19:32:17 +01:00
Martin Diehl 4ffb4a4321 fixed several typos 2018-11-16 19:28:24 +01:00
Martin Diehl 9922f5f646 adjusted to python3
translate is more complicated now:
https://stackoverflow.com/questions/41708770
2018-11-16 12:23:45 +01:00
Martin Diehl 26811b74d6 known to work with python3 2018-11-16 09:18:29 +01:00
Martin Diehl a3647cc587 more files with confirmed python3 compatibility 2018-11-16 09:03:12 +01:00
Martin Diehl f47891e292 booleans not allowed as indeces any more 2018-11-16 09:03:12 +01:00
Martin Diehl e9e3fef8d4 more python3 compatible scripts 2018-11-15 16:40:54 +01:00
Martin Diehl fe2c7efa27 seem to work 2018-11-15 13:56:48 +01:00
Martin Diehl 8f80152a03 use floor division of integers
1/2 = 0.5 in python3 (would be 0 in python2)
2018-11-15 12:28:36 +01:00
Martin Diehl efd29e62f7 verbose should be optional
- causes problems on many systems (screwed up output)
- does not work with python 3 since threading class has changed
2018-11-15 12:16:55 +01:00
Philip Eisenlohr 0cbcb028aa fixed problem with "ValueError: Mixing iteration and read methods would lose data" for string-containing tables 2018-10-21 15:39:30 -04:00
Martin Diehl 7480d1a842 fixes for Python3 2018-10-19 07:35:59 +02:00
Martin Diehl a00d15b889 geom files are not labeled 2018-09-29 11:18:35 +02:00
Martin Diehl 8616a92309 unused module 2018-07-20 03:50:07 +02:00
Martin Diehl 24d1528e04 on the way to full python 3 compatibility 2018-07-20 03:31:46 +02:00
Martin Diehl 2632be2a76 polishing 2018-07-20 03:09:53 +02:00
Martin Diehl 784ae28dbb now working with python 3 2018-07-20 00:39:50 +02:00
Martin Diehl 1f637a0c49 python3 compatible map requires conversion to list 2018-07-19 18:01:38 +02:00
Martin Diehl 0438b7113a using util function where possible, ensuring python3 compatibility 2018-07-19 16:38:25 +02:00
Martin Diehl f928bd5e5b more python 3 compatibility 2018-07-19 16:26:30 +02:00
Martin Diehl 35e470ff4d needed for python3 2018-07-19 16:19:05 +02:00
Martin Diehl 9821654aae iteritems does not exist in python3 anymore
items also works for python2 (might be slower though)
2018-07-19 16:16:10 +02:00
Martin Diehl d138993c1d using util functionality to be compatible with python3 2018-07-19 16:12:36 +02:00
Martin Diehl aadcd61824 polishing 2018-06-18 00:05:55 +02:00
Philip Eisenlohr 1b12457fe6 vicinityOffset to specific triggering IDs instead of just any other ID 2018-03-30 11:48:02 -04:00
Philip Eisenlohr 0570a49ed5 fixed broken logic of restoring and preventing immutable microstructures 2018-03-27 16:53:49 -04:00
Philip Eisenlohr 2c3eae6bf0 fixed tests and bug for very small unit cube fractions when grid is also small 2018-03-07 18:59:27 -05:00
Philip Eisenlohr 32c34457c2 direct selection of valid seed coordinates within subfraction of unit cube instead of check and repeat 2018-03-07 17:45:22 -05:00
Martin Diehl 1bbaa7cefe reverted last commit, scipy.linalg is different from numpy.linalg 2018-02-26 23:50:44 +01:00
Martin Diehl 6046a7ae3d there is no scipy.linalg (at least on my system)
numpy.linalg is automatically imported together with numpy
2018-02-26 20:22:57 +01:00
Philip Eisenlohr b078234644 added scipy and scipy.linalg as known modules for calculations 2018-02-25 14:19:22 -05:00
Philip Eisenlohr f5177b6d2d [skip ci] added option for non-periodic geometries 2018-02-20 10:20:35 -05:00
Martin Diehl 2254746177 Merge branch 'development' of magit1.mpie.de:damask/DAMASK into development 2018-02-12 11:23:05 +01:00
Fengbo Han 9249e7db2b Merge branch 'development' into HMS 2018-02-07 11:44:17 +01:00
Martin Diehl ba3a4e1254 indicating vectors with 1_, ..., n_ is standard now, "euler" also (more or less) 2018-02-05 17:34:08 +01:00
Philip Eisenlohr e304ce35da forgot to rename function call to read "coordGridAndSize" 2018-01-30 12:58:43 -05:00
Philip Eisenlohr 355d576b4d shortened code with utility function coordGridAndSize 2018-01-30 09:20:47 -05:00
Philip Eisenlohr 710970d728 updated option --label for addCurl/Div/Grad 2018-01-29 21:27:05 -05:00
Philip Eisenlohr 1d71a52133 further simplifcation of scripts 2018-01-29 15:10:41 -05:00
Philip Eisenlohr b45b43c5ac bug fix in addCurl, simplified scripts 2018-01-29 14:12:19 -05:00
Philip Eisenlohr 622d038932 einsum now compatible with numpy 1.14 2018-01-29 09:18:05 -05:00
Philip Eisenlohr 30272fc355 generalized addCurl with --data instead of --tensor and --vector 2018-01-28 18:25:50 -05:00
Philip Eisenlohr 8fb127f31c better description of activity 2018-01-28 18:08:02 -05:00
Philip Eisenlohr 761670f218 generalized addGradient with --data instead of --scalar and --vector 2018-01-28 18:02:35 -05:00
Philip Eisenlohr 532d669d33 switched to more robust line based output 2018-01-27 17:45:53 -05:00
Brendan Vande Kieft ceb0ff09e6 Subdivide vertex data with geometry when converting Marc input to VTK 2018-01-15 17:20:24 -05:00
brendanvk a03bb1ec3e Add MSC.Marc to VTK conversion support
marc_to_vtk.py takes Marc input file, subdivides it and creates a
vtkUnstructuredGrid .vtu file with the resulting geometry.  Currently
supports hexahedron elements.

vtk_addGridData.py adds nodal/cell data to some VTK grid.  It is
essentially vtk_addRectilinearGridData with support for unstructured
grid (.vtu) format, which is marc_to_vtk.py's output.
2017-12-11 12:32:38 -05:00
Philip Eisenlohr c33655b479 fixed pyflakes issues 2017-11-28 11:14:22 -05:00
Philip Eisenlohr 0c8c4b54aa Merge branch 'development' of magit1.mpie.de:damask/DAMASK into development 2017-11-28 11:12:05 -05:00
Philip Eisenlohr 3b96fac8bd added script to calculate numerical derivative of ASCIItable data 2017-11-28 10:59:53 -05:00
Martin Diehl 4dfb52c792 unfinished HDF5 should not be part of the next release 2017-11-21 10:23:50 +01:00
Martin Diehl b4f4527ad1 Merge branch 'development' of magit1.mpie.de:damask/DAMASK into development 2017-11-05 08:31:59 +01:00
Fengbo Han 2b69cb8ea9 removed unnecessary liens 2017-10-24 13:23:44 +02:00
Fengbo Han d77789b89f minor change 2017-10-24 12:01:10 +02:00
Fengbo Han d599aec37f Merge branch 'development' into HMS 2017-10-24 11:24:54 +02:00
Fengbo Han 82758bd90f added yield criterion of facet potential 2017-10-24 11:15:34 +02:00
Franz Roters eddc2a6acf numpy actually not needed 2017-10-20 10:17:08 +02:00
Franz Roters 0c24f113c1 split overlong line 2017-10-20 10:14:15 +02:00
Franz Roters 26b8788c06 script to colocate 2D ang files into one §D file and optionally creat geometry and Paraview files 2017-10-20 09:36:57 +02:00
Martin Diehl eda8c24b7d Merge branch 'development' of magit1.mpie.de:damask/DAMASK into development 2017-10-07 17:24:59 +02:00
Philip Eisenlohr 14c1291046 added "--quiet" option to suppress online messaging 2017-10-03 14:03:50 -04:00
Tias Maiti f46d721750 Merge branch 'development' of magit1.mpie.de:damask/DAMASK into development 2017-09-03 17:42:02 -07:00
Philip Eisenlohr 64259d9239 bug fixed in whitelist sorting, more robust against numpy parsing errors 2017-08-28 19:38:14 -04:00
Philip Eisenlohr 5b8bc65d37 exchanged string 'n/a' for 'nan' to allow smooth parsing as float value 2017-08-28 19:32:59 -04:00
Philip Eisenlohr 9e5896a6c5 large speedup (10x) for unconditional filtering by using read/writeArray 2017-08-23 20:54:02 -04:00
Philip Eisenlohr fc4fb43d48 aborting when NO data columns found 2017-08-23 17:53:30 -04:00
Philip Eisenlohr ff072ae3c4 fixed bug (lost orgin info) 2017-08-23 15:14:22 -04:00
Philip Eisenlohr e82df723d1 added Rodrigues vector as possible input format 2017-08-23 14:10:56 -04:00
Philip Eisenlohr b3ac200c17 report linking column in screen output 2017-08-23 14:10:22 -04:00
Philip Eisenlohr 9b6e092b5c changed location where script appends itself to info trail
used to be sometimes at top, sometimes at bottom; now always after predecessor and above standard geom header
2017-08-23 14:09:33 -04:00
Philip Eisenlohr f825e91bf1 script to straighten numbering in geom 2017-08-23 14:08:11 -04:00
Philip Eisenlohr 12fed7a38f added option to use seed coordinates that are not normalized to a unit cube 2017-08-16 16:24:45 -04:00
Philip Eisenlohr 255a465e8b sharpened error detection and reporting 2017-08-16 15:18:29 -04:00
Philip Eisenlohr e18c2fd74c slight layout tweak 2017-08-16 12:52:46 -04:00
Philip Eisenlohr 91c70fc823 sharpened error detection and reporting 2017-08-16 12:51:32 -04:00
Philip Eisenlohr a2947789b5 clarified help and reporting 2017-08-15 16:12:06 -04:00
Philip Eisenlohr 4eff7cfdd8 fixed wrong name for "pos" options destination 2017-08-15 16:11:21 -04:00
Martin Diehl 95c0179945 labeling vectors and values independenty in addSpectralDecomposition 2017-08-13 02:14:34 +02:00
Philip Eisenlohr e6cc948ddf added vector-valued conditions and cleaned obsolete code 2017-08-11 15:19:47 -04:00
Zhuowen Zhao b7d4b3d190 simplified internal handling of conditions and added vector capability to it 2017-08-11 11:56:27 -04:00
Tias Maiti 3860eecb7c Merge branch 'development' of magit1.mpie.de:damask/DAMASK into development 2017-08-10 11:09:37 -04:00
Fengbo Han 9bbc0d4803 implemented fast yield surface fitting with yield stop criteria 2017-08-08 17:29:14 +02:00
Fengbo Han 36c370e668 implemented fast yield surface fitting with yield stop criteria 2017-08-08 17:25:38 +02:00
Philip Eisenlohr 1a423617c2 combined assignement of curvature exponent to deal with negative dimensions 2017-08-03 12:12:47 -04:00
Philip Eisenlohr 84a3885af8 negated option from "voxelspace" to "realspace".
introduced logarithmic sense of curvature exponents, additional polishing
2017-08-03 12:08:51 -04:00
Martin Diehl cb62066667 Merge branch 'development' of magit1.mpie.de:damask/DAMASK into development 2017-07-31 23:00:24 +02:00
Philip Eisenlohr 68493a00f5 fixed PEP line continuation warning 2017-07-31 10:04:04 -04:00
Philip Eisenlohr c8222d6f82 Merge remote-tracking branch 'origin/development' into development 2017-07-31 09:51:10 -04:00
Philip Eisenlohr 837b14592a addLinked can now link between vector-valued columns 2017-07-31 09:34:30 -04:00
Unknown 269eacb11d added flag for skipping right-handedness check of eigenvector basis
separate names for min,mid,max eigvals and vecs
2017-07-28 13:44:17 -04:00
Martin Diehl 6547ab8c69 not needed, ASCII table ensures shape (Npoints,Nvalues) 2017-07-05 04:43:20 +02:00
Martin Diehl f085f61c4d testing hook that checks for executable bit 2017-06-02 09:25:58 +02:00
Martin Diehl 6599f7299d correct description 2017-06-01 10:00:29 +02:00
Martin Diehl e5af0630fe gaussian filter (wrapper no ndimage) 2017-05-29 10:33:05 +02:00
Martin Diehl 691f338f5d executable bit got lost 2017-05-19 09:33:58 +02:00
Franz Roters ed85ce5bdb changed argument handling in line with other scripts
now also works with stdin/out
2017-04-28 12:36:10 +02:00
Philip Eisenlohr d35df1df49 Operate on MFD file to apply servo links, not client-server communication
Speed up by many orders of magnitude... 64 x 64 x 64 mesh less than a minute! Thanks Brendan!
2017-04-26 17:32:01 -04:00
Philip Eisenlohr c34716a0da modern form of croaking, added '*draw_automatic' as final output 2017-04-14 15:07:43 -04:00
Philip Eisenlohr d1c2e2114d switch auto drawing back on at end of pipeline 2017-04-13 19:00:19 -04:00
Martin Diehl 95a982e002 default type for muliple arguments (not extend) is tuple, not list 2017-04-13 12:54:26 +02:00
Philip Eisenlohr 88809863ba Merge branch 'development' of magit1.mpie.de:damask/DAMASK into development 2017-03-20 15:14:15 -04:00
Philip Eisenlohr 66b4e24ab7 solver.Marc.version has no argument anymore 2017-03-20 15:13:54 -04:00
brendanvk 0d648b8de0 Change script to use resolution-independent coords
- Use the --voxelspace flag to get the old behavior
2017-03-07 20:37:30 -05:00
Martin Diehl de57d9514e removed code doubling and unused variables 2017-03-05 17:50:17 +01:00
brendanvk f010aa97d9 Fix non-cube geometry structure, reduce memory 2017-02-24 22:30:04 -05:00
Brendan Vande Kieft e5e6bed5de Improve performance and generalize primitive shape
- Behavior is mostly unchanged, but the primitive may be shifted by a voxel when compared to the previous version, which had rounding issues near the edge of the primitive.
- exponent flag specifies the exponents that satisfy the equation x^e1 + y^e2 + z^e3 < 1.  (1,1,1) gives an octahedron, (2,2,2) a sphere, and large values (1e10, 1e10, 1e10) gives a hexahedral box for any reasonable resolution. Mixing the two can produce a cylinder, (1e10, 2, 2) gives one with rotational symmetry about the x-axis.
2017-02-24 00:42:28 -05:00
Martin Diehl a9d72c54b6 was not python3 conforming 2017-02-04 01:07:24 +01:00
Philip Eisenlohr 746cb9c306 nicer code layout 2017-01-19 15:10:38 +01:00
Philip Eisenlohr c80b02dd72 avoid reporting "none" as STDIN filename 2017-01-19 15:10:17 +01:00
Philip Eisenlohr 49eb7aa1be fixed nasty ABS that caused wrong packing for 1,2,1,1,1,... and the like 2016-12-25 12:39:49 -05:00
Philip Eisenlohr 3628deb30e changed option name from "no-config" to more common "without-config" 2016-12-23 17:46:16 -05:00
Philip Eisenlohr d67be0e3f3 reduced memory footprint (substantially) by switching to 32bit precision 2016-12-08 23:36:19 -05:00
Philip Eisenlohr c8f321356d prefill immutable indices with closest mutable one
Retain only orginially immutable locations, not those where immutability bled into.
Changed threshold for change from 0.5 to 0.95 of max diffusedEnergy.
2016-12-08 09:47:20 -05:00
Philip Eisenlohr 9bb4f89e78 removed leftover debug output 2016-12-06 21:36:45 -05:00
Philip Eisenlohr a2db7e9ba1 added option to suppress writing of material.config part in header 2016-12-06 21:36:25 -05:00
Philip Eisenlohr cb95f3b244 fixed systematic drift of grain structure along -[1,1,1]
correction of periodic Gauss kernel extension, inclusion of ndimage.gaussian_filter alternative (same runtime as FFT), proper output handling of grids <3D
2016-11-30 09:39:13 -05:00
Philip Eisenlohr 40de6910b8 added --float option to translate real-valued grid data 2016-11-29 23:59:42 -05:00
Philip Eisenlohr 814b05e2f6 renamed to hopefully clearer express functionality 2016-11-29 16:30:24 -05:00
Philip Eisenlohr 0f04ddd88e polishing of whitespace, usage help, etc. 2016-11-29 14:44:34 -05:00
Philip Eisenlohr 43c1880195 fixed periodic averaging to work with multi-dimensional data
option --periodic now takes list of labels that undergo periodoc domain averaging, i.e. incompatible to former API!
2016-11-29 14:44:06 -05:00
Philip Eisenlohr 231f05e142 corrected bug that added index column values as first output 2016-11-29 11:16:50 -05:00
Philip Eisenlohr c9ec2e0f46 New table mapping based on shared column values
renamed old addMapped to addRowMapped to better reflect true functionality.
2016-11-29 09:33:35 -05:00
Martin Diehl 873c52cceb using 3 way merge to have syntax as similar as possible 2016-11-07 19:51:12 +01:00
Chuanlai Liu 6d91ce866e Merge branch 'development' of magit1.mpie.de:damask/DAMASK into development 2016-11-07 09:10:39 +01:00
Chuanlai Liu 551b4369a1 improved readability 2016-11-07 09:06:35 +01:00
Martin Diehl 8179a703fb now more flexible, works for synthetic data and user selected data 2016-11-06 23:07:12 +01:00
Chuanlai Liu d35c9dd431 using Einstein sum to replace 'for loop' 2016-11-04 18:50:39 +01:00
Martin Diehl a04968d43f Merge branch 'development' into negativeRange 2016-11-01 17:20:56 +01:00
Martin Diehl 9e76b51014 fixing global variables handling (need to be defined before being used) 2016-10-31 22:53:14 +01:00
Martin Diehl 8593fb3ed7 unifying scripts 2016-10-31 22:11:16 +01:00
Philip Eisenlohr 4acfc73fa1 Merge branch 'Python3' into development 2016-10-31 11:28:40 -04:00
Philip Eisenlohr 94fcc9ad24 fixed language and syntax 2016-10-31 10:40:58 -04:00
Martin Diehl 8eb93a3274 python scripts now pack "a a-1 a-2 ... a-n" to "a to a-n" 2016-10-29 10:49:40 +02:00
Martin Diehl aa3dc56949 fixed handling of last line (bug fix for second but last commit) 2016-10-29 10:30:42 +02:00
Martin Diehl 7e6e2e1c84 not using reserverd keyword "type" 2016-10-29 10:28:34 +02:00
Martin Diehl 1a56ad7a72 no logic change yet 2016-10-29 10:21:00 +02:00
Martin Diehl 6d9d25ea43 python 3 compatible and modernized 2016-10-28 15:40:17 +02:00
Martin Diehl e43e37aae1 new style option setting 2016-10-27 23:06:17 +02:00
Martin Diehl 99dc75c2fd proper capitalization 2016-10-25 21:53:32 +02:00
Martin Diehl a62ab3b5d4 fixes (mainly tuple arguments for functions and lambda functions) 2016-10-25 21:52:51 +02:00
Martin Diehl 8a94f55a2e python 3 compatibility 2016-10-25 06:44:12 +02:00
Martin Diehl a84e7310f5 fixed prospector hints 2016-10-24 20:30:51 +02:00
chen 96349ebf53 add log to each dataset 2016-10-17 18:24:47 -04:00
chen 703ae3c6d6 add script for adding von Mises equivalent to HDF5 file 2016-10-17 17:29:44 -04:00
chen 4d849219f7 will come back for this later 2016-10-17 16:59:42 -04:00
chen 8e7f0c255b fix some syntax error 2016-10-17 16:58:04 -04:00
chen 74b29881f3 strain tensor calculation script for HDF5 2016-10-17 16:24:11 -04:00
chen 1a2194f042 remove useless functions 2016-10-17 16:23:21 -04:00
chen fb1e4f0c39 add IPF color tuple for HDF5 file 2016-10-17 12:24:29 -04:00
chen b04c5801a5 syntax polish 2016-10-14 14:38:09 -04:00
chen 0a35761636 delete unused module 2016-10-14 14:33:22 -04:00
chen dfb49c3138 as script for calc Cauchy stress in HDF5
no safe net in the script, following 'let-it-fail' design
2016-10-14 14:32:20 -04:00
chen fd4b495de2 adding interface for addCalc with HDF5 2016-10-14 14:30:46 -04:00
chen 05a3b569fc adding parallel version of addCalc for H5 table 2016-10-14 12:26:46 -04:00
chen 33de9cf2b9 script for adding data from HDF5 to vtk file 2016-10-14 12:06:59 -04:00
chen 1f01dce862 use 4 space indentation 2016-10-14 12:06:09 -04:00
chen 2f2490e784 remove unused import 2016-10-14 10:48:08 -04:00
chen e5e2eef375 add script generate vtr file from HDF5
following "let-it-fail" design
2016-10-14 10:45:42 -04:00
chen 353b5b6994 avoid doctring as argument 2016-10-14 10:42:03 -04:00
chen 9ac3f564c8 syntax fix 2016-10-13 13:45:25 -04:00
chen 8cdc7c0b10 add xdmf wrapper generator for HDF5
Not recommended for large dataset due to potential memory leak currently plaguing Xdmf ilbrary.
2016-10-13 13:41:04 -04:00
chen ec59dfeec0 do not reshape data
since xdmf is not stable right now, there is no need to reshape the data to tie it to the mesh. comment them out for future reference
2016-10-13 13:22:37 -04:00
chen ace06fd0e1 skip dulplicated columns in ascii table
also add a todo list at the top
2016-10-13 11:33:38 -04:00
chen c311ac47ca force using rectangular mesh
Paraview cannot handle large number of polyvertices using xdmf, forcing a meshed structure to by pass the problem.
2016-10-12 20:20:15 -04:00
chen ffcfe67c73 remove debug output, fix name handling error 2016-10-10 09:46:11 -04:00
chen 7278605004 fix naming error 2016-10-09 19:13:44 -04:00
chen 6450cb3003 fix syntax error 2016-10-09 19:12:45 -04:00
chen 6eb111dc7c add script convert ASCII table to HDF5
using H5Table
2016-10-09 19:01:38 -04:00
chen 4e8bd83d4b syntax error fix 2016-10-07 15:32:10 -04:00
Martin Diehl 5951b45259 only grain file type 1 seems to make sense (type 2 has average values).
For type one, data is fixed i.e. flexible labels are not useful
2016-10-06 15:22:05 +02:00
Martin Diehl de88bebe99 handling defaults correctly for extend option 2016-10-06 12:14:07 +02:00
Martin Diehl f78f89fb12 periodic microstructure needs to be updated per iteration (N).
now calling script twice gives the same result as one call with N=2.
results for N=1 are not affected
2016-10-05 15:24:37 +02:00
Martin Diehl 3abf0bc2d3 Merge branch 'development' of magit1.mpie.de:damask/DAMASK into miscImprovements 2016-09-27 06:22:52 +02:00
Aritra Chakraborty 0ffd74d536 correct flag "data" for updated vtk_addRectilinearGridData 2016-09-26 16:32:39 -04:00