Commit Graph

1499 Commits

Author SHA1 Message Date
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
Aritra Chakraborty 1d06e82700 grain circumference identification
fixed right most path selection criteria for grain circumference
2016-09-26 16:30:50 -04:00
Philip Eisenlohr 5345b42d71 improved robustness against faulty RCB data
deals gracefully with duplicate segments, new option to export cleaned up RCB
2016-09-25 21:18:53 -04:00
Martin Diehl fb23c49b41 should be executable 2016-09-24 15:58:13 +02:00
Martin Diehl e20623845a Merge branch 'development' of magit1.mpie.de:damask/DAMASK into miscImprovements 2016-09-22 16:14:07 +02:00
Jennifer Nastola 0f09a66b62 pyflake was complaining 2016-09-22 15:36:28 +02:00
Jennifer Nastola f8901220ab Merge branch 'development' of magit1.mpie.de:damask/DAMASK into development 2016-09-22 15:34:28 +02:00
Martin Diehl 25103205a8 bug fix, adjust to options change of vtk_addXXXData 2016-09-21 22:01:16 +02:00
Martin Diehl 0f636bf6c3 not needed 2016-09-21 17:47:37 +02:00
Martin Diehl 4cd8fe7f36 indices should be integers (visible warning) 2016-09-21 17:45:23 +02:00
Martin Diehl 43457dcfc5 flexible selection of axes 2016-09-21 17:43:07 +02:00
Martin Diehl 4ccc0cf5a1 tool to mirror geometries (enforce periodicity on measured data) 2016-09-21 17:06:50 +02:00
Brendan Robert Vande Kieft 1180c8bb88 Fix calculation of interfaceEnergy 2016-09-15 17:36:43 -04:00
chen f3308dbef6 replace scalar/vector option with data
vtk does not care 1D data array length
2016-09-14 19:59:26 -04:00
chen 38d1a2c254 Merged branch development into development 2016-09-14 19:50:18 -04:00
Philip Eisenlohr eb69d6f4f1 Merged branch development into development 2016-09-14 19:42:15 -04:00
Philip Eisenlohr 59c1eee16b added possibility to restrict seed coordinates to fraction of unit box 2016-09-14 19:42:05 -04:00
chen ae16ccae61 need to use deep copy when converting np array to vtk array
for batch array conversion, it is necessary to use the deep copy to ensure numpy_support.numpy_to_vtk works as it should.
2016-09-14 15:06:00 -04:00
chen 53d2df6058 vector support 1D vector with arbitrary lenght
simple hack to bypass the size check for vectors since vtk does not care the vector size.
2016-09-14 12:37:07 -04:00
chen 804931db9e force type cast index to int for numpy array
Force type casting indices into int array to avoid warning:
 
VisibleDeprecationWarning: using a non-integer number instead of an integer will result in an error in the future

For more info, see http://stackoverflow.com/questions/20084218/deprecation-warning-in-scikit-learn-svmlight-format-loader
2016-09-12 19:09:48 -04:00
Martin Diehl 77729f39e3 commenting last commit 2016-09-11 14:41:48 +02:00
tiasmaiti 06405bc251 fixed coordinate system convention to be right handed always instead of random left and right handed assignment 2016-09-10 16:39:25 -04:00
tiasmaiti 2daad7542e added option for periodic averaging 2016-09-10 16:39:25 -04:00
chen ee322be870 use np.histogram2d, fixed list.append bug when using weight column 2016-09-09 16:17:00 -04:00
Chen 8c4767d58c syntax fix 2016-09-09 07:28:54 -04:00
Chen 017c08a7bb syntax fix 2016-09-09 07:28:31 -04:00
chen da538fbce9 speed up of VTK data transformation 2016-09-08 18:05:49 -04:00
Martin Diehl c05307a273 Merge branch 'development' of magit1.mpie.de:damask/DAMASK into miscImprovements 2016-09-03 14:35:53 +02:00
Chen a2f3839ca8 add missing numpy import 2016-09-02 14:37:15 -04:00
chen d9077805e4 Forced symetric tensor when adding tensor to vtk
VTK addTensor by default using the lower triangle to populate its tensor object. Enforcing the tensor to be symmetric to avoid necessary confusion when adding data (most stress/strain tensor should symmetric by default, so it should not affect the results)
2016-09-02 09:30:49 -04:00
Chen 20d1164e5d add tensor support for vtk_addRectlinearGridData 2016-09-01 16:57:29 -04:00
Chen 6db0a42eae addvtk data now support tensor type (9 components) 2016-09-01 12:47:26 -04:00
Philip Eisenlohr 4b02a55f4d explicit type casting from boolean to int 2016-08-30 16:08:47 -04:00
Philip Eisenlohr 891ac4d585 fixed comma syntax error 2016-08-25 12:17:27 -04:00
Philip Eisenlohr 55d6adf1b8 renamed to reflect more general nature of script 2016-08-25 12:15:41 -04:00
Philip Eisenlohr 85abf84186 generalized to user-specified mapping function instead of hardwired avg 2016-08-25 12:15:03 -04:00
Zhuowen Zhao f984f1ebea enable floating point data and corrected counting of microstructures 2016-08-24 16:05:50 -04:00
Martin Diehl 7710f4d444 hybridIA (stand alone script and DAMASK) need standard ASCII table
export of TSL OIM is similar to standard ASCII table, simply add correct header
including labels
2016-08-23 17:21:17 +02:00
Martin Diehl c2b1499d84 Merge branch 'development' of magit1.mpie.de:damask/DAMASK into miscImprovements 2016-08-16 12:46:03 +02:00
Philip Eisenlohr 64ac05fc26 removed left-over debug output 2016-08-11 14:24:40 -04:00
Philip Eisenlohr 600731b15c modernized, gracefully add NaN for out-of-bounds mapping 2016-08-11 14:23:29 -04:00
Martin Diehl d239cab3ae corrected help 2016-08-11 13:48:15 +02:00
Jennifer Nastola a0567e8642 added FeatureID and right coordniates to table 2016-08-04 11:11:24 +02:00
Jennifer Nastola ccc0ac35ac copied from ang_toTable 2016-08-02 11:30:36 +02:00
Martin Diehl 6c82641713 added defaults (bugfix) 2016-08-01 16:43:14 +02:00
Philip Eisenlohr fa3387486d clarified meaning of possible (global) rotation (lab/crystal frame) 2016-07-31 19:35:10 -04:00
Philip Eisenlohr 79ff040426 sorting and clarification of help, shortening of output labels 2016-07-30 15:07:44 -04:00
Philip Eisenlohr 23a57ec78f reinstalled "NOQA" keyword for "import math" 2016-07-30 12:52:49 -04:00
Philip Eisenlohr ab3415d44e polishing and rearrangement of code snippets 2016-07-30 12:46:00 -04:00
Martin Diehl c3650a1b00 shebang got reverted 2016-07-30 08:20:57 +02:00
Aritra Chakraborty 6a80c71c0b Merge branch 'development' of magit1.mpie.de:damask/DAMASK into development 2016-07-29 20:42:38 -04:00
Aritra Chakraborty 304fdf1ebe can deal with "veterans" and "newbies" meaning over ride existing with new 2016-07-29 20:41:15 -04:00
Philip Eisenlohr b39915afe1 Merged branch development into development 2016-07-29 17:51:16 -04:00
Philip Eisenlohr 0bbf54e0e4 switched to string.format() method 2016-07-29 17:49:29 -04:00
Philip Eisenlohr afff0b8614 fixed STDOUT error
no files on command line translate to "filename" being empty list. Cannot test for filename[0] then...
2016-07-29 17:48:40 -04:00
Martin Diehl 2a0be6d232 Merge branch 'development' of magit1.mpie.de:damask/DAMASK into miscImprovements 2016-07-27 08:57:13 +02:00