Commit Graph

558 Commits

Author SHA1 Message Date
Christoph Kords 13227dff0f corrected calculation of origin 2013-06-22 14:13:29 +00:00
Philip Eisenlohr 8b5ba9f8f0 now understands packed geom-files (much faster processing...) 2013-06-21 21:19:14 +00:00
Philip Eisenlohr 4cf2e75dc1 justification of numbers done with space instead of "0"s 2013-06-21 21:18:10 +00:00
Philip Eisenlohr e53c67f0e0 added black list for immutable microstructures.
now able to parse packed geom-files.
2013-06-21 21:17:03 +00:00
Philip Eisenlohr 3b4573301c removed now obsolete Moore neighborhood array 2013-06-21 19:10:10 +00:00
Philip Eisenlohr 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
Pratheek Shanthraj 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
Philip Eisenlohr 45951e27c5 script to smooth out interface roughness in a (polycrystal) geom 2013-06-20 19:45:25 +00:00
Christoph Kords 0740845d81 allow coordinates to not be in consecutive columns
keep origin of original data set
2013-06-20 07:36:35 +00:00
Christoph Kords e6499e1a39 renamed script in order to distinguish from "add" scripts that act on ascii tables 2013-06-13 09:05:30 +00:00
Ding Wang 920195809c fixed bug in auto determination of size and grid 2013-06-11 10:11:14 +00:00
Martin Diehl becacb675a linear reconstruction no longer needed for odd resolution 2013-06-05 14:05:11 +00:00
Martin Diehl e635b06270 last polishing on preprocessing scripts, documentation and scripts are all up to date.
added addSchmidfactors to post processing scripts
2013-06-04 12:56:57 +00:00
Philip Eisenlohr 32a16f9745 wildcard matching for column headings, e.g. "[159]_p" to extract only the diagonal elements (scalars) of stress, or "[1-9]_p" to extract all nine values.
fixed VTK file format problem where double precision floats were incorrectly interpreted because they were announced as "float" (now "double").
2013-05-29 10:24:00 +00:00
Martin Diehl 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
Christoph Kords 837574278e removed (now) unused function for reading of configFile 2013-05-28 14:47:50 +00:00
Christoph Kords 10a32dc17b use predefined maps in damask.Colormap class; no need for a colorMap config file anymore 2013-05-28 14:18:21 +00:00
Philip Eisenlohr 8fd590d7bd added red--blue map 2013-05-24 07:41:44 +00:00
Christoph Kords 19dc95a915 now able to choose vector that is used for warpvector filter via option.dispLabel 2013-05-22 21:23:01 +00:00
Christoph Kords 75ee54146b deleted unused function 2013-05-22 21:20:00 +00:00
Martin Diehl b3a90a8a3b last changes on preprocessing tools, only documentation needs to be done 2013-05-17 16:44:03 +00:00
Martin Diehl 17b81fda7c still improving preprocessing scripts 2013-05-15 17:23:21 +00:00
Martin Diehl 53348db000 tested the modified scripts, all scripts generating geometry now named geom_from... 2013-05-15 16:02:38 +00:00
Martin Diehl 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
Martin Diehl 9093cf2072 polishing, unifying,simplifying 2013-05-14 17:51:53 +00:00
Martin Diehl 2acd737859 polishing, unifying,simplifying 2013-05-14 17:19:36 +00:00
Martin Diehl 563e74c832 now also using numpy 2013-05-14 17:00:41 +00:00
Martin Diehl b2c50124b5 more improvements on structure, comments and header generation of pre processing tools 2013-05-13 13:10:31 +00:00
Martin Diehl 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
Christoph Kords deb2bd7dca added option to only process ip or node based geometry/data 2013-05-13 10:06:40 +00:00
Christoph Kords 7f7cd0732d improved visualization of script results 2013-05-13 09:36:19 +00:00
Christoph Kords 193c77f526 corrected prediction of computation time 2013-05-09 11:33:40 +00:00
Christoph Kords ed1674ee1c changed default value of eulerangles label 2013-05-09 11:32:34 +00:00
Christoph Kords 2d4cb6d128 first point on slice always starts at (0,0)
added option to visualize results
2013-05-08 15:59:51 +00:00
Christoph Kords bd33169118 mistakenly committed table2ang in rev 2380, instead of vtk2ang. reverted changes in table2ang 2013-05-08 15:58:17 +00:00
Christoph Kords ed9413a008 added simple output about progress 2013-05-07 14:32:38 +00:00
Christoph Kords 543cbf3a14 first point on slice always starts at (0,0) 2013-05-07 13:18:26 +00:00
Christoph Kords c7f987a3c1 "unitlength" parameter, which determines the physical size of the mesh, now available as a global mesh variable "mesh_unitlength" and written to the .mesh file during init.
Hence, it is available to the marc_deformedGeometry.py script via "mesh_init_postprocessing()" and "mesh_get_unitlength()", so no need for setting the scaling of the displacement vectors explicitly through an option; now displacements and nodal positions are always consistent
2013-05-07 13:06:29 +00:00
Christoph Kords 9656d06fcc - all length in nag file in micrometer
- "size" option replaced by "scale": uniform scaling of all length
- default normal in negative z-direction
- more output in verbose mode
- ang file numbering starts with 1
- positions in ang file in TSL, not lab frame
2013-05-07 12:57:34 +00:00
Christoph Kords 278198121d only import vtk classes that were used 2013-05-06 16:55:44 +00:00
Christoph Kords 2371bd9f57 correct extension ".py" for "table2ang" and "vtk2ang" 2013-05-06 16:43:05 +00:00
Christoph Kords f5482ffbf4 new script that generates ang files for slices through vtk data set 2013-05-06 16:37:54 +00:00
Christoph Kords 43647fc5e6 use datatype double instead of float for ouputs 2013-04-30 14:45:29 +00:00
Christoph Kords 12ca2c1931 added scaling option for displacements 2013-04-29 16:02:30 +00:00
Christoph Kords 9afaa9f4d0 set "line breaks" and "keywords" property 2013-04-29 09:24:07 +00:00
Christoph Kords fbb8353bba check if data set attribute is already present 2013-04-29 09:23:16 +00:00
Christoph Kords cc72c0b17b added two new scripts:
"marc_extractData" is a simple variant of the "postResult" script that extracts all data from a macro *.t16 file (quadratic elements not yet supported) and writes it into an asciitable
"addDataToGeometry" searches for corresponding *.txt and *.vtk file in a given directory and adds the data from the *.txt file as SCALARS to the *.vtk file

first script needed an additional function in mesh that returns the corresponding node of a given ip in a specific element
2013-04-28 20:56:17 +00:00
Martin Diehl a003d14824 grid and size for vicinityOffset, small changes for other scripts 2013-04-25 16:51:32 +00:00
Martin Diehl 5d8664e230 updated to new keywords + more verbosity 2013-04-25 15:53:41 +00:00
Martin Diehl 7cbf107751 removed misplaced new line statement 2013-04-24 11:07:05 +00:00
Christoph Kords 650b7ef4ac added python script that produces vtk files with the (node based and ip based) deformed mesh from marc output file 2013-04-23 18:30:56 +00:00
Pratheek Shanthraj aa07656a90 exchanged final two occurrences of "grains" to "microstructures" 2013-04-18 13:53:13 +00:00
Martin Diehl 06c872d404 added libs.f90 to core module compilation, didn't work because kdtree2 wasn't there 2013-04-17 17:39:52 +00:00
Philip Eisenlohr b572c71db0 fixed small bug in error reporting (missing column head complaint was broken...) 2013-04-16 20:10:17 +00:00
Martin Diehl d971a32516 changed keywords, now also printing out altered size/grid/microstructures information 2013-04-16 18:00:14 +00:00
Martin Diehl 2ff0f1b93e keywords update from resolution/dimension to grid/size 2013-04-12 14:13:32 +00:00
Martin Diehl b4f67248a5 deleted two simple scripts used for debugging but with almost no use any more 2013-04-12 13:22:15 +00:00
Martin Diehl 7bcf1d6072 added ID information of creator script to header, changed keywords (resolution->grid, dimension->size) 2013-04-12 12:48:39 +00:00
Martin Diehl 4314ab236e added ID information of creator script to header 2013-04-12 11:15:17 +00:00
Martin Diehl 6f0308844f geom packing/unpacking won't throw away unknown header information any more (might contain comments) 2013-04-12 10:47:44 +00:00
Martin Diehl 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
Martin Diehl 770712529d one more bug fix related to scaling 2013-03-26 16:16:59 +00:00
Martin Diehl ccef9d4f73 fixed scaling option 2013-03-26 14:18:29 +00:00
Philip Eisenlohr 5b96c1d62a scaling of deformation gradient fluctuations now possible in x,y,z independently (give array). 2013-03-22 15:09:55 +00:00
Martin Diehl cd86a80c2b corrected handling of default value and cases where the deformation gradient is not f 2013-03-19 18:22:14 +00:00
Martin Diehl 43ec1d2051 added output of perceptual unfiform colormaps to GOM (DIC Aramis) format, deleted some old files in the documentation folder 2013-03-19 15:19:46 +00:00
Martin Diehl 757c3e5a04 fixed bug in averageDown and updated test 2013-03-13 16:23:02 +00:00
Martin Diehl 010d4c6e26 added script to make 27 periodic copies (3 in each dimension) 2013-03-11 13:40:30 +00:00
Martin Diehl 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
Philip Eisenlohr 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
Philip Eisenlohr 565c532546 fixed bugs (grain index start, alpha orientation for elliptic osteons).
added option to rotate osteon relative to periodic box.
2013-02-27 10:56:30 +00:00
Pratheek Shanthraj 1cc990c7ac osteon geom and config generator 2013-02-25 17:12:13 +00:00
Martin Diehl 831ad6d9c8 added leading zeros to names of microstructures and phases, spaces caused problems during initialization 2013-02-20 14:50:01 +00:00
Philip Eisenlohr 7461e13c1e relocated spectral_quit() into driver code.
added (dummy) core_quit() for Python damask module.
2013-02-19 14:54:34 +00:00
Philip Eisenlohr 30024af6c2 polished string concatenations 2013-02-14 21:33:11 +00:00
Martin Diehl d715ec769b removed debug statements from symlink_Code.py, added autodetection for fortran compiler and disabled compiling on default 2013-02-13 18:45:49 +00:00
Christoph Kords a90f15a3d3 corrected usage of "append" (which does not copy list items but only creates references) 2013-02-13 16:00:02 +00:00
Martin Diehl cc9eb685fe fixed wrong setting of coordinates in spectral solvers and removed old python scripts for setup of code and processing 2013-02-05 12:31:44 +00:00
Philip Eisenlohr a7e7a857c3 readjusted color values to work nicely with Msh colorspace (as in ParaView) 2013-02-02 20:17:54 +00:00
Philip Eisenlohr ac562f4b8b changed internal color mapping to damask.Colormap class 2013-02-02 15:12:43 +00:00
Martin Diehl b0263a8aab added possibility to parse options for setup_code.sh and setup_processing.sh + other improvements in setup functionality 2013-02-01 12:21:56 +00:00
Martin Diehl e74b5da19a changed all remaining routines to fortran-fast arrays (geometry reconstruction etc.)
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
Mahesh Balasubramaniam 55957dd99e compile_CoreModule.py split seperately from the previous setup_processing.py 2013-01-29 15:33:20 +00:00
Mahesh Balasubramaniam d713ef79d0 a simple shell script that runs compile_CoreModule.py and symLink_Processing.py in the said order 2013-01-29 15:32:43 +00:00
Mahesh Balasubramaniam bd1f8044fb symLink_Processing.py split seperately from the previous setup_processing.py 2013-01-29 15:31:57 +00:00
Philip Eisenlohr 963ff0c3ae added support for tetrahedron element with 4 integration points (Marc ID 127) 2013-01-28 16:25:43 +00:00
Pratheek Shanthraj e691ff1ea1 updated setup_processing and corrected descriptions for new scripts 2013-01-22 09:56:36 +00:00
Pratheek Shanthraj a4abebfcbb some potentially useful postprocessing scripts 2013-01-21 23:15:23 +00:00
Mahesh Balasubramaniam 4af855c755 added perceptualUniformColorMap.py to the list of post-processing files 2013-01-18 17:39:09 +00:00
Mahesh Balasubramaniam 5676330e93 parsing options and file handling for perceptually linear diverging and sequential colormaps 2013-01-18 17:15:30 +00:00
Philip Eisenlohr e51779579e removed (unsupported) "--geom" option. 2013-01-18 13:01:43 +00:00
Philip Eisenlohr c8aaf8f6d4 added $id flags and specified line ending types when missing.
setup script missed ".py" extension for geom_euclideanDistance.
2013-01-18 12:59:26 +00:00
Pratheek Shanthraj 0e93d51fed adopted same algorithm as in addEuclideanDistance 2013-01-18 11:42:27 +00:00
Pratheek Shanthraj 096204cd79 corrected missing file renaming of output 2013-01-18 11:39:53 +00:00
Mahesh Balasubramaniam 7ac7d1a657 new tool for creation of colormaps, now using proper classes 2013-01-15 18:24:10 +00:00
Mahesh Balasubramaniam cd5197556b sequential colormapping with options for desired color and type(increasing or decreasing) is now working 2013-01-04 19:50:39 +00:00
Mahesh Balasubramaniam 820b8eb2c1 put colormap related functions into library, renamed and added scripts for creation of colormaps 2013-01-04 13:57:36 +00:00
Mahesh Balasubramaniam 6ab79d5593 added options for parsing and the colormap. Customized colormap is written out as an xml file importable into paraview. 2013-01-04 12:04:05 +00:00
Mahesh Balasubramaniam 3242361c91 added a minor change to the string expression and the for loop. 2013-01-04 12:01:34 +00:00
Mahesh Balasubramaniam 7157e8f03c changed some of the color-space conversion formulae. 2013-01-04 12:00:10 +00:00
Pratheek Shanthraj a69aaa1315 Use scipy euclidean distance function instead of FMM (runs without skfmm
module installed)
2012-12-19 14:50:45 +00:00
Martin Diehl 260e4191a0 replaced tabs by spaces 2012-12-13 18:15:10 +00:00
Philip Eisenlohr dfb791bcaf only complain about missing Mentat release if needed... 2012-12-12 08:33:42 +00:00
Christoph Kords 34645a7222 write warning about missing Mentat release to stderr instead of stdout 2012-12-12 08:21:59 +00:00
Christoph Kords 93d822aaa1 symmetric colormap always with pure white in the middle 2012-12-11 16:50:34 +00:00
Pratheek Shanthraj 726d1173e5 polishing 2012-12-07 17:46:28 +00:00
Pratheek Shanthraj c4ef2e5925 bug fixes 2012-12-07 17:41:50 +00:00
Pratheek Shanthraj eaf7072bc1 Vectorized checking of neighbourhood for unique microstructure
(faster) 

M    addEuclideanDistance.py
2012-12-07 10:50:34 +00:00
Philip Eisenlohr 89867a198c forgot to adopt addEuclideanDistance into the auto-setup... 2012-12-06 21:51:30 +00:00
Philip Eisenlohr a37250eef4 script to add the Euclidean distance map from boundaries, triple lines, and quadruple points to an ASCIItable of a regular grid.
requires numpy, scipy, and skfmm...
2012-12-06 21:49:49 +00:00
Philip Eisenlohr 2d4cf7da74 conditions can handle string data.
use "#s#label#" format to indicate that column headed by "label" contains strings (not floats)...
2012-12-03 14:29:21 +00:00
Philip Eisenlohr 7d96bb7ce8 Add column(s) containing directional stiffness based on given cubic stiffness values C11, C12, and C44 (in consecutive columns) 2012-12-03 13:10:16 +00:00
Philip Eisenlohr faa5f3c459 corrected severe bug in (non-logarithmic) strain calculations..! 2012-11-30 15:02:25 +00:00
Philip Eisenlohr 72159e867c fixed buggy file handling for multiple input files 2012-11-30 11:03:53 +00:00
Philip Eisenlohr 74f62c891d slightly safer file closing strategy 2012-11-30 08:38:52 +00:00
Philip Eisenlohr 9fb838fd28 changed switch from "sequential" to "column" 2012-11-30 08:29:34 +00:00
Philip Eisenlohr 1bd6bcfe3d script to list info, labels, and/or data of an ASCIItable 2012-11-30 08:26:13 +00:00
Pratheek Shanthraj e498719dcf forgot to add to last commit 2012-11-29 21:57:07 +00:00
Pratheek Shanthraj 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
Philip Eisenlohr f446d4d87e added wildcard matching ( "?", "*", "[(!)sequence_of_characters]" ) for ASCII table labels 2012-11-29 10:42:13 +00:00
Philip Eisenlohr 05507a6240 removed opening of unused _tmp file 2012-11-27 17:59:56 +00:00
Philip Eisenlohr 255af58434 post processing script to add eigenvalues and eigenvectors to tensorial data in ASCII tables. 2012-11-23 21:49:30 +00:00
Martin Diehl 78c22d8449 corrected label in case of divergence of tensor, now using correct notation for scalar: divFFT(data) instead of 1_divFFT(data) 2012-11-21 10:31:52 +00:00
Martin Diehl b5945ced5e changed counting of rows from pythonic (starting at 0) to human way (starting at 1) 2012-11-20 10:27:09 +00:00
Martin Diehl b988caa6ba added script to add deviatoric and hydrostatic part of a tensor to ASCII table 2012-11-14 10:46:51 +00:00
Martin Diehl c3926efd93 introduced logic to use gfortran as default if ifort is not found 2012-11-13 19:12:00 +00:00
Philip Eisenlohr 1df9be233d changed default threshold to 0.0 2012-11-08 17:08:41 +00:00
Philip Eisenlohr 682a98b704 forgot to alter name of 'geom_fromAng' in setup script... 2012-11-08 16:29:26 +00:00
Philip Eisenlohr 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
Philip Eisenlohr af2aa8500d added option to specify crystallite index 2012-11-08 15:43:38 +00:00
Philip Eisenlohr c4c27860b2 renamed script
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
Philip Eisenlohr 7cf2024be3 fixed buggy parameter checking 2012-11-07 16:51:17 +00:00
Philip Eisenlohr e11d107956 fixed reporting to STDOUT/STDERR
fixed buggy parameter checking
2012-11-07 16:49:47 +00:00
Philip Eisenlohr cfc8823328 missed those three in former commit... 2012-11-05 21:28:01 +00:00
Philip Eisenlohr 1bd4262cfb renaming of (loosely related) "spectral" scripts to (more tightly related) "geom" versions. 2012-11-05 21:19:12 +00:00
Martin Diehl 1fc59107fa removed debug statement in averageDown.py, deleted obsolete spectral_iterationCount.py (new solver will report statistics anyway and most probably the current count does not work as the screen output was modified) 2012-10-31 10:06:11 +00:00
Philip Eisenlohr afaf1f4e8c made errors report to STDERR.
maxMicrostructure remains silent if not present.
2012-10-30 16:32:00 +00:00
Philip Eisenlohr f2229883b5 exchanged "maxGrainCount" for "maxMicrostructure", since this is what it really means... 2012-10-30 16:15:10 +00:00
Philip Eisenlohr 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
Philip Eisenlohr 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
Martin Diehl b9aa50c59a improved performance for large packing values 2012-10-26 12:59:43 +00:00
Martin Diehl 868984cb89 import of damask.core will not complain any more if done in setup_processing.py, however setup_processing.py will check if core.so exist after compilation and delete it before compilation 2012-10-25 07:55:27 +00:00
Philip Eisenlohr 17bfc3b284 added explanation of script purpose to its usage output (-h) 2012-10-18 07:24:44 +00:00
Martin Diehl 573c4702eb fixed bug in averageDown.py and added test to check its features 2012-10-17 15:05:26 +00:00
Martin Diehl dcff640926 fixed handling of given resolution and dimension 2012-10-17 10:04:13 +00:00
Martin Diehl 6c7affc43f improved performance (hopefully)
now each new element gets a new ID, running from 1 to N for N elements
2012-10-16 18:06:02 +00:00
Philip Eisenlohr 1004d744f2 output speed-up by *show_table/*show_model masking 2012-10-05 21:49:33 +00:00
Martin Diehl c377dae9a6 added option to create hexagonal grid (2D slices only, according to P. Konijnenbergs experience on 3D ang) 2012-10-05 17:25:54 +00:00
Martin Diehl 124451ac1a added missing comment sign # 2012-10-04 08:42:13 +00:00
Martin Diehl 0a961bef55 made test for spectral packing/unpacking working again, small fixes in the 2 scripts 2012-09-28 14:49:07 +00:00