[cig-commits] r6787 - short/3D/PyLith/branches/pylith-0.8
leif at geodynamics.org
leif at geodynamics.org
Fri May 4 14:17:26 PDT 2007
Author: leif
Date: 2007-05-04 14:17:26 -0700 (Fri, 04 May 2007)
New Revision: 6787
Modified:
short/3D/PyLith/branches/pylith-0.8/ChangeLog
short/3D/PyLith/branches/pylith-0.8/INSTALL
short/3D/PyLith/branches/pylith-0.8/NEWS
short/3D/PyLith/branches/pylith-0.8/README
Log:
Updated info files.
Modified: short/3D/PyLith/branches/pylith-0.8/ChangeLog
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/ChangeLog 2007-05-04 20:46:22 UTC (rev 6786)
+++ short/3D/PyLith/branches/pylith-0.8/ChangeLog 2007-05-04 21:17:26 UTC (rev 6787)
@@ -1,3 +1,1566 @@
+2007-05-04 20:46 leif
+
+ * [r6786] Updated Makefile.
+
+2007-05-04 20:26 willic3
+
+ * [r6785] Removed parmetis .cfg file from tractest, since it won't
+ work, but added one for splittest. Viscosity values for
+ powertest have been changed.
+
+2007-05-04 03:00 leif
+
+ * [r6783] Updated 'setup.py'.
+
+2007-05-03 20:13 leif
+
+ * [r6765] ParMETIS partitioning is broken for traction BC; fail
+ with an error message when partitioner=parmetis and there is a
+ .traction file.
+
+2007-05-03 15:46 willic3
+
+ * [r6764] Moved partitioner parameter to pylith3d list rather than
+ pylith3d.petsc. Added a Chaco .cfg file for testing, even though
+ this is already the default.
+
+2007-05-03 15:42 willic3
+
+ * [r6763] Removed partitioner from PETSc arguments.
+
+2007-05-03 00:05 leif
+
+ * [r6760] Using a Perl script, updated all shell scripts to use
+ the new property/facility/component layout. Removed shell
+ scripts that still used 'mpiexec' or had 'lithomop' in the
+ filename.
+
+2007-05-02 20:25 leif
+
+ * [r6757] Removed kludgey support for old 'pl3dscan.xxx' and
+ 'scanner.xxx' options.
+
+2007-05-02 20:09 leif
+
+ * [r6756] Updated all *.cfg files to use the new
+ property/facility/component layout.
+
+2007-05-02 19:29 sue
+
+ * [r6754] image prob solved using .ai image version
+
+2007-05-02 19:20 sue
+
+ * [r6753] working image problem; pdf pg 62, figure b.1, runs off
+ page bottom no matter what I do. still troubleshooting
+
+2007-05-02 18:26 sue
+
+ * [r6752] working image problem
+
+2007-05-02 17:18 sue
+
+ * [r6751] minor edits
+
+2007-05-02 06:55 leif
+
+ * [r6750] Updated PyLith for Pythia v0.8.1.3b5.
+ PetscCommandlineParser and PetscProperty are no longer
+ supported. Use Pyre command line syntax. Use the "petsc"
+ facility/component ("petsc.xxx=yyy") to set PETSc options.
+
+2007-05-02 02:45 leif
+
+ * [r6748] Removed quotes around quadratureOrder values;
+ prestressAutoChangeElasticProperties ->
+ prestressAutoChangeElasticProps.
+
+2007-05-02 02:28 leif
+
+ * [r6747] Mechanically converted remaining *.keyval files to *.cfg
+ files: keyval=`find . -name \*.keyval` for kv in $keyval; do
+ cfg=`dirname $kv`/`basename $kv .keyval`.cfg; svn cp $kv $cfg ;
+ echo "[pylith3d]" > $cfg; cat $kv >> $cfg ; svn rm $kv ; done
+
+2007-05-02 02:04 leif
+
+ * [r6746] Removed all references to *.keyval files from the
+ manual; they are no longer read by PyLith.
+
+2007-05-02 01:31 leif
+
+ * [r6745] Removed remaining 'runex' scripts, to avoid confusion.
+
+2007-05-01 22:04 leif
+
+ * [r6743] Build fixes: install pylith3dapp.py ~ install examples ~
+ allow tarball to work without Pyrex installed ~ made sure
+ tarball is complete. Unfortunately, "make distcheck" does not
+ work, due to an egg-related issue.
+
+2007-05-01 20:27 sue
+
+ * [r6741] a few edits; more tomorrow
+
+2007-05-01 18:55 leif
+
+ * [r6739] Added one more PETSc config example.
+
+2007-05-01 16:17 willic3
+
+ * [r6736] Minor format fix when writing out material model name.
+
+2007-05-01 03:31 leif
+
+ * [r6735] Final draft of installation chapter.
+
+2007-04-30 23:19 leif
+
+ * [r6732] Wrote PETSc installation section.
+
+2007-04-28 01:15 leif
+
+ * [r6725] Temporarily disabled outputFile(). Without ${rank} in
+ the filenames, there is a race condition revolving around O_EXCL
+ with more than one processor.
+
+2007-04-27 23:09 leif
+
+ * [r6723] Initial rewrite of installation chapter.
+
+2007-04-27 23:03 sue
+
+ * [r6722] made journal no. standard format
+
+2007-04-27 22:52 sue
+
+ * [r6721] various edits, spacing fixes, image positioning, and
+ long lines running off the page fixed
+
+2007-04-27 21:47 willic3
+
+ * [r6720] Finished draft of materials. It's a little sketchy
+ toward the end.
+
+2007-04-27 20:49 willic3
+
+ * [r6718] Added another reference to userguide. Material models
+ are complete through generalized Maxwell. Still need Z&T
+ formulation for power-law Maxwell.
+
+2007-04-27 03:27 willic3
+
+ * [r6706] Mostly finished through power-law ESF.
+
+2007-04-27 01:05 willic3
+
+ * [r6704] More work on materials. Nearly finished fixing things
+ through ESF formulation of linear Maxwell. Table and figure
+ references still need fixing. Still to do: Power-law ESF
+ Generalized Maxwell Power-law Maxwell using Z&T formulation
+
+2007-04-26 00:11 sue
+
+ * [r6688] small changes
+
+2007-04-25 21:31 willic3
+
+ * [r6687] Completely reworking materials section: Adding figure of
+ material models. Changing layout. Changing equations to be
+ consistent with what we're doing for 1.0. Adding new material
+ models. Section is still incomplete. I need to finish fixing
+ after the first subsection in the ESF section.
+
+2007-04-25 02:42 willic3
+
+ * [r6681] Multiprocessor .cfg file.
+
+2007-04-24 22:42 sue
+
+ * [r6678] finished up standardizing subheader format
+
+2007-04-24 22:36 sue
+
+ * [r6677] standardized subsection headers in install file
+
+2007-04-24 22:33 sue
+
+ * [r6676] fixed spacing in table and other minor edits
+
+2007-04-24 22:05 sue
+
+ * [r6670] edits to tutorials incl standardizing quote marks and
+ subsection titles, and fixing over long lines
+
+2007-04-24 21:48 willic3
+
+ * [r6664] Modified .cfg file to let ParMetis be the partitioner.
+
+2007-04-24 21:44 willic3
+
+ * [r6663] Handled case where file could be empty due to
+ partitioning.
+
+2007-04-24 21:43 willic3
+
+ * [r6662] Added 'partitioner' as a PETSc option of interest to
+ PyLith.
+
+2007-04-24 21:15 willic3
+
+ * [r6660] Fixed end of section and created a revised table of
+ PETSc settings.
+
+2007-04-24 20:38 sue
+
+ * [r6659] fixed problem with preface in preview mode in file
+ userguide.lyx which was causing lyx program to hang when edited,
+ e.g., turned off preview mode
+
+2007-04-24 20:17 willic3
+
+ * [r6658] Updated reversenog tutorial for new utilities, new usage
+ of .cfg files, etc.
+
+2007-04-24 20:16 sue
+
+ * [r6657] various edits, incl. resized table in Materials and
+ changed quotes to match other manuals
+
+2007-04-24 19:40 willic3
+
+ * [r6655] Forgot to change version number.
+
+2007-04-24 19:37 willic3
+
+ * [r6654] Updated splitcube tutorial for new utilities, new usage
+ of .cfg files, etc.
+
+2007-04-24 15:50 willic3
+
+ * [r6647] Updated features for current version.
+
+2007-04-23 03:04 willic3
+
+ * [r6631] Changed method for determining how many vertices per
+ face for traction BC.
+
+2007-04-23 03:02 willic3
+
+ * [r6630] Changed method for determining how many vertices per
+ face for traction BC.
+
+2007-04-20 20:33 willic3
+
+ * [r6624] Updated .cfg files.
+
+2007-04-20 20:24 willic3
+
+ * [r6623] Deleted old shell scripts and added a couple of new .cfg
+ files.
+
+2007-04-20 19:34 knepley
+
+ * [r6622] Small fixes
+
+2007-04-20 17:36 willic3
+
+ * [r6620] Added .cfg file to launch multi-processor job. Removed
+ launcher info from pylith3d.cfg specific to Matt's setup.
+
+2007-04-20 17:19 willic3
+
+ * [r6619] Put in changes to ntimdat array (removal of ndtot) that
+ had been done for fortran code.
+
+2007-04-20 15:37 knepley
+
+ * [r6617] Minimally running 0.8 with new PETSc
+
+2007-04-19 20:08 knepley
+
+ * [r6609] Fixed compile bug with new PETSc
+
+2007-04-19 17:09 knepley
+
+ * [r6607] Trial integration into mainline
+
+2007-04-19 04:11 willic3
+
+ * [r6605] Updated vistest examples for current code (no more
+ scanner), and fixed some timestep stuff.
+
+2007-04-19 02:33 willic3
+
+ * [r6604] Removed ndtot, which was no longer being used, along
+ with corresponding entry in the ntimdat array.
+
+2007-04-19 00:02 willic3
+
+ * [r6600] Checked in current version of documentation, which still
+ needs work.
+
+2007-04-18 18:43 leif
+
+ * [r6596] Creating my own forward declarations of "petscmesh.h"
+ functions turns out to be a bad idea, because such functions can
+ have different linkage (C or C+) depending upon how PETSC was
+ configured.
+
+2007-04-18 00:38 leif
+
+ * [r6595] Fixed VTK output.
+
+2007-04-17 23:13 leif
+
+ * [r6594] Don't open xxx.ascii file when 'asciiOutput' is set to
+ 'none'. Corrected "category" for output files.
+
+2007-04-17 18:47 leif
+
+ * [r6591] Re-implemented memory-usage-report feature, but this
+ time with only a few lines of code. Factored-out
+ Python-list-to-C-array code. Added __get__() methods so that
+ public list/array properties are readable as well as writeable.
+
+2007-04-17 17:53 willic3
+
+ * [r6587] Fixed incorrect format statement number.
+
+2007-04-17 04:37 leif
+
+ * [r6586] Open output files once at the beginning of the run, and
+ close them once at the end (instead of repeatedly opening and
+ appending to them). This change elminates the need for the
+ CIT_FC_OPEN_APPEND Autoconf test and the FORTRAN_POSITION_APPEND
+ and FORTRAN_ACCESS_APPEND preprocessor macros. It also (quite
+ incidentally) made the Fortran routine viscos_setup() redundant.
+ Also, I fixed a bug I introduced. In the Pyrex call to
+ scan_timdat(), I wrote "len(time_units)" instead of
+ "sizeof(time_units)". D'oh! Mostly, the Pyrex calls are a
+ transcription/merging of the old C++ bindings into the Python
+ code, so hopefully this is the only bug of its kind.
+
+2007-04-14 02:02 leif
+
+ * [r6570] Eliminated the bindings by converting the bulk of the
+ Python code to Pyrex.
+
+2007-04-12 17:30 willic3
+
+ * [r6555] More changes to documentation.
+
+2007-04-12 17:29 willic3
+
+ * [r6554] Did a little more on Green's functions, but it is
+ commented out because it still doesn't work.
+
+2007-04-11 20:20 willic3
+
+ * [r6546] Started making changes for 0.8.2. There is still a fair
+ bit to do.
+
+2007-04-10 21:26 willic3
+
+ * [r6540] Altered to use pythonTimestep and minor fix to time step
+ info.
+
+2007-04-10 21:14 willic3
+
+ * [r6539] Updated tutorial to use *.cfg files and new methods of
+ dealing with filenames.
+
+2007-04-10 20:25 willic3
+
+ * [r6538] Updated tutorial to use *.cfg files and new ways of
+ dealing with filenames.
+
+2007-04-09 18:03 willic3
+
+ * [r6531] Fixed direction of normal (it was backwards).
+
+2007-04-06 20:06 willic3
+
+ * [r6514] Added new 'prescomp' code to source list.
+
+2007-04-06 20:05 willic3
+
+ * [r6513] Simple utility code to compute boundary-normal tractions
+ (pressures) over a specified set of faces.
+
+2007-04-05 21:54 leif
+
+ * [r6509] Renamed almost all the variables in the Python code and
+ in the C++ bindings such that the variable names are consistent
+ with the Fortran code. E.g., rotationUnits -> rotation_units,
+ numberRotationEntries -> numrot. This makes the code much easier
+ to understand and much easier to follow as control flows from
+ Python through C++ into Fortran, and back again. For instance,
+ if I grep for 'numrot' (actually I use 'gid' from the 'mkid'
+ package), I now get matches in the Python and C++ code, and I
+ can easily see that 'numrot' is defined as the return value of
+ scan_skew(). Sample matches from the output of "gid numrot": #
+ ---- snip ---- PyLith.py:558: self.numrot = pylith3d.scan_skew(
+ # [...] ../module/libpylith3d.cc:5319: scan_skew_f(&numrot,
+ ../module/libpylith3d.cc:5336: << "numrot:" << numrot
+ ../module/libpylith3d.cc:5341: return Py_BuildValue((char *)
+ "i", numrot); # [...] ../libpylith3d/scan_skew.f:31: subroutine
+ scan_skew(numrot,kr,rotation_units,skfile,ierr, # [...] # ----
+ snip ---- The light is so much better now!
+
+2007-04-04 20:28 willic3
+
+ * [r6508] Minor optimization.
+
+2007-03-30 21:05 leif
+
+ * [r6475] Merged all the Fortran bindings into a single file, in
+ preparation for the next step.
+
+2007-03-30 18:22 leif
+
+ * [r6473] Removed 'unused' files.
+
+2007-03-27 22:33 willic3
+
+ * [r6444] Made some changes related to generating Green's
+ functions.
+
+2007-03-27 20:51 sue
+
+ * [r6435] standardized typefaces on cover
+
+2007-03-27 02:24 leif
+
+ * [r6415] Cleaning, step 10: Removed *all* instance variables used
+ as temporaries, and *all* unused instance variables. If an
+ instance variable was only used in a single function (but was
+ more than a mere temporary), I changed it to an ordinary local
+ variable. I found all these ill-begotten instance variables with
+ the help of some introspective scaffolding (__getattribute__,
+ __settattr__). Refactored/tweaked some code so that temporary
+ arrays are automatically deallocated (without the goofy "xxx =
+ None").
+
+2007-03-26 23:19 leif
+
+ * [r6414] Cleaning, step 9: Removed 'memorySize' computations.
+ Maintaining a manual tally such as this one is a tedius and
+ error-prone way to keep track of memory usage. (I promise to
+ re-implement this feature later.) Also, I temporarily labeled
+ all the explicit deallocations, so I can grep for them later.
+
+2007-03-26 22:51 leif
+
+ * [r6413] Cleaning, step 8: Eliminated more redundant variable
+ initializations. Specifically, the (now former) PyLith
+ convention self.pointerToX = None # ...later... self.pointerToX
+ = pylith3d.allocateDouble(...) is meaningless in Python.
+ Variables do not need to be declared or initialized in Python.
+ Rest assured that any attempt to read 'pointerToX' before it is
+ defined will result in an attribute error.
+
+2007-03-24 19:07 leif
+
+ * [r6389] Fixed Makefile.
+
+2007-03-24 01:21 leif
+
+ * [r6387] Cleaning, step 7 {in initialize()}: Eliminated redundant
+ variable initializations. Moved constants to 'constants.py'.
+ Eliminated instance variables used as temporaries. Eliminated
+ unused variables.
+
+2007-03-23 23:39 leif
+
+ * [r6383] Cleaning, step 6: Moved all properties out of the nested
+ Inventory class. They are now properties of the PyLith
+ application itself. CIG-Pyre automatically makes such properties
+ accessible as "self.xxx" (which is much less verbose than
+ "self.inventory.xxx"). This eliminates the especially tiresome
+ "self.xxx = self.inventory.xxx" mantra.
+
+2007-03-23 22:48 leif
+
+ * [r6382] Cleaning, step 5: Merged Application and Pylith3d_scan
+ into a new class, PyLith. (Removing meaningless Component
+ structure... done.) There is now a single, top-level component
+ (the PyLith application class). However, this isn't a
+ user-visible change (yet), as I added a hack so that old
+ 'pl3dscan.xxx' and 'scanner.xxx' options still work.
+
+2007-03-23 21:26 leif
+
+ * [r6379] Cleaning, step 4: Merged GreenFunctionApp with
+ Application. (Removing meaningless Component structure... 90%
+ complete...)
+
+2007-03-23 21:00 leif
+
+ * [r6377] Cleaning, step 3: Merged Pylith3d_run with
+ Pylith3d_scan. (Removing meaningless Component structure... 66%
+ complete...)
+
+2007-03-23 20:40 leif
+
+ * [r6375] Cleaning, step 2: Merged Pylith3d_setup with
+ Pylith3d_scan. (Removing meaningless Component structure...)
+
+2007-03-23 20:21 leif
+
+ * [r6373] Cleaning, step 1: removed the leading underscore on
+ instance variables in Pylith3d_scan, so that they will match the
+ identifiers used elsewhere in the code. (I'm tired of mold...)
+
+2007-03-23 20:14 willic3
+
+ * [r6372] Incomplete and non-functional version of Greeen function
+ application. Some C code needs to be converted to Python, and
+ some logic still needs to be worked out.
+
+2007-03-23 17:42 leif
+
+ * [r6369] Utilize the new _validate() hook in pythia v0.8.1.3b2,
+ which PyLith-0.8 now requires. Help and command-completion now
+ works.
+
+2007-03-22 21:04 willic3
+
+ * [r6355] Added sampleLocationFile to inventory for sample
+ locations of Green's functions. Setup is kludgy right now,
+ because file is listed as 'optional'. It should actually be
+ listed as 'required' if Green's functions are being computed,
+ but I don't have a way of signaling that right now.
+
+2007-03-22 18:13 willic3
+
+ * [r6351] Removed debugging statements.
+
+2007-03-21 21:38 willic3
+
+ * [r6338] Directory containing simple tests for all of the
+ viscoelastic models presently available. The default model is a
+ linear Maxwell model based on the Zienkiewiecz & Taylor
+ formulation. Other models are obtained simply by putting the
+ appropriate *.cfg file on the command-line.
+
+2007-03-21 20:23 willic3
+
+ * [r6337] Changed call to processMesh so we're now sending it the
+ base bcInputFile rather than the outputFileRoot.
+
+2007-03-21 20:18 willic3
+
+ * [r6336] Made some changes so the per-processor BC filenames are
+ based on the global BC filename. For everything to be
+ consistent, this should also be done for coordinates,
+ connectivities, split nodes, and tractions. That would involve
+ changes to PETSc, however.
+
+2007-03-21 18:37 leif
+
+ * [r6333] Avoid (r)partition, which is new in Python 2.5.
+
+2007-03-21 17:56 willic3
+
+ * [r6332] Altered output of BC so that the filenames are based in
+ the inputFileRoot basename. Now that I think of it, I should add
+ a new argument so it is based on bcInputFile.
+
+2007-03-21 17:53 willic3
+
+ * [r6331] Made some changes to get things working in parallel
+ again.
+
+2007-03-19 17:01 willic3
+
+ * [r6290] Updated makefile for new file names.
+
+2007-03-19 16:59 willic3
+
+ * [r6289] Fixed all material models to conform to new arrangement,
+ and added some documentation strings. Also replaced
+ commented-out print statements with journal calls.
+
+2007-03-19 16:56 willic3
+
+ * [r6288] Completely rearranged material models to correspond with
+ current preferred methods, although more testing is needed. Also
+ removed Numerical Recipes linear algebra routines and replaced
+ them with LAPACK calls.
+
+2007-03-19 16:50 willic3
+
+ * [r6287] Parameters for material model 9 (power-law viscoelastic
+ using Zienkiewicz & Taylor formulation).
+
+2007-03-15 19:39 willic3
+
+ * [r6263] Added exception for case where maximum number of
+ Newton-Raphson iterations is exceeded.
+
+2007-03-15 19:38 willic3
+
+ * [r6262] Major fixes to Newton-Raphson solution for power-law.
+
+2007-03-10 21:12 willic3
+
+ * [r6220] Updated code to deal with multiple element types.
+
+2007-03-09 21:58 willic3
+
+ * [r6215] Traction test for hexahedral elements.
+
+2007-03-08 22:48 leif
+
+ * [r6205] Fixed the makefile I broke.
+
+2007-03-08 00:12 leif
+
+ * [r6185] Removed support for .keyval files (this is a bit
+ premature, since I still haven't finished updating the
+ examples). Moved PETSc/Pyre integration stuff into the
+ framework. PyLith v0.8 now requires Pythia v0.8.1.3b1. Re-run
+ 'configure' to get it.
+
+2007-03-06 02:32 willic3
+
+ * [r6178] Temporarily added Numerical Recipes-derived routines for
+ LU decomposition and backsubstitution. This should be replaced
+ with LAPACK calls to routines that take advantage of matrix
+ symmetry and packed storage.
+
+2007-03-02 19:06 willic3
+
+ * [r6161] New and altered routines for new method of dealing with
+ power-law rheology. Things should compile, but testing/debugging
+ is needed.
+
+2007-02-28 01:54 leif
+
+ * [r6127] Updated about half of the PyLith examples to use *.cfg
+ files instead of *.keyval files. The other half is linhex/*,
+ which I will update later.
+
+2007-02-14 00:27 leif
+
+ * [r6017] Reverted unintentional check-in of
+ ComponentHarness-related changes.
+
+2007-02-14 00:23 leif
+
+ * [r6016] Ripped-out calls to PetscCommSynchronizeTags, per Matt's
+ instructions. The function no longer exists in the development
+ version of PETSc: changeset: 10000:21bdefd4c2d2 user:
+ bsmith at barry-smiths-computer.local date: Fri Feb 9 19:34:16 2007
+ -0600 summary: removed PetscCommSynchronizeTags and
+ PetscCommCheckTags
+
+2007-02-12 20:06 willic3
+
+ * [r6010] Fixed 2D Jacobian determinant (needed square root).
+ Fixed problem where element contributions were replacing
+ traction vector contents rather than updating them.
+
+2007-02-12 20:05 willic3
+
+ * [r6009] Fixed BC to give constant stress throughout cube. Fixed
+ incorrect node position.
+
+2007-02-12 17:15 willic3
+
+ * [r6008] Made nodal spacing more regular so it is easier to
+ figure out what areas should be.
+
+2007-02-12 17:14 willic3
+
+ * [r6007] This file must have been added accidentally, and has
+ been deleted.
+
+2007-02-05 17:27 willic3
+
+ * [r5964] Fixed error in updating viscous strain.
+
+2007-02-03 03:27 leif
+
+ * [r5962] Added a "keyval codec" so that *.keyval files can be
+ processed by the Pyre framework. Keyval parameters are now
+ ordinary Inventory items, so they can also be set from the
+ command line or a .cfg file. Another advantage of this is error
+ reporting: try inserting a bogus key or value into a '.keyval'
+ file. I still haven't got the implementation exactly right,
+ however: with this change, errors in .cfg files (for example)
+ are reported twice. Since the filename of the .keyval file is
+ itself a Pyre property, this creates order-of-initialization
+ problems which exceed the limitations of the Pyre framework. I
+ have one or two ideas about how to fix this, but they are still
+ in the oven, only half-baked...
+
+2007-02-01 20:26 willic3
+
+ * [r5948] Added *.cfg file specifically for debugging to make life
+ easier.
+
+2007-02-01 17:03 willic3
+
+ * [r5947] Fixed mistake in units for viscosityCoefficient.
+
+2007-02-01 16:29 willic3
+
+ * [r5946] Fixed stupid typo.
+
+2007-02-01 16:11 willic3
+
+ * [r5945] Removed old run scripts and replaced them with *.cfg
+ files. Fixed time stepping and added option for running
+ power-law example using older ESF-based solution method. At
+ present, PyLith is no longer able to parse the material
+ properties files correctly. I'm not sure why.
+
+2007-01-30 21:28 leif
+
+ * [r5936] Moved Python egg stuff into our Autoconf macro library.
+
+2007-01-30 20:50 willic3
+
+ * [r5932] Removed python run script, which isn't really necessary
+ with the new *.cfg files.
+
+2007-01-30 20:45 willic3
+
+ * [r5931] Initial version of *.cfg file for tractest example. This
+ is about the simplest possible file, with nothing related to
+ MPI, etc.
+
+2007-01-27 20:28 willic3
+
+ * [r5920] Fixed parsing of units.
+
+2007-01-27 17:52 willic3
+
+ * [r5919] Added new utility to alter boundary conditions along
+ specified line segments, and added it to the Makefile. This
+ utility is somewhat specific to the CFEM benchmarks, but may
+ have some other uses.
+
+2007-01-27 00:19 leif
+
+ * [r5918] Removed extraneous quotes around 'traction_units' in the
+ lintet/tractest example (I'm not sure how this ever worked).
+
+2007-01-26 16:20 willic3
+
+ * [r5907] Fixed logic for getting minimum value for a point.
+
+2007-01-26 15:13 willic3
+
+ * [r5906] Added faultbm.f to utilities.
+
+2007-01-26 15:12 willic3
+
+ * [r5905] Initial version of code to calculate fault BC for CFEM
+ benchmarks. I need to test it.
+
+2007-01-26 03:02 leif
+
+ * [r5900] Removed unused files.
+
+2007-01-24 03:18 leif
+
+ * [r5882] Perform I/O file checks earlier, in _configure(), so
+ that errors are caught before launching. Also, turned the error
+ message into a 'journal' log message.
+
+2007-01-24 00:44 leif
+
+ * [r5879] Cleanly separate input files from output files by giving
+ their filenames different roots. This allows PyLith to read
+ input files directly, instead of relying upon symlinks.
+
+2007-01-22 15:47 willic3
+
+ * [r5853] Fixed incorrect call to td_matinit.
+
+2007-01-19 21:47 leif
+
+ * [r5840] Added 'sys.executable' to the arguments for
+ PetscInitialize(), so that -start_in_debugger works. Also,
+ recognize -debugger_pause (the default is too short on my
+ system).
+
+2007-01-19 00:35 leif
+
+ * [r5834] Fix for "Fortran 77 source seen but `F77' is undefined"
+ error with Automake 1.10.
+
+2007-01-18 16:49 willic3
+
+ * [r5826] New example to test ESF version of power-law rheology.
+
+2007-01-18 16:46 willic3
+
+ * [r5825] Corrected time info for double precision. Removed gdb
+ history file that had accidentally been committed.
+
+2007-01-18 16:41 willic3
+
+ * [r5824] Starting the process of revising benchmarks. Old Make.mm
+ and test.sh files have been removed and replaced by runex.py
+ script to run the benchmark. Time information has been corrected
+ to yield correct viscoelastic solution. Files originally used
+ from bm1a have been copied over to make this a standalone
+ example. The time info needs to be tested to see if it is
+ overkill.
+
+2007-01-18 16:30 willic3
+
+ * [r5823] Starting the process of revising benchmarks. Old Make.mm
+ and test.sh files have been removed and replaced by runex.py
+ script to run the benchmark. Time information has been corrected
+ to yield correct viscoelastic solution.
+
+2007-01-18 16:25 willic3
+
+ * [r5822] Starting the process of revising benchmarks. Old Make.mm
+ and test.sh files have been removed and replaced by runex.py
+ script to run the benchmark. Time information has been corrected
+ to yield correct viscoelastic solution.
+
+2007-01-18 15:21 willic3
+
+ * [r5821] Added descriptions to stdout info.
+
+2007-01-17 22:24 willic3
+
+ * [r5804] Fixed incorrect routine calls.
+
+2007-01-17 21:59 willic3
+
+ * [r5803] Fixed incorrect calls.
+
+2007-01-17 21:09 willic3
+
+ * [r5801] Fixed incorrect call to td_strs_1.
+
+2007-01-17 20:29 willic3
+
+ * [r5800] Fixed time stepping so viscous solution is correct.
+
+2007-01-12 21:34 willic3
+
+ * [r5784] Added new material model.
+
+2007-01-12 21:30 willic3
+
+ * [r5783] Added new material model to hold original ESF-based
+ power-law model.
+
+2007-01-12 21:24 willic3
+
+ * [r5782] Added exceptions for problems with Cholesky inversion.
+
+2007-01-12 21:23 willic3
+
+ * [r5781] Update all material model routines and associated
+ drivers to make use of iteration counter, which is useful for
+ some material models. Added option to tangent computation
+ routines to let them know whether tangent is being computed
+ using current stresses or stresses from previous time step.
+ Fixed test makefile to add top-level PETSc directory to include
+ path.
+
+2007-01-12 21:20 willic3
+
+ * [r5780] Replaced original power-law model (model 6) with new
+ implementation and moved original implementation to material
+ model 9.
+
+2007-01-12 21:19 willic3
+
+ * [r5779] New implementation of Maxwell power-law material model,
+ using formulation based on Zienkiewicz & Taylor rather than
+ original ESF-based version. Routines compile but have not yet
+ been tested.
+
+2007-01-12 21:17 willic3
+
+ * [r5778] This material model now corresponds to the original
+ ESF-version of the Maxwell power-law model.
+
+2007-01-10 03:19 leif
+
+ * [r5751] Tied PyLith's configuration even more closely to
+ PETSc's: use 'petscconf' to determine both CXX and the MPI
+ flags. I'm not sure why this 'configure' script didn't grab MPI
+ configuration from PETSc. But, I remember why it didn't grab CXX
+ from PETSc: Lithomop didn't require PETSc to be configured with
+ C++, so it couldn't assume that 'petscconf' defined CXX. Now,
+ with the addition of the Sieve dependency, it can be assumed
+ that 'petscconf' defines CXX. It is almost certainly an error to
+ configure PyLith with a C++ compiler different from the one used
+ to configure PETSc; this change avoids that potential mistake.
+ This change also avoids confusing 'configure' error messages
+ about MPIINCLUDES and MPILIBS, which aren't relevant to PyLith
+ -- PyLith should simply be configured with the MPI library
+ defined by the PETSc configuration.
+
+2007-01-10 00:45 leif
+
+ * [r5746] Use CIG-Pythia's 'launcher' and 'scheduler' facilities.
+ Users no longer execute 'mpirun'. Instead, they execute
+ 'pylith3dapp.py' directly, and the framework re-executes PyLith
+ under 'mpirun' automatically. On a cluster with a scheduler
+ (PBS, LSF, ...) the framework automatically generates a batch
+ script and submits a job to the queue. One uses
+ "--launcher.nodes=XXX" to specify the number of processors.
+ Currently, the framework defaults to MPICH1 with no scheduler;
+ using PBS, LSF, MPICH2, LAM/MPI, etc. may require additional
+ configuration, which is beyond the scope of this log comment.
+ This change breaks the "--disable-embedding" configuration. I
+ will revisit this later.
+
+2007-01-09 03:02 leif
+
+ * [r5698] Transformed "Hello" print statements into 'journal' log
+ messages. Made MaterialModel subclasses call
+ MaterialModel.__init__(). Nuked gratuitous use of 'exec'.
+
+2007-01-08 23:27 leif
+
+ * [r5696] Issue32: "make install" is now optional. Users can now
+ simply "configure", "make", and then add the "pylith3d"
+ subdirectory of the source/build directory to their PATH. In
+ this mode, changes to C++ simply require a "make" from the
+ top-level directory. Changes to the Python code do not require
+ you to run "make" at all -- simply re-run 'pylith3dapp.py'.
+ Also: Changed the 'configure' option '--with-embedding' to
+ '--enable-embedding', for consistency with CitcomS. Note: when
+ configured with '--disable-embedding', "make install" is NOT
+ optional. This is because the PyLith extension module has the
+ same name as the top-level package ('pylith3d'). The extension
+ module must be installed under the package directory in order
+ for everything to work. There are two possible fixes: 1) tweak
+ the build so that 'pylith3dmodule.so' lands under 'pylith3d'; or
+ 2) rename the extension module.
+
+2007-01-06 02:11 leif
+
+ * [r5688] Implemented strict command-line processing. Previously,
+ Pyre-based PyLith command-line options and PETSc options were
+ mixed together. This caused Pyre to issue warnings about the
+ unrecognized PETSc options, and PETSc to warn about the
+ unrecognized Pyre options. (Pyre errors were degraded to
+ warnings by giving "--typos=relaxed" as a matter for course.)
+ Now, PETSc and Pyre options are cleanly separated. (The use of
+ "--typos=relaxed" is discouraged.) This is implemented as
+ follows: PETSc options are designated explicitly using a 'petsc'
+ dummy facility+component, which allows passing arbitrary options
+ to PETSc: "--petsc.xxx". In addition,
+ commonly-used/highly-relevant PETSc options are listed in
+ PyLith's inventory; so, for example, on can give "-log_summary"
+ instead of "-petsc.log_summary" (either one will work). Finally,
+ PyLith overrides the standard Pyre CommandlineParser with
+ PetscCommandlineParser, which mimics PETSc's command-line
+ processing logic. This lets one write "-ksp_rtol 1e-09" (as is
+ customary) instead of "-ksp_rtol=1e-09". ~~~ Also:
+ PetscInitialize() was being called twice; I removed the second
+ occurance. The binding for PetscInitialize() was free()ing the
+ 'argv' passed to PETSc; this is potentially dangerous since
+ PETSc maintains a reference to this block, so now the 'argv' is
+ not freed.
+
+2007-01-05 01:15 leif
+
+ * [r5637] Transitioned PyLith v0.8 to the egg-based "CIG Edition"
+ of Pythia.
+
+2006-12-15 00:55 leif
+
+ * [r5600] Replaced lnblnk with len_trim for portability (ifort has
+ only the latter).
+
+2006-12-06 21:25 willic3
+
+ * [r5485] Changed integer output format to allow larger values for
+ ASCII UCD files.
+
+2006-12-06 20:59 willic3
+
+ * [r5483] Updated code to allow coordinate ranges to be specified.
+ Nodes outside those ranges get no slip.
+
+2006-12-04 21:31 willic3
+
+ * [r5439] Added an extra field to ivfamily so we can output
+ material ID rather than material model, which is much more
+ useful.
+
+2006-12-04 21:30 willic3
+
+ * [r5438] Added an extra field to ivfamily so that we can output
+ material ID rather than material type, which is much more useful.
+
+2006-12-04 18:44 sue
+
+ * [r5433] copied materials.lyx custom preamble line to
+ userguide.lyx to solve pdf generation problem
+
+2006-11-30 01:53 willic3
+
+ * [r5384] Forgot to put in slip scaling earlier.
+
+2006-11-30 01:44 willic3
+
+ * [r5383] Finished fixing Makefile.am.
+
+2006-11-30 01:29 willic3
+
+ * [r5382] Added new code to compute split node entries given
+ LaGriT auxiliary fault files plus UCD file specifying slip
+ values. Also added associated parameter file.
+
+2006-11-29 22:47 willic3
+
+ * [r5381] Quick and dirty code to compute fault slip using a
+ combination of LaGriT auxiliary fault info files and UCD files
+ containing slip values. Code needs testing (hasn't even been
+ compiled yet).
+
+2006-11-29 19:14 willic3
+
+ * [r5378] Added ESF version of Maxwell model.
+
+2006-11-29 18:03 willic3
+
+ * [r5373] Fixed error in computation of tangent matrix.
+
+2006-11-29 03:35 willic3
+
+ * [r5372] Changed old ESF-based Maxwell model to correspond to a
+ new material model.
+
+2006-11-29 03:33 willic3
+
+ * [r5371] Changed name of compdq function to avoid conflicts with
+ other material models that might use the same (or similar)
+ function.
+
+2006-11-29 03:32 willic3
+
+ * [r5370] Added python module for new material model.
+
+2006-11-29 03:28 willic3
+
+ * [r5369] Instead of replacing Maxwell model with new method, keep
+ old one as a different material model.
+
+2006-11-28 22:14 willic3
+
+ * [r5367] Initial version of linear Maxwell model that uses Prony
+ series approach rather than ESF. This hasn't been tested yet and
+ I may revert back to the previous version, depending on how
+ tests go.
+
+2006-11-22 02:06 willic3
+
+ * [r5341] Altered relaxation time to be consistent with uniaxial
+ test problem.
+
+2006-11-21 22:20 willic3
+
+ * [r5337] Changed relaxation time definitions, but still not sure
+ it's correct.
+
+2006-11-21 21:41 willic3
+
+ * [r5336] Fixed errors in computation of tangent stress-strain
+ matrix.
+
+2006-11-17 22:36 willic3
+
+ * [r5319] Fixed some bugs, mostly related to intializing viscous
+ strain variables. Test based on bm1 seems to work OK. Need to do
+ a shear test to make sure I haven't mixed up engineering/tensor
+ strain.
+
+2006-11-17 19:52 willic3
+
+ * [r5316] New generalized Maxwell model, consisting of 3 Maxwell
+ models in parallel with a spring. Still needs testing.
+
+2006-11-16 21:08 willic3
+
+ * [r5305] Increased maximum number of state variables for a model
+ to 30.
+ * [r5304] More work on generalized Maxwell model. Still need to
+ finish mat_7.f.
+
+2006-11-16 20:36 willic3
+
+ * [r5303] For now, let the number of state variables be 30 for the
+ current formulation using 3 Maxwell models in parallel
+ (Zienkiewicz and Taylor formulation). I may switch to the Simo
+ and Hughes formulation later, since this appears to only require
+ one additional state variable per Maxwell element (rather than
+ 6).
+
+2006-11-15 20:08 willic3
+
+ * [r5275] Changed parameter definitions and temporarily altered
+ things so the number of Maxwell elements is fixed at 3.
+
+2006-11-15 20:07 willic3
+
+ * [r5274] Added python file for generalized Maxwell model.
+
+2006-11-15 20:06 willic3
+
+ * [r5273] Added new exception if sum of shear ratios is incorrect.
+
+2006-11-15 20:05 willic3
+
+ * [r5272] Updated definitions for generalized Maxwell model.
+
+2006-11-15 20:04 willic3
+
+ * [r5271] Initial incomplete set of routines for generalized
+ Maxwell model. Things should be OK through matinit computation.
+ I still need to finish the rest of it.
+
+2006-11-14 21:22 willic3
+
+ * [r5265] Added generalized Maxwell model to list.
+
+2006-11-14 21:21 willic3
+
+ * [r5264] Initial python code to describe a Generalized Maxwell
+ model, which consists of a series of linear Maxwell models in
+ parallel. The standard linear solid can also be obtained as a
+ special case.
+
+2006-11-13 15:39 willic3
+
+ * [r5247] Minor fix to blockrot3.f. Updated blockrot3.par to be
+ consistent with dipblock4-sin example. Added readucd3.par
+ parameter file for new readucd3.f code. Added readucd3.f to
+ Makefile.am.
+
+2006-11-10 22:16 willic3
+
+ * [r5236] New code to deal with new LaGriT method for flagging
+ boundaries. This version does not deal with faults, since the
+ plan now is to use other codes to do this that no longer require
+ global mesh info to use the new LaGriT fault description files.
+
+2006-11-09 14:11 willic3
+
+ * [r5214] Fixed silly mistake in computation of tangent matrix.
+
+2006-11-04 01:01 leif
+
+ * [r5176] Fix for issue62: "PETSc autoconf macro CIT_PETSC_SIEVE
+ out of date". Also, use AC_HELP_STRING.
+
+2006-11-03 01:57 willic3
+
+ * [r5173] Put in same fix Matt did for matinit_drv.F, syncing tags
+ before assembly.
+
+2006-11-03 01:31 knepley
+
+ * [r5172] Sync tags before assembly
+
+2006-11-02 18:42 brad
+
+ * [r5171] Added 2 more bc to keep block from rotating.
+
+2006-11-02 17:06 brad
+
+ * [r5170] Added use of SIEVE_FLAGS and PETSC_LIB in module
+ Makefile. Temporarily hardwired setting SIEVE_FLAGS in
+ configure.ac (real solution is to get value from petscconf in
+ m4/cit_petsc.m4, which Leif will add when he has time).
+
+2006-10-30 21:35 knepley
+
+ * [r5118] Fixed preallocateMatrix() call
+
+2006-10-30 15:17 willic3
+
+ * [r5116] Updated blockrot utility to use new LaGriT fault
+ definition format. Hopefully, this is the final version.
+
+2006-10-26 19:53 willic3
+
+ * [r5102] Fixed routine so BC arrays are zeroed out before
+ returning even when there are no BC entries.
+
+2006-10-26 19:43 willic3
+
+ * [r5101] Fixed routine to pass up error codes from stress_drv and
+ stress_mat_drv.
+
+2006-10-26 19:42 willic3
+
+ * [r5100] Fixed stupid bug when computing current stress estimate.
+ Fixed problem when I was not transferring current stress
+ estimate to the necessary temporary variable. Fixed root-finding
+ tolerance to be a function of the current stress estimate.
+ Otherwise, the tolerance was typically too small.
+
+2006-10-26 19:39 willic3
+
+ * [r5099] Cleaned up code with some parentheses and a few other
+ fixes to avoid ambiguity.
+ * [r5098] Cleaned up viscous stress computation and fixed some
+ potential bugs.
+
+2006-10-26 19:33 willic3
+
+ * [r5097] Updated run scripts to pay attention to .keyval files.
+
+2006-10-26 18:47 brad
+
+ * [r5096] Partial fix to bug where PyLith can't handle cases where
+ processors don't have BCs. BC file is now empty when there are
+ no BCs as opposed to creating BC file with header. Still dies
+ later on for this case. Created bctest which exposes remaining
+ problems with this case.
+
+2006-10-26 17:39 willic3
+
+ * [r5095] Altered BC routines so they will not return an error if
+ there are no BC defined for a process.
+
+2006-10-26 17:03 knepley
+
+ * [r5094] Fixed problem with BC - Was figuring numElements
+ incorrectly
+
+2006-10-25 14:19 willic3
+
+ * [r5092] New power-law rheology test for linear hexes, for
+ comparison with results from TECTON and TEKTON.
+
+2006-10-25 14:15 willic3
+
+ * [r5091] Removed obsolete loop, since slippery nodes are not
+ presently available.
+
+2006-10-25 14:12 willic3
+
+ * [r5090] Added power-law Maxwell definitions.
+
+2006-10-25 14:11 willic3
+
+ * [r5089] Fixed string returned on error.
+
+2006-10-25 14:10 willic3
+
+ * [r5088] Minor efficiency change, but it chould be significant
+ since this routine is used many times.
+ * [r5087] Numerous bug fixes and efficiency improvements. Also
+ made much more use of parentheses in long expressions, since
+ some were not being evaluated correctly. At some point, I need
+ to determine whether the evaluations were consistent with
+ fortran standards or are a result of using g95.
+
+2006-10-25 14:05 willic3
+
+ * [r5086] Put in return for case where root-finding algorithm
+ finds the exact root (to machine precision) during function
+ evaluation. Original algorithm did not seem to detect this case
+ and took many more iterations to converge.
+
+2006-10-25 00:36 brad
+
+ * [r5084] Green's functions stuff is turned on with
+ --enable-greensfns argument to configure. Still need to add test
+ for Numeric/arrayobject.h to configure.ac.
+
+2006-10-25 00:30 brad
+
+ * [r5082] Moved interpolatePoints from scanner.cc to
+ interpolate.cc. Green's functions stuff is turned on with
+ --enable-greensfns argument to configure. Still need to add test
+ for Numeric/arrayobject.h to configure.ac.
+
+2006-10-23 16:55 willic3
+
+ * [r5079] Added power-law rheology.
+
+2006-10-23 15:08 willic3
+
+ * [r5077] Added python module for power-law rheology.
+
+2006-10-23 14:56 willic3
+
+ * [r5076] Fixed silly error in derivative of effective stress
+ function to be used for Newton's method (equation 46).
+
+2006-10-20 20:20 willic3
+
+ * [r5073] Completely reworked materials chapter, and added
+ equations for power-law Maxwell rheology. I need to double-check
+ the equations and cross-referencing.
+
+2006-10-16 19:55 knepley
+
+ * [r5054] Added Green Function application: - Needs to be updated
+ to run multiple problems Put in interpolation
+
+2006-10-16 00:13 knepley
+
+ * [r5053] Finally running with new PETSc
+
+2006-10-15 23:27 willic3
+
+ * [r5052] Added new routines rtsafe.f and zbrac.f.
+
+2006-10-15 23:24 knepley
+
+ * [r5051] This compiles, but has link errors
+
+2006-10-13 22:41 sue
+
+ * [r4991] added pdf manual
+
+2006-10-13 20:24 sue
+
+ * [r4990] went over all urls to remove http since not needed
+
+2006-10-13 19:30 sue
+
+ * [r4989] added latex feature to put urls in parentheses
+
+2006-10-13 19:29 sue
+
+ * [r4988] miniscule punc. and typos fixed; added feature to put
+ urls in parentheses)
+
+2006-10-13 18:29 willic3
+
+ * [r4987] Definitions for Maxwell power-law material.
+
+2006-10-13 18:27 willic3
+
+ * [r4986] Initial test for power-law rheology. I may need to alter
+ the viscosity coefficient to get anything interesting.
+
+2006-10-13 16:43 willic3
+
+ * [r4985] Updated all routine for computation of Maxwell time.
+
+2006-10-13 02:22 willic3
+
+ * [r4964] Nearly finished. Still need to finish Maxwell time
+ computations.
+
+2006-10-13 00:25 sue
+
+ * [r4963] small typos corrected
+
+2006-10-12 21:07 willic3
+
+ * [r4960] Added error return.
+
+2006-10-12 21:06 willic3
+
+ * [r4959] More effective stress function stuff. Still need to
+ finish tangent matrix.
+
+2006-10-11 23:25 sue
+
+ * [r4954] correct a few typos and format
+
+2006-10-11 19:02 willic3
+
+ * [r4788] More progress with effective stress formulation.
+
+2006-10-11 00:53 willic3
+
+ * [r4784] Added more stuff for power-law (initialization of
+ material matrix at the beginning of a time step.
+
+2006-10-11 00:13 sue
+
+ * [r4783] updated cover per brad and added layered psd cover file
+
+2006-10-10 20:55 willic3
+
+ * [r4779] Updated to compute Maxwell time from elastic solution
+ for consistency with other rheologies. More changes will be
+ needed, primarily in fixing the calling routines.
+
+2006-10-10 20:53 willic3
+
+ * [r4778] Started updating these routines for power-law Maxwell
+ viscoelastic rheology. Additional changes will be needed. Also,
+ all other material models will need to be updated to the new
+ calling conventions.
+
+2006-10-10 15:38 willic3
+
+ * [r4774] Added new errors related to root bracketing/finding.
+
+2006-10-10 15:36 willic3
+
+ * [r4773] Initial version of a root finding routine modified from
+ Numerical Recipes. This will be needed for power-law rheology.
+
+2006-10-10 15:35 willic3
+
+ * [r4772] Initial version of a root bracketing routine modified
+ from Numerical Recipes. This will be needed for power-law
+ rheology.
+
+2006-10-10 15:20 willic3
+
+ * [r4770] Added some new exceptions related to root
+ bracketing/finding.
+
+2006-10-06 23:22 brad
+
+ * [r4729] Increased resolution of sample images. Removed
+ superfluous print statement in tutor.
+
+2006-10-06 23:02 baagaard
+
+ * [r4728] Removed obsolete xml (docbook) file.
+
+2006-10-06 23:00 baagaard
+
+ * [r4727] Updated user guide to 0.8.1. Fixed size of tutorial
+ figures. Removed obsolete xml (docbook) and tex (latex) files.
+
+2006-10-06 22:46 brad
+
+ * [r4726] Replaced figures with higher resolution versions.
+
+2006-10-05 00:25 baagaard
+
+ * [r4707] Updated to reflect inclusion of readnetgen and faultcalc
+ in bin directory. Updated estimate for 1.0.
+
+2006-10-04 18:35 willic3
+
+ * [r4696] Fixed incorrect error return for scan_tractions
+ (tractions are optional). Fixed read_tractions to return with no
+ error when there are no tractions.
+
+2006-10-04 18:33 willic3
+
+ * [r4694] Fixed argument lists and inventory for traction BC.
+
+2006-10-04 16:05 willic3
+
+ * [r4691] Fixed bindings for scan_tractions and read_tractions,
+ which had been commented out.
+
+2006-10-04 15:53 willic3
+
+ * [r4690] Fixed name from scan_traction to scan_tractions.
+
+2006-10-03 16:36 willic3
+
+ * [r4682] Added missing entries for write_tractions and preshape2d.
+
+2006-10-02 20:55 knepley
+
+ * [r4676] Fixed setup.cc Upgraded to new PETSc Sieve interface
+
+2006-09-29 01:57 willic3
+
+ * [r4665] Removed obsolete sources.
+
+2006-09-29 01:49 willic3
+
+ * [r4664] Updated makefile for new sources.
+
+2006-09-28 21:35 willic3
+
+ * [r4663] Updated all bindings for traction BC.
+
+2006-09-28 21:20 willic3
+
+ * [r4662] Routine to write out traction BC.
+
+2006-09-28 21:07 willic3
+
+ * [r4661] Updated call to write_tractions.
+
+2006-09-28 20:49 willic3
+
+ * [r4660] Added bindings for preshape2d.
+
+2006-09-28 20:38 willic3
+
+ * [r4659] Updated to reflect changes in read_tractions.
+
+2006-09-28 20:36 willic3
+
+ * [r4658] Updated bindings to reflect change in argument list for
+ scan_tractions.
+ * [r4657] Get degrees of freedom from parameter include file
+ rather than being passed in.
+
+2006-09-28 20:34 willic3
+
+ * [r4656] Added routine to read traction BC. Time histories should
+ be added later.
+
+2006-09-28 20:32 willic3
+
+ * [r4655] Added bindings for read_tractions.
+
+2006-09-28 20:12 willic3
+
+ * [r4654] Fixed call to scan_tractions.
+
+2006-09-28 20:09 willic3
+
+ * [r4653] Put in bindings for scan_tractions.
+
+2006-09-28 20:08 willic3
+
+ * [r4652] Initial version of routine to scan traction BC. Once
+ things are working OK, we should add time histories.
+
+2006-09-28 16:01 willic3
+
+ * [r4644] Updated all routines for traction BC.
+
+2006-09-27 21:11 willic3
+
+ * [r4638] This obsolete routine has been replaced by the routines
+ traction_drv and traction_cmp_ss.
+
+2006-09-27 21:09 willic3
+
+ * [r4637] This obsolete routine has been superceded by the
+ traction_drv and traction_cmp_ss routines.
+
+2006-09-27 21:08 willic3
+
+ * [r4636] Altered arguments lists to be consistent with
+ computation routine.
+
+2006-09-27 21:07 willic3
+
+ * [r4635] Initial version of routine to compute contributions to
+ global load vector for tractions applied to a given face. This
+ version does not include load histories and assumes a constant
+ value applied over the entire face.
+
+2006-09-27 20:08 willic3
+
+ * [r4632] Initial version of routine to compute Jacobian for a 2D
+ surface in 3D.
+
+2006-09-26 22:18 leif
+
+ * [r4627] Updated info files.
+
2006-09-26 21:56 leif
* [r4626] Version 0.8.1a -> 0.8.1.
Modified: short/3D/PyLith/branches/pylith-0.8/INSTALL
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/INSTALL 2007-05-04 20:46:22 UTC (rev 6786)
+++ short/3D/PyLith/branches/pylith-0.8/INSTALL 2007-05-04 21:17:26 UTC (rev 6787)
@@ -10,8 +10,6 @@
* A Fortran compiler. Both older Fortran-77 and modern Fortran-9x
compilers will work.
-* A C compiler.
-
* A C++ compiler.
* Python 2.3 or later; see <http://www.python.org/>.
@@ -19,82 +17,72 @@
If you are using a modern UN*X system, there is a good chance that all
of the above tools are already installed.
-In addition, PyLith v0.8.1 requires the following software packages:
+In addition, PyLith v0.8.2 requires the following software packages:
-* An MPI library. Both PETSc and Pythia (detailed below)
- should be configured to use MPI. A popular choice is MPICH:
+* An MPI library. PETSc must be configured to use MPI. A popular
+ choice is MPICH:
<http://www-unix.mcs.anl.gov/mpi/mpich>
MPICH is recommended by the PETSc installation instructions; in
fact, PETSc's `configure.py' can automatically download and install
- MPICH for you (`--download-mpich=yes').
+ MPICH for you (`--download-mpich=1').
-* The development version of PETSc, which you can download using
- Mercurial:
+* The development version of PETSc. You can download the nightly
+ tarball snapshot:
- hg clone http://mercurial.mcs.anl.gov/petsc/petsc-dev
+ ftp://info.mcs.anl.gov/pub/petsc/petsc-dev.tar.gz
+
+ Or, check-out the source using Mercurial:
+
+ hg clone http://petsc.cs.iit.edu/petsc/petsc-dev
cd petsc-dev/python
- hg clone http://mercurial.mcs.anl.gov/petsc/BuildSystem
+ hg clone http://petsc.cs.iit.edu/petsc/BuildSystem BuildSystem
- As of this writing, the latest source code revision is r9506.
Mercurial may be obtained here:
<http://www.selenic.com/mercurial/>
PETSc must be configured with the Sieve package (--with-sieve=1).
This, in turn, requires that it be built with a C++ compiler
- (--with-clanguage=C++) and that you have Boost headers installed:
-
- <http://www.boost.org/>
-
- Use '--with-boost-dir=' to specify the full path to Boost's parent
- directory. You will also need Chaco (--with-chaco=1
+ (--with-clanguage=C++) and Boost (--with-boost=1
+ --download-boost=1). You will also need Chaco (--with-chaco=1
--download-chaco=1).
For more information about installing PETSc, see the MCS web site at
Argonne National Laboratory:
- <http://www-unix.mcs.anl.gov/petsc/petsc-2>
+ <http://www.mcs.anl.gov/petsc>
-* Pythia version 0.8. The easiest way to install Pythia is to
- download the GNU-style `pythia-0.8.tar.gz' source package from the
- CIG web site under `Software -> Software Packages -> Pythia':
+* Pythia version 0.8.1.3 or later. PyLith's 'configure' script will
+ download and install Pythia for you.
+ General information about Pythia can be found at the CIG website:
+
<http://www.geodynamics.org/cig/software/packages/pythia>
- General information about Pythia can be found at the Pyre project
- page:
+Note that releases of PETSc are generally not backwards-compatible
+with prior versions. Therefore, you must install the development
+version PETSc from May 2007 (or perhaps the equivalent release
+version, when it becomes available); future versions of PETSc would
+not be expected to work with PyLith v0.8.2.
- <http://www.cacr.caltech.edu/projects/pyre>
-
-Note that releases of both PETSc and Pythia are generally not
-backwards-compatible with prior versions. Therefore, you must install
-PETSc r9506 (or perhaps the equivalent final release) and Pythia v0.8
-specifically; future versions of PETSc and Pythia would not be
-expected to work with PyLith v0.8.1.
-
Installing PyLith
=================
To install PyLith, perform the following:
- gunzip -c pylith3d-0.8.1.tar.gz | tar xf -
- cd pylith3d-0.8.1
+ gunzip -c pylith3d-0.8.2.tar.gz | tar xf -
+ cd pylith3d-0.8.2
./configure
make
- make install
+ make install # optional
If you will be running `make install' as a non-root user, specify a
prefix when running `configure'; e.g.,
./configure --prefix=$HOME/pylith3d
-After installing, you may optionally run `make check' to run the
-examples. However, `check' takes a long time; instead, you may
-perform `cd pylith3d/examples; make quickcheck' to run only a
-handful of short examples.
-
More information about `configure' and the build system may be found
under "Generic GNU Installation Instructions", below.
@@ -112,11 +100,10 @@
Python rather than embedding it -- instead creating a dynamic
extension module (`pylith3dmodule.so') which is loaded by the
standard Python interpreter -- give PyLith's `configure' the
-`--without-embedding' option. However, this is not guaranteed to work
+`--disable-embedding' option. However, this is not guaranteed to work
properly unless you installed MPI as a shared library.
-PyLith v0.8.1 was tested on Linux (x86), Mac OS X (PowerPC), and
-Windows NT/2000/XP (Cygwin 1.5.19-4).
+PyLith v0.8.2 was tested on Linux (x86) and Mac OS X (PowerPC).
Generic GNU Installation Instructions
*************************************
Modified: short/3D/PyLith/branches/pylith-0.8/NEWS
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/NEWS 2007-05-04 20:46:22 UTC (rev 6786)
+++ short/3D/PyLith/branches/pylith-0.8/NEWS 2007-05-04 21:17:26 UTC (rev 6787)
@@ -1,9 +1,14 @@
-PyLith NEWS -- history of user-visible changes. 2006-09-26
+PyLith NEWS -- history of user-visible changes. 2007-05-04
Please report bugs at <http://geodynamics.org/roundup>.
Send questions to cig-short at geodynamics.org.
+Version 0.8.2
+
+* Numerous enhancements. See the file ChangeLog for details.
+
+
Version 0.8.1
* Numerous bug fixes and enhancements. See the file ChangeLog for
Modified: short/3D/PyLith/branches/pylith-0.8/README
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/README 2007-05-04 20:46:22 UTC (rev 6786)
+++ short/3D/PyLith/branches/pylith-0.8/README 2007-05-04 21:17:26 UTC (rev 6787)
@@ -1,4 +1,4 @@
-We are pleased to announce the version 0.8.1 release of PyLith.
+We are pleased to announce the version 0.8.2 release of PyLith.
See the file INSTALL for building and installation instructions.
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