[cig-commits] r4651 - in short/3D/PyLith/tags/v0.8.1: . pylith3d
pylith3d/utils
leif at geodynamics.org
leif at geodynamics.org
Thu Sep 28 12:25:43 PDT 2006
Author: leif
Date: 2006-09-28 12:25:42 -0700 (Thu, 28 Sep 2006)
New Revision: 4651
Removed:
short/3D/PyLith/tags/v0.8.1/pylith3d/utils/makefile
Modified:
short/3D/PyLith/tags/v0.8.1/ChangeLog
short/3D/PyLith/tags/v0.8.1/INSTALL
short/3D/PyLith/tags/v0.8.1/NEWS
short/3D/PyLith/tags/v0.8.1/README
short/3D/PyLith/tags/v0.8.1/configure.ac
short/3D/PyLith/tags/v0.8.1/pylith3d/Makefile.am
Log:
Merged v0.8.1 changes from v0.8 branch and regenerated ChangeLog.
Modified: short/3D/PyLith/tags/v0.8.1/ChangeLog
===================================================================
--- short/3D/PyLith/tags/v0.8.1/ChangeLog 2006-09-28 19:12:47 UTC (rev 4650)
+++ short/3D/PyLith/tags/v0.8.1/ChangeLog 2006-09-28 19:25:42 UTC (rev 4651)
@@ -1,3 +1,447 @@
+2006-09-28 19:12 leif
+
+ * [r4650] Tagged PyLith v0.8.1.
+
+2006-09-22 15:50 willic3
+
+ * [r4588] Fixed dependency for blockrot3.
+
+2006-09-15 03:54 willic3
+
+ * [r4552] Simple test for traction boundary conditions.
+
+2006-09-14 17:48 willic3
+
+ * [r4531] Another attempt at fixing string.
+
+2006-09-14 17:41 willic3
+
+ * [r4530] Fixed string problem.
+
+2006-09-14 17:36 willic3
+
+ * [r4529] Added options to get partitioner from command-line.
+ * [r4528] Added in options for getting partitioner from
+ command-line.
+
+2006-09-12 15:38 knepley
+
+ * [r4517] Error checking for MatAssembly
+
+2006-09-10 03:05 willic3
+
+ * [r4507] Added additional blockrot code that works with present
+ auxiliary fault file. Once we settle on formats, these codes
+ will be merged. Added entries to makefiles.
+
+2006-09-06 21:30 willic3
+
+ * [r4486] Added initial version of blockrot2 program, which still
+ needs to be tested and possibly debugged. This code takes UCD
+ and auxiliary fault info from LaGriT, as well as a parameter
+ file, and creates split node input from block rotation info.
+ Also added sample parameter file and entries in Makefile.am and
+ makefile.
+
+2006-09-06 00:40 baagaard
+
+ * [r4478] Tutorial. Made tutor.py executable.
+
+2006-09-06 00:25 baagaard
+
+ * [r4477] User guide. Fixed typo in xx.time comment. <<0 should be
+ <0.
+
+2006-09-05 19:40 sue
+
+ * [r4472] fixed typos found in readthru
+
+2006-09-05 19:17 sue
+
+ * [r4471] fixed typos found in readthru
+
+2006-09-05 18:54 sue
+
+ * [r4470] fixed typos found in readthru
+
+2006-09-05 13:38 knepley
+
+ * [r4469] Looks like parallel bm1b is working
+
+2006-09-05 03:24 knepley
+
+ * [r4468] Now bm1b works in serial for me
+
+2006-09-04 22:19 knepley
+
+ * [r4467] Now comiling with new Sieve
+
+2006-08-29 16:37 baagaard
+
+ * [r4447] User guide. Fixed typos related to description of fault
+ geometry for reversenog benchmark. Fixed corresponding figure of
+ geometry.
+
+2006-08-28 20:18 sue
+
+ * [r4441] fixed URLs to enable hotlink, suppressed pg no on title
+ page, changed url to pylith binaries from leif shipping per
+ Walter, other small errors fixed
+
+2006-08-28 16:15 baagaard
+
+ * [r4440] Removed latex title stuff which is now replaced by cover
+ page.
+
+2006-08-28 01:11 willic3
+
+ * [r4439] Altered routine, bindings and calls to include missing
+ array (nprint).
+
+2006-08-26 22:39 sue
+
+ * [r4438] added edited lyx files
+
+2006-08-25 22:57 sue
+
+ * [r4435] added lyx file and all files edited
+
+2006-08-25 21:44 leif
+
+ * [r4433] Bumped version number.
+
+2006-08-25 18:41 willic3
+
+ * [r4432] Replaced BLAS call in makeucd.f with call to an included
+ subroutine. Makefile has been modified so that BLAS is no longer
+ linked.
+
+2006-08-24 23:27 baagaard
+
+ * [r4428] Tutorial files. Moved figures to archive (where they
+ belong) from workarea.
+
+2006-08-24 23:26 baagaard
+
+ * [r4427] Tutorial files. Added sample Paraview figs.
+
+2006-08-24 23:17 baagaard
+
+ * [r4426] User guide. Added figures of output. Fixed text of
+ splitcube visualizations to use y-disp (only meaningful
+ component.
+
+2006-08-24 22:29 baagaard
+
+ * [r4425] Switched from copyfile() to copy() to preserve
+ permissions on executable scripts.
+
+2006-08-24 22:23 sue
+
+ * [r4424] added lyx file
+
+2006-08-24 22:22 sue
+
+ * [r4423] added lyx file
+
+2006-08-24 22:10 baagaard
+
+ * [r4422] Fixed bug in ReadBounary_PyLith where units were ignored
+ incorrectly. The line with displacement units is read as the
+ last thing in IgnoreComments_PyLith (which causes it to stop).
+ Fix is to remove line reading displacement units.
+
+2006-08-24 21:27 baagaard
+
+ * [r4421] Fixed bug in scanner wherein iIgnoreComments_PyLith
+ didn't terminate on encountering '\0'. This brings the ignore
+ comments functionality in line with what is in meshpylith.c in
+ PETSc.
+
+2006-08-24 20:56 baagaard
+
+ * [r4420] Created utils/Makefile.am. Updated configure.ac
+ accordingly.
+
+2006-08-24 18:35 baagaard
+
+ * [r4413] User guide. Added not on compiler bug in gcc-4.1.
+
+2006-08-24 15:10 willic3
+
+ * [r4412] Added new blockrot.f code to compute split node
+ displacements corresponding to given block rotations, using the
+ UCD output from LaGriT, and updated the makefile to include the
+ new code. Increased the dimensions on makeucd.f to handle some
+ of the bigger meshes.
+
+2006-08-23 23:27 baagaard
+
+ * [r4409] User guide. Brought splitcube up to date. Added figures
+ for splitcube tutorial.
+
+2006-08-23 23:19 sue
+
+ * [r4407] added lyx files
+ * [r4406] added lyx files
+
+2006-08-23 23:18 sue
+
+ * [r4405] added lyx files
+
+2006-08-23 19:39 baagaard
+
+ * [r4403] Updated to split cube problem. Fixed units in .par file.
+
+2006-08-23 03:34 baagaard
+
+ * [r4402] Added files for splitsube tutorial.
+
+2006-08-22 21:44 baagaard
+
+ * [r4401] Changed name of splittest to splitcube.
+
+2006-08-22 21:42 baagaard
+
+ * [r4400] Continued docbook to LaTeX conversion. Cleaned up
+ fileformats.
+
+2006-08-22 15:30 baagaard
+
+ * [r4398] First stab at converting docbook files to LaTeX.
+
+2006-08-21 14:49 willic3
+
+ * [r4393] Changed readucd2.par to conform to new version of
+ readucd2 code. Added makeucd utility to makefile.
+
+2006-08-18 21:34 knepley
+
+ * [r4392] Activated matrix preallocation in serial - This will
+ break parallel code right now
+
+2006-08-18 21:13 willic3
+
+ * [r4391] Changed the way I deal with faults, which was wrong
+ before. At present, the UCD file needs to contain one nodal
+ attribute and one element attribute per fault, to allow for
+ nodes and elements that lie on more than one fault. This still
+ does not solve the problem when a node/element pair lie on more
+ than one fault, which can not be handled with split or slippery
+ nodes anyway. The problem of duplicate entries will have to be
+ dealt with somehow in postprocessing. Also added in options for
+ reading fault normals if they are available. The accompanying
+ parameter file needs to be updated.
+
+2006-08-15 21:59 knepley
+
+ * [r4299] Fixed prototype
+
+2006-08-12 20:45 knepley
+
+ * [r4277] Now split nodes seem to work
+
+2006-08-12 15:42 knepley
+
+ * [r4276] Looks like its working in parallel now
+
+2006-08-04 22:14 knepley
+
+ * [r4229] Fix mesh viewer name
+
+2006-08-04 20:51 willic3
+
+ * [r4227] Initial version of code to turn UCD pieces from
+ LithoMop/PyLith into complete UCD files. All behavior is
+ controlled by command-line arguments including options for
+ interpolating state variables to nodes and averaging Gauss point
+ values to element centroids. The code definitely needs more
+ testing. So far, it produces a valid UCD file and the results
+ look reasonable, but no quantitative testing has been done.
+ Likely future enhancements include the ability to deal with
+ binary UCD files.
+
+2006-08-04 19:18 knepley
+
+ * [r4226] Fixed ALE::Point refrences to Sieve points
+
+2006-08-03 19:39 willic3
+
+ * [r4219] Initial (unfinished) version of code to create complete
+ UCD files out of pieces created by LithoMop and PyLith. Includes
+ options to interpolate stresses to nodes and average stresses to
+ Gauss points. Current limitations: Only works for linear hexes
+ and tets. Only works for ASCII UCD format. Somewhat primitive
+ stress interpolation algorithm.
+
+2006-08-01 16:48 knepley
+
+ * [r4187] Changes which allow serial running with new Sieve fields
+
+2006-07-20 14:33 willic3
+
+ * [r4039] Dimension parameters have been changed to deal with the
+ high resolution benchmarks.
+
+2006-07-18 21:55 cassie
+
+ * [r4025] just testing
+
+2006-07-14 17:47 knepley
+
+ * [r4019] Small fix
+
+2006-07-14 17:20 knepley
+
+ * [r4018] Updates for new Sieve stuff
+
+2006-07-13 15:22 willic3
+
+ * [r4015] Updated file to reflect actual values used for BM5.
+
+2006-07-13 02:23 willic3
+
+ * [r4014] Fixed stupid indexing error.
+
+2006-07-12 21:51 willic3
+
+ * [r4013] Added utilities and sample parameter files, as well as a
+ README containing brief code descriptions. The scaling codes are
+ simple and appear to work OK. The readucd2 code has been tested
+ on a single example (BM5 created with LaGriT) and appears to
+ work OK, but more testing is probably needed. I still need to
+ make this whole directory part of the GNU build procedure and
+ install the executables.
+
+2006-07-11 19:02 willic3
+
+ * [r4004] Added new version of faultcalc that uses essentially no
+ memory. This code should be at least as efficient as the
+ previous version, and relies only on the presence of the .fbc
+ and .fcoord files created by readucd or readnetgen, as well as a
+ parameter file.
+
+2006-07-11 17:50 willic3
+
+ * [r4003] Two utility codes that were previously available only
+ with the tutorial have been added to the repository.
+
+2006-07-11 17:49 willic3
+
+ * [r4002] Update code to more recent version that includes
+ features such as getting BC directly from an auxiliary values
+ file.
+
+2006-07-07 14:48 willic3
+
+ * [r3980] Kludgy fix for the case where Sieve produces an empty
+ split node file. In this case the file does not contain an EOF
+ and an error would ordinarily be returned.
+
+2006-07-05 23:40 baagaard
+
+ * [r3921] User guide. Fixed mercurial version number.
+
+2006-07-05 23:19 baagaard
+
+ * [r3920] User guide. Fixed orientation of hex8 element. Added
+ more notes on building developer version.
+
+2006-07-05 18:14 baagaard
+
+ * [r3917] User guide. Added instructions for building developers
+ version. Added info on support for hex element.
+
+2006-07-03 23:18 baagaard
+
+ * [r3915] User guide, tutorial. Added workflow diagram for how
+ input files are created.
+
+2006-07-03 21:02 baagaard
+
+ * [r3914] User guide. Changed name of tutorial.
+
+2006-07-03 21:01 baagaard
+
+ * [r3913] User guide. Changed name of tutorial.
+
+2006-07-03 20:43 baagaard
+
+ * [r3912] Tutorial. Updated tutor to use Python runbm.
+
+2006-07-03 20:36 baagaard
+
+ * [r3911] Tutorial. Converted runbm5 from bash script to Python
+ script. Changed name to runbm. This removes dependency on bash
+ shell for running a job.
+
+2006-07-03 19:38 baagaard
+
+ * [r3910] Tutorial. Finished converting tutor shell script to
+ Python. This removed reliance on bash shell for tutor.
+
+2006-07-03 16:24 baagaard
+
+ * [r3909] Created tutorials subdir with input files (don't include
+ sim output). reversenog is the old bm5.
+
+2006-06-30 21:52 baagaard
+
+ * [r3907] User guide. Fixed fault dimensions in tutorialbm5.
+
+2006-06-30 17:13 willic3
+
+ * [r3906] Increased max dimensions for readnetgen and changed some
+ makefile options. Need to create a Makefile.am for these codes
+ and make all utilities part of the GNU build procedure.
+
+2006-06-28 17:58 willic3
+
+ * [r3905] Removed blank line that makes parser blow up.
+
+2006-06-28 16:59 willic3
+
+ * [r3904] Added fuldat file and simple shell script to run pt1.
+
+2006-06-28 16:57 willic3
+
+ * [r3903] Added simple split node test for hexes.
+
+2006-06-28 14:13 knepley
+
+ * [r3902] Turned off mesh interpolation by default - Now
+ controlled by -scanner.interpolateMesh Fixed patchtest to run
+ with new stuff
+
+2006-06-26 21:27 baagaard
+
+ * [r3892] User guide. Added ps target for makefile. Fixed install
+ instructions for linux (LD_LIBRARY_PATH). Fixed long lines in
+ tutorial.
+
+2006-06-24 23:25 baagaard
+
+ * [r3882] User guide. Added figures illustrating output for bm5
+ tutorial. Added how to run on Windows.
+
+2006-06-24 00:35 leif
+
+ * [r3879] Updated license headers to MIT license using my
+ 'licencetool' Perl script.
+
+2006-06-24 00:31 leif
+
+ * [r3878] Minor tweak to 'configure': Pythia's MPI packages are
+ not actually required.
+
+2006-06-24 00:20 leif
+
+ * [r3877] Added boilerplate GNU-style text info files: AUTHORS,
+ INSTALL, ChangeLog, COPYING, NEWS, README. "ChangeLog" generated
+ with svn2cl (http://ch.tudelft.nl/~arthur/svn2cl/) using the
+ following command: svn log --xml | xsltproc --stringparam
+ include-rev yes ~/install/svn2cl-0.3/svn2cl.xsl - > ChangeLog
+
2006-06-23 22:45 cassie
* [r3874] updated cover for manual
Modified: short/3D/PyLith/tags/v0.8.1/INSTALL
===================================================================
--- short/3D/PyLith/tags/v0.8.1/INSTALL 2006-09-28 19:12:47 UTC (rev 4650)
+++ short/3D/PyLith/tags/v0.8.1/INSTALL 2006-09-28 19:25:42 UTC (rev 4651)
@@ -19,7 +19,7 @@
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 v0.8.0 requires the following software packages:
+In addition, PyLith v0.8.1 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:
@@ -37,7 +37,7 @@
cd petsc-dev/python
hg clone http://mercurial.mcs.anl.gov/petsc/BuildSystem
- As of this writing, the latest source code revision is r8951.
+ As of this writing, the latest source code revision is r9506.
Mercurial may be obtained here:
<http://www.selenic.com/mercurial/>
@@ -49,9 +49,12 @@
<http://www.boost.org/>
Use '--with-boost-dir=' to specify the full path to Boost's parent
- directory. For more information about installing PETSc, see the MCS
- web site at Argonne National Laboratory:
+ directory. 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>
* Pythia version 0.8. The easiest way to install Pythia is to
@@ -67,17 +70,17 @@
Note that releases of both PETSc and Pythia are generally not
backwards-compatible with prior versions. Therefore, you must install
-PETSc r8951 (or perhaps the equivalent final release) and Pythia v0.8
+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 v0.8.0.
+expected to work with PyLith v0.8.1.
Installing PyLith
=================
To install PyLith, perform the following:
- gunzip -c pylith3d-0.8.0.tar.gz | tar xf -
- cd pylith3d-0.8.0
+ gunzip -c pylith3d-0.8.1.tar.gz | tar xf -
+ cd pylith3d-0.8.1
./configure
make
make install
@@ -112,7 +115,7 @@
`--without-embedding' option. However, this is not guaranteed to work
properly unless you installed MPI as a shared library.
-PyLith v0.8.0 was tested on Linux (x86), Mac OS X (PowerPC), and
+PyLith v0.8.1 was tested on Linux (x86), Mac OS X (PowerPC), and
Windows NT/2000/XP (Cygwin 1.5.19-4).
Generic GNU Installation Instructions
Modified: short/3D/PyLith/tags/v0.8.1/NEWS
===================================================================
--- short/3D/PyLith/tags/v0.8.1/NEWS 2006-09-28 19:12:47 UTC (rev 4650)
+++ short/3D/PyLith/tags/v0.8.1/NEWS 2006-09-28 19:25:42 UTC (rev 4651)
@@ -1,9 +1,15 @@
-PyLith NEWS -- history of user-visible changes. 2006-04-06
+PyLith NEWS -- history of user-visible changes. 2006-09-26
Please report bugs at <http://geodynamics.org/roundup>.
Send questions to cig-short at geodynamics.org.
+Version 0.8.1
+
+* Numerous bug fixes and enhancements. See the file ChangeLog for
+ details.
+
+
Version 0.8.0
* This first version of PyLith is a direct descendant of Lithomop and
Modified: short/3D/PyLith/tags/v0.8.1/README
===================================================================
--- short/3D/PyLith/tags/v0.8.1/README 2006-09-28 19:12:47 UTC (rev 4650)
+++ short/3D/PyLith/tags/v0.8.1/README 2006-09-28 19:25:42 UTC (rev 4651)
@@ -1,4 +1,4 @@
-We are pleased to announce the version 0.8.0 release of PyLith.
+We are pleased to announce the version 0.8.1 release of PyLith.
See the file INSTALL for building and installation instructions.
Modified: short/3D/PyLith/tags/v0.8.1/configure.ac
===================================================================
--- short/3D/PyLith/tags/v0.8.1/configure.ac 2006-09-28 19:12:47 UTC (rev 4650)
+++ short/3D/PyLith/tags/v0.8.1/configure.ac 2006-09-28 19:25:42 UTC (rev 4651)
@@ -3,7 +3,7 @@
# $Id: configure.ac,v 1.1 2005/08/24 22:45:51 leif Exp $
AC_PREREQ(2.59)
-AC_INIT([PyLith3D], [0.8.1a], [cig-short at geodynamics.org])
+AC_INIT([PyLith3D], [0.8.1], [cig-short at geodynamics.org])
AC_CONFIG_AUX_DIR([./aux-config])
AC_CONFIG_SRCDIR([pylith3d/applications/pylith3dapp.py])
AC_CONFIG_HEADER([portinfo])
Modified: short/3D/PyLith/tags/v0.8.1/pylith3d/Makefile.am
===================================================================
--- short/3D/PyLith/tags/v0.8.1/pylith3d/Makefile.am 2006-09-28 19:12:47 UTC (rev 4650)
+++ short/3D/PyLith/tags/v0.8.1/pylith3d/Makefile.am 2006-09-28 19:25:42 UTC (rev 4651)
@@ -1,7 +1,7 @@
## Process this file with automake to produce Makefile.in
# $Id: Makefile.am 2370 2005-09-09 19:49:10Z leif $
-SUBDIRS = libpylith3d module
+SUBDIRS = libpylith3d module utils
bin_PROGRAMS =
if COND_EMBEDDING
Deleted: short/3D/PyLith/tags/v0.8.1/pylith3d/utils/makefile
===================================================================
--- short/3D/PyLith/tags/v0.8.1/pylith3d/utils/makefile 2006-09-28 19:12:47 UTC (rev 4650)
+++ short/3D/PyLith/tags/v0.8.1/pylith3d/utils/makefile 2006-09-28 19:25:42 UTC (rev 4651)
@@ -1,99 +0,0 @@
-#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-#
-# Example makefile for TECTON sources
-#
-# This makefile was set up for a Macintosh (Mac OSX) using the g77
-# compiler. If you use a different compiler, change the FCOMPL
-# variable. You will also probably need to specify a different
-# location for the BLAS and LAPACK libraries (LINALG variable).
-#
-#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-FFLAGC= -Wall -fbackslash -v
-
-CFLAGC=
-
-opt = -g
-
-# opt = -O3 -funroll-loops
-
-# load = -lcc_dynamic
-
-# load =
-
-FCOMPL= g95
-
-CCOMPL= gcc
-
-INCD= includes
-
-# LINALG= -L/sw/lib -llapack -lf77blas -lcblas -latlas
-
-LINALG= -Wl,-framework -Wl,vecLib
-
-.SUFFIXES: .F .f .c .s .o .fil
-
-.F.f:
- $(FCOMPL) -F $<
-
-.f.o:
- $(FCOMPL) -c $(FFLAGC) $(opt) $<
-
-.f.fil:
- $(FCOMPL) -il $(FFLAGC) $<
-
-.s.o:
- as $<
-
-.c.o:
- $(CCOMPL) -c $(CFLAGC) $(opt) $<
-
-lh2qh: lh2qh.o
- $(FCOMPL) $(opt) -o lh2qh lh2qh.o
-
-lt2qt: lt2qt.o
- $(FCOMPL) $(opt) -o lt2qt lt2qt.o
-
-fixqt: fixqt.o
- $(FCOMPL) $(opt) -o fixqt fixqt.o
-
-blockrot: blockrot.o
- $(FCOMPL) $(opt) -o blockrot blockrot.o
-
-blockrot2: blockrot2.o
- $(FCOMPL) $(opt) -o blockrot2 blockrot2.o
-
-blockrot3: blockrot3.o
- $(FCOMPL) $(opt) -o blockrot3 blockrot3.o
-
-makeucd: makeucd.o
- $(FCOMPL) $(opt) -o makeucd makeucd.o
-
-pylith2ucd: pylith2ucd.o
- $(FCOMPL) $(opt) -o pylith2ucd pylith2ucd.o
-
-readnetgen: readnetgen.o
- $(FCOMPL) $(opt) -o readnetgen readnetgen.o
-
-readucd: readucd.o
- $(FCOMPL) $(opt) -o readucd readucd.o
-
-readucd2: readucd2.o
- $(FCOMPL) $(opt) -o readucd2 readucd2.o
-
-tetcmp: tetcmp.o
- $(FCOMPL) $(opt) -o tetcmp tetcmp.o
-
-faultcalc: faultcalc.o
- $(FCOMPL) $(opt) -o faultcalc faultcalc.o
-
-faultcalc2: faultcalc2.o
- $(FCOMPL) $(opt) -o faultcalc2 faultcalc2.o
-
-scalecoord: scalecoord.o
- $(FCOMPL) $(opt) -o scalecoord scalecoord.o
-
-scaleucd: scaleucd.o
- $(FCOMPL) $(opt) -o scaleucd scaleucd.o
-
-clean:
- /bin/rm -f *.o
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