[cig-commits] r18614 - in short/3D/PyLith/trunk: doc/userguide tests/refinefaulttip
brad at geodynamics.org
brad at geodynamics.org
Mon Jun 13 20:39:07 PDT 2011
Author: brad
Date: 2011-06-13 20:39:07 -0700 (Mon, 13 Jun 2011)
New Revision: 18614
Added:
short/3D/PyLith/trunk/doc/userguide/makepdf.sh
short/3D/PyLith/trunk/tests/refinefaulttip/tet4.cfg
short/3D/PyLith/trunk/tests/refinefaulttip/tet4.mesh
Modified:
short/3D/PyLith/trunk/doc/userguide/Makefile.am
short/3D/PyLith/trunk/tests/refinefaulttip/Makefile.am
short/3D/PyLith/trunk/tests/refinefaulttip/Makefile.in
Log:
Added tet4 refine fault tip test. Added script to generate userguide PDF (on linux).
Modified: short/3D/PyLith/trunk/doc/userguide/Makefile.am
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/Makefile.am 2011-06-14 02:56:16 UTC (rev 18613)
+++ short/3D/PyLith/trunk/doc/userguide/Makefile.am 2011-06-14 03:39:07 UTC (rev 18614)
@@ -16,11 +16,6 @@
# ----------------------------------------------------------------------
#
-dist_noinst_DATA =
+dist_noinst_DATA = makepdf.sh
-default: userguide.pdf
-
-userguide.pdf:
- lyx -e pdf userguide.lyx
-
# End of file
Added: short/3D/PyLith/trunk/doc/userguide/makepdf.sh
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/makepdf.sh (rev 0)
+++ short/3D/PyLith/trunk/doc/userguide/makepdf.sh 2011-06-14 03:39:07 UTC (rev 18614)
@@ -0,0 +1,22 @@
+#!/bin/bash
+#
+# ----------------------------------------------------------------------
+#
+# Brad T. Aagaard, U.S. Geological Survey
+# Charles A. Williams, GNS Science
+# Matthew G. Knepley, University of Chicago
+#
+# This code was developed as part of the Computational Infrastructure
+# for Geodynamics (http://geodynamics.org).
+#
+# Copyright (c) 2010 University of California, Davis
+#
+# See COPYING for license information.
+#
+# ----------------------------------------------------------------------
+#
+
+for i in `find . -name "*.eps"`; do epstopdf $i; done
+lyx -e pdf userguide.lyx
+
+# End of file
\ No newline at end of file
Modified: short/3D/PyLith/trunk/tests/refinefaulttip/Makefile.am
===================================================================
--- short/3D/PyLith/trunk/tests/refinefaulttip/Makefile.am 2011-06-14 02:56:16 UTC (rev 18613)
+++ short/3D/PyLith/trunk/tests/refinefaulttip/Makefile.am 2011-06-14 03:39:07 UTC (rev 18614)
@@ -16,11 +16,15 @@
# ----------------------------------------------------------------------
#
-dist_noinst_DATA =\
+dist_noinst_DATA = \
tri3.cfg \
tri3.mesh \
quad4.cfg \
- quad4.mesh
+ quad4.mesh \
+ tet4.cfg \
+ tet4.mesh \
+ hex8.cfg \
+ hex8.mesh
# End of file
Modified: short/3D/PyLith/trunk/tests/refinefaulttip/Makefile.in
===================================================================
--- short/3D/PyLith/trunk/tests/refinefaulttip/Makefile.in 2011-06-14 02:56:16 UTC (rev 18613)
+++ short/3D/PyLith/trunk/tests/refinefaulttip/Makefile.in 2011-06-14 03:39:07 UTC (rev 18614)
@@ -1,9 +1,8 @@
-# Makefile.in generated by automake 1.11.1 from Makefile.am.
+# Makefile.in generated by automake 1.10 from Makefile.am.
# @configure_input@
# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
-# Inc.
+# 2003, 2004, 2005, 2006 Free Software Foundation, Inc.
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
@@ -35,9 +34,8 @@
VPATH = @srcdir@
pkgdatadir = $(datadir)/@PACKAGE@
-pkgincludedir = $(includedir)/@PACKAGE@
pkglibdir = $(libdir)/@PACKAGE@
-pkglibexecdir = $(libexecdir)/@PACKAGE@
+pkgincludedir = $(includedir)/@PACKAGE@
am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
install_sh_DATA = $(install_sh) -c -m 644
install_sh_PROGRAM = $(install_sh) -c
@@ -72,7 +70,6 @@
mkinstalldirs = $(install_sh) -d
CONFIG_HEADER = $(top_builddir)/portinfo
CONFIG_CLEAN_FILES =
-CONFIG_CLEAN_VPATH_FILES =
SOURCES =
DIST_SOURCES =
DATA = $(dist_noinst_DATA)
@@ -125,7 +122,6 @@
NMEDIT = @NMEDIT@
NUMPY_INCDIR = @NUMPY_INCDIR@
NVCC = @NVCC@
-OBJDUMP = @OBJDUMP@
OBJEXT = @OBJEXT@
OTOOL = @OTOOL@
OTOOL64 = @OTOOL64@
@@ -134,7 +130,6 @@
PACKAGE_NAME = @PACKAGE_NAME@
PACKAGE_STRING = @PACKAGE_STRING@
PACKAGE_TARNAME = @PACKAGE_TARNAME@
-PACKAGE_URL = @PACKAGE_URL@
PACKAGE_VERSION = @PACKAGE_VERSION@
PATH_SEPARATOR = @PATH_SEPARATOR@
PETSC_ARCH = @PETSC_ARCH@
@@ -242,14 +237,17 @@
srcdir = @srcdir@
sysconfdir = @sysconfdir@
target_alias = @target_alias@
-top_build_prefix = @top_build_prefix@
top_builddir = @top_builddir@
top_srcdir = @top_srcdir@
dist_noinst_DATA = \
tri3.cfg \
tri3.mesh \
quad4.cfg \
- quad4.mesh
+ quad4.mesh \
+ tet4.cfg \
+ tet4.mesh \
+ hex8.cfg \
+ hex8.mesh
all: all-am
@@ -258,14 +256,14 @@
@for dep in $?; do \
case '$(am__configure_deps)' in \
*$$dep*) \
- ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
- && { if test -f $@; then exit 0; else break; fi; }; \
+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh \
+ && exit 0; \
exit 1;; \
esac; \
done; \
- echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign tests/refinefaulttip/Makefile'; \
- $(am__cd) $(top_srcdir) && \
- $(AUTOMAKE) --foreign tests/refinefaulttip/Makefile
+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign tests/refinefaulttip/Makefile'; \
+ cd $(top_srcdir) && \
+ $(AUTOMAKE) --foreign tests/refinefaulttip/Makefile
.PRECIOUS: Makefile
Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
@case '$?' in \
@@ -283,7 +281,6 @@
cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
$(ACLOCAL_M4): $(am__aclocal_m4_deps)
cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-$(am__aclocal_m4_deps):
mostlyclean-libtool:
-rm -f *.lo
@@ -313,17 +310,13 @@
if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
if test -d $$d/$$file; then \
dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
- if test -d "$(distdir)/$$file"; then \
- find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
- fi; \
if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
- cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
- find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+ cp -pR $(srcdir)/$$file $(distdir)$$dir || exit 1; \
fi; \
- cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
+ cp -pR $$d/$$file $(distdir)$$dir || exit 1; \
else \
- test -f "$(distdir)/$$file" \
- || cp -p $$d/$$file "$(distdir)/$$file" \
+ test -f $(distdir)/$$file \
+ || cp -p $$d/$$file $(distdir)/$$file \
|| exit 1; \
fi; \
done
@@ -351,7 +344,6 @@
distclean-generic:
-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
- -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
maintainer-clean-generic:
@echo "This command is intended for maintainers to use"
@@ -370,8 +362,6 @@
html: html-am
-html-am:
-
info: info-am
info-am:
@@ -380,28 +370,18 @@
install-dvi: install-dvi-am
-install-dvi-am:
-
install-exec-am:
install-html: install-html-am
-install-html-am:
-
install-info: install-info-am
-install-info-am:
-
install-man:
install-pdf: install-pdf-am
-install-pdf-am:
-
install-ps: install-ps-am
-install-ps-am:
-
installcheck-am:
maintainer-clean: maintainer-clean-am
@@ -437,7 +417,6 @@
# End of file
-
# Tell versions [3.59,3.63) of GNU make to not export all variables.
# Otherwise a system limit (for SysV at least) may be exceeded.
.NOEXPORT:
Added: short/3D/PyLith/trunk/tests/refinefaulttip/tet4.cfg
===================================================================
--- short/3D/PyLith/trunk/tests/refinefaulttip/tet4.cfg (rev 0)
+++ short/3D/PyLith/trunk/tests/refinefaulttip/tet4.cfg 2011-06-14 03:39:07 UTC (rev 18614)
@@ -0,0 +1,144 @@
+# -*- Python -*-
+[pylithapp]
+
+# ----------------------------------------------------------------------
+# journal
+# ----------------------------------------------------------------------
+# Turn on some journals to show progress.
+[pylithapp.journal.info]
+timedependent = 1
+implicit = 1
+petsc = 1
+meshiocubit = 1
+implicitelasticity = 1
+quadrature2d = 1
+fiatlagrange = 1
+faultcohesivedyn = 1
+
+[pylithapp.journal.debug]
+pylithapp = 1
+problem = 1
+implicit = 1
+
+# ----------------------------------------------------------------------
+# mesh_generator
+# ----------------------------------------------------------------------
+[pylithapp.mesh_generator]
+reader = pylith.meshio.MeshIOAscii
+debug = 1
+distributor.write_partition = True
+distributor.data_writer.filename = partition.vtk
+
+# SWITCH FOR REFINEMENT
+refiner = pylith.topology.RefineUniform
+
+
+[pylithapp.mesh_generator.reader]
+filename = tet4.mesh
+coordsys.space_dim = 3
+
+# ----------------------------------------------------------------------
+# problem
+# ----------------------------------------------------------------------
+[pylithapp.timedependent]
+dimension = 3
+
+formulation = pylith.problems.Implicit
+
+normalizer = spatialdata.units.NondimElasticQuasistatic
+normalizer.length_scale = 1.0*m
+normalizer.relaxation_time = 1.0*s
+
+bc = [xpos,xneg]
+interfaces = [fault]
+materials = [elastic]
+
+[pylithapp.timedependent.implicit.time_step]
+total_time = 0.0*s
+dt = 0.1*s
+
+# ----------------------------------------------------------------------
+# materials
+# ----------------------------------------------------------------------
+[pylithapp.timedependent.materials.elastic]
+label = Elastic material
+id = 0
+db_properties = spatialdata.spatialdb.UniformDB
+db_properties.label = Elastic properties
+db_properties.values = [density, vp, vs]
+db_properties.data = [2500.0*km/m**3, 5.1962*km/s, 3.0*km/s]
+
+quadrature.cell = pylith.feassemble.FIATSimplex
+quadrature.cell.shape = tetrahedron
+quadrature.cell.quad_order = 2
+
+# ----------------------------------------------------------------------
+# boundary conditions
+# ----------------------------------------------------------------------
+[pylithapp.timedependent.bc]
+
+# Dirichlet BC on -x
+[pylithapp.timedependent.bc.xneg]
+bc_dof = [0, 1, 2]
+label = xneg
+
+
+# Dirichlet BC on +x
+[pylithapp.timedependent.bc.xpos]
+bc_dof = [0, 1, 2]
+label = xpos
+
+# ----------------------------------------------------------------------
+# faults
+# ----------------------------------------------------------------------
+[pylithapp.timedependent.interfaces.fault]
+id = 100
+label = fault
+quadrature.cell = pylith.feassemble.FIATSimplex
+quadrature.cell.shape = triangle
+quadrature.cell.quad_order = 2
+
+[pylithapp.timedependent.interfaces.fault.eq_srcs.rupture.slip_function]
+slip = spatialdata.spatialdb.UniformDB
+slip.label = Final slip
+slip.values = [left-lateral-slip,reverse-slip,fault-opening]
+slip.data = [0.1*m, 0.0*m, 0.0*m]
+
+slip_time = spatialdata.spatialdb.UniformDB
+slip_time.label = Slip initiation time
+slip_time.values = [slip-time]
+slip_time.data = [0.0*s]
+
+# ----------------------------------------------------------------------
+# PETSc
+# ----------------------------------------------------------------------
+[pylithapp.petsc]
+
+# Preconditioner settings.
+pc_type = asm
+sub_pc_factor_shift_type = nonzero
+
+# KSP
+ksp_rtol = 1.0e-12
+ksp_atol = 1.0e-15
+ksp_max_it = 500
+ksp_gmres_restart = 100
+
+ksp_monitor = true
+#ksp_view = true
+ksp_converged_reason = true
+
+# ----------------------------------------------------------------------
+# output
+# ----------------------------------------------------------------------
+[pylithapp.problem.formulation.output.output]
+vertex_data_fields = [displacement]
+writer.filename = tet4.vtk
+
+[pylithapp.timedependent.interfaces.fault.output]
+vertex_data_fields=[slip]
+writer.filename = tet4-fault.vtk
+
+[pylithapp.timedependent.materials.elastic.output]
+cell_filter = pylith.meshio.CellFilterAvgMesh
+writer.filename = tet4-statevars.vtk
Added: short/3D/PyLith/trunk/tests/refinefaulttip/tet4.mesh
===================================================================
--- short/3D/PyLith/trunk/tests/refinefaulttip/tet4.mesh (rev 0)
+++ short/3D/PyLith/trunk/tests/refinefaulttip/tet4.mesh 2011-06-14 03:39:07 UTC (rev 18614)
@@ -0,0 +1,90 @@
+// Original mesh
+//
+// Bottom
+// 3
+// / | \
+// / | \
+// / 1 | 3 \
+// 0 ----- 2 ----- 4
+// \ 0 | 2 /
+// \ | /
+// \ | /
+// 1
+//
+// Top
+//
+//
+//
+// 5 7
+// 5 ----- 6 ----- 7
+// 4 6
+//
+//
+//
+//
+mesh = {
+ dimension = 3
+ use-index-zero = true
+ vertices = {
+ dimension = 3
+ count = 8
+ coordinates = {
+ 0 -1.0 0.0 0.0
+ 1 0.0 -1.0 0.0
+ 2 0.0 0.0 0.0
+ 3 0.0 1.0 0.0
+ 4 1.0 0.0 0.0
+ 5 -1.0 0.0 1.0
+ 6 0.0 0.0 1.0
+ 7 1.0 0.0 1.0
+ }
+ }
+ cells = {
+ count = 8
+ num-corners = 4
+ simplices = {
+ 0 0 1 2 6
+ 1 0 2 3 6
+ 2 1 4 2 6
+ 3 3 2 4 6
+ 4 0 1 6 5
+ 5 0 6 3 5
+ 6 1 4 6 7
+ 7 3 6 4 7
+ }
+ material-ids = {
+ 0 0
+ 1 0
+ 2 0
+ 3 0
+ 4 0
+ 5 0
+ 6 0
+ 7 0
+ }
+ }
+ group = {
+ name = fault
+ type = vertices
+ count = 3
+ indices = {
+ 2 3 6
+ }
+ }
+ group = {
+ name = xpos
+ type = vertices
+ count = 2
+ indices = {
+ 4 7
+ }
+ }
+ group = {
+ name = xneg
+ type = vertices
+ count = 2
+ indices = {
+ 0 5
+ }
+ }
+}
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