Merge branch 'baagaard/increment-version-2.1.3'

* baagaard/increment-version-2.1.3:
  Increment to version 2.1.3.
  Remove duplicate call to function.

Author: baagaard-usgs

CHANGES

@@ -9,6 +9,23 @@ MIGRATING FROM VERSION 2.0 TO 2.1
 The points file for OutputSolnPoints must now contain station names as
 the first column.
 
+----------------------------------------------------------------------
+Version 2.1.3
+----------------------------------------------------------------------
+
+* Add generate_statedb.py and postseismic.pvsm files missing from
+  examples/2d/gravity.
+
+* Update handling of fault intersection when creating boundary
+  condition nodesets in examples/meshing/surface_nurbs/subduction.
+
+* Fixes to Darwin binary package.
+
+  + Fix linking of netCDF4 Python module.
+
+  + Fix linking and executable mode permissions for Python scripts in
+    binary by using nemesis so relative links are valid.
+
 ----------------------------------------------------------------------
 Version 2.1.2
 ----------------------------------------------------------------------

configure.ac

@@ -17,7 +17,7 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ(2.59)
-AC_INIT([PyLith], [2.1.2], [[email protected]])
+AC_INIT([PyLith], [2.1.3], [[email protected]])
 AC_CONFIG_AUX_DIR([./aux-config])
 AC_CONFIG_HEADER([portinfo])
 AC_CONFIG_MACRO_DIR([m4])

doc/releasenotes/announce_v2.1.3.txt

@@ -0,0 +1,89 @@
+Greetings,
+
+I am pleased to announce the release of PyLith 2.1.3, a finite-element
+code designed to solve dynamic elastic problems and quasi-static
+viscoelastic problems in tectonic deformation.
+
+This release provides a few new minor features and bugfixes.
+
+You can download the source code and binaries from
+
+    http://geodynamics.org/cig/software/pylith
+
+Detailed installation instructions for the binary packages are in the
+User Manual with detailed building instructions for a few platforms in
+the INSTALL file bundled with the PyLith Installer utility.
+
+
+======================================================================
+MIGRATING FROM VERSION 2.0 TO 2.1
+======================================================================
+
+The points file for OutputSolnPoints must now contain station names as
+the first column.
+
+======================================================================
+RELEASE NOTES
+======================================================================
+
+----------------------------------------------------------------------
+Version 2.1.3
+----------------------------------------------------------------------
+
+* Add generate_statedb.py and postseismic.pvsm files missing from
+  examples/2d/gravity.
+
+* Update handling of fault intersection when creating boundary
+  condition nodesets in examples/meshing/surface_nurbs/subduction.
+
+* Fixes to Darwin binary package.
+
+  + Fix linking of netCDF4 Python module.
+
+  + Fix linking and executable mode permissions for Python scripts in
+    binary by using nemesis so relative links are valid.
+
+----------------------------------------------------------------------
+Version 2.1.2
+----------------------------------------------------------------------
+
+* Bugfixes for finite-strain formulation.
+
+  + Added output of the Cauchy stresses (cauchy_stress). The second
+    Pioloa-Kirchoff stresses are output via the stress field.
+
+  + Material properties and state variables were not retrieved
+    properly when updating state variables.
+
+* Bugfixes for setting initial stress and state variables for
+  viscoelastic materials. The deviatoric stress state is carried
+  forward using the state variables, so the initial deviatoric stress
+  should not be considered when computing the stresses.
+
+* Created new examples showing how to use gravity, initial stress, and
+  finite-strain in 2-D (examples/2d/gravity).
+
+* Reintroduced check (that had been inadvertently removed in v2.x) for
+  ambiguous description of fault surface based on groups of vertices
+  defining faces of cells.
+
+* Flush the output of the progress monitor so progress reports are
+  updated promptly.
+
+* Updates to the user manual.
+
+  + Added section on the debugging examples covered in recent
+    tutorials.
+
+  + Added tables describing the spatial database values for each
+    material.
+
+  + Included a more complete discussion of the finite-strain
+    formulation.
+
+* PETSc
+
+  + Updated to PETSc v3.7.1 (knepley/pylith branch).
+
+  + Fixed Trilinos/ML configuration and code so that it can be built
+    without a Fortran compiler.

doc/userguide/install/install.lyx

@@ -249,7 +249,7 @@ Unpack the tarball.
 
 \begin_deeper
 \begin_layout LyX-Code
-$ tar -xzf pylith-2.1.2-linux-i686.tgz
+$ tar -xzf pylith-2.1.3-linux-i686.tgz
 \end_layout
 
 \end_deeper
@@ -323,7 +323,7 @@ Unpack the tarball.
 
 \begin_deeper
 \begin_layout LyX-Code
-$ tar -xzf pylith-2.1.2-darwin-10.10.5.tgz
+$ tar -xzf pylith-2.1.3-darwin-10.10.5.tgz
 \end_layout
 
 \end_deeper
@@ -446,11 +446,11 @@ The easiest way to verify that PyLith has been installed correctly is to
  run one or more of the examples supplied with the binary and source code.
  In the binary distribution, the examples are located in 
 \family typewriter
-src/pylith-2.1.2/examples
+src/pylith-2.1.3/examples
 \family default
  while in the source distribution, they are located in 
 \family typewriter
-pylith-2.1.2/examples
+pylith-2.1.3/examples
 \family default
 .
  Chapter 

doc/userguide/intro/intro.lyx

@@ -83,7 +83,7 @@ PyLith is a multi-scale simulation software package for earthquake physics.
 \end_layout
 
 \begin_layout Section
-New in PyLith Version 2.1.2
+New in PyLith Version 2.1.3
 \end_layout
 
 \begin_layout Itemize

doc/userguide/preface.lyx

@@ -146,14 +146,14 @@ To cite this manual, use:
 \begin_layout Itemize
 Aagaard, B., M. Knepley, C. Williams (2016), 
 \emph on
-PyLith User Manual, Version 2.1.2.
+PyLith User Manual, Version 2.1.3.
 
 \emph default
  Davis, CA: Computational Infrastructure of Geodynamics.
 \begin_inset Newline newline
 \end_inset
 
-URL: geodynamics.org/cig/software/pylith/pylith_manual-2.1.2.pdf
+URL: geodynamics.org/cig/software/pylith/pylith_manual-2.1.3.pdf
 \end_layout
 
 \begin_layout Section

doc/userguide/userguide.lyx

@@ -136,7 +136,7 @@ PyLith User Manual
 \begin_inset Newline newline
 \end_inset
 
-Version 2.1.2
+Version 2.1.3
 \end_layout
 
 \begin_layout Date

libsrc/pylith/feassemble/ElasticityImplicitLgDeform.cc

@@ -352,8 +352,6 @@ pylith::feassemble::ElasticityImplicitLgDeform::integrateJacobian(topology::Jaco
   scalar_array coordsCell(numBasis*spaceDim); // :KLUDGE: numBasis to numCorners after switching to higher order
   topology::CoordsVisitor coordsVisitor(dmMesh);
 
-  _material->createPropsAndVarsVisitors();
-
   // Get sparse matrix
   const PetscMat jacobianMat = jacobian->matrix();assert(jacobianMat);
   topology::MatVisitorMesh jacobianVisitor(jacobianMat, fields->get("disp(t)"));