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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 v3.7.2 (knepley/pylith branch).
Fixed Trilinos/ML configuration and code so that it can be built without a Fortran compiler.