[cig-commits] r6012 - in short/3D/PyLith/trunk: . pylith pylith/feassemble

[brad at geodynamics.org]

Author: brad
Date: 2007-02-13 11:04:17 -0800 (Tue, 13 Feb 2007)
New Revision: 6012

Added:
   short/3D/PyLith/trunk/DEPENDENCIES
Modified:
   short/3D/PyLith/trunk/TODO
   short/3D/PyLith/trunk/pylith/PyLithApp.py
   short/3D/PyLith/trunk/pylith/feassemble/Integrator.py
Log:
Added bare bones initialization of PETSc using petsc4py (we do not yet get PETSc options from command line arguments). Fixed typo in documentation.

Added: short/3D/PyLith/trunk/DEPENDENCIES
===================================================================
--- short/3D/PyLith/trunk/DEPENDENCIES	2007-02-13 09:34:27 UTC (rev 6011)
+++ short/3D/PyLith/trunk/DEPENDENCIES	2007-02-13 19:04:17 UTC (rev 6012)
@@ -0,0 +1,14 @@
+REQUIRED DEPENDENCIES
+
+MPI
+PETSc
+petsc2py (http://cheeseshop.python.org/pypi/petsc4py)
+pythia
+spatialdata
+  proj
+numpy
+
+OPTIONAL DEPENDENCIES
+
+cppunit
+doxygen

Modified: short/3D/PyLith/trunk/TODO
===================================================================
--- short/3D/PyLith/trunk/TODO	2007-02-13 09:34:27 UTC (rev 6011)
+++ short/3D/PyLith/trunk/TODO	2007-02-13 19:04:17 UTC (rev 6012)
@@ -1,36 +1,40 @@
 MAIN PRIORITIES
 
-1. Implement unit tests for MeshIO at Python level.
-   a. write()/read()
-   b. checkVals()
+0. Add in PETSc initialize/finalize using petsc2py.
 
-  STATUS: 
+  STATUS:
 
-    Postponed. Easiest implementation requires semi-messy build
-    on top of libtests/meshio classes and initializing/finalizing
-    PETSc from Python. May be easier to include in higher-level unit
-    test.
+    Initial implementation. Still need to get PETSc options from
+    command line. See comment in PyLithApp.py.
 
-2. Finish implementing IntegratorInertia.
+1. Debug reading mesh via pylithic
+
+2. Bridge gap b/t Problem and Formulation (advance versus calcResidual)
+
+3. Finish implementing ExplicitElasticity
+   a. C++
    a. Python object
    b. bindings
-   c. unit tests at Python level
+   c. unit tests at C++ level
+   d. unit tests at Python level
 
-  Status: Implemented a & b.
+  Status: Started on a.
 
-3. Implement WFInertia object (manager for integrating inertia over ALL patches)
-   a. C++ object
-   b. unit tests at C++ level
+4.  Finish implementing Python Formulation
+    (e.g., Explicit) with initialization of solid element families.
    c. Python object
-   d. bindings
    e. unit tests at Python level
 
-4. Construct test case for integrating inertia term for a mesh
-   a. Mesh input file (ascii)
-   b. Python driver
+5. Implement unit tests for MeshIO at Python level.
+   a. write()/read()
+   b. checkVals()
 
-5. Specify material properties using spatial database
+  STATUS: 
 
+    Postponed. Easiest implementation requires semi-messy build
+    on top of libtests/meshio classes and initializing/finalizing
+    PETSc from Python. May be easier to include in higher-level unit
+    test.
 
 SECONDARY PRIORITIES
 
@@ -41,9 +45,14 @@
    c. bindings
    d. unit tests at Python level
 
-1. Implement MeshIOCubit
+2. Implement MeshIOCubit
    a. C++ objects
    b. unit tests at C++ level
    b. Python object (MeshIOCubit)
    c. bindings
    d. unit tests at Python level
+
+UNRESOLVED ISSUES
+
+1. Integration of nemesis (pylithic.py as mpi/python application)
+

Modified: short/3D/PyLith/trunk/pylith/PyLithApp.py
===================================================================
--- short/3D/PyLith/trunk/pylith/PyLithApp.py	2007-02-13 09:34:27 UTC (rev 6011)
+++ short/3D/PyLith/trunk/pylith/PyLithApp.py	2007-02-13 19:04:17 UTC (rev 6012)
@@ -63,6 +63,14 @@
     Run the application.
     """
 
+    import petsc4py
+    # :TODO: Add PETSc command line arguments using something like
+    # PetscUtil.py in 0.8. Some update may be necessary to be
+    # compatible with petsc4py. Brad doesn' like mixing different
+    # formats of command line arguments and he would like to require
+    # Pyre style formats.
+    petsc4py.init()
+
     #mesh = self.mesher.create()
     #self.problem.mesh = mesh.distribute()
     self.problem.run(self)

Modified: short/3D/PyLith/trunk/pylith/feassemble/Integrator.py
===================================================================
--- short/3D/PyLith/trunk/pylith/feassemble/Integrator.py	2007-02-13 09:34:27 UTC (rev 6011)
+++ short/3D/PyLith/trunk/pylith/feassemble/Integrator.py	2007-02-13 19:04:17 UTC (rev 6012)
@@ -39,7 +39,6 @@
     ##
     ## \b Facilities
     ## @li \b quadrature Quadrature object for integration
-    ## @li \b db Database for material properties.
 
     import pyre.inventory