Merge pull request #856 from baagaard-usgs/fix-default-nondimensionalization

Improve nondimensionalization adding a displacement scale

Author: baagaard-usgs

configure.ac

@@ -114,7 +114,7 @@ AC_CHECK_HEADER([mpi.h], [], [AC_MSG_ERROR([header 'mpi.h' not found])])
 
 dnl PETSC
 AC_LANG(C)
-CIT_PATH_PETSC([3.23.5])
+CIT_PATH_PETSC([3.24.0])
 CIT_HEADER_PETSC
 CIT_CHECK_LIB_PETSC
 
@@ -205,6 +205,7 @@ AC_CONFIG_FILES([Makefile
 		libsrc/pylith/problems/Makefile
 		libsrc/pylith/topology/Makefile
 		libsrc/pylith/utils/Makefile
+		libsrc/pylith/scales/Makefile
         libsrc/pylith/testing/Makefile
 		modulesrc/Makefile
 		modulesrc/include/Makefile
@@ -216,6 +217,7 @@ AC_CONFIG_FILES([Makefile
 		modulesrc/meshio/Makefile
 		modulesrc/mpi/Makefile
 		modulesrc/problems/Makefile
+		modulesrc/scales/Makefile
 		modulesrc/topology/Makefile
 		modulesrc/utils/Makefile
 		tests/Makefile
@@ -233,6 +235,7 @@ AC_CONFIG_FILES([Makefile
 		tests/libtests/problems/Makefile
 		tests/libtests/problems/data/Makefile
 		tests/libtests/meshio/data/Makefile
+		tests/libtests/scales/Makefile
 		tests/libtests/topology/Makefile
 		tests/libtests/topology/data/Makefile
 		tests/libtests/testing/Makefile

developer/uncrustify.cfg

@@ -51,8 +51,8 @@ sp_endif_cmt = Add
 sp_after_new = Add
 sp_paren_brace = Add
 sp_fparen_brace = Add
-sp_before_tr_emb_cmt = Force
-sp_num_before_tr_emb_cmt = 1
+sp_before_tr_cmt = Force
+sp_num_before_tr_cmt = 1
 
 # Align
 align_left_shift = True
@@ -98,7 +98,7 @@ nl_if_leave_one_liners = True
 nl_after_brace_open = False
 nl_after_brace_close = False
 nl_after_brace_open_cmt = False
-nl_max = 2
+nl_max = 3
 nl_after_func_proto = 2
 nl_after_func_body = 3
 nl_after_func_body_class = 2

docs/Makefile.am

@@ -679,6 +679,7 @@ dist_noinst_DATA = \
 	user/problems/figs/hdf5layout.svg \
 	user/problems/figs/hdf5layout.tex \
 	user/problems/index.md \
+	user/problems/nondimensionalization.md \
 	user/problems/output.md \
 	user/problems/problems.md \
 	user/run-pylith/figs/cells2d.pdf \

docs/developer/implementation/figs/classdiagram_problem.tex

@@ -19,7 +19,7 @@
   \node (pyre-component) [abstract-class, anchor=west] at ($(pythia-component.east)+(2em,0)$) {\umlemptyclass{PyreComponent}};
 
   \node (python-problem) [abstract-class] at ($(petsc-component.south)-(0,4em)$) {\umlclass{Python Problem}{%
-      normalizer\\
+      scales\\
       materials\\
       bc\\
       interfaces\\
@@ -28,7 +28,7 @@
       observers
 }};
   \node (cxx-problem) [abstract-class, anchor=north] at ($(python-problem.north)+(12em,0)$) {\umlclass{C++ Problem}{%
-      normalizer\\
+      scales\\
       materials\\
       bc\\
       interfaces\\
@@ -53,8 +53,8 @@
 }};
 
 
-  \node (normalizer) [abstract-class, anchor=west] at ($(cxx-problem.east)+(12em,12em)$) {\umlemptyclass{spatialdata::units::Nondimensional}};
-  \node (material) [abstract-class] at ($(normalizer.south)-(0,1em)$) {\umlemptyclass{Material}};
+  \node (scales) [abstract-class, anchor=west] at ($(cxx-problem.east)+(12em,12em)$) {\umlemptyclass{pylith::scales::Scales}};
+  \node (material) [abstract-class] at ($(scales.south)-(0,1em)$) {\umlemptyclass{Material}};
   \node (bc) [abstract-class] at ($(material.south)-(0,1em)$) {\umlemptyclass{BoundaryCondition}};
   \node (interface) [abstract-class] at ($(bc.south)-(0,1em)$) {\umlemptyclass{FaultCohesive}};
   \node (gravity-field) [concrete-class] at ($(interface.south)-(0,1em)$) {\umlemptyclass{spatialdata::spatialdb::GravityField}};
@@ -76,7 +76,7 @@
   \draw[inherit] (cxx-problem) -- (pyre-component);
   \draw[inherit] (cxx-time-dependent) -- (cxx-problem);
 
-  \draw[aggregate] ($(cxx-problem.east)+(0,8ex)$) -- (normalizer.west);
+  \draw[aggregate] ($(cxx-problem.east)+(0,8ex)$) -- (scales.west);
   \draw[aggregate] ($(cxx-problem.east)+(0,5.5ex)$) -- (material.west);
   \draw[aggregate] ($(cxx-problem.east)+(0,3.0ex)$) -- (bc.west);
   \draw[aggregate] ($(cxx-problem.east)+(0,0.5ex)$) -- (interface.west);

docs/developer/testing/libtests.md

@@ -60,7 +60,7 @@ namespace pylith {
 class pylith::problems::TestPhysics : public CppUnit::TestFixture {
     CPPUNIT_TEST_SUITE(TestPhysics); // CppUnit macro used to define the `TestPhysics` test suite.
 
-    CPPUNIT_TEST(testSetNormalizer); // CppUnit macro to add test implemented by class method.
+    CPPUNIT_TEST(testSetScales); // CppUnit macro to add test implemented by class method.
     CPPUNIT_TEST(testSetAuxiliaryFieldDB);
     CPPUNIT_TEST(testSetAuxiliarySubfieldDiscretization);
     CPPUNIT_TEST(testObservers);
@@ -81,7 +81,7 @@ public:
 
     // Methods that implement tests. The naming convention is testMethodName.
     // All test methods must return void and not have any arguments.
-    void testSetNormalizer(void);
+    void testSetScales(void);
     void testSetAuxiliaryFieldDB(void);
     void testSetAuxiliarySubfieldDiscretization(void);
     void testObservers(void);
@@ -129,20 +129,20 @@ pylith::problems::TestPhysics::tearDown(void) {
 
 
 void
-pylith::problems::TestPhysics::testSetNormalizer(void) {
+pylith::problems::TestPhysics::testSetScales(void) {
     PYLITH_METHOD_BEGIN;
 
-    spatialdata::units::Nondimensional normalizer;
+    pylith::scales::Scales scales;
     const PylithReal lengthScale = 3.0;
-    normalizer.setLengthScale(lengthScale);
+    scales.setLengthScale(lengthScale);
 
     CPPUNIT_ASSERT(_physics);
-    _physics->setNormalizer(normalizer);
+    _physics->setScales(scales);
 
-    CPPUNIT_ASSERT_DOUBLES_EQUAL(lengthScale, _physics->_normalizer->getLengthScale(), 1.0e-6);
+    CPPUNIT_ASSERT_DOUBLES_EQUAL(lengthScale, _physics->_scales->getLengthScale(), 1.0e-6);
 
     PYLITH_METHOD_END;
-} // testSetNormalizer
+} // testSetScales
 
 
 void

docs/user/components/problems/GreensFns.md

@@ -25,9 +25,9 @@ Implements `Problem`.
 * `materials`: Materials in problem.
   - **current value**: 'homogeneous', from {default}
   - **configurable as**: homogeneous, materials
-* `normalizer`: Nondimensionalizer for problem.
+* `scales`: Nondimensionalizer for problem.
   - **current value**: 'nondimelasticquasistatic', from {default}
-  - **configurable as**: nondimelasticquasistatic, normalizer
+  - **configurable as**: nondimelasticquasistatic, scales
 * `petsc_defaults`: Flags controlling which default PETSc options to use.
   - **current value**: 'petscdefaults', from {default}
   - **configurable as**: petscdefaults, petsc_defaults

docs/user/components/problems/Problem.md

@@ -29,9 +29,9 @@ If the nonlinear (SNES) solver requires multiple iterations to converge for thes
 * `materials`: Materials in problem.
   - **current value**: 'homogeneous', from {default}
   - **configurable as**: homogeneous, materials
-* `normalizer`: Nondimensionalizer for problem.
+* `scales`: Nondimensionalizer for problem.
   - **current value**: 'nondimelasticquasistatic', from {default}
-  - **configurable as**: nondimelasticquasistatic, normalizer
+  - **configurable as**: nondimelasticquasistatic, scales
 * `petsc_defaults`: Flags controlling which default PETSc options to use.
   - **current value**: 'petscdefaults', from {default}
   - **configurable as**: petscdefaults, petsc_defaults

docs/user/components/problems/TimeDependent.md

@@ -28,9 +28,9 @@ Implements `Problem`.
 * `materials`: Materials in problem.
   - **current value**: 'homogeneous', from {default}
   - **configurable as**: homogeneous, materials
-* `normalizer`: Nondimensionalizer for problem.
+* `scales`: Nondimensionalizer for problem.
   - **current value**: 'nondimelasticquasistatic', from {default}
-  - **configurable as**: nondimelasticquasistatic, normalizer
+  - **configurable as**: nondimelasticquasistatic, scales
 * `petsc_defaults`: Flags controlling which default PETSc options to use.
   - **current value**: 'petscdefaults', from {default}
   - **configurable as**: petscdefaults, petsc_defaults
@@ -89,8 +89,8 @@ ic = [domain]
 # Turn on gravitational body forces
 gravity_field = spatialdata.spatialdb.GravityField
 
-# Set the normalizer for nondimensionalizing the problem
-normalizer = spatialdata.units.NondimElasticQuasistatic
+# Set the scales for nondimensionalizing the problem
+scales = pylith.scales.NondimElasticQuasistatic
 
 # Set the subfields in the solution
 solution = = pylith.problems.SolnDispLagrange

docs/user/examples/box-2d/step05-sheardisptractrate.md

@@ -34,7 +34,7 @@ start_time = -1.0*year
 end_time = 5.0*year
 initial_dt = 1.0*year
 
-[pylithapp.problem.normalizer]
+[pylithapp.problem.scales]
 relaxation_time = 10.0*year
 ```
 

docs/user/examples/box-3d/step05-sheardisptractrate.md

@@ -34,7 +34,7 @@ initial_dt = 1.0*year
 start_time = -1.0*year
 end_time = 5.0*year
 
-[pylithapp.problem.normalizer]
+[pylithapp.problem.scales]
 relaxation_time = 10.0*year
 ```