Merge pull request #147 from mesnardo/bugfix-probe

Bugfix (ProbeVolume): Output IS (with natural ordering) to re-arrange sub-data (post-processing)

CHANGELOG.md

@@ -2,6 +2,22 @@
 
 ---
 
+## 0.5.1
+
+---
+
+### Added
+
+### Changed
+
+### Fixed
+
+* `ProbeVolume`: write a PETSc Index Set to the output file (HDF5 or ASCII) for the volume probe. The index set contains the natural index of the points located inside the volume being monitored. During post-processing stage, the index set can be used to re-arrange field values of the sub-volume and visualize the solution. Without this index set, the PETSc vector for the sub-volume (obtained with the PETSc routine `VecGetSubVector`) did not output the values in the natural ordering of the vector. `VecGetSubVector` simply concatenates the values in the parallel ordering of the vector. This problem only affected simulations running with multiple MPI processes where the window being monitored span over multiple process domains.
+
+### Removed
+
+---
+
 ## 0.5.0
 
 ---

configure

@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for PetIBM 0.5.
+# Generated by GNU Autoconf 2.69 for PetIBM 0.5.1.
 #
 # Report bugs to <mesnardo@gwu.edu, pychuang@gwu.edu>.
 #
@@ -590,8 +590,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='PetIBM'
 PACKAGE_TARNAME='petibm'
-PACKAGE_VERSION='0.5'
-PACKAGE_STRING='PetIBM 0.5'
+PACKAGE_VERSION='0.5.1'
+PACKAGE_STRING='PetIBM 0.5.1'
 PACKAGE_BUGREPORT='mesnardo@gwu.edu, pychuang@gwu.edu'
 PACKAGE_URL=''
 
@@ -1376,7 +1376,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures PetIBM 0.5 to adapt to many kinds of systems.
+\`configure' configures PetIBM 0.5.1 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1447,7 +1447,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of PetIBM 0.5:";;
+     short | recursive ) echo "Configuration of PetIBM 0.5.1:";;
    esac
   cat <<\_ACEOF
 
@@ -1589,7 +1589,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-PetIBM configure 0.5
+PetIBM configure 0.5.1
 generated by GNU Autoconf 2.69
 
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -2395,7 +2395,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by PetIBM $as_me 0.5, which was
+It was created by PetIBM $as_me 0.5.1, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   $ $0 $@
@@ -3262,7 +3262,7 @@ fi
 
 # Define the identity of the package.
  PACKAGE='petibm'
- VERSION='0.5'
+ VERSION='0.5.1'
 
 
 cat >>confdefs.h <<_ACEOF
@@ -20826,7 +20826,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by PetIBM $as_me 0.5, which was
+This file was extended by PetIBM $as_me 0.5.1, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -20892,7 +20892,7 @@ _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-PetIBM config.status 0.5
+PetIBM config.status 0.5.1
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"
 

configure.ac

@@ -4,7 +4,7 @@
 
 # set-up
 AC_PREREQ([2.69])
-AC_INIT([PetIBM], [0.5], [mesnardo@gwu.edu, pychuang@gwu.edu])
+AC_INIT([PetIBM], [0.5.1], [mesnardo@gwu.edu, pychuang@gwu.edu])
 AC_CONFIG_AUX_DIR([config])
 AC_CONFIG_MACRO_DIR([m4])
 AM_INIT_AUTOMAKE([foreign subdir-objects])

doc/Doxyfile

@@ -38,7 +38,7 @@ PROJECT_NAME           = PetIBM
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 0.5
+PROJECT_NUMBER         = 0.5.1
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a

include/petibm/probes.h

@@ -144,8 +144,11 @@ class ProbeVolume : public ProbeBase
     /** \brief Limits of the volume. */
     type::RealVec2D box;
 
-    /** \brief Index set for the grid points to monitor. */
-    IS is;
+    /** \brief Index set for the grid points to monitor (PETSc ordering). */
+    IS isPetsc;
+
+    /** \brief Index set for the grid points to monitor (Natural ordering). */
+    IS isNatural;
 
     /** \brief Sub-vector of the region to monitor. */
     Vec dvec;
@@ -182,8 +185,8 @@ class ProbeVolume : public ProbeBase
      * \param box [in] Box area to monitor
      * \return PetscErrorCode
      */
-    PetscErrorCode getSubMeshInfo(const type::Mesh &mesh,
-                                  const type::RealVec2D &box);
+    PetscErrorCode getInfo(const type::Mesh &mesh,
+                           const type::RealVec2D &box);
 
     /** \brief Create the index set for the points to monitor.
      *
@@ -197,28 +200,53 @@ class ProbeVolume : public ProbeBase
      * \param mesh [in] Cartesian mesh object
      * \return PetscErrorCode
      */
-    PetscErrorCode createSubMesh(const type::Mesh &mesh);
+    PetscErrorCode createGrid(const type::Mesh &mesh);
 
     /** \brief Write the sub mesh grid points into a file.
+     *
+     * Supported formats are HDF5 and ASCII.
      *
      * \param filePath [in] Path of the file to write in
      * \return PetscErrorCode
      */
-    PetscErrorCode writeSubMesh(const std::string &filePath);
+    PetscErrorCode writeGrid(const std::string &filePath);
 
     /** \brief Write the sub mesh into an ASCII file.
      *
      * \param filePath [in] Path of the file to write in
      * \return PetscErrorCode
      */
-    PetscErrorCode writeSubMeshASCII(const std::string &filePath);
+    PetscErrorCode writeGrid_ASCII(const std::string &filePath);
 
     /** \brief Write the sub mesh into a HDF5 file.
      *
      * \param filePath [in] Path of the file to write in
      * \return PetscErrorCode
      */
-    PetscErrorCode writeSubMeshHDF5(const std::string &filePath);
+    PetscErrorCode writeGrid_HDF5(const std::string &filePath);
+
+    /** \brief Write index set (natural ordering) into a file.
+     *
+     * Supported formats are HDF5 and ASCII.
+     *
+     * \param filePath [in] Path of the file to write in
+     * \return PetscErrorCode
+     */
+    PetscErrorCode writeIS(const std::string &filePath);
+
+    /** \brief Write index set (natural ordering) into a HDF5 file.
+     *
+     * \param filePath [in] Path of the file to write in
+     * \return PetscErrorCode
+     */
+    PetscErrorCode writeIS_HDF5(const std::string &filePath);
+
+    /** \brief Write index set (natural ordering) into a HDF5 file.
+     *
+     * \param filePath [in] Path of the file to write in
+     * \return PetscErrorCode
+     */
+    PetscErrorCode writeIS_ASCII(const std::string &filePath);
 
     /** \copydoc ProbeBase::monitorVec() */
     PetscErrorCode monitorVec(const DM &da,
@@ -242,15 +270,15 @@ class ProbeVolume : public ProbeBase
      * \param t [in] Time
      * \return PetscErrorCode
      */
-    PetscErrorCode writeVecASCII(const Vec &vec, const PetscReal &t);
+    PetscErrorCode writeVec_ASCII(const Vec &vec, const PetscReal &t);
 
     /** \brief Output a PETSc Vec object to a HDF5 file.
      *
      * \param vec [in] PETSc Vec object to output
      * \param t [in] Time
      * \return PetscErrorCode
      */
-    PetscErrorCode writeVecHDF5(const Vec &vec, const PetscReal &t);
+    PetscErrorCode writeVec_HDF5(const Vec &vec, const PetscReal &t);
 
 };  // ProbeVolume