Merge pull request #146 from mesnardo/fix-write-bodies

Fix output filenames of immersed bodies (and cleaning)

Author: mesnardo

CHANGELOG.md

@@ -2,6 +2,30 @@
 
 ---
 
+## Current development
+
+---
+
+### Added
+
+* Allow to configure PetIBM against PETSc 3.12.x.
+
+### Changed
+
+* Default directory to output files generated by PetIBM is now the `output` folder in the current working directory. (User has the possibility to change the path of the output directory with the command-line option `-output <path of the folder>`.)
+* Use PETSc-3.12.2 to test PetIBM with Travis CI.
+* Copy `examples` folder into installation directory upon `make install`.
+
+### Fixed
+
+* Fix name of the file used to output the body coordinates; bug only affected simulations dealing with multiple immersed bodies with prescribed kinematics.
+
+### Removed
+
+* Dockerfile files and Singularity recipes. These files are now version-controlled in a separate GitHub repository: [`petibm-recipes`](https://github.com/barbagroup/petibm-recipes).
+
+---
+
 ## 0.4.2
 
 ---

Makefile.am

@@ -10,13 +10,9 @@ SUBDIRS = \
 
 EXTRA_DIST = autogen.sh
 
-EXAMPLES_DIR=$(top_builddir)/examples
-
-copy-examples:
-	@if test $(EXAMPLES_DIR) != "$(top_srcdir)/examples" ; then \
-		echo "Copying examples folders into $(EXAMPLES_DIR)..." ; \
-		mkdir -p $(EXAMPLES_DIR) ; \
-		rsync -a $(top_srcdir)/examples/* $(EXAMPLES_DIR) ; \
+install-data-hook:
+	@if test "$(prefix)/examples" != "$(top_srcdir)/examples" ; then \
+		echo "Copying examples into $(prefix)..." ; \
+		rsync -a $(top_srcdir)/examples $(prefix) ; \
+		rm -rf $(prefix)/examples/api_examples ; \
 	fi ;
-
-.PHONY: copy-examples

Makefile.in

@@ -363,7 +363,6 @@ SUBDIRS = \
 	include
 
 EXTRA_DIST = autogen.sh
-EXAMPLES_DIR = $(top_builddir)/examples
 all: all-recursive
 
 .SUFFIXES:
@@ -777,7 +776,8 @@ info: info-recursive
 info-am:
 
 install-data-am:
-
+	@$(NORMAL_INSTALL)
+	$(MAKE) $(AM_MAKEFLAGS) install-data-hook
 install-dvi: install-dvi-recursive
 
 install-dvi-am:
@@ -824,7 +824,8 @@ ps-am:
 
 uninstall-am:
 
-.MAKE: $(am__recursive_targets) install-am install-strip
+.MAKE: $(am__recursive_targets) install-am install-data-am \
+	install-strip
 
 .PHONY: $(am__recursive_targets) CTAGS GTAGS TAGS all all-am \
 	am--refresh check check-am clean clean-cscope clean-generic \
@@ -834,27 +835,25 @@ uninstall-am:
 	distclean-hdr distclean-libtool distclean-tags distcleancheck \
 	distdir distuninstallcheck dvi dvi-am html html-am info \
 	info-am install install-am install-data install-data-am \
-	install-dvi install-dvi-am install-exec install-exec-am \
-	install-html install-html-am install-info install-info-am \
-	install-man install-pdf install-pdf-am install-ps \
-	install-ps-am install-strip installcheck installcheck-am \
-	installdirs installdirs-am maintainer-clean \
+	install-data-hook install-dvi install-dvi-am install-exec \
+	install-exec-am install-html install-html-am install-info \
+	install-info-am install-man install-pdf install-pdf-am \
+	install-ps install-ps-am install-strip installcheck \
+	installcheck-am installdirs installdirs-am maintainer-clean \
 	maintainer-clean-generic mostlyclean mostlyclean-generic \
 	mostlyclean-libtool pdf pdf-am ps ps-am tags tags-am uninstall \
 	uninstall-am
 
 .PRECIOUS: Makefile
 
 
-copy-examples:
-	@if test $(EXAMPLES_DIR) != "$(top_srcdir)/examples" ; then \
-		echo "Copying examples folders into $(EXAMPLES_DIR)..." ; \
-		mkdir -p $(EXAMPLES_DIR) ; \
-		rsync -a $(top_srcdir)/examples/* $(EXAMPLES_DIR) ; \
+install-data-hook:
+	@if test "$(prefix)/examples" != "$(top_srcdir)/examples" ; then \
+		echo "Copying examples into $(prefix)..." ; \
+		rsync -a $(top_srcdir)/examples $(prefix) ; \
+		rm -rf $(prefix)/examples/api_examples ; \
 	fi ;
 
-.PHONY: copy-examples
-
 # Tell versions [3.59,3.63) of GNU make to not export all variables.
 # Otherwise a system limit (for SysV at least) may be exceeded.
 .NOEXPORT:

applications/createxdmf/main.cpp

@@ -75,15 +75,15 @@ int main(int argc, char **argv)
     if (!isSet) step = setting["parameters"]["nsave"].as<PetscInt>();
 
     // u
-    ierr = writeSingleXDMF(setting["directory"].as<std::string>(), "u",
+    ierr = writeSingleXDMF(setting["output"].as<std::string>(), "u",
                            mesh->dim, mesh->n[0], bg, ed, step); CHKERRQ(ierr);
 
     // v
-    ierr = writeSingleXDMF(setting["directory"].as<std::string>(), "v",
+    ierr = writeSingleXDMF(setting["output"].as<std::string>(), "v",
                            mesh->dim, mesh->n[1], bg, ed, step); CHKERRQ(ierr);
 
     // p
-    ierr = writeSingleXDMF(setting["directory"].as<std::string>(), "p",
+    ierr = writeSingleXDMF(setting["output"].as<std::string>(), "p",
                            mesh->dim, mesh->n[3], bg, ed, step); CHKERRQ(ierr);
 
     // wz
@@ -92,28 +92,28 @@ int main(int argc, char **argv)
     wn[0] = mesh->n[4][0];
     wn[1] = mesh->n[4][1];
     wn[2] = mesh->n[3][2];
-    ierr = writeSingleXDMF(setting["directory"].as<std::string>(), "wz",
+    ierr = writeSingleXDMF(setting["output"].as<std::string>(), "wz",
                            mesh->dim, wn, bg, ed, step); CHKERRQ(ierr);
 
     if (mesh->dim == 3)
     {
         // w
-        ierr = writeSingleXDMF(setting["directory"].as<std::string>(), "w",
+        ierr = writeSingleXDMF(setting["output"].as<std::string>(), "w",
                                mesh->dim, mesh->n[2], bg, ed, step);
         CHKERRQ(ierr);
 
         // wx
         wn[0] = mesh->n[3][0];
         wn[1] = mesh->n[4][1];
         wn[2] = mesh->n[4][2];
-        ierr = writeSingleXDMF(setting["directory"].as<std::string>(), "wx",
+        ierr = writeSingleXDMF(setting["output"].as<std::string>(), "wx",
                                mesh->dim, wn, bg, ed, step); CHKERRQ(ierr);
 
         // wy
         wn[0] = mesh->n[4][0];
         wn[1] = mesh->n[3][1];
         wn[2] = mesh->n[4][2];
-        ierr = writeSingleXDMF(setting["directory"].as<std::string>(), "wy",
+        ierr = writeSingleXDMF(setting["output"].as<std::string>(), "wy",
                                mesh->dim, wn, bg, ed, step); CHKERRQ(ierr);
     }
 
@@ -150,7 +150,8 @@ PetscErrorCode writeSingleXDMF(const std::string &directory,
     ierr = PetscViewerASCIIPrintf(viewer,
                                   "<!DOCTYPE Xdmf SYSTEM \"Xdmf.dtd\" [\n");
     CHKERRQ(ierr);
-    ierr = PetscViewerASCIIPrintf(viewer, "\t<!ENTITY CaseDir \"%s\">\n", "./");
+    ierr = PetscViewerASCIIPrintf(
+        viewer, "\t<!ENTITY CaseDir \"%s\">\n", directory.c_str());
     CHKERRQ(ierr);
 
     // always use 3D XDMF format, so both Visit and Paraview works
@@ -247,7 +248,7 @@ PetscErrorCode writeSingleXDMF(const std::string &directory,
         CHKERRQ(ierr);
         ierr = PetscViewerASCIIPrintf(viewer,
                                       "\t\t\t\t\t"
-                                      "&CaseDir;/solution/%07d.h5:/%s\n",
+                                      "&CaseDir;/%07d.h5:/%s\n",
                                       t, name.c_str()); CHKERRQ(ierr);
         ierr = PetscViewerASCIIPrintf(viewer,
                                       "\t\t\t\t"

applications/decoupledibpm/decoupledibpm.cpp

@@ -85,7 +85,7 @@ PetscErrorCode DecoupledIBPMSolver::init(const MPI_Comm &world,
 
     // create an ASCII PetscViewer to output the body forces
     ierr = createPetscViewerASCII(
-        config["directory"].as<std::string>() +
+        config["output"].as<std::string>() +
         "/forces-" + std::to_string(ite) + ".txt",
         FILE_MODE_WRITE, forcesViewer); CHKERRQ(ierr);
 

applications/ibpm/ibpm.cpp

@@ -68,7 +68,7 @@ PetscErrorCode IBPMSolver::init(const MPI_Comm &world, const YAML::Node &node)
 
     // create an ASCII PetscViewer to output the body forces
     ierr = createPetscViewerASCII(
-        config["directory"].as<std::string>() +
+        config["output"].as<std::string>() +
         "/forces-" + std::to_string(ite) + ".txt",
         FILE_MODE_WRITE, forcesViewer); CHKERRQ(ierr);
 

applications/navierstokes/navierstokes.cpp

@@ -125,7 +125,7 @@ PetscErrorCode NavierStokesSolver::init(const MPI_Comm &world, const YAML::Node
     // create the Cartesian mesh
     ierr = petibm::mesh::createMesh(comm, config, mesh); CHKERRQ(ierr);
     // write the grid points into a HDF5 file
-    std::string filePath = config["directory"].as<std::string>() + "/grid.h5";
+    std::string filePath = config["output"].as<std::string>() + "/grid.h5";
     ierr = mesh->write(filePath); CHKERRQ(ierr);
 
     // create the data object for the boundary conditions
@@ -167,13 +167,18 @@ PetscErrorCode NavierStokesSolver::init(const MPI_Comm &world, const YAML::Node
     probes.resize(config["probes"].size());
     for (unsigned int i = 0; i < probes.size(); ++i)
     {
+         // Prepend relative path with output directory.
+        config["probes"][i]["path"] =
+            config["output"].as<std::string>() + "/" +
+            config["probes"][i]["path"].as<std::string>();
+        // Create the probe.
         ierr = petibm::misc::createProbe(mesh->comm, config["probes"][i],
                                          mesh, probes[i]); CHKERRQ(ierr);
     }
 
     // create an ASCII PetscViewer to output linear solvers info
     ierr = createPetscViewerASCII(
-        config["directory"].as<std::string>() +
+        config["output"].as<std::string>() +
         "/iterations-" + std::to_string(ite) + ".txt",
         FILE_MODE_WRITE, solversViewer); CHKERRQ(ierr);
 

applications/rigidkinematics/rigidkinematics.cpp

@@ -166,16 +166,16 @@ PetscErrorCode RigidKinematicsSolver::writeBodies()
     PetscFunctionBeginUser;
 
     std::string directory = config["output"].as<std::string>(".");
-    std::stringstream ss;
-    ss << std::setfill('0') << std::setw(7) << ite;
+    std::stringstream ss_ite;
+    ss_ite << std::setfill('0') << std::setw(7) << ite;
     std::string filepath;
     for (PetscInt i = 0; i < bodies->nBodies; ++i)
     {
         petibm::type::SingleBody &body = bodies->bodies[i];
-        filepath = directory + "/" + body->name + "_" + ss.str();
-        ss.str("");
-        ss << "." << body->dim << "D";
-        filepath = filepath + ss.str();
+        filepath = directory + "/" + body->name + "_" + ss_ite.str();
+        std::stringstream ss_suffix;
+        ss_suffix << "." << body->dim << "D";
+        filepath = filepath + ss_suffix.str();
         ierr = body->writeBody(filepath); CHKERRQ(ierr);
     }
 

applications/vorticity/main.cpp

@@ -101,7 +101,7 @@ int main(int argc, char **argv)
         {
             ierr = petibm::io::writeHDF5Vecs(
                 PETSC_COMM_SELF,
-                setting["directory"].as<std::string>() + "/grid.h5", wNames[i],
+                setting["output"].as<std::string>() + "/grid.h5", wNames[i],
                 {"x", "y", "z"}, wCoord[i], FILE_MODE_APPEND); CHKERRQ(ierr);
         }
     }

applications/writemesh/main.cpp

@@ -38,7 +38,7 @@ int main(int argc, char **argv)
     CHKERRQ(ierr);
 
     // write grid data into HDF5 file
-    std::string filePath = config["directory"].as<std::string>() + "/grid.h5";
+    std::string filePath = config["output"].as<std::string>() + "/grid.h5";
     char s[PETSC_MAX_PATH_LEN];
     PetscBool flag = PETSC_FALSE;
     ierr = PetscOptionsGetString(nullptr, nullptr, "-file", s, sizeof(s),