Minor bug fixes

.gitignore

@@ -2,12 +2,10 @@ build/*.o
 build/libibpm.a
 build/checkgeom
 build/ibpm
-examples/*.cmd
-examples/*.force
-examples/*.bin
-examples/*.plt
-examples/*.cholesky
-TAGS
+examples/oseen_out
+examples/pitching_out
+examples/plunging_out
+plunging_outTAGS
 test/*.o
 test/runner
 test/runner.err
@@ -30,3 +28,4 @@ doc/examples/*.out
 doc/snippets/*.out
 callgrind.out.*
 .depend
+*.exe   

examples/Oseen.cc

@@ -50,7 +50,7 @@ const double alpha = 1.256431208626170;
 
 int main(int argc, char* argv[]) {
 	cout << "Test of Oseen vortex\n";
-	
+
 	// Setup grid
 	int nx = 100;
 	int ny = 100;
@@ -59,20 +59,19 @@ int main(int argc, char* argv[]) {
     double xOffset = -5;
     double yOffset = -5;
 	Grid grid( nx, ny, ngrid, length, xOffset, yOffset );
-	
+
 	// Empty geometry -- no body
 	Geometry geom;
     int numPoints = 0;
 
 	// Setup equations to solve
 	double Reynolds=100;
     // No background flow
-    Flux q0( grid );
-    q0 = 0;
+    BaseFlow q0( grid );
 
 	NavierStokesModel model( grid, geom, Reynolds, q0 );
     model.init();
-    
+
 	// Setup timestepper
 	double dt = 0.05;
     NonlinearIBSolver solver( grid, model, dt, Scheme::EULER );
@@ -87,22 +86,22 @@ int main(int argc, char* argv[]) {
 
     // Create output directory, if does not already exist
     mkdir( "oseen_out", S_IRWXU | S_IRWXG | S_IRWXO );
-    
+
     // Setup output routines
     OutputTecplot outputComputed( "oseen_out/ibpm%03d.plt",
-        "Oseen vortex, numerical, step %03d" );
+                                  "Oseen vortex, numerical, step %03d" );
     OutputTecplot outputExact( "oseen_out/exact%03d.plt",
-        "Oseen vortex, exact, step %03d");
+                               "Oseen vortex, exact, step %03d" );
     OutputTecplot outputError( "oseen_out/error%03d.plt",
-        "Oseen vortex, error, step %03d");
-    
+                               "Oseen vortex, error, step %03d" );
+
     // Output initial condition
     outputComputed.doOutput( x );
     outputExact.doOutput( exact );
     outputError.doOutput( error );
 
-	// Step
-	int numSteps = 200;
+    // Step
+    int numSteps = 200;
     int iskip = 20;
 	for(int i=1; i <= numSteps; ++i) {
 		cout << "step " << i << endl;
@@ -183,7 +182,7 @@ void initializeOseenVortex(
     double Reynolds,
     State& x
     ) {
-    
+
     double t0 = Reynolds / (4 * alpha);
-    computeExactSolution( Reynolds, t0, 0, x );    
+    computeExactSolution( Reynolds, t0, 0, x );
 }

examples/pitching.cc

@@ -11,6 +11,7 @@
 
 #include <iostream>
 #include <iomanip>
+#include <sys/stat.h>
 #include "ibpm.h"
 
 using namespace std;
@@ -22,36 +23,35 @@ int main(int argc, char* argv[]) {
     // lift and drag
     double lift = 0.;
     double drag = 0.;
-    
+
     // Setup grid
     int nx = 100;
     int ny = 100;
     int ngrid = 1;
-    double length = 4.0;
+    double length = 4;
     double xOffset = -1;
     double yOffset = -2;
     Grid grid( nx, ny, ngrid, length, xOffset, yOffset );
-
-
+
     // Make a flat plate, length 1, with center at 1/4 chord
     RigidBody plate;
     plate.addLine( 0, 0, 1, 0, grid.Dx() );
     plate.setCenter( 0.25, 0 );
-    
+
     // Set the motion to pitching, amplitude = 0.25, period 10 time units
     double amplitude = 0.25;
     double freq = 0.1;
     PitchPlunge motion( amplitude, freq, 0, 0 );
     plate.setMotion( motion );
     Geometry geom;
     geom.addBody( plate );
-    geom.moveBodies(0);
+    geom.moveBodies( 0 );
 
     // Setup equations to solve
-    double Reynolds=100;
+    double Reynolds = 100;
     double magnitude = 1;
     double alpha = 0;  // angle of background flow
-    Flux q_potential = Flux::UniformFlow( grid, magnitude, alpha );
+    BaseFlow q_potential( grid, magnitude, alpha );
     cout << "Setting up Navier Stokes model..." << flush;
     NavierStokesModel model( grid, geom, Reynolds, q_potential );
     model.init();
@@ -65,17 +65,22 @@ int main(int argc, char* argv[]) {
     // Build the state variable, zero initial conditions
     State x(grid, geom.getNumPoints());
     x.omega = 0.;
+    x.f = 0.;
+    x.q = 0.;
+
+    // Create output directory, if does not already exist
+    mkdir( "pitching_out", S_IRWXU | S_IRWXG | S_IRWXO );
 
     // Setup output routines
-    OutputForce force( "tecplot/force.dat" );
-    OutputTecplot tecplot( "tecplot/pitch%03d.plt", "Pitching plate, step %03d" );
+    OutputForce force( "pitching_out/force.dat" );
+    OutputTecplot tecplot( "pitching_out/pitch%03d.plt", "Pitching plate, step %03d" );
     Logger logger;
     // Output Tecplot file every few timesteps
     logger.addOutput( &tecplot, 25 );
-    logger.addOutput( &force, 1 ); 
+    logger.addOutput( &force, 1 );
     logger.init();
     logger.doOutput( x );
-    
+
     // Step
     const double PI = 4. * atan(1.);
     int numSteps = 250;
@@ -85,7 +90,7 @@ int main(int argc, char* argv[]) {
             << "  time = " << setw(5) << x.time
             << "  theta = " << theta << endl;
         solver.advance( x );
-        x.computeNetForce( drag, lift);
+        x.computeNetForce( drag, lift );
         cout << " x force : " << setw(16) << drag*2 << " , y force : "
             << setw(16) << lift*2 << "\n";
         logger.doOutput( x );

examples/plunging.cc

@@ -12,6 +12,7 @@
 #include <iostream>
 #include <iomanip>
 #include <fstream>
+#include <sys/stat.h>
 #include <string>
 #include "ibpm.h"
 
@@ -24,60 +25,64 @@ int main(int argc, char* argv[]) {
     // lift and drag
     double lift = 0.;
     double drag = 0.;
-    
+
     // Setup grid
-    int nx = 200;
-    int ny = 200;
+    int nx = 100;
+    int ny = 100;
     int ngrid = 1;
-    double length = 4.0;
+    double length = 4;
     double xOffset = -1;
     double yOffset = -2;
     Grid grid( nx, ny, ngrid, length, xOffset, yOffset );
-
-
+
     // Make a flat plate, length 1, with center at 1/4 chord
     RigidBody plate;
     plate.addLine( 0, 0, 1, 0, grid.Dx() );
     plate.setCenter( 0.25, 0 );
-    
-    // Set the motion to plunging: amplitude = 0.1, period 0.25 time unit
-    double amplitude = 0.1;
-    double freq = 0.25;
+
+    // Set the motion to plunging: amplitude = 0.25, period 10 time units
+    double amplitude = 0.25;
+    double freq = 0.1;
     PitchPlunge motion( 0, 0, amplitude, freq );
     plate.setMotion( motion );
     Geometry geom;
     geom.addBody( plate );
-    geom.moveBodies(0);
+    geom.moveBodies( 0 );
 
     // Setup equations to solve
-    double Reynolds=100;
+    double Reynolds = 100;
     double magnitude = 1;
     double alpha = 0;  // angle of background flow
-    Flux q_potential = Flux::UniformFlow( grid, magnitude, alpha );
+    BaseFlow q_potential( grid, magnitude, alpha );
     cout << "Setting up Navier Stokes model..." << flush;
     NavierStokesModel model( grid, geom, Reynolds, q_potential );
     model.init();
     cout << "done" << endl;
 
     // Setup timestepper
-    double dt = 0.001;
+    double dt = 0.005;
     NonlinearIBSolver solver( grid, model, dt, Scheme::AB2 );
     solver.init();
 
     // Build the state variable, zero initial conditions
     State x(grid, geom.getNumPoints());
     x.omega = 0.;
+    x.f = 0.;
+    x.q = 0;
+
+    // Create output directory, if does not already exist
+    mkdir( "plunging_out", S_IRWXU | S_IRWXG | S_IRWXO );
 
     // Setup output routines
-    OutputTecplot tecplot( "tecplot/plunge%03d.plt", "Plunging plate, step %03d" );
-    OutputForce force( "tecplot/force.dat" );
+    OutputTecplot tecplot( "plunging_out/plunge%03d.plt", "Plunging plate, step %03d" );
+    OutputForce force( "plunging_out/force.dat" );
     Logger logger;
     // Output Tecplot file every few timesteps
-    logger.addOutput( &tecplot, 10 );
-    logger.addOutput( &force, 1 ); 
+    logger.addOutput( &tecplot, 25 );
+    logger.addOutput( &force, 1 );
     logger.init();
     logger.doOutput( x );
-    
+
     // Step
     const double PI = 4. * atan(1.);
     int numSteps = 250;

src/OutputTecplot.cc

@@ -26,37 +26,43 @@ using namespace std;
 
 namespace ibpm {
 
+OutputTecplot::OutputTecplot( string filename, string title ) {
+    _filename = filename;
+    _title = title;
+    _TecplotAllGrids = false;
+}
+
 OutputTecplot::OutputTecplot( string filename, string title, bool TecplotAllGrids ) {
     _filename = filename;
     _title = title;
     _TecplotAllGrids = TecplotAllGrids;
 }
-    
+
 bool OutputTecplot::doOutput(const State& state) {
     // Add timestep to filename and title
     char filename[256];
     sprintf( filename, _filename.c_str(), state.timestep );
     char title[256];
     sprintf( title, _title.c_str(), state.timestep );
-    bool status = false;    
-    const Grid& grid = state.omega.getGrid();	
-		
+    bool status = false;
+    const Grid& grid = state.omega.getGrid();
+
     // Calculate velocities
     Scalar u( state.omega.getGrid() );
     Scalar v( state.omega.getGrid() );
     FluxToVelocity( state.q, u, v );
-    
+
     // Create vector of Scalar fields
     vector<const Scalar*> varVec;
     varVec.push_back( &u );
     varVec.push_back( &v);
     varVec.push_back( &state.omega );
-    
+
     vector<string> varNameVec;
     varNameVec.push_back( "u" );
     varNameVec.push_back( "v" );
     varNameVec.push_back( "Vorticity" );
-        
+
     // Write the tecplot file
     if(_TecplotAllGrids) {
         status = true;
@@ -69,19 +75,19 @@ bool OutputTecplot::doOutput(const State& state) {
     else status = ScalarToTecplot( varVec, varNameVec, filename, title );
     return status;
 }
-    
+
 bool OutputTecplot::doOutput(const BaseFlow& q, const State& x) {
-    // Currently no use for baseflow, but this method is defined for future 
+    // Currently no use for baseflow, but this method is defined for future
     // flexibility
     return doOutput(x);
 }
-    
+
 void OutputTecplot::setFilename( string filename ) {
     _filename = filename;
 }
-    
+
 void OutputTecplot::setTitle( string title ) {
     _title = title;
 }
-    
+
 } // namespace ibpm

src/OutputTecplot.h

@@ -9,7 +9,7 @@
 using std::string;
 
 namespace ibpm {
-    
+
 /*!
 \file OutputTecplot.h
 \class OutputTecplot
@@ -24,26 +24,32 @@ namespace ibpm {
 \version $Revision$
 */
 
-   
+
 class OutputTecplot : public Output {
 public:
     /// \brief Constructor
     /// \param[in] filename Filename in the standard printf format (e.g. "file%06d.plt"), where timestep will be supplied
     /// \param[in] title Title in the standard printf format
+    OutputTecplot( string filename, string title );
+
+    /// \brief Constructor
+    /// \param[in] filename Filename in the standard printf format (e.g. "file%06d.plt"), where timestep will be supplied
+    /// \param[in] title Title in the standard printf format
+    /// \param[in] TecplotAllGrids bool describing whether or not to save Tecplot data for all grid levels
     OutputTecplot( string filename, string title, bool TecplotAllGrids );
-    
+
     /// \brief Write the Tecplot file
     bool doOutput(const State& x);
-    
+
     /// \brief Write the Tecplot file
     bool doOutput(const BaseFlow& q, const State& x);
-    
+
     /// \brief Change the filename for the output file
     void setFilename( string filename );
-    
+
     /// \brief Change the title for the output file
     void setTitle( string title );
-    
+
 private:
     string _filename;
     string _title;