git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13833 f3b2605a-c512-4ea7-a41b-209d697bcdaa

tools/smd/Makefile

@@ -0,0 +1,7 @@
+all:
+	clang++ -o dump2vtk_tris dump2vtk_tris.cpp -I/usr/include/vtk-5.8/ -lvtkCommon -lvtkIO -lvtkFiltering -lvtkRendering
+
+
+clean:
+	rm -f *.o
+	

tools/smd/dump2vtk_tris.cpp

@@ -0,0 +1,235 @@
+/*
+ * convert a LAMMPS / Smooth-Mach Dynamics triangle output file into a VTK unstructured grid file.
+ * LAMMPS output file contains STL triangle vertices
+ *
+ * ASSUMPTIONS:
+ *
+ * A compute exists for and STL triangulated surface, which computes the triangl vertices with a command like this:
+ * compute  F tri_group smd/triangle_vertices
+ * c_F[1-9] now hold the triangle vertices.
+ *
+ * LAMMPS dump file has the following entries per atom line:
+ * id type mol x y z c_F[1] c_F[2] c_F[3] c_F[4] c_F[5] c_F[6] c_F[7] c_F[8] c_F[9]
+ *
+ */
+
+#include <vtkVersion.h>
+#include <vtkSmartPointer.h>
+#include <vtkTriangle.h>
+#include <vtkCellArray.h>
+#include <vtkXMLUnstructuredGridReader.h>
+#include <vtkDataSetMapper.h>
+#include <vtkActor.h>
+#include <vtkRenderer.h>
+#include <vtkRenderWindow.h>
+#include <vtkRenderWindowInteractor.h>
+#include <vtkXMLUnstructuredGridWriter.h>
+#include <vtkUnstructuredGridWriter.h>
+#include <vtkUnstructuredGrid.h>
+#include <vtkPointData.h>
+
+#include <iostream>
+#include <fstream>
+#include <sstream>
+#include <vector>
+#include <algorithm>
+#include <iterator>
+
+using namespace std;
+
+#define RENDER 0 // switch on / off rendering of snapshots
+
+void WriteVTU(std::string filename, int ntime, vtkSmartPointer<vtkUnstructuredGrid> unstructuredGrid) {
+	vtkSmartPointer<vtkXMLUnstructuredGridWriter> writer = vtkSmartPointer<vtkXMLUnstructuredGridWriter>::New();
+	// create filename with the current timestep
+					std::ostringstream oss;
+					oss << ntime;
+					filename += "." + oss.str() + ".vtu";
+
+					writer->SetFileName(filename.c_str());
+	#if VTK_MAJOR_VERSION <= 5
+					writer->SetInput(unstructuredGrid);
+	#else
+					writer->SetInputData(unstructuredGrid);
+	#endif
+					writer->Write();
+}
+
+void WriteVTK(std::string filename, int ntime, vtkSmartPointer<vtkUnstructuredGrid> unstructuredGrid) {
+	vtkSmartPointer<vtkUnstructuredGridWriter> writer = vtkSmartPointer<vtkUnstructuredGridWriter>::New();
+	// create filename with the current timestep
+					std::ostringstream oss;
+					oss << ntime;
+					filename += "_" + oss.str() + ".vtk";
+
+					writer->SetFileName(filename.c_str());
+	#if VTK_MAJOR_VERSION <= 5
+					writer->SetInput(unstructuredGrid);
+	#else
+					writer->SetInputData(unstructuredGrid);
+	#endif
+					writer->Write();
+}
+
+int main(int argc, char *argv[]) {
+
+	string line;
+	vtkSmartPointer<vtkPoints> points;
+	vtkSmartPointer<vtkCellArray> vertices;
+	vtkSmartPointer<vtkCellArray> cellArray;
+	vtkIdType id_v1, id_v2, id_v3;
+	vtkSmartPointer<vtkTriangle> tri = vtkSmartPointer<vtkTriangle>::New(); // create an empty tri;
+	vtkSmartPointer<vtkUnstructuredGrid> unstructuredGrid;
+
+
+	unstructuredGrid = vtkSmartPointer<vtkUnstructuredGrid>::New();
+
+	// Parse command line arguments
+	if (argc != 3) {
+		std::cout << "Required arguments: InputFilename OutputFile_Basename"
+				<< std::endl;
+		return EXIT_FAILURE;
+	}
+
+	std::string lammps_dump = argv[1];
+	std::string filename = argv[2];
+
+	ifstream myfile(lammps_dump.c_str());
+
+	int nlines_read = 0;
+	int count = -1;
+	int ntime;
+	int N; // number of atoms in this timestep
+	int id, type, mol;
+	double x, y, z, v1x, v1y, v1z, v2x, v2y, v2z, v3x, v3y, v3z;
+	if (myfile.is_open()) {
+
+		while (getline(myfile, line)) {
+			std::size_t found = line.find("TIMESTEP");
+			if (found != std::string::npos) {
+				cout << line << endl;
+				count = 0;
+				nlines_read = 0;
+
+				// reinitialize VTK arrays so they are empty
+				points = vtkSmartPointer<vtkPoints>::New();
+				vertices = vtkSmartPointer<vtkCellArray>::New();
+				cellArray = vtkSmartPointer<vtkCellArray>::New();
+			}
+			if (count >= 0)
+				count++;
+
+			if (count == 2) {
+				istringstream convert(line);
+				convert >> ntime;
+				cout << "timestep is: " << ntime << endl;
+			}
+
+			if (count == 4) {
+				istringstream convert(line);
+				convert >> N;
+				cout << "number of particles is: " << N << endl;
+			}
+
+			if (count > 9) {
+				//cout << line << endl;
+				//const vector<string> words = split(line, " ");
+
+				std::istringstream is(line);
+				std::istream_iterator<float> eos;
+				std::vector<float> out(std::istream_iterator<float>(is), eos);
+
+				/*
+				 * we expect the following entries in a data line:
+				 * id type mol x y z v1x v1y v1z v2x v2y v2z v3x v3y v3z
+				 */
+
+				id = out[0];
+				type = out[1];
+				mol = out[2];
+				x = out[3];  // triangle center
+				y = out[4];
+				z = out[5];
+				v1x = out[6]; // triangle vertex 1
+				v1y = out[7];
+				v1z = out[8];
+				v2x = out[9]; // triangle vertex 2
+				v2y = out[10];
+				v2z = out[11];
+				v3x = out[12]; // triangle vertex 3
+				v3y = out[13];
+				v3z = out[14];
+
+				id_v1 = points->InsertNextPoint(v1x, v1y, v1z); // store tri vertices in points array and retain indices
+				id_v2 = points->InsertNextPoint(v2x, v2y, v2z);
+				id_v3 = points->InsertNextPoint(v3x, v3y, v3z);
+
+
+
+				tri->GetPointIds()->SetId(0, id_v1); // fill triangle with retained indices
+				tri->GetPointIds()->SetId(1, id_v2);
+				tri->GetPointIds()->SetId(2, id_v3);
+
+				cellArray->InsertNextCell(tri); // insert tri into array of cells
+
+				nlines_read += 1;
+
+			}
+
+			if (count % (9 + N) == 0) { // we have reached the end of this snapshot
+				printf(
+						"----------------------------------------------------\n");
+				printf("number of lines read from lammps dump file: %d\n",
+						nlines_read);
+
+
+				unstructuredGrid->SetPoints(points);
+				unstructuredGrid->SetCells(VTK_TRIANGLE, cellArray);
+
+				WriteVTK(filename, ntime, unstructuredGrid);
+
+
+//				if (ntime > 100) {
+//					return 0;
+//				}
+
+#if RENDER == 1
+				// Read and display file for verification that it was written correclty
+				vtkSmartPointer<vtkXMLUnstructuredGridReader> reader =
+						vtkSmartPointer<vtkXMLUnstructuredGridReader>::New();
+				reader->SetFileName(filename.c_str());
+				reader->Update();
+
+				vtkSmartPointer<vtkDataSetMapper> mapper = vtkSmartPointer<
+						vtkDataSetMapper>::New();
+				mapper->SetInputConnection(reader->GetOutputPort());
+
+				vtkSmartPointer<vtkActor> actor =
+						vtkSmartPointer<vtkActor>::New();
+				actor->SetMapper(mapper);
+
+				vtkSmartPointer<vtkRenderer> renderer = vtkSmartPointer<
+						vtkRenderer>::New();
+				vtkSmartPointer<vtkRenderWindow> renderWindow = vtkSmartPointer<
+						vtkRenderWindow>::New();
+				renderWindow->AddRenderer(renderer);
+				vtkSmartPointer<vtkRenderWindowInteractor> renderWindowInteractor =
+						vtkSmartPointer<vtkRenderWindowInteractor>::New();
+				renderWindowInteractor->SetRenderWindow(renderWindow);
+
+				renderer->AddActor(actor);
+				renderer->SetBackground(.3, .6, .3); // Background color green
+
+				renderWindow->Render();
+				renderWindowInteractor->Start();
+#endif
+			}
+
+		}
+		myfile.close();
+	} else {
+		cout << "Unable to open file";
+	}
+
+	return EXIT_SUCCESS;
+}