Merge branch 'issue17-Unified_formatting_in_example_code'

.gitignore

@@ -7,7 +7,9 @@
 *.dvi
 *.log
 *.out
+*.png
 *.toc
+*.directory
 doc/MMSP.manual.pdf
 
 # MMSP utility binaries
@@ -26,6 +28,9 @@ utility/mmsp2topo
 utility/mmsp2z
 utility/wrongendian
 
+# unit testing
+test/unitTestSuite
+
 # Compiled Object files
 *.slo
 *.lo

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "test/gtest"]
+	path = test/gtest
+	url = https://github.com/google/googletest.git

.travis.yml

@@ -0,0 +1,27 @@
+# Mesoscale Microstructure Simulation Project
+# Travis Continuous Integration build script
+# Questions/comments to trevor.keller@gmail.com (Trevor Keller)
+
+language: cpp
+dist: trusty
+sudo: required
+
+compiler:
+  - gcc
+
+env:
+  - MPI=mpich2
+  - MPI=openmpi
+
+notifications:
+  email: false
+
+install:
+  - sudo apt-get update -qq -y
+  - sh test/travis-mpi.sh $MPI
+
+before_script:
+  - cd test
+
+script:
+  ./build_examples.sh --np 2 --noviz --clean

README.md

@@ -1,5 +1,6 @@
 Mesoscale Microstructure Simulation Project
 ====
+[![Build Status](https://travis-ci.org/mesoscale/mmsp.svg?branch=develop)](https://travis-ci.org/mesoscale/mmsp)
 
 The goal of the Mesoscale Microstructure Simulation Project (MMSP) is to provide a simple,
 consistent, and extensible programming interface for all grid and mesh based microstructure

algorithms/evolvers.cpp

@@ -14,30 +14,6 @@
 
 #include "evolvers.h"
 
-void print_progress(const int step, const int steps, const int iterations)
-{
-	 char* timestring;
-	static unsigned long tstart;
-	struct tm* timeinfo;
-
-	if (step==0) {
-		tstart = time(NULL);
-		std::time_t rawtime;
-		std::time( &rawtime );
-		timeinfo = std::localtime( &rawtime );
-		timestring = std::asctime(timeinfo);
-		timestring[std::strlen(timestring)-1] = '\0';
-		std::cout<<"Pass "<<std::setw(3)<<std::right<<iterations<<": "<<timestring<<" ["<<std::flush;
-	} else if (step==steps) {
-		unsigned long deltat = time(NULL)-tstart;
-		std::cout << "•] "
-							<<std::setw(2)<<std::right<<deltat/3600<<"h:"
-							<<std::setw(2)<<std::right<<(deltat%3600)/60<<"m:"
-							<<std::setw(2)<<std::right<<deltat%60<<"s"
-							<<" (File "<<std::setw(5)<<std::right<<iterations*steps<<")."<<std::endl;
-	} else if ((20 * step) % steps == 0) std::cout<<"• "<<std::flush;
-}
-
 template<int dim, typename T>
 void interface_field_evolves(const T& dt, const T& width, const T& gamma, const T& epsilon, const T& w, const T& mu,
 														 const MMSP::grid<dim,MMSP::sparse<T> >& former, MMSP::grid<dim,MMSP::sparse<T> >& latter, const int node)

algorithms/evolvers.h

@@ -2,8 +2,6 @@
 // Definitions of methods to evolve MMSP grids
 #ifndef _EVOLVERS_H_
 #define _EVOLVERS_H_
-void print_progress(const int step, const int steps, const int iterations);
-
 template<int dim, typename T>
 void interface_field_evolves(const T& dt, const T& width, const T& gamma, const T& epsilon, const T& w, const T& mu,
 														 const MMSP::grid<dim,MMSP::sparse<T> >& former, MMSP::grid<dim,MMSP::sparse<T> >& latter, const int node);

algorithms/generators.cpp

@@ -44,7 +44,7 @@ int seeds_to_buffer(const std::vector<MMSP::vector<int> >& vp, int* &q) {
   // q should already point to an array of T[size]
   if (q == NULL) {
     std::cerr << "\nError in seeds_to_buffer: send_buffer not initialized." << std::endl;
-    exit(1);
+    MMSP::Abort(-1);
   }
   int* p = q;
   for (unsigned int i=0; i<vp.size(); ++i) {
@@ -61,7 +61,7 @@ int seeds_to_buffer(const std::vector<MMSP::vector<int> >& vp, int* &q) {
 void seeds_from_buffer(std::vector<MMSP::vector<int> >& vp, int* &q, const int& size) {
   if (q == NULL) {
     std::cerr << "\nError in seeds_from_buffer: recv_buffer not initialized." << std::endl;
-    exit(1);
+    MMSP::Abort(-1);
   }
   MMSP::vector<int> v(3);
   for (int* p = q + 2; p < q + size; p += 3) {
@@ -90,8 +90,8 @@ void exact_voronoi(MMSP::grid<dim, MMSP::sparse<T> >& grid, const std::vector<st
   #ifdef DEBUG
   unsigned long tstart=time(NULL);
   #endif
-	if (id==0) print_progress(0,nodes(grid));
 	for (int n=0; n<nodes(grid); ++n) {
+		if (id==0) print_progress(n,nodes(grid));
 		const MMSP::vector<int> x=position(grid,n);
 		int min_distance=std::numeric_limits<int>::max();
 		int identity=-1, min_identity=identity;
@@ -115,7 +115,6 @@ void exact_voronoi(MMSP::grid<dim, MMSP::sparse<T> >& grid, const std::vector<st
 				}
 			}
 		}
-		if (id==0) print_progress(n+1,nodes(grid));
 		MMSP::set(grid(n), min_identity) = 1.;
 	}
 	#ifdef DEBUG
@@ -397,7 +396,7 @@ void approximate_voronoi(MMSP::grid<dim, MMSP::sparse<T> >& grid, const std::vec
   else
   {
     std::cerr << "Error: Invalid dimension (" << dim << ") in tessellation." << std::endl;
-    std::exit(1);
+    MMSP::Abort(-1);
   }
 	#ifdef DEBUG
 	#ifdef MPI_VERSION
@@ -513,13 +512,13 @@ void seeds_from_file(const int x0[dim], const int x1[dim], const int g0[dim], co
 	std::ifstream input(seedfilename);
 	if (!input) {
 		std::cerr<<"\nError: "<<seedfilename<<" does not exist.\n"<<std::endl;
-		std::exit(-1);
+		MMSP::Abort(-1);
 	}
 	int seed_dim;
 	input >> seed_dim;
 	if (dim!=seed_dim) {
 		std::cerr<<"\nError: "<<seedfilename<<" is "<<seed_dim<<"-dimensional.\n"<<std::endl;
-		std::exit(-1);
+		MMSP::Abort(-1);
 	}
   std::vector<MMSP::vector<int> > local_seeds; // blank for now
   seeds.clear();
@@ -532,7 +531,7 @@ void seeds_from_file(const int x0[dim], const int x1[dim], const int g0[dim], co
 			input >> s;
 			if (s>1.0001) {
 				std::cerr<<"\nError: Seeds in "<<seedfilename<<" need to be normalized (found s="<<s<<").\n"<<std::endl;
-				std::exit(-1);
+				MMSP::Abort(-1);
 			}
 			// Seeds in file should be normalized (unit line, square, or cube).
 			seed[d]=g0[d]+(g1[d]-g0[d]-1)*s;
@@ -570,7 +569,7 @@ void honeycomb_seeds(const int x0[dim], const int x1[dim], const int g0[dim], co
 		}
 	} else {
 		std::cerr<<"\nError: "<<dim<<"-dimensional honeycomb is not implemented yet.\n"<<std::endl;
-		std::exit(-1);
+		MMSP::Abort(-1);
 	}
 	seedswap(seeds);
 }
@@ -602,26 +601,4 @@ void tessellate(MMSP::grid<dim, MMSP::sparse<T> >& grid, const int& nseeds) {
 	#endif
 } // tessellate
 
-void print_progress(const int i, const int N) {
-  char* timestring;
-  static unsigned long tstart;
-  struct tm* timeinfo;
-
-  if (i==0) {
-    tstart = time(NULL);
-    std::time_t rawtime;
-    std::time( &rawtime );
-    timeinfo = std::localtime( &rawtime );
-    timestring = std::asctime(timeinfo);
-    timestring[std::strlen(timestring)-1] = '\0';
-    std::cout<<timestring<<" ["<<std::flush;
-  } else if (i==N) {
-    unsigned long deltat = time(NULL)-tstart;
-    std::cout<<"•] "<<std::setw(2)<<std::right<<deltat/3600<<"h:"
-                    <<std::setw(2)<<std::right<<(deltat%3600)/60<<"m:"
-                    <<std::setw(2)<<std::right<<deltat%60<<"s"
-                    <<'.'<<std::endl;
-  } else if ((20 * i) % N == 0) std::cout<<"• "<<std::flush;
-}
-
 #endif // _GENERATORS_

algorithms/generators.h

@@ -36,6 +36,4 @@ void seeds_from_file(const int x0[dim], const int x1[dim], const int g0[dim], co
 template<int dim>
 void honeycomb_seeds(const int x0[dim], const int x1[dim], const int g0[dim], const int g1[dim], const int a, std::vector<std::vector<MMSP::vector<int> > >& seeds);
 
-void print_progress(const int i, const int N);
-
 #endif // _GENERATORS_H_

algorithms/tessellate.hpp

@@ -16,8 +16,6 @@
 #include <cassert>
 #include "MersenneTwister.h"
 
-void print_progress(const int i, const int N);
-
 template <int dim, typename T> double radius(const MMSP::vector<T>& a, const MMSP::vector<T>& b) {
   double radius=0.0;
 	for (int d=0; d<dim; ++d) radius+=std::pow(double(b[d]-a[d]), 2.0);
@@ -604,25 +602,4 @@ void tessellate(MMSP::grid<dim, sparse<T> >& grid, const std::string& seed_filen
 
 } // namespace
 
-void print_progress(const int i, const int N) {
-  char* timestring;
-  static unsigned long tstart;
-  struct tm* timeinfo;
-
-  if (i==0) {
-    tstart = time(NULL);
-    std::time_t rawtime;
-    std::time( &rawtime );
-    timeinfo = std::localtime( &rawtime );
-    timestring = std::asctime(timeinfo);
-    timestring[std::strlen(timestring)-1] = '\0';
-    std::cout<<timestring<<" ["<<std::flush;
-  } else if (i==N-1) {
-    unsigned long deltat = time(NULL)-tstart;
-    std::cout<<"•] "<<std::setw(2)<<std::right<<deltat/3600<<"h:"
-                    <<std::setw(2)<<std::right<<(deltat%3600)/60<<"m:"
-                    <<std::setw(2)<<std::right<<deltat%60<<"s"
-                    <<'.'<<std::endl;
-  } else if ((20 * i) % N == 0) std::cout<<"• "<<std::flush;
-}
 #endif