Update documentation

src/IsingModel.cpp

@@ -10,7 +10,6 @@
  *  @bug No known bugs
  * */
 #include "IsingModel.hpp"
-#include <random>
 
 IsingModel::IsingModel()
 {
@@ -34,8 +33,7 @@ IsingModel::IsingModel(int L, double T, int val)
     this->L = L;
     this->T = T;
     this->initialize_engine();
-    this->lattice.set_size(this->L, this->L);
-    this->lattice.fill(val);
+    this->initialize_lattice(val);
     this->initialize_neighbors();
     this->initialize_energy_diff();
     this->initialize_magnetization();
@@ -58,6 +56,17 @@ void IsingModel::initialize_lattice()
         this->lattice(i) = 2 * coin_flip(this->engine) - 1;
 }
 
+void IsingModel::initialize_lattice(int val)
+{
+    // If val is neither 1 or -1, then initialize random values.
+    if (val != 1 && val != -1) {
+        this->initialize_lattice();
+        return;
+    }
+    this->lattice.set_size(this->L, this->L);
+    this->lattice.fill(val);
+}
+
 void IsingModel::initialize_neighbors()
 {
     this->neighbors.set_size(this->L, 2);
@@ -133,13 +142,3 @@ data_t IsingModel::Metropolis()
     return data_t((double)this->E, (double)(this->E * this->E), (double)this->M,
                   (double)(this->M * this->M), std::fabs((double)this->M));
 }
-
-int IsingModel::get_E()
-{
-    return this->E;
-}
-
-int IsingModel::get_M()
-{
-    return this->M;
-}

src/Makefile

@@ -1,66 +0,0 @@
-#CC=g++
-CC=mpic++
-
-LIBSRCS=utils.cpp testlib.cpp data_type.cpp
-LIBOBJS=$(LIBSRCS:.cpp=.o)
-LIBPROFOBJS=$(addprefix prof/, $(LIBOBJS))
-
-CLASSSRCS=IsingModel.cpp monte_carlo.cpp
-CLASSOBJS=$(CLASSSRCS:.cpp=.o)
-CLASSPROFOBJS=$(addprefix prof/, $(CLASSOBJS))
-
-INCLUDE=../include
-
-CFLAGS=-Wall -larmadillo -std=c++11 -O3 -fomit-frame-pointer
-#CFLAGS=-Wall -larmadillo -lblas -llapack -std=c++11 -O3 -fomit-frame-pointer
-OPENMP=-fopenmp
-
-# Add a debug flag when compiling (For the DEBUG macro in utils.hpp)
-DEBUG ?= 0
-ifeq ($(DEBUG), 1)
-	DBGFLAG=-DDBG -g
-else
-	DBGFLAG=
-endif
-
-# Add profiling for serial code
-PROFILE ?= 0
-ifeq ($(PROFILE), 1)
-	PROFFLAG=-pg -fno-inline-functions
-else
-	PROFFLAG=
-endif
-
-.PHONY: clean instrument
-
-all: main phase_transition_mpi test_suite  time
-#all: main 
-
-# Instrumentation using scorep for parallel analysis
-instrument: prof/phase_transition_mpi.o $(LIBPROFOBJS) $(CLASSPROFOBJS)
-	scorep $(CC) $(LIBPROFOBJS) $(CLASSPROFOBJS) $< -o phase_transition_mpi_prof $(CFLAGS) $(DBGFLAG) $(PROFFLAG) -I$(INCLUDE) $(OPENMP)
-	
-# Rules for executables
-main: main.o $(LIBOBJS) $(CLASSOBJS)
-	$(CC) $^ -o $@ $(CFLAGS) $(DBGFLAG) $(PROFFLAG) -I$(INCLUDE) $(OPENMP)
-
-phase_transition_mpi: phase_transition_mpi.o $(LIBOBJS) $(CLASSOBJS)
-	$(CC) $^ -o $@ $(CFLAGS) $(DBGFLAG) $(PROFFLAG) -I$(INCLUDE) $(OPENMP)
-
-test_suite: test_suite.o $(LIBOBJS) $(CLASSOBJS)
-	$(CC) $^ -o $@ $(CFLAGS) $(DBGFLAG) $(PROFFLAG) -I$(INCLUDE) $(OPENMP)
-
-time: time.o $(LIBOBJS) $(CLASSOBJS)
-	$(CC) $^ -o $@ $(CFLAGS) $(DBGFLAG) $(PROFFLAG) -I$(INCLUDE) $(OPENMP)
-
-# Rule for object files
-%.o: %.cpp
-	$(CC) -c $^ -o $@ $(CFLAGS) $(DBGFLAG) $(PROFFLAG) -I$(INCLUDE) $(OPENMP)
-
-# Rule for instrumented object files
-prof/%.o: %.cpp
-	scorep $(CC) -c $^ -o $@ $(CFLAGS) $(DBGFLAG) $(PROFFLAG) -I$(INCLUDE) $(OPENMP)
-
-clean:
-	find . -maxdepth 2 -name "*.o" -type f -delete
-	rm test_suite main phase_transition_mpi phase_transition_mpi_prof time

src/main.cpp

@@ -43,14 +43,17 @@ void create_pd_estimate_data()
                             "../output/pd_estimate/estimate_2_4.txt");
 }
 
+/** @brief Create data using the same parameters except one uses burn-in time,
+ *  while the other doesn't.
+ * */
 void test_burn_in_time()
 {
     montecarlo::phase_transition(
         100, 2.1, 2.4, 40, 1e5, montecarlo::mcmc_serial,
-        "../output/test_burn_in_time/no_burn_in.txt", 0);
+        "../output/test_burn_in_time/burn_in.txt", 5000);
     montecarlo::phase_transition(
         100, 2.1, 2.4, 40, 1e5, montecarlo::mcmc_serial,
-        "../output/test_burn_in_time/burn_in.txt", 5000);
+        "../output/test_burn_in_time/no_burn_in.txt", 0);
 }
 
 /** @brief Test how much Openmp speeds up.*/
@@ -103,6 +106,7 @@ void create_phase_transition_data()
     std::cout << "Time: " << t1 - t0 << std::endl;
 }
 
+/** @brief A function that displays how to use the program and quits.*/
 void usage(std::string filename)
 {
     std::cout << "Usage: " << filename << " OPTION ...\n"

src/mcmc_progression.cpp

@@ -18,6 +18,7 @@
 #include <omp.h>
 #include <string>
 
+/** @brief A function that displays how to use the program and quits.*/
 void usage(std::string filename)
 {
     std::cout << "Usage: " << filename
@@ -27,9 +28,7 @@ void usage(std::string filename)
     exit(-1);
 }
 
-/** @brief The main function
- *
- *  */
+/** @brief The main function.*/
 int main(int argc, char **argv)
 {
     // Command options

src/pd_estimate.cpp

@@ -18,6 +18,7 @@
 #include <omp.h>
 #include <string>
 
+/** @brief A function that displays how to use the program and quits.*/
 void usage(std::string filename)
 {
     std::cout << "Usage: " << filename

src/phase_transition.cpp

@@ -21,6 +21,7 @@
 #include <omp.h>
 #include <string>
 
+/** @brief A function that displays how to use the program and quits.*/
 void usage(std::string filename)
 {
     std::cout << "Usage: " << filename
@@ -30,9 +31,7 @@ void usage(std::string filename)
     exit(-1);
 }
 
-/** @brief The main function
- *
- *  */
+/** @brief The main function.*/
 int main(int argc, char **argv)
 {
     // Command options

src/phase_transition_mpi.cpp

@@ -21,6 +21,7 @@
 #include <mpi.h>
 #include <string>
 
+/** @brief A function that displays how to use the program and quits.*/
 void usage(std::string filename)
 {
     std::cout
@@ -33,9 +34,7 @@ void usage(std::string filename)
     exit(-1);
 }
 
-/** @brief The main function
- *
- *  */
+/** @brief The main function.*/
 int main(int argc, char **argv)
 {
     // Command options

src/test_suite.cpp

@@ -12,13 +12,21 @@
 #include "IsingModel.hpp"
 #include "testlib.hpp"
 
+/** @brief The analytic expected energy for a \f$ 2 \times 2 \f$ lattice.
+ * */
 #define EPS_2 (-2 * std::sinh(8.)) / (std::cosh(8.) + 3)
 
+/** @brief The analytic expected magnetization for a \f$ 2 \times 2 \f$
+ *  lattice.
+ * */
 #define MAG_2 (std::exp(8.) + 1) / (2 * (cosh(8.) + 3))
 
+/** @brief The analytic heat capacity for a \f$ 2 \times 2 \f$ lattice.
+ * */
 #define CV_2                                                                   \
     16 * (3 * std::cosh(8.) + 1) / ((std::cosh(8.) + 3) * (std::cosh(8.) + 3))
 
+/** @brief The analytic susceptibility for a \f$ 2 \times 2 \f$ lattice.*/
 #define X_2                                                                    \
     (3 * std::exp(8.) + std::exp(-8.) + 3)                                     \
         / ((std::cosh(8.) + 3) * (std::cosh(8.) + 3))
@@ -87,10 +95,10 @@ public:
             tmp = data / cycles;
             if (testlib::close_to(EPS_2, tmp.E / n_spins, tol)
                 && testlib::close_to(MAG_2, tmp.M_abs / n_spins, tol)
-                && testlib::close_to(CV_2, (tmp.E2 - tmp.E * tmp.E) / (T * T)
-                                               / n_spins, tol)
-                && testlib::close_to(X_2, (tmp.M2 - tmp.M_abs * tmp.M_abs) / T
-                                              / n_spins, tol)) {
+                && testlib::close_to(
+                    CV_2, (tmp.E2 - tmp.E * tmp.E) / (T * T) / n_spins, tol)
+                && testlib::close_to(
+                    X_2, (tmp.M2 - tmp.M_abs * tmp.M_abs) / T / n_spins, tol)) {
                 return cycles;
             }
         }
@@ -111,7 +119,7 @@ int main()
     int accepted_values = 0;
 
     // Run through the test multiple times to get a better estimate.
-    for (size_t i=0; i < iterations; i++) {
+    for (size_t i = 0; i < iterations; i++) {
         tmp = test.test_2x2_lattice(1e-2, 1e5);
         if (tmp == 0) {
             continue;
@@ -119,7 +127,7 @@ int main()
         accepted_values++;
         res += tmp;
     }
-    
+
     std::cout << "Res: " << res / accepted_values << std::endl;
 
     return 0;

src/time.cpp

@@ -5,7 +5,7 @@
  *
  *  @version 0.1
  *
- *  @brief Timing various things
+ *  @brief Timing various things.
  *
  *  @bug No known bugs
  * */
@@ -17,9 +17,11 @@
 #include <omp.h>
 #include <ostream>
 
+/** @brief Time phase transition using different lattice sizes.
+ * */
 void time_lattice_sizes()
 {
-    std::string outfile = "output/timing/lattice_sizes.txt";
+    std::string outfile = "data/timing/lattice_sizes.txt";
     std::ofstream ofile;
 
     int lattice_sizes[] = {20, 40, 60, 80, 100};
@@ -38,9 +40,11 @@ void time_lattice_sizes()
     ofile.close();
 }
 
+/** @brief Time phase transition using different sample sizes.
+ * */
 void time_sample_sizes()
 {
-    std::string outfile = "output/timing/sample_sizes.txt";
+    std::string outfile = "data/timing/sample_sizes.txt";
     std::ofstream ofile;
 
     int sample_sizes[] = {1000, 10000, 100000};
@@ -59,6 +63,7 @@ void time_sample_sizes()
     ofile.close();
 }
 
+/** @brief A function that displays how to use the program and quits.*/
 void usage(std::string filename)
 {
     std::cout << "Usage: " << filename << " OPTION ...\n"
@@ -70,6 +75,7 @@ void usage(std::string filename)
     exit(-1);
 }
 
+/** @brief The main function.*/
 int main(int argc, char **argv)
 {
     struct option long_options[] = {{"all", 0, 0, 0},