Merge branch 'master' into sink_20190723

Hopefully the merge isssues were resolved.

src/standalone/CMakeLists.txt

@@ -25,10 +25,11 @@ add_compile_options(-pipe ${OpenMP_CXX_FLAGS})
 add_compile_options(-Wall -Wextra -Werror -Wdouble-promotion -Wfloat-conversion)# -Wshadow)
 
 ## Compile and link
-add_library(astaroth_standalone ${SOURCES})
+add_library(astaroth_standalone STATIC ${SOURCES})
+target_link_libraries(astaroth_standalone PRIVATE astaroth_core "${OpenMP_CXX_FLAGS}" ${SDL2_LIBRARY})
 
 add_executable(ac_run main.cc)
-target_link_libraries(ac_run PRIVATE astaroth_standalone astaroth_core "${OpenMP_CXX_FLAGS}" ${SDL2_LIBRARY})
+target_link_libraries(ac_run PRIVATE astaroth_standalone)
 
 # Define the config directory
 if (ALTER_CONF)

src/standalone/autotest.cc

@@ -75,6 +75,12 @@ static const InitType test_cases[] = {INIT_TYPE_RANDOM, INIT_TYPE_XWAVE,
                                       INIT_TYPE_GAUSSIAN_RADIAL_EXPL, INIT_TYPE_ABC_FLOW};
 // #define ARRAY_SIZE(arr) (sizeof(arr) / sizeof(arr[0]))
 
+static inline bool
+is_valid(const ModelScalar a)
+{
+    return !isnan(a) && !isinf(a);
+}
+
 #if TEST_TYPE ==                                                                                   \
     QUICK_TEST // REGULAR TEST START HERE
                // --------------------------------------------------------------------------------------------------------------

src/standalone/config_loader.cc

@@ -34,15 +34,6 @@
 #include "src/core/errchk.h"
 #include "src/core/math_utils.h"
 
-static inline void
-print(const AcMeshInfo& config)
-{
-    for (int i = 0; i < NUM_INT_PARAMS; ++i)
-        printf("[%s]: %d\n", intparam_names[i], config.int_params[i]);
-    for (int i = 0; i < NUM_REAL_PARAMS; ++i)
-        printf("[%s]: %g\n", realparam_names[i], double(config.real_params[i]));
-}
-
 /**
  \brief Find the index of the keyword in names
  \return Index in range 0...n if the keyword is in names. -1 if the keyword was
@@ -163,7 +154,7 @@ update_config(AcMeshInfo* config)
 #if VERBOSE_PRINTING // Defined in astaroth.h
     printf("###############################################################\n");
     printf("Config dimensions recalculated:\n");
-    print(*config);
+    acPrintMeshInfo(*config);
     printf("###############################################################\n");
 #endif
 }

src/standalone/model/host_forcing.cc

@@ -26,7 +26,9 @@
  */
 #include "host_forcing.h"
 
-#include "src/core/math_utils.h"
+// #include "src/core/math_utils.h"
+#include <cmath>
+using namespace std;
 
 // The is a wrapper for genering random numbers with a chosen system.
 AcReal
@@ -36,7 +38,7 @@ get_random_number_01()
     return AcReal(rand()) / AcReal(RAND_MAX);
 }
 
-AcReal3
+static AcReal3
 cross(const AcReal3& a, const AcReal3& b)
 {
     AcReal3 c;
@@ -48,13 +50,13 @@ cross(const AcReal3& a, const AcReal3& b)
     return c;
 }
 
-AcReal
+static AcReal
 dot(const AcReal3& a, const AcReal3& b)
 {
     return a.x * b.x + a.y * b.y + a.z * b.z;
 }
 
-AcReal3
+static AcReal3
 vec_norm(const AcReal3& a)
 {
     AcReal3 c;
@@ -67,7 +69,7 @@ vec_norm(const AcReal3& a)
     return c;
 }
 
-AcReal3
+static AcReal3
 vec_multi_scal(const AcReal scal, const AcReal3& a)
 {
     AcReal3 c;

src/standalone/model/host_forcing.h

@@ -32,14 +32,6 @@
 
 AcReal get_random_number_01();
 
-AcReal3 cross(const AcReal3& a, const AcReal3& b);
-
-AcReal dot(const AcReal3& a, const AcReal3& b);
-
-AcReal3 vec_norm(const AcReal3& a);
-
-AcReal3 vec_multi_scal(const AcReal scal, const AcReal3& a);
-
 AcReal3 helical_forcing_k_generator(const AcReal kmax, const AcReal kmin);
 
 void helical_forcing_e_generator(AcReal3* e_force, const AcReal3 k_force);

src/standalone/model/model_rk3.cc

@@ -31,6 +31,16 @@
 #include "host_memory.h"
 #include "model_boundconds.h"
 
+// Standalone flags
+#define LDENSITY (1)
+#define LHYDRO (1)
+#define LMAGNETIC (1)
+#define LENTROPY (1)
+#define LTEMPERATURE (0)
+#define LFORCING (1)
+#define LUPWD (1)
+#define AC_THERMAL_CONDUCTIVITY (AcReal(0.001)) // TODO: make an actual config parameter
+
 typedef struct {
     ModelScalar x, y, z;
 } ModelVector;

src/standalone/model/modelmesh.h

@@ -27,6 +27,7 @@
 #pragma once
 #include "astaroth.h"
 
+#include "math.h"
 
 typedef long double ModelScalar;