Merge branch 'master' into sink_20190723

Hopefully the merge isssues were resolved.

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;