Merge branch 'master' into sink_20190723

Conflicts:
	acc/mhd_solver/stencil_defines.h
	src/standalone/simulation.cc

src/standalone/simulation.cc

@@ -27,13 +27,13 @@
 #include "run.h"
 
 #include "config_loader.h"
-#include "src/core/errchk.h"
-#include "src/core/math_utils.h"
 #include "model/host_forcing.h"
 #include "model/host_memory.h"
 #include "model/host_timestep.h"
 #include "model/model_reduce.h"
 #include "model/model_rk3.h"
+#include "src/core/errchk.h"
+#include "src/core/math_utils.h"
 #include "timer_hires.h"
 
 #include <string.h>
@@ -216,6 +216,7 @@ run_simulation(void)
     write_mesh_info(&mesh_info);
     print_diagnostics(0, AcReal(.0), t_step, diag_file);
 
+    acBoundcondStep();
     acStore(mesh);
     save_mesh(*mesh, 0, t_step);
 
@@ -229,13 +230,13 @@ run_simulation(void)
     /* initialize random seed: */
     srand(312256655);
 
-    //TODO_SINK. init_sink_particle()
+    // TODO_SINK. init_sink_particle()
     //  Initialize the basic variables of the sink particle to a suitable initial value.
     //  1. Location of the particle
     //  2. Mass of the particle
     //  (3. Velocity of the particle)
-    //  This at the level of Host in this case. 
-    //  acUpdate_sink_particle() will do the similar trick to the device. 
+    //  This at the level of Host in this case.
+    //  acUpdate_sink_particle() will do the similar trick to the device.
 
     /* Step the simulation */
     for (int i = 1; i < max_steps; ++i) {
@@ -247,28 +248,28 @@ run_simulation(void)
         loadForcingParamsToDevice(forcing_params);
 #endif
 
+
        //TODO_SINK acUpdate_sink_particle()
        //  Update properties of the sing particle for acIntegrate(). Essentially:
        //  1. Location of the particle
        //  2. Mass of the particle
-       //  (3. Velocity of the particle)
+       //  3. Velocity of the particle)
        //  These can be used for calculating he gravitational field. 
        //  This is my first comment! by Jack
        //  This is my second comment! by Jack
-
         acIntegrate(dt);
-       //TODO_SINK acAdvect_sink_particle()
-       //  THIS IS OPTIONAL. We will start from unmoving particle. 
-       //  1. Calculate the equation of motion for the sink particle. 
-       //  NOTE: Might require embedding with acIntegrate(dt). 
+        // TODO_SINK acAdvect_sink_particle()
+        //  THIS IS OPTIONAL. We will start from unmoving particle.
+        //  1. Calculate the equation of motion for the sink particle.
+        //  NOTE: Might require embedding with acIntegrate(dt).
 
-       //TODO_SINK acAccrete_sink_particle()
-       //  Calculate accretion of the sink particle from the surrounding medium 
-       //  1. Transfer density into sink particle mass
-       //  2. Transfer momentum into sink particle 
-       //  (OPTIONAL: Affection the motion of the particle)
-       //  NOTE: Might require embedding with acIntegrate(dt).
-       //  This is the hardest part. Please see Lee et al. ApJ 783 (2014) for reference. 
+        // TODO_SINK acAccrete_sink_particle()
+        //  Calculate accretion of the sink particle from the surrounding medium
+        //  1. Transfer density into sink particle mass
+        //  2. Transfer momentum into sink particle
+        //  (OPTIONAL: Affection the motion of the particle)
+        //  NOTE: Might require embedding with acIntegrate(dt).
+        //  This is the hardest part. Please see Lee et al. ApJ 783 (2014) for reference.
 
         t_step += dt;
 
@@ -311,9 +312,10 @@ run_simulation(void)
                 assumed to be asynchronous, so the meshes must be also synchronized
                 before transferring the data to the CPU. Like so:
 
-                acSynchronize();
+                acBoundcondStep();
                 acStore(mesh);
             */
+            acBoundcondStep();
             acStore(mesh);
 
             save_mesh(*mesh, i, t_step);