Merge branch 'master' of https://bitbucket.org/jpekkila/astaroth

README.md

@@ -32,7 +32,7 @@ Edit `config/astaroth.conf` to change the numerical setup.
 
 1. `source sourceme.sh` to add relevant directories to the `PATH`
 1. `ac_mkbuilddir.sh -b my_build_dir/` to set up a custom build directory. There are also other options available. See `ac_mkbuilddir.sh -h` for more. 
-1. `$AC_HOME/scripts/compile_acc.sh` to generate kernels from the Domain Specific Language 
+1. `compile_acc.sh` to generate kernels from the Domain Specific Language 
 1. `cd my_build_dir/` 
 1. `make -j`
 1. `./ac_run <options>`

analysis/python/jupyter/notebook_example.ipynb

@@ -7,7 +7,8 @@
    "outputs": [],
    "source": [
     "import astar.data as ad\n",
-    "import astar.visual as vis"
+    "import astar.visual as vis\n",
+    "import numpy as np"
    ]
   },
   {
@@ -23,7 +24,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "meshdir  = \"/scratch/data/mvaisala/iotest/\""
+    "meshdir  = \"/scratch/data/mvaisala/forcingtest/\""
    ]
   },
   {
@@ -32,10 +33,26 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "imesh = 0\n",
+    "imesh = 10000\n",
     "mesh = ad.read.Mesh(imesh, fdir=meshdir)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Auxuliary variables"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "uu_tot = np.sqrt(mesh.uu[0]**2.0 + mesh.uu[1]**2.0 + mesh.uu[2]**2.0)"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -51,7 +68,11 @@
    },
    "outputs": [],
    "source": [
-    "vis.slices.plot_3(mesh, mesh.uu[0], title = r'$u_x$', bitmap = False, fname = 'uux')"
+    "vis.slices.plot_3(mesh, uu_tot, title = r'$\\|u\\|$')\n",
+    "vis.slices.plot_3(mesh, mesh.uu[0], title = r'$u_x$')\n",
+    "vis.slices.plot_3(mesh, mesh.uu[1], title = r'$u_y$')\n",
+    "vis.slices.plot_3(mesh, mesh.uu[2], title = r'$u_z$')\n",
+    "vis.slices.plot_3(mesh, mesh.lnrho, title = r'$\\ln_\\rho$')"
    ]
   },
   {
@@ -86,6 +107,13 @@
    "outputs": [],
    "source": []
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
   {
    "cell_type": "code",
    "execution_count": null,

analysis/python/samples/readtest.py

@@ -45,7 +45,7 @@ print("sys.argv", sys.argv)
 #meshdir = "/tiara/home/mvaisala/astaroth-code/astaroth_2.0/build/"
 #meshdir  = "/tiara/ara/data/mvaisala/tmp/astaroth-code/astaroth_2.0/build/"
 #meshdir = "/tiara/ara/data/mvaisala/asth_testbed_double/"
-meshdir  = "/scratch/data/mvaisala/iotest/"
+meshdir  = "/scratch/data/mvaisala/forcingtest/"
 
 if "xtopbound" in sys.argv: 
     for i in range(0, 171):
@@ -169,7 +169,7 @@ if '1d' in sys.argv:
 if 'sl' in sys.argv:
     #maxfiles = 200002
     #stride = 10000
-    maxfiles = 1001
+    maxfiles = 5001
     stride = 100
     for i in range(0, maxfiles, stride):
         mesh = ad.read.Mesh(i, fdir=meshdir) 

src/core/kernels/kernels.cuh

@@ -545,10 +545,12 @@ normalized(const AcReal3& vec)
 
 // Sinusoidal forcing
 // https://arxiv.org/pdf/1704.04676.pdf
+// NOTE: This method of forcing is depracated. However, it will remain in here
+// until a corresponding scheme exists in the new code. 
 __constant__ AcReal3 forcing_vec;
 __constant__ AcReal forcing_phi;
 static __device__ __forceinline__ AcReal3
-forcing(const int i, const int j, const int k)
+DEPRECATED_forcing(const int i, const int j, const int k)
 {
 #define DOMAIN_SIZE_X (DCONST_INT(AC_nx) * DCONST_REAL(AC_dsx))
 #define DOMAIN_SIZE_Y (DCONST_INT(AC_ny) * DCONST_REAL(AC_dsy))

src/standalone/simulation.cc

@@ -202,6 +202,7 @@ run_simulation(void)
     load_config(&mesh_info);
 
     AcMesh* mesh = acmesh_create(mesh_info);
+    //TODO: This need to be possible to define in astaroth.conf 
     acmesh_init_to(INIT_TYPE_GAUSSIAN_RADIAL_EXPL, mesh);
 
     acInit(mesh_info);