Merge branch 'analysis_tools'

analysis/python/astar/data/read.py

@@ -96,9 +96,9 @@ class Mesh:
             aay = [] 
             aaz = []
 
-            self.xx =  self.minfo.contents['AC_inv_dsx']*np.arange(self.minfo.contents['AC_mx'])
-            self.yy =  self.minfo.contents['AC_inv_dsy']*np.arange(self.minfo.contents['AC_my'])
-            self.zz =  self.minfo.contents['AC_inv_dsz']*np.arange(self.minfo.contents['AC_mz'])
+            self.xx =  np.arange(self.minfo.contents['AC_mx']) * self.minfo.contents['AC_dsx']
+            self.yy =  np.arange(self.minfo.contents['AC_my']) * self.minfo.contents['AC_dsy']
+            self.zz =  np.arange(self.minfo.contents['AC_mz']) * self.minfo.contents['AC_dsz']
 
             self.xmid = int(self.minfo.contents['AC_mx']/2)
             self.ymid = int(self.minfo.contents['AC_my']/2)

analysis/python/jupyter/README.md

@@ -0,0 +1,11 @@
+# Setting up a remote jupyter session 
+
+1. In remote machine write: `jupyter notebook --no-browser --port=8889`
+
+2. In the local machine write:  `ssh -N -L localhost:8888:localhost:8889 username@remote.machine`
+
+3. Access jupyter seession with a browser: `http://localhost:8888`
+
+Now it should work. 
+
+*PLEASE NOTE: Never commit `.ipyb` files without clearing them to the github repo.*

analysis/python/jupyter/notebook_example.ipynb

@@ -0,0 +1,78 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import astar.data as ad\n",
+    "import astar.visual as vis"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Here we read data from the run directory"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "imesh = 0\n",
+    "meshdir  = \"/scratch/data/mvaisala/iotest/\"\n",
+    "mesh = ad.read.Mesh(imesh, fdir=meshdir)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Example visualization funtion call. "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "scrolled": true
+   },
+   "outputs": [],
+   "source": [
+    "vis.slices.plot_3(mesh, mesh.uu[0], title = r'$u_x$', bitmap = False, fname = 'uux')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.7.2"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

src/standalone/simulation.cc

@@ -90,6 +90,9 @@ void write_mesh_info(const AcMeshInfo* config)
     fprintf(infotxt, "int  AC_nz_max    %i \n", config->int_params[AC_nz_max]);
 
     // Spacing
+    fprintf(infotxt, "real AC_dsx       %e \n", (double)config->real_params[AC_dsx]);
+    fprintf(infotxt, "real AC_dsy       %e \n", (double)config->real_params[AC_dsy]);
+    fprintf(infotxt, "real AC_dsz       %e \n", (double)config->real_params[AC_dsz]);
     fprintf(infotxt, "real AC_inv_dsx   %e \n", (double)config->real_params[AC_inv_dsx]);
     fprintf(infotxt, "real AC_inv_dsy   %e \n", (double)config->real_params[AC_inv_dsy]);
     fprintf(infotxt, "real AC_inv_dsz   %e \n", (double)config->real_params[AC_inv_dsz]);