Add files via upload

Author: HeydenLabASU

demos/NAMD/ionFlux/mda/demo.ipynb

@@ -39,8 +39,7 @@
     "    dataLabel = \"ion current\",\n",
     "    mode = 'append'\n",
     ")\n",
-    "# Have fixed axis for better visualization\n",
-    "#plot[\"ax\"].set_xlim(0, 100)\n",
+    "# fixed y-axis for visualization\n",
     "plot[\"ax\"].set_ylim(-25,25)\n",
     "\n",
     "u = mda.Universe(NAMD_TOPOL, \"imd://10.206.72.141:8888\", buffersize = 1024*1024*1024)\n",
@@ -61,8 +60,8 @@
     "        # correct for PBC jumps\n",
     "        deltas[deltas>zdist/2.] -= zdist\n",
     "        deltas[deltas<-zdist/2.] += zdist\n",
-    "        cd = deltas*charges\n",
-    "        current = np.sum(cd)/zdist/dt*unitConv\n",
+    "        Qd = deltas*charges\n",
+    "        current = np.sum(Qd)/zdist/dt*unitConv\n",
     "        ionRef = ionPos\n",
     "        plot['update'](time, current)\n",
     "    i = i + 1"
@@ -84,8 +83,7 @@
     "    dataLabels = [\"cation current\", \"anion current\"],\n",
     "    mode = 'append'\n",
     ")\n",
-    "# Have fixed axis for better visualization\n",
-    "#plot[\"ax\"].set_xlim(0, 100)\n",
+    "# fixed y-axis for visualization\n",
     "plot[\"ax\"].set_ylim(-25,25)\n",
     "\n",
     "u = mda.Universe(NAMD_TOPOL, \"imd://10.206.72.141:8888\", buffersize = 1024*1024*1024)\n",