Remove Make.py reference in PyLammps examples

Also fixes some regressions due to command syntax changes

python/examples/pylammps/.gitignore

@@ -1 +1,4 @@
 *.orig
+*-checkpoint.ipynb
+*.png
+*.mp4

python/examples/pylammps/interface_usage.ipynb

@@ -29,8 +29,7 @@
     "2. Compile LAMMPS as a shared library and enable exceptions and PNG support\n",
     "   ```bash\n",
     "   cd $LAMMPS_DIR/src\n",
-    "   python Make.py -m mpi -png -s exceptions -a file\n",
-    "   make mode=shlib auto\n",
+    "   make mpi mode=shlib LMP_INC=\"-DLAMMPS_PNG -DLAMMPS_EXCEPTIONS\" JPG_LIB=\"-lpng\"\n",
     "   ```\n",
     "\n",
     "3. Create a python virtualenv\n",
@@ -67,7 +66,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "collapsed": true
+   },
    "outputs": [],
    "source": [
     "from lammps import IPyLammps"
@@ -204,7 +205,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "collapsed": true
+   },
    "outputs": [],
    "source": [
     "L.variable(\"a index 2\")"
@@ -222,7 +225,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "collapsed": true
+   },
    "outputs": [],
    "source": [
     "L.variable(\"t equal temp\")"
@@ -278,7 +283,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "collapsed": true
+   },
    "outputs": [],
    "source": [
     "L.variable(\"b index a b c\")"
@@ -314,7 +321,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "collapsed": true
+   },
    "outputs": [],
    "source": [
     "L.variable(\"i loop 10\")"
@@ -467,7 +476,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "L.runs[0].thermo.Temp"
+    "L.runs[0].thermo"
    ]
   },
   {
@@ -480,12 +489,23 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "collapsed": true
+   },
    "outputs": [],
    "source": [
     "L.write_script(\"in.output\")"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "dir(L.runs[0].thermo)"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -509,9 +529,10 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3"
+   "pygments_lexer": "ipython3",
+   "version": "3.6.2"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 0
+ "nbformat_minor": 1
 }

python/examples/pylammps/interface_usage_bonds.ipynb

@@ -30,8 +30,7 @@
     "   ```bash\n",
     "   cd $LAMMPS_DIR/src\n",
     "   make yes-molecule\n",
-    "   python Make.py -m mpi -png -s exceptions -a file\n",
-    "   make mode=shlib auto\n",
+    "   make mpi mode=shlib LMP_INC=\"-DLAMMPS_PNG -DLAMMPS_EXCEPTIONS\" JPG_LIB=\"-lpng\"\n",
     "   ```\n",
     "\n",
     "3. Create a python virtualenv\n",
@@ -68,7 +67,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "collapsed": true
+   },
    "outputs": [],
    "source": [
     "from lammps import IPyLammps"
@@ -123,7 +124,7 @@
     "L.bond_style(\"harmonic\")\n",
     "L.bond_coeff(1, 10.0, 1.2)\n",
     "\n",
-    "L.create_bonds(\"all\", \"all\", 1, 1.0, 1.5)\n",
+    "L.create_bonds(\"many\", \"all\", \"all\", 1, 1.0, 1.5)\n",
     "\n",
     "L.neighbor(0.3, \"bin\")\n",
     "L.neigh_modify(\"delay\", 0, \"every\", 1, \"check yes\")\n",
@@ -253,7 +254,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "collapsed": true
+   },
    "outputs": [],
    "source": [
     "L.variable(\"a index 2\")"
@@ -271,7 +274,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "collapsed": true
+   },
    "outputs": [],
    "source": [
     "L.variable(\"t equal temp\")"
@@ -327,7 +332,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "collapsed": true
+   },
    "outputs": [],
    "source": [
     "L.variable(\"b index a b c\")"
@@ -363,7 +370,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "collapsed": true
+   },
    "outputs": [],
    "source": [
     "L.variable(\"i loop 10\")"
@@ -470,7 +479,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "collapsed": true
+   },
    "outputs": [],
    "source": []
   }
@@ -490,9 +501,10 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3"
+   "pygments_lexer": "ipython3",
+   "version": "3.6.2"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 0
+ "nbformat_minor": 1
 }

python/examples/pylammps/simple.ipynb

@@ -29,8 +29,7 @@
     "2. Compile LAMMPS as a shared library and enable exceptions and PNG support\n",
     "   ```bash\n",
     "   cd $LAMMPS_DIR/src\n",
-    "   python Make.py -m mpi -png -s exceptions -a file\n",
-    "   make mode=shlib auto\n",
+    "   make mpi mode=shlib LMP_INC=\"-DLAMMPS_PNG -DLAMMPS_EXCEPTIONS\" JPG_LIB=\"-lpng\"\n",
     "   ```\n",
     "\n",
     "3. Create a python virtualenv\n",
@@ -67,7 +66,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "collapsed": true
+   },
    "outputs": [],
    "source": [
     "from lammps import IPyLammps"
@@ -144,9 +145,10 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3"
+   "pygments_lexer": "ipython3",
+   "version": "3.6.2"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 0
+ "nbformat_minor": 1
 }