Merge Development to master

docs/source/tutorials/after_training.ipynb

@@ -21,7 +21,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -45,24 +45,16 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 2,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "Final name of the gp instance is default_gp_2\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "gp_model = otf_object.make_gp(hyp_no=hyp_no)\n",
     "gp_model.parallel = True\n",
     "gp_model.hyp_labels = ['sig2', 'ls2', 'sig3', 'ls3', 'noise']\n",
     "\n",
     "# write model to a binary file\n",
-    "gp_model.write_model('AgI.gp', format='pickle')"
+    "gp_model.write_model('AgI.gp', format='json')"
    ]
   },
   {
@@ -75,21 +67,13 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 3,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "Final name of the gp instance is default_gp_2_2\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "from flare.gp import GaussianProcess\n",
     "\n",
-    "gp_model = GaussianProcess.from_file('AgI.gp.pickle')"
+    "gp_model = GaussianProcess.from_file('AgI.gp.json')"
    ]
   },
   {
@@ -106,20 +90,33 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 4,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/Users/xiey/Google Drive/flare/flare/mgp/mapxb.py:525: UserWarning: The minimal distance in training data is lower than the current lower bound, will reset lower bound to 2.129780094032895\n",
+      "  f\"The minimal distance in training data is lower than \"\n",
+      "/Users/xiey/Google Drive/flare/flare/mgp/mapxb.py:525: UserWarning: The minimal distance in training data is lower than the current lower bound, will reset lower bound to 2.129780094032895\n",
+      "  f\"The minimal distance in training data is lower than \"\n",
+      "/Users/xiey/Google Drive/flare/flare/mgp/mapxb.py:525: UserWarning: The minimal distance in training data is lower than the current lower bound, will reset lower bound to 2.129780094032895\n",
+      "  f\"The minimal distance in training data is lower than \"\n"
+     ]
+    }
+   ],
    "source": [
     "from flare.mgp import MappedGaussianProcess\n",
     "\n",
     "grid_params = {'twobody':   {'grid_num': [64]}, \n",
     "               'threebody': {'grid_num': [20, 20, 20]}}\n",
     "\n",
     "data = gp_model.training_statistics\n",
-    "lammps_location = 'AgI_Molten_15.txt'\n",
+    "lammps_location = 'AgI_Molten'\n",
     "\n",
     "mgp_model = MappedGaussianProcess(grid_params, data['species'], \n",
-    "    map_force=False, lmp_file_name='AgI_Molten_15.txt', n_cpus=1)\n",
+    "    var_map=None, lmp_file_name='AgI_Molten', n_cpus=1)\n",
     "mgp_model.build_map(gp_model)"
    ]
   },
@@ -145,28 +142,36 @@
     "pair_coeff * * <lmp_file_name> <chemical_symbols> yes/no yes/no\n",
     "```\n",
     "\n",
-    "An example is using coefficient file `AgI_Molten_15.txt` for AgI system, \n",
+    "An example is using coefficient file `AgI_Molten.mgp` for AgI system, \n",
     "with two-body (the 1st `yes`) together with three-body (the 2nd `yes`).\n",
     "\n",
     "```\n",
-    "pair_coeff * * AgI_Molten_15.txt Ag I yes yes\n",
-    "```\n",
-    "\n",
-    "**Note**: if you build force mapping (`map_force=True`) instead of energy mapping, please use\n",
-    "```\n",
-    "pair_style mgpf\n",
+    "pair_coeff * * AgI_Molten.mgp Ag I yes yes\n",
     "```\n",
     "\n",
-    "2. The third way is to use the ASE LAMMPS interface"
+    "2. Another way is to use the ASE LAMMPS interface"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 5,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/Users/xiey/anaconda3/lib/python3.7/site-packages/ase/calculators/lammpsrun.py:189: UserWarning: You are using an old syntax to set 'parameters'.\n",
+      "Please use LAMMPSRUN.set().\n",
+      "  warnings.warn(self.legacy_warn_string.format(\"parameters\"))\n"
+     ]
+    }
+   ],
    "source": [
+    "import os\n",
+    "from flare.utils.element_coder import _Z_to_mass, _element_to_Z\n",
     "from flare.ase.calculator import FLARE_Calculator\n",
+    "from ase.calculators.lammpsrun import LAMMPS\n",
     "\n",
     "# get chemical symbols, masses etc.\n",
     "species = gp_model.training_statistics['species']\n",
@@ -177,9 +182,9 @@
     "parameters = {'command': os.environ.get('lmp'), # set up executable for ASE\n",
     "              'newton': 'off',\n",
     "              'pair_style': 'mgp',\n",
-    "              'pair_coeff': [f'* * {lammps_location} {specie_symbol_list} yes yes'],\n",
+    "              'pair_coeff': [f'* * {lammps_location + \".mgp\"} {specie_symbol_list} yes yes'],\n",
     "              'mass': masses}\n",
-    "files = [lammps_location]\n",
+    "files = [lammps_location + \".mgp\"]\n",
     "\n",
     "# create ASE calc\n",
     "lmp_calc = LAMMPS(label=f'tmp_AgI', keep_tmp_files=True, tmp_dir='./tmp/',\n",
@@ -190,7 +195,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "3. The second way to run LAMMPS is using our LAMMPS interface, please set the\n",
+    "3. The third way to run LAMMPS is using our LAMMPS interface, please set the\n",
     "environment variable `$lmp` to the executable."
    ]
   },