Merge pull request #219 from Exabyte-io/update/cif-import

update/cif import

Author: timurbazhirov

other/materials_designer/import_materials_from_files.ipynb

@@ -20,11 +20,11 @@
     "The following happens in the script below:\n",
     "\n",
     "1. Install the required packages\n",
-    "1. The files are extracted from `user_uploads` folder assuming their extensions represent the format - e.g. `SiO2.poscar`.\n",
+    "1. The files are extracted from `uploads` folder assuming their extensions represent the format - e.g. `SiO2.poscar`, `Ni.pwi`.\n",
     "1. Structural information is read from files into ASE Atoms objects.\n",
     "1. ASE Atoms objects are converted to `poscar` format \n",
     "1. `poscar` structures are converted to ESSE\n",
-    "1. The results are passed to the outside runtime"
+    "1. The results are visualized and passed to the outside runtime"
    ]
   },
   {
@@ -42,12 +42,15 @@
    "source": [
     "# Upload files to this folder\n",
     "FOLDER_PATH = \"./uploads\"\n",
-    "# Attempt to guess the format from file extension\n",
-    "# If set to specific format, it will only accept that format\n",
-    "ENFORCED_FORMAT = None\n",
+    "\n",
+    "# By default, format will be guessed from file extension\n",
+    "# If set to specific format, notebook will only read that format\n",
+    "ENFORCED_FORMATS = None # e.g. [\"cif\", \"espresso-in\"]\n",
+    "\n",
     "# If set to true, the file extension will be included in the resulting material name\n",
     "USE_FILE_NAME_NO_EXTENSION = False\n",
-    "# If set to true, the supported formats will be printed below\n",
+    "\n",
+    "# If set to true, the supported formats and required extensions will be printed below\n",
     "SHOW_SUPPORTED_FORMATS = False"
    ],
    "outputs": [],
@@ -86,7 +89,7 @@
    "source": [
     "## 3. Data Processing\n",
     "\n",
-    "### 3.1. Read data from files"
+    "### 3.1. Read data from files in `uploads` folder"
    ]
   },
   {
@@ -101,22 +104,26 @@
     "from pathlib import Path\n",
     "from ase.io import read\n",
     "\n",
-    "materials = []\n",
-    "unreadable_files = []\n",
+    "ase_atoms, readable_file_names, unreadable_file_names = [], [], []\n",
     "file_names = os.listdir(FOLDER_PATH)\n",
     "\n",
     "for file_name in file_names:\n",
     "    file_path = os.path.join(FOLDER_PATH, file_name)\n",
-    "    try:\n",
-    "        atoms = read(file_path, format=ENFORCED_FORMAT)\n",
+    "    formats = ENFORCED_FORMATS or [None]\n",
     "\n",
-    "        atoms.info[\"file_name\"] = Path(file_name).stem if USE_FILE_NAME_NO_EXTENSION else file_name\n",
-    "        materials.append(atoms)\n",
-    "        \n",
-    "    except Exception as e:\n",
-    "        print(e)\n",
-    "        unreadable_files.append(file_name)\n",
-    "        continue"
+    "    for fmt in formats:\n",
+    "        try:\n",
+    "            atoms = read(file_path, format=fmt)\n",
+    "            atoms.info[\"file_name\"] = Path(file_name).stem if USE_FILE_NAME_NO_EXTENSION else file_name\n",
+    "            ase_atoms.append(atoms)\n",
+    "            readable_file_names.append(file_name)\n",
+    "            print(\"Successfully read:\", atoms.info[\"file_name\"], \"using format:\", fmt)\n",
+    "            break\n",
+    "        except Exception:\n",
+    "            continue\n",
+    "    else:\n",
+    "        unreadable_file_names.append(file_name)\n",
+    "        print(\"Failed to read:\", file_name)"
    ],
    "outputs": [],
    "execution_count": null
@@ -125,17 +132,15 @@
    "cell_type": "markdown",
    "id": "57b0d358",
    "metadata": {},
-   "source": [
-    "### 3.2. Preview the data"
-   ]
+   "source": "### 3.2. List imported the data"
   },
   {
    "cell_type": "code",
    "id": "0e34472a",
    "metadata": {},
    "source": [
-    "print(f\"Successfully read {len(materials)} files\")\n",
-    "print(f\"Unreadable files: {unreadable_files}. \")\n"
+    "print(f\"Successfully read {len(ase_atoms)} files: {readable_file_names}. \")\n",
+    "print(f\"Unreadable files: {unreadable_file_names}. \")"
    ],
    "outputs": [],
    "execution_count": null
@@ -153,12 +158,11 @@
    "id": "a771a36a",
    "metadata": {},
    "source": [
-    "# Uncomment to see the list of supported formats and their file extensions\n",
     "from ase.io.formats import ioformats\n",
     "import pandas as pd\n",
     "\n",
-    "if len(unreadable_files) > 0 or SHOW_SUPPORTED_FORMATS:\n",
-    "    print(f\"Unreadable files found: {unreadable_files}. See formats/extensions below.\")\n",
+    "if len(unreadable_file_names) > 0 or SHOW_SUPPORTED_FORMATS:\n",
+    "    print(f\"Unreadable files found: {unreadable_file_names}. See formats/extensions below.\")\n",
     "    data = [[frmt.name, frmt.extensions, frmt.description] for frmt in ioformats.values()]\n",
     "    dataframe = pd.DataFrame(data, columns=[\"Format Name\", \"File Extensions\", \"Description\"])\n",
     "    print(dataframe.to_markdown())"
@@ -188,37 +192,40 @@
     "from express import ExPrESS\n",
     "\n",
     "def ase_to_poscar(atoms: Atoms):\n",
-    "    \"\"\"\n",
-    "    Converts ase.Atoms object to POSCAR format\n",
-    "\n",
-    "    Args:\n",
-    "        atoms (ase.Atoms): ase.Atoms object\n",
-    "\n",
-    "    Returns:\n",
-    "        str: POSCAR string\n",
-    "    \"\"\"\n",
     "    output = io.StringIO()\n",
-    "    write(output, atoms, format=\"vasp\")\n",
-    "    content = output.getvalue()\n",
-    "    output.close()\n",
+    "    try:\n",
+    "        write(output, atoms, format=\"vasp\")\n",
+    "        content = output.getvalue()\n",
+    "    except Exception as e:\n",
+    "        print(f\"Error converting ASE atoms to POSCAR: {e}\")\n",
+    "        content = None\n",
+    "    finally:\n",
+    "        output.close()\n",
     "\n",
     "    return content\n",
     "\n",
     "def convert_ase_entry_to_esse(ase_entry):\n",
-    "    poscar = ase_to_poscar(ase_entry)\n",
-    "    kwargs = {\n",
-    "        \"structure_string\": poscar,\n",
-    "        \"structure_format\": \"poscar\"\n",
-    "    }\n",
+    "    try:\n",
+    "        poscar = ase_to_poscar(ase_entry)\n",
+    "        if poscar is None:\n",
+    "            raise ValueError(\"Failed to generate POSCAR string\")\n",
     "\n",
-    "    handler = ExPrESS(\"structure\", **kwargs)\n",
-    "    esse = handler.property(\"material\", **kwargs)\n",
-    "    \n",
-    "    esse[\"name\"] = ase_entry.info[\"file_name\"]\n",
-    "    \n",
-    "    return esse\n",
+    "        kwargs = {\n",
+    "            \"structure_string\": poscar,\n",
+    "            \"structure_format\": \"poscar\"\n",
+    "        }\n",
+    "\n",
+    "        handler = ExPrESS(\"structure\", **kwargs)\n",
+    "        esse = handler.property(\"material\", **kwargs)\n",
+    "\n",
+    "        esse[\"name\"] = ase_entry.info.get(\"file_name\", \"Unknown\")\n",
+    "\n",
+    "        return esse\n",
+    "    except Exception as e:\n",
+    "        print(f\"Error processing ASE entry: {e}\")\n",
+    "        return None\n",
     "\n",
-    "esse_entries = list(map(convert_ase_entry_to_esse, materials))"
+    "esse_entries = [entry for entry in map(convert_ase_entry_to_esse, ase_atoms) if entry is not None]"
    ],
    "outputs": [],
    "execution_count": null

other/materials_designer/uploads/Graphene.cif

@@ -0,0 +1,51 @@
+# C, Graphene, HEX (P6/mmm) 2D (Monolayer), 2dm-3993
+
+data_findsym-output
+
+_symmetry_space_group_name_H-M 'P 6/m 2/m 2/m'
+_symmetry_Int_Tables_number 191
+
+_cell_length_a       2.46500
+_cell_length_b       2.46500
+_cell_length_c      19.99700
+_cell_angle_alpha   90.00000
+_cell_angle_beta    90.00000
+_cell_angle_gamma  120.00000
+
+loop_
+_space_group_symop_operation_xyz
+x,y,z
+x-y,x,z
+-y,x-y,z
+-x,-y,z
+-x+y,-x,z
+y,-x+y,z
+x-y,-y,-z
+x,x-y,-z
+y,x,-z
+-x+y,y,-z
+-x,-x+y,-z
+-y,-x,-z
+-x,-y,-z
+-x+y,-x,-z
+y,-x+y,-z
+x,y,-z
+x-y,x,-z
+-y,x-y,-z
+-x+y,y,z
+-x,-x+y,z
+-y,-x,z
+x-y,-y,z
+x,x-y,z
+y,x,z
+
+loop_
+_atom_site_label
+_atom_site_type_symbol
+_atom_site_fract_x
+_atom_site_fract_y
+_atom_site_fract_z
+_atom_site_occupancy
+C1  C    0.33333   0.66667   0.50000   1.00000
+
+# end_of_file

other/materials_designer/uploads/Ni.poscar

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:7ad33a418661557756dce79ca7afddfbe54f86a4ede07446918fbfaba1a16755
+size 250