update vasp

pyscal · Oct 21, 2024 · 32a1bd0 · 32a1bd0
1 parent 10de082
commit 32a1bd0
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Showing 2 changed files with 78 additions and 45 deletions.
diff --git a/atomrdf/workflow/pyiron/vasp.py b/atomrdf/workflow/pyiron/vasp.py
@@ -99,17 +99,50 @@ def identify_method(job, method_dict):
     method_dict['method'] = method
     method_dict['dof'] = dof
 
-    encut = mdict['ENCUT'] 
-    method_dict['encut'] = encut
-
+    inputs = []
+    inputs.append(
+        {
+            "label": "EnergyCutoff",
+            "value": encut,
+            "unit": "EV",
+        }
+    )
+
     indf = job.input.to_dict()['kpoints/data_dict']
     params = indf['Parameter']
     vals = indf['Value']   
 
     kpoint_type = vals[2]
     kpoint_grid = vals[3]
-    method_dict['kpoint_type'] = kpoint_type
-    method_dict['kpoint_grid'] = kpoint_grid
+
+    if kpoint_type == 'Monkhorst-pack':
+        inputs.append(
+            {
+                "label": "MonkhorstPackKPointMesh",
+                "value": kpoint_grid,
+            }
+        )
+    elif kpoint_type == 'Gamma':
+        inputs.append(
+            {
+                "label": "GammaCenteredKPointMesh",
+                "value": kpoint_grid,
+            }
+        )
+    elif kpoint_type in ['Reciprocal', 'Cartesian']:
+        inputs.append(
+            {
+                "label": "ExplicitKPointMesh",
+                "value": kpoint_grid,
+            }
+        )
+    else:
+        inputs.append(
+            {
+                "label": "KPointMesh",
+                "value": kpoint_grid,
+            }
+        )
 
     indf = job.input.to_dict()['potcar/data_dict']
     xc = indf['Value'][0]
@@ -153,39 +186,19 @@ def extract_calculated_quantities(job, method_dict):
     )
     outputs.append(
         {
-            "label": "TotalVolume",
-            "value": np.round(job.output.volume[-1], decimals=5),
-            "unit": "ANGSTROM3",
-            "associate_to_sample": True,
-        }
-    )
-    structure = job.get_structure(frame=-1)
-    lx = np.linalg.norm(structure.cell[0])
-    ly = np.linalg.norm(structure.cell[1])
-    lz = np.linalg.norm(structure.cell[2])
-
-    outputs.append(
-        {
-            "label": "SimulationCellLength_x",
-            "value": np.round(lx, decimals=4),
-            "unit": "ANGSTROM",
+            "label": "PotentialEnergy",
+            "value": np.round(job.output.energy_pot[-1], decimals=5),
+            "unit": "EV",
             "associate_to_sample": True,
         }
     )
     outputs.append(
         {
-            "label": "SimulationCellLength_y",
-            "value": np.round(ly, decimals=4),
-            "unit": "ANGSTROM",
+            "label": "Volume",
+            "value": np.round(job.output.volume[-1], decimals=5),
+            "unit": "ANGSTROM3",
             "associate_to_sample": True,
         }
     )
-    outputs.append(
-        {
-            "label": "SimulationCellLength_z",
-            "value": np.round(lz, decimals=4),
-            "unit": "ANGSTROM",
-            "associate_to_sample": True,
-        }
-    )   
+
     method_dict['outputs'] =  outputs
diff --git a/examples/workflow_examples/02_vasp.ipynb b/examples/workflow_examples/02_vasp.ipynb
@@ -22,7 +22,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "fe747ff19deb48f78e4a3641d148c6c1",
+       "model_id": "7d2179bc22d84ea8a30013374dbdad2c",
        "version_major": 2,
        "version_minor": 0
       },
@@ -43,7 +43,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "pr = Project('wfy1')"
+    "pr = Project('wfy1e')"
    ]
   },
   {
@@ -63,7 +63,7 @@
      "output_type": "stream",
      "text": [
       "fccSi fccSi\n",
-      "job was stored with the job ID  468\n"
+      "job was stored with the job ID  1199\n"
      ]
     }
    ],
@@ -117,14 +117,14 @@
        "  <tbody>\n",
        "    <tr>\n",
        "      <th>0</th>\n",
-       "      <td>468</td>\n",
+       "      <td>1199</td>\n",
        "      <td>finished</td>\n",
        "      <td>Si</td>\n",
        "      <td>fccSi</td>\n",
        "      <td>/fccSi</td>\n",
        "      <td>None</td>\n",
-       "      <td>/mnt/c/Users/menon/Documents/repos/projects-iuc17/atomRDF/examples/workflow_examples/wfy1/</td>\n",
-       "      <td>2024-05-08 16:32:24.518895</td>\n",
+       "      <td>/mnt/c/Users/menon/Documents/repos/projects-iuc17/atomRDF/examples/workflow_examples/wfy1e/</td>\n",
+       "      <td>2024-10-21 11:32:41.253871</td>\n",
        "      <td>None</td>\n",
        "      <td>None</td>\n",
        "      <td>pyiron@cmleo26#1</td>\n",
@@ -138,14 +138,14 @@
        "</div>"
       ],
       "text/plain": [
-       "    id    status chemicalformula    job  subjob projectpath  \\\n",
-       "0  468  finished              Si  fccSi  /fccSi        None   \n",
+       "     id    status chemicalformula    job  subjob projectpath  \\\n",
+       "0  1199  finished              Si  fccSi  /fccSi        None   \n",
        "\n",
-       "                                                                                      project  \\\n",
-       "0  /mnt/c/Users/menon/Documents/repos/projects-iuc17/atomRDF/examples/workflow_examples/wfy1/   \n",
+       "                                                                                       project  \\\n",
+       "0  /mnt/c/Users/menon/Documents/repos/projects-iuc17/atomRDF/examples/workflow_examples/wfy1e/   \n",
        "\n",
        "                   timestart timestop totalcputime          computer hamilton  \\\n",
-       "0 2024-05-08 16:32:24.518895     None         None  pyiron@cmleo26#1     Vasp   \n",
+       "0 2024-10-21 11:32:41.253871     None         None  pyiron@cmleo26#1     Vasp   \n",
        "\n",
        "  hamversion parentid masterid  \n",
        "0       None     None     None  "
@@ -162,13 +162,33 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [],
    "source": [
     "job = pr.load('fccSi')"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 12,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "(array([-4.87738472]), array([-4.87738472]))"
+      ]
+     },
+     "execution_count": 12,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "job.output.energy_tot, job.output.energy_pot"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 6,
@@ -683,7 +703,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.1.-1"
+   "version": "3.11.10"
   }
  },
  "nbformat": 4,