[NbConvertApp] Converting notebook /home/pyiron/energy_volume_curve.ipynb to notebook
1185[NbConvertApp] Executing notebook with kernel: python3
1186Traceback (most recent call last):
1187 File "/opt/conda/bin/jupyter-nbconvert", line 11, in <module>
1188 sys.exit(main())
1189 File "/opt/conda/lib/python3.8/site-packages/jupyter_core/application.py", line 270, in launch_instance
1190 return super(JupyterApp, cls).launch_instance(argv=argv, **kwargs)
1191 File "/opt/conda/lib/python3.8/site-packages/traitlets/config/application.py", line 837, in launch_instance
1192 app.start()
1193 File "/opt/conda/lib/python3.8/site-packages/nbconvert/nbconvertapp.py", line 350, in start
1194 self.convert_notebooks()
1195 File "/opt/conda/lib/python3.8/site-packages/nbconvert/nbconvertapp.py", line 524, in convert_notebooks
1196 self.convert_single_notebook(notebook_filename)
1197 File "/opt/conda/lib/python3.8/site-packages/nbconvert/nbconvertapp.py", line 489, in convert_single_notebook
1198 output, resources = self.export_single_notebook(notebook_filename, resources, input_buffer=input_buffer)
1199 File "/opt/conda/lib/python3.8/site-packages/nbconvert/nbconvertapp.py", line 418, in export_single_notebook
1200 output, resources = self.exporter.from_filename(notebook_filename, resources=resources)
1201 File "/opt/conda/lib/python3.8/site-packages/nbconvert/exporters/exporter.py", line 181, in from_filename
1202 return self.from_file(f, resources=resources, **kw)
1203 File "/opt/conda/lib/python3.8/site-packages/nbconvert/exporters/exporter.py", line 199, in from_file
1204 return self.from_notebook_node(nbformat.read(file_stream, as_version=4), resources=resources, **kw)
1205 File "/opt/conda/lib/python3.8/site-packages/nbconvert/exporters/notebook.py", line 32, in from_notebook_node
1206 nb_copy, resources = super().from_notebook_node(nb, resources, **kw)
1207 File "/opt/conda/lib/python3.8/site-packages/nbconvert/exporters/exporter.py", line 143, in from_notebook_node
1208 nb_copy, resources = self._preprocess(nb_copy, resources)
1209 File "/opt/conda/lib/python3.8/site-packages/nbconvert/exporters/exporter.py", line 318, in _preprocess
1210 nbc, resc = preprocessor(nbc, resc)
1211 File "/opt/conda/lib/python3.8/site-packages/nbconvert/preprocessors/base.py", line 47, in __call__
1212 return self.preprocess(nb, resources)
1213 File "/opt/conda/lib/python3.8/site-packages/nbconvert/preprocessors/execute.py", line 79, in preprocess
1214 self.execute()
1215 File "/opt/conda/lib/python3.8/site-packages/nbclient/util.py", line 74, in wrapped
1216 return just_run(coro(*args, **kwargs))
1217 File "/opt/conda/lib/python3.8/site-packages/nbclient/util.py", line 53, in just_run
1218 return loop.run_until_complete(coro)
1219 File "/opt/conda/lib/python3.8/asyncio/base_events.py", line 616, in run_until_complete
1220 return future.result()
1221 File "/opt/conda/lib/python3.8/site-packages/nbclient/client.py", line 535, in async_execute
1222 await self.async_execute_cell(
1223 File "/opt/conda/lib/python3.8/site-packages/nbconvert/preprocessors/execute.py", line 123, in async_execute_cell
1224 cell, resources = self.preprocess_cell(cell, self.resources, cell_index)
1225 File "/opt/conda/lib/python3.8/site-packages/nbconvert/preprocessors/execute.py", line 146, in preprocess_cell
1226 cell = run_sync(NotebookClient.async_execute_cell)(self, cell, index, store_history=self.store_history)
1227 File "/opt/conda/lib/python3.8/site-packages/nbclient/util.py", line 74, in wrapped
1228 return just_run(coro(*args, **kwargs))
1229 File "/opt/conda/lib/python3.8/site-packages/nbclient/util.py", line 53, in just_run
1230 return loop.run_until_complete(coro)
1231 File "/opt/conda/lib/python3.8/site-packages/nest_asyncio.py", line 95, in run_until_complete
1232 return f.result()
1233 File "/opt/conda/lib/python3.8/asyncio/futures.py", line 178, in result
1234 raise self._exception
1235 File "/opt/conda/lib/python3.8/asyncio/tasks.py", line 280, in __step
1236 result = coro.send(None)
1237 File "/opt/conda/lib/python3.8/site-packages/nbclient/client.py", line 827, in async_execute_cell
1238 self._check_raise_for_error(cell, exec_reply)
1239 File "/opt/conda/lib/python3.8/site-packages/nbclient/client.py", line 735, in _check_raise_for_error
1240 raise CellExecutionError.from_cell_and_msg(cell, exec_reply['content'])
1241nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell:
1242------------------
1243for strain in np.linspace(0.95, 1.05, 7):
1244 strain_str = str(strain).replace('.', '_')
1245 job_vasp_strain = pr.create_job(job_type=pr.job_type.Gpaw, job_name='gpaw_' + strain_str)
1246 job_vasp_strain.set_encut(320.0)
1247 job_vasp_strain.structure = basis.copy()
1248 job_vasp_strain.structure.set_cell(cell=basis.cell * strain ** (1/3), scale_atoms=True)
1249 job_vasp_strain.run()
1250------------------
1251
1252---------------------------------------------------------------------------
1253RuntimeError Traceback (most recent call last)
1254<ipython-input-1-938fbdfb8715> in <module>
1255 5 job_vasp_strain.structure = basis.copy()
1256 6 job_vasp_strain.structure.set_cell(cell=basis.cell * strain ** (1/3), scale_atoms=True)
1257----> 7 job_vasp_strain.run()
1258
1259/opt/conda/lib/python3.8/site-packages/pyiron_base/job/generic.py in run(self, delete_existing_job, repair, debug, run_mode, run_again)
1260 682 status = "created"
1261 683 if status == "initialized":
1262--> 684 self._run_if_new(debug=debug)
1263 685 elif status == "created":
1264 686 que_id = self._run_if_created()
1265
1266/opt/conda/lib/python3.8/site-packages/pyiron_base/job/generic.py in _run_if_new(self, debug)
1267 1392 else:
1268 1393 self.save()
1269-> 1394 self.run()
1270 1395
1271 1396 def _run_if_created(self):
1272
1273/opt/conda/lib/python3.8/site-packages/pyiron_base/job/generic.py in run(self, delete_existing_job, repair, debug, run_mode, run_again)
1274 684 self._run_if_new(debug=debug)
1275 685 elif status == "created":
1276--> 686 que_id = self._run_if_created()
1277 687 if que_id:
1278 688 self._logger.info(
1279
1280/opt/conda/lib/python3.8/site-packages/pyiron_base/job/generic.py in _run_if_created(self)
1281 1409 self.run_if_manually()
1282 1410 elif self.server.run_mode.modal:
1283-> 1411 self.run_static()
1284 1412 elif self.server.run_mode.non_modal or self.server.run_mode.thread:
1285 1413 self.run_if_non_modal()
1286
1287/opt/conda/lib/python3.8/site-packages/pyiron/gpaw/gpaw.py in run_static(self)
1288 152 pre_run_mode = self.server.run_mode
1289 153 self.server.run_mode.interactive = True
1290--> 154 self.run_if_interactive()
1291 155 self.interactive_close()
1292 156 self.server.run_mode = pre_run_mode
1293
1294/opt/conda/lib/python3.8/site-packages/pyiron/gpaw/gpaw.py in run_if_interactive(self)
1295 177 self.structure.set_calculator(calc)
1296 178 self.status.running = True
1297--> 179 self.structure.calc.calculate(self.structure)
1298 180 self.interactive_collect()
1299 181
1300
1301/opt/conda/lib/python3.8/site-packages/gpaw/calculator.py in calculate(self, atoms, properties, system_changes)
1302 282 self.hamiltonian = None
1303 283 self.scf = None
1304--> 284 self.initialize(atoms)
1305 285
1306 286 self.set_positions(atoms)
1307
1308/opt/conda/lib/python3.8/site-packages/gpaw/calculator.py in initialize(self, atoms, reading)
1309 555 realspace = (mode.name != 'pw' and mode.interpolation != 'fft')
1310 556
1311--> 557 self.create_setups(mode, xc)
1312 558
1313 559 if not realspace:
1314
1315/opt/conda/lib/python3.8/site-packages/gpaw/calculator.py in create_setups(self, mode, xc)
1316 779
1317 780 Z_a = self.atoms.get_atomic_numbers()
1318--> 781 self.setups = Setups(Z_a,
1319 782 self.parameters.setups, self.parameters.basis,
1320 783 xc, filter, self.world)
1321
1322/opt/conda/lib/python3.8/site-packages/gpaw/setup.py in __init__(self, Z_a, setup_types, basis_sets, xc, filter, world)
1323 1358 if isinstance(basis, basestring):
1324 1359 basis = Basis(symbol, basis, world=world)
1325-> 1360 setup = create_setup(symbol, xc, 2, type,
1326 1361 basis, setupdata=setupdata,
1327 1362 filter=filter, world=world)
1328
1329/opt/conda/lib/python3.8/site-packages/gpaw/setup.py in create_setup(symbol, xc, lmax, type, basis, setupdata, filter, world)
1330 84 'the %s functional.' % xc.get_setup_name())
1331 85 else:
1332---> 86 setupdata = SetupData(symbol, xc.get_setup_name(),
1333 87 type, True,
1334 88 world=world)
1335
1336/opt/conda/lib/python3.8/site-packages/gpaw/setup_data.py in __init__(self, symbol, xcsetupname, name, readxml, zero_reference, world, generator_version)
1337 120
1338 121 if readxml:
1339--> 122 self.read_xml(world=world)
1340 123
1341 124 def __repr__(self):
1342
1343/opt/conda/lib/python3.8/site-packages/gpaw/setup_data.py in read_xml(self, source, world)
1344 138
1345 139 def read_xml(self, source=None, world=None):
1346--> 140 PAWXMLParser(self).parse(source=source, world=world)
1347 141 nj = len(self.l_j)
1348 142 self.e_kin_jj.shape = (nj, nj)
1349
1350/opt/conda/lib/python3.8/site-packages/gpaw/setup_data.py in parse(self, source, world)
1351 436 setup = self.setup
1352 437 if source is None:
1353--> 438 setup.filename, source = search_for_file(setup.stdfilename, world)
1354 439
1355 440 setup.fingerprint = hashlib.md5(source).hexdigest()
1356
1357/opt/conda/lib/python3.8/site-packages/gpaw/setup_data.py in search_for_file(name, world)
1358 421 https://wiki.fysik.dtu.dk/gpaw/install.html#install-paw-datasets
1359 422 for details."""
1360--> 423 raise RuntimeError('%s\n%s' % (err, helpful_message))
1361 424
1362 425 return filename, source
1363
1364RuntimeError: Could not find required PAW dataset file "Fe.PBE".
1365
1366You need to set the GPAW_SETUP_PATH environment variable to point to
1367the directories where PAW dataset and basis files are stored. See
1368https://wiki.fysik.dtu.dk/gpaw/install.html#install-paw-datasets
1369for details.
1370RuntimeError: Could not find required PAW dataset file "Fe.PBE".
1371
1372You need to set the GPAW_SETUP_PATH environment variable to point to
1373the directories where PAW dataset and basis files are stored. See
1374https://wiki.fysik.dtu.dk/gpaw/install.html#install-paw-datasets
1375for details.
1376
1377