Update tutorial

aiida_wannier90_workflows/utils/workflows/plot.py

@@ -83,7 +83,8 @@ def plot_scdm_fit(workchain: int, save: bool = False):
 
     formula = workchain.inputs.structure.get_formula()
 
-    w90calc = workchain.get_outgoing(link_label_filter="wannier90").one().node
+    # w90calc = workchain.get_outgoing(link_label_filter="wannier90").one().node
+    w90calc = workchain.outputs.wannier90.remote_folder.creator
     p2w_workchain = workchain.get_outgoing(link_label_filter="pw2wannier90").one().node
     p2wcalc = get_last_calcjob(p2w_workchain)
     projcalc = workchain.get_outgoing(link_label_filter="projwfc").one().node
@@ -104,7 +105,8 @@ def plot_scdm_fit(workchain: int, save: bool = False):
     # check the fitting are consistent
     eps = 1e-6
     assert abs(sigma - sigma_fit) < eps
-    sigma_factor = workchain.inputs.scdm_sigma_factor.value
+    # sigma_factor = workchain.inputs.scdm_sigma_factor.value
+    sigma_factor = 3
     assert abs(mu - (mu_fit - sigma_fit * sigma_factor)) < eps
     sorted_bands = data[0, :]
     sorted_projwfc = data[1, :]

docs/source/user_guide/get_started/scdm/include/snippets/launch_pwbands.py

@@ -0,0 +1,49 @@
+#!/usr/bin/env runaiida
+import os
+import sys
+
+from ase.io import read as aseread
+
+from aiida import orm
+from aiida.engine import submit
+
+from aiida_quantumespresso.workflows.pw.bands import PwBandsWorkChain
+
+# Code labels for `pw.x`
+# Change these according to your aiida setup.
+code = "qe-pw-6.8@localhost"
+
+# Filename of a structure.
+# filename = "GaAs.xsf"
+if len(sys.argv) != 2:
+    print(f"Please pass a filename for a structure as the argument.")
+    sys.exit(1)
+filename = sys.argv[1]
+if not os.path.exists(filename):
+    print(f"{filename} not existed!")
+    sys.exit(1)
+
+# Read a structure file and store as an `orm.StructureData`.
+structure = orm.StructureData(ase=aseread(filename))
+structure.store()
+print(f"Read and stored structure {structure.get_formula()}<{structure.pk}>")
+
+# Prepare the builder to launch the workchain.
+# We use fast protocol to converge faster.
+builder = PwBandsWorkChain.get_builder_from_protocol(
+    code,
+    structure,
+    protocol="fast",
+)
+builder.pop("relax", None)
+
+# Submit the workchain.
+workchain = submit(builder)
+print(f"Submitted {workchain.process_label}<{workchain.pk}>")
+
+print(
+    "Run any of these commands to check the progress:\n"
+    f"verdi process report {workchain.pk}\n"
+    f"verdi process show {workchain.pk}\n"
+    "verdi process list\n"
+)

docs/source/user_guide/get_started/scdm/include/snippets/launch_workflow.py → docs/source/user_guide/get_started/scdm/include/snippets/launch_wannier.py

@@ -1,4 +1,7 @@
 #!/usr/bin/env runaiida
+import os
+import sys
+
 from ase.io import read as aseread
 
 from aiida import orm
@@ -9,14 +12,21 @@
 # Code labels for `pw.x`, `pw2wannier90.x`, `projwfc.x`, and `wannier90.x`.
 # Change these according to your aiida setup.
 codes = {
-    "pw": "qe-7.0-pw@localhost",
-    "projwfc": "qe-7.0-projwfc@localhost",
-    "pw2wannier90": "qe-7.0-pw2wannier90@localhost",
-    "wannier90": "wannier90-3.1-wannier90@localhost",
+    "pw": "qe-pw-6.8@localhost",
+    "projwfc": "qe-projwfc-6.8@localhost",
+    "pw2wannier90": "qe-pw2wannier90-6.8@localhost",
+    "wannier90": "wannier90-3.1@localhost",
 }
 
 # Filename of a structure.
-filename = "GaAs.xsf"
+# filename = "GaAs.xsf"
+if len(sys.argv) != 2:
+    print(f"Please pass a filename for a structure as the argument.")
+    sys.exit(1)
+filename = sys.argv[1]
+if not os.path.exists(filename):
+    print(f"{filename} not existed!")
+    sys.exit(1)
 
 # Read a structure file and store as an `orm.StructureData`.
 structure = orm.StructureData(ase=aseread(filename))
@@ -36,8 +46,8 @@
 print(f"Submitted {workchain.process_label}<{workchain.pk}>")
 
 print(
-    "Run any of these commands to check the progress:"
-    "verdi process report {workchain.pk}"
-    "verdi process show {workchain.pk}"
-    "verdi process list"
+    "Run any of these commands to check the progress:\n"
+    f"verdi process report {workchain.pk}\n"
+    f"verdi process show {workchain.pk}\n"
+    "verdi process list\n"
 )

docs/source/user_guide/get_started/scdm/include/snippets/workchain_report.txt

@@ -1,32 +1,27 @@
-2020-03-19 07:58:27 [88  | REPORT]: [495|Wannier90BandsWorkChain|setup_protocol]: running the workchain with the "testing" protocol
-2020-03-19 07:58:27 [89  | REPORT]: [495|Wannier90BandsWorkChain|setup]: workchain controls found in inputs: valence + conduction bands
-2020-03-19 07:58:27 [90  | REPORT]: [495|Wannier90BandsWorkChain|run_seekpath]: running seekpath to get primitive structure for: CsH
-2020-03-19 07:58:28 [91  | REPORT]: [495|Wannier90BandsWorkChain|setup_parameters]: number of machines 1 auto-set according to number of atoms
-2020-03-19 07:58:30 [92  | REPORT]: [495|Wannier90BandsWorkChain|run_wannier_workchain]: launching Wannier90WorkChain<514>
-2020-03-19 07:58:31 [93  | REPORT]:   [514|Wannier90WorkChain|run_scf]: scf step - launching PwBaseWorkChain<517> in scf mode
-2020-03-19 07:58:33 [94  | REPORT]:     [517|PwBaseWorkChain|run_calculation]: launching PwCalculation<523> iteration #1
-2020-03-19 07:58:46 [95  | REPORT]:     [517|PwBaseWorkChain|inspect_calculation]: PwCalculation<523> completed successfully
-2020-03-19 07:58:46 [96  | REPORT]:     [517|PwBaseWorkChain|results]: work chain completed after 1 iterations
-2020-03-19 07:58:46 [97  | REPORT]:     [517|PwBaseWorkChain|on_terminated]: remote folders will not be cleaned
-2020-03-19 07:58:47 [98  | REPORT]:   [514|Wannier90WorkChain|inspect_scf]: scf PwBaseWorkChain successfully finished
-2020-03-19 07:58:47 [99  | REPORT]:   [514|Wannier90WorkChain|run_nscf]: nscf number of bands set as 24
-2020-03-19 07:58:48 [100 | REPORT]:   [514|Wannier90WorkChain|run_nscf]: nscf step - launching PwBaseWorkChain<537> in nscf mode
-2020-03-19 07:58:49 [101 | REPORT]:     [537|PwBaseWorkChain|run_calculation]: launching PwCalculation<540> iteration #1
-2020-03-19 08:01:16 [102 | REPORT]:     [537|PwBaseWorkChain|inspect_calculation]: PwCalculation<540> completed successfully
-2020-03-19 08:01:16 [103 | REPORT]:     [537|PwBaseWorkChain|results]: work chain completed after 1 iterations
-2020-03-19 08:01:16 [104 | REPORT]:     [537|PwBaseWorkChain|on_terminated]: remote folders will not be cleaned
-2020-03-19 08:01:17 [105 | REPORT]:   [514|Wannier90WorkChain|inspect_nscf]: nscf PwBaseWorkChain successfully finished
-2020-03-19 08:01:17 [106 | REPORT]:   [514|Wannier90WorkChain|should_do_projwfc]: SCDM mu & sigma are auto-set using projectability
-2020-03-19 08:01:18 [107 | REPORT]:   [514|Wannier90WorkChain|run_projwfc]: projwfc step - launching ProjwfcCalculation<546>
-2020-03-19 08:01:27 [108 | REPORT]:   [514|Wannier90WorkChain|inspect_projwfc]: projwfc ProjwfcCalculation successfully finished
-2020-03-19 08:01:28 [109 | REPORT]:   [514|Wannier90WorkChain|run_wannier90_pp]: number of Wannier functions extracted from projections: 14
-2020-03-19 08:01:29 [110 | REPORT]:   [514|Wannier90WorkChain|run_wannier90_pp]: wannier90 postproc step - launching Wannier90Calculation<559> in postproc mode
-2020-03-19 08:01:35 [111 | REPORT]:   [514|Wannier90WorkChain|inspect_wannier90_pp]: wannier90 postproc Wannier90Calculation successfully finished
-2020-03-19 08:01:38 [112 | REPORT]:   [514|Wannier90WorkChain|run_pw2wannier90]: pw2wannier90 step - launching Pw2Wannier90Calculation<567>
-2020-03-19 08:02:16 [113 | REPORT]:   [514|Wannier90WorkChain|inspect_pw2wannier90]: Pw2wannier90Calculation successfully finished
-2020-03-19 08:02:16 [114 | REPORT]:   [514|Wannier90WorkChain|run_wannier90]: wannier90 step - launching Wannier90Calculation<572>
-2020-03-19 08:03:06 [115 | REPORT]:   [514|Wannier90WorkChain|inspect_wannier90]: Wannier90Calculation successfully finished
-2020-03-19 08:03:06 [116 | REPORT]:   [514|Wannier90WorkChain|results]: final step - preparing outputs
-2020-03-19 08:03:06 [117 | REPORT]:   [514|Wannier90WorkChain|results]: Wannier90WorkChain successfully completed
-2020-03-19 08:03:07 [118 | REPORT]: [495|Wannier90BandsWorkChain|results]: wannier90 interpolated bands pk: 575
-2020-03-19 08:03:07 [119 | REPORT]: [495|Wannier90BandsWorkChain|results]: Wannier90BandsWorkChain successfully completed
+2022-05-12 22:07:11 [179 | REPORT]: [446|Wannier90BandsWorkChain|run_seekpath]: launching seekpath: CsH -> CsH
+2022-05-12 22:07:11 [180 | REPORT]: [446|Wannier90BandsWorkChain|run_scf]: launching PwBaseWorkChain<454> in scf mode
+2022-05-12 22:07:12 [181 | REPORT]:   [454|PwBaseWorkChain|run_process]: launching PwCalculation<459> iteration #1
+2022-05-12 22:07:55 [182 | REPORT]:   [454|PwBaseWorkChain|results]: work chain completed after 1 iterations
+2022-05-12 22:07:55 [183 | REPORT]:   [454|PwBaseWorkChain|on_terminated]: remote folders will not be cleaned
+2022-05-12 22:07:55 [184 | REPORT]: [446|Wannier90BandsWorkChain|run_nscf]: launching PwBaseWorkChain<466> in nscf mode
+2022-05-12 22:07:56 [185 | REPORT]:   [466|PwBaseWorkChain|run_process]: launching PwCalculation<469> iteration #1
+2022-05-12 22:19:39 [187 | REPORT]:   [466|PwBaseWorkChain|results]: work chain completed after 1 iterations
+2022-05-12 22:19:40 [188 | REPORT]:   [466|PwBaseWorkChain|on_terminated]: remote folders will not be cleaned
+2022-05-12 22:19:40 [189 | REPORT]: [446|Wannier90BandsWorkChain|run_projwfc]: launching ProjwfcBaseWorkChain<476>
+2022-05-12 22:19:40 [190 | REPORT]:   [476|ProjwfcBaseWorkChain|run_process]: launching ProjwfcCalculation<477> iteration #1
+2022-05-12 22:19:50 [191 | REPORT]:   [476|ProjwfcBaseWorkChain|results]: work chain completed after 1 iterations
+2022-05-12 22:19:50 [192 | REPORT]:   [476|ProjwfcBaseWorkChain|on_terminated]: remote folders will not be cleaned
+2022-05-12 22:19:50 [193 | REPORT]: [446|Wannier90BandsWorkChain|run_wannier90_pp]: launching Wannier90BaseWorkChain<487> in postproc mode
+2022-05-12 22:19:51 [194 | REPORT]:   [487|Wannier90BaseWorkChain|run_process]: launching Wannier90Calculation<489> iteration #1
+2022-05-12 22:19:59 [195 | REPORT]:   [487|Wannier90BaseWorkChain|results]: work chain completed after 1 iterations
+2022-05-12 22:19:59 [196 | REPORT]:   [487|Wannier90BaseWorkChain|on_terminated]: remote folders will not be cleaned
+2022-05-12 22:20:00 [197 | REPORT]: [446|Wannier90BandsWorkChain|run_pw2wannier90]: launching Pw2wannier90BaseWorkChain<495>
+2022-05-12 22:20:02 [198 | REPORT]:   [495|Pw2wannier90BaseWorkChain|run_process]: launching Pw2wannier90Calculation<497> iteration #1
+2022-05-12 22:20:39 [199 | REPORT]:   [495|Pw2wannier90BaseWorkChain|results]: work chain completed after 1 iterations
+2022-05-12 22:20:39 [200 | REPORT]:   [495|Pw2wannier90BaseWorkChain|on_terminated]: remote folders will not be cleaned
+2022-05-12 22:20:40 [201 | REPORT]: [446|Wannier90BandsWorkChain|run_wannier90]: launching Wannier90BaseWorkChain<506>
+2022-05-12 22:20:41 [202 | REPORT]:   [506|Wannier90BaseWorkChain|run_process]: launching Wannier90Calculation<508> iteration #1
+2022-05-12 22:21:00 [203 | REPORT]:   [506|Wannier90BaseWorkChain|results]: work chain completed after 1 iterations
+2022-05-12 22:21:00 [204 | REPORT]:   [506|Wannier90BaseWorkChain|on_terminated]: remote folders will not be cleaned
+2022-05-12 22:21:00 [205 | REPORT]: [446|Wannier90BandsWorkChain|results]: Wannier90BandsWorkChain successfully completed
+2022-05-12 22:21:01 [206 | REPORT]: [446|Wannier90BandsWorkChain|on_terminated]: remote folders will not be cleaned