Add element check + new scheme

mpds_aiida/calc_templates/ext_metallic.yml

@@ -0,0 +1,146 @@
+codes:
+  crystal:
+    Pcrystal@yascheduler
+
+options:
+  need_phonons: true
+  need_elastic_constants: true
+  need_properties: false
+  recursive_update: true
+  try_oxi_if_fails: true
+  is_magnetic: true
+  optimize_structure: optimise
+
+basis_family: MPDSBSL_NEUTRAL_24
+
+default:
+  crystal:
+    scf:
+      k_points: [18, 54]
+      dft:
+        SPIN: True
+        xc: PBE0
+        grid: XLGRID
+        numerical:
+          TOLLDENS: 8
+          TOLLGRID: 16
+      numerical:
+        TOLDEE: 9
+        BIPOSIZE: 256000000
+        EXCHSIZE: 256000000 
+        TOLINTEG: [20, 20, 20, 20, 40]
+        FMIXING: 80
+        SMEAR: 0.001
+        MAXCYCLE: 500
+      fock_mixing: ANDERSON
+      post_scf: ['PPAN']
+
+calculations:
+  optimise:
+    metadata:
+      label: 'Geometry optimization'
+    parameters:
+      crystal:
+        geometry:
+          optimise:
+            hessian: HESSIDEN
+            convergence:
+              TOLDEE: 9
+    on_error:
+      300:
+        crystal:
+          scf:
+            numerical:
+              MAXCYCLE: 1000
+      301:
+        crystal:
+          scf:
+            k_points: [36, 72]
+            numerical:
+              TOLLDENS: 10
+              TOLLGRID: 18
+          numerical:
+            TOLPSEUD: 10
+      303:
+        crystal:
+          scf:
+            k_points: [36, 72]
+            numerical:
+              TOLLDENS: 10
+              TOLLGRID: 18
+          numerical:
+            TOLPSEUD: 10
+      304:
+        crystal:
+          scf:
+            k_points: [36, 72]
+            numerical:
+              TOLLDENS: 10
+              TOLLGRID: 18
+          numerical:
+            TOLPSEUD: 10
+      305:
+        crystal:
+          scf:
+            k_points: [36, 72]
+            numerical:
+              TOLLDENS: 10
+              TOLLGRID: 18
+          numerical:
+            TOLPSEUD: 10
+      306:
+        crystal:
+          scf:
+            k_points: [36, 72]
+            numerical:
+              TOLLDENS: 10
+              TOLLGRID: 18
+          numerical:
+            TOLPSEUD: 10
+  phonons:
+    metadata:
+      label: 'Phonon frequencies'
+    parameters:
+      crystal:
+        geometry:
+          phonons:
+            TEMPERAT: [35, 5.7125, 1000]
+            SCELPHONO: [[1, 1, 0], [-1, 1, 0], [0, 0, 2]]
+    on_error:
+      300:
+        crystal:
+          scf:
+            numerical:
+              MAXCYCLE: 1000
+      303:
+        crystal:
+          scf:
+            k_points: [36, 72]
+            numerical:
+              TOLLDENS: 10
+              TOLLGRID: 18
+          numerical:
+            TOLPSEUD: 10
+  elastic_constants:
+    metadata:
+      label: 'Elastic constants'
+    parameters:
+      crystal:
+        geometry:
+          elastic_constants:
+            type: ELASTCON
+    on_error:
+      300:
+        crystal:
+          scf:
+            numerical:
+              MAXCYCLE: 1000
+      303:
+        crystal:
+          scf:
+            k_points: [36, 72]
+            numerical:
+              TOLLDENS: 10
+              TOLLGRID: 18
+          numerical:
+            TOLPSEUD: 10

mpds_aiida/workflows/mpds.py

@@ -3,14 +3,15 @@
 The MPDS workflow for AiiDA that gets structure with MPDS query
 """
 import os
-import time
 import random
+import time
 
 import numpy as np
+from aiida_crystal_dft.utils import get_data_class
 from httplib2 import ServerNotFoundError
+from mpds_client import APIError, MPDSDataRetrieval
 
-from aiida_crystal_dft.utils import get_data_class
-from mpds_client import MPDSDataRetrieval, APIError
+from ..chemical_formulae import parse_formula
 from .crystal import MPDSCrystalWorkChain
 
 
@@ -29,7 +30,7 @@ def define(cls, spec):
         spec.exit_code(503, 'ERROR_NO_HITS', message='Request returned nothing')
         spec.exit_code(504, 'ERROR_SERVER_NOT_FOUND', message='MPDS server not found')
 
-    def get_geometry(self):
+    def get_geometry(self, elements_check=False):
         """ Getting geometry from MPDS database
         """
         # check for API key
@@ -50,6 +51,7 @@ def get_geometry(self):
             answer = client.get_data(
                 query_dict,
                 fields={'S': [
+                    'chemical_formula',
                     'cell_abc',
                     'sg_n',
                     'basis_noneq',
@@ -69,7 +71,18 @@ def get_geometry(self):
             self.report(f'MPDS API error: {str(ex)}')
             return self.exit_codes.ERROR_SERVER_NOT_FOUND
 
-        structs = [client.compile_crystal(line, flavor='ase') for line in answer]
+        structs = []
+        for line in answer:
+            if line:
+                structs.append(
+                    client.compile_crystal(
+                        line,
+                        flavor='ase',
+                        elements_check=elements_check,
+                        elements_counter=parse_formula(line[0])
+                        )
+                               )
+
         structs = list(filter(None, structs))
         if not structs:
             return self.exit_codes.ERROR_NO_HITS

scripts/aiida_submit_ext_scheme.py

@@ -0,0 +1,57 @@
+import argparse
+import sys
+
+import yaml
+from aiida import load_profile
+from aiida.engine import submit
+from aiida.plugins import DataFactory
+from mpds_aiida.workflows.mpds import MPDSStructureWorkChain
+
+
+def main():
+    load_profile()
+
+    parser = argparse.ArgumentParser(description="Submit an MPDSStructureWorkChain job")
+    parser.add_argument("phase",
+                        nargs="?",
+                        default="MgO/225",
+                        help="Phase information in the format 'formula/sgs/pearson'")
+    parser.add_argument("--scheme", default=None, help="Full path to the scheme file")
+    args = parser.parse_args()
+
+    phase = args.phase.split("/")
+
+    if len(phase) == 3:
+        formula, sgs, pearson = phase
+    else:
+        formula, sgs, pearson = phase[0], phase[1], None
+
+    try:
+        sgs = int(sgs)
+    except ValueError:
+        print(f"Error: space group should be an integer, got {sgs}")
+        sys.exit(1)
+
+    inputs = MPDSStructureWorkChain.get_builder()
+
+    if args.scheme:
+        try:
+            with open(args.scheme) as f:
+                inputs.workchain_options = yaml.safe_load(f)
+        except FileNotFoundError:
+            print(f"Error: Scheme file {args.scheme} not found")
+            sys.exit(1)
+        except yaml.YAMLError as exc:
+            print(f"Error parsing YAML file: {exc}")
+            sys.exit(1)
+    else:
+        inputs.workchain_options = {}
+
+    inputs.metadata = {"label": "/".join(phase)}
+    inputs.mpds_query = DataFactory('dict')(dict={'formulae': formula, 'sgs': sgs})
+    calc = submit(MPDSStructureWorkChain, **inputs)
+    print(f"Submitted WorkChain; calc=WorkCalculation(PK={calc.pk})")
+
+
+if __name__ == "__main__":
+    main()