Merge pull request #153 from pyscal/add_calphy

Add calphy

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.9.7
+current_version = 0.9.8
 commit = True
 tag = False
 

CITATION.cff

@@ -19,4 +19,4 @@ url: 'https://atomrdf.pyscal.org'
 license: "MIT"
 repository-code: https://github.com/pyscal/atomRDF
 type: software
-version: 0.9.7
+version: 0.9.8

atomrdf/workflow/pyiron/calphy.py

@@ -0,0 +1,160 @@
+import os
+import numpy as np
+import ast
+from atomrdf.structure import System
+import atomrdf.workflow.pyiron.lammps as lammps
+
+def process_job(job):
+    method_dict = {}
+    method_dict['intermediate'] = False
+    lammps.get_structures(job, method_dict)
+
+    identify_method(job, method_dict)
+    extract_calculated_quantities(job, method_dict)
+    add_software(method_dict)
+    get_simulation_folder(job, method_dict)
+    return method_dict
+
+def get_simulation_folder(job, method_dict):
+    method_dict['path'] = os.path.join(job.project.path, f'{job.name}_hdf5')
+
+
+def identify_method(job, method_dict):
+    pressure = job.input.pressure
+    if pressure is None:
+        iso = True
+        fix_lattice = True
+    elif np.isscalar(pressure):
+        iso = True
+        fix_lattice = False
+    elif np.shape(pressure) == (1,):
+        iso = True
+        fix_lattice = False
+    elif np.shape(pressure) == (2,):
+        iso = True
+        fix_lattice = False
+    elif np.shape(pressure) == (1, 3):
+        iso = False
+        fix_lattice = False
+    elif np.shape(pressure) == (2, 3):
+        iso = False
+        fix_lattice = False
+
+    dof = []
+    dof.append("AtomicPositionRelaxation")
+    ensemble = 'IsothermalIsobaricEnsemble'
+
+    if not fix_lattice:
+        dof.append("CellVolumeRelaxation")
+        ensemble = "CanonicalEnsemble"
+
+    if not iso:
+        dof.append("CellShapeRelaxation")
+
+    method_dict["dof"] = dof
+    method_dict["ensemble"] = ensemble
+
+    #now potential
+    ps = job.potential.Config.values[0][0].strip().split('pair_style ')[-1]
+    name = job.potential.Name.values[0]
+    potstr = job.potential.Citations.values[0]
+    potdict = ast.literal_eval(potstr[1:-1])
+    url = None
+    if "url" in potdict[list(potdict.keys())[0]].keys():
+        url = potdict[list(potdict.keys())[0]]["url"]
+
+    method_dict["potential"] = {}
+    method_dict["potential"]["type"] = ps
+    method_dict["potential"]["label"] = name
+    if url is not None:
+        method_dict["potential"]["uri"] = url
+    else:
+        method_dict["potential"]["uri"] = name
+    method_dict['method'] = 'ThermodynamicIntegration'
+    method_dict["temperature"] = job.input.temperature
+    method_dict["pressure"] = job.input.pressure
+
+def add_software(method_dict):
+    method_dict["workflow_manager"] = {}
+    method_dict["workflow_manager"]["uri"] = "http://demo.fiz-karlsruhe.de/matwerk/E457491"
+    method_dict["workflow_manager"]["label"] = "pyiron"
+    # and finally code details
+
+    software1 = {
+        "uri": "http://demo.fiz-karlsruhe.de/matwerk/E447986",
+        "label": "LAMMPS",
+    }
+
+    software2 = {
+        "uri": "https://doi.org/10.5281/zenodo.10527452",
+        "label": "Calphy",
+    }
+    method_dict["software"] = [software1, software2]
+
+def extract_calculated_quantities(job, method_dict):
+
+    outputs = []
+    outputs.append(
+        {
+            "label": "FreeEnergy",
+            "value": np.round(job['output/energy_free'], decimals=4),
+            "unit": "EV",
+            "associate_to_sample": True,
+        }
+    )
+    outputs.append(
+        {
+            "label": "Pressure",
+            "value": np.round(job['output/pressure'], decimals=4),
+            "unit": "GigaPA",
+            "associate_to_sample": True,
+        }
+    )
+    outputs.append(
+        {
+            "label": "Temperature",
+            "value": np.round(job['output/temperature'], decimals=2),
+            "unit": "K",
+            "associate_to_sample": True,
+        }
+    )
+    outputs.append(
+        {
+            "label": "AtomicVolume",
+            "value": np.round(job['output/atomic_volume'], decimals=4),
+            "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",
+            "associate_to_sample": True,
+        }
+    )
+    outputs.append(
+        {
+            "label": "SimulationCellLength_y",
+            "value": np.round(ly, decimals=4),
+            "unit": "ANGSTROM",
+            "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

atomrdf/workflow/pyiron/pyiron.py

@@ -11,6 +11,7 @@
 import atomrdf.workflow.pyiron.vasp as vasp
 import atomrdf.workflow.pyiron.murnaghan as murnaghan
 import atomrdf.workflow.pyiron.quasiharmonic as qha
+import atomrdf.workflow.pyiron.calphy as calphy
 
 def process_job(job):
     """
@@ -35,6 +36,8 @@ def process_job(job):
         return murnaghan.process_job(job)
     elif type(job).__name__ == 'QuasiHarmonicJob':
         return qha.process_job(job)
+    elif type(job).__name__ == 'Calphy':
+        return calphy.process_job(job)
     else:
         raise TypeError("These type of pyiron Job is not currently supported")
 

atomrdf/workflow/workflow.py

@@ -310,6 +310,11 @@ def _add_method(
         elif job_dict["method"] == "QuasiHarmonicModel":            
             self.kg.add((activity, RDF.type, Namespace("http://purls.helmholtz-metadaten.de/asmo/").QuasiHarmonicModel))
 
+        elif job_dict["method"] == "ThermodynamicIntegration":     
+            self._add_dof(job_dict, activity)
+            self._add_md(job_dict, activity)       
+            self.kg.add((activity, RDF.type, Namespace("http://purls.helmholtz-metadaten.de/asmo/").ThermodynamicIntegration))
+
         # add that structure was generated
         self.kg.add((activity, ASMO.hasComputationalMethod, method))
         self.kg.add((job_dict['sample']['final'], PROV.wasGeneratedBy, activity))

examples/workflow_examples/01_lammps_pyiron.ipynb

@@ -653,7 +653,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.1.-1"
+   "version": "3.11.8"
   }
  },
  "nbformat": 4,

setup.py

@@ -6,7 +6,7 @@
 
 setup(
     name='atomrdf',
-    version='0.9.7',
+    version='0.9.8',
     author='Abril Azocar Guzman, Sarath Menon',
     author_email='[email protected]',
     description='Ontology based structural manipulation and quering',