calphy 1.4.2__tar.gz → 1.4.4__tar.gz

{calphy-1.4.2/calphy.egg-info → calphy-1.4.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: calphy
-Version: 1.4.2
+Version: 1.4.4
 Summary: free energy calculation for python
 Home-page: https://github.com/ICAMS/calphy
 Author: Sarath Menon, Yury Lysogorskiy, Ralf Drautz

{calphy-1.4.2 → calphy-1.4.4}/calphy/__init__.py

@@ -4,7 +4,7 @@ from calphy.solid import Solid
 from calphy.alchemy import Alchemy
 from calphy.routines import MeltingTemp
 
-__version__ = "1.4.2"
+__version__ = "1.4.4"
 
 def addtest(a,b):
     return a+b

{calphy-1.4.2 → calphy-1.4.4}/calphy/input.py

@@ -28,6 +28,7 @@ from pydantic import (
     Field,
     ValidationError,
     model_validator,
+    field_validator,
     conlist,
     PrivateAttr,
 )
@@ -48,7 +49,7 @@ from pyscal3.core import structure_dict, element_dict, _make_crystal
 from ase.io import read, write
 import shutil
 
-__version__ = "1.4.2"
+__version__ = "1.4.4"
 
 
 def _check_equal(val):
@@ -180,6 +181,22 @@ class MeltingTemperature(BaseModel, title="Input options for melting temperature
     step: Annotated[int, Field(default=200, ge=20)]
     attempts: Annotated[int, Field(default=5, ge=1)]
 
+class MaterialsProject(BaseModel, title='Input options for materials project'):
+    api_key: Annotated[str, Field(default="", exclude=True)]
+    conventional: Annotated[bool, Field(default=True)]
+    target_natoms: Annotated[int, Field(default=1500, description='The structure parsed from materials project would be repeated to approximately this value')]
+
+    @field_validator("api_key", mode="after")
+    def resolve_api_key(cls, v: str) -> str:
+        if not v:
+            return v
+        value = os.getenv(v)
+        if not value:
+            raise ValueError(
+                f"Environment variable '{v}' not found or empty. "
+                f"Set it before running, e.g.:\n  export {v}='your_api_key_here'"
+            )
+        return value
 
 class Calculation(BaseModel, title="Main input class"):
     monte_carlo: Optional[MonteCarlo] = MonteCarlo()
@@ -191,6 +208,8 @@ class Calculation(BaseModel, title="Main input class"):
     tolerance: Optional[Tolerance] = Tolerance()
     uhlenbeck_ford_model: Optional[UFMP] = UFMP()
     melting_temperature: Optional[MeltingTemperature] = MeltingTemperature()
+    materials_project: Optional[MaterialsProject] = MaterialsProject()
+
     element: Annotated[List[str], BeforeValidator(to_list), Field(default=[])]
     n_elements: Annotated[int, Field(default=0)]
     mass: Annotated[List[float], BeforeValidator(to_list), Field(default=[])]
@@ -496,6 +515,44 @@ class Calculation(BaseModel, title="Main input class"):
             self._original_lattice = self.lattice.lower()
             write_structure_file = True
 
+        elif self.lattice.split('-')[0] == 'mp':
+            #confirm here that API key exists
+            if not self.materials_project.api_key:
+                raise ValueError('could not find API KEY, pls set it.')
+            #now we need to fetch the structure
+            try:
+                from mp_api.client import MPRester
+            except ImportError:
+                raise ImportError('Could not import mp_api, make sure you install mp_api package!')
+            #now all good
+            rest = {
+                    "use_document_model": False,
+                    "include_user_agent": True,
+                    "api_key": self.materials_project.api_key, 
+                }
+            with MPRester(**rest) as mpr:
+                docs = mpr.materials.summary.search(material_ids=[self.lattice])
+
+            structures = []
+            for doc in docs:
+                struct = doc['structure']
+                if self.materials_project.conventional:
+                    aseatoms = struct.to_conventional().to_ase_atoms()
+                else:
+                    aseatoms = struct.to_primitive().to_ase_atoms()
+                structures.append(aseatoms)
+            structure = structures[0]
+            
+            if np.prod(self.repeat) == 1:
+                x = int(np.ceil((self.materials_project.target_natoms/len(structure))**(1/3)))
+                structure = structure.repeat(x)
+            else:
+                structure = structure.repeat(self.repeat)
+
+            self._natoms = len(structure)
+            self._original_lattice = self.lattice.lower()
+            write_structure_file = True
+
         else:
             # this is a file
             if not os.path.exists(self.lattice):

{calphy-1.4.2 → calphy-1.4.4}/calphy/integrators.py

@@ -226,6 +226,7 @@ def integrate_rs(simfolder, f0, t,
     
     """
     ws = []
+    es = []
     p = p/(10000*160.21766208)
     
     for i in range(1, nsims+1):
@@ -245,9 +246,12 @@ def integrate_rs(simfolder, f0, t,
         wf = cumtrapz(fdx, flambda,initial=0)
         wb = cumtrapz(bdx[::-1], blambda[::-1],initial=0)
         w = (wf + wb) / (2*flambda)
+        e = np.max(np.abs((wf - wb)/(2*flambda)))
+
         ws.append(w)
-    
+        es.append(e)
 
+    e_diss = np.min(es)
     wmean = np.mean(ws, axis=0)
     werr = np.std(ws, axis=0)
     temp = t/flambda
@@ -257,8 +261,9 @@ def integrate_rs(simfolder, f0, t,
     if not return_values:
         outfile = os.path.join(simfolder, "temperature_sweep.dat")
         np.savetxt(outfile, np.column_stack((temp, f, werr)))
+        return None, e_diss
     else:
-        return (temp, f, werr)
+        return (temp, f, werr), e_diss
 
 
 def integrate_ps(simfolder, f0, natoms, pi, pf, nsims=1, 

{calphy-1.4.2 → calphy-1.4.4}/calphy/phase.py

@@ -1206,7 +1206,7 @@ class Phase:
         res : list of lists of shape 1x3
             Only returned if `return_values` is True.
         """
-        res = integrate_rs(
+        res, ediss = integrate_rs(
             self.simfolder,
             self.fe,
             self.calc._temperature,
@@ -1217,6 +1217,11 @@ class Phase:
             return_values=return_values,
         )
 
+        self.logger.info(f'Maximum energy dissipation along the temperature scaling part: {ediss} eV/atom')
+        if np.abs(ediss) > 1E-4:
+            self.logger.warning(f'Found max energy dissipation of {ediss} along the temperature scaling path. Please ensure there are no structural changes!')
+
+
         if return_values:
             return res
 

{calphy-1.4.2 → calphy-1.4.4}/calphy/phase_diagram.py

@@ -314,7 +314,10 @@ def prepare_inputs_for_phase_diagram(inputyamlfile, calculation_base_name=None):
 
         comps = phase['composition']
         reference_element = comps["reference_element"]
-        use_composition_scaling = bool(comps["use_composition_scaling"])
+        if "use_composition_scaling" in comps.keys():
+            use_composition_scaling = bool(comps["use_composition_scaling"])
+        else:
+            use_composition_scaling = True
         if str(phase_reference_state) == 'liquid':
             use_composition_scaling = False
 

{calphy-1.4.2 → calphy-1.4.4}/calphy/postprocessing.py

@@ -121,7 +121,7 @@ def gather_results(mainfolder, reduce_composition=True,
         #print(inpfile)
         if not os.path.exists(outfile):
             datadict['status'].append('False')
-            datadict['free_energy'].append(np.NaN)
+            datadict['free_energy'].append(np.nan)
             #check if error file is found
             errfile = os.path.join(os.getcwd(), mainfolder, folder+'.sub.err')
             datadict['error_code'][-1] = _extract_error(errfile)

{calphy-1.4.2 → calphy-1.4.4}/calphy/solid.py

@@ -299,7 +299,7 @@ class Solid(cph.Phase):
             lmp.command(f'pair_style {self.calc._pair_style_with_options[0]}')
 
         #set up structure
-        lmp = ph.create_structure(lmp, self.calc, species=self.calc.n_elements+self.calc._ghost_element_count)
+        lmp = ph.create_structure(lmp, self.calc)
 
         if self.calc.potential_file is None:
             lmp.command(f'pair_coeff {self.calc.pair_coeff[0]}')

{calphy-1.4.2 → calphy-1.4.4/calphy.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: calphy
-Version: 1.4.2
+Version: 1.4.4
 Summary: free energy calculation for python
 Home-page: https://github.com/ICAMS/calphy
 Author: Sarath Menon, Yury Lysogorskiy, Ralf Drautz

{calphy-1.4.2 → calphy-1.4.4}/calphy.egg-info/SOURCES.txt

@@ -28,6 +28,7 @@ calphy.egg-info/entry_points.txt
 calphy.egg-info/not-zip-safe
 calphy.egg-info/requires.txt
 calphy.egg-info/top_level.txt
+tests/test_ex07.py
 tests/test_helpers.py
 tests/test_integrators.py
 tests/test_options.py

{calphy-1.4.2 → calphy-1.4.4}/setup.py

@@ -53,7 +53,7 @@ setup(
     packages=find_packages(include=['calphy', 'calphy.*']),
     test_suite='tests',
     url='https://github.com/ICAMS/calphy',
-    version='1.4.2',
+    version='1.4.4',
     zip_safe=False,
     entry_points={
         'console_scripts': [

calphy-1.4.4/tests/test_ex07.py

@@ -0,0 +1,25 @@
+def test_ex07():
+    import calphy
+    from calphy.postprocessing import read_report
+
+# def test_example07_first_cell_runs():
+#     notebook_path = os.path.abspath(os.path.join(os.path.dirname(__file__), '../examples/example_07/analysis.ipynb'))
+
+#     with open(notebook_path, "r", encoding="utf-8") as f:
+#         nb = nbformat.read(f, as_version=4)
+
+#     # Filter just the first code cell
+#     first_code_cell = next((cell for cell in nb.cells if cell.cell_type == "code"), None)
+
+#     if not first_code_cell:
+#         pytest.fail("No code cell found in example07.ipynb")
+
+#     # Create a minimal notebook with only the first cell
+#     nb_single = nbformat.v4.new_notebook()
+#     nb_single.cells = [first_code_cell]
+
+#     try:
+#         client = NotebookClient(nb_single, timeout=60, kernel_name="pyiron")
+#         client.execute()
+#     except Exception as e:
+#         pytest.fail(f"First code cell in example07.analysis.ipynb failed: {e}")