calphy 1.4.4__py3-none-any.whl → 1.4.5__py3-none-any.whl

calphy/__init__.py

@@ -4,7 +4,7 @@ from calphy.solid import Solid
 from calphy.alchemy import Alchemy
 from calphy.routines import MeltingTemp
 
-__version__ = "1.4.4"
+__version__ = "1.4.5"
 
 def addtest(a,b):
     return a+b

calphy/clitools.py

@@ -125,4 +125,5 @@ def phase_diagram():
     arg = ap.ArgumentParser()
     arg.add_argument("-i", "--input", required=True, type=str,
     help="name of the input file")
+    args = vars(arg.parse_args())
     prepare_inputs_for_phase_diagram(args['input'])

calphy/input.py

@@ -49,7 +49,7 @@ from pyscal3.core import structure_dict, element_dict, _make_crystal
 from ase.io import read, write
 import shutil
 
-__version__ = "1.4.4"
+__version__ = "1.4.5"
 
 
 def _check_equal(val):
@@ -181,10 +181,17 @@ 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'):
+
+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')]
+    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:
@@ -198,6 +205,7 @@ class MaterialsProject(BaseModel, title='Input options for materials project'):
             )
         return value
 
+
 class Calculation(BaseModel, title="Main input class"):
     monte_carlo: Optional[MonteCarlo] = MonteCarlo()
     composition_scaling: Optional[CompositionScaling] = CompositionScaling()
@@ -515,40 +523,58 @@ 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
+        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
+                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
+                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, 
-                }
+                "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']
+                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)))
+                x = int(
+                    np.ceil(
+                        (self.materials_project.target_natoms / len(structure))
+                        ** (1 / 3)
+                    )
+                )
                 structure = structure.repeat(x)
             else:
                 structure = structure.repeat(self.repeat)
 
+            # extract composition
+            types, typecounts = np.unique(
+                structure.get_chemical_symbols(), return_counts=True
+            )
+
+            for c, t in enumerate(types):
+                self._element_dict[t]["count"] = typecounts[c]
+                self._element_dict[t]["composition"] = typecounts[c] / np.sum(
+                    typecounts
+                )
+
             self._natoms = len(structure)
             self._original_lattice = self.lattice.lower()
             write_structure_file = True

calphy/postprocessing.py

@@ -30,15 +30,15 @@ def read_report(folder):
 
 def _extract_error(errfile):
     error_code = None
-    if os.path.exists(errfile):
-        with open(errfile, 'r') as fin:
-            for line in fin:
-                if 'calphy.errors' in line:
-                    break
-            try:
-                error_code = line.split(':')[0].split('.')[-1]
-            except:
-                pass
+    try:
+        if os.path.exists(errfile):
+            with open(errfile, 'r') as fin:
+                for line in fin:
+                    if 'calphy.errors' in line:
+                        break
+                    error_code = line.split(':')[0].split('.')[-1]
+    except:
+        pass
     return error_code
     
 def gather_results(mainfolder, reduce_composition=True, 

{calphy-1.4.4.dist-info → calphy-1.4.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: calphy
-Version: 1.4.4
+Version: 1.4.5
 Summary: free energy calculation for python
 Home-page: https://github.com/ICAMS/calphy
 Author: Sarath Menon, Yury Lysogorskiy, Ralf Drautz

{calphy-1.4.4.dist-info → calphy-1.4.5.dist-info}/RECORD

@@ -1,25 +1,25 @@
-calphy/__init__.py,sha256=jdtdEFX95fL5I9BhMCehg_tsIWI3TuF5BEEax1JqdCE,233
+calphy/__init__.py,sha256=ajDpPU1OkfwLqHSjYro8IgKKujLpCZhkszpGfQHA_5U,233
 calphy/alchemy.py,sha256=IEYLfsJRsjfB0zFfApmxGbYXif7IE6mUY_vjTZoXdII,17236
-calphy/clitools.py,sha256=CjADSz3nc8CLYhAmw2Os7aT-Iu_0LLIF6tdAmUMJErw,4398
+calphy/clitools.py,sha256=ZUr6ZfdopFxWMbrzNT_TQaUA16iPmZ3144oPcwcDazY,4433
 calphy/composition_transformation.py,sha256=z3X4fFVoym6QgRDpLBYZ_fM9V0IgJvBq-wITu1nwVmw,17247
 calphy/errors.py,sha256=KN47RWTLbg1H_NZMrhCiJCbqjqJScJ1pgQAuzj1-l84,1268
 calphy/helpers.py,sha256=goN_n5kceSaevjBilQDgHD5-QZxsQsOwTiWsY00jMcM,8411
-calphy/input.py,sha256=hGq4ecaxHJvZV9XI5RGM1eVIpcEpvbRkSCyr1ousTRo,35644
+calphy/input.py,sha256=3xVoJcbwq3T7y_1drIvg1Erel9dz6y9A4rgNsncEfgw,36225
 calphy/integrators.py,sha256=q5sIJX3nh4c9kmDQJ4Pqhvm38tRWKELoJwm5gW0lqws,21858
 calphy/kernel.py,sha256=wjSpQ59PN-aqHQ1kvOxTYnP2d3wE1Zx4A9ZhqQFqGlI,6311
 calphy/liquid.py,sha256=ECF3DxPZv7XHnmQzk_yz1fol-Vsd98lRojTMAR1YS3M,15025
 calphy/phase.py,sha256=F4GRrEG0IDR6f0rFabQYP7aYBzpKAyxPvol-n7vAj08,53540
 calphy/phase_diagram.py,sha256=Yu192y7bhWsj-xQL7ITSBdMHKXJ6I_4gV0cLfdXTOa4,27791
-calphy/postprocessing.py,sha256=SLHiW5lrTZ4t_t1ZGCCehQnKioS5eFvyxxLuecYS9Iw,15164
+calphy/postprocessing.py,sha256=XxpFGbR8dUoKhGb7GCPEWPA4CWl7ZftuM1cN4tz7-fQ,15164
 calphy/queuekernel.py,sha256=4GMIYnjMiAPipoLNKP5noYcfeEOI_vCqm84zgokk7Xw,5321
 calphy/routines.py,sha256=YaVoAbeAbZ3ytAP_A0o5ngkpPiXpc_lk2I0bN3nqhPs,17858
 calphy/scheduler.py,sha256=nIxlKKGj8ol_FuYMMtXrQinPGhPlYs2h-JsEGHC7_wY,8666
 calphy/solid.py,sha256=zHSqri8roW23hIQ21huxHHJqq3P5EklSj6Z0z9ywfbc,21911
 calphy/splines.py,sha256=BGwUVz_qXQxUzpUCuZo6CsELcd5JVNWzI-Ttcz22G_E,61627
 calphy/utils.py,sha256=0UpsYoxjS5N-iGs-cdm0YDMkLF8IHvKO3smXDHrj3eg,3818
-calphy-1.4.4.dist-info/licenses/LICENSE,sha256=XIHGB5RZLIhOjjoO1bPf0II-qDbjhP5Cv5HJMRE9v1g,16651
-calphy-1.4.4.dist-info/METADATA,sha256=UCs0MNKdMuusbCZkwRF7NjT07jTKdhVQ4An9_Us_0SE,4469
-calphy-1.4.4.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-calphy-1.4.4.dist-info/entry_points.txt,sha256=KX5dP2iYy9GB4Mo0lbCPAz6jo-8b1Gt9GDmsDFzt9pQ,439
-calphy-1.4.4.dist-info/top_level.txt,sha256=w871dhMqPwgjjbifBWdkT9_aOnK1ek4Odrh8UnSG3PE,7
-calphy-1.4.4.dist-info/RECORD,,
+calphy-1.4.5.dist-info/licenses/LICENSE,sha256=XIHGB5RZLIhOjjoO1bPf0II-qDbjhP5Cv5HJMRE9v1g,16651
+calphy-1.4.5.dist-info/METADATA,sha256=za1qlwUMSyzxwl2bghD8i9HdGRMLKpxslgpkX-jiM2s,4469
+calphy-1.4.5.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+calphy-1.4.5.dist-info/entry_points.txt,sha256=KX5dP2iYy9GB4Mo0lbCPAz6jo-8b1Gt9GDmsDFzt9pQ,439
+calphy-1.4.5.dist-info/top_level.txt,sha256=w871dhMqPwgjjbifBWdkT9_aOnK1ek4Odrh8UnSG3PE,7
+calphy-1.4.5.dist-info/RECORD,,