calphy 1.4.3__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__ = "1.4.3"
+__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

@@ -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__ = "1.4.3"
+__version__ = "1.4.5"
 
 
 def _check_equal(val):
@@ -181,6 +182,30 @@ class MeltingTemperature(BaseModel, title="Input options for melting temperature
     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()
     composition_scaling: Optional[CompositionScaling] = CompositionScaling()
@@ -191,6 +216,8 @@ 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 +523,62 @@ 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)
+
+            # 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
+
         else:
             # this is a file
             if not os.path.exists(self.lattice):

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/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/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, 
@@ -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-1.4.3.dist-info → calphy-1.4.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: calphy
-Version: 1.4.3
+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-1.4.3.dist-info → calphy-1.4.5.dist-info}/RECORD

@@ -1,25 +1,25 @@
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+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=sDMbnyjyUs3al0kdHpMYBKzBbe4iug2426YPLnVxhl0,33169
-calphy/integrators.py,sha256=hJYmbznsgY-x-eZm7ng8gW0qsGbopERl5gGDnw5uLms,21719
+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=rmOb_T2IsSR48HNvpACnlw9USYagzWT5zqZXymnVVA4,53231
+calphy/phase.py,sha256=F4GRrEG0IDR6f0rFabQYP7aYBzpKAyxPvol-n7vAj08,53540
 calphy/phase_diagram.py,sha256=Yu192y7bhWsj-xQL7ITSBdMHKXJ6I_4gV0cLfdXTOa4,27791
-calphy/postprocessing.py,sha256=WmCVj_xyCOU3pO5hycj8Qmfrx-bhIWcVnSfjx_yZkwQ,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-1.4.3.dist-info/licenses/LICENSE,sha256=XIHGB5RZLIhOjjoO1bPf0II-qDbjhP5Cv5HJMRE9v1g,16651
-calphy-1.4.3.dist-info/METADATA,sha256=ldKbDFVDC_C1qk1jzLw7lCV3-S558UunR2wNfZ16cbA,4469
-calphy-1.4.3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-calphy-1.4.3.dist-info/entry_points.txt,sha256=KX5dP2iYy9GB4Mo0lbCPAz6jo-8b1Gt9GDmsDFzt9pQ,439
-calphy-1.4.3.dist-info/top_level.txt,sha256=w871dhMqPwgjjbifBWdkT9_aOnK1ek4Odrh8UnSG3PE,7
-calphy-1.4.3.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
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+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
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