calphy 2.1.2__tar.gz → 2.3.1__tar.gz

{calphy-2.1.2 → calphy-2.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: calphy
-Version: 2.1.2
+Version: 2.3.1
 Summary: free energy calculation for python
 Author: Yury Lysogorskiy, Ralf Drautz
 Author-email: Sarath Menon <sarath.menon@ruhr-uni-bochum.de>
@@ -26,7 +26,8 @@ Requires-Dist: mendeleev
 Requires-Dist: tqdm
 Requires-Dist: scipy
 Requires-Dist: pydantic>=2.3.0
-Requires-Dist: pyscal3
+Requires-Dist: ase
+Requires-Dist: pyscal3>=4.0.0
 Provides-Extra: test
 Requires-Dist: pytest>=7; extra == "test"
 Provides-Extra: materials-project
@@ -42,6 +43,7 @@ Dynamic: license-file
 - <img src="https://render.githubusercontent.com/render/math?math=F(V_i,T_i)"> and <img src="https://render.githubusercontent.com/render/math?math=G(P_i,T_i)"> for both solid and liquid phases at the given thermodynamic conditions using [non-equilibrium Hamiltonian interpolation](https://linkinghub.elsevier.com/retrieve/pii/S0927025615007089).
 - <img src="https://render.githubusercontent.com/render/math?math=F(T_i \to T_f)"> and <img src="https://render.githubusercontent.com/render/math?math=G(T_i \to T_f)">, temperature dependence of Gibbs and Helmholtz free energies using the [reversible scaling](https://link.aps.org/doi/10.1103/PhysRevLett.83.3973) approach.
 - Calculation of solid-solid or solid-liquid phase transition temperatures.
+- Calculation of solid-liquid coexistence lines <img src="https://render.githubusercontent.com/render/math?math=P_{coex}(T)"> over a wide pressure range from a single known coexistence point using [dynamic Clausius-Clapeyron integration](https://doi.org/10.1063/1.1420486).
 - Calculation of specific heat <img src="https://render.githubusercontent.com/render/math?math=c_P(T)"> as a function of temperature.
 - Calculation of <img src="https://render.githubusercontent.com/render/math?math=F(x, T)"> and <img src="https://render.githubusercontent.com/render/math?math=G(x, T)"> for multicomponent systems using [alchemical transformations](https://journals.aps.org/prmaterials/abstract/10.1103/PhysRevMaterials.5.103801).
 - [Upsampling calculations](https://journals.aps.org/prmaterials/abstract/10.1103/PhysRevMaterials.5.103801).

{calphy-2.1.2 → calphy-2.3.1}/README.md

@@ -5,6 +5,7 @@
 - <img src="https://render.githubusercontent.com/render/math?math=F(V_i,T_i)"> and <img src="https://render.githubusercontent.com/render/math?math=G(P_i,T_i)"> for both solid and liquid phases at the given thermodynamic conditions using [non-equilibrium Hamiltonian interpolation](https://linkinghub.elsevier.com/retrieve/pii/S0927025615007089).
 - <img src="https://render.githubusercontent.com/render/math?math=F(T_i \to T_f)"> and <img src="https://render.githubusercontent.com/render/math?math=G(T_i \to T_f)">, temperature dependence of Gibbs and Helmholtz free energies using the [reversible scaling](https://link.aps.org/doi/10.1103/PhysRevLett.83.3973) approach.
 - Calculation of solid-solid or solid-liquid phase transition temperatures.
+- Calculation of solid-liquid coexistence lines <img src="https://render.githubusercontent.com/render/math?math=P_{coex}(T)"> over a wide pressure range from a single known coexistence point using [dynamic Clausius-Clapeyron integration](https://doi.org/10.1063/1.1420486).
 - Calculation of specific heat <img src="https://render.githubusercontent.com/render/math?math=c_P(T)"> as a function of temperature.
 - Calculation of <img src="https://render.githubusercontent.com/render/math?math=F(x, T)"> and <img src="https://render.githubusercontent.com/render/math?math=G(x, T)"> for multicomponent systems using [alchemical transformations](https://journals.aps.org/prmaterials/abstract/10.1103/PhysRevMaterials.5.103801).
 - [Upsampling calculations](https://journals.aps.org/prmaterials/abstract/10.1103/PhysRevMaterials.5.103801).

{calphy-2.1.2 → calphy-2.3.1}/calphy/__init__.py

@@ -28,7 +28,7 @@ from calphy.solid import Solid
 from calphy.alchemy import Alchemy
 from calphy.routines import MeltingTemp
 
-__version__ = "2.1.2"
+__version__ = "2.3.1"
 
 def addtest(a,b):
     return a+b

{calphy-2.1.2 → calphy-2.3.1}/calphy/alchemy.py

@@ -175,7 +175,7 @@ class Alchemy(cph.Phase):
         """Coupling-mode integration: ramp ONLY the last component 0->1
         (forward) and 1->0 (backward) over the fixed base.
         W = int <U_last>_lam dlam;  dF = (W_f + W_b)/2 per iteration."""
-        lmp = ph.create_object(self.calc, self.simfolder)
+        lmp = self._open_lammps()
         conf = os.path.join(self.simfolder, "conf.equilibration.data")
         # style only before read_data (pair_coeff needs the box)
         ns = self.calc._pair_style_with_options
@@ -253,7 +253,7 @@ class Alchemy(cph.Phase):
         Fix lattice option is not implemented at present.
         At the end of the run, the averaged box dimensions are calculated.
         """
-        lmp = ph.create_object(self.calc, self.simfolder)
+        lmp = self._open_lammps()
 
         if self.calc.alchemy_coupling:
             # equilibrate on the BASE system (lam = 0): full base, ramped
@@ -345,7 +345,7 @@ class Alchemy(cph.Phase):
         initial, final = self._end_states()
 
         # create lammps object
-        lmp = ph.create_object(self.calc, self.simfolder)
+        lmp = self._open_lammps()
 
         # Adiabatic switching parameters.
         lmp.command("variable        li       equal   1.0")

{calphy-2.1.2 → calphy-2.3.1}/calphy/composition_transformation.py

@@ -27,11 +27,9 @@ import re
 import numpy as np
 import os
 import random
-import pyscal3.core as pc
 from mendeleev import element
 from ase.io import read, write
 from ase.atoms import Atoms
-from pyscal3.core import element_dict
 from calphy.integrators import kb
 
 
@@ -163,9 +161,9 @@ class CompositionTransformation:
         entropy_term = kb * np.sum(ents)
         return entropy_term
 
-    def convert_to_pyscal(self):
+    def read_structure(self):
         """
-        Convert a given system to pyscal and give a dict of type mappings
+        Read the input structure and set up the element <-> type mappings
         """
         # Create Z_of_type mapping to properly read LAMMPS data files
         # This ensures atoms are correctly identified by their element
@@ -178,20 +176,19 @@ class CompositionTransformation:
         aseobj = read(
             self.calc.lattice, format="lammps-data", style="atomic", Z_of_type=Z_of_type
         )
-        pstruct = pc.System(aseobj, format="ase")
 
         # here we have to validate the input composition dict; and map it
-        typelist = pstruct.atoms.species
+        typelist = aseobj.get_chemical_symbols()
         types, typecounts = np.unique(typelist, return_counts=True)
         composition = {types[x]: typecounts[x] for x in range(len(types))}
 
         atomsymbols = self.calc.element
         atomtypes = [x + 1 for x in range(len(self.calc.element))]
 
-        self.pyscal_structure = pstruct
+        self.structure = aseobj
         self.typedict = dict(zip(atomsymbols, atomtypes))
         self.reversetypedict = dict(zip(atomtypes, atomsymbols))
-        self.natoms = self.pyscal_structure.natoms
+        self.natoms = len(self.structure)
 
         # Count of actual unique atom types present in the structure
         # This matches what's declared in the LAMMPS data file header
@@ -239,8 +236,9 @@ class CompositionTransformation:
             self.atom_mark.append(False)
 
         # Use species (element symbols) instead of numeric types
-        self.atom_species = self.pyscal_structure.atoms.species
-        self.atom_type = self.pyscal_structure.atoms.types
+        self.atom_species = self.structure.get_chemical_symbols()
+        # placeholder types; update_types assigns the mapping type of every atom
+        self.atom_type = [1] * self.natoms
         self.mappings = [f"{x}-{x}" for x in self.atom_species]
 
     def update_mark_atoms(self):
@@ -378,9 +376,6 @@ class CompositionTransformation:
         for x in range(len(self.atom_type)):
             self.atom_type[x] = self.mappingdict[self.mappings[x]]
 
-        # Update pyscal structure types
-        self.pyscal_structure.atoms.types = self.atom_type
-
     def iselement(self, symbol):
         try:
             _ = element(symbol)
@@ -582,9 +577,8 @@ class CompositionTransformation:
         from ase.io import write as ase_write
         from ase import Atoms as ASEAtoms
 
-        # Get positions and cell from pyscal structure
-        positions = self.pyscal_structure.atoms.positions
-        cell = self.pyscal_structure.box
+        positions = self.structure.positions
+        cell = self.structure.cell
 
         # Build per-atom type numbers and chemical symbols.
         # for_fe_mode: remap each atom to its TARGET element's typedict entry so
@@ -598,8 +592,8 @@ class CompositionTransformation:
             invert_typedict = {v: k for k, v in self.typedict.items()}
             symbols = [invert_typedict[t] for t in fe_types]
         else:
-            fe_types = None  # will use pyscal types below
-            symbols = [self.reversetypedict[t] for t in self.pyscal_structure.atoms.types]
+            fe_types = None  # will use the mapping types below
+            symbols = [self.reversetypedict[t] for t in self.atom_type]
 
         ase_atoms = ASEAtoms(symbols=symbols, positions=positions, cell=cell, pbc=True)
 
@@ -611,7 +605,7 @@ class CompositionTransformation:
             lines = f.readlines()
 
         # Choose which per-atom type list to use
-        atom_types_to_write = fe_types if for_fe_mode else list(self.pyscal_structure.atoms.types)
+        atom_types_to_write = fe_types if for_fe_mode else list(self.atom_type)
 
         # Find the Atoms section and replace type numbers
         # Support different ASE formats: "Atoms # atomic", "Atoms # full", or just "Atoms"
@@ -635,7 +629,7 @@ class CompositionTransformation:
                         break
 
         # Verify all atoms were updated
-        expected_atoms = len(self.pyscal_structure.atoms.types)
+        expected_atoms = len(self.atom_type)
         if atom_idx != expected_atoms:
             raise RuntimeError(
                 f"Failed to update all atoms in {outfilename}. "
@@ -666,7 +660,7 @@ class CompositionTransformation:
         self.unique_mappings = []
 
         self.get_composition_transformation()
-        self.convert_to_pyscal()
+        self.read_structure()
 
         self.mark_atoms()
         self.update_mark_atoms()