cosmopharm 0.1.0__py3-none-any.whl → 0.1.0a1__py3-none-any.whl

cosmopharm/actmodels/actmodel.py

@@ -35,17 +35,6 @@ class ActModel:
         # Fill gmix with calculated values where the mask is True
         gmix[mask] = _gmix
         return gmix[0] if is_scalar else gmix
-    
-    def thermofac(self, T, x):
-        """ Approximate thermodynamic factor
-        Simple derivative form, when no analytical equation is available. 
-        """
-        def f(x1):
-            x = np.array([x1, 1-x1])
-            return self.lngamma(T, x)[0]
-        h, x = 0.0001, x[0]
-        dy = (f(x+h)-f(x-h))/(2*h)
-        return 1 + x * dy
 
 
 # =============================================================================

cosmopharm/actmodels/cosmo.py

@@ -1,3 +1,4 @@
+
 import numpy as np
 import cCOSMO
 
@@ -5,9 +6,9 @@ from typing import List, Union, Literal
 from .actmodel import ActModel
 from ..components import Component
 
-class COSMOSAC(ActModel):
 
-    # Handle invalid values for free volume calculation
+class COSMOSAC(ActModel):
+    # Handling invalid values for free volume calculation
     class InvalidFreeVolumeParametersException(Exception):
         pass
 
@@ -66,6 +67,7 @@ class COSMOSAC(ActModel):
         (can replace ln_gamma_comb of normal COSMO-SAC) - Kuo2013
         x, v_298, v_hc are 1D arrays (number of elements = number of components)
         """
+        # TODO: Make sure, that v_298 and v_hc are provided, else "FV" not possible
         self.validate_free_volume_parameters()  # Ensure components are valid before proceeding
         v_298 = np.array([comp.v_298 for comp in self.mixture])
         v_hc = np.array([comp.v_hc for comp in self.mixture])

cosmopharm/equilibrium/lle.py

@@ -1,7 +1,7 @@
 import numpy as np
 import pandas as pd
 from scipy.optimize import least_squares, root
-from typing import Union, Optional, Type, List, Dict
+from typing import Union, Optional, Type, List
 
 from ..components import Component
 from ..actmodels import ActModel
@@ -17,104 +17,6 @@ class LLE:
         self.mixture = mixture
         self._validate_arguments()
 
-    def miscibility(self,
-                    T: float,
-                    x0: np.ndarray = None,
-                    x0_type: str = 'mole',
-                    max_gap: float = 0.1,
-                    max_gap_type: str = 'mole',
-                    max_T: float = 1000,
-                    dT: float = 10,
-                    exponent: float = 1
-                    ) -> pd.DataFrame:
-        """ Calculate miscibility """
-        self.config = getattr(self.actmodel, 'config', '')
-        Mw = np.array([c.Mw for c in self.mixture])
-        self.is_valid_Mw = self.is_valid_numpy_array(Mw)
-        res = {'binodal':[], 'spinodal':[]}
-        var = 'x' if max_gap_type == 'mole' else 'w'
-        print()
-        print("Calculating LLE...")
-
-        # Define column names
-        binodal_columns = ['T', 'xL1', 'xL2']
-        if self.is_valid_Mw:
-            binodal_columns += ['wL1', 'wL2']
-
-        # Check for valid molar masses
-        if x0_type == 'weight':
-            if self.is_valid_Mw:
-                x0 = self.convert_to_mole_fractions(x0, self.mixture.Mw)
-            else:
-                raise ValueError("Molar masses are not available for conversion from weight to mole fraction.")
-# =============================================================================
-# TODO: Implement all edge cases (no LLE, bad approximation, ....)
-# TODO: Improve code structure
-        # Approximate initial value for LLE
-        if x0 is None:
-            print("...searching for suitable initial value...")
-            x0 = self.approx_init_x0(T)
-
-            if any(x is None for x in x0):
-                print("...no initial value at T0 was found. Try another T0.")
-                return pd.DataFrame(columns=binodal_columns)
-
-            # Check if initial guess is reasonable - otherwise increase T
-            # TODO: Check whether it might be an LCST if isLower
-            binodal = self.solve_lle(T, x0, show_output=False)
-            isEqual = np.diff(binodal['x'])[0] < 1e-8 # check if both phases have equal composition
-            if isEqual:
-                print("...no initial value at T0 was found. Try another T0.")
-                return pd.DataFrame(columns=binodal_columns)
-            isLower = min(binodal['x']) < min(x0) # lower bound below min(x0)
-            while isLower and T <= max_T:
-                print('LLE: ', f"{T=:.2f}", "...no feasbible initial value found.")
-                T += 10  # Increase T by 10
-                x0 = self.approx_init_x0(T)
-                binodal = self.solve_lle(T, x0, show_output=False)
-            print("Suitable initial value found! Proceed with calculating LLE...")
-# =============================================================================
-        # First iteration step
-        binodal = self.solve_lle(T, x0)
-        gap = np.diff(binodal[var])[0]
-        res['binodal'].append((T, *[val for vals in binodal.values() for val in vals]))
-
-        # Subsequent iteration steps
-        while gap > max_gap and T <= max_T:
-            T += dT * gap**exponent
-            x0 = binodal['x']
-            binodal = self.solve_lle(T, x0)
-            gap = np.diff(binodal[var])[0]
-            res['binodal'].append((T, *[val for vals in binodal.values() for val in vals]))
-
-        # Convert lists to DataFrames
-        res = pd.DataFrame(res['binodal'], columns=binodal_columns)
-        return res
-
-# =============================================================================
-# MATHEMATICS
-# =============================================================================
-
-    def solve_lle(self, T: float, x0: np.ndarray, show_output=True) -> Dict[str, np.ndarray]:
-        """ Solve for liquid-liquid equilibrium (LLE) at a given temperature and initial composition. """
-        binodal = {'x': self.binodal(T, x0)}
-        output = [f"{k}={v:.4f}" for k,v in zip(['xL1', 'xL2'], binodal['x'])]
-
-        if self.is_valid_Mw:
-            binodal['w'] = self.actmodel._convert(binodal['x'])
-            output += [f"{k}={v:.4f}" for k,v in zip(['wL1', 'wL2'], binodal['w'])]
-
-        if show_output:
-            prefix = f'LLE ({self.config})' if self.config else 'LLE'
-            print(f'{prefix}: ', f"{T=:.2f}", *output)
-        return binodal
-
-
-
-
-# =============================================================================
-# THERMODYNAMICS
-# =============================================================================
     def fobj_binodal(self, x1, T):
         # Equilibrium: Isoactivity criterion (aL1 - aL2 = 0)
         x = np.array([x1, 1-x1])
@@ -127,23 +29,29 @@ class LLE:
         x = np.array([x1, 1-x1])
         return self.actmodel.thermofac(T, x)
 
-    def binodal(self, T, x0=None):
+    def binodal(self, T, x0=None, solver='least_squares'):
         if x0 is None:
-            x0 = [0.1, 0.999]
-        kwargs = dict(bounds=(0,1), ftol=1e-15, xtol=1e-15)
-        res = least_squares(self.fobj_binodal, x0, args=(T,), **kwargs)
-        return res.x
+            x0 = [0.1, 0.999]    # 1_N2_Ethan
 
-    def spinodal(self, T, x0=None):
-        if x0 is None:
-            x0 = self.binodal(T, x0)
-        kwargs = dict(bounds=(0,1), ftol=1e-15, xtol=1e-15)
-        res = least_squares(self.fobj_spinodal, x0, args=(T,), **kwargs)
-        return res.x
+        if solver == 'least_squares':
+            kwargs = dict(bounds=(0,1), ftol=1e-15, xtol=1e-15)
+            res = least_squares(self.fobj_binodal, x0, args=(T,), **kwargs)
+            # print(res.nfev)
+            return res.x, res.nfev
+        else:
+            kwargs = dict(method='krylov', options={'maxiter': 5})
+            res = root(self.fobj_binodal, x0, args=(T,), **kwargs)
+            # print(res.nit)
+            return res.x, 30
 
+    def spinodal(self, x0=None):
+        if x0 is None:
+            x0 = self.binodal()
+        return least_squares(self.fobj_spinodal, x0).x
 
 # =============================================================================
-# AUXILLIARY FUNCTIONS
+# TODO: (1) Add some "approx_initial_values" function based on gmix
+# TODO: (2) Overall improve this code to match the SLE code
 # =============================================================================
     def approx_init_x0(self, T):
         x1 = spacing(0,1,51,'poly',n=3)
@@ -151,10 +59,59 @@ class LLE:
         xL, xR, yL, yR = estimate_lle_from_gmix(x1, gmix, rough=True)
         return xL, xR
 
+    def solve_lle(self, T, x0, solver='least_squares', info=True):
+        binodal_x, nfev = self.binodal(T, x0, solver)
+        binodal_w = self.actmodel._convert(binodal_x)
+        formatted_w_binodal = [f"wL{i+1}={value:.4f}" for i, value in enumerate(binodal_w)]
+        formatted_x_binodal = [f"xL{i+1}={value:.6f}" for i, value in enumerate(binodal_x)]
+        msg = ('LLE: ', f"{T=:.2f}", *formatted_w_binodal, *formatted_x_binodal)
+        if info:
+            print(*msg)
+            return binodal_x, binodal_w, nfev
+        return binodal_x, binodal_w, nfev, msg
+
+    def miscibility(self, T, x0=None, max_gap=0.1, max_T=500, dT=25, exponent=2):
+        """ Calculate miscibility """
+        print()
+        print("Calculating LLE...")
+        res = []
+
+        if x0 is None:
+            print("...searching for suitable initial value...")
+            x0 = self.approx_init_x0(T)
+        binodal_x, binodal_w, nfev, msg = self.solve_lle(T, x0, info=False)
+
+        # Check if initial guess is reasonalble - otherwise increase T
+        while binodal_x[0] < x0[0] and T <= max_T:
+            print('LLE: ', f"{T=:.2f}", "...no feasbible initial value found.")
+            T += 10  # Increase T by 10
+            x0 = self.approx_init_x0(T)
+            binodal_x, binodal_w, nfev, msg = self.solve_lle(T, x0, info=False)
+        print("Suitable initial value found! Proceed with calculating LLE...")
+        print(*msg)
+        gap = np.diff(binodal_w)[0]
+        res.append((T, *binodal_w, *binodal_x))
+
+        while gap > max_gap and T <= max_T:
+            solver = 'least_squares' if nfev <= 30 else 'root'
+            solver = 'least_squares'
+            # print(solver)
+            T += dT * gap**exponent
+            x0 = binodal_x
+            binodal_x, binodal_w, nfev = self.solve_lle(T, x0, solver)
+            gap = np.diff(binodal_w)[0]
+            res.append((T, *binodal_w, *binodal_x))
+
+        columns = ['T', 'wL1', 'wL2', 'xL1', 'xL2']
+        res = pd.DataFrame(res, columns=columns)
+        return res
+
+# =============================================================================
+# AUXILLIARY FUNCTIONS
+# =============================================================================
     def _validate_arguments(self):
         """Validate the arguments for the LLE class."""
-        # TODO: Insert case where both actmodel and mixture are provided
-        # (check if acmodel.mixture == mixture, if not raise warning)
+        # TODO: Insert case where both actmodel and mixture are provided (check if acmodel.mixture == mixture, if not raise warning)
         if isinstance(self.actmodel, ActModel):
             # If actmodel is an instance of ActModel
             self.mixture: List[Component] = self.mixture or self.actmodel.mixture
@@ -167,12 +124,3 @@ class LLE:
             # If actmodel is neither an instance nor a subclass of ActModel
             err = "'actmodel' must be an instance or a subclass of 'ActModel'"
             raise ValueError(err)
-
-    def is_valid_numpy_array(self, arr: np.ndarray) -> bool:
-        """Check if a numpy array contains only numbers and no None values."""
-        if not isinstance(arr, np.ndarray):
-            return False
-        if arr.dtype == object:  # Check if the array contains objects (which could include None)
-            return not np.any(arr == None)
-        else:
-            return np.issubdtype(arr.dtype, np.number)

cosmopharm/equilibrium/sle.py

@@ -77,7 +77,7 @@ class SLE:
             x0 = out if not is_iterable else x0
             res = {key: arg, lock: out, 'vary': self._vary}
             res['w'] = self.actmodel._convert(res['x'])[0]
-            text = (f"T={res['T']:.2f}", f"x={res['x']:.4f}", f"w={res['w']:.4f}")
+            text = (f"T={res['T']:.2f}", f"w={res['w']:.4f}", f"x={res['x']:.4f}")
             if self.show_progress:
                 print(f'SLE ({self.config}): ', *text)
             yield res

{cosmopharm-0.1.0.dist-info → cosmopharm-0.1.0a1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cosmopharm
-Version: 0.1.0
+Version: 0.1.0a1
 Summary: Predictive modeling for drug-polymer compatibility in pharmaceutical formulations using COSMO-SAC.
 Home-page: https://github.com/ivanantolo/cosmopharm,
 Author: Ivan Antolovic
@@ -38,7 +38,7 @@ Requires-Dist: matplotlib >=3.0 ; extra == 'examples'
 
 # COSMOPharm
 
-Welcome to the COSMOPharm package, accompanying [our paper in *Molecular Pharmaceutics*](https://doi.org/10.1021/acs.molpharmaceut.4c00342). This project and its associated publication offer insights and a practical toolkit for researching drug-polymer and drug-solvent systems, aiming to provide the scientific community with the means to reproduce our findings and further the development of COSMO-SAC-based models.
+Welcome to the COSMOPharm package, accompanying [our paper in *Molecular Pharmaceutics*](https://dx.doi.org/10.1021/acs.jctc.9b01016). This project and its associated publication offer insights and a practical toolkit for researching drug-polymer and drug-solvent systems, aiming to provide the scientific community with the means to reproduce our findings and further the development of COSMO-SAC-based models.
 
 <p align="center">
   <!-- <img src="https://github.com/usnistgov/COSMOSAC/raw/master/JCTC2020.PNG" alt="TOC Figure" width="500"> -->

cosmopharm-0.1.0a1.dist-info/RECORD

@@ -0,0 +1,18 @@
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+cosmopharm/actmodels/actmodel.py,sha256=69jluNR7Tb4BHwtkCQLI3NQ_0AEZcTDM69IdRPz9--w,5072
+cosmopharm/actmodels/cosmo.py,sha256=tpYboI369rEOIkYgGqLyqgQSfKEgxwONULC4ZKDKIHI,5962
+cosmopharm/equilibrium/__init__.py,sha256=5NsIbQEwELjeeoFEiWelnzHnhTzt5zsBh3r5icn_AIQ,44
+cosmopharm/equilibrium/lle.py,sha256=Ru0_mso43vZNjy8ybdVQeweAsaZoa_yJiUBljn8qoNU,5472
+cosmopharm/equilibrium/sle.py,sha256=E89JHAq-0XpJvSf2ybeVoNuV8OH55DHiJL6-8r33ggc,11187
+cosmopharm/utils/__init__.py,sha256=qfUPovmZ9ukj6ZbTfndUOH6EX0ZrzRNjLZEDIVS8UvM,113
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cosmopharm-0.1.0.dist-info/RECORD

@@ -1,18 +0,0 @@
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-cosmopharm/components.py,sha256=wEQQ0ZNOrFvG9SdhKAzBgqTbT6DtuoTreNBEdLw8Lm0,981
-cosmopharm/actmodels/__init__.py,sha256=9iH67yrdSaf10Fj8LwRikUDUMeMxsvUHRPEaWc3384k,59
-cosmopharm/actmodels/actmodel.py,sha256=rm3-3oWX71IrgdxjcO90bAtlBBsYWOu4cr_oIQH-zZ4,5437
-cosmopharm/actmodels/cosmo.py,sha256=Dj7kjFYSvJWESG2Y_dP5b6yCCpWYzD5tkh3ATvXIfjg,5873
-cosmopharm/equilibrium/__init__.py,sha256=5NsIbQEwELjeeoFEiWelnzHnhTzt5zsBh3r5icn_AIQ,44
-cosmopharm/equilibrium/lle.py,sha256=-xGnJg_7paMPMVaL1pzkF1UNWtnAPSnk1UbMPB11eqM,7814
-cosmopharm/equilibrium/sle.py,sha256=ScyVq0hNqpWgAbWSKoPARZdO2wf3I9uGzv8L9oDlCtY,11187
-cosmopharm/utils/__init__.py,sha256=qfUPovmZ9ukj6ZbTfndUOH6EX0ZrzRNjLZEDIVS8UvM,113
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