calphy 1.3.11__tar.gz → 1.3.13__tar.gz

{calphy-1.3.11/calphy.egg-info → calphy-1.3.13}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: calphy
-Version: 1.3.11
+Version: 1.3.13
 Summary: free energy calculation for python
 Home-page: https://github.com/ICAMS/calphy
 Author: Sarath Menon, Yury Lysogorskiy, Ralf Drautz

{calphy-1.3.11 → calphy-1.3.13}/calphy/__init__.py

@@ -4,7 +4,7 @@ from calphy.solid import Solid
 from calphy.alchemy import Alchemy
 from calphy.routines import MeltingTemp
 
-__version__ = "1.3.11"
+__version__ = "1.3.13"
 
 def addtest(a,b):
     return a+b

{calphy-1.3.11 → calphy-1.3.13}/calphy/input.py

@@ -40,7 +40,7 @@ from pyscal3.core import structure_dict, element_dict, _make_crystal
 from ase.io import read, write
 import shutil
 
-__version__ = "1.3.11"
+__version__ = "1.3.13"
 
 def _check_equal(val):
     if not (val[0]==val[1]==val[2]):

{calphy-1.3.11 → calphy-1.3.13}/calphy/phase.py

@@ -598,8 +598,12 @@ class Phase:
         
         #now we can check if it converted
         file = os.path.join(self.simfolder, "avg.dat")
-        lx, ly, lz, ipress = np.loadtxt(file, usecols=(1, 2, 3, 4), unpack=True)
-        lxpc = ipress
+        #we have to clean the data, so as just the last block is selected
+        lx, ly, lz, lxpc = np.loadtxt(file, usecols=(1, 2, 3, 4), unpack=True)
+        lx = lx[-ncount+1:]
+        ly = ly[-ncount+1:]
+        lz = lx[-ncount+1:]
+        lxpc = lxpc[-ncount+1:]
         mean = np.mean(lxpc)
         std = np.std(lxpc)
         volatom = np.mean((lx*ly*lz)/self.natoms)
@@ -612,16 +616,20 @@ class Phase:
             ncount = int(self.calc.md.n_small_steps)//int(self.calc.md.n_every_steps*self.calc.md.n_repeat_steps)
 
         file = os.path.join(self.simfolder, "avg.dat")
-        lx, ly, lz, ipress = np.loadtxt(file, usecols=(1, 2, 3, 4), unpack=True)        
-        lxpc = ipress
+        lx, ly, lz, lxpc = np.loadtxt(file, usecols=(1, 2, 3, 4), unpack=True)        
+        lx = lx[-ncount+1:]
+        ly = ly[-ncount+1:]
+        lz = lx[-ncount+1:]
+        lxpc = lxpc[-ncount+1:]
+
         mean = np.mean(lxpc)
         std = np.std(lxpc)
         volatom = np.mean((lx*ly*lz)/self.natoms)
 
         self.calc._pressure = mean
-        self.lx = np.round(np.mean(lx[-ncount+1:]), decimals=3)
-        self.ly = np.round(np.mean(ly[-ncount+1:]), decimals=3)
-        self.lz = np.round(np.mean(lz[-ncount+1:]), decimals=3)
+        self.lx = np.round(np.mean(lx), decimals=3)
+        self.ly = np.round(np.mean(ly), decimals=3)
+        self.lz = np.round(np.mean(lz), decimals=3)
         self.volatom = volatom
         self.vol = self.lx*self.ly*self.lz
         self.rho = self.natoms/(self.lx*self.ly*self.lz)

{calphy-1.3.11 → calphy-1.3.13}/calphy/postprocessing.py

@@ -1,6 +1,8 @@
 import os
 import numpy as np
 import yaml
+import matplotlib.pyplot as plt
+import warnings
 
 def read_report(folder):
     """
@@ -145,4 +147,83 @@ def gather_results(mainfolder):
                 datadict['error_code'][-1] = _extract_error(errfile)
 
     df = pd.DataFrame(data=datadict)
-    return df
+    return df
+
+def find_transition_temperature(folder1, folder2, fit_order=4, plot=True):
+    """
+    Find transition temperature where free energy of two phases are equal.
+
+    Parameters
+    ----------
+    folder1: string
+        directory with temperature scale calculation
+
+    folder2: string
+        directory with temperature scale calculation
+
+    fit_order: int, optional
+        default 4. Order for polynomial fit of temperature vs free energy
+    
+    plot: bool, optional
+        default True. Plot the results.
+    """
+    file1 = os.path.join(folder1, 'temperature_sweep.dat')
+    file2 = os.path.join(folder2, 'temperature_sweep.dat')
+    if not os.path.exists(file1):
+        raise FileNotFoundError(f'{file1} does not exist')
+    if not os.path.exists(file2):
+        raise FileNotFoundError(f'{file2} does not exist')
+
+    t1, f1 = np.loadtxt(file1, unpack=True, usecols=(0,1))
+    t2, f2 = np.loadtxt(file2, unpack=True, usecols=(0,1))
+
+    #do some fitting to determine temps
+    t1min = np.min(t1)
+    t2min = np.min(t2)
+    t1max = np.max(t1)
+    t2max = np.max(t2)
+
+    tmin = np.min([t1min, t2min])
+    tmax = np.max([t1max, t2max])
+
+    #warn about extrapolation
+    if not t1min == t2min:
+        warnings.warn(f'free energy is being extrapolated!')
+    if not t1max == t2max:
+        warnings.warn(f'free energy is being extrapolated!')
+
+    #now fit
+    f1fit = np.polyfit(t1, f1, fit_order)
+    f2fit = np.polyfit(t2, f2, fit_order)
+
+    #reevaluate over the new range
+    fit_t = np.arange(tmin, tmax+1, 1)
+    fit_f1 = np.polyval(f1fit, fit_t)
+    fit_f2 = np.polyval(f2fit, fit_t)
+
+    #now evaluate the intersection temp
+    arg = np.argsort(np.abs(fit_f1-fit_f2))[0]
+    transition_temp = fit_t[arg]
+
+    #warn if the temperature is shady
+    if np.abs(transition_temp-tmin) < 1E-3:
+        warnings.warn('It is likely there is no intersection of free energies')
+    elif np.abs(transition_temp-tmax) < 1E-3:
+        warnings.warn('It is likely there is no intersection of free energies')
+
+    #plot
+    if plot:
+        c1lo = '#ef9a9a'
+        c1hi = '#b71c1c'
+        c2lo = '#90caf9'
+        c2hi = '#0d47a1'
+
+        plt.plot(fit_t, fit_f1, color=c1lo, label=f'{folder1} fit')
+        plt.plot(fit_t, fit_f2, color=c2lo, label=f'{folder2} fit')
+        plt.plot(t1, f1, color=c1hi, label=folder1, ls='dashed')
+        plt.plot(t2, f2, color=c2hi, label=folder2, ls='dashed')
+        plt.axvline(transition_temp, ls='dashed', c='#37474f')
+        plt.ylabel('Free energy (eV/atom)')
+        plt.xlabel('Temperature (K)')
+        plt.legend(frameon=False)
+    return transition_temp

{calphy-1.3.11 → calphy-1.3.13/calphy.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: calphy
-Version: 1.3.11
+Version: 1.3.13
 Summary: free energy calculation for python
 Home-page: https://github.com/ICAMS/calphy
 Author: Sarath Menon, Yury Lysogorskiy, Ralf Drautz

{calphy-1.3.11 → calphy-1.3.13}/setup.py

@@ -53,7 +53,7 @@ setup(
     packages=find_packages(include=['calphy', 'calphy.*']),
     test_suite='tests',
     url='https://github.com/ICAMS/calphy',
-    version='1.3.11',
+    version='1.3.13',
     zip_safe=False,
     entry_points={
         'console_scripts': [