calphy 1.3.9__tar.gz → 1.3.11__tar.gz

{calphy-1.3.9/calphy.egg-info → calphy-1.3.11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: calphy
-Version: 1.3.9
+Version: 1.3.11
 Summary: free energy calculation for python
 Home-page: https://github.com/ICAMS/calphy
 Author: Sarath Menon, Yury Lysogorskiy, Ralf Drautz

{calphy-1.3.9 → calphy-1.3.11}/calphy/__init__.py

@@ -4,7 +4,7 @@ from calphy.solid import Solid
 from calphy.alchemy import Alchemy
 from calphy.routines import MeltingTemp
 
-__version__ = "1.3.9"
+__version__ = "1.3.11"
 
 def addtest(a,b):
     return a+b

{calphy-1.3.9 → calphy-1.3.11}/calphy/input.py

@@ -40,19 +40,7 @@ from pyscal3.core import structure_dict, element_dict, _make_crystal
 from ase.io import read, write
 import shutil
 
-__version__ = "1.3.9"
-
-def read_report(folder):
-    """
-    Read the finished calculation report
-    """
-    repfile = os.path.join(folder, "report.yaml")
-    if not os.path.exists(repfile):
-        raise FileNotFoundError(f"file {repfile} not found")
-
-    with open(repfile, 'r') as fin:
-        data = yaml.safe_load(fin)
-    return data
+__version__ = "1.3.11"
 
 def _check_equal(val):
     if not (val[0]==val[1]==val[2]):

{calphy-1.3.9 → calphy-1.3.11}/calphy/integrators.py

@@ -28,19 +28,23 @@ import math
 import os
 import warnings
 from calphy.splines import splines, sum_spline1, sum_spline25, sum_spline50, sum_spline75, sum_spline100
-from scipy.integrate import cumtrapz
+try:
+    from scipy.integrate import cumtrapz
+except ImportError:
+    from scipy.integrate import cumulative_trapezoid as cumtrapz
 from tqdm import tqdm
 import pyscal3.core as pc
 from ase.io import read
 
 #Constants
 h = const.physical_constants["Planck constant in eV/Hz"][0]
+hJ = const.physical_constants["Planck constant"][0]
 hbar = h/(2*np.pi)
 kb = const.physical_constants["Boltzmann constant in eV/K"][0]
 kbJ = const.physical_constants["Boltzmann constant"][0]
 Na = const.physical_constants["Avogadro constant"][0]
 eV2J = const.eV
-
+J2eV = 6.242E18
 
 #--------------------------------------------------------------------
 #             TI PATH INTEGRATION ROUTINES
@@ -466,23 +470,18 @@ def get_einstein_crystal_fe(
     calc,
     vol, 
     k, 
-    cm_correction=True):
+    cm_correction=True,
+    return_contributions=False):
     """
     Get the free energy of einstein crystal
 
     Parameters
     ----------
-    temp : temperature, float
-        units - K
-
-    natoms : int
-        no of atoms in the system
-
-    mass : float
-        units - g/mol
+    calc : Calculation object
+        contains all input parameters
 
-    a : lattice constant, float
-        units - Angstrom
+    vol : float
+        converged volume per atom
 
     k : spring constant, float
         units - eV/Angstrom^2
@@ -490,40 +489,77 @@ def get_einstein_crystal_fe(
     cm_correction : bool, optional, default - True
         add the centre of mass correction to free energy
 
+    return_contributions: bool, optional, default - True
+        If True, return individual contributions to the reference free energy.
+
     Returns
     -------
-    fe : float
-        free energy of Einstein crystal
+    F_tot : float
+        total free energy of reference crystal
+
+    F_e : float
+        Free energy of Einstein crystal without centre of mass correction. Only if `return_contributions` is True.
+
+    F_cm : float
+        centre of mass correction. Only if `return_contributions` is True.
+
+    Notes
+    -----
+    The equations for free energy of Einstein crystal and centre of mass correction are from https://doi.org/10.1063/5.0044833.
 
     """
-    #convert mass first for single particle in kg
-    mass = np.array([calc._element_dict[x]['mass'] for x in calc.element])
-    mass = (mass/Na)*1E-3
-    natoms = np.sum([calc._element_dict[x]['count'] for x in calc.element])
-    concentration = np.array([calc._element_dict[x]['composition'] for x in calc.element])
+    #temperature
+    temp = calc._temperature
 
-    #convert k from ev/A2 to J/m2
-    k = np.array(k)*(eV2J/1E-20)
-    omega = np.sqrt(k/mass)
+    #natoms
+    natoms = np.sum([calc._element_dict[x]['count'] for x in calc.element])
 
     #convert a to m3
     vol = vol*1E-30
 
-    F_harm = 0
-    F_cm = 0
+    #whats the beta
+    beta = (1/(kbJ*temp))   
 
-    for count, om in enumerate(omega):
-        if concentration[count] > 0:
-            F_harm += concentration[count]*np.log((hbar*om)/(kb*calc._temperature))
-            if cm_correction:
-                F_cm += np.log((natoms*concentration[count]/vol)*(2*np.pi*kbJ*calc._temperature/(natoms*concentration[count]*k[count]))**1.5)
-            #F_cm = 0
-    F_harm = 3*kb*calc._temperature*F_harm
-    F_cm = (kb*calc._temperature/natoms)*F_cm
-
-    F_harm = F_harm + F_cm
+    #create an array of mass
+    mass = []
+    for x in calc.element:
+        for count in range(calc._element_dict[x]['count']):
+            mass.append(calc._element_dict[x]['mass'])
+    mass = np.array(mass)
+    
+    #convert mass to kg
+    mass = (mass/Na)*1E-3
 
-    return F_harm
+    #create an array of k as well
+    karr = []
+    for c, x in enumerate(calc.element):
+        for count in range(calc._element_dict[x]['count']):
+            karr.append(k[c])
+    k = np.array(karr)
+    #convert k from ev/A2 to J/m2
+    k = k*(eV2J/1E-20)
+
+    #fe of Einstein crystal
+    Z_e = ((beta**2*k*hJ**2)/(4*np.pi**2*mass))**1.5
+    F_e = np.log(Z_e)
+    F_e = kb*temp*np.sum(F_e)/natoms #*J2eV #convert back to eV
+
+    #now get the cm correction
+    if cm_correction:
+        mass_sum = np.sum(mass)
+        mu = mass/mass_sum
+        mu2_over_k = mu**2/k
+        mu2_over_k_sum = np.sum(mu2_over_k) 
+        prefactor = vol
+        F_cm = np.log(prefactor*(beta/(2*np.pi*mu2_over_k_sum))**1.5)
+        F_cm = kb*temp*F_cm/natoms #convert to eV
+    else:
+        F_cm = 0
+    
+    F_tot = F_e - F_cm
+    if return_contributions:
+        return F_e, -F_cm
+    return F_tot
 
 #--------------------------------------------------------------------
 #             REF. STATE ROUTINES: LIQUID

{calphy-1.3.9 → calphy-1.3.11}/calphy/phase.py

@@ -163,6 +163,8 @@ class Phase:
 
         self.ferr = 0
         self.fref = 0
+        self.feinstein = 0
+        self.fcm = 0
         self.fideal = 0
         
         self.w = 0
@@ -682,6 +684,8 @@ class Phase:
         report["results"]["free_energy"] = float(self.fe)
         report["results"]["error"] = float(self.ferr)
         report["results"]["reference_system"] = float(self.fref)
+        report["results"]["einstein_crystal"] = float(self.feinstein)
+        report["results"]["com_correction"] = float(self.fcm)
         report["results"]["work"] = float(self.w)
         report["results"]["pv"] = float(self.pv)
         report["results"]["unit"] = "eV/atom"

calphy-1.3.11/calphy/postprocessing.py

@@ -0,0 +1,148 @@
+import os
+import numpy as np
+import yaml
+
+def read_report(folder):
+    """
+    Read the finished calculation report
+
+    Parameters
+    ----------
+    folder: string
+        folder from which calculation is to be read
+    
+    Returns
+    -------
+    data: dict
+        dictionary with results
+
+    """
+    repfile = os.path.join(folder, "report.yaml")
+    if not os.path.exists(repfile):
+        raise FileNotFoundError(f"file {repfile} not found")
+
+    with open(repfile, 'r') as fin:
+        data = yaml.safe_load(fin)
+    return data
+
+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
+    return error_code
+    
+def gather_results(mainfolder):
+    """
+    Gather results from all subfolders in a given folder into a Pandas DataFrame
+
+    Parameters
+    ----------
+    mainfolder: string
+        folder where calculations are stored
+    
+    Returns
+    -------
+    df: pandas DataFrame
+        DataFrame with results
+    """
+    try:
+        import pandas as pd
+    except ImportError:
+        raise ImportError('Please install pandas to use this function')
+     
+    datadict = {}
+    datadict['mode'] = []
+    datadict['status'] = []
+    datadict['temperature'] = []
+    datadict['pressure'] = []
+    datadict['free_energy'] = []
+    datadict['reference_phase'] = []
+    datadict['error_code'] = []
+    datadict['composition'] = []
+    datadict['calculation'] = []
+    
+    folders = next(os.walk(mainfolder))[1]
+    for folder in folders:
+        #adjust for pyiron folder, see
+        if folder.split('_')[-1] == 'hdf5':
+            #this could be a pyiron calc
+            withouthdf = folder.split('_hdf5')[0]
+            folder = f'{folder}/{withouthdf}'
+            
+        inpfile = os.path.join(mainfolder, folder, 'input_file.yaml')
+        #print(inpfile)
+        if not os.path.exists(inpfile):
+            continue;
+        
+        #ok, valid calculation, try to parse input file to get info
+        with open(inpfile, 'r') as fin:
+            inp = yaml.safe_load(fin)
+        #grab the first calculation
+        inp = inp['calculations'][0]
+        #mode
+        mode = inp['mode']
+        datadict['mode'].append(mode)
+        datadict['temperature'].append(inp['temperature'])
+        datadict['pressure'].append(inp['pressure'])
+        datadict['reference_phase'].append(inp['reference_phase'])
+        datadict['composition'].append(None)
+        datadict['calculation'].append(folder)
+    
+        #check output file
+        outfile = os.path.join(mainfolder, folder, 'report.yaml')
+        datadict['error_code'].append(None)
+        
+        #print(inpfile)
+        if not os.path.exists(outfile):
+            datadict['status'].append('False')
+            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)
+            continue;
+    
+        if mode in ['fe', 'alchemy', 'composition_scaling']:
+            datadict['status'].append('True')
+        
+        #ok, valid calculation, try to parse input file to get info
+        with open(outfile, 'r') as fin:
+            out = yaml.safe_load(fin)
+    
+        datadict['free_energy'].append(out['results']['free_energy'])
+        
+        #add normal composition
+        el_arr = np.array(out['input']['element'].split(' ')).astype(str)
+        comp_arr = np.array(out['input']['concentration'].split(' ')).astype(float)
+        composition = {x:y for x,y in zip(el_arr, comp_arr)}
+        datadict['composition'][-1] = composition
+
+        if mode == 'composition_scaling':
+            #we need to update composition
+            compdict = inp['composition_scaling']['output_chemical_composition']
+            maxatoms = np.sum([val for key, val in compdict.items()])
+            for key, val in compdict.items():
+                compdict[key] = val/maxatoms
+            datadict['composition'][-1] = compdict
+
+        #parse extra info
+        if mode in ['ts', 'tscale']:
+            datafile = os.path.join(os.getcwd(), mainfolder, folder, 'temperature_sweep.dat')
+            if os.path.exists(datafile):
+                datadict['status'].append('True')
+                t, f = np.loadtxt(datafile, unpack=True, usecols=(0,1))
+                datadict['temperature'][-1] = t
+                datadict['free_energy'][-1] = f
+            else:
+                datadict['status'].append('False')
+                errfile = os.path.join(os.getcwd(), mainfolder, folder+'.sub.err')
+                datadict['error_code'][-1] = _extract_error(errfile)
+
+    df = pd.DataFrame(data=datadict)
+    return df

{calphy-1.3.9 → calphy-1.3.11}/calphy/scheduler.py

@@ -90,6 +90,7 @@ class SLURM:
         """
         self.queueoptions = {"scheduler": "slurm",
                              "jobname": "tis",
+                             "queuename": None,
                              "walltime": "23:59:00",
                              "memory": "3GB",
                              "cores": cores,
@@ -125,7 +126,8 @@ class SLURM:
             #write the main header options
             fout.write("#SBATCH --job-name=%s\n" %self.queueoptions["jobname"])
             fout.write("#SBATCH --time=%s\n"     %self.queueoptions["walltime"])
-            fout.write("#SBATCH --partition=%s\n"%self.queueoptions["queuename"])
+            if self.queueoptions["queuename"] is not None:
+                fout.write("#SBATCH --partition=%s\n"%self.queueoptions["queuename"])
             fout.write("#SBATCH --ntasks=%s\n"   %str(self.queueoptions["cores"]))
             fout.write("#SBATCH --mem-per-cpu=%s\n"%self.queueoptions["memory"])
             fout.write("#SBATCH --hint=%s\n"     %self.queueoptions["hint"])

{calphy-1.3.9 → calphy-1.3.11}/calphy/solid.py

@@ -516,17 +516,20 @@ class Solid(cph.Phase):
         Calculates the final work, energy dissipation and free energy by
         matching with Einstein crystal
         """
-        f1 = get_einstein_crystal_fe(
+        fe, fcm = get_einstein_crystal_fe(
             self.calc,  
             self.vol, 
-            self.k)
+            self.k,
+            return_contributions=True)
         
         w, q, qerr = find_w(self.simfolder, 
             self.calc,
             full=True, 
             solid=True)
         
-        self.fref = f1
+        self.fref = fe + fcm
+        self.feinstein = fe
+        self.fcm = fcm
         self.w = w
         self.ferr = qerr
 

{calphy-1.3.9 → calphy-1.3.11/calphy.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: calphy
-Version: 1.3.9
+Version: 1.3.11
 Summary: free energy calculation for python
 Home-page: https://github.com/ICAMS/calphy
 Author: Sarath Menon, Yury Lysogorskiy, Ralf Drautz

{calphy-1.3.9 → calphy-1.3.11}/calphy.egg-info/SOURCES.txt

@@ -14,6 +14,7 @@ calphy/kernel.py
 calphy/liquid.py
 calphy/phase.py
 calphy/phase_diagram.py
+calphy/postprocessing.py
 calphy/queuekernel.py
 calphy/routines.py
 calphy/scheduler.py

{calphy-1.3.9 → calphy-1.3.11}/setup.py

@@ -53,7 +53,7 @@ setup(
     packages=find_packages(include=['calphy', 'calphy.*']),
     test_suite='tests',
     url='https://github.com/ICAMS/calphy',
-    version='1.3.9',
+    version='1.3.11',
     zip_safe=False,
     entry_points={
         'console_scripts': [