calphy 1.3.8__tar.gz → 1.3.10__tar.gz

{calphy-1.3.8/calphy.egg-info → calphy-1.3.10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: calphy
-Version: 1.3.8
+Version: 1.3.10
 Summary: free energy calculation for python
 Home-page: https://github.com/ICAMS/calphy
 Author: Sarath Menon, Yury Lysogorskiy, Ralf Drautz

{calphy-1.3.8 → calphy-1.3.10}/calphy/__init__.py

@@ -4,7 +4,7 @@ from calphy.solid import Solid
 from calphy.alchemy import Alchemy
 from calphy.routines import MeltingTemp
 
-__version__ = "1.3.8"
+__version__ = "1.3.10"
 
 def addtest(a,b):
     return a+b

{calphy-1.3.8 → calphy-1.3.10}/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__ = "1.3.8"
+__version__ = "1.3.10"
 
 def read_report(folder):
     """
@@ -72,7 +72,12 @@ def _to_int(val):
     if np.isscalar(val):
         return int(val)
     else:
-        return [int(x) for x in val] 
+        return [int(x) for x in val]
+
+def _to_none(val):
+    if val in ['none', 'None',]:
+        return None 
+    return val
 
 def _to_float(val):
     if np.isscalar(val):
@@ -558,6 +563,8 @@ def _read_inputfile(file):
     for count, calc in enumerate(data['calculations']):
         calc['kernel'] = count
         calc['inputfile'] = file
+        if 'pressure' in calc.keys():
+            calc['pressure'] = _to_none(calc['pressure'])
         calculations.append(Calculation(**calc))
     return calculations
 

{calphy-1.3.8 → calphy-1.3.10}/calphy/integrators.py

@@ -28,7 +28,10 @@ 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

{calphy-1.3.8 → calphy-1.3.10}/calphy/liquid.py

@@ -56,7 +56,12 @@ class Liquid(cph.Phase):
 
     def melt_structure(self, lmp):
         """
-        """        
+        """
+        if self.calc._fix_lattice and self.calc.melting_cycle:
+            
+            raise ValueError("Cannot fix lattice and melt structure (set to False) at the same time")
+            
+
         melted = False
         
         #this is the multiplier for thigh to try melting routines
@@ -136,11 +141,14 @@ class Liquid(cph.Phase):
         if self.calc.melting_cycle:
             self.melt_structure(lmp)
 
-        #now assign correct temperature and equilibrate
-        self.run_zero_pressure_equilibration(lmp)
+        if not self.calc._fix_lattice:
+            #now assign correct temperature and equilibrate
+            self.run_zero_pressure_equilibration(lmp)
 
-        #converge pressure
-        self.run_pressure_convergence(lmp)
+            #converge pressure
+            self.run_pressure_convergence(lmp)
+        else:
+            self.run_constrained_pressure_convergence(lmp)
 
         #check melted error
         self.dump_current_snapshot(lmp, "traj.equilibration_stage1.dat")

{calphy-1.3.8 → calphy-1.3.10}/calphy/phase.py

@@ -622,6 +622,7 @@ class Phase:
         self.lz = np.round(np.mean(lz[-ncount+1:]), decimals=3)
         self.volatom = volatom
         self.vol = self.lx*self.ly*self.lz
+        self.rho = self.natoms/(self.lx*self.ly*self.lz)
         self.logger.info("finalized vol/atom %f at pressure %f"%(self.volatom, mean))
         self.logger.info("Avg box dimensions x: %f, y: %f, z:%f"%(self.lx, self.ly, self.lz))
 

{calphy-1.3.8 → calphy-1.3.10}/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-1.3.8 → calphy-1.3.10/calphy.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: calphy
-Version: 1.3.8
+Version: 1.3.10
 Summary: free energy calculation for python
 Home-page: https://github.com/ICAMS/calphy
 Author: Sarath Menon, Yury Lysogorskiy, Ralf Drautz

{calphy-1.3.8 → calphy-1.3.10}/setup.py

@@ -53,7 +53,7 @@ setup(
     packages=find_packages(include=['calphy', 'calphy.*']),
     test_suite='tests',
     url='https://github.com/ICAMS/calphy',
-    version='1.3.8',
+    version='1.3.10',
     zip_safe=False,
     entry_points={
         'console_scripts': [