calphy 1.3.7__tar.gz → 1.3.9__tar.gz

{calphy-1.3.7/calphy.egg-info → calphy-1.3.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: calphy
-Version: 1.3.7
+Version: 1.3.9
 Summary: free energy calculation for python
 Home-page: https://github.com/ICAMS/calphy
 Author: Sarath Menon, Yury Lysogorskiy, Ralf Drautz

{calphy-1.3.7 → calphy-1.3.9}/calphy/__init__.py

@@ -4,7 +4,7 @@ from calphy.solid import Solid
 from calphy.alchemy import Alchemy
 from calphy.routines import MeltingTemp
 
-__version__ = "1.3.7"
+__version__ = "1.3.9"
 
 def addtest(a,b):
     return a+b

{calphy-1.3.7 → calphy-1.3.9}/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__ = "1.3.7"
+__version__ = "1.3.9"
 
 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-1.3.7 → calphy-1.3.9}/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-1.3.7 → calphy-1.3.9}/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-1.3.7 → calphy-1.3.9}/calphy/phase_diagram.py

@@ -329,6 +329,7 @@ def get_common_tangents(dict_list,
     tangents = []
     energies = []    
     tangent_colors = []
+    phases = []
     
     for d in dist:
         t = [convex_x[sargs][d], convex_x[sargs][d+1]]
@@ -339,6 +340,7 @@ def get_common_tangents(dict_list,
             tangents.append(t)
             energies.append(e)
             tangent_colors.append(color_dict[phase_str])
+            phases.append(phase_str.split("-"))
     
     if plot:
         for d in dict_list:
@@ -347,7 +349,7 @@ def get_common_tangents(dict_list,
             plt.plot(t, e, color="black", ls="dashed")
         plt.ylim(top=0.0)
     
-    return np.array(tangents), np.array(energies), np.array(tangent_colors), color_dict
+    return np.array(tangents), np.array(energies), np.array(tangent_colors), color_dict, np.array(phases)
 
 
 def plot_phase_diagram(tangents, temperature,

{calphy-1.3.7 → calphy-1.3.9}/calphy/scheduler.py

@@ -106,7 +106,7 @@ class SLURM:
         for (key, val) in options.items():
             if key in self.queueoptions.keys():
                 if val is not None:
-                    if val is not "":
+                    if val != "":
                         self.queueoptions[key] = val
         self.maincommand = ""
 

{calphy-1.3.7 → calphy-1.3.9/calphy.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: calphy
-Version: 1.3.7
+Version: 1.3.9
 Summary: free energy calculation for python
 Home-page: https://github.com/ICAMS/calphy
 Author: Sarath Menon, Yury Lysogorskiy, Ralf Drautz

{calphy-1.3.7 → calphy-1.3.9}/setup.py

@@ -53,7 +53,7 @@ setup(
     packages=find_packages(include=['calphy', 'calphy.*']),
     test_suite='tests',
     url='https://github.com/ICAMS/calphy',
-    version='1.3.7',
+    version='1.3.9',
     zip_safe=False,
     entry_points={
         'console_scripts': [