calphy 1.3.8__py3-none-any.whl → 1.3.9__py3-none-any.whl

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__ = "1.3.9"
 
 def addtest(a,b):
     return a+b

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__ = "1.3.9"
 
 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/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/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.dist-info → calphy-1.3.9.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: calphy
-Version: 1.3.8
+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-1.3.8.dist-info → calphy-1.3.9.dist-info}/RECORD

@@ -1,14 +1,14 @@
-calphy/__init__.py,sha256=jJPLUeJFKfa7dCVgQ0_d1yXSSgim9KpQLN3LbiBlRws,233
+calphy/__init__.py,sha256=RKi3orWUQRK_qYHCQKFzfbyTptYDonS9673vtVdelso,233
 calphy/alchemy.py,sha256=epv_vJoAMVbj-S1TuPSbBGr4w_a9qEr4EIxKlgwdlSo,12893
 calphy/clitools.py,sha256=oDqaw0s-LJ7tAdW_Njk2SFljVx6K34Rs8sdMz48SNSI,4125
 calphy/composition_transformation.py,sha256=Hh240-iVGC8ATlJ3nQK757qVZIBrE2aw7dsF46mi3oo,15353
 calphy/errors.py,sha256=KN47RWTLbg1H_NZMrhCiJCbqjqJScJ1pgQAuzj1-l84,1268
 calphy/helpers.py,sha256=nj8g53H6ScohQtyV7Enzms8Rv_89PRrDDY1IHjFSZdQ,8292
-calphy/input.py,sha256=BNSxEKTvORN-TJs5fqlmUnK-yqv2Iul4wNftUTYbqSo,29533
+calphy/input.py,sha256=Z8h-Y3dz5HJy6eOGYffMtUV9Q-NPall8dnPiFKkXUEw,29717
 calphy/integrators.py,sha256=CcK3oqIwZ3z41v3fh3IvswY_l-ZbLRluWuDNJlXCXfg,20680
 calphy/kernel.py,sha256=rd_-EfCiBhQjkxcVaoLtVJB2_qDgS-g-dQ0BZBTJQ_A,6190
-calphy/liquid.py,sha256=8KH4t0mcpumR1KlOoWHjlr8lcQaWLXQPcA438A08hfM,13450
-calphy/phase.py,sha256=5ZA7tn6ZyZozZW7wMiZSfkRQZAa5Wg9XtIjNofu21cg,44730
+calphy/liquid.py,sha256=a5NTAjc3VsrPBQoEMGe9O1WXfv1vxGoB0xPguf0fOyM,13762
+calphy/phase.py,sha256=ukqad4MJ-MNGiyOsq2_jntG2s10UHbJVi2Ounpg_S2U,44787
 calphy/phase_diagram.py,sha256=2EwmT_qkT5BEP6Sx0_rm09kPP2RWh5JY4sogIBK_AhA,12992
 calphy/queuekernel.py,sha256=4GMIYnjMiAPipoLNKP5noYcfeEOI_vCqm84zgokk7Xw,5321
 calphy/routines.py,sha256=W6OZEPv6HEG11EYsoIbum2WVrO3Ly36i5UWsYQ4oBdQ,17473
@@ -16,9 +16,9 @@ calphy/scheduler.py,sha256=9p1MdMlB2QtMV6-LmjBU9E0GOxx-fdDEvAb3LOVsRPM,8468
 calphy/solid.py,sha256=49gT0wNOP3h8lRDXarULP-bU09lIrnDCTUcyxE7X-UE,19795
 calphy/splines.py,sha256=BGwUVz_qXQxUzpUCuZo6CsELcd5JVNWzI-Ttcz22G_E,61627
 calphy/utils.py,sha256=0UpsYoxjS5N-iGs-cdm0YDMkLF8IHvKO3smXDHrj3eg,3818
-calphy-1.3.8.dist-info/LICENSE,sha256=XIHGB5RZLIhOjjoO1bPf0II-qDbjhP5Cv5HJMRE9v1g,16651
-calphy-1.3.8.dist-info/METADATA,sha256=IczeMseQTEJMkgpGF6A7gNfzwuFiJzzIvfulp-n291c,4215
-calphy-1.3.8.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-calphy-1.3.8.dist-info/entry_points.txt,sha256=W9qq254koyWnAgo1jtfQP9bO5Q7sgZrzc8BMnfo3vf4,386
-calphy-1.3.8.dist-info/top_level.txt,sha256=w871dhMqPwgjjbifBWdkT9_aOnK1ek4Odrh8UnSG3PE,7
-calphy-1.3.8.dist-info/RECORD,,
+calphy-1.3.9.dist-info/LICENSE,sha256=XIHGB5RZLIhOjjoO1bPf0II-qDbjhP5Cv5HJMRE9v1g,16651
+calphy-1.3.9.dist-info/METADATA,sha256=OoDJsMjXCuKp1w4IxKX-RL9baeg3b4Co_BzHtaydQnc,4215
+calphy-1.3.9.dist-info/WHEEL,sha256=cpQTJ5IWu9CdaPViMhC9YzF8gZuS5-vlfoFihTBC86A,91
+calphy-1.3.9.dist-info/entry_points.txt,sha256=W9qq254koyWnAgo1jtfQP9bO5Q7sgZrzc8BMnfo3vf4,386
+calphy-1.3.9.dist-info/top_level.txt,sha256=w871dhMqPwgjjbifBWdkT9_aOnK1ek4Odrh8UnSG3PE,7
+calphy-1.3.9.dist-info/RECORD,,

{calphy-1.3.8.dist-info → calphy-1.3.9.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.43.0)
+Generator: setuptools (70.1.0)
 Root-Is-Purelib: true
 Tag: py3-none-any