fixes to add_to_dict

ammber/__init__.py

@@ -4,6 +4,6 @@
 A Python package for parametrizing gibbs free energy curves for phase-field modeling.
 """
 
-__version__ = "0.1.6"
+__version__ = "0.1.7"
 __author__ = 'W. Beck Andrews, Xander Mensah, Katsuyo Thornton'
 __credits__ = 'University of Michigan'

ammber/utils.py

@@ -1,11 +1,11 @@
-def add_to_dict(binaryIsothermalSys, dict, add_templates=False, c0={}, Vm=None, convert_to_volumetric_energy=True):
+def add_to_dict(binaryIsothermalSys, system_dict, add_templates=False, c0={}, Vm=None, convert_to_volumetric_energy=True):
     """
     Adds the parameters of a BinaryIsothermal2ndOrderSystem to a dictionary
     Parameters
     ----------
     binaryIsothermalSys : BinaryIsothermal2ndOrderSystem
         system to draw parameters from
-    dict : dict
+    system_dict : dict
         dictionary to add parameters to
     add_templates : bool
         add templates or additional values needed for kinetics simulation
@@ -16,36 +16,36 @@ def add_to_dict(binaryIsothermalSys, dict, add_templates=False, c0={}, Vm=None,
     convert_to_volumetric_energy : bool
         a setting for AMMBER kinetics. true if binaryIsothermalSys composition axes are number fraction
     """
-    dict["solution_component"] = binaryIsothermalSys.solution_component
-    dict["components"] = [binaryIsothermalSys.component]
-    dict["convert_fractional_to_volumetric_energy"] = convert_to_volumetric_energy
-    if "phases" not in dict:
-        dict["phases"] = {}
+    system_dict["solution_component"] = binaryIsothermalSys.solution_component
+    system_dict["components"] = [binaryIsothermalSys.component]
+    system_dict["convert_fractional_to_volumetric_energy"] = convert_to_volumetric_energy
+    if "phases" not in system_dict:
+        system_dict["phases"] = {}
     comp = binaryIsothermalSys.component
     for phase_name in binaryIsothermalSys.phases.keys():
         phase = binaryIsothermalSys.phases[phase_name]
-        if phase_name not in dict:
-            dict["phases"][phase_name] = {}
+        if phase_name not in system_dict["phases"]:
+            system_dict["phases"][phase_name] = {}
 
-        if comp not in dict["phases"][phase_name]:
-            dict["phases"][phase_name][comp] = {}
-        dict["phases"][phase_name][comp]["k_well"] = phase.kwell
-        dict["phases"][phase_name][comp]["c_min"] = phase.cmin
-        dict["phases"][phase_name]["f_min"] = phase.fmin
+        if comp not in system_dict["phases"][phase_name]:
+            system_dict["phases"][phase_name][comp] = {}
+        system_dict["phases"][phase_name][comp]["k_well"] = phase.kwell
+        system_dict["phases"][phase_name][comp]["c_min"] = phase.cmin
+        system_dict["phases"][phase_name]["f_min"] = phase.fmin
 
         if add_templates:
             c0_phase_keys = list(c0.keys())
-            if "c0" not in dict["phases"][phase_name][comp]:
-                dict["phases"][phase_name][comp]["c0"] = c0[phase_name] if phase_name in c0_phase_keys else -1.0
+            if "x0" not in system_dict["phases"][phase_name][comp]:
+                system_dict["phases"][phase_name][comp]["x0"] = c0[phase_name] if phase_name in c0_phase_keys else -1.0
             for phase_prop in ["mu_int", "D", "sigma"]:
-                if phase_prop not in dict["phases"][phase_name]:
-                    dict["phases"][phase_name][phase_prop] = -1.0
+                if phase_prop not in system_dict["phases"][phase_name]:
+                    system_dict["phases"][phase_name][phase_prop] = -1.0
     if add_templates:
-        if "l_int" not in dict:
-            dict["l_int"] = -1.0
-        if "Vm" not in dict:
-            dict["Vm"] = Vm if Vm is not None else -1.0
-        if "order_parameters" not in dict:
-            dict["order_parameters"] = list(binaryIsothermalSys.phases.keys())
-        if "dimensions" not in dict:
-            dict["dimensions"] = { "length_scale": 0.0, "time_scale": 0.0, "energy_density_scale": 0.0 }
+        if "l_int" not in system_dict:
+            system_dict["l_int"] = -1.0
+        if "Vm" not in system_dict:
+            system_dict["Vm"] = Vm if Vm is not None else -1.0
+        if "order_parameters" not in system_dict:
+            system_dict["order_parameters"] = list(binaryIsothermalSys.phases.keys())
+        if "dimensions" not in system_dict:
+            system_dict["dimensions"] = { "length_scale": 0.0, "time_scale": 0.0, "energy_density_scale": 0.0 }

pyproject.toml

@@ -29,7 +29,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "ammber"
-version = "0.1.6"
+version = "0.1.7"
 description = "A Python package for parametrizing Gibbs free energy curves for phase-field modeling"
 authors = [
     { name = "W. Beck Andrews", email = "wband@umich.edu" },