Merge pull request #6 from GES-mpalermo/main

Miscellaneous code fixes

echemsuite/cellcycling/read_input.py

@@ -1,6 +1,8 @@
 import pandas as pd
 import numpy as np
 import scipy.integrate as integrate
+import sys
+import warnings
 
 
 class CellCycling:
@@ -9,6 +11,13 @@ class CellCycling:
     """
     def __init__(self, cycles):
         self._cycles = cycles
+        self._number_of_cycles = len(self._cycles)
+
+        self._capacity_retentions = None  # to be initialized in calculate_retention()
+        self._capacity_efficiencies = None  # to be initialized in calculate_efficiency()
+
+        self.calculate_capacity_efficiencies()
+        self.calculate_capacity_retention()
 
     def __getitem__(self, cycle):
         return self._cycles[cycle]
@@ -17,39 +26,41 @@ def __iter__(self):
         for obj in self._cycles:
             yield obj
 
-    def calculate_retention(self, reference = 0):
+    def calculate_capacity_retention(self, reference = 0):
         """
         Calculates capacity retention between cycles, as the ratio between 
         capacity of cycle n (discharge) minus cycle 1 (discharge)
         """
 
         initial_capacity = self._cycles[reference].capacity_discharge
 
-        self._retention = []
+        self._capacity_retentions = []
 
         for cycle in self._cycles:
-            self._retention.append(cycle.capacity_discharge / initial_capacity * 100)
+            self._capacity_retentions.append(cycle.capacity_discharge / initial_capacity * 100)
 
-        return self._retention
-
-    def calculate_efficiency(self):
+    def calculate_capacity_efficiencies(self):
         """
         Calculates capacity efficiency of the cycles, as the ratio between 
         capacity of cycle n in charge and discharge
         """
 
-        self._efficiency = []
+        self._capacity_efficiencies = []
 
         for cycle in self._cycles:
-            self._efficiency.append(cycle.capacity_discharge / cycle.capacity_charge * 100) 
+            self._capacity_efficiencies.append(cycle.capacity_discharge / cycle.capacity_charge * 100) 
 
     @property
-    def retention(self):
-        return self._retention
+    def capacity_retention(self):
+        return self._capacity_retentions
 
     @property
-    def efficiency(self):
-        return self._efficiency
+    def capacity_efficiency(self):
+        return self._capacity_efficiencies
+
+    @property
+    def number_of_cycles(self):
+        return self._number_of_cycles
 
 
 class Cycle:
@@ -59,6 +70,8 @@ class Cycle:
 
     def __init__(self, number):
         self._number = number
+
+        # DEV NOTE: move all variable initializations here to default value
 
     @property
     def number(self):
@@ -198,10 +211,18 @@ def calculate_efficiencies(self):
         Computes the coulombic and energy efficiency of the cycle as the ratio 
         between the discharge and charge energies.
         """
-
-        self._coulomb_efficiency = self._capacity_discharge / self._capacity_charge * 100
-        self._energy_efficiency = self._total_energy_discharge / self._total_energy_charge * 100
-        self._voltage_efficiency = self._energy_efficiency / self._coulomb_efficiency * 100
+        if any((self._capacity_charge <= 0, self._total_energy_charge <= 0)):
+            print(f"Warning: cycle {self._number} will be removed due to unphysical charge/discharge value")
+            #warnings.warn(f"Cycle {self._number} will be removed due to unphysical charge/discharge value")
+
+            # 101 is a sentinel value
+            self._coulomb_efficiency = 101
+            self._energy_efficiency = 101
+            self._voltage_efficiency = 101
+        else:
+            self._coulomb_efficiency = self._capacity_discharge / self._capacity_charge * 100
+            self._energy_efficiency = self._total_energy_discharge / self._total_energy_charge * 100
+            self._voltage_efficiency = self._energy_efficiency / self._coulomb_efficiency * 100
 
         return self._coulomb_efficiency, self._energy_efficiency, self._voltage_efficiency
 
@@ -221,13 +242,13 @@ def voltage_efficiency(self):
 def build_DTA_cycles(filelist):
 
     cycles = []
-    cycle_number = 1
+    cycle_number = 0
 
     for filepath in filelist:
 
         print("Loading:", filepath, "\n")
 
-        if filepath.endswith(".DTA"):                                        
+        if filepath.endswith(".DTA".lower()):                                        
 
             with open(filepath, "r", encoding="utf8", errors="ignore") as file:
 
@@ -291,21 +312,21 @@ def build_DTA_cycles(filelist):
 
         else:
             print("This is not a .DTA file!")
-            exit()  
+            sys.exit()  
 
     return cycles
 
 
 def read_mpt_cycles(filelist):
 
     cycles = []
-    cycle_number = 1
+    cycle_number = 0
 
     for filepath in filelist:
 
         print("Loading:", filepath, "\n")
 
-        if filepath.endswith(".mpt"):  
+        if filepath.endswith(".mpt".lower()):  
 
             with open(filepath, "r", encoding="utf8", errors="ignore") as file:
 
@@ -382,32 +403,38 @@ def read_mpt_cycles(filelist):
 
         else:
             print("This is not a .mpt file!")
-            exit() 
+            sys.exit() 
 
     return cycles
 
 
 def read_cycles(filelist):
-
+    for filepath in filelist:
+        filepath = r'%s' %filepath
+
     cycles = read_mpt_cycles(filelist)
 
     return CellCycling(cycles)
 
 
 def build_cycles(filelist):
-
+    for filepath in filelist:
+        filepath = r'%s' %filepath
     cycles = build_DTA_cycles(filelist)
 
     return CellCycling(cycles)    
 
 
-def time_adjust(cycle):
+def time_adjust(cycle, reverse=False):
 
     if cycle.time_discharge.iloc[0] != cycle.time_charge.iloc[0]:
         time_charge = cycle.time_charge.subtract(cycle.time_charge.iloc[0])
         time_discharge = cycle.time_discharge.subtract(cycle.time_charge.iloc[-1])
     else:
         time_charge = cycle.time_charge
         time_discharge = cycle.time_discharge
+
+    if reverse is True:
+        time_discharge=time_discharge.sort_values(ascending=False)
 
     return time_charge, time_discharge

meta.yaml

@@ -1,5 +1,5 @@
 {% set name = "GES-echem-suite" %}
-{% set version = "0.1.3a" %}
+{% set version = "0.1.4a" %}
 
 
 

setup.py

@@ -3,7 +3,7 @@
 
 setuptools.setup(
     name="GES-echem-suite",
-    version="0.1.3a",
+    version="0.1.4a",
     description="",
     long_description="",
     packages=["echemsuite"],