Merge branch 'master' of gitlab.tubit.tu-berlin.de:m_huelsberg/analyzebd

 Conflicts:
	analyzebd/stress.py

.idea/analyzebd.iml

@@ -4,7 +4,7 @@
     <content url="file://$MODULE_DIR$">
       <excludeFolder url="file://$MODULE_DIR$/.venv" />
     </content>
-    <orderEntry type="jdk" jdkName="Python 3.7 (analyzebd)" jdkType="Python SDK" />
+    <orderEntry type="inheritedJdk" />
     <orderEntry type="sourceFolder" forTests="false" />
   </component>
   <component name="TestRunnerService">

analyzebd/strain.py

@@ -13,10 +13,10 @@ class Strain:
         if(filename is None):
             self.generate()
         else:
-            self.read_from_file(filename)
+            self.readFromFile(filename)
 
     def reset(self, filename):
-        self.read_from_file(filename)
+        self.readFromFile(filename)
 
     def generate(self):
         self.T = 1
@@ -28,7 +28,7 @@ class Strain:
         self.strainUnit = "y0"
         self.strainConversion = self.A
     
-    def read_from_file(self, filename):
+    def readFromFile(self, filename):
         self.dt = float(find_setting_in_file(filename.parent / "shearedSlitporeBD.out", "dt"))
         self.T = float(find_setting_in_file(filename.parent / "shearedSlitporeBD.out", "oscillationPeriod"))
         self.A = float(find_setting_in_file(filename.parent / "shearedSlitporeBD.out", "amplitude")) * self.T / (2 * math.pi)

analyzebd/stress.py

+import math
 import numpy as np
 import matplotlib.pyplot as plt
 from matplotlib import cm
@@ -43,7 +44,8 @@ class Stress:
         i0 = int(tStart * self.timeConversion / self.dt_stress)
         iEnd = None
         if (tEnd is not None):
-            iEnd = int(tEnd * self.timeConversion / self.dt_stress)
+            # not optimal
+            iEnd = round(tEnd * self.timeConversion / self.dt_stress)
         self.time = np.loadtxt(filename, skiprows=i0, max_rows=iEnd, usecols=0) * self.dt / self.timeConversion
         self.shearRate = np.loadtxt(filename, skiprows=i0, max_rows=iEnd, usecols=1)
         self.stress = np.loadtxt(filename, skiprows=i0, max_rows=iEnd, usecols=6)
@@ -83,9 +85,9 @@ class Stress:
         if(tStart is not None):
             self.time -= tStart
             # translated starting index due to shift
-            i0 = int(tStart * self.timeConversion / self.dt_stress)
+            i0 = round(tStart * self.timeConversion / self.dt_stress)
         if(tEnd is not None):
-            iEnd = int(tEnd * self.timeConversion / self.dt_stress)
+            iEnd = round(tEnd * self.timeConversion / self.dt_stress)
         self.time = self.time[i0:iEnd]
         self.shearRate = self.shearRate[i0:iEnd]
         self.stress = self.stress[i0:iEnd]
@@ -111,6 +113,9 @@ class Stress:
         self.stress = newStress
         return self
 
+    def getTotalAverage(self):
+        return self.stress.mean()
+
     def plotOverTime(self, ax=None, **kwargs):
         if(ax is None):
             ax = plt.subplot()
@@ -125,13 +130,28 @@ class Stress:
         ax.set_title("$T=$" f"{self.T}" "$\\tau_B, \\dot{\\gamma}_0=$" f"{self.A}" "$\\tau_B^{-1}$")
         return ax
 
-    def plotVLB(self, ax=None, normalize=False, withColor=True, withColorBar=False, colormap="viridis", **kwargs):
+    def plotLB(self, ax=None, kind="viscous", normalize=False, withColor=True, withColorBar=False, colormap="viridis", **kwargs):
         if(ax is None):
             ax = plt.subplot()
+        if(kind == "viscous"):
+            x = self.shearRate
+            ax.set_xlabel("$\\dot{\\gamma}(t)/\\tau_B^{-1}$")
+            ax.set_title("Viscous Lissajou-Bowditch figure")
+        elif(kind == "elastic"):
+            x = np.array([self.A * self.T / self.timeConversion / (2 * math.pi) * math.sin(2*math.pi * t / self.T * self.timeConversion) for t in self.time])
+            ax.set_xlabel("$\\gamma(t)$")
+            ax.set_title("Elastic Lissajou-Bowditch figure")
+        else:
+            raise AttributeError(f"kind='{kind}' not supported. Choose either 'viscous' or 'elastic'.")
+        y = self.stress
+        ax.set_ylabel("$\\sigma_{xz}(t)/\\tilde{\\epsilon}d^{-3}$")
         if(normalize):
-            x = self.shearRate / np.absolute(self.shearRate).max()
-            y = self.stress / np.absolute(self.stress).max()
-            ax.set_xlabel("$\\dot{\\gamma}(t)/\\dot{\\gamma}_0$")
+            x /= np.absolute(x).max()
+            y /= np.absolute(y).max()
+            if(kind == "viscous"):
+                ax.set_xlabel("$\\dot{\\gamma}(t)/\\dot{\\gamma}_0$")
+            else:
+                ax.set_xlabel("$\\gamma(t)/\\gamma_0$")
             ax.set_ylabel("$\\sigma_{xz}(t)/\\sigma_{xz}^{max}$")
         else:
             x = self.shearRate