Added examples

CMakeLists.txt

@@ -4,6 +4,7 @@ enable_language(CXX)
 
 project(mythical VERSION "0.0.0")
 
+set(SOVERSION 0)
 set(CMAKE_CXX_STANDARD 14)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_CXX_EXTENSIONS OFF)

CoarseGrainSites/include/mythical/version.hpp.in

@@ -4,10 +4,11 @@
 #include <string>
 
 namespace mythical {
-  const std::string PROJECT_NAME = "@PROJECT_NAME@";
-  const std::string PROJECT_VER = "@PROJECT_VERSION@";
-  const int PROJECT_VER_MAJOR = @PROJECT_VERSION_MAJOR@;
-  const int PROJECT_VER_MINOR = @PROJECT_VERSION_MINOR@;
-  const int PROJECT_VER_PATCH = @PROJECT_VERSION_PATCH@;
+  const std::string mythical_NAME = "@PROJECT_NAME@";
+  const std::string mythical_VER = "@PROJECT_VERSION@";
+  const std::string mythnical_SOVERSION = "@SOVERSION@";
+  const int mythical_VER_MAJOR = @PROJECT_VERSION_MAJOR@;
+  const int mythical_VER_MINOR = @PROJECT_VERSION_MINOR@;
+  const int mythical_VER_PATCH = @PROJECT_VERSION_PATCH@;
 }
 #endif // MYTHICAL_VERSION_HPP

cmake/MythiCaLInstall.cmake

@@ -1,3 +1,6 @@
+
+set_target_properties(mythical PROPERTIES VERSION ${mythical_VERSION} SOVERSION ${SOVERSION})
+
 target_include_directories(mythical PUBLIC
   $<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/src/libmythical>
   $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/mythical>

examples/1D_hopping/1D_example.cpp

@@ -0,0 +1,64 @@
+#include <mythical/coarsegrainsystem.hpp>
+#include <mythical/walker.hpp>
+
+#include <unordered_map>
+#include <vector>
+#include <iostream>
+#include <fstream>
+
+using namespace std;
+
+namespace my = mythical;
+
+typedef std::pair<int,shared_ptr<my::Walker>> walker_t;
+
+unordered_map<int,unordered_map<int, double>> 
+generateRates(const int number_of_sites) {
+  unordered_map<int,unordered_map<int, double>> rates;
+  for(int i=1 ; i<number_of_sites; ++i){
+    rates[i][i+1]=3.0;
+    rates[i+1][i]=1.0;
+  }
+  return rates;
+}
+
+int main(){
+
+  int number_of_sites = 20;
+
+  unordered_map<int,unordered_map<int, double>> rates =  generateRates(number_of_sites);
+
+  my::CoarseGrainSystem CGsystem;
+  CGsystem.setTimeResolution(3.0);
+  CGsystem.initializeSystem(rates);
+
+  class Charge : public my::Walker {};
+
+  int charge_id;
+  vector<walker_t> charges;
+  charges.emplace_back(charge_id, std::shared_ptr<my::Walker>( new Charge));
+  charges.back().second->occupySite(1);
+  CGsystem.initializeWalkers(charges);
+
+  const int iterations = 50;
+
+  ofstream traj_file;
+  traj_file.open("Trajectory.txt");
+  traj_file << "Number of Sites: " << number_of_sites << endl;
+  traj_file << "Number of iterations: " << iterations << endl;
+  traj_file << endl;
+  traj_file << "Site    Dwell Time" << std::endl;
+
+  for(int iteration = 0; iteration<iterations;++iteration){
+    CGsystem.hop(charges.at(0));
+    const int site_id = charges.at(0).second->getIdOfSiteCurrentlyOccupying();
+    const double dwell_time = charges.at(0).second->getDwellTime();
+    cout << "Charge occupying site: " << site_id << " dwell time " << dwell_time << endl;
+    traj_file << site_id << "      " << dwell_time << endl;
+  }
+
+  CGsystem.removeWalkerFromSystem(charges.at(0));
+  traj_file.close();
+
+  return 0;
+}

examples/1D_hopping/CMakeLists.txt

@@ -0,0 +1,9 @@
+cmake_minimum_required(VERSION 3.12)
+project(1D_example)
+
+enable_language(CXX)
+
+find_package(MythiCaL REQUIRED)
+add_executable(1D_example 1D_example.cpp)
+
+target_link_libraries(1D_example PUBLIC mythical::mythical)

examples/1D_hopping/scripts/create_images.py

@@ -0,0 +1,44 @@
+import numpy as np
+import matplotlib.pyplot as plt
+import matplotlib.patches as pat
+
+site=[]
+dwell_Time=[]
+
+with open("Trajectory.txt") as fid:
+
+    line = fid.readline()
+    words = line.split()
+    num_sites = int(words[3])
+
+    line = fid.readline()
+    words = line.split()
+    iterations = int(words[3])
+
+    line = fid.readline()
+    line = fid.readline()
+
+
+    for line in fid:
+        site.append(int(line.split()[0]))
+        dwell_Time.append(float(line.split()[1]))
+
+sites = np.asarray(site)
+
+for i in range(0,iterations):
+    fig = plt.figure(figsize = (num_sites+1,5))
+    ax = plt.gca()
+    for j in range(1,num_sites+1):
+        draw_circ = plt.Circle((j,0),0.4, color='r')
+        ax.add_artist(draw_circ)
+
+    draw_circ = plt.Circle((sites[i],0),0.4, color='b')
+    ax.add_artist(draw_circ)
+
+    ax.set_xlim(0, num_sites+1)
+    ax.set_ylim(-2,2)
+    ax.set_aspect('equal')
+    plt.xlabel("x axis")
+    plt.savefig("hop_" + str(i) + ".png")
+
+    plt.close()

examples/1D_hopping/scripts/create_movie.sh

@@ -0,0 +1 @@
+ffmpeg.exe -r 4 -i hop_%d.png -vcodec libx264 -pix_fmt yuv420p output.mp4

examples/ToF/scripts/plot_current_transient.py

@@ -0,0 +1,56 @@
+
+import numpy as np
+import matplotlib.pyplot as plt
+
+moving_avg = 5
+
+with open("transient_current.txt",'r') as tc:
+    tc.readline() # Ignore header
+    num_pts = int(tc.readline())
+    time = np.zeros(num_pts)
+    current = np.zeros(num_pts)
+    current_moving_avg = np.zeros(num_pts)
+    charges = np.zeros(num_pts)
+
+    lines = tc.readlines()
+    count = 0
+    # Strips the newline character 
+    for line in lines: 
+        words = line.split()
+        time[count] = float(words[0])
+        current[count] = float(words[1])
+        charges[count] = int(words[2])
+        count = count + 1
+
+    value = 0.0
+    for ind in range(0,num_pts):
+        value = value + current[ind]
+        if ind < moving_avg:
+            current_moving_avg[ind] = value/float(ind+1)
+        elif ind > num_pts - moving_avg:
+            value = value - current[ind-moving_avg]
+            current_moving_avg[ind] = value/float(num_pts - ind)
+        else:
+            value = value - current[ind-moving_avg]
+            current_moving_avg[ind] = value/float(moving_avg)
+
+    xlim_val = 2E-9
+    plt.plot(time,current)
+    plt.plot(time,current_moving_avg)
+    params = {'mathtext.default': 'regular' }          
+    plt.rcParams.update(params)
+    plt.xlabel("Time $[s]$")
+    plt.ylabel("Displacement Current $[A / cm^2]$")
+    plt.yscale('log')
+    plt.xscale('log')
+    plt.savefig("DisplacementCurrentLogLog.png")
+    plt.xscale('linear')
+    plt.yscale('linear')
+    ax = plt.gca()
+    plt.xlim(0,xlim_val)
+#    plt.ylim(0,20000)
+    ax2 = ax.twinx()
+    ax2.plot(time,charges,color='g')
+    ax2.set_ylabel("Number of Charges Remaining")
+    plt.ylim(0,210)
+    plt.savefig("DisplacementCurrent.png")