commit fe6942ce0dd1e38d092defdcc4117918aa369bba
Author: JesusMSM <jesusm.sanchez93@gmail.com>
Date:   Fri Dec 4 11:41:42 2015 +0100

    First commit

diff --git a/settings.py b/settings.py
new file mode 100644
index 0000000..86acbd5
--- /dev/null
+++ b/settings.py
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+# settings.py
+def init():
+    global number_of_nodes
+    global max_time
+    global num_trials
+    global bite_prob
+    global network_type
+    global heal_prob
+    global innovation_prob
+    global imitation_prob
+    global timeout
+    global outside_effects_prob
+    global anger_prob
+    global joy_prob
+    global sadness_prob
+    global disgust_prob
+
+    network_type=1
+    number_of_nodes=200
+    max_time=1000
+    num_trials=1
+    timeout=10
+
+    #Zombie model
+    bite_prob=0.01 # 0-1
+    heal_prob=0.01 # 0-1
+
+    #Bass model
+    innovation_prob=0.01
+    imitation_prob=0.01
+
+    #SentimentCorrelation model
+    outside_effects_prob = 0.2
+    anger_prob = 0.08
+    joy_prob = 0.05
+    sadness_prob = 0.02
+    disgust_prob = 0.02
diff --git a/soil.py b/soil.py
new file mode 100644
index 0000000..d6d6204
--- /dev/null
+++ b/soil.py
@@ -0,0 +1,394 @@
+from nxsim import NetworkSimulation
+from nxsim import BaseNetworkAgent
+from nxsim import BaseLoggingAgent
+from random import randint
+from matplotlib import pyplot as plt
+import random
+import numpy as np
+import networkx as nx
+import settings
+
+
+settings.init()
+
+if settings.network_type == 0:
+    G = nx.complete_graph(settings.number_of_nodes)
+if settings.network_type == 1:
+    G = nx.barabasi_albert_graph(settings.number_of_nodes,3)
+if settings.network_type == 2:
+    G = nx.margulis_gabber_galil_graph(settings.number_of_nodes, None)
+
+
+myList=[]
+networkStatus=[]
+for x in range(0, settings.number_of_nodes):
+    networkStatus.append({'id':x})
+
+
+
+# # Just like subclassing a process in SimPy
+# class MyAgent(BaseNetworkAgent):
+#     def __init__(self, environment=None, agent_id=0, state=()):  # Make sure to have these three keyword arguments
+#         super().__init__(environment=environment, agent_id=agent_id, state=state)
+#         # Add your own attributes here
+
+#     def run(self):
+#         # Add your behaviors here
+
+
+
+
+class SentimentCorrelationModel(BaseNetworkAgent):
+    def __init__(self, environment=None, agent_id=0, state=()):
+        super().__init__(environment=environment, agent_id=agent_id, state=state)
+        self.outside_effects_prob = settings.outside_effects_prob
+        self.anger_prob = settings.anger_prob
+        self.joy_prob = settings.joy_prob
+        self.sadness_prob = settings.sadness_prob
+        self.disgust_prob = settings.disgust_prob
+        self.time_awareness=[]
+        for i in range(4):
+            self.time_awareness.append(0)     #0-> Anger, 1-> joy, 2->sadness, 3 -> disgust
+        networkStatus[self.id][self.env.now]=0
+
+
+    def run(self):
+        while True:
+            if self.env.now > 10:
+                G.add_node(205)
+                G.add_edge(205,0)
+            angry_neighbors_1_time_step=[]
+            joyful_neighbors_1_time_step=[]
+            sad_neighbors_1_time_step=[]
+            disgusted_neighbors_1_time_step=[]
+
+
+            angry_neighbors = self.get_neighboring_agents(state_id=1)
+            for x in angry_neighbors:
+                if x.time_awareness[0] > (self.env.now-500):
+                    angry_neighbors_1_time_step.append(x)
+            num_neighbors_angry = len(angry_neighbors_1_time_step)
+
+
+            joyful_neighbors = self.get_neighboring_agents(state_id=2)
+            for x in joyful_neighbors:
+                if x.time_awareness[1] > (self.env.now-500):
+                    joyful_neighbors_1_time_step.append(x)
+            num_neighbors_joyful = len(joyful_neighbors_1_time_step)
+
+
+            sad_neighbors = self.get_neighboring_agents(state_id=3)
+            for x in sad_neighbors:
+                if x.time_awareness[2] > (self.env.now-500):
+                    sad_neighbors_1_time_step.append(x)
+            num_neighbors_sad = len(sad_neighbors_1_time_step)
+
+
+            disgusted_neighbors = self.get_neighboring_agents(state_id=4)
+            for x in disgusted_neighbors:
+                if x.time_awareness[3] > (self.env.now-500):
+                    disgusted_neighbors_1_time_step.append(x)
+            num_neighbors_disgusted = len(disgusted_neighbors_1_time_step)
+
+            # #Outside effects. Asignamos un estado aleatorio
+            # if random.random() < settings.outside_effects_prob:
+            #     if self.state['id'] == 0:
+            #         self.state['id'] = random.randint(1,4)
+            #         myList.append(self.id)
+            #         networkStatus[self.id][self.env.now]=self.state['id'] #Almaceno cuando se ha infectado para la red dinamica
+            #         self.time_awareness = self.env.now #Para saber cuando se han contagiado
+            #         yield self.env.timeout(settings.timeout)
+            #     else:
+            #         yield self.env.timeout(settings.timeout)
+
+
+            # #Imitation effects-Joy
+
+            # if random.random() < (settings.joy_prob*(num_neighbors_joyful)/10):
+            #     myList.append(self.id)
+            #     self.state['id'] = 2
+            #     networkStatus[self.id][self.env.now]=2
+            #     yield self.env.timeout(settings.timeout)
+
+
+            # #Imitation effects-Sadness
+
+            # if random.random() < (settings.sadness_prob*(num_neighbors_sad)/10):
+            #     myList.append(self.id)
+            #     self.state['id'] = 3
+            #     networkStatus[self.id][self.env.now]=3
+            #     yield self.env.timeout(settings.timeout)
+
+
+            # #Imitation effects-Disgust
+
+            # if random.random() < (settings.disgust_prob*(num_neighbors_disgusted)/10):
+            #     myList.append(self.id)
+            #     self.state['id'] = 4
+            #     networkStatus[self.id][self.env.now]=4
+            #     yield self.env.timeout(settings.timeout)
+
+            # #Imitation effects-Anger
+
+            # if random.random() < (settings.anger_prob*(num_neighbors_angry)/10):
+            #     myList.append(self.id)
+            #     self.state['id'] = 1
+            #     networkStatus[self.id][self.env.now]=1
+            #     yield self.env.timeout(settings.timeout)
+
+            # yield self.env.timeout(settings.timeout)
+
+###########################################
+
+
+            anger_prob= settings.anger_prob+(len(angry_neighbors_1_time_step)*settings.anger_prob)
+            print("anger_prob " + str(anger_prob))
+            joy_prob= settings.joy_prob+(len(joyful_neighbors_1_time_step)*settings.joy_prob)
+            print("joy_prob " + str(joy_prob))
+            sadness_prob = settings.sadness_prob+(len(sad_neighbors_1_time_step)*settings.sadness_prob)
+            print("sadness_prob "+ str(sadness_prob))
+            disgust_prob = settings.disgust_prob+(len(disgusted_neighbors_1_time_step)*settings.disgust_prob)
+            print("disgust_prob " + str(disgust_prob))
+            outside_effects_prob= settings.outside_effects_prob
+            print("outside_effects_prob " + str(outside_effects_prob))
+
+
+            num = random.random()
+
+
+            if(num<outside_effects_prob):
+                self.state['id'] = random.randint(1,4)
+                myList.append(self.id)
+                networkStatus[self.id][self.env.now]=self.state['id'] #Almaceno cuando se ha infectado para la red dinamica
+                self.time_awareness[self.state['id']-1] = self.env.now
+                yield self.env.timeout(settings.timeout)
+
+
+            if(num<anger_prob):
+
+                myList.append(self.id)
+                self.state['id'] = 1
+                networkStatus[self.id][self.env.now]=1
+                self.time_awareness[self.state['id']-1] = self.env.now
+            elif (num<joy_prob+anger_prob and num>anger_prob):
+
+                myList.append(self.id)
+                self.state['id'] = 2
+                networkStatus[self.id][self.env.now]=2
+                self.time_awareness[self.state['id']-1] = self.env.now
+            elif (num<sadness_prob+anger_prob+joy_prob and num>joy_prob+anger_prob):
+
+                myList.append(self.id)
+                self.state['id'] = 3
+                networkStatus[self.id][self.env.now]=3
+                self.time_awareness[self.state['id']-1] = self.env.now
+            elif (num<disgust_prob+sadness_prob+anger_prob+joy_prob and num>sadness_prob+anger_prob+joy_prob):
+
+                myList.append(self.id)
+                self.state['id'] = 4
+                networkStatus[self.id][self.env.now]=4
+                self.time_awareness[self.state['id']-1] = self.env.now
+
+            yield self.env.timeout(settings.timeout)
+
+
+            # anger_propagation = settings.anger_prob*num_neighbors_angry/10
+            # joy_propagation = anger_propagation + (settings.joy_prob*num_neighbors_joyful/10)
+            # sadness_propagation = joy_propagation + (settings.sadness_prob*num_neighbors_sad/10)
+            # disgust_propagation = sadness_propagation + (settings.disgust_prob*num_neighbors_disgusted/10)
+            # outside_effects_propagation = disgust_propagation + settings.outside_effects_prob
+
+            # if (num<anger_propagation):
+            #     if(self.state['id'] !=0):
+            #         myList.append(self.id)
+            #         self.state['id'] = 1
+            #         networkStatus[self.id][self.env.now]=1
+            #         yield self.env.timeout(settings.timeout)
+            # if (num<joy_propagation):
+            #     if(self.state['id'] !=0):
+            #         myList.append(self.id)
+            #         self.state['id'] = 2
+            #         networkStatus[self.id][self.env.now]=2
+            #         yield self.env.timeout(settings.timeout)
+            # if(num<sadness_propagation):
+            #     if(self.state['id'] !=0):
+            #         myList.append(self.id)
+            #         self.state['id'] = 3
+            #         networkStatus[self.id][self.env.now]=3
+            #         yield self.env.timeout(settings.timeout)
+            # # if(num<disgust_propagation):
+            # #     if(self.state['id'] !=0):
+            # #         myList.append(self.id)
+            # #         self.state['id'] = 4
+            # #         networkStatus[self.id][self.env.now]=4
+            # #         yield self.env.timeout(settings.timeout)
+            # if(num <outside_effects_propagation):
+            #     if self.state['id'] == 0:
+            #         self.state['id'] = random.randint(1,4)
+            #         myList.append(self.id)
+            #         networkStatus[self.id][self.env.now]=self.state['id'] #Almaceno cuando se ha infectado para la red dinamica
+            #         self.time_awareness = self.env.now #Para saber cuando se han contagiado
+            #         yield self.env.timeout(settings.timeout)
+            #     else:
+            #         yield self.env.timeout(settings.timeout)
+            # else:
+            #     yield self.env.timeout(settings.timeout)
+
+
+
+
+
+class BassModel(BaseNetworkAgent):
+    def __init__(self, environment=None, agent_id=0, state=()):
+        super().__init__(environment=environment, agent_id=agent_id, state=state)
+        self.innovation_prob = settings.innovation_prob
+        self.imitation_prob = settings.imitation_prob
+        networkStatus[self.id][self.env.now]=0
+
+    def run(self):
+        while True:
+
+
+            #Outside effects
+            if random.random() < settings.innovation_prob:
+                if self.state['id'] == 0:
+                    self.state['id'] = 1
+                    myList.append(self.id)
+                    networkStatus[self.id][self.env.now]=1
+                    yield self.env.timeout(settings.timeout)
+                else:
+                    yield self.env.timeout(settings.timeout)
+
+            #Imitation effects
+            if self.state['id'] == 0:
+                aware_neighbors = self.get_neighboring_agents(state_id=1)
+                num_neighbors_aware = len(aware_neighbors)
+                if random.random() < (settings.imitation_prob*num_neighbors_aware):
+                    myList.append(self.id)
+                    self.state['id'] = 1
+                    networkStatus[self.id][self.env.now]=1
+                    yield self.env.timeout(settings.timeout)
+                else:
+                    yield self.env.timeout(settings.timeout)
+
+class IndependentCascadeModel(BaseNetworkAgent):
+    def __init__(self, environment=None, agent_id=0, state=()):
+        super().__init__(environment=environment, agent_id=agent_id, state=state)
+        self.innovation_prob = settings.innovation_prob
+        self.imitation_prob = settings.imitation_prob
+        self.time_awareness = 0
+        networkStatus[self.id][self.env.now]=0
+
+    def run(self):
+        while True:
+            aware_neighbors_1_time_step=[]
+            #Outside effects
+            if random.random() < settings.innovation_prob:
+                if self.state['id'] == 0:
+                    self.state['id'] = 1
+                    myList.append(self.id)
+                    networkStatus[self.id][self.env.now]=1
+                    self.time_awareness = self.env.now #Para saber cuando se han contagiado
+                    yield self.env.timeout(settings.timeout)
+                else:
+                    yield self.env.timeout(settings.timeout)
+
+            #Imitation effects
+            if self.state['id'] == 0:
+                aware_neighbors = self.get_neighboring_agents(state_id=1)
+                for x in aware_neighbors:
+                    if x.time_awareness == (self.env.now-1):
+                        aware_neighbors_1_time_step.append(x)
+                num_neighbors_aware = len(aware_neighbors_1_time_step)
+                if random.random() < (settings.imitation_prob*num_neighbors_aware):
+                    myList.append(self.id)
+                    self.state['id'] = 1
+                    networkStatus[self.id][self.env.now]=1
+                    yield self.env.timeout(settings.timeout)
+                else:
+                    yield self.env.timeout(settings.timeout)
+
+
+class ZombieOutbreak(BaseNetworkAgent):
+    def __init__(self, environment=None, agent_id=0, state=()):
+        super().__init__(environment=environment, agent_id=agent_id, state=state)
+        self.bite_prob = settings.bite_prob
+        networkStatus[self.id][self.env.now]=0
+
+
+    def run(self):
+        while True:
+            if random.random() < settings.heal_prob:
+                if self.state['id'] == 1:
+                    self.zombify()
+                    yield self.env.timeout(settings.timeout)
+                else:
+                    yield self.env.timeout(settings.timeout)
+            else:
+                if self.state['id'] == 1:
+                    print("Soy el zombie " + str(self.id) + " y me voy a curar porque el num aleatorio ha sido " + str(num))
+                    networkStatus[self.id][self.env.now]=0
+                    if self.id in myList:
+                        myList.remove(self.id)
+                    self.state['id'] = 0
+                    yield self.env.timeout(settings.timeout)
+                else:
+                    yield self.env.timeout(settings.timeout)
+
+
+    def zombify(self):
+        normal_neighbors = self.get_neighboring_agents(state_id=0)
+        for neighbor in normal_neighbors:
+            if random.random() < self.bite_prob:
+                print("Soy el zombie " + str(self.id) + " y voy a contagiar a " + str(neighbor.id))
+                neighbor.state['id'] = 1 # zombie
+                myList.append(neighbor.id)
+                networkStatus[self.id][self.env.now]=1
+                networkStatus[neighbor.id][self.env.now]=1
+                print(self.env.now, "Soy el zombie: "+ str(self.id), "Mi vecino es: "+ str(neighbor.id), sep='\t')
+                break
+
+
+# Initialize agent states. Let's assume everyone is normal.
+init_states = [{'id': 0, } for _ in range(settings.number_of_nodes)]  # add keys as as necessary, but "id" must always refer to that state category
+
+# Seed a zombie
+#init_states[5] = {'id': 1}
+#init_states[3] = {'id': 1}
+
+sim = NetworkSimulation(topology=G, states=init_states, agent_type=SentimentCorrelationModel,
+                        max_time=settings.max_time, num_trials=settings.num_trials, logging_interval=1.0)
+
+
+sim.run_simulation()
+
+myList = sorted(myList, key=int)
+#print("Los zombies son: " + str(myList))
+
+trial = BaseLoggingAgent.open_trial_state_history(dir_path='sim_01', trial_id=0)
+zombie_census = [sum([1 for node_id, state in g.items() if state['id'] == 1]) for t,g in trial.items()]
+
+#for x in range(len(myList)):
+#    G.node[myList[x]]['viz'] = {'color': {'r': 255, 'g': 0, 'b': 0, 'a': 0}}
+
+#G.node[1]['viz'] = {'color': {'r': 255, 'g': 0, 'b': 0, 'a': 0}}
+
+#lista = nx.nodes(G)
+#print('Nodos: ' + str(lista))
+for x in range(0, settings.number_of_nodes):
+    networkStatusAux=[]
+    for tiempo in networkStatus[x]:
+        if tiempo != 'id':
+	        networkStatusAux.append((networkStatus[x][tiempo],tiempo,None))
+    G.add_node(x, zombie= networkStatusAux)
+#print(networkStatus)
+
+
+nx.write_gexf(G,"test.gexf", version="1.2draft")
+plt.plot(zombie_census)
+plt.draw()  # pyplot draw()
+plt.savefig("zombie.png")
+#print(networkStatus)
+#nx.draw(G)
+#plt.show()
+#plt.savefig("path.png")