piegy 1.1.6__py3-none-any.whl → 2.0.0__py3-none-any.whl

piegy/simulation.py

@@ -27,229 +27,78 @@ NOTE: Only model class and run function are intended for direct usages.
 '''
 
 
-import math
 import numpy as np
-from timeit import default_timer as timer
-
-
-# data type used by model.U and model.V
-UV_DTYPE = 'float64'
-
-# data type used by model.Upi and V_pi
-PI_DTYPE = 'float64'
-
-# data type for storing rates in single_test an single_init
-RATES_DTYPE = 'float64'
-
-
-class patch:
-    '''
-    A single patch in the N x M space.
-    Interacts with neighboring patches, assuming no spatial structure within a patch.
-    Initialized in single_init function.
+import os
+import ctypes
+from ctypes import c_size_t, c_uint32, c_int32, c_double, c_bool, c_char_p, c_char
+import numpy as np
+from numpy.ctypeslib import ndpointer
 
-    Class Functions:
 
-        __init__:
-            Inputs:
-                U, V:       initial value of U and V
-                matrix:     payoff matrix for U and V. The canonical form is 2x2, here we ask for a flattened 1x4 form.
-                patch_var:  np.array of [mu1, mu2, w1, w2, kappa1, kappa2]
-        
-        __str__:
-            Print patch object in a nice way.
 
-        set_nb_pointers:
-            Set pointers to neighbors of this patch object.
 
-        update_pi:
-            Update Upi, V_pi and payoff rates (payoff rates are the first two numbers in self.pi_death_rates).
-        
-        update_k:
-            Update natural death rates (the last two numbers in self.pi_death_rates).
+'''
+The C core
+'''
 
-        update_mig:
-            Update migration rates.
+# path to the C shared libary
+C_LIB_PATH = os.path.join(os.path.dirname(__file__), 'C_core', 'piegyc.so')
 
-        get_pi_death_rates, get_mig_rates:
-            Return respective members.
 
-        change_popu:
-            Change U, V based on input signal.
+class model_c(ctypes.Structure):
+    '''
+    The C-cored model
     '''
-    
-    def __init__(self, U, V, matrix = [-0.1, 0.4, 0, 0.2], patch_var = [0.5, 0.5, 100, 100, 0.001, 0.001]):
-
-        self.U = U                          # int, U population. Initialized upon creating object.
-        self.V = V                          # int, V population
-        self.Upi = 0                       # float, payoff
-        self.Vpi = 0
-
-        self.matrix = matrix                # np.array or list, len = 4, payoff matrix
-        self.mu1 = patch_var[0]             # float, how much proportion of the population migrates (U) each time
-        self.mu2 = patch_var[1]
-        self.w1 = patch_var[2]              # float, strength of payoff-driven effect. Larger w <=> stronger payoff-driven motion
-        self.w2 = patch_var[3]
-        self.kappa1 = patch_var[4]          # float, carrying capacity, determines death rates
-        self.kappa2 = patch_var[5]
-
-        self.nb = None                                  # list of patch objects (pointers), point to neighbors, initialized seperatedly (after all patches are created)
-        self.pi_death_rates = [0 for _ in range(4)]     # list, len = 4, rates of payoff & death
-                                                        # first two are payoff rates, second two are death rates
-        self.mig_rates = [0 for _ in range(8)]          # list, len = 8, migration rates, stored in an order: up, down, left, right, 
-                                                        # first 4 are U's mig_rate, the last 4 are V's
-        self.sum_pi_death_rates = 0                     # float, sum of pi_death_rates
-        self.sum_mig_rates = 0                          # float, sum of mig_rates
-        
-
-    def __str__(self):
-        self_str = ''
-        self_str += 'U, V = ' + str(self.U) + ', ' + str(self.V) + '\n'
-        self_str += 'pi = ' + str(self.Upi) + ', ' + str(self.Vpi) + '\n'
-        self_str += 'matrix = ' + str(self.matrix) + '\n'
-        self_str += 'mu1, mu2 = ' + str(self.mu1) + ', ' + str(self.mu2) + '\n'
-        self_str += 'w1, w2 = ' + str(self.w1) + ', ' + str(self.w2) + '\n'
-        self_str += 'kappa1, kappa2 = ' + str(self.kappa1) + ', ' + str(self.kappa2) + '\n'
-        self_str += '\n'
-        self_str += 'nb = ' + str(self.nb)
-        self_str += 'pi_death_rates = ' + str(self.pi_death_rates) + '\n'
-        self_str += 'mig_rates = ' + str(self.mig_rates) + '\n'
-        self_str += 'sum_pi_death_rates = ' + str(self.sum_pi_death_rates) + '\n'
-        self_str += 'sum_mig_rates = ' + str(self.sum_mig_rates) + '\n'
-
-        return self_str
-    
-    
-    def set_nb_pointers(self, nb):
-        # nb is a list of pointers (point to patches)
-        # nb is passed from the model class
-        self.nb = nb
-    
-    
-    def update_pi_k(self):
-        # calculate payoff and natural death rates
-
-        U = self.U  # bring the values to front
-        V = self.V
-        sum_minus_1 = U + V - 1  # this value is used several times
-        
-        if sum_minus_1 > 0:
-            # interaction happens only if there is more than 1 individual
-            
-            if U != 0:
-                # no payoff if U == 0
-                self.Upi = (U - 1) / sum_minus_1 * self.matrix[0] + V / sum_minus_1 * self.matrix[1]
-            else:
-                self.Upi = 0
-                
-            if V != 0:
-                self.Vpi = U / sum_minus_1 * self.matrix[2] + (V - 1) / sum_minus_1 * self.matrix[3]
-            else:
-                self.Vpi = 0
-                
-        else:
-            # no interaction, hence no payoff, if only 1 individual
-            self.Upi = 0
-            self.Vpi = 0
-
-        # update payoff rates
-        self.pi_death_rates[0] = abs(U * self.Upi)
-        self.pi_death_rates[1] = abs(V * self.Vpi)
-
-        # update natural death rates
-        self.pi_death_rates[2] = self.kappa1 * U * (sum_minus_1 + 1)
-        self.pi_death_rates[3] = self.kappa2 * V * (sum_minus_1 + 1)
-
-        # update sum of rates
-        self.sum_pi_death_rates = sum(self.pi_death_rates)
-    
-
-    def update_mig(self):
-        # calculate migration rates
-
-        # store the 'weight' of migration, i.e. value of f/g functions for neighbors
-        U_weight = [0, 0, 0, 0]
-        V_weight = [0, 0, 0, 0]
-
-        for i in range(4):
-            if self.nb[i] != None:
-                U_weight[i] = 1 + pow(math.e, self.w1 * self.nb[i].Upi)
-                V_weight[i] = 1 + pow(math.e, self.w2 * self.nb[i].Vpi)
-
-        mu1_U = self.mu1 * self.U
-        mu2_V = self.mu2 * self.V
-
-        mu1_U_divide_sum = mu1_U / sum(U_weight)
-        mu2_V_divide_sum = mu2_V / sum(V_weight)
-        
-        for i in range(4):
-            self.mig_rates[i] = mu1_U_divide_sum * U_weight[i]
-            self.mig_rates[i + 4] = mu2_V_divide_sum * V_weight[i]
-
-        # update sum of rates
-        self.sum_mig_rates = mu1_U + mu2_V
-    
-
-    def get_sum_rates(self):
-        # return sum of all 12 rates
-        return self.sum_pi_death_rates + self.sum_mig_rates
-
-
-    def find_event(self, expected_sum):
-        # find the event within the 12 events based on expected sum-of-rates within this patch
 
-        if expected_sum < self.sum_pi_death_rates:
-            # in the first 4 events (payoff and death events)
-            event = 0
-            current_sum = 0
-            while current_sum < expected_sum:
-                current_sum += self.pi_death_rates[event]
-                event += 1
-            event -= 1
+    _fields_ = [
+        ('N', c_size_t),
+        ('M', c_size_t),
+        ('maxtime', c_double),
+        ('record_itv', c_double),
+        ('sim_time', c_size_t),
+        ('boundary', c_bool),
+
+        ('I', ctypes.POINTER(c_uint32)),
+        ('X', ctypes.POINTER(c_double)),
+        ('P', ctypes.POINTER(c_double)),
+
+        ('print_pct', c_int32),
+        ('seed', c_int32),
+
+        ('data_empty', c_bool),
+        ('max_record', c_size_t),
+        ('arr_size', c_size_t),
+        ('compress_itv', c_uint32),
+
+        ('U1d', ctypes.POINTER(c_double)),
+        ('V1d', ctypes.POINTER(c_double)),
+        ('Upi_1d', ctypes.POINTER(c_double)),
+        ('Vpi_1d', ctypes.POINTER(c_double)),
+    ]
+    def get_array(self, name):
+        """Return internal data as NumPy array, e.g. .get_array('U')"""
+        ptr = getattr(self, name)
+        return np.ctypeslib.as_array(ptr, shape=(self.arr_size,))
+
+lib = ctypes.CDLL(C_LIB_PATH, winmode = 0)
+lib.mod_init.argtypes = [
+    ctypes.POINTER(model_c), c_size_t, c_size_t,
+    c_double, c_double, c_size_t, c_bool,
+    ndpointer(dtype=np.uint32, flags="C_CONTIGUOUS"),
+    ndpointer(dtype=np.float64, flags="C_CONTIGUOUS"),
+    ndpointer(dtype=np.float64, flags="C_CONTIGUOUS"),
+    c_int32, c_int32
+]
+lib.mod_init.restype = c_bool
+
+lib.run.argtypes = [ctypes.POINTER(model_c), ctypes.POINTER(c_char), c_size_t]
+lib.run.restype = None
 
-        else:
-            # in the last 8 events (migration events):
-            event = 0
-            current_sum = self.sum_pi_death_rates
-            while current_sum < expected_sum:
-                current_sum += self.mig_rates[event]
-                event += 1
-            event += 3  # i.e., -= 1, then += 4 (to account for the first 4 payoff & death rates)
 
-        return event
-
-    
-    def change_popu(self, s):
-        # convert s (a signal, passed from model class) to a change in population
-        
-        # s = 0, 1, 2 are for U
-        # s = 0 for migration IN, receive an immigrant
-        if s == 0:
-            self.U += 1       # receive an immigrant
-        # s = 1 for migration OUT / death due to carrying capacity
-        elif s == 1:
-            if self.U > 0:
-                self.U -= 1
-        # s = 2 for natural birth / death, due to payoff
-        elif s == 2:
-            if self.Upi > 0:
-                self.U += 1   # natural growth due to payoff
-            elif self.U > 0:
-                self.U -= 1   # natural death due to payoff
-        
-        # s = 3, 4, 5 are for V
-        elif s == 3:
-            self.V += 1
-        elif s == 4:
-            if self.V > 0:
-                self.V -= 1
-        else:
-            if self.Vpi > 0:
-                self.V += 1
-            elif self.V > 0:
-                self.V -= 1
-                
 
+'''
+For access by Python
+'''             
 
 class model:
     '''
@@ -268,7 +117,7 @@ class model:
             Return a deep copy of self. Can choose whether to copy data as well. Default is to copy.
 
         clear_data:
-            clear all data stored, set U, V, Upi, V_pi to zero arrays
+            clear all data stored, set U, V, Upi, Vpi to zero arrays
 
         change_maxtime:
             Changes maxtime of self. Update data storage as well.
@@ -280,47 +129,42 @@ class model:
             compress data by only storing average values
     '''
 
-    def __init__(self, N, M, maxtime, record_itv, sim_time, boundary, I, X, P, print_pct = 25, seed = None, UV_dtype = UV_DTYPE, pi_dtype = PI_DTYPE):
+    def __init__(self, N, M, maxtime, record_itv, sim_time, boundary, I, X, P, print_pct = 25, seed = None):
 
         self.check_valid_input(N, M, maxtime, record_itv, sim_time, boundary, I, X, P, print_pct)
         
         self.N = N                      # int, N x M is spatial dimension
         self.M = M                      # int, can't be 1. If want to make 1D space, use N = 1. And this model doesn't work for 1x1 space (causes NaN)
         self.maxtime = maxtime          # float or int, run model for how long time
-        self.record_itv = record_itv        # float, record data every record_itv of time
+        self.record_itv = record_itv    # float, record data every record_itv of time
         self.sim_time = sim_time        # int, run this many of rounds (of single_test)
         self.boundary = boundary        # bool, the N x M space have boundary or not (i.e., zero-flux (True) or periodical (False))
         self.I = np.array(I)            # N x M x 2 np.array, initial population. Two init-popu for every patch (U and V)
         self.X = np.array(X)            # N x M x 4 np.array, matrices. The '4' comes from 2x2 matrix flattened to 1D
         self.P = np.array(P)            # N x M x 6 np.array, 'patch variables', i.e., mu1&2, w1&2, kappa1&2
         self.print_pct = print_pct      # int, print how much percent is done, need to be non-zero
-        self.seed = seed                # non-negative int, seed for random generator
-        self.UV_dtype = UV_dtype        # what data type to store population, should be a float format. This value is passed to np.array. 
-                                        # Default is 'float64', use lower accuracy to reduce data size.
-        self.pi_dtype = pi_dtype        # what data type to store payoff, should be a float format. This value is passed to np.array. 
-                                        # Default is 'float64'
+        self.seed = seed                # non-negative int, seed for random number generation
 
-        self.init_storage()                         # initialize storage bins. Put in a separate function because might want to change maxtime 
-                                                    # and that doesn't need to initialze the whole object again
+        self.init_storage()             # initialize storage bins. Put in a separate function because might want to change maxtime 
+                                        # and that doesn't need to initialze the whole object again
 
 
     def init_storage(self):
         # initialize storage bins
-        self.data_empty = True                      # whether data storage bins are empty. model.run will refuse to run (raise error) if not empty.
-        self.max_record = int(self.maxtime / self.record_itv)                         # int, how many data points to store sin total
-        self.compress_itv = 1                       # int, intended to reduce size of data (if not 1). Updated by compress_data function
-                                                    # if set to an int, say 20, mod will take average over every 20 data points and save them as new data.
-                                                    # May be used over and over again to recursively reduce data size. 
-                                                    # Default is 1, not to take average.
-        self.U = np.zeros((self.N, self.M, self.max_record), dtype = self.UV_dtype)      # N x M x max_record np.array, float32, stores population of U in every patch over tiem
-        self.V = np.zeros((self.N, self.M, self.max_record), dtype = self.UV_dtype)
-        self.Upi = np.zeros((self.N, self.M, self.max_record), dtype = self.pi_dtype)   # similar to U, but for U's payoff and float 64
-        self.Vpi = np.zeros((self.N, self.M, self.max_record), dtype = self.pi_dtype)
+        self.data_empty = True      # whether data storage bins are empty. model.run will refuse to run (raise error) if not empty.
+        self.max_record = int(self.maxtime / self.record_itv)   # int, how many data points to store sin total
+        self.compress_itv = 1       # int, intended to reduce size of data (if not 1). Updated by compress_data function
+                                    # if set to an int, say 20, mod will take average over every 20 data points and save them as new data.
+                                    # May be used over and over again to recursively reduce data size. 
+                                    # Default is 1, not to take average.
+        self.U = None               # initialized by simulation.run or data_tools.read_data
+        self.V = None
+        self.Upi = None
+        self.Vpi = None
 
 
     def check_valid_input(self, N, M, maxtime, record_itv, sim_time, boundary, I, X, P, print_pct):
         # check whether the inputs are valid
-        # seed, UV_dtype, pi_dtype is handled by numpy
 
         if (N < 1) or (M < 1):
             raise ValueError('N < 1 or M < 1')
@@ -384,8 +228,7 @@ class model:
         self_str += 'boundary = ' + str(self.boundary) + '\n'
         self_str += 'print_pct = ' + str(self.print_pct) + '\n'
         self_str += 'seed = ' + str(self.seed) + '\n'
-        self_str += 'UV_dtype = \'' + self.UV_dtype + '\'\n'
-        self_str += 'pi_dtype = \'' + self.pi_dtype + '\'\n'
+        self_str += 'data_empty = ' + str(self.data_empty) + '\n'
         self_str += 'compress_itv = ' + str(self.compress_itv) + '\n'
         self_str += '\n'
 
@@ -445,7 +288,7 @@ class model:
 
         sim2 = model(N = self.N, M = self.M, maxtime = self.maxtime, record_itv = self.record_itv, sim_time = self.sim_time, boundary = self.boundary,
                           I = np.copy(self.I), X = np.copy(self.X), P = np.copy(self.P), 
-                          print_pct = self.print_pct, seed = self.seed, UV_dtype = self.UV_dtype, pi_dtype = self.pi_dtype)
+                          print_pct = self.print_pct, seed = self.seed)
 
         if copy_data:
             # copy data as well
@@ -486,7 +329,7 @@ class model:
         self.init_storage()
 
 
-    def set_data(self, data_empty, max_record, compress_itv, U, V, Upi, V_pi):
+    def set_data(self, data_empty, max_record, compress_itv, U, V, Upi, Vpi):
         # set data to the given data values
         # copies are made
         self.check_valid_data(data_empty, max_record, compress_itv)
@@ -497,12 +340,14 @@ class model:
         self.U = np.copy(U)
         self.V = np.copy(V)
         self.Upi = np.copy(Upi)
-        self.Vpi = np.copy(V_pi)
+        self.Vpi = np.copy(Vpi)
 
 
     def compress_data(self, compress_itv = 5):
         # compress data by only storing average values
-        
+        if self.data_empty:
+            raise RuntimeError('Model has empty data. Cannot compress')
+
         if type(compress_itv) != int:
             raise TypeError('Please use an int as compress_itv')
         if compress_itv < 1:
@@ -513,10 +358,10 @@ class model:
         self.compress_itv *= compress_itv  # may be reduced over and over again
         self.max_record = int(self.max_record / compress_itv)  # number of data points after reducing
 
-        U_reduced = np.zeros((self.N, self.M, self.max_record), dtype = self.UV_dtype)
-        V_reduced = np.zeros((self.N, self.M, self.max_record), dtype = self.UV_dtype)
-        Upi_reduced = np.zeros((self.N, self.M, self.max_record), dtype = self.pi_dtype)
-        V_pi_reduced = np.zeros((self.N, self.M, self.max_record), dtype = self.pi_dtype)
+        U_reduced = np.zeros((self.N, self.M, self.max_record), dtype = np.float64)
+        V_reduced = np.zeros((self.N, self.M, self.max_record), dtype = np.float64)
+        Upi_reduced = np.zeros((self.N, self.M, self.max_record), dtype = np.float64)
+        Vpi_reduced = np.zeros((self.N, self.M, self.max_record), dtype = np.float64)
 
         for i in range(self.N):
             for j in range(self.M):
@@ -526,597 +371,41 @@ class model:
                     U_reduced[i][j][k] = np.mean(self.U[i, j, lower : upper])
                     V_reduced[i][j][k] = np.mean(self.V[i, j, lower : upper])
                     Upi_reduced[i][j][k] = np.mean(self.Upi[i, j, lower : upper])
-                    V_pi_reduced[i][j][k] = np.mean(self.Vpi[i, j, lower : upper])
+                    Vpi_reduced[i][j][k] = np.mean(self.Vpi[i, j, lower : upper])
         
         self.U = U_reduced
         self.V = V_reduced
         self.Upi = Upi_reduced
-        self.Vpi = V_pi_reduced
-
-
-
-
-def find_nb_zero_flux(N, M, i, j):
-    '''
-    Find neighbors of patch (i, j) in zero-flux boundary condition. i.e., the space is square with boundary.
-    Return neighbors' indices in an order: up, down, left, right.
-    Index will be None if no neighbor exists in that direction.
-    '''
-    nb_indices = []
-    
-    if i != 0: 
-        nb_indices.append([i - 1, j])  # up
-    else:
-        nb_indices.append(None)    # neighbor doesn't exist
-    
-    if i != N - 1:
-        nb_indices.append([i + 1, j])  # down
-    else:
-        nb_indices.append(None)
-    
-    if j != 0:
-        nb_indices.append([i, j - 1])  # left
-    else:
-        nb_indices.append(None)
-    
-    if j != M - 1:
-        nb_indices.append([i, j + 1])  # right
-    else:
-        nb_indices.append(None)
-    
-    return nb_indices
-
-
-
-
-def find_nb_periodical(N, M, i, j):
-    '''
-    Find neighbors of patch (i, j) in periodical boundary condition. i.e., the space is a sphere.
-    Return neighbors' indices in an order: up, down, left, right.
-    If space not 1D, a neighbor always exists.
-    If space is 1D, say N = 1, we don't allow (0, j) to migrate up & down (self-self migration is considered invalid)
-    '''
-    nb_indices = []
-    
-    # up
-    if N != 1:
-        if i != 0: 
-            nb_indices.append([i - 1, j])
-        else:
-            nb_indices.append([N - 1, j])
-    else:
-        nb_indices.append(None)  # can't migrate to itself
-    
-    # down
-    if N != 1:
-        if i != N - 1:
-            nb_indices.append([i + 1, j])
-        else:
-            nb_indices.append([0, j])
-    else:
-        nb_indices.append(None)
-    
-    # left
-    # No need to check M == 1 because we explicitly asked for M > 1
-    if j != 0:
-        nb_indices.append([i, j - 1])
-    else:
-        nb_indices.append([i, M - 1])
-    
-    # right
-    if j != M - 1:
-        nb_indices.append([i, j + 1])
-    else:
-        nb_indices.append([i, 0])
-        
-    return nb_indices
-
-
-
-
-def find_patch(expected_sum, patch_rates, sum_rates_by_row, sum_rates):
-    '''
-    Find which patch the event is in. Only patch index is found, patch.find_event find which event it is exactly.
-
-    Inputs:
-        expected_sum:       a random number * sum of all rates. Essentially points to a random event.
-                            We want to find the patch that contains this pointer.
-        patch_rates:        a N x M np.array. Stores sum of the 12 rates in every patch.
-        sum_rates_by_row:   a 1D np.array with len = N. Stores the sum of the M x 12 rates in every row.
-        sum_rates:          sum of all N x M x 12 rates.
-    
-    Returns:
-        row, col:           row and column number of where the patch.
-    '''
-    
-    # Find row first
-    if expected_sum < sum_rates / 2:
-        # search row forwards if in the first half of rows
-        current_sum = 0
-        row = 0
-        while current_sum < expected_sum:
-            current_sum += sum_rates_by_row[row]
-            row += 1
-        row -= 1
-        current_sum -= sum_rates_by_row[row]  # need to subtract that row (which caused current sum to exceed expected_sum)
-    else:
-        # search row backwards if in the second half of rows
-        current_sum = sum_rates
-        row = len(patch_rates) - 1
-        while current_sum > expected_sum:
-            current_sum -= sum_rates_by_row[row]
-            row -= 1
-        row += 1
-        # don't need subtraction here, as current_sum is already < expected same
-
-    # Find col in that row
-    if (expected_sum - current_sum) < sum_rates_by_row[row] / 2:
-        # search col forwards if in the first half of that row
-        col = 0
-        while current_sum < expected_sum:
-            current_sum += patch_rates[row][col]
-            col += 1
-        col -= 1
-        current_sum -= patch_rates[row][col]  # need a subtraction
-    else:
-        # search col backwards if in the second half of that row
-        current_sum += sum_rates_by_row[row]
-        col = len(patch_rates[0]) - 1
-        while current_sum > expected_sum:
-            current_sum -= patch_rates[row][col]
-            col -= 1
-        col += 1
-        # don't need subtraction
-
-    return row, col, current_sum
-
-
-
-
-def make_signal_zero_flux(i, j, e):
-    '''
-    Find which patch to change what based on i, j, e (event number) value, for the zero-flux boundary condition
-
-    Inputs: 
-        i, j is the position of the 'center' patch, e is which event to happen there.
-        Another patch might be influenced as well if a migration event was picked.
-
-        Possible values for e:
-            e = 0 or 1: natural change of U/V due to payoff. 
-                        Can be either brith or death (based on payoff is positive or negative).
-                        Cooresponds to s = 2 or 5 in the patch class
-            e = 2 or 3: death of U/V due to carrying capacity. 
-                        Cooresponds to s = 1 or 4 in patch: make U/V -= 1
-            e = 4 ~ 7:  migration events of U, patch (i, j) loses an individual, and another patch receives one.
-                        we use the up-down-left-right rule for the direction. 4 means up, 5 means down, ...
-                        Cooresponds to s = 0 for the mig-in patch (force U += 1), and s = 1 for the mig-out patch (force U -= 1)
-            e = 8 ~ 11: migration events of V.
-                        Cooresponds to s = 3 for the mig-in patch (force V += 1), and s = 4 for the mig-out patch (force V -= 1)
-    '''
-    if e < 6:
-        if e == 0:
-            return [[i, j, 2]]
-        elif e == 1:
-            return [[i, j, 5]]
-        elif e == 2:
-            return [[i, j, 1]]
-        elif e == 3:
-            return [[i, j, 4]]
-        elif e == 4:
-            return [[i, j, 1], [i - 1, j, 0]]
-        else:
-            return [[i, j, 1], [i + 1, j, 0]]
-    else:
-        if e == 6:
-            return [[i, j, 1], [i, j - 1, 0]]
-        elif e == 7:
-            return [[i, j, 1], [i, j + 1, 0]]
-        elif e == 8:
-            return [[i, j, 4], [i - 1, j, 3]]
-        elif e == 9:
-            return [[i, j, 4], [i + 1, j, 3]]
-        elif e == 10:
-            return [[i, j, 4], [i, j - 1, 3]]
-        elif e == 11:
-            return [[i, j, 4], [i, j + 1, 3]]
-        else:
-            raise RuntimeError('A bug in code: invalid event number encountered:', e)  # debug line
-
-
-
-def make_signal_periodical(N, M, i, j, e):
-    '''
-    Find which patch to change what based on i, j, e value, for the periodical boundary condition
-    Similar to make_signal_zero_flux.
-    '''
-    
-    if e < 6:
-        if e == 0:
-            return [[i, j, 2]]
-        elif e == 1:
-            return [[i, j, 5]]
-        elif e == 2:
-            return [[i, j, 1]]
-        elif e == 3:
-            return [[i, j, 4]]
-        elif e == 4:
-            if i != 0:
-                return [[i, j, 1], [i - 1, j, 0]]
-            else:
-                return [[i, j, 1], [N - 1, j, 0]]
-        else:
-            if i != N - 1:
-                return [[i, j, 1], [i + 1, j, 0]]
-            else:
-                return [[i, j, 1], [0, j, 0]]
-    else:
-        if e == 6:
-            if j != 0:
-                return [[i, j, 1], [i, j - 1, 0]]
-            else:
-                return [[i, j, 1], [i, M - 1, 0]]
-        elif e == 7:
-            if j != M - 1:
-                return [[i, j, 1], [i, j + 1, 0]]
-            else:
-                return [[i, j, 1], [i, 0, 0]]
-        elif e == 8:
-            if i != 0:
-                return [[i, j, 4], [i - 1, j, 3]]
-            else:
-                return [[i, j, 4], [N - 1, j, 3]]
-        elif e == 9:
-            if i != N - 1:
-                return [[i, j, 4], [i + 1, j, 3]]
-            else:
-                return [[i, j, 4], [0, j, 3]]
-        elif e == 10:
-            if j != 0:
-                return [[i, j, 4], [i, j - 1, 3]]
-            else:
-                return [[i, j, 4], [i, M - 1, 3]]
-        elif e == 11:
-            if j != M - 1:
-                return [[i, j, 4], [i, j + 1, 3]]
-            else:
-                return [[i, j, 4], [i, 0, 3]]
-        else:
-            raise RuntimeError('A bug in code: invalid event number encountered:', e)  # debug line
-
-
-
-
-def nb_need_change(ni, signal):
-    '''
-    Check whether a neighbor needs to change.
-    Two cases don't need change: either ni is None (doesn't exist) or in signal (is a last-change patch and already updated)
-
-    Inputs:
-        ni:         index of a neighbor, might be None if patch doesn't exist.
-        signal:     return value of make_signal_zero_flux or make_signal_periodical.
-    
-    Returns:
-        True or False, whether the neighboring patch specified by ni needs change
-    '''
-    
-    if ni == None:
-        return False
-    
-    for si in signal:
-        if ni[0] == si[0] and ni[1] == si[1]:
-            return False
-    
-    return True
-
-
-
-
-def single_init(mod, rng):
-    '''
-    The first major function for the model.
-    Initialize all variables and run 1 round, then pass variables and results to single_test.
-
-    Input:
-        mod is a model object
-        rng is random number generator (np.random.default_rng), initialized by model.run
-    '''
-
-    #### Initialize Data Storage ####
-
-    world = [[patch(mod.I[i][j][0], mod.I[i][j][1], mod.X[i][j], mod.P[i][j]) for j in range(mod.M)] for i in range(mod.N)]  # N x M patches
-    patch_rates = np.zeros((mod.N, mod.M), dtype = RATES_DTYPE)  # every patch's sum-of-12-srates
-    sum_rates_by_row = np.zeros((mod.N), dtype = RATES_DTYPE)  # every row's sum-of-patch, i.e., sum of 12 * M rates in every row.
-    sum_rates = 0  # sum of all N x M x 12 rates
-
-    signal = None
-
-    nb_indices = None
-    if mod.boundary:
-        nb_indices = [[find_nb_zero_flux(mod.N, mod.M, i, j) for j in range(mod.M)] for i in range(mod.N)]
-    else:
-        nb_indices = [[find_nb_periodical(mod.N, mod.M, i, j) for j in range(mod.M)] for i in range(mod.N)]
-        
-    for i in range(mod.N):
-        for j in range(mod.M):
-            nb = []
-            for k in range(4):
-                if nb_indices[i][j][k] != None:
-                    # append a pointer to the patch
-                    nb.append(world[nb_indices[i][j][k][0]][nb_indices[i][j][k][1]])
-                else:
-                    # nb doesn't exist
-                    nb.append(None)
-            # pass it to patch class and store
-            world[i][j].set_nb_pointers(nb)
-    
-
-    #### Begin Running ####
+        self.Vpi = Vpi_reduced
 
-    # initialize payoff & natural death rates
-    for i in range(mod.N):
-        for j in range(mod.M):
-            world[i][j].update_pi_k()
-    
-    # initialize migration rates & the rates list
-    for i in range(mod.N):
-        for j in range(mod.M):
-            world[i][j].update_mig()
-            # store rates & sum of rates
-            patch_rates[i][j] = world[i][j].get_sum_rates()
-        sum_rates_by_row[i] = sum(patch_rates[i])
-
-    sum_rates = sum(sum_rates_by_row)
-    
-    # pick the first random event
-    expected_sum = rng.random() * sum_rates
-    # find patch first
-    i0, j0, current_sum = find_patch(expected_sum, patch_rates, sum_rates_by_row, sum_rates)
-    # then find which event in that patch
-    e0 = world[i0][j0].find_event(expected_sum - current_sum)
-
-    # initialize signal
-    if mod.boundary:
-        signal = make_signal_zero_flux(i0, j0, e0)   # walls around world
-    else:
-        signal = make_signal_periodical(mod.N, mod.M, i0, j0, e0)  # no walls around world
-    
-    # change U&V based on signal
-    for si in signal:
-        world[si[0]][si[1]].change_popu(si[2])
-        
-    # time increment
-    time = (1 / sum_rates) * math.log(1 / rng.random())
-    
-    # record
-    if time > mod.record_itv:
-        record_index = int(time / mod.record_itv)
-        for i in range(mod.N):
-            for j in range(mod.M):
-                for k in range(record_index):
-                    mod.U[i][j][k] += world[i][j].U
-                    mod.V[i][j][k] += world[i][j].V
-                    mod.Upi[i][j][k] += world[i][j].Upi
-                    mod.Vpi[i][j][k] += world[i][j].Vpi
-                    # we simply add to that entry, and later divide by sim_time to get the average (division in run function)
-    
-    return time, world, nb_indices, patch_rates, sum_rates_by_row, sum_rates, signal
 
 
-
-
-def single_test(mod, front_info, end_info, update_sum_frequency, rng):
+def run(mod, message = ""):
     '''
-    Runs a single model, from time = 0 to mod.maxtime.
-    run recursively calls single_test to get the average data. 
-
-    Inputs:
-        sim:                    a model object, created by user and carries all parameters & storage bins.
-        front_info, end_info:   passed by run to show messages, like the current round number in run. Not intended for direct usages.
-        update_sum_frequency:   re-calculate sums this many times in model. 
-                                Our sums are gradually updated over time. So might have precision errors for large maxtime.
-        rng:                    np.random.default_rng. Initialized by model.run
+    C-cored simulation
     '''
-
-    # initialize helper variables
-    # used to print progress, i.e., how much percent is done
-    one_time = mod.maxtime / max(100, update_sum_frequency) 
-    one_progress = 0
-    if mod.print_pct != None:
-        # print progress, x%
-        print(front_info +  ' 0%' + end_info, end = '\r')
-        one_progress = mod.maxtime * mod.print_pct / 100
-    else:
-        one_progress = 2 * mod.maxtime     # not printing
-
-    # our sums (sum_rates_by_row and sum_rates) are gradually updated over time. This may have precision errors for large maxtime.
-    # So re-sum everything every some percentage of maxtime.
-    one_update_sum = mod.maxtime / update_sum_frequency
-
-    current_time = one_time
-    current_progress = one_progress
-    current_update_sum = one_update_sum
-
-    max_record = int(mod.maxtime / mod.record_itv)
-
-    
-    # initialize
-    time, world, nb_indices, patch_rates, sum_rates_by_row, sum_rates, signal = single_init(mod, rng)
-    record_index = int(time / mod.record_itv)
-    # record_time is how much time has passed since the last record
-    # if record_time > record_itv:
-    #    we count how many record_itvs are there in record_time, denote the number by multi_records
-    #    then store the current data in multi_records number of cells in the list
-    #    and subtract record_time by the multiple of record_itv, so that record_time < record_itv
-    record_time = time - record_index * mod.record_itv
-
-    ### Large while loop ###
+    msg_len = len(message)
+    msg_bytes = message.encode('utf-8')
+    msg_buffer = ctypes.create_string_buffer(msg_bytes, msg_len) 
     
-    while time < mod.maxtime:
-    
-        # print progress & correct error of sum_rates
-        if time > current_time:
-            # a new 1% of time
-            current_time += one_time
-            if time > current_progress:
-                # print progress
-                print(front_info +  ' ' + str(round(time / mod.maxtime * 100)) + '%' + end_info, end = '\r')
-                current_progress += one_progress
-
-            if time > current_update_sum:
-                current_update_sum += one_update_sum
-                for i in range(mod.N):
-                    sum_rates_by_row[i] = sum(patch_rates[i])
-                sum_rates = sum(sum_rates_by_row)
-
-        
-        # before updating last-changed patches, subtract old sum of rates (so as to update sum of rates by adding new rates later)
-        for si in signal:
-            # si[0] is row number, si[1] is col number
-            old_patch_rate = world[si[0]][si[1]].get_sum_rates()
-            sum_rates_by_row[si[0]] -= old_patch_rate
-            sum_rates -= old_patch_rate
-
-        # update last-changed patches
-        # update payoff and death rates first
-        for si in signal:
-            world[si[0]][si[1]].update_pi_k()
-        # then update migration rates, as mig_rates depend on neighbor's payoff
-        for si in signal:
-            world[si[0]][si[1]].update_mig()
-            
-            # update rates stored
-            new_patch_rate = world[si[0]][si[1]].get_sum_rates()
-            # update patch_rates
-            patch_rates[si[0]][si[1]] = new_patch_rate
-            # update sum_rate_by_row and sum_rates_by_row by adding new rates
-            sum_rates_by_row[si[0]] += new_patch_rate
-            sum_rates += new_patch_rate
-
-        # update neighbors of last-changed patches
-        for si in signal:
-            for ni in nb_indices[si[0]][si[1]]:
-                # don't need to update if the patch is a last-change patch itself or None
-                # use helper function to check
-                if nb_need_change(ni, signal):
-                    # update migratino rates
-                    world[ni[0]][ni[1]].update_mig()
-                    # Note: no need to update patch_rates and sum of rates, as update_mig doesn't change total rates in a patch.
-                    # sum_mig_rate is decided by mu1 * U + mu2 * V, and pi_death_rate is not changed.
-               
-        # pick the first random event
-        expected_sum = rng.random() * sum_rates
-        # find patch first
-        i0, j0, current_sum = find_patch(expected_sum, patch_rates, sum_rates_by_row, sum_rates)
-        # then find which event in that patch
-        e0 = world[i0][j0].find_event(expected_sum - current_sum)
-
-        # make signal
-        if mod.boundary:
-            signal = make_signal_zero_flux(i0, j0, e0)
-        else:
-            signal = make_signal_periodical(mod.N, mod.M, i0, j0, e0)
+    I = np.ascontiguousarray(mod.I.flatten(), dtype = np.uint32)
+    X = np.ascontiguousarray(mod.X.flatten(), dtype = np.float64)
+    P = np.ascontiguousarray(mod.P.flatten(), dtype = np.float64)
 
-        # let the event happen
-        for si in signal:
-            world[si[0]][si[1]].change_popu(si[2])
-        
-        # increase time
-        r1 = rng.random()
-        dt = (1 / sum_rates) * math.log(1 / r1)
-        time += dt
-        record_time += dt
+    mod_c = model_c()
+    success = lib.mod_init(ctypes.byref(mod_c), 
+                           mod.N, mod.M, mod.maxtime, mod.record_itv, mod.sim_time, mod.boundary,
+                           I, X, P, mod.print_pct, mod.seed)
+    if not success:
+        raise RuntimeError("mod_init failed")
     
-        if time < mod.maxtime:
-            # if not exceeds maxtime
-            if record_time > mod.record_itv:
-                multi_records = int(record_time / mod.record_itv)
-                record_time -= multi_records * mod.record_itv
-
-                for i in range(mod.N):
-                    for j in range(mod.M):
-                        for k in range(record_index, record_index + multi_records):
-                            mod.U[i][j][k] += world[i][j].U
-                            mod.V[i][j][k] += world[i][j].V
-                            mod.Upi[i][j][k] += world[i][j].Upi
-                            mod.Vpi[i][j][k] += world[i][j].Vpi
-                record_index += multi_records
-        else:
-            # if already exceeds maxtime
-            for i in range(mod.N):
-                for j in range(mod.M):
-                    for k in range(record_index, max_record):
-                        mod.U[i][j][k] += world[i][j].U
-                        mod.V[i][j][k] += world[i][j].V
-                        mod.Upi[i][j][k] += world[i][j].Upi
-                        mod.Vpi[i][j][k] += world[i][j].Vpi
-
-    ### Large while loop ends ###
+    lib.run(ctypes.byref(mod_c), msg_buffer, msg_len)
     
-    if mod.print_pct != None:
-        print(front_info + ' 100%' + ' ' * 20, end = '\r')  # empty spaces to overwrite predicted runtime
-
-
-
-
-def run(mod, predict_runtime = False, message = ''):
-    '''
-    Main function. Recursively calls single_test to run many models and then takes the average.
-
-    Inputs:
-    - mod is a model object.
-    - predict_runtime = False will not predict how much time still needed, set to True if you want to see.
-    - message is used by some functions in figures.py to print messages.
-    '''
-
-    if not mod.data_empty:
-        raise RuntimeError('mod has non-empty data')
-    
-    start = timer()   # runtime
-
     mod.data_empty = False
-    rng = np.random.default_rng(mod.seed)
-    
-    # passed to single_test to print progress
-    if mod.print_pct == 0:
-        mod.print_pct = 5    # default print_pct
-
-    update_sum_frequency = 4   # re-calculate sums this many times. See input desciption of single_test
-    
-    ### models ###
-    i = 0
-    
-    while i < mod.sim_time:
-        # use while loop so that can go backwards if got numerical issues
-
-        end_info = ''
-        if predict_runtime:
-            if i > 0:
-                time_elapsed = timer() - start
-                pred_runtime = time_elapsed / i * (mod.sim_time - i)
-                end_info = ', ~' + str(round(pred_runtime, 2)) + 's left'
-        
-        front_info = ''
-        if mod.print_pct != None:
-            front_info = message + 'round ' + str(i) + ':'
-            print(front_info + ' ' * 30, end = '\r')  # the blank spaces are to overwrite percentages, e.g. 36 %
-        
-        try:
-            single_test(mod, front_info, end_info, update_sum_frequency, rng)
-            i += 1
-        except IndexError:
-            update_sum_frequency *= 4
-            print('Numerical issue at round ' + str(i) + '. Trying higher precision now. See doc if err repeats')
-            # not increasing i: redo current round.
-        
-    ### models end ###
-
-    mod.calculate_ave()
-    
-    stop = timer()
-    print(' ' * 30, end = '\r')  # overwrite all previous prints
-    print(message + 'runtime: ' + str(round(stop - start, 2)) + ' s')
-    return
-
+    mod.U = mod_c.get_array('U1d').reshape(mod.N, mod.M, mod.max_record)
+    mod.V = mod_c.get_array('V1d').reshape(mod.N, mod.M, mod.max_record)
+    mod.Upi = mod_c.get_array('Upi_1d').reshape(mod.N, mod.M, mod.max_record)
+    mod.Vpi = mod_c.get_array('Vpi_1d').reshape(mod.N, mod.M, mod.max_record)
 
 
 
@@ -1143,13 +432,12 @@ def demo_model():
 
     print_pct = 5           # print progress
     seed = 36               # seed for random number generation
-    UV_dtype = 'float32'    # data type for population
-    pi_dyna = 'float64'    # data type for payoff
 
     # create a model object
     mod = model(N, M, maxtime, record_itv, sim_time, boundary, I, X, P, 
-                            print_pct = print_pct, seed = seed, UV_dtype = UV_dtype, pi_dtype = pi_dyna)
+                            print_pct = print_pct, seed = seed)
     
     return mod
 
 
+