update some dysts json metadata

- parameterize some hardcoded constants - clean up circadian rhythm - update unbounded indices
williamgilpin · Dec 29, 2024 · 6166f96 · 6166f96
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commit 6166f96
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diff --git a/dysts/data/chaotic_attractors.json b/dysts/data/chaotic_attractors.json
@@ -349,7 +349,7 @@
     },
     "period": 2.9520625,
     "pesin_entropy": 5.617567417119514,
-    "unbounded_indices": [0, 1, 2],
+    "unbounded_indices": [1, 2],
     "mean": [0.20578754423965043, -0.022789280675006653, 0.006181954059999296],
     "std": [0.47387058648171193, 0.39966045251784715, 0.7098035797292681]
   },
@@ -379,7 +379,7 @@
     },
     "period": 2.7616666666666667,
     "pesin_entropy": 4.877593783333199,
-    "unbounded_indices": [0, 1, 2],
+    "unbounded_indices": [1, 2],
     "mean": [0.09628302338811898, 0.051081909007632376, 0.014044835128269546],
     "std": [0.5173893273874359, 0.5621146168812219, 0.7058063557135066]
   },
@@ -751,12 +751,13 @@
       "km": 0.4,
       "ks": 1,
       "n": 4,
+      "ps": 24,
+      "vc": 2.5,
       "vd": 6,
       "vdn": 1.5,
       "vm": 0.7,
       "vmax": 4.7,
-      "vmin": 1.0,
-      "vs": 6
+      "vmin": 1.0
     },
     "period": 27.0,
     "pesin_entropy": 0.09372724379002938,
@@ -978,8 +979,11 @@
     "multiscale_entropy": 0.5591104791210428,
     "nonautonomous": false,
     "parameters": {
-      "d": 1.0,
-      "m": 1.0
+      "g": 9.81,
+      "l1": 1.0,
+      "l2": 1.0,
+      "m1": 1.0,
+      "m2": 1.0
     },
     "period": 4.0234,
     "pesin_entropy": 8.928560651305366,
@@ -1045,12 +1049,31 @@
     "multiscale_entropy": 0.7807524009298388,
     "nonautonomous": false,
     "parameters": {
+      "aho": 2.5,
+      "ahr": 0.05,
+      "ahs": 0.07,
+      "ams": 0.1,
+      "amvb": 25,
+      "amvo": 2.5,
+      "ans": 0.01,
+      "anvb": 20,
+      "anvo": 2,
+      "ar": 0.1,
+      "bho": 2.0,
+      "bhr": 0.1,
+      "bmo": 2.7777777777777777778,
+      "bmr": 0.0555555555555555556,
+      "bms": 4.0,
+      "bno": 0.375,
+      "bnr": 0.0125,
+      "bns": 0.125,
       "gi": 1800,
       "gkc": 11,
       "gkv": 1700,
       "gl": 7,
       "kc": 0.183333,
       "rho": 0.27,
+      "tscl": 230,
       "vc": 100,
       "vi": 100,
       "vk": -75,
@@ -1144,7 +1167,7 @@
       "w": 0.81
     },
     "period": 20.411,
-    "pesin_entropy": 0.0028307087627546254,
+    "entropy": 0.0028307087627546254,
     "unbounded_indices": [2],
     "mean": [0.39605874701368277, 2.7397572605387843, -0.008946634312398942],
     "std": [0.14966981525041267, 0.3908426287195323, 0.7076296217622412]
@@ -2024,7 +2047,7 @@
     },
     "period": 28.822573200111794,
     "pesin_entropy": 0.9110009439099345,
-    "unbounded_indices": [2],
+    "unbounded_indices": [1,2],
     "mean": [-0.08706186157906316, 0.003099475891320229, 0.001757118959650587],
     "std": [0.4963566077805293, 0.5089387987269263, 0.7072246055642845]
   },
@@ -2775,7 +2798,7 @@
     },
     "period": 23.857,
     "pesin_entropy": 0.4274159768365288,
-    "unbounded_indices": [0, 1],
+    "unbounded_indices": [0, 2],
     "mean": [-0.0017403093986211205, 1.6642129379690616, 0.010636631704986098],
     "std": [0.6958702046098053, 0.9076069739985229, 0.7071664907860569]
   },
@@ -3900,7 +3923,7 @@
     },
     "period": 0.3417647058823529,
     "pesin_entropy": 10.773094126465404,
-    "unbounded_indices": [],
+    "unbounded_indices": [1],
     "mean": [
       0.09117893552133338, 0.07467874204049706, -0.1279534926442416,
       0.08471804040163511
@@ -4044,6 +4067,7 @@
       "e": 0.5,
       "g": 0.1,
       "h": 0.8,
+      "lamb": 1.0,
       "r": 8.12,
       "s": 1.25
     },

diff --git a/dysts/flows.py b/dysts/flows.py
@@ -142,23 +142,23 @@ class ThomasLabyrinth(Thomas):
 
 class DoublePendulum(DynSys):
     @staticjit
-    def _rhs(th1, th2, p1, p2, t, d, m):
-        g = 9.82
-        pre = 6 / (m * d**2)
-        denom = 16 - 9 * np.cos(th1 - th2) ** 2
-        th1_dot = pre * (2 * p1 - 3 * np.cos(th1 - th2) * p2) / denom
-        th2_dot = pre * (8 * p2 - 3 * np.cos(th1 - th2) * p1) / denom
-        p1_dot = (
-            -0.5
-            * (m * d**2)
-            * (th1_dot * th2_dot * np.sin(th1 - th2) + 3 * (g / d) * np.sin(th1))
-        )
-        p2_dot = (
-            -0.5
-            * (m * d**2)
-            * (-th1_dot * th2_dot * np.sin(th1 - th2) + 3 * (g / d) * np.sin(th2))
-        )
-        return th1_dot, th2_dot, p1_dot, p2_dot
+    def _rhs(th1, th2, p1, p2, t, g, l1, l2, m1, m2):
+        cos_diff = np.cos(th1 - th2)
+        sin_diff = np.sin(th1 - th2)
+        denom = l1 * l2 * (m1 + m2 * sin_diff**2)
+
+        th1dot = (l2 * p1 - l1 * p2 * cos_diff) / (l1 * denom)
+        th2dot = ((m1 + m2) * l1 * p2 - m2 * l2 * p1 * cos_diff) / (m2 * l2 * denom)
+
+        h1 = p1 * p2 * sin_diff / denom
+        h2 = (m2 * l2 * p1**2) / (2 * l1 * denom**2)
+        h2 += 0.5 * m2 * p2 * l2 * l1 * th2dot / denom
+        h2 *= np.sin(2 * (th1 - th2))
+
+        p1dot = -(m1 + m2) * g * l1 * np.sin(th1) - h1 + h2
+        p2dot = -m2 * g * l2 * np.sin(th2) + h1 - h2
+
+        return th1dot, th2dot, p1dot, p2dot
 
     @staticmethod
     @staticjit
@@ -736,8 +736,7 @@ def _rhs(
         z0,
     ):
         ybar = (1 / y0) * yb1 * z * v / (yb2 * x + yb3 + kf)
-        if x < 0.0:
-            x = 0
+        x = max(0, x)
         rf = (ci - z0 * z) * np.sqrt(x)
         xdot = c1 * x * ybar + c2 * ybar + c3 * x**2 + c4 * rf + c5 * x * z - kf * x
         zdot = (c6 / z0) * rf + c7 * x * z + c8 * z * v + c9 * z - kf * z
@@ -1409,14 +1408,14 @@ class ChenLee(DynSys):
     def _rhs(x, y, z, t, a, b, c):
         xdot = a * x - y * z
         ydot = b * y + x * z
-        zdot = c * z + 0.3333333333333333333333333 * x * y
+        zdot = c * z + (1 / 3) * x * y
         return xdot, ydot, zdot
 
     @staticjit
     def _jac(x, y, z, t, a, b, c):
         row1 = [a, -z, -y]
         row2 = [z, b, x]
-        row3 = [0.3333333333333333333333333 * y, 0.3333333333333333333333333 * x, c]
+        row3 = [(1 / 3) * y, (1 / 3) * x, c]
         return row1, row2, row3
 
 
@@ -1698,18 +1697,18 @@ class ExcitableCell(DynSys):
     def rhs(self, X, t):
         v, n, c = X
 
-        alpham = 0.1 * (25 + v) / (1 - np.exp(-0.1 * v - 2.5))
-        betam = 4 * np.exp(-(v + 50) / 18)
+        alpham = self.ams * (self.amvb + v) / (1 - np.exp(-self.ar * v - self.amvo))
+        betam = self.bms * np.exp(-self.bmr * v - self.bmo)
         minf = alpham / (alpham + betam)
 
-        alphah = 0.07 * np.exp(-0.05 * v - 2.5)
-        betah = 1 / (1 + np.exp(-0.1 * v - 2))
+        alphah = self.ahs * np.exp(-self.ahr * v - self.aho)
+        betah = 1 / (1 + np.exp(-self.bhr * v - self.bho))
         hinf = alphah / (alphah + betah)
 
-        alphan = 0.01 * (20 + v) / (1 - np.exp(-0.1 * v - 2))
-        betan = 0.125 * np.exp(-(v + 30) / 80)
+        alphan = self.ans * (self.anvb + v) / (1 - np.exp(-self.ar * v - self.anvo))
+        betan = self.bns * np.exp(-self.bnr * v - self.bno)
         ninf = alphan / (alphan + betan)
-        tau = 1 / (230 * (alphan + betan))
+        tau = 1 / (self.tscl * (alphan + betan))
 
         ca = c / (1 + c)
 
@@ -1774,36 +1773,16 @@ def rhs(self, X, t):
 
 
 class CircadianRhythm(DynSys):
-    @staticjit
-    def _rhs(
-        m,
-        fc,
-        fs,
-        fn,
-        th,
-        t,
-        Ki,
-        k,
-        k1,
-        k2,
-        kd,
-        kdn,
-        km,
-        ks,
-        n,
-        vd,
-        vdn,
-        vm,
-        vmax,
-        vmin,
-        v,
-    ):
-        vs = 2.5 * ((0.5 + 0.5 * np.cos(th)) + vmin) * (vmax - vmin)
-        mdot = vs * (Ki**n) / (Ki**n + fn**n) - vm * m / (km + m)
-        fcdot = ks * m - k1 * fc + k2 * fn - k * fc
-        fsdot = k * fc - vd * fs / (kd + fs)
-        fndot = k1 * fc - k2 * fn - vdn * fn / (kdn + fn)
-        thdot = 2 * np.pi / 24
+    def rhs(self, X, t):
+        m, fc, fs, fn, th = X
+        vs = self.vc * ((0.5 + 0.5 * np.cos(th)) + self.vmin) * (self.vmax - self.vmin)
+        mdot = vs * (self.Ki**self.n) / (self.Ki**self.n + fn**self.n) - self.vm * m / (
+            self.km + m
+        )
+        fcdot = self.ks * m - self.k1 * fc + self.k2 * fn - self.k * fc
+        fsdot = self.k * fc - self.vd * fs / (self.kd + fs)
+        fndot = self.k1 * fc - self.k2 * fn - self.vdn * fn / (self.kdn + fn)
+        thdot = 2 * np.pi / self.ps
         return mdot, fcdot, fsdot, fndot, thdot
 
     @staticjit
@@ -1817,7 +1796,7 @@ def _rhs(x, y, th, t, gamma, psi, w):
         xdot = y
         ydot = -1 - np.heaviside(-x, 0) * (x + psi * y * np.abs(y)) + gamma * np.cos(th)
         thdot = w
-        return (xdot, ydot, thdot)
+        return xdot, ydot, thdot
 
     @staticjit
     def _postprocessing(x, y, th):
@@ -1999,15 +1978,15 @@ def _rhs(x, y, z, t, a, alpha1, alpha2, b, c, k1, k2, zs):
 
 class TurchinHanski(DynSys):
     @staticjit
-    def _rhs(n, p, z, t, a, d, e, g, h, r, s):
+    def _rhs(n, p, z, t, a, d, e, g, h, lamb, r, s):
         ndot = (
             r * (1 - e * np.sin(z)) * n
             - r * (n**2)
             - g * (n**2) / (n**2 + h**2)
             - a * n * p / (n + d)
         )
         pdot = s * (1 - e * np.sin(z)) * p - s * (p**2) / n
-        zdot = 2 * np.pi
+        zdot = 2 * np.pi * lamb
         return ndot, pdot, zdot
 
     @staticjit

diff --git a/tests/test_ensemble.py b/tests/test_ensemble.py
@@ -109,7 +109,6 @@ def test_ensemble_generation_parameter_sampling(self):
             scale=1e-4, random_seed=random.randint(0, 1000000)
         )
         system_sample = random.sample(get_attractor_list(sys_class="continuous"), 4)
-        system_sample += ["InteriorSquirmer"]
         systems = [getattr(dfl, sys)() for sys in system_sample]
         unperturbed_sols = make_trajectory_ensemble(
             256,