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Fixed quickstart notebook #294

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Mar 15, 2023
Merged

Fixed quickstart notebook #294

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4 changes: 2 additions & 2 deletions tests/dynamics/test_synchronization.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ def test_simulate_kuramoto():
H1 = xgi.random_hypergraph(N, [0.05, 0.001], seed=0)
theta_time, times = xgi.simulate_kuramoto(H1, 1, 1, np.ones(N), theta0, n_steps, dt)

assert theta_time.shape == (N, n_steps)
assert theta_time.shape == (n_steps, N)
assert np.all(times == np.arange(n_steps) * dt)

output = np.array(
Expand Down Expand Up @@ -81,7 +81,7 @@ def test_simulate_kuramoto():
]
)

assert norm(theta_time - output) < 1e-07
assert norm(theta_time - output.T) < 1e-07


def test_compute_kuramoto_order_parameter():
Expand Down
20 changes: 10 additions & 10 deletions tutorials/quickstart.ipynb
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Expand Up @@ -185,9 +185,7 @@
" multiedges=False, singletons=False, isolates=False, relabel=True, in_place=False\n",
")\n",
"\n",
"print(\n",
" f\"The hypergraph has {H_enron_cleaned.num_nodes} nodes and {H_enron_cleaned.num_edges} edges\"\n",
")\n",
"print(f\"The hypergraph has {H_enron_cleaned.num_nodes} nodes and {H_enron_cleaned.num_edges} edges\")\n",
"\n",
"print(\"The first 10 node IDs are:\")\n",
"print(list(H_enron_cleaned.nodes)[:10])"
Expand Down Expand Up @@ -716,13 +714,15 @@
"source": [
"n = 100\n",
"H = xgi.random_hypergraph(n, [0.05, 0.001], seed=None)\n",
"w = 2 * np.random.normal(1, 0.05, n)\n",
"omega = 2 * np.random.normal(1, 0.05, n)\n",
"theta = np.linspace(0, 2 * np.pi, n)\n",
"timesteps = 1000\n",
"dt = 0.002\n",
"R = xgi.compute_kuramoto_order_parameter(\n",
" H, k2=2, k3=3, w=w, theta=theta, timesteps=timesteps, dt=dt\n",
")"
"dt = 0.01\n",
"\n",
"theta, t = xgi.simulate_kuramoto(\n",
" H, k2=2, k3=3, omega=omega, theta=theta, timesteps=timesteps, dt=dt\n",
")\n",
"R = xgi.compute_kuramoto_order_parameter(theta)"
]
},
{
Expand All @@ -732,7 +732,7 @@
"outputs": [],
"source": [
"plt.figure()\n",
"plt.plot(np.arange(0, timesteps * dt, dt), R)\n",
"plt.plot(t, R)\n",
"plt.xlabel(\"time\")\n",
"plt.ylabel(\"Kuramoto order parameter\")\n",
"plt.show()"
Expand Down Expand Up @@ -762,7 +762,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.6 | packaged by conda-forge | (main, Aug 22 2022, 20:38:29) [Clang 13.0.1 ]"
"version": "3.10.0"
},
"vscode": {
"interpreter": {
Expand Down
10 changes: 5 additions & 5 deletions xgi/dynamics/synchronization.py
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Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,7 @@ def simulate_kuramoto(H, k2, k3, omega=None, theta=None, timesteps=10000, dt=0.0
Returns
-------
theta_time: numpy array of floats
Timeseries of phases from the Kuramoto model, of dimension (N, T)
Timeseries of phases from the Kuramoto model, of dimension (T, N)
times: numpy array of floats
Times corresponding to the simulate phases

Expand All @@ -67,7 +67,7 @@ def simulate_kuramoto(H, k2, k3, omega=None, theta=None, timesteps=10000, dt=0.0
triangles = H_int.edges.filterby("size", 3).members()
n = H_int.num_nodes

theta_time = np.zeros((n, timesteps))
theta_time = np.zeros((timesteps, n))
times = np.arange(timesteps) * dt

if omega is None:
Expand All @@ -78,7 +78,7 @@ def simulate_kuramoto(H, k2, k3, omega=None, theta=None, timesteps=10000, dt=0.0

for t in range(timesteps):

theta_time[:, t] = theta
theta_time[t] = theta

r1 = np.zeros(n, dtype=complex)
r2 = np.zeros(n, dtype=complex)
Expand Down Expand Up @@ -118,7 +118,7 @@ def compute_kuramoto_order_parameter(theta_time):
Parameters
----------
theta_time: numpy array of floats
Timeseries of phases from the Kuramoto model, of dimension (N, T)
Timeseries of phases from the Kuramoto model, of dimension (T, N)

Returns
-------
Expand All @@ -127,7 +127,7 @@ def compute_kuramoto_order_parameter(theta_time):

"""

z = np.mean(np.exp(1j * theta_time), axis=0)
z = np.mean(np.exp(1j * theta_time), axis=1)
r_time = np.abs(z)

return r_time
Expand Down