Merge pull request #126 from PKU-NIP-Lab/changes

fix bugs

Author: chaoming0625

brainpy/__init__.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = "2.1.2"
+__version__ = "2.1.3"
 
 
 try:

brainpy/datasets/chaotic_systems.py

@@ -112,7 +112,9 @@ def modified_lu_chen_series(duration, dt=0.001, a=36, c=20, b=3, d1=1, d2=0., ta
   eq.x[:] = inits['x']
   eq.y[:] = inits['y']
   eq.z[:] = inits['z']
-  runner = dyn.DSRunner(eq, monitors=['x', 'y', 'z'], dt=dt, progress_bar=False,
+  runner = dyn.DSRunner(eq,
+                        monitors=['x', 'y', 'z'],
+                        dt=dt, progress_bar=False,
                         numpy_mon_after_run=numpy_mon)
   runner.run(duration)
   return {'ts': runner.mon.ts,
@@ -167,19 +169,20 @@ def mackey_glass_series(duration, dt=0.1, beta=2., gamma=1., tau=2., n=9.65,
     assert isinstance(inits, (bm.ndarray, jnp.ndarray))
 
   rng = bm.random.RandomState(seed)
-  xdelay = bm.TimeDelay(inits, tau, dt=dt)
-  xdelay.data = inits + 0.2 * (rng.random((xdelay.num_delay_step,) + inits.shape) - 0.5)
+  xdelay = bm.TimeDelay(inits, tau, dt=dt, interp_method='round')
+  xdelay.data.value = inits + 0.2 * (rng.random((xdelay.num_delay_step,) + inits.shape) - 0.5)
 
-  @ddeint(method=method, state_delays={'x': xdelay})
+  @ddeint(method=method,
+          state_delays={'x': xdelay})
   def mg_eq(x, t):
-    return beta * xdelay(t - tau) / (1 + xdelay(t - tau) ** n) - gamma * x
+    xtau = xdelay(t - tau)
+    return beta * xtau / (1 + xtau ** n) - gamma * x
 
   runner = IntegratorRunner(mg_eq,
                             inits={'x': inits},
                             monitors=['x'],
-                            fun_monitors={'x(tau)': lambda t, dt: xdelay(t - tau)},
-                            progress_bar=progress_bar,
-                            dt=dt,
+                            fun_monitors={'x(tau)': lambda t, _: xdelay(t - tau)},
+                            progress_bar=progress_bar, dt=dt,
                             numpy_mon_after_run=numpy_mon)
   runner.run(duration)
   return {'ts': runner.mon.ts,

brainpy/integrators/dde/base.py

@@ -119,15 +119,23 @@ def __call__(self, *args, **kwargs):
           delay.update(new_dvars[key])
         elif isinstance(delay, bm.TimeDelay):
           delay.update(kwargs['t'] + dt, new_dvars[key])
-        raise ValueError('Unknown delay variable.')
+        else:
+          raise ValueError('Unknown delay variable. We only supports '
+                           'brainpy.math.LengthDelay, brainpy.math.TimeDelay, '
+                           'brainpy.math.NeutralDelay. '
+                           f'While we got {delay}')
 
     # update state delay variables
     for key, delay in self.state_delays.items():
       if isinstance(delay, bm.LengthDelay):
         delay.update(dict_vars[key])
       elif isinstance(delay, bm.TimeDelay):
         delay.update(kwargs['t'] + dt, dict_vars[key])
-      raise ValueError('Unknown delay variable.')
+      else:
+        raise ValueError('Unknown delay variable. We only supports '
+                         'brainpy.math.LengthDelay, brainpy.math.TimeDelay, '
+                         'brainpy.math.NeutralDelay. '
+                         f'While we got {delay}')
 
     return new_vars
 

brainpy/integrators/dde/explicit_rk.py

@@ -1,5 +1,8 @@
 # -*- coding: utf-8 -*-
 
+from typing import Dict
+import brainpy.math as bm
+
 from brainpy.integrators.constants import F, DT
 from brainpy.integrators.dde.base import DDEIntegrator
 from brainpy.integrators.ode import common
@@ -102,11 +105,14 @@ class Ralston2(ExplicitRKIntegrator):
 
 
 class RK2(ExplicitRKIntegrator):
-  def __init__(self, f, beta=2 / 3, var_type=None, dt=None, name=None, show_code=False):
+  def __init__(self, f, beta=2 / 3, var_type=None, dt=None, name=None,
+               state_delays: Dict[str, bm.TimeDelay] = None,
+               neutral_delays: Dict[str, bm.NeutralDelay] = None):
     self.A = [(), (beta,)]
     self.B = [1 - 1 / (2 * beta), 1 / (2 * beta)]
     self.C = [0, beta]
-    super(RK2, self).__init__(f=f, var_type=var_type, dt=dt, name=name, show_code=show_code)
+    super(RK2, self).__init__(f=f, var_type=var_type, dt=dt, name=name,
+                              state_delays=state_delays, neutral_delays=neutral_delays)
 
 
 register_dde_integrator('rk2', RK2)

brainpy/integrators/dde/tests/test_explicit_rk.py

@@ -0,0 +1,155 @@
+# -*- coding: utf-8 -*-
+
+
+import unittest
+
+import brainpy as bp
+import brainpy.math as bm
+
+
+class TestExplicitRKStateDelay(unittest.TestCase):
+  def test_euler(self):
+    xdelay = bm.TimeDelay(bm.zeros((1,)), 1., before_t0=-1., interp_method='round')
+
+    @bp.ddeint(method='euler', state_delays={'x': xdelay})
+    def equation(x, t, ):
+      return -xdelay(t - 1)
+
+    runner = bp.integrators.IntegratorRunner(equation, monitors=['x'])
+    runner.run(20.)
+
+    bp.visualize.line_plot(runner.mon.ts, runner.mon['x'], show=True)
+
+  def test_midpoint(self):
+    xdelay = bm.TimeDelay(bm.zeros((1,)), 1., before_t0=-1., interp_method='round')
+
+    @bp.ddeint(method='midpoint', state_delays={'x': xdelay})
+    def equation(x, t, ):
+      return -xdelay(t - 1)
+
+    runner = bp.integrators.IntegratorRunner(equation, monitors=['x'])
+    runner.run(20.)
+
+    bp.visualize.line_plot(runner.mon.ts, runner.mon['x'], show=True)
+
+  def test_heun2(self):
+    xdelay = bm.TimeDelay(bm.zeros((1,)), 1., before_t0=-1., interp_method='round')
+
+    @bp.ddeint(method='heun2', state_delays={'x': xdelay})
+    def equation(x, t, ):
+      return -xdelay(t - 1)
+
+    runner = bp.integrators.IntegratorRunner(equation, monitors=['x'])
+    runner.run(20.)
+
+    bp.visualize.line_plot(runner.mon.ts, runner.mon['x'], show=True)
+
+  def test_ralston2(self):
+    xdelay = bm.TimeDelay(bm.zeros((1,)), 1., before_t0=-1., interp_method='round')
+
+    @bp.ddeint(method='ralston2', state_delays={'x': xdelay})
+    def equation(x, t, ):
+      return -xdelay(t - 1)
+
+    runner = bp.integrators.IntegratorRunner(equation, monitors=['x'])
+    runner.run(20.)
+
+    bp.visualize.line_plot(runner.mon.ts, runner.mon['x'], show=True)
+
+  def test_rk2(self):
+    xdelay = bm.TimeDelay(bm.zeros((1,)), 1., before_t0=-1., interp_method='round')
+
+    @bp.ddeint(method='rk2',
+               state_delays={'x': xdelay})
+    def equation(x, t, ):
+      return -xdelay(t - 1)
+
+    runner = bp.integrators.IntegratorRunner(equation, monitors=['x'])
+    runner.run(20.)
+
+    bp.visualize.line_plot(runner.mon.ts, runner.mon['x'], show=True)
+
+  def test_rk3(self):
+    xdelay = bm.TimeDelay(bm.zeros((1,)), 1., before_t0=-1., interp_method='round')
+
+    @bp.ddeint(method='rk3', state_delays={'x': xdelay})
+    def equation(x, t, ):
+      return -xdelay(t - 1)
+
+    runner = bp.integrators.IntegratorRunner(equation, monitors=['x'])
+    runner.run(20.)
+
+    bp.visualize.line_plot(runner.mon.ts, runner.mon['x'], show=True)
+
+  def test_heun3(self):
+    xdelay = bm.TimeDelay(bm.zeros((1,)), 1., before_t0=-1., interp_method='round')
+
+    @bp.ddeint(method='heun3', state_delays={'x': xdelay})
+    def equation(x, t, ):
+      return -xdelay(t - 1)
+
+    runner = bp.integrators.IntegratorRunner(equation, monitors=['x'])
+    runner.run(20.)
+
+    bp.visualize.line_plot(runner.mon.ts, runner.mon['x'], show=True)
+
+  def test_ralston3(self):
+    xdelay = bm.TimeDelay(bm.zeros((1,)), 1., before_t0=-1., interp_method='round')
+
+    @bp.ddeint(method='ralston3', state_delays={'x': xdelay})
+    def equation(x, t, ):
+      return -xdelay(t - 1)
+
+    runner = bp.integrators.IntegratorRunner(equation, monitors=['x'])
+    runner.run(20.)
+
+    bp.visualize.line_plot(runner.mon.ts, runner.mon['x'], show=True)
+
+  def test_ssprk3(self):
+    xdelay = bm.TimeDelay(bm.zeros((1,)), 1., before_t0=-1., interp_method='round')
+
+    @bp.ddeint(method='ssprk3', state_delays={'x': xdelay})
+    def equation(x, t, ):
+      return -xdelay(t - 1)
+
+    runner = bp.integrators.IntegratorRunner(equation, monitors=['x'])
+    runner.run(20.)
+
+    bp.visualize.line_plot(runner.mon.ts, runner.mon['x'], show=True)
+
+  def test_rk4(self):
+    xdelay = bm.TimeDelay(bm.zeros((1,)), 1., before_t0=-1., interp_method='round')
+
+    @bp.ddeint(method='rk4', state_delays={'x': xdelay})
+    def equation(x, t, ):
+      return -xdelay(t - 1)
+
+    runner = bp.integrators.IntegratorRunner(equation, monitors=['x'])
+    runner.run(20.)
+
+    bp.visualize.line_plot(runner.mon.ts, runner.mon['x'], show=True)
+
+  def test_ralston4(self):
+    xdelay = bm.TimeDelay(bm.zeros((1,)), 1., before_t0=-1., interp_method='round')
+
+    @bp.ddeint(method='ralston4', state_delays={'x': xdelay})
+    def equation(x, t, ):
+      return -xdelay(t - 1)
+
+    runner = bp.integrators.IntegratorRunner(equation, monitors=['x'])
+    runner.run(20.)
+
+    bp.visualize.line_plot(runner.mon.ts, runner.mon['x'], show=True)
+
+  def test_rk4_38rule(self):
+    xdelay = bm.TimeDelay(bm.zeros((1,)), 1., before_t0=-1., interp_method='round')
+
+    @bp.ddeint(method='rk4_38rule', state_delays={'x': xdelay})
+    def equation(x, t, ):
+      return -xdelay(t - 1)
+
+    runner = bp.integrators.IntegratorRunner(equation, monitors=['x'])
+    runner.run(20.)
+
+    bp.visualize.line_plot(runner.mon.ts, runner.mon['x'], show=True)
+

brainpy/nn/nodes/RC/nvar.py

@@ -133,7 +133,7 @@ def init_state(self, num_batch=1):
     if self.store is None:
       self.store = bm.Variable(state)
     else:
-      self.store._value = state
+      self.store._value = state.value
 
   def forward(self, ff, fb=None, **shared_kwargs):
     all_parts = []