Merge 20706ac into f22955b

brian2/stateupdaters/exact.py

@@ -40,22 +40,25 @@ def get_linear_system(eqs, variables):
     ValueError
         If the equations cannot be converted into an M * X + B form.
     '''
-    diff_eqs = eqs.get_substituted_expressions(variables)
-    diff_eq_names = [name for name, _ in diff_eqs]
+    diff_eqs = {name: str_to_sympy(expr.code, variables).expand()
+                for name, expr in eqs.get_substituted_expressions(variables)}
 
-    symbols = [Symbol(name, real=True) for name in diff_eq_names]
+    # Sometimes, in particular in testing, variables defined as differential
+    # equations are actually constant (e.g. `dv/dt = 0/second`). We ignore
+    # them here
+    symbols = [Symbol(name, real=True) for name, expr in diff_eqs.items()
+               if expr != 0]
 
-    coefficients = sp.zeros(len(diff_eq_names))
-    constants = sp.zeros(len(diff_eq_names), 1)
-
-    for row_idx, (name, expr) in enumerate(diff_eqs):
-        s_expr = str_to_sympy(expr.code, variables).expand()
+    coefficients = sp.zeros(len(symbols))
+    constants = sp.zeros(len(symbols), 1)
 
+    for row_idx, symbol in enumerate(symbols):
+        s_expr = diff_eqs[symbol.name]
         current_s_expr = s_expr
         for col_idx, symbol in enumerate(symbols):
             current_s_expr = current_s_expr.collect(symbol)
             constant_wildcard = Wild('c', exclude=[symbol])
-            factor_wildcard = Wild('c_'+name, exclude=symbols)
+            factor_wildcard = Wild('c_'+symbol.name, exclude=symbols)
             one_pattern = factor_wildcard*symbol + constant_wildcard
             matches = current_s_expr.match(one_pattern)
             if matches is None:
@@ -64,15 +67,16 @@ def get_linear_system(eqs, variables):
                                                      '%s, could not be '
                                                      'separated into linear '
                                                      'components.') %
-                                                    (expr, name))
+                                                    (sympy_to_str(s_expr),
+                                                     symbol.name))
 
             coefficients[row_idx, col_idx] = matches[factor_wildcard]
             current_s_expr = matches[constant_wildcard]
 
         # The remaining constant should be a true constant
         constants[row_idx] = current_s_expr
 
-    return (diff_eq_names, coefficients, constants)
+    return [s.name for s in symbols], coefficients, constants
 
 
 class IndependentStateUpdater(StateUpdateMethod):
@@ -191,40 +195,49 @@ def __call__(self, equations, variables=None, method_options=None):
                     ('Expression "{}" is not guaranteed to be constant over a '
                      'time step').format(sympy_to_str(entry)))
 
-        symbols = [Symbol(variable, real=True) for variable in varnames]
-        solution = sp.solve_linear_system(matrix.row_join(constants), *symbols)
-        if solution is None or set(symbols) != set(solution.keys()):
-            raise UnsupportedEquationsException('Cannot solve the given '
-                                                'equations with this '
-                                                'stateupdater.')
-        b = sp.ImmutableMatrix([solution[symbol] for symbol in symbols])
-
         # Solve the system
         dt = Symbol('dt', real=True, positive=True)
+        # Add the constant terms as new variables
+        const_vars = []
+        const_terms = []
+        for idx, (varname, const_term) in enumerate(zip(varnames, constants)):
+            if const_term != 0:
+                matrix = matrix.col_insert(matrix.cols, sp.Matrix([1 if i == idx else 0
+                                                                   for i in range(matrix.rows)]))
+                matrix = matrix.row_insert(matrix.rows, sp.zeros(1, matrix.cols))
+                const_vars.append('_const_term_' + varname)
+                const_terms.append(const_term)
+
         try:
             A = (matrix * dt).exp()
         except NotImplementedError:
             raise UnsupportedEquationsException('Cannot solve the given '
                                                 'equations with this '
                                                 'stateupdater.')
+
         if method_options['simplify']:
             A = A.applyfunc(lambda x:
                             sp.factor_terms(sp.cancel(sp.signsimp(x))))
-        C = sp.ImmutableMatrix(A * b) - b
-        _S = sp.MatrixSymbol('_S', len(varnames), 1)
-        updates = A * _S + C
+
+        _S = sp.MatrixSymbol('_S', len(varnames) + len(const_vars), 1)
+        updates = A * _S
         updates = updates.as_explicit()
+        abstract_code = []
+
+        # Add code for the constant terms:
+        for const_var, const_term in zip(const_vars, const_terms):
+            abstract_code.append(const_var + ' = ' + sympy_to_str(const_term))
 
         # The solution contains _S[0, 0], _S[1, 0] etc. for the state variables,
-        # replace them with the state variable names 
-        abstract_code = []
-        for idx, (variable, update) in enumerate(zip(varnames, updates)):
+        # replace them with the state variable names
+        for variable, update in zip(varnames, updates[:len(varnames)]):
             rhs = update
             if rhs.has(I, re, im):
                 raise UnsupportedEquationsException('The solution to the linear system '
                                                     'contains complex values '
                                                     'which is currently not implemented.')
-            for row_idx, varname in enumerate(varnames):
+
+            for row_idx, varname in enumerate(itertools.chain(varnames, const_vars)):
                 rhs = rhs.subs(_S[row_idx, 0], varname)
 
             # Do not overwrite the real state variables yet, the update step

brian2/tests/test_synapses.py

@@ -1585,6 +1585,8 @@ def test_event_driven_dependency_error():
 
 @pytest.mark.codegen_independent
 def test_event_driven_dependency_error2():
+    pytest.xfail("This will be fixed with the rewrite of the equation "
+                 "dependency check.")
     stim = SpikeGeneratorGroup(1, [0], [0]*ms, period=5*ms)
     tau = 5*ms
     syn = Synapses(stim, stim, '''
@@ -1962,7 +1964,8 @@ def test_vectorisation_STDP_like():
     neurons = NeuronGroup(6, '''dv/dt = rate : 1
                                 ge : 1
                                 rate : Hz
-                                dA/dt = -A/(1*ms) : 1''', threshold='v>1', reset='v=0')
+                                dA/dt = -A/(1*ms) : 1''', threshold='v>1',
+                          reset='v=0', method='euler')
     # Note that the synapse does not actually increase the target v, we want
     # to have simple control about when neurons spike. Also, we separate the
     # "depression" and "facilitation" completely. The example also uses