def test_ode_system(tb_args): fvarspecs = { "w": "k*w + a*itable + sin(t) + myauxfn1(t)*myauxfn2(w)", 'aux_wdouble': 'w*2 + globalindepvar(t)', 'aux_other': 'myauxfn1(2*t) + initcond(w)' } fnspecs = { 'myauxfn1': (['t'], '2.5*cos(3*t)'), 'myauxfn2': (['w'], 'w/2') } DSargs = { 'tdomain': [0.1, 2.1], 'pars': {'k': 2, 'a': -0.5}, 'inputs': {'itable': InterpolateTable(tb_args).variables['x1']}, 'auxvars': ['aux_wdouble', 'aux_other'], 'algparams': {'init_step': 0.01, 'strict': False}, 'checklevel': 2, 'name': 'ODEtest', 'fnspecs': fnspecs, 'varspecs': fvarspecs } testODE = Vode_ODEsystem(DSargs) assert testODE.pars == DSargs['pars'] assert (not testODE.defined) testODE.set( ics={'w': 3.0}, tdata=[0.11, 2.1] ) testtraj = testODE.compute('test1') assert testODE.defined assert_almost_equal(testtraj(0.5, 'w'), 6.05867901304, 3) assert_almost_equal(testtraj(0.2, 'aux_other'), 3.90581993688, 3) assert testODE.indepvariable.depdomain == Interval( 't', float64, [0.11, 2.1]) assert testODE.diagnostics.hasWarnings() assert testODE.diagnostics.findWarnings(21) != [] # Now adding a terminating co-ordinate threshold event... ev_args = { 'name': 'threshold', 'eventtol': 1e-4, 'eventdelay': 1e-5, 'starttime': 0, 'active': True, # = default 'term': True, 'precise': True # = default } thresh_ev = Events.makePythonStateZeroCrossEvent('w', 20, 1, ev_args) testODE.eventstruct.add(thresh_ev) traj2 = testODE.compute('test2') assert testODE.diagnostics.hasWarnings() assert testODE.diagnostics.findWarnings(10) != [] print(testODE.diagnostics.showWarnings()) assert_almost_equal(traj2.getEventTimes()['threshold'][0], 1.51449456, 3) assert testODE.indepvariable.depdomain == Interval( 't', float64, [0.11, 2.1])
def test_saveload_vode_odesystem(interptable): """Test pickling for saving and loading 'Vode_ODEsystem' Generator""" # Vode object with event and external input trajectory (defined earlier) fvarspecs = { "w": "k*w + a*itable + sin(t) + myauxfn1(t)*myauxfn2(w)", 'aux_wdouble': 'w*2 + globalindepvar(t)', 'aux_other': 'myauxfn1(2*t) + initcond(w)' } fnspecs = {'myauxfn1': (['t'], '2.5*cos(3*t)'), 'myauxfn2': (['w'], 'w/2')} ev_args = { 'name': 'threshold', 'eventtol': 1e-4, 'eventdelay': 1e-5, 'starttime': 0, 'term': True, } thresh_ev = Events.makePythonStateZeroCrossEvent('w', 20, 1, ev_args) DSargs = { 'tdomain': [0.1, 2.1], 'tdata': [0.11, 2.1], 'ics': { 'w': 3.0 }, 'pars': { 'k': 2, 'a': -0.5 }, 'inputs': { 'itable': interptable.variables['x1'] }, 'auxvars': ['aux_wdouble', 'aux_other'], 'algparams': { 'init_step': 0.01, 'strict': False }, 'events': thresh_ev, 'checklevel': 2, 'name': 'ODEtest', 'fnspecs': fnspecs, 'varspecs': fvarspecs } testODE = Vode_ODEsystem(DSargs) odetraj = testODE.compute('testode') saveObjects([odetraj, testODE], 'temp_objects.pkl', True) objs_ode = loadObjects('temp_objects.pkl') objs_ode[1].diagnostics.clearWarnings() assert len(objs_ode[1].diagnostics.warnings) == 0 odetraj2 = objs_ode[1].compute('testode2') assert odetraj2(0.6) == odetraj(0.6) assert len(objs_ode[1].diagnostics.warnings) == 1 os.remove('temp_objects.pkl')
def ode(): return Vode_ODEsystem({ 'name': 'ode', 'vars': ['x'], 'varspecs': { 'x': 'x' }, })
def ode(): return Vode_ODEsystem({ 'name': 'ode', 'vars': ['x'], 'pars': {'p': 0.5}, 'varspecs': {'x': 'x+p'}, 'pdomain': {'p': [0,1]} })
def test_saveload_vode_odesystem(interptable): """Test pickling for saving and loading 'Vode_ODEsystem' Generator""" # Vode object with event and external input trajectory (defined earlier) fvarspecs = { "w": "k*w + a*itable + sin(t) + myauxfn1(t)*myauxfn2(w)", 'aux_wdouble': 'w*2 + globalindepvar(t)', 'aux_other': 'myauxfn1(2*t) + initcond(w)' } fnspecs = { 'myauxfn1': (['t'], '2.5*cos(3*t)'), 'myauxfn2': (['w'], 'w/2') } ev_args = { 'name': 'threshold', 'eventtol': 1e-4, 'eventdelay': 1e-5, 'starttime': 0, 'term': True, } thresh_ev = Events.makePythonStateZeroCrossEvent('w', 20, 1, ev_args) DSargs = { 'tdomain': [0.1, 2.1], 'tdata': [0.11, 2.1], 'ics': {'w': 3.0}, 'pars': {'k': 2, 'a': -0.5}, 'inputs': {'itable': interptable.variables['x1']}, 'auxvars': ['aux_wdouble', 'aux_other'], 'algparams': {'init_step': 0.01, 'strict': False}, 'events': thresh_ev, 'checklevel': 2, 'name': 'ODEtest', 'fnspecs': fnspecs, 'varspecs': fvarspecs } testODE = Vode_ODEsystem(DSargs) odetraj = testODE.compute('testode') saveObjects([odetraj, testODE], 'temp_objects.pkl', True) objs_ode = loadObjects('temp_objects.pkl') objs_ode[1].diagnostics.clearWarnings() assert len(objs_ode[1].diagnostics.warnings) == 0 odetraj2 = objs_ode[1].compute('testode2') assert odetraj2(0.6) == odetraj(0.6) assert len(objs_ode[1].diagnostics.warnings) == 1 os.remove('temp_objects.pkl')
def test_ode_system(tb_args): fvarspecs = { "w": "k*w + a*itable + sin(t) + myauxfn1(t)*myauxfn2(w)", 'aux_wdouble': 'w*2 + globalindepvar(t)', 'aux_other': 'myauxfn1(2*t) + initcond(w)' } fnspecs = {'myauxfn1': (['t'], '2.5*cos(3*t)'), 'myauxfn2': (['w'], 'w/2')} DSargs = { 'tdomain': [0.1, 2.1], 'pars': { 'k': 2, 'a': -0.5 }, 'inputs': { 'itable': InterpolateTable(tb_args).variables['x1'] }, 'auxvars': ['aux_wdouble', 'aux_other'], 'algparams': { 'init_step': 0.01, 'strict': False }, 'checklevel': 2, 'name': 'ODEtest', 'fnspecs': fnspecs, 'varspecs': fvarspecs } testODE = Vode_ODEsystem(DSargs) assert testODE.pars == DSargs['pars'] assert (not testODE.defined) testODE.set(ics={'w': 3.0}, tdata=[0.11, 2.1]) testtraj = testODE.compute('test1') assert testODE.defined assert_almost_equal(testtraj(0.5, 'w'), 6.05867901304, 3) assert_almost_equal(testtraj(0.2, 'aux_other'), 3.90581993688, 3) assert testODE.indepvariable.depdomain == Interval('t', float64, [0.11, 2.1]) assert testODE.diagnostics.hasWarnings() assert testODE.diagnostics.findWarnings(21) != [] # Now adding a terminating co-ordinate threshold event... ev_args = { 'name': 'threshold', 'eventtol': 1e-4, 'eventdelay': 1e-5, 'starttime': 0, 'active': True, # = default 'term': True, 'precise': True # = default } thresh_ev = Events.makePythonStateZeroCrossEvent('w', 20, 1, ev_args) testODE.eventstruct.add(thresh_ev) traj2 = testODE.compute('test2') assert testODE.diagnostics.hasWarnings() assert testODE.diagnostics.findWarnings(10) != [] print(testODE.diagnostics.showWarnings()) assert_almost_equal(traj2.getEventTimes()['threshold'][0], 1.51449456, 3) assert testODE.indepvariable.depdomain == Interval('t', float64, [0.11, 2.1])
def test_python_funcspec_with_for_loop(): args = { 'name': 'fs_with_loop', 'varspecs': { 'z[i]': 'for(i, 1, 6, t**[i]/2)' }, } # XXX: FuncSpec doesn't support 'for' loop directly fs = Vode_ODEsystem(args).funcspec assert fs.spec[0].split('\n') == [ 'def _specfn(ds, t, x, parsinps):', ' xnew0 = t/2 ', ' xnew1 = math.pow(t,2)/2 ', ' xnew2 = math.pow(t,3)/2 ', ' xnew3 = math.pow(t,4)/2 ', ' xnew4 = math.pow(t,5)/2 ', ' xnew5 = math.pow(t,6)/2 ', ' return array([xnew0, xnew1, xnew2, xnew3, xnew4, xnew5])', '', ]
def test_vode_event(dsargs): """ Test Vode_ODEsystem with events involving external inputs. """ _run_checks(Vode_ODEsystem(dsargs))
def test_vode_events_compare_with_euler(): """ Test terminal and non-terminal event testing with VODE integrator, including some comparisons and tests of Euler integrator too. """ DSargs = args(varspecs={'w': 'k*sin(2*t) - w'}, name='ODEtest') DSargs.tdomain = [0, 10] DSargs.pars = {'k': 1, 'p_thresh': -0.25} DSargs.algparams = {'init_step': 0.001, 'atol': 1e-12, 'rtol': 1e-13} DSargs.checklevel = 2 DSargs.ics = {'w': -1.0} DSargs.tdata = [0, 10] ev_args_nonterm = {'name': 'monitor', 'eventtol': 1e-4, 'eventdelay': 1e-5, 'starttime': 0, 'active': True, 'term': False, 'precise': True} thresh_ev_nonterm = Events.makeZeroCrossEvent('w', 0, ev_args_nonterm, varnames=['w']) ev_args_term = {'name': 'threshold', 'eventtol': 1e-4, 'eventdelay': 1e-5, 'starttime': 0, 'active': True, 'term': True, 'precise': True} thresh_ev_term = Events.makeZeroCrossEvent('w-p_thresh', -1, ev_args_term, varnames=['w'], parnames=['p_thresh']) DSargs.events = [thresh_ev_nonterm, thresh_ev_term] testODE = Vode_ODEsystem(DSargs) # diagnostics and other possible user-defined python functions # for python solvers only (currently only Euler) # def before_func(euler): # print(euler.algparams['init_step']) # # def after_func(euler): # print(euler._solver.y) # ##DSargs.user_func_beforestep = before_func ##DSargs.user_func_afterstep = after_func testODE_Euler = Euler_ODEsystem(DSargs) traj = testODE.compute('traj') traj2 = testODE_Euler.compute('traj') pts = traj.sample() testODE.diagnostics.showWarnings() mon_evs_found = testODE.getEvents('monitor') term_evs_found = testODE.getEvents('threshold') # test Euler assert allclose(array(testODE.getEventTimes('monitor')), array(traj2.getEventTimes('monitor')), atol=1e-3) assert all(traj.getEvents('monitor') == mon_evs_found) assert all(traj.getEventTimes('threshold') == testODE.getEventTimes('threshold')) term_evs_found.info() # Alternative way to extract events: they are labelled in the # pointset! These return dictionaries indexing into the pointset. mon_evs_dict = pts.labels.by_label['Event:monitor'] mon_ev_points = pts[sort(list(mon_evs_dict.keys()))] assert len(mon_evs_found) == len(mon_ev_points) == 2 assert all(mon_evs_found == mon_ev_points)
def test_vode_events_with_external_input(my_input): """ Test Vode_ODEsystem with events involving external inputs. Robert Clewley, September 2006. """ xs = ['x1', 'x2', 'x3'] ys = [0, 0.5, 1] fvarspecs = {"w": "k*w + pcwfn(sin(t)) + myauxfn1(t)*myauxfn2(w)", 'aux_wdouble': 'w*2 + globalindepvar(t)', 'aux_other': 'myauxfn1(2*t) + initcond(w)'} fnspecs = {'myauxfn1': (['t'], '2.5*cos(3*t)'), 'myauxfn2': (['w'], 'w/2'), 'pcwfn': makeMultilinearRegrFn('x', xs, ys)} # targetlang is optional if the default python target is desired DSargs = args(fnspecs=fnspecs, name='ODEtest') DSargs.varspecs = fvarspecs DSargs.tdomain = [0.1, 2.1] DSargs.pars = {'k': 2, 'a': -0.5, 'x1': -3, 'x2': 0.5, 'x3': 1.5} DSargs.vars = 'w' DSargs.inputs = {'in': my_input.variables['example_input']} DSargs.algparams = {'init_step': 0.01} DSargs.checklevel = 2 testODE = Vode_ODEsystem(DSargs) assert not testODE.defined testODE.set(ics={'w': 3.0}, tdata=[0.11, 2.1]) traj1 = testODE.compute('traj1') assert testODE.defined assert_almost_equal(traj1(0.5, 'w'), 8.9771499, 5) assert not testODE.diagnostics.hasWarnings() assert_almost_equal(traj1(0.2, ['aux_other']), 3.905819936, 5) print("\nNow adding a terminating co-ordinate threshold event") print(" and non-terminating timer event") # Show off the general-purpose, language-independent event creator: # 'makeZeroCrossEvent' ev_args_nonterm = {'name': 'monitor', 'eventtol': 1e-4, 'eventdelay': 1e-5, 'starttime': 0, 'active': True, 'term': False, 'precise': True} thresh_ev_nonterm = Events.makeZeroCrossEvent('in', 0, ev_args_nonterm, inputnames=['in']) # Now show use of the python-target specific creator: # 'makePythonStateZeroCrossEvent', which is also only # able to make events for state variable threshold crossings ev_args_term = {'name': 'threshold', 'eventtol': 1e-4, 'eventdelay': 1e-5, 'starttime': 0, 'active': True, 'term': True, 'precise': True} thresh_ev_term = Events.makePythonStateZeroCrossEvent('w', 20, 1, ev_args_term) testODE.eventstruct.add([thresh_ev_nonterm, thresh_ev_term]) print("Recomputing trajectory:") print("traj2 = testODE.compute('traj2')") traj2 = testODE.compute('traj2') print("\ntestODE.diagnostics.showWarnings() => ") testODE.diagnostics.showWarnings() print("\ntraj2.indepdomain.get() => ", traj2.indepdomain.get()) indep1 = traj2.indepdomain[1] assert indep1 < 1.17 and indep1 > 1.16 mon_evs_found = testODE.getEvents('monitor') assert len(mon_evs_found) == 1
def test_vode_events_compare_with_euler(): """ Test terminal and non-terminal event testing with VODE integrator, including some comparisons and tests of Euler integrator too. """ DSargs = args(varspecs={'w': 'k*sin(2*t) - w'}, name='ODEtest') DSargs.tdomain = [0, 10] DSargs.pars = {'k': 1, 'p_thresh': -0.25} DSargs.algparams = {'init_step': 0.001, 'atol': 1e-12, 'rtol': 1e-13} DSargs.checklevel = 2 DSargs.ics = {'w': -1.0} DSargs.tdata = [0, 10] ev_args_nonterm = {'name': 'monitor', 'eventtol': 1e-4, 'eventdelay': 1e-5, 'starttime': 0, 'active': True, 'term': False, 'precise': True} thresh_ev_nonterm = Events.makeZeroCrossEvent('w', 0, ev_args_nonterm, varnames=['w']) ev_args_term = {'name': 'threshold', 'eventtol': 1e-4, 'eventdelay': 1e-5, 'starttime': 0, 'active': True, 'term': True, 'precise': True} thresh_ev_term = Events.makeZeroCrossEvent('w-p_thresh', -1, ev_args_term, varnames=['w'], parnames=['p_thresh']) DSargs.events = [thresh_ev_nonterm, thresh_ev_term] testODE = Vode_ODEsystem(DSargs) # diagnostics and other possible user-defined python functions # for python solvers only (currently only Euler) # def before_func(euler): # print(euler.algparams['init_step']) # # def after_func(euler): # print(euler._solver.y) # ##DSargs.user_func_beforestep = before_func ##DSargs.user_func_afterstep = after_func testODE_Euler = Euler_ODEsystem(DSargs) traj = testODE.compute('traj') traj2 = testODE_Euler.compute('traj') pts = traj.sample() testODE.diagnostics.showWarnings() mon_evs_found = testODE.getEvents('monitor') term_evs_found = testODE.getEvents('threshold') # test Euler assert allclose(array(testODE.getEventTimes('monitor')), array(traj2.getEventTimes('monitor')), atol=1e-3) assert all(traj.getEvents('monitor') == mon_evs_found) assert all(traj.getEventTimes('threshold') == testODE.getEventTimes('threshold')) term_evs_found.info() # Alternative way to extract events: they are labelled in the # pointset! These return dictionaries indexing into the pointset. mon_evs_dict = pts.labels.by_label['Event:monitor'] mon_ev_points = pts[sort(mon_evs_dict.keys())] assert len(mon_evs_found) == len(mon_ev_points) == 2 assert all(mon_evs_found == mon_ev_points)