def addMethods(self):
# override to add _solver function
ODEsystem.addMethods(self)
# Jacobian ignored
self._solver = euler_solver(getattr(self,self.funcspec.spec[1]))
self._funcreg['_solver'] = ('self', 'euler_solver(getattr(self,' \
+ 'self.funcspec.spec[1]))')
def __init__(self, kw):
ODEsystem.__init__(self, kw)
self.diagnostics._errorcodes = \
{0: 'Unrecognized error code returned (see stderr output)',
-1: 'Excess work done on this call. (Perhaps wrong method MF.)',
-2: 'Excess accuracy requested. (Tolerances too small.)',
-3: 'Illegal input detected. (See printed message.)',
-4: 'Repeated error test failures. (Check all input.)',
-5: 'Repeated convergence failures. (Perhaps bad'
' Jacobian supplied or wrong choice of method MF or tolerances.)',
-6: 'Error weight became zero during problem. (Solution'
' component i vanished, and ATOL or ATOL(i) = 0.)'
}
self.diagnostics.outputStatsInfo = {'errorStatus': 'Error status on completion.'}
# note: VODE only supports array atol, not rtol.
algparams_def = {'poly_interp': False,
'rtol': 1e-9,
'atol': [1e-12 for dimix in range(self.dimension)],
'stiff': False,
'max_step': 0.0,
'min_step': 0.0,
'init_step': 0.01,
'max_pts': 1000000,
'strictdt': False,
'use_special': False,
'specialtimes': []
}
for k, v in algparams_def.items():
if k not in self.algparams:
self.algparams[k] = v
def __init__(self, kw):
if 'user_func_beforestep' in kw:
self.ufunc_before = kw['user_func_beforestep']
# delete because not covered in ODEsystem
del kw['user_func_beforestep']
else:
self.ufunc_before = _dummy_userfunc
if 'user_func_afterstep' in kw:
self.ufunc_after = kw['user_func_afterstep']
# delete because not covered in ODEsystem
del kw['user_func_afterstep']
else:
self.ufunc_after = _dummy_userfunc
ODEsystem.__init__(self, kw)
self._paraminfo = {'init_step': 'Fixed step size for time mesh.'}
self.diagnostics._errorcodes = {1: 'Step OK'}
self.diagnostics.outputStatsInfo = {
'errorStatus': 'Error status on completion.'
}
algparams_def = {
'poly_interp': False,
'init_step': 0.01,
'max_pts': 100000
}
for k, v in algparams_def.items():
if k not in self.algparams:
self.algparams[k] = v
def __init__(self, kw):
ODEsystem.__init__(self, kw)
self.diagnostics._errorcodes = \
{0: 'Unrecognized error code returned (see stderr output)',
-1: 'Excess work done on this call. (Perhaps wrong method MF.)',
-2: 'Excess accuracy requested. (Tolerances too small.)',
-3: 'Illegal input detected. (See printed message.)',
-4: 'Repeated error test failures. (Check all input.)',
-5: 'Repeated convergence failures. (Perhaps bad'
' Jacobian supplied or wrong choice of method MF or tolerances.)',
-6: 'Error weight became zero during problem. (Solution'
' component i vanished, and ATOL or ATOL(i) = 0.)'
}
self.diagnostics.outputStatsInfo = {
'errorStatus': 'Error status on completion.'
}
# note: VODE only supports array atol, not rtol.
algparams_def = {
'poly_interp': False,
'rtol': 1e-9,
'atol': [1e-12 for dimix in range(self.dimension)],
'stiff': False,
'max_step': 0.0,
'min_step': 0.0,
'init_step': 0.01,
'max_pts': 1000000,
'strictdt': False,
'use_special': False,
'specialtimes': []
}
for k, v in algparams_def.items():
if k not in self.algparams:
self.algparams[k] = v
def __init__(self, kw):
ODEsystem.__init__(self, kw)
assert self.funcspec.targetlang == 'python', \
('Wrong target language for functional specification. '
'Python needed for this class')
assert isinstance(self.funcspec, RHSfuncSpec), ('Vode '
'requires RHSfuncSpec type to proceed')
self._paraminfo = {'init_step': 'Fixed step size for time mesh.',
'strictdt': 'Boolean determining whether to evenly space time mesh (default=False), or to use exactly dt spacing.',
'stiff': 'Boolean to activate the BDF method, otherwise Adams method used. Default False.'}
self._errorcodes = {0: 'Unrecognized error code returned (see stderr output)',
-1: 'Excess work done on this call. (Perhaps wrong method MF.)',
-2: 'Excess accuracy requested. (Tolerances too small.)',
-3: 'Illegal input detected. (See printed message.)',
-4: 'Repeated error test failures. (Check all input.)',
-5: 'Repeated convergence failures. (Perhaps bad'
' Jacobian supplied or wrong choice of method MF or tolerances.)',
-6: 'Error weight became zero during problem. (Solution'
' component i vanished, and ATOL or ATOL(i) = 0.)'
}
self._outputinfo = {'errorStatus': 'Error status on completion.'}
# note: VODE only supports array atol, not rtol.
algparams_def = {'rtol': 1e-9,
'atol': [1e-12 for dimix in xrange(self.dimension)],
'stiff': False,
'max_step': 0.0,
'min_step': 0.0,
'init_step': 0.01,
'max_pts': 1000000,
'strictdt': False
}
for k, v in algparams_def.iteritems():
if k not in self._algparams:
self._algparams[k] = v
self.outputstats = {}
def addMethods(self):
# override to add _solver function
ODEsystem.addMethods(self, usePsyco=False)
if self.haveJacobian():
self._solver = ode(getattr(self,self.funcspec.spec[1]),
getattr(self,self.funcspec.auxfns["Jacobian"][1]))
self._funcreg['_solver'] = ('self',
'ode(getattr(self,self.funcspec.spec[1]),' \
+ 'getattr(self,self.funcspec.auxfns["Jacobian"][1]))')
else:
self._solver = ode(getattr(self,self.funcspec.spec[1]))
self._funcreg['_solver'] = ('self', 'ode(getattr(self,' \
+ 'self.funcspec.spec[1]))')
def addMethods(self):
# override to add _solver function
ODEsystem.addMethods(self, usePsyco=False)
if self.haveJacobian():
self._solver = ode(getattr(self,self.funcspec.spec[1]),
getattr(self,self.funcspec.auxfns["Jacobian"][1]))
self._funcreg['_solver'] = ('self',
'ode(getattr(self,self.funcspec.spec[1]),' \
+ 'getattr(self,self.funcspec.auxfns["Jacobian"][1]))')
else:
self._solver = ode(getattr(self,self.funcspec.spec[1]))
self._funcreg['_solver'] = ('self', 'ode(getattr(self,' \
+ 'self.funcspec.spec[1]))')
def __init__(self, kw):
ODEsystem.__init__(self, kw)
assert self.funcspec.targetlang == 'python', \
('Wrong target language for functional specification. '
'Python needed for this class')
assert isinstance(
self.funcspec,
RHSfuncSpec), ('Vode '
'requires RHSfuncSpec type to proceed')
self._paraminfo = {
'init_step':
'Fixed step size for time mesh.',
'strictdt':
'Boolean determining whether to evenly space time mesh (default=False), or to use exactly dt spacing.',
'stiff':
'Boolean to activate the BDF method, otherwise Adams method used. Default False.'
}
self._errorcodes = {
0:
'Unrecognized error code returned (see stderr output)',
-1:
'Excess work done on this call. (Perhaps wrong method MF.)',
-2:
'Excess accuracy requested. (Tolerances too small.)',
-3:
'Illegal input detected. (See printed message.)',
-4:
'Repeated error test failures. (Check all input.)',
-5:
'Repeated convergence failures. (Perhaps bad'
' Jacobian supplied or wrong choice of method MF or tolerances.)',
-6:
'Error weight became zero during problem. (Solution'
' component i vanished, and ATOL or ATOL(i) = 0.)'
}
self._outputinfo = {'errorStatus': 'Error status on completion.'}
# note: VODE only supports array atol, not rtol.
algparams_def = {
'rtol': 1e-9,
'atol': [1e-12 for dimix in xrange(self.dimension)],
'stiff': False,
'max_step': 0.0,
'min_step': 0.0,
'init_step': 0.01,
'max_pts': 1000000,
'strictdt': False
}
for k, v in algparams_def.iteritems():
if k not in self._algparams:
self._algparams[k] = v
self.outputstats = {}
def __init__(self, kw):
if 'user_func_beforestep' in kw:
self.ufunc_before = kw['user_func_beforestep']
# delete because not covered in ODEsystem
del kw['user_func_beforestep']
else:
self.ufunc_before = _dummy_userfunc
if 'user_func_afterstep' in kw:
self.ufunc_after = kw['user_func_afterstep']
# delete because not covered in ODEsystem
del kw['user_func_afterstep']
else:
self.ufunc_after = _dummy_userfunc
ODEsystem.__init__(self, kw)
self._paraminfo = {'init_step': 'Fixed step size for time mesh.'}
self.diagnostics._errorcodes = {1: 'Step OK'}
self.diagnostics.outputStatsInfo = {'errorStatus': 'Error status on completion.'}
algparams_def = {'poly_interp': False,
'init_step': 0.01,
'max_pts': 100000
}
for k, v in algparams_def.items():
if k not in self.algparams:
self.algparams[k] = v
def __init__(self, kw):
"""Use the nobuild key to postpone building of the library, e.g. in
order to provide additional build options to makeLibSource and
compileLib methods or to make changes to the C code by hand.
No build options can be specified otherwise."""
# Building is just doing make
if 'nobuild' in kw:
nobuild = kw['nobuild']
del kw['nobuild']
else:
nobuild = False
ODEsystem.__init__(self, kw)
self._solver = None
assert self.funcspec.targetlang == 'matlab', \
('Wrong target language for functional specification. '
'matlab needed for this class')
assert isinstance(self.funcspec, RHSfuncSpec), ('ADMC++ '
'requires RHSfuncSpec type to proceed')
assert not self.inputs, \
'ADMC++ does not support external inputs feature'
self._errorcodes = {}
self._paraminfo = {}
self.vftype = 'vfieldts'
# currently the final four of these params are for event handling
# NEED TO CHECK WHICH ONES ARE SUPPORTED BY ADMC -- LOOKS LIKE EVTOLS ONLY FOR NOW
# HACK: vftype is alg param for now, tells us whether parent class is hybridvf, vfieldts, etc.
algparams_def = {'evtols' : 0.0001, 'vftype' : 'vfieldts'}
# Remove this later
for k, v in algparams_def.iteritems():
if k not in self.algparams:
self.algparams[k] = v
# verify that no additional keys are present in algparams, after
# defaults are added above
if len(self.algparams) != len(algparams_def):
raise ValueError("Invalid keys present in algparams argument: " \
+ str(remain(self.algparams.keys(),algparams_def.keys())))
thisplatform = platform.system()
self._compilation_tempdir = os.path.join(os.getcwd(),
"admcpp_temp")
if not os.path.isdir(self._compilation_tempdir):
try:
assert not os.path.isfile(self._compilation_tempdir), \
"A file already exists with the same name"
os.mkdir(self._compilation_tempdir)
except:
print "Could not create compilation temp directory " + \
self._compilation_tempdir
raise
# ADMC targets must go in their own directories with appropriate names
self._model_dir = "@"+self.name
self._target_dir = os.path.join(self._compilation_tempdir,self._model_dir)
# Make the target directory
if not os.path.isdir(self._target_dir):
try:
assert not os.path.isfile(self._target_dir), \
"A file already exists with the same name"
os.mkdir(self._target_dir)
except:
print "Could not creat target ADMC model directory " + \
self._target_dir
raise
""" An ADMC model has the following files:
vfield.m -- contains code for the RHS of the vector field
set.m -- a generic method that overload matlab's set method; only need to insert vfield name
get.m -- a generic method that overloads matlab's get method; only need to insert appropriate parent name
"""
# model.m, get.m, set.m, vfield.m are minimal files required. TO DO: EVENTS
self._model_file = self.name+".m"
self._ic_file = self.name+"_ics.m"
self._param_file = self.name+"_params.m"
self._set_file = "set.m"
self._get_file = "get.m"
self._vfield_file = "vfield.m"
self._events_file = "events.m"
self._vf_filename_ext = "_"+self._model_file[:-2]
if not nobuild:
self.makeLibSource()
else:
print "Build the library using the makeLib method, or in "
print "stages using the makeLibSource and compileLib methods."
def __del__(self):
ODEsystem.__del__(self)
def compute(self, trajname, dirn='f', ics=None):
continue_integ = ODEsystem.prepDirection(self, dirn)
if self._dircode == -1:
raise NotImplementedError(
'Backwards integration is not implemented')
if ics is not None:
self.set(ics=ics)
self.validateICs()
self.diagnostics.clearWarnings()
self.diagnostics.clearErrors()
pnames = sortedDictKeys(self.pars)
xnames = self._var_ixmap # ensures correct order
# Check i.c.'s are well defined (finite)
self.checkInitialConditions()
if self.algparams['stiff']:
methstr = 'bdf'
methcode = 2
else:
methstr = 'adams'
methcode = 1
haveJac = int(self.haveJacobian())
if isinstance(self.algparams['atol'], list):
if len(self.algparams['atol']) != self.dimension:
raise ValueError('atol list must have same length as phase '
'dimension')
else:
atol = self.algparams['atol']
self.algparams['atol'] = [atol for dimix in range(self.dimension)]
indepdom0, indepdom1 = self.indepvariable.depdomain.get()
if continue_integ:
if indepdom0 > self._solver.t:
print("Previous end time is %f" % self._solver.t)
raise ValueError("Start time not correctly updated for "
"continuing orbit")
x0 = self._solver.y
indepdom0 = self._solver.t
self.indepvariable.depdomain.set((indepdom0, indepdom1))
else:
x0 = sortedDictValues(self.initialconditions, self.funcspec.vars)
t0 = indepdom0
if self.algparams['use_special']:
tmesh_special = list(self.algparams['specialtimes'])
if continue_integ:
if self._solver.t not in tmesh_special:
raise ValueError("Invalid time to continue integration:"
"it is not in 'special times'")
tmesh_special = tmesh_special[tmesh_special.index(self._solver.
t):]
try:
dt = min([tmesh_special[1] - t0, self.algparams['init_step']])
except:
raise ValueError("Invalid list of special times")
if not isincreasing(tmesh_special):
raise ValueError("special times must be given in increasing "
"order")
if self.indepvariable.depdomain.contains(t0) is notcontained or \
self.indepvariable.depdomain.contains(tmesh_special[-1]) is notcontained:
raise PyDSTool_BoundsError(
"special times were outside of independent "
"variable bounds")
else:
tmesh_special = []
dt = self.algparams['init_step']
# speed up repeated access to solver by making a temp name for it
solver = self._solver
if solver._integrator is None:
# Banded Jacobians not yet supported
#
# start a new integrator, because method may have been
# switched
solver.set_integrator('vode',
method=methstr,
rtol=self.algparams['rtol'],
atol=self.algparams['atol'],
nsteps=self.algparams['max_pts'],
max_step=self.algparams['max_step'],
min_step=self.algparams['min_step'],
first_step=dt / 2.,
with_jacobian=haveJac)
else:
solver.with_jacobian = haveJac
# self.mu = lband
# self.ml = uband
solver.rtol = self.algparams['rtol']
solver.atol = self.algparams['atol']
solver.method = methcode
# self.order = order
solver.nsteps = self.algparams['max_pts']
solver.max_step = self.algparams['max_step']
solver.min_step = self.algparams['min_step']
solver.first_step = dt / 2.
solver.set_initial_value(x0, t0)
## Broken code for going backwards (doesn't respect 'continue' option
## either)
## if self._dircode == 1:
## solver.set_initial_value(x0, t0)
## else:
## solver.set_initial_value(x0, indepdom1)
# wrap up each dictionary initial value as a singleton list
alltData = [t0]
allxDataDict = dict(zip(xnames, map(listid, x0)))
plist = sortedDictValues(self.pars)
extralist = copy(plist)
if self.inputs:
# inputVarList is a list of Variables
inames = sortedDictKeys(self.inputs)
listend = self.numpars + len(self.inputs)
inputVarList = sortedDictValues(self.inputs)
ilist = _pollInputs(inputVarList, alltData[0] + self.globalt0,
self.checklevel)
else:
ilist = []
inames = []
listend = self.numpars
inputVarList = []
extralist.extend(ilist)
solver.set_f_params(extralist)
if haveJac:
solver.set_jac_params(extralist)
do_poly = self.algparams['poly_interp']
if do_poly:
rhsfn = getattr(self, self.funcspec.spec[1])
dx0 = rhsfn(t0, x0, extralist)
alldxDataDict = dict(zip(xnames, map(listid, dx0)))
auxvarsfn = getattr(self, self.funcspec.auxspec[1])
strict = self.algparams['strictdt']
# Make t mesh if it wasn't given as 'specialtimes'
if not all(isfinite(self.indepvariable.depdomain.get())):
print("Time domain was: %f" % self.indepvariable.depdomain.get())
raise ValueError("Ensure time domain is finite")
if dt == indepdom1 - indepdom0:
# single-step integration required
# special times will not have been set (unless trivially
# they are [indepdom0, indepdom1])
tmesh = [indepdom0, indepdom1]
else:
notDone = True
repeatTol = 10
count = 0
while notDone and count <= repeatTol:
try:
tmesh = self.indepvariable.depdomain.sample(
dt, strict=strict, avoidendpoints=self.checklevel > 2)
notDone = False
except AssertionError:
count += 1
dt = dt / 3.0
if count == repeatTol:
raise AssertionError("Supplied time step is too large for "
"selected time interval")
# incorporate tmesh_special, if used, ensuring uniqueness
if tmesh_special != []:
tmesh.extend(tmesh_special)
tmesh = list(unique(tmesh))
tmesh.sort()
if len(tmesh) <= 2:
# safety net, in case too few points in mesh
# too few points unless we can add endpoint
if tmesh[-1] != indepdom1:
# dt too large for tmesh to have more than one point
tmesh.append(indepdom1)
if not strict: # get actual time step used
# don't use [0] in case avoided end points
try:
dt = tmesh[2] - tmesh[1]
except IndexError:
# can't avoid end points for such a small mesh
dt = tmesh[1] - tmesh[0]
#if self.eventstruct.query(['lowlevel']) != []:
# raise ValueError("Only high level events can be passed to VODE")
eventslist = self.eventstruct.query(['active', 'notvarlinked'])
termevents = self.eventstruct.query(['term'], eventslist)
# reverse time by reversing mesh doesn't work
## if self._dircode == -1:
## tmesh.reverse()
tmesh.pop(0) # get rid of first entry for initial condition
xnames = self.funcspec.vars
# storage of all auxiliary variable data
allaDataDict = {}
anames = self.funcspec.auxvars
avals = auxvarsfn(t0, x0, extralist)
for aix in range(len(anames)):
aname = anames[aix]
try:
allaDataDict[aname] = [avals[aix]]
except IndexError:
print("\nVODE generator: There was a problem evaluating " \
+ "an auxiliary variable")
print("Debug info: avals (length %d) was %r" %
(len(avals), avals))
print("Index out of range was %d" % aix)
print(self.funcspec.auxspec[1])
print(hasattr(self, self.funcspec.auxspec[1]))
print("Args were:%r" % [t0, x0, extralist])
raise
# Initialize signs of event detection objects at IC
self.setEventICs(self.initialconditions, self.globalt0)
if self.inputs:
parsinps = copy(self.pars)
parsinps.update(dict(zip(inames, ilist)))
else:
parsinps = self.pars
if eventslist != []:
dataDict = copy(self.initialconditions)
dataDict.update(dict(zip(anames, avals)))
dataDict['t'] = t0
## Removed this "belt and braces" pre-check because it messes
## up some events in the middle of hybrid regime switches.
## Not sure yet what the problem is. (Oct 2013)
#evsflagged = self.eventstruct.pollHighLevelEvents(None,
# dataDict,
# parsinps,
# eventslist)
#if len(evsflagged) > 0:
# raise RuntimeError("Some events flagged at initial condition")
if continue_integ:
# revert to prevprevsign, since prevsign changed after call
self.eventstruct.resetHighLevelEvents(t0, eventslist, 'prev')
elif self._for_hybrid_DS:
# self._for_hybrid_DS is set internally by HybridModel class
# to ensure not to reset events, because they may be about to
# flag on first step if previous hybrid state was the same
# generator and, for example, two variables are synchronizing
# so that their events get very close together.
# Just reset the starttimes of these events
for evname, ev in eventslist:
ev.starttime = t0
else:
# default state is a one-off call to this generator
self.eventstruct.resetHighLevelEvents(t0, eventslist, None)
self.eventstruct.validateEvents(self.funcspec.vars + \
self.funcspec.auxvars + \
self.funcspec.inputs + \
['t'], eventslist)
# temp storage of first time at which terminal events found
# (this is used for keeping the correct end point of new mesh)
first_found_t = None
# list of precise non-terminal events to be resolved after integration
nontermprecevs = []
evnames = [ev[0] for ev in eventslist]
lastevtime = {}.fromkeys(evnames, None)
# initialize new event info dictionaries
Evtimes = {}
Evpoints = {}
if continue_integ:
for evname in evnames:
try:
# these are in global time, so convert to local time
lastevtime[evname] = self.eventstruct.Evtimes[evname][-1] \
- self.globalt0
except (IndexError, KeyError):
# IndexError: Evtimes[evname] was None
# KeyError: Evtimes does not have key evname
pass
for evname in evnames:
Evtimes[evname] = []
Evpoints[evname] = []
# temp storage for repeatedly used object attributes (for lookup efficiency)
depdomains = dict(
zip(range(self.dimension),
[self.variables[xn].depdomain for xn in xnames]))
# Main integration loop
num_points = 0
breakwhile = False
while not breakwhile:
try:
new_t = tmesh.pop(0) # this destroys tmesh for future use
except IndexError:
# empty
break
last_t = solver.t # a record of previous time for use by event detector
try:
errcode = solver.integrate(new_t)
except:
print("Error calling right hand side function:")
self.showSpec()
print("Numerical traceback information (current state, " \
+ "parameters, etc.)")
print("in generator dictionary 'traceback'")
self.traceback = {
'vars': dict(zip(xnames, solver.y)),
'pars': dict(zip(pnames, plist)),
'inputs': dict(zip(inames, ilist)),
self.indepvariable.name: new_t
}
raise
avals = auxvarsfn(new_t, solver.y, extralist)
# Uncomment the following assertion for debugging
# assert all([isfinite(a) for a in avals]), \
# "Some auxiliary variable values not finite"
if eventslist != []:
dataDict = dict(zip(xnames, solver.y))
dataDict.update(dict(zip(anames, avals)))
dataDict['t'] = new_t
if self.inputs:
parsinps = copy(self.pars)
parsinps.update(
dict(
zip(
inames,
_pollInputs(inputVarList,
new_t + self.globalt0,
self.checklevel))))
else:
parsinps = self.pars
evsflagged = self.eventstruct.pollHighLevelEvents(
None, dataDict, parsinps, eventslist)
## print new_t, evsflagged
## evsflagged = [ev for ev in evsflagged if solver.t-indepdom0 > ev[1].eventinterval]
termevsflagged = [e for e in termevents if e in evsflagged]
nontermevsflagged = [
e for e in evsflagged if e not in termevsflagged
]
# register any non-terminating events in the warnings
# list, unless they are 'precise' in which case flag
# them to be resolved after integration completes
if len(nontermevsflagged) > 0:
evnames = [ev[0] for ev in nontermevsflagged]
precEvts = self.eventstruct.query(['precise'],
nontermevsflagged)
prec_evnames = [e[0] for e in precEvts]
# first register non-precise events
nonprecEvts = self.eventstruct.query(['notprecise'],
nontermevsflagged)
nonprec_evnames = [e[0] for e in nonprecEvts]
# only record events if they have not been previously
# flagged within their event interval
if nonprec_evnames != []:
temp_names = []
for evname, ev in nonprecEvts:
prevevt_time = lastevtime[evname]
if prevevt_time is None:
ignore_ev = False
else:
if solver.t - prevevt_time < ev.eventinterval:
ignore_ev = True
else:
ignore_ev = False
if not ignore_ev:
temp_names.append(evname)
lastevtime[evname] = solver.t
self.diagnostics.warnings.append(
(W_NONTERMEVENT, (solver.t, temp_names)))
for evname in temp_names:
Evtimes[evname].append(solver.t)
xv = solver.y
av = array(avals)
Evpoints[evname].append(concatenate((xv, av)))
for evname, ev in precEvts:
# only record events if they have not been previously
# flagged within their event interval
prevevt_time = lastevtime[evname]
if prevevt_time is None:
ignore_ev = False
else:
if last_t - prevevt_time < ev.eventinterval:
ignore_ev = True
else:
ignore_ev = False
if not ignore_ev:
nontermprecevs.append(
(last_t, solver.t, (evname, ev)))
# be conservative as to where the event is, so
# that don't miss any events.
lastevtime[evname] = last_t # solver.t-dt
ev.reset() #ev.prevsign = None #
do_termevs = []
if termevsflagged != []:
# only record events if they have not been previously
# flagged within their event interval
for e in termevsflagged:
prevevt_time = lastevtime[e[0]]
## print "Event %s flagged."%e[0]
## print " ... last time was ", prevevt_time
## print " ... event interval = ", e[1].eventinterval
## print " ... t = %f, dt = %f"%(solver.t, dt)
if prevevt_time is None:
ignore_ev = False
else:
## print " ... comparison = %f < %f"%(solver.t-dt-prevevt_time, e[1].eventinterval)
if last_t - prevevt_time < e[1].eventinterval:
ignore_ev = True
## print "VODE ignore ev"
else:
ignore_ev = False
if not ignore_ev:
do_termevs.append(e)
if len(do_termevs) > 0:
# >= 1 active terminal event flagged at this time point
if all([not ev[1].preciseFlag for ev in do_termevs]):
# then none of the events specify greater accuracy
# register the event in the warnings
evnames = [ev[0] for ev in do_termevs]
self.diagnostics.warnings.append((W_TERMEVENT, \
(solver.t, evnames)))
for evname in evnames:
Evtimes[evname].append(solver.t)
xv = solver.y
av = array(avals)
Evpoints[evname].append(concatenate((xv, av)))
# break while loop after appending t, x
breakwhile = True
else:
# find which are the 'precise' events that flagged
precEvts = self.eventstruct.query(['precise'],
do_termevs)
# these events have flagged once so eventdelay has
# been used. now switch it off while finding event
# precisely (should be redundant after change to
# eventinterval and eventdelay parameters)
evnames = [ev[0] for ev in precEvts]
if first_found_t is None:
## print "first time round at", solver.t
numtries = 0
first_found_t = solver.t
restore_evts = deepcopy(precEvts)
minbisectlimit = min(
[ev[1].bisectlimit for ev in precEvts])
for ev in precEvts:
ev[1].eventdelay = 0.
else:
numtries += 1
## print "time round: ", numtries
if numtries > minbisectlimit:
self.diagnostics.warnings.append(
(W_BISECTLIMIT, (solver.t, evnames)))
breakwhile = True
# get previous time point
if len(alltData) >= 1:
# take one step back -> told, which will
# get dt added back to first new meshpoint
# (solver.t is the step *after* the event was
# detected)
told = last_t # solver.t-dt without the loss of precision from subtraction
else:
raise ValueError("Event %s found too "%evnames[0]+\
"close to local start time: try decreasing "
"initial step size (current size is "
"%f @ t=%f)"%(dt,solver.t+self.globalt0))
# absolute tolerance check on event function values (not t)
in_tols = [
abs(e[1].fval) < e[1].eventtol for e in precEvts
]
if all(in_tols):
## print "Registering event:", dt_min, dt
# register the event in the warnings
self.diagnostics.warnings.append(
(W_TERMEVENT, (solver.t, evnames)))
for evname in evnames:
Evtimes[evname].append(solver.t)
xv = solver.y
av = array(avals)
Evpoints[evname].append(concatenate((xv, av)))
# Cannot continue -- dt_min no smaller than
# previous dt. If this is more than the first time
# in this code then have found the event to within
# the minimum 'precise' event's eventtol, o/w need
# to set eventtol smaller.
# Before exiting event-finding loop, reset prevsign
# of flagged events
self.eventstruct.resetHighLevelEvents(0, precEvts)
breakwhile = True # while loop, but append point first
if not breakwhile:
dt_new = dt / 5.0
# calc new tmesh
trangewidth = 2 * dt #first_found_t - told
numpoints = int(math.ceil(trangewidth / dt_new))
# choose slightly smaller dt to fit trange exactly
dt = trangewidth / numpoints
tmesh = [
told + i * dt for i in range(1, numpoints + 1)
]
# linspace version is *much* slower for numpoints ~ 10 and 100
#tmesh = list(told+linspace(dt, numpoints*dt, numpoints))
# reset events according to new time mesh,
# setting known previous event state to be their
# "no event found" state
self.eventstruct.resetHighLevelEvents(told,
precEvts,
state='off')
# build new ic with last good values (at t=told)
if len(alltData) > 1:
new_ic = [allxDataDict[xname][-1] \
for xname in xnames]
else:
new_ic = x0
# reset integrator
solver.set_initial_value(new_ic, told)
extralist[self.numpars:listend] = _pollInputs(
inputVarList, told + self.globalt0,
self.checklevel)
solver.set_f_params(extralist)
# continue integrating over new mesh
continue # while
# after events have had a chance to be detected at a state boundary
# we check for any that have not been caught by an event (will be
# much less accurately determined)
if not breakwhile:
# only here if a terminal event hasn't just flagged
for xi in range(self.dimension):
if not self.contains(depdomains[xi], solver.y[xi],
self.checklevel):
self.diagnostics.warnings.append(
(W_TERMSTATEBD,
(solver.t, xnames[xi], solver.y[xi],
depdomains[xi].get())))
breakwhile = True
break # for loop
if breakwhile:
break # while loop
alltData.append(solver.t)
if do_poly:
dxvals = rhsfn(solver.t, solver.y, extralist)
for xi, xname in enumerate(xnames):
allxDataDict[xname].append(solver.y[xi])
alldxDataDict[xname].append(dxvals[xi])
else:
for xi, xname in enumerate(xnames):
allxDataDict[xname].append(solver.y[xi])
for aix, aname in enumerate(anames):
allaDataDict[aname].append(avals[aix])
num_points += 1
if not breakwhile:
try:
extralist[self.numpars:listend] = [f(solver.t+self.globalt0,
self.checklevel) \
for f in inputVarList]
except ValueError:
print('External input call caused value out of range error:',\
't = %f' % solver.t)
for f in inputVarList:
if f.diagnostics.hasWarnings():
print('External input variable %s out of range:' %
f.name)
print(' t = %r, %s, %r' %
(repr(f.diagnostics.warnings[-1][0]), f.name,
repr(f.diagnostics.warnings[-1][1])))
raise
except AssertionError:
print(
'External input call caused t out of range error: t = %f'
% solver.t)
raise
solver.set_f_params(extralist)
breakwhile = not solver.successful()
# Check that any terminal events found terminated the code correctly
if first_found_t is not None:
# ... then terminal events were found. Those that were 'precise' had
# their 'eventdelay' attribute temporarily set to 0. It now should
# be restored.
for evname1, ev1 in termevents:
# restore_evts are copies of the originally flagged 'precise'
# events
for evname2, ev2 in restore_evts:
if evname2 == evname1:
ev1.eventdelay = ev2.eventdelay
try:
if self.diagnostics.warnings[-1][0] not in [
W_TERMEVENT, W_TERMSTATEBD
]:
print("t =%f" % solver.t)
print("state =%r" % dict(zip(xnames, solver.y)))
raise RuntimeError("Event finding code for terminal event "
"failed in Generator " + self.name + \
": try decreasing eventdelay or "
"eventinterval below eventtol, or the "
"atol and rtol parameters")
except IndexError:
info(self.diagnostics.outputStats, "Output statistics")
print("t =%f" % solver.t)
print("x =%f" % solver.y)
raise RuntimeError("Event finding failed in Generator " + \
self.name + ": try decreasing eventdelay "
"or eventinterval below eventtol, or the "
"atol and rtol parameters")
# Package up computed trajectory in Variable variables
# Add external inputs warnings to self.diagnostics.warnings, if any
for f in inputVarList:
for winfo in f.diagnostics.warnings:
self.diagnostics.warnings.append(
(W_NONTERMSTATEBD, (winfo[0], f.name, winfo[1],
f.depdomain.get())))
# check for non-unique terminal event
termcount = 0
for (w, i) in self.diagnostics.warnings:
if w == W_TERMEVENT or w == W_TERMSTATEBD:
termcount += 1
if termcount > 1:
self.diagnostics.errors.append(
(E_NONUNIQUETERM, (alltData[-1], i[1])))
# uncomment the following lines for debugging
# assert len(alltData) == len(allxDataDict.values()[0]) \
# == len(allaDataDict.values()[0]), "Output data size mismatch"
# for val_list in allaDataDict.values():
# assert all([isfinite(x) for x in val_list])
# Create variables (self.variables contains no actual data)
# These versions of the variables are only final if no non-terminal
# events need to be inserted.
variables = copyVarDict(self.variables)
for x in xnames:
if len(alltData) > 1:
if do_poly:
xvals = array([allxDataDict[x], alldxDataDict[x]]).T
interp = PiecewisePolynomial(alltData, xvals, 2)
else:
xvals = allxDataDict[x]
interp = interp1d(alltData, xvals)
variables[x] = Variable(interp, 't', x, x)
else:
print("Error in Generator:%s" % self.name)
print("t = %r" % alltData)
print("x = %r" % allxDataDict)
raise PyDSTool_ValueError("Fewer than 2 data points computed")
for a in anames:
if len(alltData) > 1:
variables[a] = Variable(interp1d(alltData, allaDataDict[a]),
't', a, a)
else:
print("Error in Generator:%s" % self.name)
print("t = %r" % alltData)
print("x = %r" % allxDataDict)
raise PyDSTool_ValueError("Fewer than 2 data points computed")
# Resolve non-terminal 'precise' events that were flagged, using the
# variables created. Then, add them to a new version of the variables.
ntpe_tdict = {}
for (et0, et1, e) in nontermprecevs:
lost_evt = False
# problem if eventinterval > et1-et0 !!
# was: search_dt = max((et1-et0)/5,e[1].eventinterval)
search_dt = (et1 - et0) / 5
try:
et_precise_list = e[1].searchForEvents(
trange=[et0, et1],
dt=search_dt,
checklevel=self.checklevel,
parDict=self.pars,
vars=variables,
inputs=self.inputs,
abseps=self._abseps,
eventdelay=False,
globalt0=self.globalt0)
except (ValueError, PyDSTool_BoundsError):
# dt too large for trange, e.g. if event tol is smaller than time mesh
et_precise_list = [(et0, (et0, et1))]
if et_precise_list == []:
lost_evt = True
for et_precise in et_precise_list:
if et_precise[0] is not None:
if et_precise[0] in ntpe_tdict:
# add event name at this time (that already exists in the dict)
ntpe_tdict[et_precise[0]].append(e[0])
else:
# add event name at this time (when time is not already in dict)
ntpe_tdict[et_precise[0]] = [e[0]]
else:
lost_evt = True
if lost_evt:
print(
"Error: A non-terminal, 'precise' event was lost -- did you reset",
end=' ')
print("events prior to integration?")
raise PyDSTool_ExistError(
"Internal error: A non-terminal, "
"'precise' event '%s' was lost after integration!" % e[0])
# add non-terminal event points to variables
if ntpe_tdict != {}:
# find indices of times at which event times will be inserted
tix = 0
evts = list(ntpe_tdict.keys())
evts.sort()
for evix in range(len(evts)):
evt = evts[evix]
evnames = ntpe_tdict[evt]
self.diagnostics.warnings.append(
(W_NONTERMEVENT, (evt, evnames)))
xval = [variables[x](evt) for x in xnames]
ilist = _pollInputs(inputVarList, evt + self.globalt0,
self.checklevel)
# find accurate dx and aux vars value at this time
if do_poly:
dxval = rhsfn(evt, xval, plist + ilist)
aval = list(auxvarsfn(evt, xval, plist + ilist))
for evname in evnames:
Evtimes[evname].append(evt)
Evpoints[evname].append(array(xval + aval))
tcond = less_equal(alltData[tix:], evt).tolist()
try:
tix = tcond.index(0) + tix # lowest index for t > evt
do_insert = (alltData[tix - 1] != evt)
except ValueError:
# evt = last t value so no need to add it
do_insert = False
if do_insert:
alltData.insert(tix, evt)
for ai, a in enumerate(anames):
allaDataDict[a].insert(tix, aval[ai])
if do_poly:
for xi, x in enumerate(xnames):
allxDataDict[x].insert(tix, xval[xi])
alldxDataDict[x].insert(tix, dxval[xi])
else:
for xi, x in enumerate(xnames):
allxDataDict[x].insert(tix, xval[xi])
for x in xnames:
if do_poly:
# use asarray in case points added to sequences as a list
xvals = array(
[asarray(allxDataDict[x]),
asarray(alldxDataDict[x])]).T
interp = PiecewisePolynomial(alltData, xvals, 2)
else:
xvals = allxDataDict[x]
interp = interp1d(alltData, xvals)
variables[x] = Variable(interp, 't', x, x)
for a in anames:
variables[a] = Variable(interp1d(alltData, allaDataDict[a]),
't', a, a)
self.diagnostics.outputStats = {
'last_step': dt,
'num_fcns': num_points,
'num_steps': num_points,
'errorStatus': errcode
}
if solver.successful():
#self.validateSpec()
for evname, evtlist in Evtimes.items():
try:
self.eventstruct.Evtimes[evname].extend([et+self.globalt0 \
for et in evtlist])
except KeyError:
self.eventstruct.Evtimes[evname] = [et+self.globalt0 \
for et in evtlist]
# build event pointset information (reset previous trajectory's)
self.trajevents = {}
for (evname, ev) in eventslist:
evpt = Evpoints[evname]
if evpt == []:
self.trajevents[evname] = None
else:
evpt = transpose(array(evpt))
self.trajevents[evname] = Pointset({
'coordnames':
xnames + anames,
'indepvarname':
't',
'coordarray':
evpt,
'indepvararray':
Evtimes[evname],
'indepvartype':
float
})
self.defined = True
return Trajectory(trajname,
list(variables.values()),
abseps=self._abseps,
globalt0=self.globalt0,
checklevel=self.checklevel,
FScompatibleNames=self._FScompatibleNames,
FScompatibleNamesInv=self._FScompatibleNamesInv,
events=self.trajevents,
modelNames=self.name,
modelEventStructs=self.eventstruct)
else:
try:
self.diagnostics.errors.append(
(E_COMPUTFAIL, (solver.t,
self.diagnostics._errorcodes[errcode])))
except TypeError:
# e.g. when errcode has been used to return info list
print("Error information: %d" % errcode)
self.diagnostics.errors.append(
(E_COMPUTFAIL, (solver.t,
self.diagnostics._errorcodes[0])))
self.defined = False
def __del__(self):
genDB.unregister(self)
ODEsystem.__del__(self)
def compute(self, trajname, dirn='f', ics=None):
continue_integ = ODEsystem.prepDirection(self, dirn)
if ics is not None:
self.set(ics=ics)
self.validateICs()
self.diagnostics.clearWarnings()
self.diagnostics.clearErrors()
if isinstance(self.algparams['rtol'], list):
if len(self.algparams['rtol']) != self.dimension:
raise ValueError('rtol list must have same length as phase dimension')
else:
rtol = self.algparams['rtol']
self.algparams['rtol'] = [rtol for dimix in range(self.dimension)]
if isinstance(self.algparams['atol'], list):
if len(self.algparams['atol']) != self.dimension:
raise ValueError('atol list must have same length as phase dimension')
else:
atol = self.algparams['atol']
self.algparams['atol'] = [atol for dimix in range(self.dimension)]
anames = self.funcspec.auxvars
# Check i.c.'s are well defined (finite)
self.checkInitialConditions()
self.setEventICs(self.initialconditions, self.globalt0)
# update event params in case changed since last run
self._prepareEventSpecs()
# Main integration
t0 = self.indepvariable.depdomain[0]
t1 = self.indepvariable.depdomain[1]
plist = sortedDictValues(self.pars)
self.algparams['hasJac'] = self.haveJacobian()
self.algparams['hasJacP'] = self.haveJacobian_pars()
if self._solver is None:
self._solver = dopri(self.modname,
rhs=self.name, phaseDim=self.dimension,
paramDim=len(plist), nAux=len(anames),
nEvents=len(self._eventNames),
nExtInputs=len(self.inputs),
hasJac=self.algparams['hasJac'],
hasJacP=self.algparams['hasJacP'],
hasMass=self.haveMass(),
extraSpace=self.algparams['extraspace'],
)
try:
genDB.register(self)
except PyDSTool_KeyError:
errstr = "Generator " + self.name + ": this vector field's " +\
"DLL is already in use"
raise RuntimeError(errstr)
if self._dircode == 1:
tbegin = t0
tend = t1
elif self._dircode == -1:
# dopri does reverse time integration simply by switching t0 and t1
# and using negative steps
tbegin = t1
tend = t0
if len(self.algparams['specialtimes'])>0:
use_special = self.algparams['use_special']
else:
use_special = 0
bounds = [[],[]] # lower, then upper
for v in self.funcspec.vars:
bds = self.xdomain[v]
bounds[0].append(bds[0])
bounds[1].append(bds[1])
for p in self.funcspec.pars:
bds = self.pdomain[p]
bounds[0].append(bds[0])
bounds[1].append(bds[1])
if continue_integ:
x0 = self._solver.lastPoint
# overwrite t0 from self.indepvariable.domain, but use its t1
tbegin = self._solver.lastTime
if abs(self._solver.lastStep) < abs(self.algparams['init_step']):
self.algparams['init_step'] = self._solver.lastStep
if abs(t1-tbegin) < abs(self.algparams['init_step']):
raise ValueError("Integration end point too close to initial "
"point")
# if self.inputs and self._extInputsChanged:
# self._extInputsChanged = False
# self._solver.setContParams(tend, plist,
# use_special,
# self.algparams['verbose'],
# True, deepcopy(self._inputVarList),
# deepcopy(self._inputTimeList))
else:
if self._solver.numRuns > 0:
self._solver.clearAll()
x0 = sortedDictValues(self.initialconditions, self.funcspec.vars)
self._solver.setInteg(maxpts=self.algparams['max_pts'],
rtol=self.algparams['rtol'], atol=self.algparams['atol'])
self._solver.setRunParams(ic=x0, params=plist,
t0=tbegin, tend=tend, gt0=self.globalt0,
refine=self.algparams['refine'],
specTimes=self.algparams['specialtimes'],
bounds=bounds)
if self.inputs:
# self._extInputsChanged if global t0 changed so that can
# adjust times given to the integrator (it is blind to global t0
# when accesses input variable times)
self._ensure_inputs(self._extInputsChanged)
# hinit only set if not continue_integ
if len(anames)>0:
check_aux = self.algparams['check_aux']
else:
check_aux = 0
if self.algparams['max_step'] == 0:
max_step = tend-tbegin
else:
max_step = self.algparams['max_step']
init_step = self.algparams['init_step']
if self._dircode == 1:
if init_step < 0:
init_step = -init_step
if max_step < 0:
max_step = -max_step
else:
if init_step > 0:
init_step = -init_step
if max_step > 0:
max_step = -max_step
if continue_integ:
# record needed for bounds checking and truncation
old_highest_ix = self._solver.points.shape[1]
alltData, X, A, Stats, H, Err, Evtimes, \
Evpoints = self._solver.Continue(tend, plist,
use_special, self.algparams['verbose'],
self._extInputsChanged,
deepcopy(self._inputVarList),
deepcopy(self._inputTimeList),
bounds)
else:
old_highest_ix = 0
self._solver.setEvents(eventActive=self.algparams['eventActive'],
eventTerm=self.algparams['eventTerm'],
eventDir=self.algparams['eventDir'],
eventDelay=self.algparams['eventDelay'],
eventInt=self.algparams['eventInt'],
eventTol=self.algparams['eventTol'],
maxevtpts=self.algparams['maxevtpts'],
maxbisect=self.algparams['maxbisect'])
alltData, X, A, Stats, H, Err, Evtimes, \
Evpoints = self._solver.Run(init_step,
max_step,
check_aux,
use_special,
self.algparams['verbose'],
self.algparams['fac1'],
self.algparams['fac2'],
self.algparams['safety'],
self.algparams['beta'],
self.algparams['checkBounds'],
self.algparams['boundsCheckMaxSteps'],
self.algparams['magBound'])
self._extInputsChanged = False # reset this now
self.diagnostics.outputStats = {'last_step': H,
'last_time': self._solver.lastTime,
'last_point': self._solver.lastPoint,
'num_fcns': Stats[0],
'num_steps': Stats[1],
'num_accept': Stats[2],
'num_reject': Stats[3],
'errorStatus': Err
}
if self._dircode == -1:
# reverse the array object (no reverse method!)
alltData = alltData[::-1]
X = X[:,::-1]
if anames != []:
A = A[:,::-1]
xnames = self._var_ixmap
# Package up computed trajectory in Variable variables
# Add external inputs warnings to self.diagnostics.warnings, if any
# (not presently supported)
## for f in inputVarList:
## for winfo in f.diagnostics.warnings:
## self.diagnostics.warnings.append((W_NONTERMSTATEBD,
## (winfo[0], f.name, winfo[1],
## f.depdomain)))
eventslist = self.eventstruct.query(['lowlevel', 'active'])
termevents = self.eventstruct.query(['term'], eventslist)
if self._eventNames != []:
# build self.diagnostics.warnings because events happened --
# and keep a record of which times terminal events happened because
# Model.py's event handling procedure assumes multiple events
# happening at one time are listed in one warning
termevtimes = {}
nontermevtimes = {}
try:
for evix in range(len(self._eventNames)):
if Evpoints[evix] is None:
continue
evname = self._eventNames[evix]
numevs = len(Evtimes[evix])
if self.algparams['eventTerm'][evix]:
if numevs > 1:
print("Event info:%r, %r" % (Evpoints, Evtimes))
assert numevs <= 1, ("Internal error: more than one "
"terminal event of same type found")
# For safety, we should assert that this event
# also appears in termevents, but we don't
if Evtimes[evix][0] in termevtimes.keys():
# append event name to this warning
warning_ix = termevtimes[Evtimes[evix][0]]
self.diagnostics.warnings[warning_ix][1][1].append(evname)
else:
# make new termevtime entry for the new warning
termevtimes[Evtimes[evix][0]] = len(self.diagnostics.warnings)
self.diagnostics.warnings.append((W_TERMEVENT,
(Evtimes[evix][0],
[self._eventNames[evix]])))
else:
for ev in range(numevs):
if Evtimes[evix][ev] in nontermevtimes.keys():
# append event name to this warning
warning_ix = nontermevtimes[Evtimes[evix][ev]]
self.diagnostics.warnings[warning_ix][1][1].append(evname)
else:
# make new nontermevtime entry for the new warning
nontermevtimes[Evtimes[evix][ev]] = \
len(self.diagnostics.warnings)
self.diagnostics.warnings.append((W_NONTERMEVENT,
(Evtimes[evix][ev],
[evname])))
except IndexError:
print("Events returned from integrator are the wrong size.")
print(" Did you change the system and not refresh the C " \
+ "library using the forcelibrefresh() method?")
raise
termcount = 0
for (w,i) in self.diagnostics.warnings:
if w == W_TERMEVENT or w == W_TERMSTATEBD:
if termcount > 0:
raise ValueError("Internal error: more than one terminal "
"event found")
termcount += 1
# post-process check of variable bounds (if defined and algparams['checkBounds'] True)
if self._dircode > 0:
compare = operator.lt
last_ix = Inf
else:
compare = operator.gt
last_ix = -Inf
highest_ix = X.shape[1]-1
last_t = Inf
if self.algparams['checkBounds'] > 0:
# temp storage for repeatedly used object attributes (for lookup efficiency)
depdomains = dict(zip(range(self.dimension),
[self.variables[xn].depdomain for xn in xnames]))
offender_ix = None
for xi in range(self.dimension):
if not any(depdomains[xi].isfinite()):
# no point in checking when the bounds are +/- infinity
continue
next_last_ix = array_bounds_check(X[xi][old_highest_ix:],
depdomains[xi], self._dircode) + old_highest_ix
if compare(next_last_ix, last_ix):
# won't count as truncating unless the following checks
# hold
last_ix = next_last_ix
offender_ix = xi
if not isfinite(last_ix) and last_ix < 0:
# only use +Inf hereon to flag no truncation needed
last_ix = Inf
elif last_ix >= 0 and last_ix < highest_ix:
# truncate data
last_t = alltData[last_ix]
print("Warning; domain bound reached (because algparams['checkBounds'] > 0)")
self.diagnostics.warnings.append((W_TERMSTATEBD,
(last_t, xnames[offender_ix],
X[offender_ix, last_ix],
depdomains[offender_ix].get())))
# Create variables (self.variables contains no actual data)
variables = copyVarDict(self.variables)
# build event pointset information (reset previous trajectory's)
# don't include events after any truncation due to state bound violation
self.trajevents = {}
for evix in range(len(self._eventNames)):
evname = self._eventNames[evix]
if Evpoints[evix] is None:
self.trajevents[evname] = None
else:
try:
ev_a_list = []
for t in Evtimes[evix]:
tix = find(alltData, t)
ev_a_list.append(A[:,tix])
ev_array = concatenate((Evpoints[evix],
transpose(array(ev_a_list, 'd'))))
del ev_a_list, tix
except TypeError:
# A is empty
ev_array = Evpoints[evix]
if last_ix >= 0 and last_ix < highest_ix:
# don't count last_ix = -1 which is the same as highest_ix
last_ev_tix = npy.argmax(Evtimes[evix] >= alltData[last_ix])
if last_ev_tix == 0 and Evtimes[evix][0] >= last_t:
# checks that there was actually a violation
# - so no events to record
self.trajevents[evname] = None
else:
# truncation needed
ev_array = ev_array[:, :last_ev_tix+1]
ev_times = Evtimes[evix][:last_ev_tix+1]
self.trajevents[evname] = Pointset({'coordnames': xnames+anames,
'indepvarname': 't',
'coordarray': ev_array,
'indepvararray': ev_times})
else:
# no truncation needed
self.trajevents[evname] = Pointset({'coordnames': xnames+anames,
'indepvarname': 't',
'coordarray': ev_array,
'indepvararray': Evtimes[evix]})
if last_ix >= 0 and last_ix < highest_ix:
# truncate
X = X[:, :last_ix]
alltData = alltData[:last_ix]
try:
allxDataDict = dict(zip(xnames,X))
except IndexError:
print("Integration returned variable values of unexpected dimensions.")
print(" Did you change the system and not refresh the C library" \
+ " using the forcelibrefresh() method?")
raise
# storage of all auxiliary variable data
try:
if anames != []:
if last_ix < highest_ix:
A = A[:, :last_ix]
try:
allaDataDict = dict(zip(anames,A))
except TypeError:
print("Internal error! Type of A: %s" % type(A))
raise
except IndexError:
print("Integration returned auxiliary values of unexpected dimensions.")
print(" Did you change the system and not refresh the C library" \
+ " using the forcelibrefresh() method?")
raise
if int(Err) == 1 or (int(Err) == 2 and termcount == 1):
# output OK
if self.algparams['poly_interp']:
rhsfn = self._solver.Rhs
# when Dopri can output the Rhs values alongside variable
# values then this won't be necessary
dxvals = zeros((len(alltData),self.dimension),float)
for tix, tval in enumerate(alltData):
# solver's Rhs function already contains the inputs so no
# need to recompute and provide here.
#i = _pollInputs(sortedDictValues(self.inputs), tval,
# self.checklevel)
# X is the output variable array, but rhsfn demands a list
dxvals[tix] = rhsfn(tval, list(X[:,tix]), plist)[0]
for xi, x in enumerate(xnames):
if len(alltData) > 1:
if self.algparams['poly_interp']:
interp = PiecewisePolynomial(alltData,
array([allxDataDict[x], dxvals[:,xi]]).T, 2)
else:
interp = interp1d(alltData, allxDataDict[x])
variables[x] = Variable(interp, 't', x, x)
else:
raise PyDSTool_ValueError("Fewer than 2 data points "
"computed")
for a in anames:
if len(alltData) > 1:
variables[a] = Variable(interp1d(alltData,allaDataDict[a]),
't', a, a)
else:
raise PyDSTool_ValueError("Fewer than 2 data points "
"computed")
# final checks
#self.validateSpec()
self.defined = True
return Trajectory(trajname, list(variables.values()),
abseps=self._abseps, globalt0=self.globalt0,
checklevel=self.checklevel,
FScompatibleNames=self._FScompatibleNames,
FScompatibleNamesInv=self._FScompatibleNamesInv,
modelNames=self.name, events=self.trajevents,
modelEventStructs=self.eventstruct)
else:
try:
diagnost_info = self.diagnostics._errorcodes[int(Err)]
except TypeError:
# errcode messed up from Dopri
print("Error code: %d" % Err)
diagnost_info = self.diagnostics._errorcodes[0]
if self._solver.verbose:
info(self.diagnostics.outputStats, "Output statistics")
self.defined = False
# Did the solver run out of memory?
if (len(alltData) == self.algparams['max_pts'] or \
self.diagnostics.outputStats['num_steps'] >= self.algparams['max_pts']) \
and alltData[-1] < tend:
print("max_pts algorithmic parameter too small: current " + \
"value is %i"%self.algparams['max_pts'])
# avstep = (self.algparams['init_step']+self.diagnostics.outputStats['last_step'])/2.
if self.diagnostics.outputStats['last_time']-tbegin > 0:
ms = str(int(round(self.algparams['max_pts'] / \
(self.diagnostics.outputStats['last_time'] - \
tbegin)*(tend-tbegin))))
else:
ms = 'Inf'
print("(recommended value for this trajectory segment is " + \
"estimated to be %s (saved in diagnostics.errors attribute))"%str(ms))
diagnost_info += " -- recommended value is " + ms
self.diagnostics.errors.append((E_COMPUTFAIL,
(self._solver.lastTime, diagnost_info)))
raise PyDSTool_ExistError("No trajectory created")
def compute(self, trajname, dirn='f', ics=None):
continue_integ = ODEsystem.prepDirection(self, dirn)
if self._dircode == -1:
raise NotImplementedError('Backwards integration is not implemented')
if ics is not None:
self.set(ics=ics)
self.validateICs()
self.diagnostics.clearWarnings()
self.diagnostics.clearErrors()
pnames = sortedDictKeys(self.pars)
xnames = self._var_ixmap # ensures correct order
# Check i.c.'s are well defined (finite)
self.checkInitialConditions()
haveJac = int(self.haveJacobian())
indepdom0, indepdom1 = self.indepvariable.depdomain.get()
if continue_integ:
if indepdom0 > self._solver.t:
print("Previous end time is %f"%self._solver.t)
raise ValueError("Start time not correctly updated for "
"continuing orbit")
x0 = self._solver.y
indepdom0 = self._solver.t
self.indepvariable.depdomain.set((indepdom0,indepdom1))
else:
x0 = sortedDictValues(self.initialconditions,
self.funcspec.vars)
t0 = indepdom0
dt = self.algparams['init_step']
# speed up repeated access to solver by making a temp name for it
solver = self._solver
solver.set_initial_value(x0, t0)
solver.dt = dt
# wrap up each dictionary initial value as a singleton list
alltData = [t0]
allxDataDict = dict(zip(xnames, map(listid, x0)))
plist = sortedDictValues(self.pars)
extralist = copy(plist)
if self.inputs:
# inputVarList is a list of Variables
inames = sortedDictKeys(self.inputs)
listend = self.numpars + len(self.inputs)
inputVarList = sortedDictValues(self.inputs)
ilist = _pollInputs(inputVarList, alltData[0]+self.globalt0,
self.checklevel)
else:
ilist = []
inames = []
listend = self.numpars
inputVarList = []
extralist.extend(ilist)
solver.set_f_params(extralist)
if haveJac:
solver.set_jac_params(extralist)
do_poly = self.algparams['poly_interp']
if do_poly:
rhsfn = getattr(self, self.funcspec.spec[1])
dx0 = rhsfn(t0, x0, extralist)
alldxDataDict = dict(zip(xnames, map(listid, dx0)))
auxvarsfn = getattr(self,self.funcspec.auxspec[1])
# Make t mesh if it wasn't given as 'specialtimes'
if not all(isfinite(self.indepvariable.depdomain.get())):
print("Time domain was: %r" % self.indepvariable.depdomain.get())
raise ValueError("Ensure time domain is finite")
if dt == indepdom1 - indepdom0:
# single-step integration required
# special times will not have been set (unless trivially
# they are [indepdom0, indepdom1])
tmesh = [indepdom0, indepdom1]
else:
notDone = True
while notDone:
tmesh = self.indepvariable.depdomain.sample(dt,
strict=True,
avoidendpoints=True)
notDone = False
first_found_t = None
eventslist = self.eventstruct.query(['active', 'notvarlinked'])
termevents = self.eventstruct.query(['term'], eventslist)
tmesh.pop(0) # get rid of first entry for initial condition
xnames = self.funcspec.vars
# storage of all auxiliary variable data
allaDataDict = {}
anames = self.funcspec.auxvars
avals = auxvarsfn(t0, x0, extralist)
for aix in range(len(anames)):
aname = anames[aix]
try:
allaDataDict[aname] = [avals[aix]]
except IndexError:
print("\nEuler generator: There was a problem evaluating " \
+ "an auxiliary variable")
print("Debug info: avals (length %d) was %r" % (len(avals), avals))
print("Index out of range was %d" % aix)
print(self.funcspec.auxspec[1])
print(hasattr(self, self.funcspec.auxspec[1]))
print("Args were: %r" % [t0, x0, extralist])
raise
# Initialize signs of event detection objects at IC
self.setEventICs(self.initialconditions, self.globalt0)
if self.inputs:
parsinps = copy(self.pars)
parsinps.update(dict(zip(inames,ilist)))
else:
parsinps = self.pars
if eventslist != []:
dataDict = copy(self.initialconditions)
dataDict.update(dict(zip(anames, avals)))
dataDict['t'] = t0
evsflagged = self.eventstruct.pollHighLevelEvents(None,
dataDict,
parsinps,
eventslist)
if len(evsflagged) > 0:
raise RuntimeError("Some events flagged at initial condition")
if continue_integ:
# revert to prevprevsign, since prevsign changed after call
self.eventstruct.resetHighLevelEvents(t0, eventslist, 'prev')
elif self._for_hybrid_DS:
# self._for_hybrid_DS is set internally by HybridModel class
# to ensure not to reset events, because they may be about to
# flag on first step if previous hybrid state was the same
# generator and, for example, two variables are synchronizing
# so that their events get very close together.
# Just reset the starttimes of these events
for evname, ev in eventslist:
ev.starttime = t0
else:
# default state is a one-off call to this generator
self.eventstruct.resetHighLevelEvents(t0, eventslist, None)
self.eventstruct.validateEvents(self.funcspec.vars + \
self.funcspec.auxvars + \
self.funcspec.inputs + \
['t'], eventslist)
evnames = [ev[0] for ev in eventslist]
lastevtime = {}.fromkeys(evnames, None)
# initialize new event info dictionaries
Evtimes = {}
Evpoints = {}
if continue_integ:
for evname in evnames:
try:
# these are in global time, so convert to local time
lastevtime[evname] = self.eventstruct.Evtimes[evname][-1] \
- self.globalt0
except (IndexError, KeyError):
# IndexError: Evtimes[evname] was None
# KeyError: Evtimes does not have key evname
pass
for evname in evnames:
Evtimes[evname] = []
Evpoints[evname] = []
# temp storage for repeatedly used object attributes (for lookup efficiency)
depdomains = dict(zip(range(self.dimension),
[self.variables[xn].depdomain for xn in xnames]))
# Main integration loop
num_points = 0
breakwhile = False
while not breakwhile:
try:
new_t = tmesh.pop(0) # this destroys tmesh for future use
except IndexError:
# empty
break
# optional user function (not a method)
self.ufunc_before(self)
try:
errcode = solver.integrate(dt)
except:
print("Error calling right hand side function:")
self.showSpec()
print("Numerical traceback information (current state, " \
+ "parameters, etc.)")
print("in generator dictionary 'traceback'")
self.traceback = {'vars': dict(zip(xnames,solver.y)),
'pars': dict(zip(pnames,plist)),
'inputs': dict(zip(inames,ilist)),
self.indepvariable.name: new_t}
raise
avals = auxvarsfn(new_t, solver.y, extralist)
# Uncomment the following assertion for debugging
# assert all([isfinite(a) for a in avals]), \
# "Some auxiliary variable values not finite"
if eventslist != []:
dataDict = dict(zip(xnames,solver.y))
dataDict.update(dict(zip(anames,avals)))
dataDict['t'] = new_t
if self.inputs:
parsinps = copy(self.pars)
parsinps.update(dict(zip(inames,
_pollInputs(inputVarList, new_t+self.globalt0,
self.checklevel))))
else:
parsinps = self.pars
evsflagged = self.eventstruct.pollHighLevelEvents(None,
dataDict,
parsinps,
eventslist)
## print new_t, evsflagged
## evsflagged = [ev for ev in evsflagged if solver.t-indepdom0 > ev[1].eventinterval]
termevsflagged = [e for e in termevents if e in evsflagged]
nontermevsflagged = [e for e in evsflagged if e not in termevsflagged]
# register any non-terminating events in the warnings
# list, unless they are 'precise' in which case flag
# them to be resolved after integration completes
if len(nontermevsflagged) > 0:
evnames = [ev[0] for ev in nontermevsflagged]
precEvts = self.eventstruct.query(['precise'],
nontermevsflagged)
# register both precise and non-precise events the same
# (Euler currently ignores precise events with its fixed time step)
nonprecEvts = self.eventstruct.query(['notprecise'],
nontermevsflagged) + precEvts
nonprec_evnames = [e[0] for e in nonprecEvts] + [e[0] for e in precEvts]
# only record events if they have not been previously
# flagged within their event interval
if nonprec_evnames != []:
temp_names = []
for evname, ev in nonprecEvts:
prevevt_time = lastevtime[evname]
if prevevt_time is None:
ignore_ev = False
else:
if solver.t-prevevt_time < ev.eventinterval:
ignore_ev = True
else:
ignore_ev = False
if not ignore_ev:
temp_names.append(evname)
lastevtime[evname] = solver.t
self.diagnostics.warnings.append((W_NONTERMEVENT,
(solver.t, temp_names)))
for evname in temp_names:
Evtimes[evname].append(solver.t)
xv = solver.y
av = array(avals)
Evpoints[evname].append(concatenate((xv, av)))
do_termevs = []
if termevsflagged != []:
# only record events if they have not been previously
# flagged within their event interval
for e in termevsflagged:
prevevt_time = lastevtime[e[0]]
## print "Event %s flagged."%e[0]
## print " ... last time was ", prevevt_time
## print " ... event interval = ", e[1].eventinterval
## print " ... t = %f, dt = %f"%(solver.t, dt)
if prevevt_time is None:
ignore_ev = False
else:
## print " ... comparison = %f < %f"%(solver.t-dt-prevevt_time, e[1].eventinterval)
if solver.t-dt-prevevt_time < e[1].eventinterval:
ignore_ev = True
## print "Euler ignore ev"
else:
ignore_ev = False
if not ignore_ev:
do_termevs.append(e)
if len(do_termevs) > 0:
# >= 1 active terminal event flagged at this time point
evnames = [ev[0] for ev in do_termevs]
self.diagnostics.warnings.append((W_TERMEVENT, \
(solver.t, evnames)))
first_found_t = solver.t
for evname in evnames:
Evtimes[evname].append(solver.t)
xv = solver.y
av = array(avals)
Evpoints[evname].append(concatenate((xv, av)))
# break while loop after appending t, x
breakwhile = True
# after events have had a chance to be detected at a state boundary
# we check for any that have not been caught by an event (will be
# much less accurately determined)
if not breakwhile:
# only here if a terminal event hasn't just flagged
for xi in range(self.dimension):
if not self.contains(depdomains[xi],
solver.y[xi],
self.checklevel):
self.diagnostics.warnings.append((W_TERMSTATEBD,
(solver.t,
xnames[xi],solver.y[xi],
depdomains[xi].get())))
breakwhile = True
break # for loop
if breakwhile:
break # while loop
alltData.append(solver.t)
if do_poly:
dxvals = rhsfn(solver.t, solver.y, extralist)
for xi, xname in enumerate(xnames):
allxDataDict[xname].append(solver.y[xi])
alldxDataDict[xname].append(dxvals[xi])
else:
for xi, xname in enumerate(xnames):
allxDataDict[xname].append(solver.y[xi])
for aix, aname in enumerate(anames):
allaDataDict[aname].append(avals[aix])
num_points += 1
if not breakwhile:
try:
extralist[self.numpars:listend] = [f(solver.t+self.globalt0,
self.checklevel) \
for f in inputVarList]
except ValueError:
print('External input call caused value out of range error:',\
't = %f' % solver.t)
for f in inputVarList:
if f.diagnostics.hasWarnings():
print('External input variable %s out of range:'%f.name)
print(' t = %r, %s = %r' % (
repr(f.diagnostics.warnings[-1][0]),
f.name,
repr(f.diagnostics.warnings[-1][1])))
raise
except AssertionError:
print('External input call caused t out of range error: t = %f' % solver.t)
raise
solver.set_f_params(extralist)
breakwhile = not solver.successful()
# optional user function (not a method)
self.ufunc_after(self)
# Check that any terminal events found terminated the code correctly
if first_found_t is not None:
# ... then terminal events were found.
try:
if self.diagnostics.warnings[-1][0] not in [W_TERMEVENT,
W_TERMSTATEBD]:
print("t =%f" % solver.t)
print("state =%r" % dict(zip(xnames,solver.y)))
raise RuntimeError("Event finding code for terminal event "
"failed in Generator " + self.name + \
": try decreasing eventdelay or "
"eventinterval below eventtol, or the "
"atol and rtol parameters")
except IndexError:
info(self.diagnostics.outputStats, "Output statistics")
print("t =%f" % solver.t)
print("x =%f" % solver.y)
raise RuntimeError("Event finding failed in Generator " + \
self.name + ": try decreasing eventdelay "
"or eventinterval below eventtol")
# Package up computed trajectory in Variable variables
# Add external inputs warnings to self.diagnostics.warnings, if any
for f in inputVarList:
for winfo in f.diagnostics.warnings:
self.diagnostics.warnings.append((W_NONTERMSTATEBD,
(winfo[0], f.name, winfo[1],
f.depdomain.get())))
# check for non-unique terminal event
termcount = 0
for (w,i) in self.diagnostics.warnings:
if w == W_TERMEVENT or w == W_TERMSTATEBD:
termcount += 1
if termcount > 1:
self.diagnostics.errors.append((E_NONUNIQUETERM,
(alltData[-1], i[1])))
# uncomment the following lines for debugging
# assert len(alltData) == len(allxDataDict.values()[0]) \
# == len(allaDataDict.values()[0]), "Output data size mismatch"
# for val_list in allaDataDict.values():
# assert all([isfinite(x) for x in val_list])
# Create variables (self.variables contains no actual data)
# These versions of the variables are only final if no non-terminal
# events need to be inserted.
variables = copyVarDict(self.variables)
for x in xnames:
if len(alltData) > 1:
if do_poly:
xvals = array([allxDataDict[x], alldxDataDict[x]]).T
interp = PiecewisePolynomial(alltData, xvals, 2)
else:
xvals = allxDataDict[x]
interp = interp1d(alltData, xvals)
variables[x] = Variable(interp, 't', x, x)
else:
print("Error in Generator:%s" % self.name)
print("t = %r" % alltData)
print("x = %r" % allxDataDict)
raise PyDSTool_ValueError("Fewer than 2 data points computed")
for a in anames:
if len(alltData) > 1:
variables[a] = Variable(interp1d(alltData, allaDataDict[a]),
't', a, a)
else:
print("Error in Generator:%s" % self.name)
print("t = %r" % alltData)
print("x = %r" % allxDataDict)
raise PyDSTool_ValueError("Fewer than 2 data points computed")
self.diagnostics.outputStats = {'last_step': dt,
'num_fcns': num_points,
'num_steps': num_points,
'errorStatus': errcode
}
if solver.successful():
#self.validateSpec()
for evname, evtlist in Evtimes.items():
try:
self.eventstruct.Evtimes[evname].extend([et+self.globalt0 \
for et in evtlist])
except KeyError:
self.eventstruct.Evtimes[evname] = [et+self.globalt0 \
for et in evtlist]
# build event pointset information (reset previous trajectory's)
self.trajevents = {}
for (evname, ev) in eventslist:
evpt = Evpoints[evname]
if evpt == []:
self.trajevents[evname] = None
else:
evpt = transpose(array(evpt))
self.trajevents[evname] = Pointset({'coordnames': xnames+anames,
'indepvarname': 't',
'coordarray': evpt,
'indepvararray': Evtimes[evname],
'indepvartype': float})
self.defined = True
return Trajectory(trajname, list(variables.values()),
abseps=self._abseps, globalt0=self.globalt0,
checklevel=self.checklevel,
FScompatibleNames=self._FScompatibleNames,
FScompatibleNamesInv=self._FScompatibleNamesInv,
events=self.trajevents,
modelNames=self.name,
modelEventStructs=self.eventstruct)
else:
try:
self.diagnostics.errors.append((E_COMPUTFAIL, (solver.t,
self.diagnostics._errorcodes[errcode])))
except TypeError:
# e.g. when errcode has been used to return info list
print("Error information: %d" % errcode)
self.diagnostics.errors.append((E_COMPUTFAIL, (solver.t,
self.diagnostics._errorcodes[0])))
self.defined = False
def __init__(self, kw):
"""Use the nobuild key to postpone building of the library, e.g. in
order to provide additional build options to makeLibSource and
compileLib methods or to make changes to the C code by hand.
No build options can be specified otherwise."""
# Building is just doing make
if 'nobuild' in kw:
nobuild = kw['nobuild']
del kw['nobuild']
else:
nobuild = False
ODEsystem.__init__(self, kw)
self._solver = None
assert self.funcspec.targetlang == 'matlab', \
('Wrong target language for functional specification. '
'matlab needed for this class')
assert isinstance(
self.funcspec,
RHSfuncSpec), ('ADMC++ '
'requires RHSfuncSpec type to proceed')
assert not self.inputs, \
'ADMC++ does not support external inputs feature'
self._errorcodes = {}
self._paraminfo = {}
self.vftype = 'vfieldts'
# currently the final four of these params are for event handling
# NEED TO CHECK WHICH ONES ARE SUPPORTED BY ADMC -- LOOKS LIKE EVTOLS ONLY FOR NOW
# HACK: vftype is alg param for now, tells us whether parent class is hybridvf, vfieldts, etc.
algparams_def = {'evtols': 0.0001, 'vftype': 'vfieldts'}
# Remove this later
for k, v in algparams_def.items():
if k not in self.algparams:
self.algparams[k] = v
# verify that no additional keys are present in algparams, after
# defaults are added above
if len(self.algparams) != len(algparams_def):
raise ValueError("Invalid keys present in algparams argument: " \
+ str(remain(self.algparams.keys(),algparams_def.keys())))
thisplatform = platform.system()
self._compilation_tempdir = os.path.join(os.getcwd(), "admcpp_temp")
if not os.path.isdir(self._compilation_tempdir):
try:
assert not os.path.isfile(self._compilation_tempdir), \
"A file already exists with the same name"
os.mkdir(self._compilation_tempdir)
except:
print("Could not create compilation temp directory " + \
self._compilation_tempdir)
raise
# ADMC targets must go in their own directories with appropriate names
self._model_dir = "@" + self.name
self._target_dir = os.path.join(self._compilation_tempdir,
self._model_dir)
# Make the target directory
if not os.path.isdir(self._target_dir):
try:
assert not os.path.isfile(self._target_dir), \
"A file already exists with the same name"
os.mkdir(self._target_dir)
except:
print("Could not creat target ADMC model directory " + \
self._target_dir)
raise
""" An ADMC model has the following files:
vfield.m -- contains code for the RHS of the vector field
set.m -- a generic method that overload matlab's set method; only need to insert vfield name
get.m -- a generic method that overloads matlab's get method; only need to insert appropriate parent name
"""
# model.m, get.m, set.m, vfield.m are minimal files required. TO DO: EVENTS
self._model_file = self.name + ".m"
self._ic_file = self.name + "_ics.m"
self._param_file = self.name + "_params.m"
self._set_file = "set.m"
self._get_file = "get.m"
self._vfield_file = "vfield.m"
self._events_file = "events.m"
self._vf_filename_ext = "_" + self._model_file[:-2]
if not nobuild:
self.makeLibSource()
else:
print("Build the library using the makeLib method, or in ")
print("stages using the makeLibSource and compileLib methods.")
def compute(self, trajname, dirn='f', ics=None):
continue_integ = ODEsystem.prepDirection(self, dirn)
if self._dircode == -1:
raise NotImplementedError('Backwards integration is not implemented')
if ics is not None:
self.set(ics=ics)
self.validateICs()
self.diagnostics.clearWarnings()
self.diagnostics.clearErrors()
pnames = sortedDictKeys(self.pars)
xnames = self._var_ixmap # ensures correct order
# Check i.c.'s are well defined (finite)
self.checkInitialConditions()
if self.algparams['stiff']:
methstr = 'bdf'
methcode = 2
else:
methstr = 'adams'
methcode = 1
haveJac = int(self.haveJacobian())
if isinstance(self.algparams['atol'], list):
if len(self.algparams['atol']) != self.dimension:
raise ValueError('atol list must have same length as phase '
'dimension')
else:
atol = self.algparams['atol']
self.algparams['atol'] = [atol for dimix in range(self.dimension)]
indepdom0, indepdom1 = self.indepvariable.depdomain.get()
if continue_integ:
if indepdom0 > self._solver.t:
print("Previous end time is %f"%self._solver.t)
raise ValueError("Start time not correctly updated for "
"continuing orbit")
x0 = self._solver.y
indepdom0 = self._solver.t
self.indepvariable.depdomain.set((indepdom0,indepdom1))
else:
x0 = sortedDictValues(self.initialconditions,
self.funcspec.vars)
t0 = indepdom0
if self.algparams['use_special']:
tmesh_special = list(self.algparams['specialtimes'])
if continue_integ:
if self._solver.t not in tmesh_special:
raise ValueError("Invalid time to continue integration:"
"it is not in 'special times'")
tmesh_special = tmesh_special[tmesh_special.index(self._solver.t):]
try:
dt = min([tmesh_special[1]-t0, self.algparams['init_step']])
except:
raise ValueError("Invalid list of special times")
if not isincreasing(tmesh_special):
raise ValueError("special times must be given in increasing "
"order")
if self.indepvariable.depdomain.contains(t0) is notcontained or \
self.indepvariable.depdomain.contains(tmesh_special[-1]) is notcontained:
raise PyDSTool_BoundsError("special times were outside of independent "
"variable bounds")
else:
tmesh_special = []
dt = self.algparams['init_step']
# speed up repeated access to solver by making a temp name for it
solver = self._solver
if solver._integrator is None:
# Banded Jacobians not yet supported
#
# start a new integrator, because method may have been
# switched
solver.set_integrator('vode', method=methstr,
rtol=self.algparams['rtol'],
atol=self.algparams['atol'],
nsteps=self.algparams['max_pts'],
max_step=self.algparams['max_step'],
min_step=self.algparams['min_step'],
first_step=dt/2.,
with_jacobian=haveJac)
else:
solver.with_jacobian = haveJac
# self.mu = lband
# self.ml = uband
solver.rtol = self.algparams['rtol']
solver.atol = self.algparams['atol']
solver.method = methcode
# self.order = order
solver.nsteps = self.algparams['max_pts']
solver.max_step = self.algparams['max_step']
solver.min_step = self.algparams['min_step']
solver.first_step = dt/2.
solver.set_initial_value(x0, t0)
## Broken code for going backwards (doesn't respect 'continue' option
## either)
## if self._dircode == 1:
## solver.set_initial_value(x0, t0)
## else:
## solver.set_initial_value(x0, indepdom1)
# wrap up each dictionary initial value as a singleton list
alltData = [t0]
allxDataDict = dict(zip(xnames, map(listid, x0)))
plist = sortedDictValues(self.pars)
extralist = copy(plist)
if self.inputs:
# inputVarList is a list of Variables
inames = sortedDictKeys(self.inputs)
listend = self.numpars + len(self.inputs)
inputVarList = sortedDictValues(self.inputs)
ilist = _pollInputs(inputVarList, alltData[0]+self.globalt0,
self.checklevel)
else:
ilist = []
inames = []
listend = self.numpars
inputVarList = []
extralist.extend(ilist)
solver.set_f_params(extralist)
if haveJac:
solver.set_jac_params(extralist)
do_poly = self.algparams['poly_interp']
if do_poly:
rhsfn = getattr(self, self.funcspec.spec[1])
dx0 = rhsfn(t0, x0, extralist)
alldxDataDict = dict(zip(xnames, map(listid, dx0)))
auxvarsfn = getattr(self,self.funcspec.auxspec[1])
strict = self.algparams['strictdt']
# Make t mesh if it wasn't given as 'specialtimes'
if not all(isfinite(self.indepvariable.depdomain.get())):
print("Time domain was: %f" % self.indepvariable.depdomain.get())
raise ValueError("Ensure time domain is finite")
if dt == indepdom1 - indepdom0:
# single-step integration required
# special times will not have been set (unless trivially
# they are [indepdom0, indepdom1])
tmesh = [indepdom0, indepdom1]
else:
notDone = True
repeatTol = 10
count = 0
while notDone and count <= repeatTol:
try:
tmesh = self.indepvariable.depdomain.sample(dt,
strict=strict,
avoidendpoints=self.checklevel>2)
notDone = False
except AssertionError:
count += 1
dt = dt/3.0
if count == repeatTol:
raise AssertionError("Supplied time step is too large for "
"selected time interval")
# incorporate tmesh_special, if used, ensuring uniqueness
if tmesh_special != []:
tmesh.extend(tmesh_special)
tmesh = list(unique(tmesh))
tmesh.sort()
if len(tmesh)<=2:
# safety net, in case too few points in mesh
# too few points unless we can add endpoint
if tmesh[-1] != indepdom1:
# dt too large for tmesh to have more than one point
tmesh.append(indepdom1)
if not strict: # get actual time step used
# don't use [0] in case avoided end points
try:
dt = tmesh[2]-tmesh[1]
except IndexError:
# can't avoid end points for such a small mesh
dt = tmesh[1]-tmesh[0]
#if self.eventstruct.query(['lowlevel']) != []:
# raise ValueError("Only high level events can be passed to VODE")
eventslist = self.eventstruct.query(['active', 'notvarlinked'])
termevents = self.eventstruct.query(['term'], eventslist)
# reverse time by reversing mesh doesn't work
## if self._dircode == -1:
## tmesh.reverse()
tmesh.pop(0) # get rid of first entry for initial condition
xnames = self.funcspec.vars
# storage of all auxiliary variable data
allaDataDict = {}
anames = self.funcspec.auxvars
avals = auxvarsfn(t0, x0, extralist)
for aix in range(len(anames)):
aname = anames[aix]
try:
allaDataDict[aname] = [avals[aix]]
except IndexError:
print("\nVODE generator: There was a problem evaluating " \
+ "an auxiliary variable")
print("Debug info: avals (length %d) was %r" % (len(avals), avals))
print("Index out of range was %d" % aix)
print(self.funcspec.auxspec[1])
print(hasattr(self, self.funcspec.auxspec[1]))
print("Args were:%r" % [t0, x0, extralist])
raise
# Initialize signs of event detection objects at IC
self.setEventICs(self.initialconditions, self.globalt0)
if self.inputs:
parsinps = copy(self.pars)
parsinps.update(dict(zip(inames,ilist)))
else:
parsinps = self.pars
if eventslist != []:
dataDict = copy(self.initialconditions)
dataDict.update(dict(zip(anames, avals)))
dataDict['t'] = t0
## Removed this "belt and braces" pre-check because it messes
## up some events in the middle of hybrid regime switches.
## Not sure yet what the problem is. (Oct 2013)
#evsflagged = self.eventstruct.pollHighLevelEvents(None,
# dataDict,
# parsinps,
# eventslist)
#if len(evsflagged) > 0:
# raise RuntimeError("Some events flagged at initial condition")
if continue_integ:
# revert to prevprevsign, since prevsign changed after call
self.eventstruct.resetHighLevelEvents(t0, eventslist, 'prev')
elif self._for_hybrid_DS:
# self._for_hybrid_DS is set internally by HybridModel class
# to ensure not to reset events, because they may be about to
# flag on first step if previous hybrid state was the same
# generator and, for example, two variables are synchronizing
# so that their events get very close together.
# Just reset the starttimes of these events
for evname, ev in eventslist:
ev.starttime = t0
else:
# default state is a one-off call to this generator
self.eventstruct.resetHighLevelEvents(t0, eventslist, None)
self.eventstruct.validateEvents(self.funcspec.vars + \
self.funcspec.auxvars + \
self.funcspec.inputs + \
['t'], eventslist)
# temp storage of first time at which terminal events found
# (this is used for keeping the correct end point of new mesh)
first_found_t = None
# list of precise non-terminal events to be resolved after integration
nontermprecevs = []
evnames = [ev[0] for ev in eventslist]
lastevtime = {}.fromkeys(evnames, None)
# initialize new event info dictionaries
Evtimes = {}
Evpoints = {}
if continue_integ:
for evname in evnames:
try:
# these are in global time, so convert to local time
lastevtime[evname] = self.eventstruct.Evtimes[evname][-1] \
- self.globalt0
except (IndexError, KeyError):
# IndexError: Evtimes[evname] was None
# KeyError: Evtimes does not have key evname
pass
for evname in evnames:
Evtimes[evname] = []
Evpoints[evname] = []
# temp storage for repeatedly used object attributes (for lookup efficiency)
depdomains = dict(zip(range(self.dimension),
[self.variables[xn].depdomain for xn in xnames]))
# Main integration loop
num_points = 0
breakwhile = False
while not breakwhile:
try:
new_t = tmesh.pop(0) # this destroys tmesh for future use
except IndexError:
# empty
break
last_t = solver.t # a record of previous time for use by event detector
try:
errcode = solver.integrate(new_t)
except:
print("Error calling right hand side function:")
self.showSpec()
print("Numerical traceback information (current state, " \
+ "parameters, etc.)")
print("in generator dictionary 'traceback'")
self.traceback = {'vars': dict(zip(xnames,solver.y)),
'pars': dict(zip(pnames,plist)),
'inputs': dict(zip(inames,ilist)),
self.indepvariable.name: new_t}
raise
avals = auxvarsfn(new_t, solver.y, extralist)
# Uncomment the following assertion for debugging
# assert all([isfinite(a) for a in avals]), \
# "Some auxiliary variable values not finite"
if eventslist != []:
dataDict = dict(zip(xnames,solver.y))
dataDict.update(dict(zip(anames,avals)))
dataDict['t'] = new_t
if self.inputs:
parsinps = copy(self.pars)
parsinps.update(dict(zip(inames,
_pollInputs(inputVarList, new_t+self.globalt0,
self.checklevel))))
else:
parsinps = self.pars
evsflagged = self.eventstruct.pollHighLevelEvents(None,
dataDict,
parsinps,
eventslist)
## print new_t, evsflagged
## evsflagged = [ev for ev in evsflagged if solver.t-indepdom0 > ev[1].eventinterval]
termevsflagged = [e for e in termevents if e in evsflagged]
nontermevsflagged = [e for e in evsflagged if e not in termevsflagged]
# register any non-terminating events in the warnings
# list, unless they are 'precise' in which case flag
# them to be resolved after integration completes
if len(nontermevsflagged) > 0:
evnames = [ev[0] for ev in nontermevsflagged]
precEvts = self.eventstruct.query(['precise'],
nontermevsflagged)
prec_evnames = [e[0] for e in precEvts]
# first register non-precise events
nonprecEvts = self.eventstruct.query(['notprecise'],
nontermevsflagged)
nonprec_evnames = [e[0] for e in nonprecEvts]
# only record events if they have not been previously
# flagged within their event interval
if nonprec_evnames != []:
temp_names = []
for evname, ev in nonprecEvts:
prevevt_time = lastevtime[evname]
if prevevt_time is None:
ignore_ev = False
else:
if solver.t-prevevt_time < ev.eventinterval:
ignore_ev = True
else:
ignore_ev = False
if not ignore_ev:
temp_names.append(evname)
lastevtime[evname] = solver.t
self.diagnostics.warnings.append((W_NONTERMEVENT,
(solver.t, temp_names)))
for evname in temp_names:
Evtimes[evname].append(solver.t)
xv = solver.y
av = array(avals)
Evpoints[evname].append(concatenate((xv, av)))
for evname, ev in precEvts:
# only record events if they have not been previously
# flagged within their event interval
prevevt_time = lastevtime[evname]
if prevevt_time is None:
ignore_ev = False
else:
if last_t-prevevt_time < ev.eventinterval:
ignore_ev = True
else:
ignore_ev = False
if not ignore_ev:
nontermprecevs.append((last_t, solver.t, (evname, ev)))
# be conservative as to where the event is, so
# that don't miss any events.
lastevtime[evname] = last_t # solver.t-dt
ev.reset() #ev.prevsign = None #
do_termevs = []
if termevsflagged != []:
# only record events if they have not been previously
# flagged within their event interval
for e in termevsflagged:
prevevt_time = lastevtime[e[0]]
## print "Event %s flagged."%e[0]
## print " ... last time was ", prevevt_time
## print " ... event interval = ", e[1].eventinterval
## print " ... t = %f, dt = %f"%(solver.t, dt)
if prevevt_time is None:
ignore_ev = False
else:
## print " ... comparison = %f < %f"%(solver.t-dt-prevevt_time, e[1].eventinterval)
if last_t-prevevt_time < e[1].eventinterval:
ignore_ev = True
## print "VODE ignore ev"
else:
ignore_ev = False
if not ignore_ev:
do_termevs.append(e)
if len(do_termevs) > 0:
# >= 1 active terminal event flagged at this time point
if all([not ev[1].preciseFlag for ev in do_termevs]):
# then none of the events specify greater accuracy
# register the event in the warnings
evnames = [ev[0] for ev in do_termevs]
self.diagnostics.warnings.append((W_TERMEVENT, \
(solver.t, evnames)))
for evname in evnames:
Evtimes[evname].append(solver.t)
xv = solver.y
av = array(avals)
Evpoints[evname].append(concatenate((xv, av)))
# break while loop after appending t, x
breakwhile = True
else:
# find which are the 'precise' events that flagged
precEvts = self.eventstruct.query(['precise'],
do_termevs)
# these events have flagged once so eventdelay has
# been used. now switch it off while finding event
# precisely (should be redundant after change to
# eventinterval and eventdelay parameters)
evnames = [ev[0] for ev in precEvts]
if first_found_t is None:
## print "first time round at", solver.t
numtries = 0
first_found_t = solver.t
restore_evts = deepcopy(precEvts)
minbisectlimit = min([ev[1].bisectlimit for ev in precEvts])
for ev in precEvts:
ev[1].eventdelay = 0.
else:
numtries += 1
## print "time round: ", numtries
if numtries > minbisectlimit:
self.diagnostics.warnings.append((W_BISECTLIMIT,
(solver.t, evnames)))
breakwhile = True
# get previous time point
if len(alltData)>=1:
# take one step back -> told, which will
# get dt added back to first new meshpoint
# (solver.t is the step *after* the event was
# detected)
told = last_t # solver.t-dt without the loss of precision from subtraction
else:
raise ValueError("Event %s found too "%evnames[0]+\
"close to local start time: try decreasing "
"initial step size (current size is "
"%f @ t=%f)"%(dt,solver.t+self.globalt0))
# absolute tolerance check on event function values (not t)
in_tols = [abs(e[1].fval) < e[1].eventtol for e in precEvts]
if all(in_tols):
## print "Registering event:", dt_min, dt
# register the event in the warnings
self.diagnostics.warnings.append((W_TERMEVENT,
(solver.t, evnames)))
for evname in evnames:
Evtimes[evname].append(solver.t)
xv = solver.y
av = array(avals)
Evpoints[evname].append(concatenate((xv, av)))
# Cannot continue -- dt_min no smaller than
# previous dt. If this is more than the first time
# in this code then have found the event to within
# the minimum 'precise' event's eventtol, o/w need
# to set eventtol smaller.
# Before exiting event-finding loop, reset prevsign
# of flagged events
self.eventstruct.resetHighLevelEvents(0,
precEvts)
breakwhile = True # while loop, but append point first
if not breakwhile:
dt_new = dt/5.0
# calc new tmesh
trangewidth = 2*dt #first_found_t - told
numpoints = int(math.ceil(trangewidth/dt_new))
# choose slightly smaller dt to fit trange exactly
dt = trangewidth/numpoints
tmesh = [told + i*dt for i in range(1, numpoints+1)]
# linspace version is *much* slower for numpoints ~ 10 and 100
#tmesh = list(told+linspace(dt, numpoints*dt, numpoints))
# reset events according to new time mesh,
# setting known previous event state to be their
# "no event found" state
self.eventstruct.resetHighLevelEvents(told,
precEvts,
state='off')
# build new ic with last good values (at t=told)
if len(alltData)>1:
new_ic = [allxDataDict[xname][-1] \
for xname in xnames]
else:
new_ic = x0
# reset integrator
solver.set_initial_value(new_ic, told)
extralist[self.numpars:listend] = _pollInputs(inputVarList,
told+self.globalt0, self.checklevel)
solver.set_f_params(extralist)
# continue integrating over new mesh
continue # while
# after events have had a chance to be detected at a state boundary
# we check for any that have not been caught by an event (will be
# much less accurately determined)
if not breakwhile:
# only here if a terminal event hasn't just flagged
for xi in range(self.dimension):
if not self.contains(depdomains[xi],
solver.y[xi],
self.checklevel):
self.diagnostics.warnings.append((W_TERMSTATEBD,
(solver.t,
xnames[xi],solver.y[xi],
depdomains[xi].get())))
breakwhile = True
break # for loop
if breakwhile:
break # while loop
alltData.append(solver.t)
if do_poly:
dxvals = rhsfn(solver.t, solver.y, extralist)
for xi, xname in enumerate(xnames):
allxDataDict[xname].append(solver.y[xi])
alldxDataDict[xname].append(dxvals[xi])
else:
for xi, xname in enumerate(xnames):
allxDataDict[xname].append(solver.y[xi])
for aix, aname in enumerate(anames):
allaDataDict[aname].append(avals[aix])
num_points += 1
if not breakwhile:
try:
extralist[self.numpars:listend] = [f(solver.t+self.globalt0,
self.checklevel) \
for f in inputVarList]
except ValueError:
print('External input call caused value out of range error:',\
't = %f' % solver.t)
for f in inputVarList:
if f.diagnostics.hasWarnings():
print('External input variable %s out of range:'%f.name)
print(' t = %r, %s, %r' % (repr(f.diagnostics.warnings[-1][0]),
f.name, repr(f.diagnostics.warnings[-1][1])))
raise
except AssertionError:
print('External input call caused t out of range error: t = %f' % solver.t)
raise
solver.set_f_params(extralist)
breakwhile = not solver.successful()
# Check that any terminal events found terminated the code correctly
if first_found_t is not None:
# ... then terminal events were found. Those that were 'precise' had
# their 'eventdelay' attribute temporarily set to 0. It now should
# be restored.
for evname1, ev1 in termevents:
# restore_evts are copies of the originally flagged 'precise'
# events
for evname2, ev2 in restore_evts:
if evname2 == evname1:
ev1.eventdelay = ev2.eventdelay
try:
if self.diagnostics.warnings[-1][0] not in [W_TERMEVENT,
W_TERMSTATEBD]:
print("t =%f" % solver.t)
print("state =%r" % dict(zip(xnames,solver.y)))
raise RuntimeError("Event finding code for terminal event "
"failed in Generator " + self.name + \
": try decreasing eventdelay or "
"eventinterval below eventtol, or the "
"atol and rtol parameters")
except IndexError:
info(self.diagnostics.outputStats, "Output statistics")
print("t =%f" % solver.t)
print("x =%f" % solver.y)
raise RuntimeError("Event finding failed in Generator " + \
self.name + ": try decreasing eventdelay "
"or eventinterval below eventtol, or the "
"atol and rtol parameters")
# Package up computed trajectory in Variable variables
# Add external inputs warnings to self.diagnostics.warnings, if any
for f in inputVarList:
for winfo in f.diagnostics.warnings:
self.diagnostics.warnings.append((W_NONTERMSTATEBD,
(winfo[0], f.name, winfo[1],
f.depdomain.get())))
# check for non-unique terminal event
termcount = 0
for (w,i) in self.diagnostics.warnings:
if w == W_TERMEVENT or w == W_TERMSTATEBD:
termcount += 1
if termcount > 1:
self.diagnostics.errors.append((E_NONUNIQUETERM,
(alltData[-1], i[1])))
# uncomment the following lines for debugging
# assert len(alltData) == len(allxDataDict.values()[0]) \
# == len(allaDataDict.values()[0]), "Output data size mismatch"
# for val_list in allaDataDict.values():
# assert all([isfinite(x) for x in val_list])
# Create variables (self.variables contains no actual data)
# These versions of the variables are only final if no non-terminal
# events need to be inserted.
variables = copyVarDict(self.variables)
for x in xnames:
if len(alltData) > 1:
if do_poly:
xvals = array([allxDataDict[x], alldxDataDict[x]]).T
interp = PiecewisePolynomial(alltData, xvals, 2)
else:
xvals = allxDataDict[x]
interp = interp1d(alltData, xvals)
variables[x] = Variable(interp, 't', x, x)
else:
print("Error in Generator:%s" % self.name)
print("t = %r" % alltData)
print("x = %r" % allxDataDict)
raise PyDSTool_ValueError("Fewer than 2 data points computed")
for a in anames:
if len(alltData) > 1:
variables[a] = Variable(interp1d(alltData, allaDataDict[a]),
't', a, a)
else:
print("Error in Generator:%s" % self.name)
print("t = %r" % alltData)
print("x = %r" % allxDataDict)
raise PyDSTool_ValueError("Fewer than 2 data points computed")
# Resolve non-terminal 'precise' events that were flagged, using the
# variables created. Then, add them to a new version of the variables.
ntpe_tdict = {}
for (et0,et1,e) in nontermprecevs:
lost_evt = False
# problem if eventinterval > et1-et0 !!
# was: search_dt = max((et1-et0)/5,e[1].eventinterval)
search_dt = (et1-et0)/5
try:
et_precise_list = e[1].searchForEvents(trange=[et0,et1],
dt=search_dt,
checklevel=self.checklevel,
parDict=self.pars,
vars=variables,
inputs=self.inputs,
abseps=self._abseps,
eventdelay=False,
globalt0=self.globalt0)
except (ValueError, PyDSTool_BoundsError):
# dt too large for trange, e.g. if event tol is smaller than time mesh
et_precise_list = [(et0, (et0, et1))]
if et_precise_list == []:
lost_evt = True
for et_precise in et_precise_list:
if et_precise[0] is not None:
if et_precise[0] in ntpe_tdict:
# add event name at this time (that already exists in the dict)
ntpe_tdict[et_precise[0]].append(e[0])
else:
# add event name at this time (when time is not already in dict)
ntpe_tdict[et_precise[0]] = [e[0]]
else:
lost_evt = True
if lost_evt:
print("Error: A non-terminal, 'precise' event was lost -- did you reset", end=' ')
print("events prior to integration?")
raise PyDSTool_ExistError("Internal error: A non-terminal, "
"'precise' event '%s' was lost after integration!"%e[0])
# add non-terminal event points to variables
if ntpe_tdict != {}:
# find indices of times at which event times will be inserted
tix = 0
evts = list(ntpe_tdict.keys())
evts.sort()
for evix in range(len(evts)):
evt = evts[evix]
evnames = ntpe_tdict[evt]
self.diagnostics.warnings.append((W_NONTERMEVENT, (evt, evnames)))
xval = [variables[x](evt) for x in xnames]
ilist = _pollInputs(inputVarList, evt+self.globalt0,
self.checklevel)
# find accurate dx and aux vars value at this time
if do_poly:
dxval = rhsfn(evt, xval, plist+ilist)
aval = list(auxvarsfn(evt, xval, plist+ilist))
for evname in evnames:
Evtimes[evname].append(evt)
Evpoints[evname].append(array(xval+aval))
tcond = less_equal(alltData[tix:], evt).tolist()
try:
tix = tcond.index(0) + tix # lowest index for t > evt
do_insert = (alltData[tix-1] != evt)
except ValueError:
# evt = last t value so no need to add it
do_insert = False
if do_insert:
alltData.insert(tix, evt)
for ai, a in enumerate(anames):
allaDataDict[a].insert(tix, aval[ai])
if do_poly:
for xi, x in enumerate(xnames):
allxDataDict[x].insert(tix, xval[xi])
alldxDataDict[x].insert(tix, dxval[xi])
else:
for xi, x in enumerate(xnames):
allxDataDict[x].insert(tix, xval[xi])
for x in xnames:
if do_poly:
# use asarray in case points added to sequences as a list
xvals = array([asarray(allxDataDict[x]),
asarray(alldxDataDict[x])]).T
interp = PiecewisePolynomial(alltData, xvals, 2)
else:
xvals = allxDataDict[x]
interp = interp1d(alltData, xvals)
variables[x] = Variable(interp, 't', x, x)
for a in anames:
variables[a] = Variable(interp1d(alltData, allaDataDict[a]),
't', a, a)
self.diagnostics.outputStats = {'last_step': dt,
'num_fcns': num_points,
'num_steps': num_points,
'errorStatus': errcode
}
if solver.successful():
#self.validateSpec()
for evname, evtlist in Evtimes.items():
try:
self.eventstruct.Evtimes[evname].extend([et+self.globalt0 \
for et in evtlist])
except KeyError:
self.eventstruct.Evtimes[evname] = [et+self.globalt0 \
for et in evtlist]
# build event pointset information (reset previous trajectory's)
self.trajevents = {}
for (evname, ev) in eventslist:
evpt = Evpoints[evname]
if evpt == []:
self.trajevents[evname] = None
else:
evpt = transpose(array(evpt))
self.trajevents[evname] = Pointset({'coordnames': xnames+anames,
'indepvarname': 't',
'coordarray': evpt,
'indepvararray': Evtimes[evname],
'indepvartype': float})
self.defined = True
return Trajectory(trajname, list(variables.values()),
abseps=self._abseps, globalt0=self.globalt0,
checklevel=self.checklevel,
FScompatibleNames=self._FScompatibleNames,
FScompatibleNamesInv=self._FScompatibleNamesInv,
events=self.trajevents,
modelNames=self.name,
modelEventStructs=self.eventstruct)
else:
try:
self.diagnostics.errors.append((E_COMPUTFAIL, (solver.t,
self.diagnostics._errorcodes[errcode])))
except TypeError:
# e.g. when errcode has been used to return info list
print("Error information: %d" % errcode)
self.diagnostics.errors.append((E_COMPUTFAIL, (solver.t,
self.diagnostics._errorcodes[0])))
self.defined = False
def __init__(self, kw):
"""Use the nobuild key to postpone building of the library, e.g. in
order to provide additional build options to makeLibSource and
compileLib methods or to make changes to the C code by hand.
No build options can be specified otherwise."""
# delete because not covered in ODEsystem
nobuild = kw.pop('nobuild', False)
ODEsystem.__init__(self, kw)
self.diagnostics.outputStatsInfo = {
'last_step': 'Predicted step size of the last accepted step (useful for a subsequent call to dop853).',
'num_steps': 'Number of used steps.',
'num_accept': 'Number of accepted steps.',
'num_reject': 'Number of rejected steps.',
'num_fcns': 'Number of function calls.',
'errorStatus': 'Error status on completion.'
}
self.diagnostics._errorcodes = {
0 : 'Unrecognized error code returned (see stderr output)',
-1 : 'input is not consistent',
-2 : 'larger nmax is needed',
2 : 'larger nmax or maxevtpts is probably needed (error raised by solout)',
-3 : 'step size becomes too small',
-4 : 'the problem is probably stiff (interrupted)',
-8 : 'The solution exceeded a magbound (poor choice of initial step)'}
self._solver = None
algparams_def = {'poly_interp': False,
'init_step': 0,
'max_step': 0,
'rtol': [1e-9 for i in range(self.dimension)],
'atol': [1e-12 for i in range(self.dimension)],
'fac1': 0.2,
'fac2': 10.0,
'safety': 0.9,
'beta': 0.04,
'max_pts': 10000,
'refine': 0,
'maxbisect': [], # for events
'maxevtpts': 1000, # for events
'eventInt': [], # set using setEventInterval only
'eventDelay': [], # set using setEventDelay only
'eventTol': [], # set using setEventTol only
'use_special': 0,
'specialtimes': [],
'check_aux': 1,
'extraspace': 100,
'verbose': 0,
'hasJac': 0,
'hasJacP': 0,
'magBound': 1e7,
'boundsCheckMaxSteps': 1000,
'checkBounds': self.checklevel
}
for k, v in algparams_def.items():
if k not in self.algparams:
self.algparams[k] = v
# verify that no additional keys are present in algparams, after
# defaults are added above
if len(self.algparams) != len(algparams_def):
raise ValueError("Invalid keys present in algparams argument: " \
+ str(remain(self.algparams.keys(),algparams_def.keys())))
if self.haveMass():
raise ValueError("Mass matrix declaration is incompatible "
"with Dopri853 integrator system specification")
self._prepareEventSpecs()
self._inputVarList = []
self._inputTimeList = []
if nobuild:
print("Build the library using the makeLib method, or in ")
print("stages using the makeLibSource and compileLib methods.")
else:
self.makeLib()
def compute(self, trajname, dirn='f'):
continue_integ = ODEsystem.prepDirection(self, dirn)
if self._dircode == -1:
raise NotImplementedError, (
'Backwards integration is not implemented')
# validate spec if there exists a prior trajectory computation
if self.defined:
self.validateSpec()
self.validateICs()
self.clearWarnings()
self.clearErrors()
pnames = sortedDictKeys(self.pars)
xnames = self._var_ixmap # ensures correct order
# Check i.c.'s are well defined (finite)
self.checkInitialConditions()
if self._algparams['stiff']:
methstr = 'bdf'
methcode = 2
else:
methstr = 'adams'
methcode = 1
if self.haveJacobian():
haveJac = 1
else:
haveJac = 0
if isinstance(self._algparams['atol'], list):
if len(self._algparams['atol']) != self.dimension:
raise ValueError, 'atol list must have same length as phase dimension'
else:
atol = self._algparams['atol']
self._algparams['atol'] = [
atol for dimix in xrange(self.dimension)
]
indepdom0 = self.indepvariable.depdomain.get(0)
indepdom1 = self.indepvariable.depdomain.get(1)
if continue_integ:
if self._tdata[0] != self._solver.t:
print "Previous end time is %f" % self._solver.t
raise ValueError, \
"Start time not correctly updated for continuing orbit"
x0 = self._solver.y
indepdom0 = self._solver.t
else:
x0 = sortedDictValues(self.initialconditions, self.funcspec.vars)
if self._solver._integrator is None:
# Banded Jacobians not yet supported
#
# start a new integrator, because method may have been
# switched
self._solver.set_integrator(
'vode',
method=methstr,
rtol=self._algparams['rtol'],
atol=self._algparams['atol'],
nsteps=self._algparams['max_pts'],
max_step=self._algparams['max_step'],
min_step=self._algparams['min_step'],
first_step=self._algparams['init_step'],
with_jacobian=haveJac)
# speed up repeated access to solver by making a temp name for it
solver = self._solver
else:
# speed up repeated access to solver by making a temp name for it
solver = self._solver
solver.with_jacobian = haveJac
# self.mu = lband
# self.ml = uband
solver.rtol = self._algparams['rtol']
solver.atol = self._algparams['atol']
solver.method = methcode
# self.order = order
solver.nsteps = self._algparams['max_pts']
solver.max_step = self._algparams['max_step']
solver.min_step = self._algparams['min_step']
solver.first_step = self._algparams['init_step']
solver.set_initial_value(x0, indepdom0)
## if self._dircode == 1:
## solver.set_initial_value(x0, indepdom0)
## else:
## solver.set_initial_value(x0, indepdom1)
# wrap up each dictionary initial value as a singleton list
alltData = [indepdom0]
allxDataDict = dict(zip(xnames, map(listid, x0)))
plist = sortedDictValues(self.pars)
extralist = copy(plist)
if self.inputs:
# inputVarList is a list of Variables
inames = sortedDictKeys(self.inputs)
listend = self.numpars + len(self.inputs)
inputVarList = sortedDictValues(self.inputs)
ilist = _pollInputs(inputVarList, alltData[0] + self.globalt0,
self.checklevel)
else:
ilist = []
inames = []
listend = self.numpars
inputVarList = []
extralist.extend(ilist)
solver.set_f_params(extralist)
if haveJac:
solver.set_jac_params(extralist)
dt = self._algparams['init_step']
strict = self._algparams['strictdt']
# Make t mesh
if not all(isfinite(self.indepvariable.depdomain.get())):
print "Time domain was: ", self.indepvariable.depdomain.get()
raise ValueError, "Ensure time domain is finite"
if dt == indepdom1 - indepdom0:
# single-step integration required
tmesh = [indepdom0, indepdom1]
else:
notDone = True
repeatTol = 10
count = 0
while notDone and count <= repeatTol:
try:
tmesh = self.indepvariable.depdomain.uniformSample(
dt, strict=strict, avoidendpoints=self.checklevel > 2)
notDone = False
except AssertionError:
count += 1
dt = dt / 3.0
if count == repeatTol:
raise AssertionError, \
("supplied time step is too large for selected time"
" interval")
if len(tmesh) <= 2:
# safety net, in case too few points in mesh
# too few points unless we can add endpoint
if tmesh[-1] != indepdom1:
# dt too large for tmesh to have more than one point
tmesh.append(indepdom1)
if not strict: # get actual time step used
# don't use [0] in case avoided end points
dt = tmesh[2] - tmesh[1]
if self.eventstruct.query(['lowlevel']) != []:
raise ValueError, "Only high level events can be passed to VODE"
eventslist = self.eventstruct.query(
['highlevel', 'active', 'notvarlinked'])
termevents = self.eventstruct.query(['term'], eventslist)
# reverse time by reversing mesh doesn't work
## if self._dircode == -1:
## tmesh.reverse()
tmesh.pop(0) # get rid of first entry for initial condition
# per-iteration storage of variable data (initial values are irrelevant)
xDataDict = {}
xnames = self.funcspec.vars
# storage of all auxiliary variable data
allaDataDict = {}
anames = self.funcspec.auxvars
avals = apply(getattr(self, self.funcspec.auxspec[1]),
[indepdom0, x0, extralist])
for aix in range(len(anames)):
aname = anames[aix]
try:
allaDataDict[aname] = [avals[aix]]
except IndexError:
print "\nVODE generator: There was a problem evaluating " \
+ "an auxiliary variable"
print "Debug info: avals (length", len(avals), ") was ", avals
print "Index out of range was ", aix
print self.funcspec.auxspec[1]
print hasattr(self, self.funcspec.auxspec[1])
print "Args were:", [indepdom0, x0, extralist]
raise
# Initialize signs of event detection objects at IC
dataDict = copy(self.initialconditions)
dataDict.update(dict(zip(anames, avals)))
dataDict['t'] = indepdom0
self.setEventICs(self.initialconditions, self.globalt0)
if self.inputs:
parsinps = copy(self.pars)
parsinps.update(dict(zip(inames, ilist)))
else:
parsinps = self.pars
if eventslist != []:
evsflagged = self.eventstruct.pollHighLevelEvents(
None, dataDict, parsinps, eventslist)
if len(evsflagged) > 0:
raise RuntimeError, "Some events flagged at initial condition"
if continue_integ:
# revert to prevprevsign, since prevsign changed after call
self.eventstruct.resetHighLevelEvents(indepdom0, eventslist,
'prev')
else:
self.eventstruct.resetHighLevelEvents(indepdom0,
eventslist) #, 'off')
self.eventstruct.validateEvents(self.funcspec.vars + \
self.funcspec.auxvars + \
self.funcspec.inputs + \
['t'], eventslist)
# temp storage of first time at which terminal events found
# (this is used for keeping the correct end point of new mesh)
first_found_t = None
# list of precise non-terminal events to be resolved after integration
nontermprecevs = []
evnames = [ev[0] for ev in eventslist]
lastevtime = {}.fromkeys(evnames, None)
# initialize new event info dictionaries
Evtimes = {}
Evpoints = {}
if continue_integ:
for evname in evnames:
try:
# these are in global time, so convert to local time
lastevtime[evname] = self.eventstruct.Evtimes[evname][
-1] - self.globalt0
except (IndexError, KeyError):
# IndexError: Evtimes[evname] was None
# KeyError: Evtimes does not have key evname
pass
for evname in evnames:
Evtimes[evname] = []
Evpoints[evname] = []
# temp storage for repeatedly used object attributes (for lookup efficiency)
depdomains = {}
for xi in xrange(self.dimension):
depdomains[xi] = self.variables[xnames[xi]].depdomain
# Main integration loop
num_points = 0
breakwhile = False
while not breakwhile:
try:
new_t = tmesh.pop(0) # this destroys tmesh for future use
except IndexError:
break
try:
errcode = solver.integrate(new_t)
except:
print "Error calling right hand side function:"
self.showSpec()
print "Numerical traceback information (current state, " \
+ "parameters, etc.)"
print "in generator dictionary 'traceback'"
self.traceback = {
'vars': dict(zip(xnames, solver.y)),
'pars': dict(zip(pnames, plist)),
'inputs': dict(zip(inames, ilist)),
self.indepvariable.name: new_t
}
raise
for xi in xrange(self.dimension):
xDataDict[xnames[xi]] = solver.y[xi]
if not self.contains(depdomains[xi], solver.y[xi],
self.checklevel):
self.warnings.append(
(W_TERMSTATEBD, (solver.t, xnames[xi], solver.y[xi],
depdomains[xi].get())))
breakwhile = True
break # for loop
if breakwhile:
break
avals = apply(
getattr(self, self.funcspec.auxspec[1]),
[new_t, sortedDictValues(xDataDict), extralist])
# Uncomment the following assertion for debugging
# assert all([isfinite(a) for a in avals]), \
# "Some auxiliary variable values not finite"
aDataDict = dict(zip(anames, avals))
if eventslist != []:
dataDict = copy(xDataDict)
dataDict.update(aDataDict)
dataDict['t'] = new_t
if self.inputs:
parsinps = copy(self.pars)
parsinps.update(
dict(
zip(
inames,
## extralist[self.numpars:listend])))
_pollInputs(inputVarList,
new_t + self.globalt0,
self.checklevel))))
else:
parsinps = self.pars
evsflagged = self.eventstruct.pollHighLevelEvents(
None, dataDict, parsinps, eventslist)
## print new_t, evsflagged
# evsflagged = [ev for ev in evsflagged if solver.t-indepdom0 > ev[1].eventinterval]
termevsflagged = filter(lambda e: e in evsflagged, termevents)
nontermevsflagged = filter(lambda e: e not in termevsflagged,
evsflagged)
# register any non-terminating events in the warnings
# list, unless they are 'precise' in which case flag
# them to be resolved after integration completes
if len(nontermevsflagged) > 0:
evnames = [ev[0] for ev in nontermevsflagged]
precEvts = self.eventstruct.query(['precise'],
nontermevsflagged)
prec_evnames = [e[0] for e in precEvts]
# first register non-precise events
nonprec_evnames = remain(evnames, prec_evnames)
# only record events if they have not been previously
# flagged within their event interval
if nonprec_evnames != []:
temp_names = []
for evname in nonprec_evnames:
prevevt_time = lastevtime[evname]
if prevevt_time is None:
ignore_ev = False
else:
if solver.t - prevevt_time < e[1].eventinterval:
ignore_ev = True
else:
ignore_ev = False
if not ignore_ev:
temp_names.append(evname)
lastevtime[evname] = solver.t
self.warnings.append(
(W_NONTERMEVENT, (solver.t, temp_names)))
for evname in temp_names:
Evtimes[evname].append(solver.t)
Evpoints[evname].append(solver.y)
for e in precEvts:
# only record events if they have not been previously
# flagged within their event interval
prevevt_time = lastevtime[e[0]]
if prevevt_time is None:
ignore_ev = False
else:
if solver.t - dt - prevevt_time < e[
1].eventinterval:
ignore_ev = True
else:
ignore_ev = False
if not ignore_ev:
nontermprecevs.append((solver.t - dt, solver.t, e))
# be conservative as to where the event is, so
# that don't miss any events.
lastevtime[e[0]] = solver.t - dt
e[1].reset() #e[1].prevsign = None #
do_termevs = []
if termevsflagged != []:
# only record events if they have not been previously
# flagged within their event interval
for e in termevsflagged:
prevevt_time = lastevtime[e[0]]
## print "Event %s flagged."%e[0]
## print " ... last time was ", prevevt_time
## print " ... event interval = ", e[1].eventinterval
## print " ... t = %f, dt = %f"%(solver.t, dt)
if prevevt_time is None:
ignore_ev = False
else:
## print " ... comparison = %f < %f"%(solver.t-dt-prevevt_time, e[1].eventinterval)
if solver.t - dt - prevevt_time < e[
1].eventinterval:
ignore_ev = True
## print "VODE ignore ev"
else:
ignore_ev = False
if not ignore_ev:
do_termevs.append(e)
if len(do_termevs) > 0:
# >= 1 active terminal event flagged at this time point
if all([not ev[1].preciseFlag for ev in do_termevs]):
# then none of the events specify greater accuracy
# register the event in the warnings
evnames = [ev[0] for ev in do_termevs]
self.warnings.append((W_TERMEVENT, \
(solver.t, evnames)))
for evname in evnames:
Evtimes[evname].append(solver.t)
Evpoints[evname].append(solver.y)
breakwhile = True # break while loop after appending t, x
else:
# find which are the 'precise' events that flagged
precEvts = self.eventstruct.query(['precise'],
do_termevs)
# these events have flagged once so eventdelay has
# been used. now switch it off while finding event
# precisely (should be redundant after change to
# eventinterval and eventdelay parameters)
evnames = [ev[0] for ev in precEvts]
if first_found_t is None:
## print "first time round at", solver.t
numtries = 0
first_found_t = solver.t
restore_evts = deepcopy(precEvts)
minbisectlimit = min(
[ev[1].bisectlimit for ev in precEvts])
for ev in precEvts:
ev[1].eventdelay = 0.
else:
numtries += 1
## print "time round: ", numtries
if numtries > minbisectlimit:
self.warnings.append(
(W_BISECTLIMIT, (solver.t, evnames)))
breakwhile = True
# find minimum eventtol in precEvts
dt_min = min([e[1].eventtol for e in precEvts])
# get previous time point
if len(alltData) >= 1:
# take one step back -> told, which will
# get dt added back to first new meshpoint
# (solver.t is the step *after* the event was
# detected)
told = solver.t - dt
else:
raise ValueError("Event %s found too "%evnames[0]+\
"close to local start time: try decreasing "
"initial step size (current size is "
"%f @ t=%f)"%(dt,solver.t+self.globalt0))
if dt_min >= dt:
## print "Registering event:", dt_min, dt
# register the event in the warnings
self.warnings.append(
(W_TERMEVENT, (solver.t, evnames)))
for evname in evnames:
Evtimes[evname].append(solver.t)
Evpoints[evname].append(solver.y)
# Cannot continue -- dt_min no smaller than
# previous dt. If this is more than the first time
# in this code then have found the event to within
# the minimum 'precise' event's eventtol, o/w need
# to set eventtol smaller.
breakwhile = True # while loop
if not breakwhile:
dt_new = dt / 5.0
# calc new tmesh
trangewidth = 2 * dt #first_found_t - told
numpoints = int(math.ceil(trangewidth / dt_new))
# choose slightly smaller dt to fit trange exactly
dt = trangewidth / numpoints
tmesh = [
told + i * dt
for i in xrange(1, numpoints + 1)
]
# reset events according to new time mesh,
# setting known previous event state to be their
# "no event found" state
self.eventstruct.resetHighLevelEvents(told,
precEvts,
state='off')
# build new ic with last good values (at t=told)
if len(alltData) > 1:
new_ic = [allxDataDict[xname][-1] \
for xname in xnames]
else:
new_ic = x0
# reset integrator
solver.set_initial_value(new_ic, told)
extralist[self.numpars:listend] = \
[apply(f, [told+self.globalt0,
self.checklevel]) \
for f in inputVarList]
solver.set_f_params(extralist)
# continue integrating over new mesh
continue # while
alltData.append(solver.t)
for xi in xrange(self.dimension):
allxDataDict[xnames[xi]].append(solver.y[xi])
for aix in xrange(len(anames)):
aname = anames[aix]
allaDataDict[aname].append(avals[aix])
num_points += 1
if not breakwhile:
try:
extralist[self.numpars:listend] = [apply(f, \
[solver.t+self.globalt0,
self.checklevel]) \
for f in inputVarList]
except ValueError:
print 'External input call caused value out of range error:',\
't = ', solver.t
for f in inputVarList:
if len(f.warnings):
print 'External input variable %s out of range:' % f.name
print ' t = ', repr(f.warnings[-1][0]), ', ', \
f.name, ' = ', repr(f.warnings[-1][1])
raise
except AssertionError:
print 'External input call caused t out of range error: t = ', \
solver.t
raise
solver.set_f_params(extralist)
breakwhile = not solver.successful()
# Check that any terminal events found terminated the code correctly
if first_found_t is not None:
# ... then terminal events were found. Those that were 'precise' had
# their 'eventdelay' attribute temporarily set to 0. It now should
# be restored.
for evname1, ev1 in termevents:
# restore_evts are copies of the originally flagged 'precise'
# events
for evname2, ev2 in restore_evts:
if evname2 == evname1:
ev1.eventdelay = ev2.eventdelay
try:
if self.warnings[-1][0] not in [W_TERMEVENT, W_TERMSTATEBD]:
raise RuntimeError("Event finding code for terminal event "
"failed in Generator " + self.name + \
": try decreasing eventdelay or "
"eventinterval below eventtol")
except IndexError:
print "Output stats: ", self.outputstats
raise RuntimeError("Event finding failed in Generator " + \
self.name + ": try decreasing eventdelay "
"or eventinterval below eventtol")
# Package up computed trajectory in Variable variables
# Add external inputs warnings to self.warnings, if any
for f in inputVarList:
for winfo in f.warnings:
self.warnings.append(
(W_NONTERMSTATEBD, (winfo[0], f.name, winfo[1],
f.depdomain.get())))
# check for non-unique terminal event
termcount = 0
for (w, i) in self.warnings:
if w == W_TERMEVENT or w == W_TERMSTATEBD:
termcount += 1
if termcount > 1:
self.errors.append((E_NONUNIQUETERM, (alltData[-1], i[1])))
# uncomment the following lines for debugging
# assert len(alltData) == len(allxDataDict.values()[0]) \
# == len(allaDataDict.values()[0]), "Output data size mismatch"
# for val_list in allaDataDict.values():
# assert all([isfinite(x) for x in val_list])
# Create variables (self.variables contains no actual data)
# These versions of the variables are only final if no non-terminal
# events need to be inserted.
variables = copyVarDict(self.variables)
for x in xnames:
if len(alltData) > 1:
variables[x] = Variable(interp1d(alltData, allxDataDict[x]),
't', x, x)
else:
print "Error in Generator:", self.name
print "t = ", alltData
print "x = ", allxDataDict
raise PyDSTool_ValueError, "Fewer than 2 data points computed"
for a in anames:
if len(alltData) > 1:
variables[a] = Variable(interp1d(alltData, allaDataDict[a]),
't', a, a)
else:
print "Error in Generator:", self.name
print "t = ", alltData
print "x = ", allxDataDict
raise PyDSTool_ValueError, "Fewer than 2 data points computed"
# Resolve non-terminal 'precise' events that were flagged, using the
# variables created. Then, add them to a new version of the variables.
ntpe_tdict = {}
for (et0, et1, e) in nontermprecevs:
lost_evt = False
search_dt = max((et1 - et0) / 5, e[1].eventinterval)
et_precise_list = e[1].searchForEvents(trange=[et0, et1],
dt=search_dt,
checklevel=self.checklevel,
parDict=self.pars,
vars=variables,
inputs=self.inputs,
abseps=self._abseps,
eventdelay=False,
globalt0=self.globalt0)
if et_precise_list == []:
lost_evt = True
for et_precise in et_precise_list:
if et_precise[0] is not None:
if et_precise[0] in ntpe_tdict:
# add event name at this time (that already exists in the dict)
ntpe_tdict[et_precise[0]].append(e[0])
else:
# add event name at this time (when time is not already in dict)
ntpe_tdict[et_precise[0]] = [e[0]]
else:
lost_evt = True
if lost_evt:
raise PyDSTool_ExistError, \
("Internal error: A non-terminal, 'precise' event '"
+e[0]+"' was lost after integration!")
# add non-terminal event points to variables
if ntpe_tdict != {}:
# find indices of times at which event times will be inserted
tix = 0
evts = ntpe_tdict.keys()
evts.sort()
for evix in xrange(len(evts)):
evt = evts[evix]
evnames = ntpe_tdict[evt]
self.warnings.append((W_NONTERMEVENT, (evt, evnames)))
xval = [variables[x](evt) for x in xnames]
for evname in evnames:
Evtimes[evname].append(evt)
Evpoints[evname].append(array(xval))
tcond = less_equal(alltData[tix:], evt).tolist()
try:
tix = tcond.index(0) + tix # lowest index for t > evt
do_insert = (alltData[tix - 1] != evt)
except ValueError:
# evt = last t value so no need to add it
do_insert = False
if do_insert:
alltData.insert(tix, evt)
xvaldict = dict(zip(xnames, xval))
for x in xnames:
allxDataDict[x].insert(tix, xvaldict[x])
for a in anames:
allaDataDict[a].insert(tix, variables[a](evt))
for x in xnames:
variables[x] = Variable(interp1d(alltData, allxDataDict[x]),
't', x, x)
for a in anames:
variables[a] = Variable(interp1d(alltData, allaDataDict[a]),
't', a, a)
self.outputstats = {
'last_step': dt,
'num_fcns': num_points,
'num_steps': num_points,
'errorStatus': errcode
}
if solver.successful():
self.validateSpec()
for evname, evtlist in Evtimes.iteritems():
try:
self.eventstruct.Evtimes[evname].extend([et+self.globalt0 \
for et in evtlist])
except KeyError:
self.eventstruct.Evtimes[evname] = [et+self.globalt0 \
for et in evtlist]
# build event pointset information (reset previous trajectory's)
self.trajevents = {}
for (evname, ev) in eventslist:
evpt = Evpoints[evname]
if evpt == []:
self.trajevents[evname] = None
else:
evpt = transpose(array(evpt))
self.trajevents[evname] = Pointset({
'coordnames':
xnames,
'indepvarname':
't',
'coordarray':
evpt,
'indepvararray':
Evtimes[evname],
'indepvartype':
Float
})
self.defined = True
return Trajectory(trajname, variables.values(), self.globalt0,
self.checklevel)
else:
try:
self.errors.append(
(E_COMPUTFAIL, (solver.t, self._errorcodes[errcode])))
except TypeError:
# e.g. when errcode has been used to return info list
print "Error information: ", errcode
self.errors.append(
(E_COMPUTFAIL, (solver.t, self._errorcodes[0])))
self.defined = False
def __del__(self):
ODEsystem.__del__(self)
def compute(self, trajname, dirn='f'):
continue_integ = ODEsystem.prepDirection(self, dirn)
if self._dircode == -1:
raise NotImplementedError, ('Backwards integration is not implemented')
# validate spec if there exists a prior trajectory computation
if self.defined:
self.validateSpec()
self.validateICs()
self.clearWarnings()
self.clearErrors()
pnames = sortedDictKeys(self.pars)
xnames = self._var_ixmap # ensures correct order
# Check i.c.'s are well defined (finite)
self.checkInitialConditions()
if self._algparams['stiff']:
methstr = 'bdf'
methcode = 2
else:
methstr = 'adams'
methcode = 1
if self.haveJacobian():
haveJac = 1
else:
haveJac = 0
if isinstance(self._algparams['atol'], list):
if len(self._algparams['atol']) != self.dimension:
raise ValueError, 'atol list must have same length as phase dimension'
else:
atol = self._algparams['atol']
self._algparams['atol'] = [atol for dimix in xrange(self.dimension)]
indepdom0 = self.indepvariable.depdomain.get(0)
indepdom1 = self.indepvariable.depdomain.get(1)
if continue_integ:
if self._tdata[0] != self._solver.t:
print "Previous end time is %f"%self._solver.t
raise ValueError, \
"Start time not correctly updated for continuing orbit"
x0 = self._solver.y
indepdom0 = self._solver.t
else:
x0 = sortedDictValues(self.initialconditions,
self.funcspec.vars)
if self._solver._integrator is None:
# Banded Jacobians not yet supported
#
# start a new integrator, because method may have been
# switched
self._solver.set_integrator('vode', method=methstr,
rtol=self._algparams['rtol'],
atol=self._algparams['atol'],
nsteps=self._algparams['max_pts'],
max_step=self._algparams['max_step'],
min_step=self._algparams['min_step'],
first_step=self._algparams['init_step'],
with_jacobian=haveJac)
# speed up repeated access to solver by making a temp name for it
solver = self._solver
else:
# speed up repeated access to solver by making a temp name for it
solver = self._solver
solver.with_jacobian = haveJac
# self.mu = lband
# self.ml = uband
solver.rtol = self._algparams['rtol']
solver.atol = self._algparams['atol']
solver.method = methcode
# self.order = order
solver.nsteps = self._algparams['max_pts']
solver.max_step = self._algparams['max_step']
solver.min_step = self._algparams['min_step']
solver.first_step = self._algparams['init_step']
solver.set_initial_value(x0, indepdom0)
## if self._dircode == 1:
## solver.set_initial_value(x0, indepdom0)
## else:
## solver.set_initial_value(x0, indepdom1)
# wrap up each dictionary initial value as a singleton list
alltData = [indepdom0]
allxDataDict = dict(zip(xnames, map(listid, x0)))
plist = sortedDictValues(self.pars)
extralist = copy(plist)
if self.inputs:
# inputVarList is a list of Variables
inames = sortedDictKeys(self.inputs)
listend = self.numpars + len(self.inputs)
inputVarList = sortedDictValues(self.inputs)
ilist = _pollInputs(inputVarList, alltData[0]+self.globalt0,
self.checklevel)
else:
ilist = []
inames = []
listend = self.numpars
inputVarList = []
extralist.extend(ilist)
solver.set_f_params(extralist)
if haveJac:
solver.set_jac_params(extralist)
dt = self._algparams['init_step']
strict = self._algparams['strictdt']
# Make t mesh
if not all(isfinite(self.indepvariable.depdomain.get())):
print "Time domain was: ", self.indepvariable.depdomain.get()
raise ValueError, "Ensure time domain is finite"
if dt == indepdom1 - indepdom0:
# single-step integration required
tmesh = [indepdom0, indepdom1]
else:
notDone = True
repeatTol = 10
count = 0
while notDone and count <= repeatTol:
try:
tmesh = self.indepvariable.depdomain.uniformSample(dt,
strict=strict,
avoidendpoints=self.checklevel>2)
notDone = False
except AssertionError:
count += 1
dt = dt/3.0
if count == repeatTol:
raise AssertionError, \
("supplied time step is too large for selected time"
" interval")
if len(tmesh)<=2:
# safety net, in case too few points in mesh
# too few points unless we can add endpoint
if tmesh[-1] != indepdom1:
# dt too large for tmesh to have more than one point
tmesh.append(indepdom1)
if not strict: # get actual time step used
# don't use [0] in case avoided end points
dt = tmesh[2]-tmesh[1]
if self.eventstruct.query(['lowlevel']) != []:
raise ValueError, "Only high level events can be passed to VODE"
eventslist = self.eventstruct.query(['highlevel', 'active',
'notvarlinked'])
termevents = self.eventstruct.query(['term'], eventslist)
# reverse time by reversing mesh doesn't work
## if self._dircode == -1:
## tmesh.reverse()
tmesh.pop(0) # get rid of first entry for initial condition
# per-iteration storage of variable data (initial values are irrelevant)
xDataDict = {}
xnames = self.funcspec.vars
# storage of all auxiliary variable data
allaDataDict = {}
anames = self.funcspec.auxvars
avals = apply(getattr(self,self.funcspec.auxspec[1]),
[indepdom0, x0, extralist])
for aix in range(len(anames)):
aname = anames[aix]
try:
allaDataDict[aname] = [avals[aix]]
except IndexError:
print "\nVODE generator: There was a problem evaluating " \
+ "an auxiliary variable"
print "Debug info: avals (length", len(avals), ") was ", avals
print "Index out of range was ", aix
print self.funcspec.auxspec[1]
print hasattr(self, self.funcspec.auxspec[1])
print "Args were:", [indepdom0, x0, extralist]
raise
# Initialize signs of event detection objects at IC
dataDict = copy(self.initialconditions)
dataDict.update(dict(zip(anames, avals)))
dataDict['t'] = indepdom0
self.setEventICs(self.initialconditions, self.globalt0)
if self.inputs:
parsinps = copy(self.pars)
parsinps.update(dict(zip(inames,ilist)))
else:
parsinps = self.pars
if eventslist != []:
evsflagged = self.eventstruct.pollHighLevelEvents(None,
dataDict,
parsinps,
eventslist)
if len(evsflagged) > 0:
raise RuntimeError, "Some events flagged at initial condition"
if continue_integ:
# revert to prevprevsign, since prevsign changed after call
self.eventstruct.resetHighLevelEvents(indepdom0, eventslist, 'prev')
else:
self.eventstruct.resetHighLevelEvents(indepdom0, eventslist) #, 'off')
self.eventstruct.validateEvents(self.funcspec.vars + \
self.funcspec.auxvars + \
self.funcspec.inputs + \
['t'], eventslist)
# temp storage of first time at which terminal events found
# (this is used for keeping the correct end point of new mesh)
first_found_t = None
# list of precise non-terminal events to be resolved after integration
nontermprecevs = []
evnames = [ev[0] for ev in eventslist]
lastevtime = {}.fromkeys(evnames, None)
# initialize new event info dictionaries
Evtimes = {}
Evpoints = {}
if continue_integ:
for evname in evnames:
try:
# these are in global time, so convert to local time
lastevtime[evname] = self.eventstruct.Evtimes[evname][-1]-self.globalt0
except (IndexError, KeyError):
# IndexError: Evtimes[evname] was None
# KeyError: Evtimes does not have key evname
pass
for evname in evnames:
Evtimes[evname] = []
Evpoints[evname] = []
# temp storage for repeatedly used object attributes (for lookup efficiency)
depdomains = {}
for xi in xrange(self.dimension):
depdomains[xi] = self.variables[xnames[xi]].depdomain
# Main integration loop
num_points = 0
breakwhile = False
while not breakwhile:
try:
new_t = tmesh.pop(0) # this destroys tmesh for future use
except IndexError:
break
try:
errcode = solver.integrate(new_t)
except:
print "Error calling right hand side function:"
self.showSpec()
print "Numerical traceback information (current state, " \
+ "parameters, etc.)"
print "in generator dictionary 'traceback'"
self.traceback = {'vars': dict(zip(xnames,solver.y)),
'pars': dict(zip(pnames,plist)),
'inputs': dict(zip(inames,ilist)),
self.indepvariable.name: new_t}
raise
for xi in xrange(self.dimension):
xDataDict[xnames[xi]] = solver.y[xi]
if not self.contains(depdomains[xi],
solver.y[xi],
self.checklevel):
self.warnings.append((W_TERMSTATEBD,
(solver.t,
xnames[xi],solver.y[xi],
depdomains[xi].get())))
breakwhile = True
break # for loop
if breakwhile:
break
avals = apply(getattr(self,self.funcspec.auxspec[1]), [new_t,
sortedDictValues(xDataDict),
extralist])
# Uncomment the following assertion for debugging
# assert all([isfinite(a) for a in avals]), \
# "Some auxiliary variable values not finite"
aDataDict = dict(zip(anames,avals))
if eventslist != []:
dataDict = copy(xDataDict)
dataDict.update(aDataDict)
dataDict['t'] = new_t
if self.inputs:
parsinps = copy(self.pars)
parsinps.update(dict(zip(inames,
## extralist[self.numpars:listend])))
_pollInputs(inputVarList, new_t+self.globalt0,
self.checklevel))))
else:
parsinps = self.pars
evsflagged = self.eventstruct.pollHighLevelEvents(None,
dataDict,
parsinps,
eventslist)
## print new_t, evsflagged
# evsflagged = [ev for ev in evsflagged if solver.t-indepdom0 > ev[1].eventinterval]
termevsflagged = filter(lambda e: e in evsflagged, termevents)
nontermevsflagged = filter(lambda e: e not in termevsflagged,
evsflagged)
# register any non-terminating events in the warnings
# list, unless they are 'precise' in which case flag
# them to be resolved after integration completes
if len(nontermevsflagged) > 0:
evnames = [ev[0] for ev in nontermevsflagged]
precEvts = self.eventstruct.query(['precise'],
nontermevsflagged)
prec_evnames = [e[0] for e in precEvts]
# first register non-precise events
nonprec_evnames = remain(evnames, prec_evnames)
# only record events if they have not been previously
# flagged within their event interval
if nonprec_evnames != []:
temp_names = []
for evname in nonprec_evnames:
prevevt_time = lastevtime[evname]
if prevevt_time is None:
ignore_ev = False
else:
if solver.t-prevevt_time < e[1].eventinterval:
ignore_ev = True
else:
ignore_ev = False
if not ignore_ev:
temp_names.append(evname)
lastevtime[evname] = solver.t
self.warnings.append((W_NONTERMEVENT,
(solver.t, temp_names)))
for evname in temp_names:
Evtimes[evname].append(solver.t)
Evpoints[evname].append(solver.y)
for e in precEvts:
# only record events if they have not been previously
# flagged within their event interval
prevevt_time = lastevtime[e[0]]
if prevevt_time is None:
ignore_ev = False
else:
if solver.t-dt-prevevt_time < e[1].eventinterval:
ignore_ev = True
else:
ignore_ev = False
if not ignore_ev:
nontermprecevs.append((solver.t-dt, solver.t,e))
# be conservative as to where the event is, so
# that don't miss any events.
lastevtime[e[0]] = solver.t-dt
e[1].reset() #e[1].prevsign = None #
do_termevs = []
if termevsflagged != []:
# only record events if they have not been previously
# flagged within their event interval
for e in termevsflagged:
prevevt_time = lastevtime[e[0]]
## print "Event %s flagged."%e[0]
## print " ... last time was ", prevevt_time
## print " ... event interval = ", e[1].eventinterval
## print " ... t = %f, dt = %f"%(solver.t, dt)
if prevevt_time is None:
ignore_ev = False
else:
## print " ... comparison = %f < %f"%(solver.t-dt-prevevt_time, e[1].eventinterval)
if solver.t-dt-prevevt_time < e[1].eventinterval:
ignore_ev = True
## print "VODE ignore ev"
else:
ignore_ev = False
if not ignore_ev:
do_termevs.append(e)
if len(do_termevs) > 0:
# >= 1 active terminal event flagged at this time point
if all([not ev[1].preciseFlag for ev in do_termevs]):
# then none of the events specify greater accuracy
# register the event in the warnings
evnames = [ev[0] for ev in do_termevs]
self.warnings.append((W_TERMEVENT, \
(solver.t, evnames)))
for evname in evnames:
Evtimes[evname].append(solver.t)
Evpoints[evname].append(solver.y)
breakwhile = True # break while loop after appending t, x
else:
# find which are the 'precise' events that flagged
precEvts = self.eventstruct.query(['precise'],
do_termevs)
# these events have flagged once so eventdelay has
# been used. now switch it off while finding event
# precisely (should be redundant after change to
# eventinterval and eventdelay parameters)
evnames = [ev[0] for ev in precEvts]
if first_found_t is None:
## print "first time round at", solver.t
numtries = 0
first_found_t = solver.t
restore_evts = deepcopy(precEvts)
minbisectlimit = min([ev[1].bisectlimit for ev in precEvts])
for ev in precEvts:
ev[1].eventdelay = 0.
else:
numtries += 1
## print "time round: ", numtries
if numtries > minbisectlimit:
self.warnings.append((W_BISECTLIMIT,
(solver.t, evnames)))
breakwhile = True
# find minimum eventtol in precEvts
dt_min = min([e[1].eventtol for e in precEvts])
# get previous time point
if len(alltData)>=1:
# take one step back -> told, which will
# get dt added back to first new meshpoint
# (solver.t is the step *after* the event was
# detected)
told = solver.t-dt
else:
raise ValueError("Event %s found too "%evnames[0]+\
"close to local start time: try decreasing "
"initial step size (current size is "
"%f @ t=%f)"%(dt,solver.t+self.globalt0))
if dt_min >= dt:
## print "Registering event:", dt_min, dt
# register the event in the warnings
self.warnings.append((W_TERMEVENT,
(solver.t, evnames)))
for evname in evnames:
Evtimes[evname].append(solver.t)
Evpoints[evname].append(solver.y)
# Cannot continue -- dt_min no smaller than
# previous dt. If this is more than the first time
# in this code then have found the event to within
# the minimum 'precise' event's eventtol, o/w need
# to set eventtol smaller.
breakwhile = True # while loop
if not breakwhile:
dt_new = dt/5.0
# calc new tmesh
trangewidth = 2*dt #first_found_t - told
numpoints = int(math.ceil(trangewidth/dt_new))
# choose slightly smaller dt to fit trange exactly
dt = trangewidth/numpoints
tmesh = [told + i*dt for i in xrange(1, numpoints+1)]
# reset events according to new time mesh,
# setting known previous event state to be their
# "no event found" state
self.eventstruct.resetHighLevelEvents(told,
precEvts,
state='off')
# build new ic with last good values (at t=told)
if len(alltData)>1:
new_ic = [allxDataDict[xname][-1] \
for xname in xnames]
else:
new_ic = x0
# reset integrator
solver.set_initial_value(new_ic, told)
extralist[self.numpars:listend] = \
[apply(f, [told+self.globalt0,
self.checklevel]) \
for f in inputVarList]
solver.set_f_params(extralist)
# continue integrating over new mesh
continue # while
alltData.append(solver.t)
for xi in xrange(self.dimension):
allxDataDict[xnames[xi]].append(solver.y[xi])
for aix in xrange(len(anames)):
aname = anames[aix]
allaDataDict[aname].append(avals[aix])
num_points += 1
if not breakwhile:
try:
extralist[self.numpars:listend] = [apply(f, \
[solver.t+self.globalt0,
self.checklevel]) \
for f in inputVarList]
except ValueError:
print 'External input call caused value out of range error:',\
't = ', solver.t
for f in inputVarList:
if len(f.warnings):
print 'External input variable %s out of range:' % f.name
print ' t = ', repr(f.warnings[-1][0]), ', ', \
f.name, ' = ', repr(f.warnings[-1][1])
raise
except AssertionError:
print 'External input call caused t out of range error: t = ', \
solver.t
raise
solver.set_f_params(extralist)
breakwhile = not solver.successful()
# Check that any terminal events found terminated the code correctly
if first_found_t is not None:
# ... then terminal events were found. Those that were 'precise' had
# their 'eventdelay' attribute temporarily set to 0. It now should
# be restored.
for evname1, ev1 in termevents:
# restore_evts are copies of the originally flagged 'precise'
# events
for evname2, ev2 in restore_evts:
if evname2 == evname1:
ev1.eventdelay = ev2.eventdelay
try:
if self.warnings[-1][0] not in [W_TERMEVENT, W_TERMSTATEBD]:
raise RuntimeError("Event finding code for terminal event "
"failed in Generator " + self.name + \
": try decreasing eventdelay or "
"eventinterval below eventtol")
except IndexError:
print "Output stats: ", self.outputstats
raise RuntimeError("Event finding failed in Generator " + \
self.name + ": try decreasing eventdelay "
"or eventinterval below eventtol")
# Package up computed trajectory in Variable variables
# Add external inputs warnings to self.warnings, if any
for f in inputVarList:
for winfo in f.warnings:
self.warnings.append((W_NONTERMSTATEBD,
(winfo[0], f.name, winfo[1],
f.depdomain.get())))
# check for non-unique terminal event
termcount = 0
for (w,i) in self.warnings:
if w == W_TERMEVENT or w == W_TERMSTATEBD:
termcount += 1
if termcount > 1:
self.errors.append((E_NONUNIQUETERM, (alltData[-1], i[1])))
# uncomment the following lines for debugging
# assert len(alltData) == len(allxDataDict.values()[0]) \
# == len(allaDataDict.values()[0]), "Output data size mismatch"
# for val_list in allaDataDict.values():
# assert all([isfinite(x) for x in val_list])
# Create variables (self.variables contains no actual data)
# These versions of the variables are only final if no non-terminal
# events need to be inserted.
variables = copyVarDict(self.variables)
for x in xnames:
if len(alltData) > 1:
variables[x] = Variable(interp1d(alltData, allxDataDict[x]),
't', x, x)
else:
print "Error in Generator:", self.name
print "t = ", alltData
print "x = ", allxDataDict
raise PyDSTool_ValueError, "Fewer than 2 data points computed"
for a in anames:
if len(alltData) > 1:
variables[a] = Variable(interp1d(alltData, allaDataDict[a]),
't', a, a)
else:
print "Error in Generator:", self.name
print "t = ", alltData
print "x = ", allxDataDict
raise PyDSTool_ValueError, "Fewer than 2 data points computed"
# Resolve non-terminal 'precise' events that were flagged, using the
# variables created. Then, add them to a new version of the variables.
ntpe_tdict = {}
for (et0,et1,e) in nontermprecevs:
lost_evt = False
search_dt = max((et1-et0)/5,e[1].eventinterval)
et_precise_list = e[1].searchForEvents(trange=[et0,et1],
dt=search_dt,
checklevel=self.checklevel,
parDict=self.pars,
vars=variables,
inputs=self.inputs,
abseps=self._abseps,
eventdelay=False,
globalt0=self.globalt0)
if et_precise_list == []:
lost_evt = True
for et_precise in et_precise_list:
if et_precise[0] is not None:
if et_precise[0] in ntpe_tdict:
# add event name at this time (that already exists in the dict)
ntpe_tdict[et_precise[0]].append(e[0])
else:
# add event name at this time (when time is not already in dict)
ntpe_tdict[et_precise[0]] = [e[0]]
else:
lost_evt = True
if lost_evt:
raise PyDSTool_ExistError, \
("Internal error: A non-terminal, 'precise' event '"
+e[0]+"' was lost after integration!")
# add non-terminal event points to variables
if ntpe_tdict != {}:
# find indices of times at which event times will be inserted
tix = 0
evts = ntpe_tdict.keys()
evts.sort()
for evix in xrange(len(evts)):
evt = evts[evix]
evnames = ntpe_tdict[evt]
self.warnings.append((W_NONTERMEVENT, (evt, evnames)))
xval = [variables[x](evt) for x in xnames]
for evname in evnames:
Evtimes[evname].append(evt)
Evpoints[evname].append(array(xval))
tcond = less_equal(alltData[tix:], evt).tolist()
try:
tix = tcond.index(0) + tix # lowest index for t > evt
do_insert = (alltData[tix-1] != evt)
except ValueError:
# evt = last t value so no need to add it
do_insert = False
if do_insert:
alltData.insert(tix, evt)
xvaldict = dict(zip(xnames, xval))
for x in xnames:
allxDataDict[x].insert(tix, xvaldict[x])
for a in anames:
allaDataDict[a].insert(tix, variables[a](evt))
for x in xnames:
variables[x] = Variable(interp1d(alltData, allxDataDict[x]),
't', x, x)
for a in anames:
variables[a] = Variable(interp1d(alltData, allaDataDict[a]),
't', a, a)
self.outputstats = {'last_step': dt,
'num_fcns': num_points,
'num_steps': num_points,
'errorStatus': errcode
}
if solver.successful():
self.validateSpec()
for evname, evtlist in Evtimes.iteritems():
try:
self.eventstruct.Evtimes[evname].extend([et+self.globalt0 \
for et in evtlist])
except KeyError:
self.eventstruct.Evtimes[evname] = [et+self.globalt0 \
for et in evtlist]
# build event pointset information (reset previous trajectory's)
self.trajevents = {}
for (evname, ev) in eventslist:
evpt = Evpoints[evname]
if evpt == []:
self.trajevents[evname] = None
else:
evpt = transpose(array(evpt))
self.trajevents[evname] = Pointset({'coordnames': xnames,
'indepvarname': 't',
'coordarray': evpt,
'indepvararray': Evtimes[evname],
'indepvartype': Float})
self.defined = True
return Trajectory(trajname, variables.values(),
self.globalt0, self.checklevel)
else:
try:
self.errors.append((E_COMPUTFAIL, (solver.t,
self._errorcodes[errcode])))
except TypeError:
# e.g. when errcode has been used to return info list
print "Error information: ", errcode
self.errors.append((E_COMPUTFAIL, (solver.t,
self._errorcodes[0])))
self.defined = False