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New features #155

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New features #155

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107b44c
add rootinfo and fix bug to pass userdata to JacRhs
sixpearls Jun 19, 2023
cdfb3bf
allow tstop of any value and setting of max_step_size after solver in…
sixpearls Jul 22, 2023
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9 changes: 5 additions & 4 deletions scikits/odes/sundials/cvode.pxd
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Original file line number Diff line number Diff line change
Expand Up @@ -23,18 +23,19 @@ cdef class CV_RootFunction:

cdef class CV_WrapRootFunction(CV_RootFunction):
cdef object _rootfn
cdef int with_userdata
cdef public int with_userdata
cpdef set_rootfn(self, object rootfn)

cdef class CV_JacRhsFunction:
cpdef int evaluate(self, DTYPE_t t,
np.ndarray[DTYPE_t, ndim=1] y,
np.ndarray[DTYPE_t, ndim=1] fy,
np.ndarray[DTYPE_t, ndim=2] J) except? -1
np.ndarray[DTYPE_t, ndim=2] J,
object userdata = *) except? -1

cdef class CV_WrapJacRhsFunction(CV_JacRhsFunction):
cdef public object _jacfn
cdef int with_userdata
cdef public int with_userdata
cpdef set_jacfn(self, object jacfn)

cdef class CV_PrecSetupFunction:
Expand Down Expand Up @@ -128,7 +129,7 @@ cdef class CVODE:
cdef N_Vector atol
cdef void* _cv_mem
cdef SUNContext sunctx
cdef dict options
cdef public dict options
cdef bint parallel_implementation, initialized, _old_api, _step_compute, _validate_flags
cdef CV_data aux_data

Expand Down
43 changes: 32 additions & 11 deletions scikits/odes/sundials/cvode.pyx
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Original file line number Diff line number Diff line change
Expand Up @@ -257,7 +257,8 @@ cdef class CV_JacRhsFunction:
cpdef int evaluate(self, DTYPE_t t,
np.ndarray[DTYPE_t, ndim=1] y,
np.ndarray[DTYPE_t, ndim=1] fy,
np.ndarray[DTYPE_t, ndim=2] J) except? -1:
np.ndarray[DTYPE_t, ndim=2] J,
object userdata = None) except? -1:
"""
Returns the Jacobi matrix of the right hand side function, as
d(rhs)/d y
Expand All @@ -275,22 +276,30 @@ cdef class CV_WrapJacRhsFunction(CV_JacRhsFunction):
"""
Set some jacobian equations as a JacRhsFunction executable class.
"""
self.with_userdata = 0
self._jacfn = jacfn
nrarg = _get_num_args(jacfn)
if nrarg > 5:
#hopefully a class method, self gives 6 arg!
self.with_userdata = 1
elif nrarg == 5 and inspect.isfunction(jacfn):
self.with_userdata = 1
self._jacfn = jacfn

cpdef int evaluate(self, DTYPE_t t,
np.ndarray[DTYPE_t, ndim=1] y,
np.ndarray[DTYPE_t, ndim=1] fy,
np.ndarray J) except? -1:
np.ndarray J,
object userdata = None) except? -1:
"""
Returns the Jacobi matrix (for dense the full matrix, for band only
bands. Result has to be stored in the variable J, which is preallocated
to the corresponding size.
"""
## if self.with_userdata == 1:
## self._jacfn(t, y, ydot, cj, J, userdata)
## else:
## self._jacfn(t, y, ydot, cj, J)
user_flag = self._jacfn(t, y, fy, J)
if self.with_userdata == 1:
user_flag = self._jacfn(t, y, fy, J, userdata)
else:
user_flag = self._jacfn(t, y, fy, J)

if user_flag is None:
user_flag = 0
Expand Down Expand Up @@ -318,7 +327,7 @@ cdef int _jacdense(sunrealtype tt,
ff_tmp = aux_data.z_tmp
nv_s2ndarray(ff, ff_tmp)

user_flag = aux_data.jac.evaluate(tt, yy_tmp, ff_tmp, jac_tmp)
user_flag = aux_data.jac.evaluate(tt, yy_tmp, ff_tmp, jac_tmp, aux_data.user_data,)

if parallel_implementation:
raise NotImplemented
Expand Down Expand Up @@ -1068,7 +1077,7 @@ cdef class CVODE:
if not supress_supported_check:
for opt in options.keys():
if not opt in ['atol', 'rtol', 'tstop', 'rootfn', 'nr_rootfns',
'verbosity', 'one_step_compute']:
'verbosity', 'one_step_compute', 'max_step_size']:
raise ValueError("Option '%s' can''t be set runtime." % opt)

# Verbosity level
Expand Down Expand Up @@ -1172,7 +1181,7 @@ cdef class CVODE:
if ('tstop' in options) and (options['tstop'] is not None):
opts_tstop = options['tstop']
self.options['tstop'] = opts_tstop
if (not opts_tstop is None) and (opts_tstop > 0.):
if (not opts_tstop is None):
flag = CVodeSetStopTime(cv_mem, <sunrealtype> opts_tstop)
if flag == CV_ILL_INPUT:
raise ValueError('CVodeSetStopTime::Stop value is beyond '
Expand Down Expand Up @@ -1644,8 +1653,12 @@ cdef class CVODE:
else:
_test = np.empty((len(y0), len(y0)), DTYPE)
_fy_test = np.zeros(len(y0), DTYPE)
jac._jacfn(t0, y0, _fy_test, _test)
if jac.with_userdata:
jac._jacfn(t0, y0, _fy_test, _test, opts['user_data'])
else:
jac._jacfn(t0, y0, _fy_test, _test)
_test = None
_fy_test = None

#now we initialize storage which is persistent over steps
self.t_roots = []
Expand Down Expand Up @@ -1896,6 +1909,14 @@ cdef class CVODE:
self.t_tstop, self.y_tstop,
)

def rootinfo(self):
#cdef int[self.options['nr_rootfns']] rootsfound
N = self.options['nr_rootfns']
cdef np.ndarray[int, ndim=1, mode='c'] rootsfound = np.empty(N, dtype=np.int32)
#cdef int rootsfound[N]
CVodeGetRootInfo(self._cv_mem, &rootsfound[0])
return rootsfound


def step(self, DTYPE_t t, np.ndarray[DTYPE_t, ndim=1] y_retn = None):
"""
Expand Down