def test_wrapArgInCall():
"""Test: wrapping delimiters around call arguments"""
fs = 'initcond(v,p)'
assert 'initcond("v",p)' == wrapArgInCall(fs, 'initcond', '"')
assert 'initcond(v,"p")' == wrapArgInCall(fs, 'initcond', '"', argnums=[1])
assert 'initcond([v],[p])' == wrapArgInCall(fs, 'initcond', '[', ']', [0, 1])
def test_wrapArgInCall():
"""Test: wrapping delimiters around call arguments"""
fs = 'initcond(v,p)'
assert 'initcond("v",p)' == wrapArgInCall(fs, 'initcond', '"')
assert 'initcond(v,"p")' == wrapArgInCall(fs, 'initcond', '"', argnums=[1])
assert 'initcond([v],[p])' == wrapArgInCall(fs, 'initcond', '[', ']',
[0, 1])
def _generate_fun(self, funcname, reusestr, specnames, pardefines,
vardefines, inpdefines, parundefines, varundefines,
inpundefines, docodeinserts):
sig = "void " + funcname + "(unsigned n_, unsigned np_, double t, double *Y_, " \
+ \
"double *p_, double *f_, unsigned wkn_, double *wk_, unsigned xvn_, double *xv_)"
# specstr = sig + "{\n\n" + pardefines + vardefines + "\n"
specstr = sig + "{" + pardefines + vardefines + inpundefines + "\n"
if docodeinserts and self.opts['start']:
specstr += self._format_user_code(self.opts['start']) + '\n'
specstr += (len(reusestr) > 0) * "/* reused term definitions */\n" \
+ reusestr + "\n"
auxdefs_parsed = {}
# add function body
for i in range(len(specnames)):
xname = specnames[i]
fbody = self.fspec.varspecs[xname]
fbody_parsed = self._processSpecialC(fbody)
if self.fspec.auxfns:
fbody_parsed = addArgToCalls(fbody_parsed,
list(self.fspec.auxfns.keys()),
"p_, wk_, xv_")
if 'initcond' in self.fspec.auxfns:
# convert 'initcond(x)' to 'initcond("x")' for
# compatibility with C syntax
fbody_parsed = wrapArgInCall(fbody_parsed,
'initcond', '"')
specstr += "f_[" + str(i) + "] = " + fbody_parsed + ";\n"
auxdefs_parsed[xname] = fbody_parsed
if docodeinserts and self.opts['end']:
specstr += '\n' + self._format_user_code(self.opts['end'])
specstr += "\n" + parundefines + varundefines + inpundefines + "}\n\n"
self.fspec._auxdefs_parsed = auxdefs_parsed
return (specstr, funcname)
def _generate_fun(self, funcname, reusestr, specnames, pardefines,
vardefines, inpdefines, parundefines, varundefines,
inpundefines, docodeinserts):
sig = "void " + funcname + "(unsigned n_, unsigned np_, double t, double *Y_, " \
+ \
"double *p_, double *f_, unsigned wkn_, double *wk_, unsigned xvn_, double *xv_)"
# specstr = sig + "{\n\n" + pardefines + vardefines + "\n"
specstr = sig + "{" + pardefines + vardefines + inpundefines + "\n"
if docodeinserts and self.opts['start']:
specstr += self._format_user_code(self.opts['start']) + '\n'
specstr += (len(reusestr) > 0) * "/* reused term definitions */\n" \
+ reusestr + "\n"
auxdefs_parsed = {}
# add function body
for i in range(len(specnames)):
xname = specnames[i]
fbody = self.fspec.varspecs[xname]
fbody_parsed = self._processSpecialC(fbody)
if self.fspec.auxfns:
fbody_parsed = addArgToCalls(fbody_parsed,
list(self.fspec.auxfns.keys()),
"p_, wk_, xv_")
if 'initcond' in self.fspec.auxfns:
# convert 'initcond(x)' to 'initcond("x")' for
# compatibility with C syntax
fbody_parsed = wrapArgInCall(fbody_parsed,
'initcond', '"')
specstr += "f_[" + str(i) + "] = " + fbody_parsed + ";\n"
auxdefs_parsed[xname] = fbody_parsed
if docodeinserts and self.opts['end']:
specstr += '\n' + self._format_user_code(self.opts['end'])
specstr += "\n" + parundefines + varundefines + inpundefines + "}\n\n"
self.fspec._auxdefs_parsed = auxdefs_parsed
return (specstr, funcname)
def makeAutoLibSource(self, include=[]):
"""makeAutoLibSource generates the C source for the vector field specification.
It should be called only once per vector field."""
# Make vector field (and event) file for compilation
assert isinstance(include, list), "includes must be in form of a list"
# codes for library types (default is USERLIB, since compiler will look in standard library d
STDLIB = 0
USERLIB = 1
libinclude = dict([('math.h', STDLIB), ('stdio.h', STDLIB), ('stdlib.h', STDLIB),
('string.h', STDLIB), ('autovfield.h', USERLIB),
('auto_c.h', USERLIB)])
include_str = '#include "auto_f2c.h"\n' # This must come first
for libstr, libtype in libinclude.items():
if libtype == STDLIB:
quoteleft = '<'
quoteright = '>'
else:
quoteleft = '"'
quoteright = '"'
include_str += "#include " + quoteleft + libstr + quoteright + "\n"
if include != []:
assert isUniqueSeq(include), "list of library includes must not contain repeats"
for libstr in include:
if libstr in libinclude:
# don't repeat libraries
print("Warning: library '" + libstr + "' already appears in list"\
+ " of imported libraries")
else:
include_str += "#include " + '"' + libstr + '"\n'
# f2c auto conventions (dirty trick!)
#define_str = "\n#define double doublereal\n#define int integer\n\n"
define_str = ""
allfilestr = "/* Vector field and other functions for Auto continuer.\n " \
+ " This code was automatically generated by PyDSTool, but may be modified " \
+ "by hand. */\n\n" + include_str + define_str + """
double *gICs;
double **gBds;
double globalt0;
static double pi = 3.1415926535897931;
"""
pardefines = ""
## parundefines = ""
vardefines = ""
## varundefines = ""
inpdefines = ""
## inpundefines = ""
# sorted version of var, par, and input names
vnames = self.gensys._var_ixmap
pnames = self.funcspec.pars
inames = self.funcspec.inputs
pnames.sort()
inames.sort()
for i in range(self.gensys.numpars):
p = pnames[i]
# add to defines (WATCH OUT FOR PERIOD _T!!!)
if (i < 10):
pardefines += self.funcspec._defstr+" "+p+"\tp_["+str(i)+"]\n"
elif (i >= 10):
pardefines += self.funcspec._defstr+" "+p+"\tp_["+str(i+40)+"]\n"
# add period _T
pardefines += self.funcspec._defstr+" _T\tp_[10]\n"
for i in range(self.gensys.dimension):
v = vnames[i]
# add to defines
vardefines += self.funcspec._defstr+" "+v+"\tY_["+str(i)+"]\n"
## # add to undefines
## varundefines += self.funcspec._undefstr+" "+v+"\n"
for i in range(len(self.funcspec.inputs)):
inp = inames[i]
# add to defines
inpdefines += self.funcspec._defstr+" "+inp+"\txv_["+str(i)+"]\n"
## # add to undefines
## inpundefines += self.funcspec._undefstr+" "+inp+"\n"
allfilestr += "\n/* Variable, parameter, and input definitions: */ \n" \
+ pardefines + vardefines + inpdefines + "\n"
# add signature for auxiliary functions
if self.funcspec.auxfns:
allfilestr += "\n"
for finfo in self.funcspec.auxfns.values():
allfilestr += finfo[1] + ";\n"
allfilestr += "\nvoid auxvars(unsigned, unsigned, double, double*, double*, " \
+ "double*, unsigned, double*, unsigned, double*);\n" \
+ """void jacobian(unsigned, unsigned, double, double*, double*, double**, unsigned, double*, unsigned, double*);
void jacobianParam(unsigned, unsigned, double, double*, double*, double**, unsigned, double*, unsigned, double*);
"""
if self.funcspec.auxvars == []:
allfilestr += "int N_AUXVARS = 0;\n\n\n"
else:
allfilestr += "int N_AUXVARS = " + str(len(self.funcspec.auxvars)) \
+ ";\n\n\n"
allfilestr += self.funcspec.spec[0] + "\n\n"
if self.funcspec.auxfns:
for fname, finfo in self.funcspec.auxfns.items():
fbody = finfo[0]
# subs _p into auxfn-to-auxfn calls (but not to the signature)
fbody_parsed = addArgToCalls(fbody,
list(self.funcspec.auxfns.keys()),
"p_, wk_, xv_", notFirst=fname)
if 'initcond' in self.funcspec.auxfns:
# convert 'initcond(x)' to 'initcond("x")' for
# compatibility with C syntax, but don't affect the
# function signature!
fbody_parsed = wrapArgInCall(fbody_parsed,
'initcond', '"', notFirst=True)
allfilestr += "\n" + fbody_parsed + "\n\n"
# add auxiliary variables (shell of the function always present)
# add event functions
allfilestr += self.funcspec.auxspec[0]
# if jacobians or mass matrix not present, fill in dummy
if not self.gensys.haveJacobian():
allfilestr += """
void jacobian(unsigned n_, unsigned np_, double t, double *Y_, double *p_, double **f_, unsigned wkn_, double *wk_, unsigned xvn_, double *xv_) {
}
"""
if not self.gensys.haveJacobian_pars():
allfilestr += """
void jacobianParam(unsigned n_, unsigned np_, double t, double *Y_, double *p_, double **f_, unsigned wkn_, double *wk_, unsigned xvn_, double *xv_) {
}
""" #+ "\n/* Variable and parameter substitutions undefined:*/\n" + parundefines + varundefines + "\n"
# write out C file
vffile = os.path.join(self._compilation_tempdir, self._vf_file)
try:
file = open(vffile, 'w')
#allfilestr = allfilestr.replace("double ","doublereal ")
#allfilestr = allfilestr.replace("double*","doublereal *")
#allfilestr = allfilestr.replace("double**","doublereal **")
file.write(allfilestr)
file.close()
except IOError as e:
print("Error opening file "+self._vf_file+" for writing")
raise IOError(e)
def generate_user_module(self, fspec, eventstruct, name="", include=None):
include = include or []
# Make vector field (and event) file for compilation
assert isinstance(include, list), "includes must be in form of a list"
# codes for library types (default is USERLIB, since compiler will look in standard library d
STDLIB = 0
USERLIB = 1
libinclude = [
("math.h", STDLIB),
("Python.h", STDLIB),
("stdio.h", STDLIB),
("stdlib.h", STDLIB),
("string.h", STDLIB),
("events.h", USERLIB),
("maxmin.h", USERLIB),
("signum.h", USERLIB),
("vfield.h", USERLIB),
]
include_str = ""
for libstr, libtype in libinclude:
if libtype == STDLIB:
quoteleft = "<"
quoteright = ">"
else:
quoteleft = '"'
quoteright = '"'
include_str += "#include " + quoteleft + libstr + quoteright + "\n"
if include != []:
incs = [libstr for libstr, _ in libinclude]
assert isUniqueSeq(
include
), "list of library includes must not contain repeats"
for libstr in include:
if libstr in incs:
# don't repeat libraries
print(
"Warning: library '%s' already appears in list" % libstr
+ " of imported libraries"
)
else:
include_str += "#include " + '"' + libstr + '"\n'
allfilestr = (
"/* Vector field function and events for %s integrator.\n" % name
+ " This code was automatically generated by PyDSTool, but may be modified "
+ "by hand. */\n\n"
+ include_str
+ """
extern double *gICs;
extern double **gBds;
extern double globalt0;
static double pi = 3.1415926535897931;
double signum(double x)
{
if (x<0) {
return -1;
}
else if (x==0) {
return 0;
}
else if (x>0) {
return 1;
}
else {
/* must be that x is Not-a-Number */
return x;
}
}
"""
)
pardefines = ""
vardefines = ""
auxvardefines = ""
inpdefines = ""
for i, p in enumerate(fspec.pars):
pardefines += fspec._defstr + " " + p + "\tp_[" + str(i) + "]\n"
for i, v in enumerate(fspec.vars):
vardefines += fspec._defstr + " " + v + "\tY_[" + str(i) + "]\n"
for i, v in enumerate(fspec.auxvars):
auxvardefines += (
fspec._defstr + " " + v + "\t(" + fspec._auxdefs_parsed[v] + ")\n"
)
for i, inp in enumerate(fspec.inputs):
inpdefines += fspec._defstr + " " + inp + "\txv_[" + str(i) + "]\n"
allfilestr += (
"\n/* Variable, aux variable, parameter, and input definitions: */ \n"
+ pardefines
+ vardefines
+ auxvardefines
+ inpdefines
+ "\n"
)
# preprocess event code
allevs = ""
eventNames = eventstruct.sortedEventNames()
numevs = len(eventNames)
for evname in eventNames:
ev = eventstruct.events[evname]
evfullfn = ""
from PyDSTool.Events import LowLevelEvent
assert isinstance(ev, LowLevelEvent), (
"Radau can only " "accept low level events"
)
evsig = ev._LLreturnstr + " " + ev.name + ev._LLargstr
assert ev._LLfuncstr.index(";") > 1, (
"Event function code "
"error: Have you included a ';' character at the end of"
"your 'return' statement?"
)
fbody = ev._LLfuncstr
# check fbody for calls to user-defined aux fns
# and add hidden p argument
if fspec.auxfns:
fbody_parsed = addArgToCalls(
fbody, list(fspec.auxfns.keys()), "p_, wk_, xv_"
)
if "initcond" in fspec.auxfns:
# convert 'initcond(x)' to 'initcond("x")' for
# compatibility with C syntax
fbody_parsed = wrapArgInCall(fbody_parsed, "initcond", '"')
else:
fbody_parsed = fbody
evbody = " {\n" + fbody_parsed + "\n}\n\n"
allevs += evsig + evbody
allfilestr += evsig + ";\n"
# add signature for auxiliary functions
if fspec.auxfns:
allfilestr += "\n"
for finfo in sorted(fspec.auxfns.values()):
allfilestr += finfo[1] + ";\n"
assignEvBody = "".join(
["events[%d] = &%s;\n" % (i, name) for i, name in enumerate(eventNames)]
)
allfilestr += (
"\nint N_EVENTS = "
+ str(numevs)
+ ";\nvoid assignEvents("
+ "EvFunType *events){\n "
+ assignEvBody
+ "\n}\n\nvoid auxvars(unsigned, unsigned, double, double*, double*, "
+ "double*, unsigned, double*, unsigned, double*);\n"
+ """void jacobian(unsigned, unsigned, double, double*, double*, double**, unsigned, double*, unsigned, double*);
void jacobianParam(unsigned, unsigned, double, double*, double*, double**, unsigned, double*, unsigned, double*);
"""
)
allfilestr += "int N_AUXVARS = %d;\n\n\n" % len(fspec.auxvars)
allfilestr += "int N_EXTINPUTS = %d;\n\n\n" % len(fspec.inputs)
allfilestr += fspec.spec[0] + "\n\n"
if fspec.auxfns:
for fname, finfo in sortedDictItems(fspec.auxfns):
fbody = finfo[0]
# subs _p into auxfn-to-auxfn calls (but not to the signature)
fbody_parsed = addArgToCalls(
fbody, list(fspec.auxfns.keys()), "p_, wk_, xv_", notFirst=fname
)
if "initcond" in fspec.auxfns:
# convert 'initcond(x)' to 'initcond("x")' for
# compatibility with C syntax, but don't affect the
# function signature!
fbody_parsed = wrapArgInCall(
fbody_parsed, "initcond", '"', notFirst=True
)
allfilestr += "\n" + fbody_parsed + "\n\n"
# add auxiliary variables (shell of the function always present)
# add event functions
allfilestr += fspec.auxspec[0] + allevs
# if jacobians or mass matrix not present, fill in dummy
if "massMatrix" not in fspec.auxfns:
allfilestr += """
void massMatrix(unsigned n_, unsigned np_, double t, double *Y_, double *p_, double **f_, unsigned wkn_, double *wk_, unsigned xvn_, double *xv_) {
}
"""
if "Jacobian" not in fspec.auxfns:
allfilestr += """
void jacobian(unsigned n_, unsigned np_, double t, double *Y_, double *p_, double **f_, unsigned wkn_, double *wk_, unsigned xvn_, double *xv_) {
}
"""
if "Jacobian_pars" not in fspec.auxfns:
allfilestr += """
void jacobianParam(unsigned n_, unsigned np_, double t, double *Y_, double *p_, double **f_, unsigned wkn_, double *wk_, unsigned xvn_, double *xv_) {
}
"""
return allfilestr
def makeAutoLibSource(self, include=[]):
"""makeAutoLibSource generates the C source for the vector field specification.
It should be called only once per vector field."""
# Make vector field (and event) file for compilation
assert isinstance(include, list), "includes must be in form of a list"
# codes for library types (default is USERLIB, since compiler will look in standard library d
STDLIB = 0
USERLIB = 1
libinclude = dict([('math.h', STDLIB), ('stdio.h', STDLIB),
('stdlib.h', STDLIB), ('string.h', STDLIB),
('autovfield.h', USERLIB), ('auto_c.h', USERLIB)])
include_str = '#include "auto_f2c.h"\n' # This must come first
for libstr, libtype in libinclude.items():
if libtype == STDLIB:
quoteleft = '<'
quoteright = '>'
else:
quoteleft = '"'
quoteright = '"'
include_str += "#include " + quoteleft + libstr + quoteright + "\n"
if include != []:
assert isUniqueSeq(
include), "list of library includes must not contain repeats"
for libstr in include:
if libstr in libinclude:
# don't repeat libraries
print("Warning: library '" + libstr + "' already appears in list"\
+ " of imported libraries")
else:
include_str += "#include " + '"' + libstr + '"\n'
# f2c auto conventions (dirty trick!)
#define_str = "\n#define double doublereal\n#define int integer\n\n"
define_str = ""
allfilestr = "/* Vector field and other functions for Auto continuer.\n " \
+ " This code was automatically generated by PyDSTool, but may be modified " \
+ "by hand. */\n\n" + include_str + define_str + """
double *gICs;
double **gBds;
double globalt0;
static double pi = 3.1415926535897931;
"""
pardefines = ""
## parundefines = ""
vardefines = ""
## varundefines = ""
inpdefines = ""
## inpundefines = ""
# sorted version of var, par, and input names
vnames = self.gensys._var_ixmap
pnames = self.funcspec.pars
inames = self.funcspec.inputs
pnames.sort()
inames.sort()
for i in range(self.gensys.numpars):
p = pnames[i]
# add to defines (WATCH OUT FOR PERIOD _T!!!)
if (i < 10):
pardefines += self.funcspec._defstr + " " + p + "\tp_[" + str(
i) + "]\n"
elif (i >= 10):
pardefines += self.funcspec._defstr + " " + p + "\tp_[" + str(
i + 40) + "]\n"
# add period _T
pardefines += self.funcspec._defstr + " _T\tp_[10]\n"
for i in range(self.gensys.dimension):
v = vnames[i]
# add to defines
vardefines += self.funcspec._defstr + " " + v + "\tY_[" + str(
i) + "]\n"
## # add to undefines
## varundefines += self.funcspec._undefstr+" "+v+"\n"
for i in range(len(self.funcspec.inputs)):
inp = inames[i]
# add to defines
inpdefines += self.funcspec._defstr + " " + inp + "\txv_[" + str(
i) + "]\n"
## # add to undefines
## inpundefines += self.funcspec._undefstr+" "+inp+"\n"
allfilestr += "\n/* Variable, parameter, and input definitions: */ \n" \
+ pardefines + vardefines + inpdefines + "\n"
# add signature for auxiliary functions
if self.funcspec.auxfns:
allfilestr += "\n"
for finfo in self.funcspec.auxfns.values():
allfilestr += finfo[1] + ";\n"
allfilestr += "\nvoid auxvars(unsigned, unsigned, double, double*, double*, " \
+ "double*, unsigned, double*, unsigned, double*);\n" \
+ """void jacobian(unsigned, unsigned, double, double*, double*, double**, unsigned, double*, unsigned, double*);
void jacobianParam(unsigned, unsigned, double, double*, double*, double**, unsigned, double*, unsigned, double*);
"""
if self.funcspec.auxvars == []:
allfilestr += "int N_AUXVARS = 0;\n\n\n"
else:
allfilestr += "int N_AUXVARS = " + str(len(self.funcspec.auxvars)) \
+ ";\n\n\n"
allfilestr += self.funcspec.spec[0] + "\n\n"
if self.funcspec.auxfns:
for fname, finfo in self.funcspec.auxfns.items():
fbody = finfo[0]
# subs _p into auxfn-to-auxfn calls (but not to the signature)
fbody_parsed = addArgToCalls(fbody,
list(self.funcspec.auxfns.keys()),
"p_, wk_, xv_",
notFirst=fname)
if 'initcond' in self.funcspec.auxfns:
# convert 'initcond(x)' to 'initcond("x")' for
# compatibility with C syntax, but don't affect the
# function signature!
fbody_parsed = wrapArgInCall(fbody_parsed,
'initcond',
'"',
notFirst=True)
allfilestr += "\n" + fbody_parsed + "\n\n"
# add auxiliary variables (shell of the function always present)
# add event functions
allfilestr += self.funcspec.auxspec[0]
# if jacobians or mass matrix not present, fill in dummy
if not self.gensys.haveJacobian():
allfilestr += """
void jacobian(unsigned n_, unsigned np_, double t, double *Y_, double *p_, double **f_, unsigned wkn_, double *wk_, unsigned xvn_, double *xv_) {
}
"""
if not self.gensys.haveJacobian_pars():
allfilestr += """
void jacobianParam(unsigned n_, unsigned np_, double t, double *Y_, double *p_, double **f_, unsigned wkn_, double *wk_, unsigned xvn_, double *xv_) {
}
""" #+ "\n/* Variable and parameter substitutions undefined:*/\n" + parundefines + varundefines + "\n"
# write out C file
vffile = os.path.join(self._compilation_tempdir, self._vf_file)
try:
file = open(vffile, 'w')
#allfilestr = allfilestr.replace("double ","doublereal ")
#allfilestr = allfilestr.replace("double*","doublereal *")
#allfilestr = allfilestr.replace("double**","doublereal **")
file.write(allfilestr)
file.close()
except IOError as e:
print("Error opening file " + self._vf_file + " for writing")
raise IOError(e)
def test_combo_wrapArgInCall_and_addArgToCalls():
"""Test combo of addArgToCalls and wrapArgInCall with embedded calls"""
fs = "1/zeta(y_rel(y,initcond(y)+initcond(z)),z-initcond(x))+zeta(0.)"
fs_p = addArgToCalls(fs, ['zeta', 'y_rel', 'initcond', 'nothing'], "p")
assert '1/zeta(y_rel(y,initcond(y, p)+initcond(z, p), p),z-initcond(x, p), p)+zeta(0., p)' == fs_p
assert '1/zeta(y_rel(y,initcond("y", p)+initcond("z", p), p),z-initcond("x", p), p)+zeta(0., p)' == wrapArgInCall(
fs_p, 'initcond', '"')
def generate_user_module(self, fspec, eventstruct, name='', include=None):
include = include or []
# Make vector field (and event) file for compilation
assert isinstance(include, list), "includes must be in form of a list"
# codes for library types (default is USERLIB, since compiler will look in standard library d
STDLIB = 0
USERLIB = 1
libinclude = [
('math.h', STDLIB),
('Python.h', STDLIB),
('stdio.h', STDLIB),
('stdlib.h', STDLIB),
('string.h', STDLIB),
('events.h', USERLIB),
('maxmin.h', USERLIB),
('signum.h', USERLIB),
('vfield.h', USERLIB),
]
include_str = ''
for libstr, libtype in libinclude:
if libtype == STDLIB:
quoteleft = '<'
quoteright = '>'
else:
quoteleft = '"'
quoteright = '"'
include_str += "#include " + quoteleft + libstr + quoteright + "\n"
if include != []:
incs = [libstr for libstr, _ in libinclude]
assert isUniqueSeq(include), "list of library includes must not contain repeats"
for libstr in include:
if libstr in incs:
# don't repeat libraries
print("Warning: library '%s' already appears in list" % libstr\
+ " of imported libraries")
else:
include_str += "#include " + '"' + libstr + '"\n'
allfilestr = "/* Vector field function and events for %s integrator.\n" % name \
+ " This code was automatically generated by PyDSTool, but may be modified " \
+ "by hand. */\n\n" + include_str + """
extern double *gICs;
extern double **gBds;
extern double globalt0;
static double pi = 3.1415926535897931;
double signum(double x)
{
if (x<0) {
return -1;
}
else if (x==0) {
return 0;
}
else if (x>0) {
return 1;
}
else {
/* must be that x is Not-a-Number */
return x;
}
}
"""
pardefines = ""
vardefines = ""
auxvardefines = ""
inpdefines = ""
for i, p in enumerate(fspec.pars):
pardefines += fspec._defstr + " " + p + "\tp_[" + str(i) + "]\n"
for i, v in enumerate(fspec.vars):
vardefines += fspec._defstr + " " + v + "\tY_[" + str(i) + "]\n"
for i, v in enumerate(fspec.auxvars):
auxvardefines += fspec._defstr+" "+v+"\t("+fspec._auxdefs_parsed[v]+")\n"
for i, inp in enumerate(fspec.inputs):
inpdefines += fspec._defstr + " " + inp + "\txv_[" + str(i) + "]\n"
allfilestr += "\n/* Variable, aux variable, parameter, and input definitions: */ \n" \
+ pardefines + vardefines + auxvardefines + inpdefines + "\n"
# preprocess event code
allevs = ""
eventNames = eventstruct.sortedEventNames()
numevs = len(eventNames)
for evname in eventNames:
ev = eventstruct.events[evname]
evfullfn = ""
from PyDSTool.Events import LowLevelEvent
assert isinstance(ev, LowLevelEvent), ("Radau can only "
"accept low level events")
evsig = ev._LLreturnstr + " " + ev.name + ev._LLargstr
assert ev._LLfuncstr.index(';') > 1, ("Event function code "
"error: Have you included a ';' character at the end of"
"your 'return' statement?")
fbody = ev._LLfuncstr
# check fbody for calls to user-defined aux fns
# and add hidden p argument
if fspec.auxfns:
fbody_parsed = addArgToCalls(fbody,
list(fspec.auxfns.keys()),
"p_, wk_, xv_")
if 'initcond' in fspec.auxfns:
# convert 'initcond(x)' to 'initcond("x")' for
# compatibility with C syntax
fbody_parsed = wrapArgInCall(fbody_parsed,
'initcond', '"')
else:
fbody_parsed = fbody
evbody = " {\n" + fbody_parsed + "\n}\n\n"
allevs += evsig + evbody
allfilestr += evsig + ";\n"
# add signature for auxiliary functions
if fspec.auxfns:
allfilestr += "\n"
for finfo in sorted(fspec.auxfns.values()):
allfilestr += finfo[1] + ";\n"
assignEvBody = ''.join([
"events[%d] = &%s;\n" % (i, name) for i, name in enumerate(eventNames)
])
allfilestr += "\nint N_EVENTS = " + str(numevs) + ";\nvoid assignEvents(" \
+ "EvFunType *events){\n " + assignEvBody \
+ "\n}\n\nvoid auxvars(unsigned, unsigned, double, double*, double*, " \
+ "double*, unsigned, double*, unsigned, double*);\n" \
+ """void jacobian(unsigned, unsigned, double, double*, double*, double**, unsigned, double*, unsigned, double*);
void jacobianParam(unsigned, unsigned, double, double*, double*, double**, unsigned, double*, unsigned, double*);
"""
allfilestr += "int N_AUXVARS = %d;\n\n\n" % len(fspec.auxvars)
allfilestr += "int N_EXTINPUTS = %d;\n\n\n" % len(fspec.inputs)
allfilestr += fspec.spec[0] + "\n\n"
if fspec.auxfns:
for fname, finfo in sortedDictItems(fspec.auxfns):
fbody = finfo[0]
# subs _p into auxfn-to-auxfn calls (but not to the signature)
fbody_parsed = addArgToCalls(fbody,
list(fspec.auxfns.keys()),
"p_, wk_, xv_", notFirst=fname)
if 'initcond' in fspec.auxfns:
# convert 'initcond(x)' to 'initcond("x")' for
# compatibility with C syntax, but don't affect the
# function signature!
fbody_parsed = wrapArgInCall(fbody_parsed,
'initcond', '"', notFirst=True)
allfilestr += "\n" + fbody_parsed + "\n\n"
# add auxiliary variables (shell of the function always present)
# add event functions
allfilestr += fspec.auxspec[0] + allevs
# if jacobians or mass matrix not present, fill in dummy
if 'massMatrix' not in fspec.auxfns:
allfilestr += """
void massMatrix(unsigned n_, unsigned np_, double t, double *Y_, double *p_, double **f_, unsigned wkn_, double *wk_, unsigned xvn_, double *xv_) {
}
"""
if 'Jacobian' not in fspec.auxfns:
allfilestr += """
void jacobian(unsigned n_, unsigned np_, double t, double *Y_, double *p_, double **f_, unsigned wkn_, double *wk_, unsigned xvn_, double *xv_) {
}
"""
if 'Jacobian_pars' not in fspec.auxfns:
allfilestr += """
void jacobianParam(unsigned n_, unsigned np_, double t, double *Y_, double *p_, double **f_, unsigned wkn_, double *wk_, unsigned xvn_, double *xv_) {
}
"""
return allfilestr
def test_combo_wrapArgInCall_and_addArgToCalls():
"""Test combo of addArgToCalls and wrapArgInCall with embedded calls"""
fs = "1/zeta(y_rel(y,initcond(y)+initcond(z)),z-initcond(x))+zeta(0.)"
fs_p = addArgToCalls(fs, ['zeta', 'y_rel', 'initcond', 'nothing'], "p")
assert '1/zeta(y_rel(y,initcond(y, p)+initcond(z, p), p),z-initcond(x, p), p)+zeta(0., p)' == fs_p
assert '1/zeta(y_rel(y,initcond("y", p)+initcond("z", p), p),z-initcond("x", p), p)+zeta(0., p)' == wrapArgInCall(fs_p, 'initcond', '"')