def smc(model, t0=0):
import sympy
from sympy.printing import fcode
cmodel = model.compile_model()
template = fortran_model #open('fortran_model.f90').read()
write_prior_file(cmodel.prior, '.')
system_matrices = model.python_sims_matrices(matrix_format='symbolic')
npara = len(model.parameters)
para = sympy.IndexedBase('para', shape=(npara + 1, ))
fortran_subs = dict(
zip([sympy.symbols('garbage')] + model.parameters, para))
fortran_subs[0] = 0.0
fortran_subs[1] = 1.0
fortran_subs[100] = 100.0
fortran_subs[2] = 2.0
fortran_subs[400] = 400.0
fortran_subs[4] = 4.0
context = dict([(p.name, p)
for p in model.parameters + model['other_para']])
context['exp'] = sympy.exp
context['log'] = sympy.log
to_replace = {}
for p in model['other_para']:
to_replace[p] = eval(str(model['para_func'][p.name]), context)
to_replace = list(to_replace.items())
print(to_replace)
from itertools import combinations, permutations
edges = [(i, j) for i, j in permutations(to_replace, 2)
if type(i[1]) not in [float, int] and i[1].has(j[0])]
from sympy import default_sort_key, topological_sort
para_func = topological_sort([to_replace, edges], default_sort_key)
to_write = [
'GAM0', 'GAM1', 'PSI', 'PPI', 'self%QQ', 'DD2', 'self%ZZ', 'self%HH'
]
fmats = [
fcode((mat.subs(para_func)).subs(fortran_subs),
assign_to=n,
source_format='free',
standard=95,
contract=False) for mat, n in zip(system_matrices, to_write)
]
sims_mat = '\n\n'.join(fmats)
template = template.format(model=model,
yy=cmodel.yy,
p0='',
t0=t0,
sims_mat=sims_mat)
return template
def test_Module():
x = Symbol('x', real=True)
v_x = Variable.deduced(x)
sq = FunctionDefinition(real, 'sqr', [v_x], [Return(x**2)])
mod_sq = Module('mod_sq', [], [sq])
sq_call = FunctionCall('sqr', [42.])
prg_sq = Program(
'foobar',
[use('mod_sq', only=['sqr']),
Print(['"Square of 42 = "', sq_call])])
if not has_fortran():
skip("No fortran compiler found.")
(stdout, stderr), info = compile_run_strings(
[('mod_sq.f90', fcode(mod_sq, standard=90)),
('main.f90', fcode(prg_sq, standard=90))],
clean=True)
assert '42' in stdout
assert str(42**2) in stdout
assert stderr == ''
def test_Subroutine():
# Code to generate the subroutine in the example from
# http://www.fortran90.org/src/best-practices.html#arrays
r = Symbol('r', real=True)
i = Symbol('i', integer=True)
v_r = Variable.deduced(r, attrs=(dimension(assumed_extent), intent_out))
v_i = Variable.deduced(i)
v_n = Variable('n', integer)
do_loop = Do([
Assignment(Element(r, [i]), literal_dp(1)/i**2)
], i, 1, v_n)
sub = Subroutine("f", [v_r], [
Declaration(v_n),
Declaration(v_i),
Assignment(v_n, size(r)),
do_loop
])
x = Symbol('x', real=True)
v_x3 = Variable.deduced(x, attrs=[dimension(3)])
mod = Module('mymod', definitions=[sub])
prog = Program('foo', [
use(mod, only=[sub]),
Declaration(v_x3),
SubroutineCall(sub, [v_x3]),
Print([sum_(v_x3), v_x3])
])
if not has_fortran():
skip("No fortran compiler found.")
(stdout, stderr), info = compile_run_strings([
('a.f90', fcode(mod, standard=90)),
('b.f90', fcode(prog, standard=90))
], clean=True)
ref = [1.0/i**2 for i in range(1, 4)]
assert str(sum(ref))[:-3] in stdout
for _ in ref:
assert str(_)[:-3] in stdout
assert stderr == ''
def test_Program():
x = Symbol('x', real=True)
vx = Variable.deduced(x, 42)
decl = Declaration(vx)
prnt = Print([x, x+1])
prog = Program('foo', [decl, prnt])
if not has_fortran():
skip("No fortran compiler found.")
(stdout, stderr), info = compile_run_strings([('main.f90', fcode(prog, standard=90))], clean=True)
assert '42' in stdout
assert '43' in stdout
assert stderr == ''
assert info['exit_status'] == os.EX_OK
def test_ImpliedDoLoop():
if not has_fortran():
skip("No fortran compiler found.")
a, i = symbols('a i', integer=True)
idl = ImpliedDoLoop(i**3, i, -3, 3, 2)
ac = ArrayConstructor([-28, idl, 28])
a = array(a, dim=[':'], attrs=[allocatable])
prog = Program(
'idlprog',
[a.as_Declaration(), Assignment(a, ac),
Print([a])])
fsrc = fcode(prog, standard=2003, source_format='free')
(stdout, stderr), info = compile_run_strings([('main.f90', fsrc)],
clean=True)
for numstr in '-28 -27 -1 1 27 28'.split():
assert numstr in stdout
assert stderr == ''
assert info['exit_status'] == os.EX_OK
def convert_to_fortran(self):
"""Returns a list with the fortran source code for the SymPy expressions
Examples
========
>>> from sympy.parsing.sym_expr import SymPyExpression
>>> src2 = '''
... integer :: a, b, c, d
... real :: p, q, r, s
... c = a/b
... d = c/a
... s = p/q
... r = q/p
... '''
>>> p = SymPyExpression(src2, 'f')
>>> p.convert_to_fortran()
[' integer*4 a', ' integer*4 b', ' integer*4 c', ' integer*4 d', ' real*8 p', ' real*8 q', ' real*8 r', ' real*8 s', ' c = a/b', ' d = c/a', ' s = p/q', ' r = q/p']
"""
self._fcode = []
for iter in self._expr:
self._fcode.append(fcode(iter))
return self._fcode
def test_size():
x = Symbol('x', real=True)
sx = size(x)
assert fcode(sx, source_format='free') == 'size(x)'
def test_literal_dp():
assert fcode(literal_dp(0), source_format='free') == '0d0'
def test_dsign():
x = Symbol('x')
assert unchanged(dsign, 1, x)
assert fcode(dsign(literal_dp(1), x), standard=95,
source_format='free') == 'dsign(1d0, x)'
def test_isign():
x = Symbol('x', integer=True)
assert unchanged(isign, 1, x)
assert fcode(isign(1, x), standard=95,
source_format='free') == 'isign(1, x)'
def smc(model, t0=0):
import sympy
from sympy.printing import fcode
cmodel = model.compile_model()
template = fortran_model # open('fortran_model.f90').read()
write_prior_file(cmodel.prior, ".")
system_matrices = model.python_sims_matrices(matrix_format="symbolic")
npara = len(model.parameters)
para = sympy.IndexedBase("para", shape=(npara + 1,))
from .symbols import Parameter
fortran_subs = dict(
zip(
[sympy.symbols("garbage")] + [Parameter(px) for px in model.parameters],
para,
)
)
fortran_subs[0] = 0.0
fortran_subs[1] = 1.0
fortran_subs[100] = 100.0
fortran_subs[2] = 2.0
fortran_subs[400] = 400.0
fortran_subs[4] = 4.0
context_tuple = [(p, Parameter(p)) for p in model.parameters] + [
(p.name, p) for p in model["other_para"]
]
context = dict(context_tuple)
context["exp"] = sympy.exp
context["log"] = sympy.log
to_replace = {}
for p in model["other_para"]:
to_replace[p] = eval(str(model["para_func"][p.name]), context)
to_replace = list(to_replace.items())
print(to_replace)
from itertools import combinations, permutations
edges = [
(i, j)
for i, j in permutations(to_replace, 2)
if type(i[1]) not in [float, int] and i[1].has(j[0])
]
from sympy import default_sort_key, topological_sort
para_func = topological_sort([to_replace, edges], default_sort_key)
to_write = ["GAM0", "GAM1", "PSI", "PPI", "self%QQ", "DD2", "self%ZZ", "self%HH"]
fmats = [
fcode(
(mat.subs(para_func)).subs(fortran_subs),
assign_to=n,
source_format="free",
standard=95,
contract=False,
)
for mat, n in zip(system_matrices, to_write)
]
sims_mat = "\n\n".join(fmats)
template = template.format(
model=model, yy=cmodel.yy, p0="", t0=t0, sims_mat=sims_mat
)
return template
