def __call__(self, pattern=None):
for i, proc in enumerate(sorted(settings.rate_constants.keys())):
if pattern is None or fnmatch(proc, pattern):
rate_expr = settings.rate_constants[proc][0]
rate_const = evaluate_rate_expression(rate_expr,
settings.parameters)
print('# %s: %s = %.2e s^{-1}' % (proc, rate_expr, rate_const))
def __call__(self, pattern=None):
for i, proc in enumerate(sorted(settings.rate_constants.keys())):
if pattern is None or fnmatch(proc, pattern):
rate_expr = settings.rate_constants[proc][0]
rate_const = evaluate_rate_expression(rate_expr,
settings.parameters)
print('# %s: %s = %.2e s^{-1}' % (proc, rate_expr, rate_const))
def inverse(self):
res = '# kMC rate constants (%i)\n' % len(settings.rate_constants)
res += '# ------------------\n'
for proc in sorted(settings.rate_constants):
rate_expr = settings.rate_constants[proc][0]
rate_const = evaluate_rate_expression(rate_expr,
settings.parameters)
res += '# %s: %.2e s^{-1} = %s\n' % (proc, rate_const, rate_expr)
res += '# ------------------\n'
return res
def inverse(self):
res = '# kMC rate constants (%i)\n' % len(settings.rate_constants)
res += '# ------------------\n'
for proc in sorted(settings.rate_constants):
rate_expr = settings.rate_constants[proc][0]
rate_const = evaluate_rate_expression(rate_expr,
settings.parameters)
res += '# %s: %.2e s^{-1} = %s\n' % (proc, rate_const, rate_expr)
res += '# ------------------\n'
return res
def __repr__(self):
"""Compact representation of all current rate_constants."""
res = '# kMC rate constants (%i)\n' % len(settings.rate_constants)
res += '# ------------------\n'
for proc in sorted(settings.rate_constants):
rate_expr = settings.rate_constants[proc][0]
rate_const = evaluate_rate_expression(rate_expr,
settings.parameters)
res += '# %s: %s = %.2e s^{-1}\n' % (proc, rate_expr, rate_const)
res += '# ------------------\n'
return res
def __repr__(self):
"""Compact representation of all current rate_constants."""
res = '# kMC rate constants (%i)\n' % len(settings.rate_constants)
res += '# ------------------\n'
for proc in sorted(settings.rate_constants):
rate_expr = settings.rate_constants[proc][0]
rate_const = evaluate_rate_expression(rate_expr,
settings.parameters)
res += '# %s: %s = %.2e s^{-1}\n' % (proc, rate_expr, rate_const)
res += '# ------------------\n'
return res
def set(self, pattern, rate_constant, parameters=None):
"""Set rate constants. Pattern can be a glob pattern,
and the rate constant will be applied to all processes,
where the pattern matches. The rate constant can be either
a number or a rate expression.
"""
if parameters is None:
parameters = settings.parameters
if type(rate_constant) is str:
rate_constant = evaluate_rate_expression(rate_constant, parameters)
try:
rate_constant = float(rate_constant)
except:
raise UserWarning("Could not convert rate constant to float")
for i, proc in enumerate(sorted(settings.rate_constants.keys())):
if pattern is None or fnmatch(proc, pattern):
base.set_rate_const(i + 1, rate_constant)
def set(self, pattern, rate_constant, parameters=None):
"""Set rate constants. Pattern can be a glob pattern,
and the rate constant will be applied to all processes,
where the pattern matches. The rate constant can be either
a number or a rate expression.
"""
if parameters is None:
parameters = settings.parameters
if type(rate_constant) is str:
rate_constant = evaluate_rate_expression(rate_constant,
parameters)
try:
rate_constant = float(rate_constant)
except:
raise UserWarning("Could not convert rate constant to float")
for i, proc in enumerate(sorted(settings.rate_constants.keys())):
if pattern is None or fnmatch(proc, pattern):
base.set_rate_const(i + 1, rate_constant)
def set_rate_constants(parameters=None, print_rates=True):
"""Tries to evaluate the supplied expression for a rate constant
to a simple real number and sets it for the corresponding process.
For the evaluation it draws on predefined natural constants, user defined
parameters and mathematical functions.
"""
if parameters is None:
parameters = settings.parameters
if print_rates:
print('-------------------')
for proc in sorted(settings.rate_constants):
rate_expr = settings.rate_constants[proc][0]
rate_const = evaluate_rate_expression(rate_expr, parameters)
try:
base.set_rate_const(eval('proclist.%s' % proc.lower()), rate_const)
if print_rates:
n = int(4 * log(rate_const))
print('%30s: %.3e s^{-1}: %s' % (proc, rate_const, '#' * n))
except Exception, e:
raise UserWarning(
"Could not set %s for process %s!\nException: %s" \
% (rate_expr, proc, e))
def set_rate_constants(parameters=None, print_rates=True):
"""Tries to evaluate the supplied expression for a rate constant
to a simple real number and sets it for the corresponding process.
For the evaluation it draws on predefined natural constants, user defined
parameters and mathematical functions.
"""
if parameters is None:
parameters = settings.parameters
if print_rates:
print('-------------------')
for proc in sorted(settings.rate_constants):
rate_expr = settings.rate_constants[proc][0]
rate_const = evaluate_rate_expression(rate_expr, parameters)
try:
base.set_rate_const(eval('proclist.%s' % proc.lower()), rate_const)
if print_rates:
n = int(4 * log(rate_const))
print('%30s: %.3e s^{-1}: %s' % (proc, rate_const, '#' * n))
except Exception, e:
raise UserWarning(
"Could not set %s for process %s!\nException: %s" \
% (rate_expr, proc, e))
scale1.set_xlim(mumin, mumax)
plt.sca(scale1)
labs_seq = []
labs_seq = [1e-18, 1e-14, 1e-10, 1e-6, 1e-2, 1e2, 1e6, 1e10]
labs_seq_strings = []
marks = []
for T in [298.15]:
#for T in [200]:
for p in labs_seq:
labs_seq_strings.append(r'$10^{%d}$' % (np.log10(p)))
print evaluate_rate_expression('mu_H2Ogas', {
'T': {
'value': T
},
'p_H2Ogas': {
'value': p
}
})
value = evaluate_rate_expression('mu_H2Ogas', {
'T': {
'value': T
},
'p_H2Ogas': {
'value': p
}
})
marks.append(value)
def by_name(self, proc):
rate_expr = settings.rate_constants[proc][0]
return evaluate_rate_expression(rate_expr, settings.parameters)
def by_name(self, proc):
rate_expr = settings.rate_constants[proc][0]
return evaluate_rate_expression(rate_expr, settings.parameters)