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Fix stable IsotopeQuantity #339

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merged 8 commits into from
May 16, 2022
Merged

Fix stable IsotopeQuantity #339

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e7f95be
add different conversions if self.is_stable
jvavrek May 2, 2022
17daadb
add tests for 0 bq/uci if stable
jvavrek May 2, 2022
d99490d
check input args for stable isotope qty
jvavrek May 2, 2022
e979c26
remove unused var
jvavrek May 2, 2022
733fdd6
Merge branch 'main' into fix-stable-isoqty
jvavrek May 2, 2022
a4ba202
update isotopes notebook
jvavrek May 2, 2022
c32cdc1
Merge branch 'fix-stable-isoqty' of github.com:lbl-anp/becquerel into…
jvavrek May 2, 2022
fc51a70
clean isotopes.ipynb
jvavrek May 16, 2022
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28 changes: 18 additions & 10 deletions becquerel/tools/isotope_qty.py
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Original file line number Diff line number Diff line change
Expand Up @@ -163,16 +163,24 @@ def _quantities_from_kwargs(self, **kwargs):

# dictionary with functions that define how to calculate all quantities
# in a circular manner
conversions = dict(
atoms=lambda: ref_quantities["g"] / self.isotope.A * N_AV,
bq=lambda: ref_quantities["atoms"] * self.decay_const,
uci=lambda: ref_quantities["bq"] / UCI_TO_BQ,
g=lambda: ref_quantities["uci"]
* UCI_TO_BQ
/ self.decay_const
/ N_AV
* self.isotope.A,
)
if self.is_stable:
conversions = dict(
atoms=lambda: ref_quantities["g"] / self.isotope.A * N_AV,
g=lambda: ref_quantities["atoms"] * self.isotope.A / N_AV,
bq=lambda: 0,
uci=lambda: 0,
)
else:
conversions = dict(
atoms=lambda: ref_quantities["g"] / self.isotope.A * N_AV,
bq=lambda: ref_quantities["atoms"] * self.decay_const,
uci=lambda: ref_quantities["bq"] / UCI_TO_BQ,
g=lambda: ref_quantities["uci"]
* UCI_TO_BQ
/ self.decay_const
/ N_AV
* self.isotope.A,
)

# rotates the order of the list so that the provided kwarg is at [0]
order = ["atoms", "bq", "uci", "g"]
Expand Down
66 changes: 32 additions & 34 deletions examples/isotopes.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -148,7 +148,7 @@
"Abundance: 0.01+/-0.00%\n",
"Stable? False\n",
"Half-life: 1.248e+09 years\n",
"Decay modes: (['B-', 'EC'], [89.28, 10.72])\n",
"Decay modes: (['EC', 'B-'], [10.72, 89.28])\n",
"\n",
"Isotope: K-41\n",
"Spin-parity: 3/2+\n",
Expand Down Expand Up @@ -202,7 +202,7 @@
{
"data": {
"text/plain": [
"8.474020543863288"
"8.00631769726367"
]
},
"execution_count": 6,
Expand Down Expand Up @@ -231,12 +231,12 @@
"name": "stdout",
"output_type": "stream",
"text": [
"Ba-133: 4.707 uCi\n",
"Cd-109: 0.016 uCi\n",
"Ba-133: 4.004 uCi\n",
"Cd-109: 0.004 uCi\n",
"Co-57: 0.000 uCi\n",
"Co-60: 1.978 uCi\n",
"Mn-54: 0.001 uCi\n",
"Na-22: 0.437 uCi\n"
"Co-60: 1.431 uCi\n",
"Mn-54: 0.000 uCi\n",
"Na-22: 0.226 uCi\n"
]
}
],
Expand Down Expand Up @@ -268,9 +268,9 @@
"name": "stdout",
"output_type": "stream",
"text": [
"37000.00000000001 Bq of Co-60 (at 2017-03-16 14:00:00)\n",
"73926311.79156348 Bq of K-40 (at 2019-11-14 16:16:17.484865)\n",
"4104.821259246284 Bq of U-238 (at 2019-11-14 16:16:17.495673)\n"
"37000.0 Bq of Co-60 (at 2017-03-16 14:00:00)\n",
"73926311.7915635 Bq of K-40 (at 2022-05-02 14:53:32.265827)\n",
"4104.821259246285 Bq of U-238 (at 2022-05-02 14:53:32.272388)\n"
]
}
],
Expand All @@ -297,7 +297,7 @@
{
"data": {
"text/plain": [
"3.831751598190806"
"3.8317515981908064"
]
},
"execution_count": 9,
Expand All @@ -317,7 +317,7 @@
{
"data": {
"text/plain": [
"576.9086036541194"
"149.24053998847538"
]
},
"execution_count": 10,
Expand Down Expand Up @@ -357,7 +357,7 @@
{
"data": {
"text/plain": [
"229361876.6085581"
"23101885.23242553"
]
},
"execution_count": 12,
Expand Down Expand Up @@ -494,7 +494,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
"11804946.77955213 Bq of Na-24 (at 2017-04-30 11:32:00)\n"
"11804946.779552134 Bq of Na-24 (at 2017-04-30 11:32:00)\n"
]
}
],
Expand Down Expand Up @@ -524,7 +524,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
"2.1776251393191668e-07 g of Na-23\n"
"2.177625139319166e-07 g of Na-23\n"
]
}
],
Expand All @@ -536,30 +536,28 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 19,
"metadata": {},
"outputs": [],
"source": []
"outputs": [
{
"data": {
"text/plain": [
"2.177625139319166e-07"
]
},
"execution_count": 19,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"na23_qty.g_at()"
]
}
],
"metadata": {
"anaconda-cloud": {},
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.3"
"name": "python"
}
},
"nbformat": 4,
Expand Down
26 changes: 26 additions & 0 deletions tests/isotope_qty_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -101,6 +101,12 @@ def test_isotopequantity_init_stable(stable_isotope, iq_date, iq_kwargs):
assert iq.isotope is stable_isotope
assert iq.half_life == stable_isotope.half_life
assert iq.decay_const == stable_isotope.decay_const
assert iq.bq_at() == iq.bq_at(iq.ref_date) == 0.0
assert iq.uci_at() == iq.uci_at(iq.ref_date) == 0.0
if "g" in iq_kwargs:
assert np.isclose(iq.g_at(), iq_kwargs["g"])
if "atoms" in iq_kwargs:
assert np.isclose(iq.atoms_at(), iq_kwargs["atoms"])


def test_isotopequantity_quantity_at(radioisotope, iq_kwargs):
Expand Down Expand Up @@ -545,6 +551,26 @@ def test_irradiation_str(start, stop, n_cm2, n_cm2_s):
print(str(ni))


def test_irradiation_nan_g():
"""Regression test for https://github.com/lbl-anp/becquerel/issues/325.

From examples/isotopes.ipynb
"""
iso = Isotope("Na-23")
iso2 = Isotope("Na-24")
barns = 2.3 # making this up for now

irradiation_start = "2017-04-30 10:32:00"
irradiation_stop = "2017-04-30 11:32:00"
flux = 3.1e11
ni = NeutronIrradiation(irradiation_start, irradiation_stop, n_cm2_s=flux)

activated_qty = IsotopeQuantity(iso2, date="2017-05-01", bq=103.2)
na23_qty = ni.activate(barns, initial=iso, activated=activated_qty)

assert not np.isnan(na23_qty.g_at())


# ----------------------------------------------------
# decay_normalize
# ----------------------------------------------------
Expand Down