{ "cells": [ { "cell_type": "markdown", "id": "median-armstrong", "metadata": {}, "source": [ "# Atomic Mass Evaluation (2016)\n", "\n", "Loading the Atomic Mass Evaluation 2016 (AME2016) is easy with`NucML`. The AME2016 library is originally split into three tables:\n", "\n", "* mass16\n", "* rct1-16\n", "* rct2-16\n", "\n", "\n", "For information on the contents including units and calculation methods please refer to the AME2016 website here.\n", "\n", "## Original AME Tables\n", "\n", "To load any of these tables simply start by importing the `nucml.datasets` module:" ] }, { "cell_type": "code", "execution_count": 2, "id": "dutch-stereo", "metadata": { "ExecuteTime": { "end_time": "2021-05-05T21:51:10.353810Z", "start_time": "2021-05-05T21:51:10.350311Z" } }, "outputs": [], "source": [ "# # Prototype\n", "# import sys\n", "# sys.path.append(\"../..\")" ] }, { "cell_type": "code", "execution_count": 1, "id": "manufactured-creature", "metadata": { "ExecuteTime": { "end_time": "2021-05-05T21:51:05.803782Z", "start_time": "2021-05-05T21:51:03.806995Z" } }, "outputs": [], "source": [ "import nucml.datasets as nuc_data" ] }, { "cell_type": "markdown", "id": "suitable-education", "metadata": {}, "source": [ "The `mass16` table contains precise atomic masses, mass excess information, the binding energy per nucleon, and the beta decay energy. As a table id, `NucML` added the `Element_w_A` feature so that joining with other tables is easier. Let us load and print the first few rows of the `mass16` table:" ] }, { "cell_type": "code", "execution_count": 3, "id": "fantastic-translator", "metadata": { "ExecuteTime": { "end_time": "2021-05-05T21:51:17.215483Z", "start_time": "2021-05-05T21:51:17.159516Z" } }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "INFO:root:AME: Reading and loading the Atomic Mass Evaluation file from: \n", " C:/Users/Pedro/Desktop/ML_Nuclear_Data/AME/CSV_Files\\AME_mass16.csv\n" ] }, { "data": { "text/html": [ "
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" ], "text/plain": [ " N Z A EL O Mass_Excess dMass_Excess Binding_Energy \\\n", "0 1 0 1 n Other 8071.31713 0.00046 0.000 \n", "1 0 1 1 H Other 7288.97061 0.00009 0.000 \n", "2 1 1 2 H Other 13135.72176 0.00011 1112.283 \n", "3 2 1 3 H Other 14949.80993 0.00022 2827.265 \n", "4 1 2 3 He Other 14931.21793 0.00021 2572.680 \n", "\n", " dBinding_Energy B_Decay_Energy dB_Decay_Energy Atomic_Mass_Micro \\\n", "0 0.0 782.347 0.0 1.008665e+06 \n", "1 0.0 NaN NaN 1.007825e+06 \n", "2 0.0 NaN NaN 2.014102e+06 \n", "3 0.0 18.592 0.0 3.016049e+06 \n", "4 0.0 -13736.000 2000.0 3.016029e+06 \n", "\n", " dAtomic_Mass_Micro Element_w_A \n", "0 0.00049 1n \n", "1 0.00009 1H \n", "2 0.00012 2H \n", "3 0.00023 3H \n", "4 0.00022 3He " ] }, "execution_count": 3, "metadata": {}, "output_type": "execute_result" } ], "source": [ "mass16 = nuc_data.load_ame(file=\"mass16\")\n", "mass16.head()" ] }, { "cell_type": "markdown", "id": "conceptual-peace", "metadata": {}, "source": [ "Similarly, we can load the `rct1` and `rct2` table." ] }, { "cell_type": "code", "execution_count": 4, "id": "sudden-fault", "metadata": { "ExecuteTime": { "end_time": "2021-05-05T21:51:19.669948Z", "start_time": "2021-05-05T21:51:19.630448Z" } }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "INFO:root:AME: Reading and loading the Atomic Mass Evaluation file from: \n", " C:/Users/Pedro/Desktop/ML_Nuclear_Data/AME/CSV_Files\\AME_rct1.csv\n" ] }, { "data": { "text/html": [ "
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" ], "text/plain": [ " S(2n) dS(2n) S(2p) dS(2p) Q(a) dQ(a) Q(2B-) dQ(2B-) Q(ep) \\\n", "0 NaN NaN NaN NaN NaN NaN NaN NaN NaN \n", "1 NaN NaN NaN NaN NaN NaN NaN NaN NaN \n", "2 NaN NaN NaN NaN NaN NaN NaN NaN NaN \n", "3 8481.79 0.0 NaN NaN NaN NaN -13717.0 2000.0 NaN \n", "4 NaN NaN 7718.04 0.0 NaN NaN NaN NaN NaN \n", "\n", " dQ(ep) Q(B-n) dQ(B-n) Element_w_A \n", "0 NaN NaN NaN 1n \n", "1 NaN NaN NaN 1H \n", "2 NaN NaN NaN 2H \n", "3 NaN NaN NaN 3H \n", "4 NaN NaN NaN 3He " ] }, "execution_count": 4, "metadata": {}, "output_type": "execute_result" } ], "source": [ "rct1 = nuc_data.load_ame(file=\"rct1\")\n", "rct1.head()" ] }, { "cell_type": "code", "execution_count": 5, "id": "ultimate-brisbane", "metadata": { "ExecuteTime": { "end_time": "2021-05-05T21:51:23.847228Z", "start_time": "2021-05-05T21:51:23.807728Z" } }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "INFO:root:AME: Reading and loading the Atomic Mass Evaluation file from: \n", " C:/Users/Pedro/Desktop/ML_Nuclear_Data/AME/CSV_Files\\AME_rct2.csv\n" ] }, { "data": { "text/html": [ "
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" ], "text/plain": [ " S(n) dS(n) S(p) dS(p) Q(4B-) dQ(4B-) Q(d,a) dQ(d,a) \\\n", "0 0.00 0.0 NaN NaN NaN NaN NaN NaN \n", "1 NaN NaN 0.00 0.0 NaN NaN NaN NaN \n", "2 2224.57 0.0 2224.57 0.0 NaN NaN 23846.53 0.0 \n", "3 6257.23 0.0 NaN NaN NaN NaN 17589.30 0.0 \n", "4 NaN NaN 5493.47 0.0 NaN NaN 18353.05 0.0 \n", "\n", " Q(p,a) dQ(p,a) Q(n,a) dQ(n,a) Element_w_A \n", "0 NaN NaN NaN NaN 1n \n", "1 NaN NaN NaN NaN 1H \n", "2 NaN NaN NaN NaN 2H \n", "3 19813.86 0.0 NaN NaN 3H \n", "4 NaN NaN 20577.62 0.0 3He " ] }, "execution_count": 5, "metadata": {}, "output_type": "execute_result" } ], "source": [ "rct2 = nuc_data.load_ame(file=\"rct2\")\n", "rct2.head()" ] }, { "cell_type": "markdown", "id": "recognized-recipient", "metadata": {}, "source": [ "You can join all tables using the `Element_w_A` feature or you can simply use the `nuc_data` module to load the merged file:" ] }, { "cell_type": "code", "execution_count": 6, "id": "coordinate-ecology", "metadata": { "ExecuteTime": { "end_time": "2021-05-05T21:51:25.087728Z", "start_time": "2021-05-05T21:51:25.015729Z" } }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "INFO:root:AME: Reading and loading Atomic Mass Evaluation files from: \n", " C:/Users/Pedro/Desktop/ML_Nuclear_Data/AME/CSV_Files\\AME_all_merged.csv\n" ] }, { "data": { "text/html": [ "
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" ], "text/plain": [ " N Z A EL O Mass_Excess dMass_Excess Binding_Energy \\\n", "0 1 0 1 n Other 8071.31713 0.00046 0.000 \n", "1 0 1 1 H Other 7288.97061 0.00009 0.000 \n", "2 1 1 2 H Other 13135.72176 0.00011 1112.283 \n", "3 2 1 3 H Other 14949.80993 0.00022 2827.265 \n", "4 1 2 3 He Other 14931.21793 0.00021 2572.680 \n", "\n", " dBinding_Energy B_Decay_Energy ... Q(n,np) Q(n,d) Q(n,2n) \\\n", "0 0.0 782.347 ... NaN NaN -0.00 \n", "1 0.0 NaN ... -0.00 2224.566 NaN \n", "2 0.0 NaN ... -2224.57 -0.004 -2224.57 \n", "3 0.0 18.592 ... NaN NaN -6257.23 \n", "4 0.0 -13736.000 ... -5493.47 -3268.904 NaN \n", "\n", " Q(n,t) Q(n,3He) Q(d,t) Q(d,3He) Q(3He,t) Q(3He,a) Q(t,a) \n", "0 NaN NaN 6257.229 NaN 763.755 20577.6194 NaN \n", "1 NaN NaN NaN 5493.4744 NaN NaN 19813.8649 \n", "2 6257.2311 NaN 4032.659 3268.9044 NaN 18353.0494 17589.2949 \n", "3 0.0011 NaN -0.001 NaN 0.000 14320.3894 NaN \n", "4 763.7511 0.0004 NaN 0.0044 -13754.592 NaN 14320.3949 \n", "\n", "[5 rows x 65 columns]" ] }, "execution_count": 6, "metadata": {}, "output_type": "execute_result" } ], "source": [ "ame = nuc_data.load_ame(file=\"merged\")\n", "ame.head()" ] }, { "cell_type": "markdown", "id": "young-angola", "metadata": {}, "source": [ "## Processed AME Tables\n", "\n", "In later sections, you will learn that the EXFOR database by itself does not contain many features for an ML model to use. The `AME` database contains a lot of useful information about every isotope that could potentially be useful if joined with `EXFOR`. Before doing this we need to bring the `AME` tables into an acceptable state. \n", "\n", "There are many missing values in the table. When preparing a dataset for ML there are a couple of strategies to deal with this. You can simply drop all rows with missing values but this means a big loss of information. Another option is filling the values with the mean of the features in the dataset. This latter option does not take into account the nature of the database. \n", "\n", "While you can personally start preparing and manipulating the `AME` tables, `NucML` offers a set of preprocessed files that are ready to use. Let us explore those." ] }, { "cell_type": "code", "execution_count": 7, "id": "pretty-river", "metadata": { "ExecuteTime": { "end_time": "2021-05-05T21:51:26.843649Z", "start_time": "2021-05-05T21:51:26.768150Z" } }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "INFO:root:AME: Reading and loading Atomic Mass Evaluation files from: \n", " C:/Users/Pedro/Desktop/ML_Nuclear_Data/AME/CSV_Files\\AME_all_merged_no_NaN.csv\n" ] }, { "data": { "text/html": [ "
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" ], "text/plain": [ " N Z A EL O Mass_Excess dMass_Excess Binding_Energy \\\n", "0 1 0 1 n Other 8071.31713 0.00046 0.000 \n", "1 0 1 1 H Other 7288.97061 0.00009 0.000 \n", "2 1 1 2 H Other 13135.72176 0.00011 1112.283 \n", "3 2 1 3 H Other 14949.80993 0.00022 2827.265 \n", "4 1 2 3 He Other 14931.21793 0.00021 2572.680 \n", "\n", " dBinding_Energy B_Decay_Energy ... Q(n,np) Q(n,d) \\\n", "0 0.0 782.347000 ... 2224.150559 4448.716559 \n", "1 0.0 -1025.364331 ... -0.000000 2224.566000 \n", "2 0.0 3792.058759 ... -2224.570000 -0.004000 \n", "3 0.0 18.592000 ... -2224.570000 -0.004000 \n", "4 0.0 -13736.000000 ... -5493.470000 -3268.904000 \n", "\n", " Q(n,2n) Q(n,t) Q(n,3He) Q(d,t) Q(d,3He) \\\n", "0 -0.000000 2086.042238 -58069.878992 6257.229000 7717.624959 \n", "1 -3814.015333 4171.487739 -43552.362241 2443.213754 5493.474400 \n", "2 -2224.570000 6257.231100 -29034.845490 4032.659000 3268.904400 \n", "3 -6257.230000 0.001100 -14517.328738 -0.001000 3268.904400 \n", "4 -12107.357125 763.751100 0.000400 -5850.128069 0.004400 \n", "\n", " Q(3He,t) Q(3He,a) Q(t,a) \n", "0 763.755000 20577.61940 22038.015459 \n", "1 -1043.956338 16763.60400 19813.864900 \n", "2 3773.466748 18353.04940 17589.294900 \n", "3 0.000000 14320.38940 17589.294900 \n", "4 -13754.592000 8470.26224 14320.394900 \n", "\n", "[5 rows x 65 columns]" ] }, "execution_count": 7, "metadata": {}, "output_type": "execute_result" } ], "source": [ "ame_imputed = nuc_data.load_ame(imputed_nan=True, file=\"merged\")\n", "ame_imputed.head()" ] }, { "cell_type": "markdown", "id": "contemporary-living", "metadata": {}, "source": [ "The `imputed_nan` option allows you to load the imputed `AME` table. This file was created by using linear interpolation feature-wise. For isotopes that do not have enough information, the mean of the feature is used to fill the values. \n", "\n", "The `EXFOR` database contains many experimental campaigns performed on natural targets. The `AME` database does not contain any information on natural data understandably. `NucML` offers two `AME` tables with natural data, one imputed and one raw. You can load them using:" ] }, { "cell_type": "code", "execution_count": 8, "id": "civilian-medline", "metadata": { "ExecuteTime": { "end_time": "2021-05-05T21:51:30.608110Z", "start_time": "2021-05-05T21:51:30.536109Z" } }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "INFO:root:AME: Reading and loading Atomic Mass Evaluation files from: \n", " C:/Users/Pedro/Desktop/ML_Nuclear_Data/AME/CSV_Files\\AME_Natural_Properties_w_NaN.csv\n" ] }, { "data": { "text/html": [ "
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NZAELOMass_ExcessdMass_ExcessBinding_EnergydBinding_EnergyB_Decay_Energy...Q(n,t)Q(n,3He)Q(d,t)Q(d,3He)Q(3He,t)Q(3He,a)Q(t,a)NeutronsMass_NumberFlag
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2516H-3n41875.72100254.12700961.63942.35424283.626...NaNNaN7169.189NaN24265.03421489.5794NaN56I
3415H-nn32892.4440089.443001336.35917.88921661.211...NaNNaN6457.229NaN21642.61920777.6194NaN45I
4314H-n24621.12700100.000001720.44925.00022196.211...NaNNaN7857.229NaN22177.61922177.6194NaN34I
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5 rows × 67 columns

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" ], "text/plain": [ " N Z A EL O Mass_Excess dMass_Excess Binding_Energy \\\n", "0 1 0 1 n Other 8071.31713 0.00046 0.000 \n", "1 6 1 7 H -nn 49135.00000 1004.00000 940.000 \n", "2 5 1 6 H -3n 41875.72100 254.12700 961.639 \n", "3 4 1 5 H -nn 32892.44400 89.44300 1336.359 \n", "4 3 1 4 H -n 24621.12700 100.00000 1720.449 \n", "\n", " dBinding_Energy B_Decay_Energy ... Q(n,t) Q(n,3He) Q(d,t) Q(d,3He) \\\n", "0 0.000 782.347 ... NaN NaN 6257.229 NaN \n", "1 143.000 23062.000 ... NaN NaN 5445.229 NaN \n", "2 42.354 24283.626 ... NaN NaN 7169.189 NaN \n", "3 17.889 21661.211 ... NaN NaN 6457.229 NaN \n", "4 25.000 22196.211 ... NaN NaN 7857.229 NaN \n", "\n", " Q(3He,t) Q(3He,a) Q(t,a) Neutrons Mass_Number Flag \n", "0 763.755 20577.6194 NaN 1 1 I \n", "1 23043.408 19765.6194 NaN 6 7 I \n", "2 24265.034 21489.5794 NaN 5 6 I \n", "3 21642.619 20777.6194 NaN 4 5 I \n", "4 22177.619 22177.6194 NaN 3 4 I \n", "\n", "[5 rows x 67 columns]" ] }, "execution_count": 8, "metadata": {}, "output_type": "execute_result" } ], "source": [ "ame_natural = nuc_data.load_ame(natural=True, file=\"merged\")\n", "ame_natural.head()" ] }, { "cell_type": "code", "execution_count": 9, "id": "executive-award", "metadata": { "ExecuteTime": { "end_time": "2021-05-05T21:51:32.854803Z", "start_time": "2021-05-05T21:51:32.783303Z" } }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "INFO:root:AME: Reading and loading Atomic Mass Evaluation files from: \n", " C:/Users/Pedro/Desktop/ML_Nuclear_Data/AME/CSV_Files\\AME_Natural_Properties_no_NaN.csv\n" ] }, { "data": { "text/html": [ "
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NZAELOMass_ExcessdMass_ExcessBinding_EnergydBinding_EnergyB_Decay_Energy...Q(n,t)Q(n,3He)Q(d,t)Q(d,3He)Q(3He,t)Q(3He,a)Q(t,a)NeutronsMass_NumberFlag
0101nOther8071.3171300.0004600.0000000.000000782.347000...0.0000000.06257.2290000.00000763.75500020577.6194000.00000011I
1011HOther-2437.418042-308.8751241124.312708-43.336286-5842.787372...5065.3777730.01666.9159104540.08726-5861.37920415987.30632718860.477844-10N
2011HOther7288.9706100.0000900.0000000.000000-1025.364293...4171.4877720.02443.2136345493.47440-1043.95616416763.60405319813.86490001I
3112HOther13135.7217600.0001101112.2830000.0000003792.058787...6257.2311000.04032.6590003268.904403773.46687618353.04940017589.29490012I
4213HOther14949.8099300.0002202827.2650000.00000018.592000...0.0011000.0-0.0010003268.904400.00000014320.38940017589.29490023I
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5 rows × 67 columns

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" ], "text/plain": [ " N Z A EL O Mass_Excess dMass_Excess Binding_Energy \\\n", "0 1 0 1 n Other 8071.317130 0.000460 0.000000 \n", "1 0 1 1 H Other -2437.418042 -308.875124 1124.312708 \n", "2 0 1 1 H Other 7288.970610 0.000090 0.000000 \n", "3 1 1 2 H Other 13135.721760 0.000110 1112.283000 \n", "4 2 1 3 H Other 14949.809930 0.000220 2827.265000 \n", "\n", " dBinding_Energy B_Decay_Energy ... Q(n,t) Q(n,3He) Q(d,t) \\\n", "0 0.000000 782.347000 ... 0.000000 0.0 6257.229000 \n", "1 -43.336286 -5842.787372 ... 5065.377773 0.0 1666.915910 \n", "2 0.000000 -1025.364293 ... 4171.487772 0.0 2443.213634 \n", "3 0.000000 3792.058787 ... 6257.231100 0.0 4032.659000 \n", "4 0.000000 18.592000 ... 0.001100 0.0 -0.001000 \n", "\n", " Q(d,3He) Q(3He,t) Q(3He,a) Q(t,a) Neutrons Mass_Number \\\n", "0 0.00000 763.755000 20577.619400 0.000000 1 1 \n", "1 4540.08726 -5861.379204 15987.306327 18860.477844 -1 0 \n", "2 5493.47440 -1043.956164 16763.604053 19813.864900 0 1 \n", "3 3268.90440 3773.466876 18353.049400 17589.294900 1 2 \n", "4 3268.90440 0.000000 14320.389400 17589.294900 2 3 \n", "\n", " Flag \n", "0 I \n", "1 N \n", "2 I \n", "3 I \n", "4 I \n", "\n", "[5 rows x 67 columns]" ] }, "execution_count": 9, "metadata": {}, "output_type": "execute_result" } ], "source": [ "ame_natural_imputed = nuc_data.load_ame(imputed_nan=True, natural=True, file=\"merged\")\n", "ame_natural_imputed.head()" ] }, { "cell_type": "markdown", "id": "promising-cedar", "metadata": {}, "source": [ "These tables are offered for you to get started and no guarantees are made. It is your responsibility to check the consistency and if needed create a new version of the table. We welcome collaboration so feel free to contribute by opening up a pull request. " ] } ], "metadata": { "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": "3.8.8" } }, "nbformat": 4, "nbformat_minor": 5 }