mirror of
https://github.com/LCPQ/EMSL_Basis_Set_Exchange_Local
synced 2024-12-31 08:35:49 +01:00
Anthony Scemama
commit
13b8c56766
43
README.md
43
README.md
@ -5,30 +5,39 @@ EMSL_Basis_Set_Exchange_Local
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Create of Local Copy of the famous [EMSL Basis Set Exchange](https://bse.pnl.gov/bse/portal) and use it easily with the API.
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* Make a slight copy (40Mo Sqlite3 database) of the EMSL Basis Set Exchange website (One database for all the basis set of one format);
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* API for scripting ;
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* Quick local access without delay ;
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* Only need [Python](https://www.python.org/) and [Request](http://docs.python-requests.org/en/latest/) module.
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* API for scripting;
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* Quick local access without delay;
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* Only need [Python](https://www.python.org/)
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##Dependancy
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##Dependency
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* Python >2.6
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* Request ```pip install requests```
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###### Optional
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If you plan to download manually some database -not using the pre existing one- you need :
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* [Request](http://docs.python-requests.org/en/latest/) python module. ```$pip install requests``` (do it in a virtual env or with sudo)
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##Installation
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* Download the git (```$ git clone https://github.com/TApplencourt/EMSL_Basis_Set_Exchange_Local.git``` for example)
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* ```cd``` into & run ```$ ./setup.py```
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* ```source EMSL_api.rc```
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* Done ! You can now, use ```EMSL_api.py``` or use all the python fonction inside ```./src```
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* Download the git repertory (```$git clone https://github.com/TApplencourt/EMSL_Basis_Set_Exchange_Local.git``` for example)
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* That all! You can now, use ```EMSL_api.py```
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##Usage
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```
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EMSL Api.
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Usage:
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EMSL_api.py get_list_basis <db_path>
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EMSL_api.py get_list_elements <db_path> <basis_name>
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EMSL_api.py get_basis_data <db_path> <basis_name> <elts>...
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EMSL_api.py get_list_formats
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EMSL_api.py create_db <db_path> <format> [--no-contraction]
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EMSL_api.py list_basis [--atom=<atom_name>...]
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[--db_path=<db_path>]
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EMSL_api.py list_atoms --basis=<basis_name>
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[--db_path=<db_path>]
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EMSL_api.py get_basis_data --basis=<basis_name>
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[--atom=<atom_name>...]
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[--db_path=<db_path>]
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[--with_l]
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[(--save [--path=<path>])]
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EMSL_api.py list_formats
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EMSL_api.py create_db --db_path=<db_path>
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--format=<format>
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[--no-contraction]
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EMSL_api.py (-h | --help)
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EMSL_api.py --version
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@ -38,7 +47,13 @@ Options:
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--no-contraction Basis functions are not contracted
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<db_path> is the path to the SQLite3 file containing the Basis sets.
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By default is $EMSL_API_ROOT/db/Gausian_uk.db
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```
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##Demonstration
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(For a beter quality see the [Source](https://asciinema.org/api/asciicasts/15380))
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##To do
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For now we can only parse Gaussian-US basis set type file. (Look at ```./src/EMSL_utility.py#EMSL_dump.basis_data_row_to_array```)
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@ -19,6 +19,29 @@ for i in data:
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dict_ele[l[1].strip().lower()] = l[2].strip().lower()
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def install_with_pip(name):
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ins = False
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d = {'y': True,
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'n': False}
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while True:
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choice = raw_input('Do you want to install it ? [Y/N]')
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try:
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ins = d[choice.lower()]
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break
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except:
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print "not a valid choice"
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if ins:
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try:
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import pip
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pip.main(['install', name])
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except:
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print "You need pip, (http://pip.readthedocs.org/en/latest/installing.html)"
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sys.exit(1)
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def cond_sql_or(table_name, l_value):
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l = []
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@ -36,8 +59,13 @@ class EMSL_dump:
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self.format = format
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self.contraction = str(contraction)
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import requests
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self.requests = requests
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try:
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import requests
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except:
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print "You need the requests package"
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install_with_pip("requests")
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finally:
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self.requests = requests
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def set_db_path(self, path):
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"""Define the database path"""
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@ -132,7 +160,7 @@ class EMSL_dump:
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data = data.replace("D+", "E+")
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data = data.replace("D-", "E-")
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data = data[b + 5:e-1].split('\n\n')
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data = data[b + 5:e - 1].split('\n\n')
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for (elt, data_elt) in zip(elts, data):
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@ -193,7 +221,7 @@ class EMSL_dump:
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q_out.put(([name, url, des, elts], basis_data))
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q_in.task_done()
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except:
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print name,url,des
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print name, url, des
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raise
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def enqueue():
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118
src/elts_abrev.dat
Normal file
118
src/elts_abrev.dat
Normal file
@ -0,0 +1,118 @@
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1 - H - Hydrogen
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2 - He - Helium
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3 - Li - Lithium
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4 - Be - Beryllium
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5 - B - Boron
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6 - C - Carbon
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7 - N - Nitrogen
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8 - O - Oxygen
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9 - F - Fluorine
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10 - Ne - Neon
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11 - Na - Sodium
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12 - Mg - Magnesium
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13 - Al - Aluminum
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14 - Si - Silicon
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15 - P - Phosphorus
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16 - S - Sulfur
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17 - Cl - Chlorine
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18 - Ar - Argon
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19 - K - Potassium
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20 - Ca - Calcium
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21 - Sc - Scandium
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22 - Ti - Titanium
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23 - V - Vanadium
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24 - Cr - Chromium
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25 - Mn - Manganese
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26 - Fe - Iron
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27 - Co - Cobalt
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28 - Ni - Nickel
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29 - Cu - Copper
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30 - Zn - Zinc
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31 - Ga - Gallium
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32 - Ge - Germanium
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33 - As - Arsenic
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34 - Se - Selenium
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35 - Br - Bromine
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36 - Kr - Krypton
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37 - Rb - Rubidium
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38 - Sr - Strontium
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39 - Y - Yttrium
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40 - Zr - Zirconium
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41 - Nb - Niobium
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42 - Mo - Molybdenum
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43 - Tc - Technetium
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44 - Ru - Ruthenium
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45 - Rh - Rhodium
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46 - Pd - Palladium
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47 - Ag - Silver
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48 - Cd - Cadmium
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49 - In - Indium
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50 - Sn - Tin
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51 - Sb - Antimony
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52 - Te - Tellurium
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53 - I - Iodine
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54 - Xe - Xenon
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55 - Cs - Cesium
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56 - Ba - Barium
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57 - La - Lanthanum
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58 - Ce - Cerium
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59 - Pr - Praseodymium
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60 - Nd - Neodymium
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61 - Pm - Promethium
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62 - Sm - Samarium
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63 - Eu - Europium
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64 - Gd - Gadolinium
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65 - Tb - Terbium
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66 - Dy - Dysprosium
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67 - Ho - Holmium
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68 - Er - Erbium
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69 - Tm - Thulium
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70 - Yb - Ytterbium
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71 - Lu - Lutetium
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72 - Hf - Hafnium
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73 - Ta - Tantalum
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74 - W - Tungsten
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75 - Re - Rhenium
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76 - Os - Osmium
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77 - Ir - Iridium
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78 - Pt - Platinum
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79 - Au - Gold
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80 - Hg - Mercury
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81 - Tl - Thallium
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82 - Pb - Lead
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83 - Bi - Bismuth
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84 - Po - Polonium
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85 - At - Astatine
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86 - Rn - Radon
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87 - Fr - Francium
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88 - Ra - Radium
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89 - Ac - Actinium
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90 - Th - Thorium
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91 - Pa - Protactinium
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92 - U - Uranium
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93 - Np - Neptunium
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94 - Pu - Plutonium
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95 - Am - Americium
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96 - Cm - Curium
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97 - Bk - Berkelium
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98 - Cf - Californium
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99 - Es - Einsteinium
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100 - Fm - Fermium
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101 - Md - Mendelevium
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102 - No - Nobelium
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103 - Lr - Lawrencium
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104 - Rf - Rutherfordium
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105 - Db - Dubnium
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106 - Sg - Seaborgium
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107 - Bh - Bohrium
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108 - Hs - Hassium
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109 - Mt - Meitnerium
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110 - Ds - Darmstadtium
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111 - Rg - Roentgenium
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112 - Cn - Copernicium
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113 - Uut - Ununtrium
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114 - Fl - Flerovium
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115 - Uup - Ununpentium
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116 - Lv - Livermorium
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117 - Uus - Ununseptium
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118 - Uuo - Ununoctium
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