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andersxcharnley
andersx
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charnley
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Fchl merge (#79)
* Commit of all 'secret' FCHL operator code * Also adding the actual FCHL operator files * Updated init for alchemy.py * Updated import of alchemy module * Removed old file * Updated manual for FCHL functionality - still needs tutorial/examples pages
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‎docs/source/qml.rst

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qml\.representations module
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---------------------------
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.. automodule:: qml.representations
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.. automodule:: qml.representations.representations
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:members:
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:undoc-members:
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:show-inheritance:
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qml\.kernels module
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-------------------
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.. automodule:: qml.kernels
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.. automodule:: qml.kernels.kernels
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:members:
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:undoc-members:
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:show-inheritance:
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qml\.math module
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----------------
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.. automodule:: qml.math
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.. automodule:: qml.math.math
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:members:
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:undoc-members:
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:show-inheritance:
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:undoc-members:
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:show-inheritance:
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.. qml\.arad module
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.. ----------------
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..
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.. .. automodule:: qml.arad
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.. :members:
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.. :show-inheritance:
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qml\.fchl module
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qml\.fchl module, representations
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----------------
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.. automodule:: qml.representations.fchl
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.. automodule:: qml.fchl.fchl_representations
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:members:
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:show-inheritance:
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qml\.fchl module, scalar kernels
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----------------
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.. automodule:: qml.fchl.fchl_scalar_kernels
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:members:
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:show-inheritance:
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qml\.wrappers module
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--------------------
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qml\.fchl module, force kernels
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----------------
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.. automodule:: qml.fchl.fchl_force_kernels
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:members:
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:show-inheritance:
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.. automodule:: qml.kernels.wrappers
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qml\.fchl module, electric-field kernels
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----------------
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.. automodule:: qml.fchl.fchl_electric_field_kernels
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:undoc-members:
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.. qml\.wrappers module
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.. --------------------
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..
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.. .. automodule:: qml.kernels.wrappers
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.. :members:
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.. :undoc-members:
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.. :show-inheritance:
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.. qml\.data module
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.. ----------------
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..
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.. :undoc-members:
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.. :show-inheritance:
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qml\.arad module
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----------------
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.. automodule:: qml.arad.arad
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:members:
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:show-inheritance:
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qml\.aglaia module
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------------------

‎qml/arad/arad.py

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from .farad_kernels import fget_atomic_kernels_arad
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from .farad_kernels import fget_atomic_symmetric_kernels_arad
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from ..representations.alchemy import PTP
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from qml.data.alchemy import PTP
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def getAngle(sp,norms):
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epsilon = 10.* np.finfo(float).eps

‎qml/data/__init__.py

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# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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# SOFTWARE.
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from .xyzdataprovider import XYZDataProvider
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from .compound import Compound
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from .alchemy import ELEMENT_NAME, NUCLEAR_CHARGE

‎qml/representations/alchemy.py ‎qml/data/alchemy.py

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import numpy as np
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from copy import copy
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ELEMENT_NAME = {
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1: 'H' ,
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2: 'He' ,
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3: 'Li' ,
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4: 'Be' ,
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5: 'B' ,
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6: 'C' ,
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7: 'N' ,
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8: 'O' ,
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9: 'F' ,
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10: 'Ne' ,
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11: 'Na' ,
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12: 'Mg' ,
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13: 'Al' ,
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14: 'Si' ,
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15: 'P' ,
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16: 'S' ,
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17: 'Cl' ,
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18: 'Ar' ,
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19: 'K' ,
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20: 'Ca' ,
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21: 'Sc' ,
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22: 'Ti' ,
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23: 'V' ,
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24: 'Cr' ,
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25: 'Mn' ,
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26: 'Fe' ,
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27: 'Co' ,
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28: 'Ni' ,
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29: 'Cu' ,
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30: 'Zn' ,
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31: 'Ga' ,
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32: 'Ge' ,
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33: 'As' ,
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34: 'Se' ,
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35: 'Br' ,
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36: 'Kr' ,
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37: 'Rb' ,
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38: 'Sr' ,
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39: 'Y' ,
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40: 'Zr' ,
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41: 'Nb' ,
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42: 'Mo' ,
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43: 'Tc' ,
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44: 'Ru' ,
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45: 'Rh' ,
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46: 'Pd' ,
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48: 'Cd' ,
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49: 'In' ,
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50: 'Sn' ,
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52: 'Te' ,
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53: 'I' ,
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54: 'Xe' ,
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55: 'Cs' ,
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57: 'La' ,
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58: 'Ce' ,
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59: 'Pr' ,
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60: 'Nd' ,
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61: 'Pm' ,
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68: 'Er' ,
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69: 'Tm' ,
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70: 'Yb' ,
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71: 'Lu' ,
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72: 'Hf' ,
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73: 'Ta' ,
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74: 'W' ,
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75: 'Re' ,
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76: 'Os' ,
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78: 'Pt' ,
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79: 'Au' ,
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80: 'Hg' ,
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81: 'Tl' ,
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82: 'Pb' ,
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83: 'Bi' ,
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84: 'Po' ,
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85: 'At' ,
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86: 'Rn' ,
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87: 'Fr' ,
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88: 'Ra' ,
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89: 'Ac' ,
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90: 'Th' ,
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91: 'Pa' ,
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92: 'U' ,
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93: 'Np' ,
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94: 'Pu' ,
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95: 'Am' ,
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96: 'Cm' ,
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97: 'Bk' ,
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98: 'Cf' ,
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99: 'Es' ,
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100: 'Fm' ,
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101: 'Md' ,
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102: 'No' ,
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103: 'Lr' ,
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104: 'Rf' ,
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105: 'Db' ,
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106: 'Sg' ,
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107: 'Bh' ,
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108: 'Hs' ,
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109: 'Mt' ,
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110: 'Ds' ,
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NUCLEAR_CHARGE = {
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'H' : 1,
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'He' : 2,

‎qml/data/compound.py

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import numpy as np
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import collections
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from ..representations.alchemy import NUCLEAR_CHARGE
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from .alchemy import NUCLEAR_CHARGE
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from ..representations import generate_coulomb_matrix
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from ..representations import generate_atomic_coulomb_matrix

‎qml/fchl/__init__.py

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# MIT License
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#
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# Copyright (c) 2017 Anders S. Christensen and Felix A. Faber
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# Copyright (c) 2017 Anders S. Christensen, Felix A. Faber
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#
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# Permission is hereby granted, free of charge, to any person obtaining a copy
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# of this software and associated documentation files (the "Software"), to deal
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# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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# SOFTWARE.
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from .fchl import *
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from .fchl_representations import *
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from .fchl_scalar_kernels import *
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from .fchl_force_kernels import *
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from .fchl_electric_field_kernels import *

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