Fchl merge

docs/source/qml.rst

@@ -8,15 +8,15 @@ Python API documentation
 qml\.representations module
 ---------------------------
 
-.. automodule:: qml.representations
+.. automodule:: qml.representations.representations
     :members:
     :undoc-members:
     :show-inheritance:
 
 qml\.kernels module
 -------------------
 
-.. automodule:: qml.kernels
+.. automodule:: qml.kernels.kernels
     :members:
     :undoc-members:
     :show-inheritance:
@@ -32,7 +32,7 @@ qml\.distance module
 qml\.math module
 ----------------
 
-.. automodule:: qml.math
+.. automodule:: qml.math.math
     :members:
     :undoc-members:
     :show-inheritance:
@@ -45,30 +45,44 @@ qml\.Compound class
     :undoc-members:
     :show-inheritance:
 
-.. qml\.arad module
-.. ----------------
-..
-.. .. automodule:: qml.arad
-..     :members:
-..     :show-inheritance:
 
-qml\.fchl module
+qml\.fchl module, representations
 ----------------
 
-.. automodule:: qml.representations.fchl
+ .. automodule:: qml.fchl.fchl_representations
     :members:
     :show-inheritance:
 
+qml\.fchl module, scalar kernels
+----------------
+ .. automodule:: qml.fchl.fchl_scalar_kernels
+    :members:
+    :show-inheritance:
 
-qml\.wrappers module
---------------------
+qml\.fchl module, force kernels 
+----------------
+
+ .. automodule:: qml.fchl.fchl_force_kernels
+    :members:
+    :show-inheritance:
 
-.. automodule:: qml.kernels.wrappers
+qml\.fchl module, electric-field kernels
+----------------
+
+ .. automodule:: qml.fchl.fchl_electric_field_kernels
     :members:
-    :undoc-members:
     :show-inheritance:
 
 
+.. qml\.wrappers module
+.. --------------------
+.. 
+.. .. automodule:: qml.kernels.wrappers
+..     :members:
+..     :undoc-members:
+..     :show-inheritance:
+
+
 .. qml\.data module
 .. ----------------
 ..
@@ -85,6 +99,12 @@ qml\.wrappers module
 ..    :undoc-members:
 ..    :show-inheritance:
 
+qml\.arad module
+----------------
+
+.. automodule:: qml.arad.arad
+    :members:
+    :show-inheritance:
 
 qml\.aglaia module
 ------------------

qml/arad/arad.py

@@ -33,7 +33,7 @@
 from .farad_kernels import fget_atomic_kernels_arad
 from .farad_kernels import fget_atomic_symmetric_kernels_arad
 
-from ..representations.alchemy import PTP
+from qml.data.alchemy import PTP
 
 def getAngle(sp,norms):
     epsilon = 10.* np.finfo(float).eps

qml/data/__init__.py

@@ -20,5 +20,7 @@
 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 # SOFTWARE.
 
+
 from .xyzdataprovider import XYZDataProvider
 from .compound import Compound
+from .alchemy import ELEMENT_NAME, NUCLEAR_CHARGE

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

@@ -26,6 +26,122 @@
 import numpy as np
 from copy import copy
 
+ELEMENT_NAME = {
+    1:  'H'  , 
+    2:  'He' , 
+    3:  'Li' , 
+    4:  'Be' , 
+    5:  'B'  , 
+    6:  'C'  , 
+    7:  'N'  , 
+    8:  'O'  , 
+    9:  'F'  , 
+   10:  'Ne' , 
+   11:  'Na' , 
+   12:  'Mg' , 
+   13:  'Al' , 
+   14:  'Si' , 
+   15:  'P'  , 
+   16:  'S'  , 
+   17:  'Cl' , 
+   18:  'Ar' , 
+   19:  'K'  , 
+   20:  'Ca' , 
+   21:  'Sc' , 
+   22:  'Ti' , 
+   23:  'V'  , 
+   24:  'Cr' , 
+   25:  'Mn' , 
+   26:  'Fe' , 
+   27:  'Co' , 
+   28:  'Ni' , 
+   29:  'Cu' , 
+   30:  'Zn' , 
+   31:  'Ga' , 
+   32:  'Ge' , 
+   33:  'As' , 
+   34:  'Se' , 
+   35:  'Br' , 
+   36:  'Kr' , 
+   37:  'Rb' , 
+   38:  'Sr' , 
+   39:  'Y'  , 
+   40:  'Zr' , 
+   41:  'Nb' , 
+   42:  'Mo' , 
+   43:  'Tc' , 
+   44:  'Ru' , 
+   45:  'Rh' , 
+   46:  'Pd' , 
+   47:  'Ag' , 
+   48:  'Cd' , 
+   49:  'In' , 
+   50:  'Sn' , 
+   51:  'Sb' , 
+   52:  'Te' , 
+   53:  'I'  , 
+   54:  'Xe' , 
+   55:  'Cs' , 
+   56:  'Ba' , 
+   57:  'La' , 
+   58:  'Ce' , 
+   59:  'Pr' , 
+   60:  'Nd' , 
+   61:  'Pm' , 
+   62:  'Sm' , 
+   63:  'Eu' , 
+   64:  'Gd' , 
+   65:  'Tb' , 
+   66:  'Dy' , 
+   67:  'Ho' , 
+   68:  'Er' , 
+   69:  'Tm' , 
+   70:  'Yb' , 
+   71:  'Lu' , 
+   72:  'Hf' , 
+   73:  'Ta' , 
+   74:  'W'  , 
+   75:  'Re' , 
+   76:  'Os' , 
+   77:  'Ir' , 
+   78:  'Pt' , 
+   79:  'Au' , 
+   80:  'Hg' , 
+   81:  'Tl' , 
+   82:  'Pb' , 
+   83:  'Bi' , 
+   84:  'Po' , 
+   85:  'At' , 
+   86:  'Rn' , 
+   87:  'Fr' , 
+   88:  'Ra' , 
+   89:  'Ac' , 
+   90:  'Th' , 
+   91:  'Pa' , 
+   92:  'U'  , 
+   93:  'Np' , 
+   94:  'Pu' , 
+   95:  'Am' , 
+   96:  'Cm' , 
+   97:  'Bk' , 
+   98:  'Cf' , 
+   99:  'Es' , 
+  100:  'Fm' , 
+  101:  'Md' , 
+  102:  'No' , 
+  103:  'Lr' , 
+  104:  'Rf' , 
+  105:  'Db' , 
+  106:  'Sg' , 
+  107:  'Bh' , 
+  108:  'Hs' , 
+  109:  'Mt' , 
+  110:  'Ds' , 
+  111:  'Rg' , 
+  112:  'Cn' , 
+  114:  'Uuq', 
+  116:  'Uuh'}
+
 NUCLEAR_CHARGE = {
  'H'  :     1, 
  'He' :     2, 

qml/data/compound.py

@@ -25,7 +25,7 @@
 import numpy as np
 import collections
 
-from ..representations.alchemy import NUCLEAR_CHARGE
+from .alchemy import NUCLEAR_CHARGE
 
 from ..representations import generate_coulomb_matrix
 from ..representations import generate_atomic_coulomb_matrix

qml/fchl/__init__.py

@@ -1,6 +1,6 @@
 # MIT License
 #
-# Copyright (c) 2017 Anders S. Christensen and Felix A. Faber
+# Copyright (c) 2017 Anders S. Christensen, Felix A. Faber
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal
@@ -20,4 +20,7 @@
 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 # SOFTWARE.
 
-from .fchl import *
+from .fchl_representations import *
+from .fchl_scalar_kernels import *
+from .fchl_force_kernels import *
+from .fchl_electric_field_kernels import *