Fchl doc

.travis.yml

@@ -7,7 +7,8 @@ group: edge
 
 deploy:
   provider: pages
-  local_dir: ${TRAVIS_BUILD_DIR}/docs/build/html
+  # local_dir: ${TRAVIS_BUILD_DIR}/docs/build/html
+  local_dir: /docs/build/html
   skip_cleanup: true
   repo: qmlcode/qmlcode.github.io
   target_branch: master

docs/source/examples.rst

@@ -261,7 +261,7 @@ The neighbors keyword is the max number of atoms with the cutoff-distance
 Generating the FCHL kernel 
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-The following example demonstrates how to calculate the local FCHL kernel elements between FCHL representations. ``X1`` and ``X2`` are numpy arrays with the shape ``(number_compounds,max_size, 5,neighbors)``, as generated in one of the previous examples. You MUST use the same cut-off distance to generate the representation and calculate the kernel.
+The following example demonstrates how to calculate the local FCHL kernel elements between FCHL representations. ``X1`` and ``X2`` are numpy arrays with the shape ``(number_compounds,max_size, 5,neighbors)``, as generated in one of the previous examples. You MUST use the same, or larger, cut-off distance to generate the representation, as to calculate the kernel.
 
 
 .. code:: python

qml/compound.py

@@ -52,7 +52,7 @@ def __init__(self, xyz = None):
         # Information about the compound
         self.natoms = float("nan")
         self.natypes = {}
-        self.atomtypes = empty_array
+        self.atomtypes = []
         self.atomtype_indices = collections.defaultdict(list)
         self.nuclear_charges = empty_array
         self.coordinates = empty_array
@@ -305,7 +305,7 @@ def read_xyz(self, filename):
         f.close()
 
         self.natoms = int(lines[0])
-        self.atomtypes = np.empty(self.natoms, dtype=str)
+        self.atomtypes = []
         self.nuclear_charges = np.empty(self.natoms, dtype=int)
         self.coordinates = np.empty((self.natoms, 3), dtype=float)
 
@@ -317,10 +317,10 @@ def read_xyz(self, filename):
             if len(tokens) < 4:
                 break
 
-            self.atomtypes[i] = tokens[0]
+            self.atomtypes.append(tokens[0])
             self.atomtype_indices[tokens[0]].append(i)
             self.nuclear_charges[i] = NUCLEAR_CHARGE[tokens[0]]
 
             self.coordinates[i] = np.asarray(tokens[1:4], dtype=float)
-    
+
         self.natypes = dict([(key, len(value)) for key,value in self.atomtype_indices.items()])

setup.py

@@ -7,7 +7,8 @@
 __copyright__ = "Copyright 2016"
 __credits__ = ["Anders S. Christensen et al. (2016) https://github.com/qmlcode/qml"]
 __license__ = "MIT"
-__version__ = "0.4.0.11"
+__version__ = "0.4.0.12"
+
 __maintainer__ = "Anders S. Christensen"
 __email__ = "andersbiceps@gmail.com"
 __status__ = "Beta"

tests/data/compound_test.xyz

@@ -0,0 +1,7 @@
+5
+
+C         -6.00533        0.91552        0.12550
+Cl        -4.22806        0.88165        0.08802
+Br        -6.62335        0.37844        1.87701
+H         -6.40470        0.21664       -0.63793
+H         -6.36029        1.94371       -0.09267

tests/test_compound.py

@@ -1 +1,49 @@
-# Test
+# MIT License
+#
+# Copyright (c) 2018 Anders Steen Christensen
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+from __future__ import print_function
+
+import os
+
+import qml
+import numpy as np
+
+def compare_lists(a, b):
+    for pair in zip(a,b):
+        if pair[0] != pair[1]:
+            return False
+    return True
+
+def test_compound():
+
+    test_dir = os.path.dirname(os.path.realpath(__file__))
+    c = qml.Compound(xyz=test_dir + "/data/compound_test.xyz")
+
+    ref_atomtypes = ['C', 'Cl', 'Br', 'H', 'H']
+    ref_charges = [ 6, 17, 35,  1 , 1]
+
+    assert compare_lists(ref_atomtypes, c.atomtypes), "Failed parsing atomtypes"
+    assert compare_lists(ref_charges, c.nuclear_charges), "Failed parsing nuclear_charges"
+
+if __name__ == "__main__":
+
+    test_compound()