qmlcode · larsbratholm · Jul 28, 2018 · Jul 26, 2018 · Jul 26, 2018 · Jul 28, 2018
diff --git a/README.rst b/README.rst
@@ -16,6 +16,8 @@ Current list of contributors:
 - Felix A. Faber (University of Basel)
 - Bing Huang (University of Basel)
 - David R. Glowacki (University of Bristol) 
+- Alexandre Tkatchenko (University of Luxembourg)
+- Klaus-Robert Müller (Technische Universitat Berlin/Korea University)
 - \O. Anatole von Lilienfeld (University of Basel)
 
 1) Citing QML:
@@ -26,7 +28,7 @@ repository as:
 
 ::
 
-    AS Christensen, LA Bratholm, S Amabilino, FA Faber, B Huang, GR Glowacki, OA von Lilienfeld (2018) "QML: A Python Toolkit for Quantum Machine Learning" https://github.com/qmlcode/qml
+    AS Christensen, LA Bratholm, S Amabilino, JC Kromann, FA Faber, B Huang, GR Glowacki, A Tkatchenko, K.R. Muller, OA von Lilienfeld (2018) "QML: A Python Toolkit for Quantum Machine Learning" https://github.com/qmlcode/qml
 
 2) Get help:
 ------------

diff --git a/docs/source/citation.rst b/docs/source/citation.rst
@@ -9,7 +9,6 @@ Until the preprint is available from arXiv, please cite use of QML as:
 
 ::
 
-    AS Christensen, LA Bratholm, S Amabilino, FA Faber, B Huang, DR Glowacki, OA von Lilienfeld (2018) "QML: A Python Toolkit for Quantum Machine Learning" https://github.com/qmlcode/qml
-
+    AS Christensen, LA Bratholm, S Amabilino, JC Kromann, FA Faber, B Huang, GR Glowacki, A Tkatchenko, K.R. Muller, OA von Lilienfeld (2018) "QML: A Python Toolkit for Quantum Machine Learning" https://github.com/qmlcode/qml
 
 
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -19,13 +19,17 @@ to make it easy for computational chemists to use these for machine-learning tas
 Current list of contributors:
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
--  Anders S. Christensen (University of Basel)
--  Lars A. Bratholm (University of Bristol)
--  Silvia Amabilino (University of Bristol)
--  Felix A. Faber (University of Basel)
--  Bing Huang (University of Basel)
--  David R. Glowacki (University of Bristol)
--  O. Anatole von Lilienfeld (University of Basel)
+- Anders S. Christensen (University of Basel)
+- Lars A. Bratholm (University of Bristol)
+- Silvia Amabilino (University of Bristol)
+- Jimmy C. Kromann (University of Basel)
+- Felix A. Faber (University of Basel)
+- Bing Huang (University of Basel)
+- David R. Glowacki (University of Bristol) 
+- Alexandre Tkatchenko (University of Luxembourg)
+- Klaus-Robert Müller (Technische Universitat Berlin/Korea University)
+- \O. Anatole von Lilienfeld (University of Basel)
+
 
 Code development
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -48,7 +52,7 @@ Until the preprint is available from arXiv, please cite use of QML as:
 
 ::
 
-    AS Christensen, LA Bratholm, S Amabilino, FA Faber, B Huang, DR Glowacki, OA von Lilienfeld (2018) "QML: A Python Toolkit for Quantum Machine Learning" https://github.com/qmlcode/qml
+    AS Christensen, LA Bratholm, S Amabilino, JC Kromann, FA Faber, B Huang, GR Glowacki, A Tkatchenko, K.R. Muller, OA von Lilienfeld (2018) "QML: A Python Toolkit for Quantum Machine Learning" https://github.com/qmlcode/qml
 
 
 For citation of the individual procedures of QML, please see the "Citing use of QML" section.

diff --git a/examples/ARMP_1.py b/examples/ARMP_1.py
@@ -1,3 +1,25 @@
+# MIT License
+#
+# Copyright (c) 2018 Silvia Amabilino
+#
+# 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.
+
 """
 This script shows how to set up the ARMP estimator where the XYZ data is used to make QML compounds and the local
 descriptors are generated from the QML compounds and then stored.
@@ -38,4 +60,4 @@
 
 print("The mean absolute error is %s kJ/mol." % (str(-score)))
 
-energies_predict = estimator.predict(idx)
+energies_predict = estimator.predict(idx)
diff --git a/examples/ARMP_2.py b/examples/ARMP_2.py
@@ -1,3 +1,25 @@
+# MIT License
+#
+# Copyright (c) 2018 Silvia Amabilino
+#
+# 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.
+
 """
 This script shows how to set up the ARMP estimator where the descriptor is set directly and stored in the class.
 """

diff --git a/examples/ARMP_3.py b/examples/ARMP_3.py
@@ -1,3 +1,25 @@
+# MIT License
+#
+# Copyright (c) 2018 Silvia Amabilino
+#
+# 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.
+
 """
 This script shows how to set up the ARMP estimator where the data to be fitted is passed directly to the fit function.
 """

diff --git a/examples/MRMP_1.py b/examples/MRMP_1.py
@@ -1,3 +1,26 @@
+# MIT License
+#
+# Copyright (c) 2018 Silvia Amabilino
+#
+# 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.
+
+
 """
 This script shows how to set up the MRMP estimator where the XYZ data is used to make QML compounds and global descriptors
 are generated from the QML compounds and stored.
@@ -37,4 +60,4 @@
 
 print("The mean absolute error is %s kJ/mol." % (str(-score)))
 
-energies_predict = estimator.predict(idx)
+energies_predict = estimator.predict(idx)
diff --git a/examples/MRMP_2.py b/examples/MRMP_2.py
@@ -1,3 +1,26 @@
+# MIT License
+#
+# Copyright (c) 2018 Silvia Amabilino
+#
+# 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.
+
+
 """
 This script shows how to set up the MRMP estimator where the descriptor is set directly and stored in the class.
 """
@@ -34,4 +57,4 @@
 
 print("The mean absolute error is %s kJ/mol." % (str(-score)))
 
-energies_predict = estimator.predict(idx)
+energies_predict = estimator.predict(idx)
diff --git a/examples/MRMP_3.py b/examples/MRMP_3.py
@@ -1,3 +1,25 @@
+# MIT License
+#
+# Copyright (c) 2018 Silvia Amabilino
+#
+# 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.
+
 """
 This script shows how to set up the MRMP estimator where the data to be fitted is passed directly to the fit function.
 """

diff --git a/examples/qm7_hyperparam_search/make_model_pickle.py b/examples/qm7_hyperparam_search/make_model_pickle.py
@@ -1,3 +1,26 @@
+# MIT License
+#
+# Copyright (c) 2018 Silvia Amabilino
+#
+# 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.
+
+
 import pickle
 import glob
 import numpy as np

diff --git a/qml/aglaia/aglaia.py b/qml/aglaia/aglaia.py
@@ -1,3 +1,25 @@
+# MIT License
+#
+# Copyright (c) 2018 Silvia Amabilino, Lars Andersen Bratholm
+#
+# 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.
+
 """
 Module containing the general neural network class and the child classes for the molecular and atomic neural networks.
 """

diff --git a/qml/aglaia/np_symm_funct.py b/qml/aglaia/np_symm_funct.py
@@ -1,3 +1,26 @@
+# MIT License
+#
+# Copyright (c) 2018 Silvia Amabilino
+#
+# 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.
+
+
 """
 This module contains an implementation of the symmetry functions used by Parkhill in the Tensormol paper:
 https://arxiv.org/pdf/1711.06385.pdf
@@ -223,4 +246,4 @@ def generate_acsf(xyzs, Zs, elements, element_pairs, radial_cutoff, angular_cuto
 
     rad_term = acsf_rad(xyzs, zs, elements, radial_cutoff, radial_rs, eta)
     ang_term = acsf_ang(xyzs, zs, element_pairs, angular_cutoff, angular_rs, theta_s, zeta, eta)
-    print(rad_term)
+    print(rad_term)
diff --git a/qml/aglaia/placeholder.py b/qml/aglaia/placeholder.py
@@ -1,3 +1,24 @@
+# MIT License
+#
+# Copyright (c) 2018 Silvia Amabilino, Lars Andersen Bratholm
+#
+# 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.
 #
 #   fit forces
 #        # Placeholders for the input/output data

diff --git a/qml/aglaia/symm_funct.py b/qml/aglaia/symm_funct.py
@@ -1,3 +1,26 @@
+# MIT License
+#
+# Copyright (c) 2018 Silvia Amabilino
+#
+# 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.
+
+
 """
 This module contains an implementation of the the symmetry functions used in the Parkhill paper https://arxiv.org/pdf/1711.06385.pdf.
 This implementation is different. It works for both data sets where all the molecules are the same but in different configurations and
@@ -377,4 +400,4 @@ def generate_parkhill_acsf(xyzs, Zs, elements, element_pairs, radial_cutoff, ang
     with tf.name_scope("ACSF"):
         acsf = tf.concat([rad_term, ang_term], axis=-1, name="acsf") # (n_samples, n_atoms, n_rad_rs*n_elements + n_thetas * n_ang_rs*n_elementpairs)
 
-    return acsf
+    return acsf
Original file line number	Diff line number	Diff line change
Expand Up		@@ -9,7 +9,6 @@ Until the preprint is available from arXiv, please cite use of QML as:

		::

		AS Christensen, LA Bratholm, S Amabilino, FA Faber, B Huang, DR Glowacki, OA von Lilienfeld (2018) "QML: A Python Toolkit for Quantum Machine Learning" https://github.com/qmlcode/qml

		AS Christensen, LA Bratholm, S Amabilino, JC Kromann, FA Faber, B Huang, GR Glowacki, A Tkatchenko, K.R. Muller, OA von Lilienfeld (2018) "QML: A Python Toolkit for Quantum Machine Learning" https://github.com/qmlcode/qml