From 2e24d6a70402cf5b7675ce267de7e488b1ab4c13 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Tue, 28 May 2024 19:39:29 +0000 Subject: [PATCH] Committing clang-format changes --- .clang-format | 14 ++++++++ .gitignore | 14 ++++++++ README.md | 16 +++++++++ docs/source/README.md | 16 +++++++++ .../background/algorithms/cap_methods/fmo.rst | 14 ++++++++ .../algorithms/cap_methods/h_capping.rst | 14 ++++++++ .../algorithms/cap_methods/index.rst | 14 ++++++++ .../algorithms/cap_methods/other_caps.rst | 14 ++++++++ .../algorithms/embed_methods/density.rst | 14 ++++++++ .../algorithms/embed_methods/index.rst | 14 ++++++++ .../algorithms/embed_methods/point_charge.rst | 14 ++++++++ .../algorithms/frag_methods/dclc.rst | 14 ++++++++ .../algorithms/frag_methods/fea.rst | 14 ++++++++ .../algorithms/frag_methods/gebf.rst | 14 ++++++++ .../algorithms/frag_methods/index.rst | 14 ++++++++ .../algorithms/frag_methods/mfcc.rst | 14 ++++++++ .../algorithms/frag_methods/mta.rst | 14 ++++++++ .../algorithms/frag_methods/other.rst | 14 ++++++++ .../algorithms/frag_methods/smf.rst | 14 ++++++++ docs/source/background/algorithms/index.rst | 14 ++++++++ .../algorithms/screening_methods/distance.rst | 14 ++++++++ .../algorithms/screening_methods/index.rst | 14 ++++++++ .../algorithms/screening_methods/smf.rst | 14 ++++++++ docs/source/background/bsse/distance.rst | 14 ++++++++ docs/source/background/bsse/history.rst | 14 ++++++++ docs/source/background/bsse/index.rst | 14 ++++++++ .../background/established_methods/dclc.rst | 14 ++++++++ .../background/established_methods/ecmfcc.rst | 14 ++++++++ .../background/established_methods/eembe.rst | 14 ++++++++ .../established_methods/efamfcc.rst | 14 ++++++++ .../background/established_methods/fea.rst | 14 ++++++++ .../background/established_methods/fmo.rst | 14 ++++++++ .../background/established_methods/gebf.rst | 14 ++++++++ .../background/established_methods/index.rst | 14 ++++++++ .../background/established_methods/kem.rst | 14 ++++++++ .../background/established_methods/mfcc.rst | 14 ++++++++ .../background/established_methods/mta.rst | 14 ++++++++ .../established_methods/overview.rst | 14 ++++++++ .../background/established_methods/smf.rst | 14 ++++++++ .../established_methods/timeline.rst | 14 ++++++++ docs/source/background/frag_v_nmer.rst | 14 ++++++++ .../background/fragment_based_methods.rst | 14 ++++++++ docs/source/background/index.rst | 14 ++++++++ docs/source/background/mbe/index.rst | 14 ++++++++ docs/source/background/terminology.rst | 14 ++++++++ docs/source/bibliography/index.rst | 14 ++++++++ docs/source/conf.py | 14 ++++++++ .../design/fragmented_molecule_driver.rst | 14 ++++++++ .../design/fragmented_nuclei_driver.rst | 14 ++++++++ .../design/fragmented_system_driver.rst | 14 ++++++++ .../developer/design/gmbe_coefficients.rst | 14 ++++++++ docs/source/developer/design/index.rst | 14 ++++++++ docs/source/developer/design/input_driver.rst | 14 ++++++++ docs/source/developer/design/nmers.rst | 14 ++++++++ docs/source/developer/design/overview.rst | 14 ++++++++ docs/source/developer/development/capping.rst | 14 ++++++++ docs/source/developer/development/index.rst | 14 ++++++++ docs/source/developer/index.rst | 14 ++++++++ docs/source/index.rst | 14 ++++++++ include/ghostfragment/equation/equation.hpp | 16 +++++++++ include/ghostfragment/equation/expression.hpp | 16 +++++++++ include/ghostfragment/equation/term.hpp | 16 +++++++++ .../charge_multiplicity_assigner.hpp | 16 +++++++++ .../property_types/expression.hpp | 16 +++++++++ .../fragmenting/capped_fragments.hpp | 16 +++++++++ .../fragmenting/fragmented_molecule.hpp | 16 +++++++++ .../property_types/input_queue.hpp | 23 +++++++++++-- .../property_types/nmer_screener.hpp | 16 +++++++++ .../property_types/property_types.hpp | 22 ++++++++++-- .../property_types/subset_map.hpp | 16 +++++++++ .../property_types/topology/broken_bonds.hpp | 18 +++++++++- .../topology/connectivity_table.hpp | 16 +++++++++ .../property_types/topology/nuclear_graph.hpp | 16 +++++++++ scripts/equations/generate_gmbe.py | 14 ++++++++ scripts/equations/index.py | 14 ++++++++ scripts/equations/intersection.py | 14 ++++++++ scripts/equations/set_base.py | 14 ++++++++ scripts/equations/tests/test_index.py | 14 ++++++++ scripts/equations/tests/test_intersection.py | 14 ++++++++ scripts/equations/tests/test_union.py | 14 ++++++++ scripts/equations/union.py | 14 ++++++++ src/ghostfragment/capping/capping.hpp | 16 +++++++++ src/ghostfragment/capping/dclc.cpp | 16 +++++++++ src/ghostfragment/capping/single_atom.cpp | 16 +++++++++ .../capping/weighted_distance.cpp | 16 +++++++++ src/ghostfragment/drivers/drivers.hpp | 16 +++++++++ src/ghostfragment/drivers/engine.hpp | 16 +++++++++ src/ghostfragment/drivers/fragment.cpp | 16 +++++++++ .../drivers/fragment_based_method.cpp | 16 +++++++++ src/ghostfragment/drivers/fragment_system.cpp | 16 +++++++++ src/ghostfragment/drivers/input_queue.cpp | 16 +++++++++ src/ghostfragment/drivers/neutral_singlet.cpp | 27 ++++++++++++--- src/ghostfragment/drivers/nmer_system.cpp | 16 +++++++++ .../equation/detail_/expression_pimpl.hpp | 16 +++++++++ .../equation/detail_/term_pimpl.hpp | 16 +++++++++ src/ghostfragment/equation/equation.cpp | 16 +++++++++ src/ghostfragment/equation/expression.cpp | 19 ++++++++++- src/ghostfragment/equation/term.cpp | 19 ++++++++++- src/ghostfragment/expressions/expressions.hpp | 16 +++++++++ src/ghostfragment/expressions/mbe.cpp | 16 +++++++++ src/ghostfragment/fragmenting/ao2atom.cpp | 16 +++++++++ src/ghostfragment/fragmenting/bond_based.cpp | 16 +++++++++ src/ghostfragment/fragmenting/cluster.cpp | 16 +++++++++ src/ghostfragment/fragmenting/heavy_atom.cpp | 16 +++++++++ .../fragmenting/inter_finder.cpp | 16 +++++++++ .../fragmenting/inter_finder.hpp | 16 +++++++++ src/ghostfragment/fragmenting/nmers.cpp | 16 +++++++++ src/ghostfragment/fragmenting/nuceli_ao.cpp | 16 +++++++++ .../screening/minimum_distance.cpp | 16 +++++++++ src/ghostfragment/screening/screening.hpp | 16 +++++++++ src/ghostfragment/topology/broken_bonds.cpp | 16 +++++++++ .../topology/covalent_radius.hpp | 2 +- src/ghostfragment/topology/distance.hpp | 16 +++++++++ .../nuclear_graph_from_connectivity.cpp | 16 +++++++++ src/python/export_ghostfragment.cpp | 16 +++++++++ tests/cxx/unit_tests/ghostfragment/README.rst | 14 ++++++++ .../unit_tests/ghostfragment/capping/dclc.cpp | 16 +++++++++ .../ghostfragment/capping/single_atom.cpp | 16 +++++++++ .../capping/weighted_distance.cpp | 16 +++++++++ tests/cxx/unit_tests/ghostfragment/caps.cpp | 16 +++++++++ .../ghostfragment/drivers/engine.cpp | 16 +++++++++ .../ghostfragment/drivers/fragment.cpp | 16 +++++++++ .../drivers/fragment_based_method.cpp | 34 ++++++++++++++----- .../drivers/fragmented_system.cpp | 16 +++++++++ .../ghostfragment/drivers/input_queue.cpp | 16 +++++++++ .../ghostfragment/drivers/neutral.cpp | 31 ++++++++++++++--- .../ghostfragment/drivers/nmer_system.cpp | 16 +++++++++ .../equation/detail_/expression_pimpl.cpp | 16 +++++++++ .../equation/detail_/term_pimpl.cpp | 16 +++++++++ .../ghostfragment/equation/expression.cpp | 16 +++++++++ .../ghostfragment/equation/term.cpp | 16 +++++++++ .../ghostfragment/expressions/mbe.cpp | 16 +++++++++ .../ghostfragment/fragmented_system.cpp | 16 +++++++++ .../ghostfragment/fragmenting/ao2atom.cpp | 20 +++++++++-- .../ghostfragment/fragmenting/bond_based.cpp | 16 +++++++++ .../ghostfragment/fragmenting/cluster.cpp | 16 +++++++++ .../ghostfragment/fragmenting/heavy_atom.cpp | 16 +++++++++ .../fragmenting/inter_finder.cpp | 16 +++++++++ .../ghostfragment/fragmenting/nmers.cpp | 16 +++++++++ .../ghostfragment/fragmenting/nuclei_ao.cpp | 16 +++++++++ tests/cxx/unit_tests/ghostfragment/main.cpp | 16 +++++++++ .../unit_tests/ghostfragment/nmer_system.cpp | 32 +++++++++++++---- .../ghostfragment/nuclear_graph.cpp | 16 +++++++++ .../ghostfragment/screening/distance.cpp | 16 +++++++++ .../ghostfragment/testing/README.rst | 14 ++++++++ .../unit_tests/ghostfragment/testing/aos.cpp | 16 +++++++++ .../unit_tests/ghostfragment/testing/aos.hpp | 16 +++++++++ .../ghostfragment/testing/are_caps_equal.hpp | 16 +++++++++ .../ghostfragment/testing/hc_fragment.cpp | 16 +++++++++ .../ghostfragment/testing/hydrocarbon.cpp | 16 +++++++++ .../testing/hydrocarbon/hydrocarbon.cpp | 16 +++++++++ .../testing/hydrocarbon/position.cpp | 2 +- .../ghostfragment/testing/sto3g.cpp | 16 +++++++++ .../ghostfragment/testing/sto3g.hpp | 16 +++++++++ .../ghostfragment/topology/broken_bonds.cpp | 16 +++++++++ .../nuclear_graph_from_connectivity.cpp | 16 +++++++++ tests/python/integration_tests/test_cap.py | 14 ++++++++ 157 files changed, 2396 insertions(+), 37 deletions(-) diff --git a/.clang-format b/.clang-format index 873a6596..d90e1f63 100644 --- a/.clang-format +++ b/.clang-format @@ -1,3 +1,17 @@ +# Copyright 2024 GhostFragment +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + --- Language: Cpp # BasedOnStyle: Mozilla diff --git a/.gitignore b/.gitignore index 36efe7bd..44d99644 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,17 @@ +# Copyright 2024 GhostFragment +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + ################################################################################ # # The master .gitignore lives at NWChemEx-Project/DeveloperTools. The .gitignore diff --git a/README.md b/README.md index e3aa6475..ed74522b 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,19 @@ + + # GhostFragment GhostFragment is a computational chemistry library focused on reusable, modular diff --git a/docs/source/README.md b/docs/source/README.md index 4a01a0ed..0ef940dd 100644 --- a/docs/source/README.md +++ b/docs/source/README.md @@ -1,3 +1,19 @@ + + # Build the Documentation for GhostFragment This directory contains the source files for GhostFragment's documentation. diff --git a/docs/source/background/algorithms/cap_methods/fmo.rst b/docs/source/background/algorithms/cap_methods/fmo.rst index 2e5db369..afd59534 100644 --- a/docs/source/background/algorithms/cap_methods/fmo.rst +++ b/docs/source/background/algorithms/cap_methods/fmo.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + ################## FMO Capping Method ################## diff --git a/docs/source/background/algorithms/cap_methods/h_capping.rst b/docs/source/background/algorithms/cap_methods/h_capping.rst index 1db31e8a..4de91637 100644 --- a/docs/source/background/algorithms/cap_methods/h_capping.rst +++ b/docs/source/background/algorithms/cap_methods/h_capping.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + ######### H Capping ######### diff --git a/docs/source/background/algorithms/cap_methods/index.rst b/docs/source/background/algorithms/cap_methods/index.rst index d76a5e94..329ccd4a 100644 --- a/docs/source/background/algorithms/cap_methods/index.rst +++ b/docs/source/background/algorithms/cap_methods/index.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + ############### Capping Methods ############### diff --git a/docs/source/background/algorithms/cap_methods/other_caps.rst b/docs/source/background/algorithms/cap_methods/other_caps.rst index 6d60f429..330a9342 100644 --- a/docs/source/background/algorithms/cap_methods/other_caps.rst +++ b/docs/source/background/algorithms/cap_methods/other_caps.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + ################### Other Types of Caps ################### diff --git a/docs/source/background/algorithms/embed_methods/density.rst b/docs/source/background/algorithms/embed_methods/density.rst index 2278e77a..592f8853 100644 --- a/docs/source/background/algorithms/embed_methods/density.rst +++ b/docs/source/background/algorithms/embed_methods/density.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + .. _density_embedding: ################# diff --git a/docs/source/background/algorithms/embed_methods/index.rst b/docs/source/background/algorithms/embed_methods/index.rst index 0fbdf5ba..d4b617e7 100644 --- a/docs/source/background/algorithms/embed_methods/index.rst +++ b/docs/source/background/algorithms/embed_methods/index.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + #################### Embedding Algorithms #################### diff --git a/docs/source/background/algorithms/embed_methods/point_charge.rst b/docs/source/background/algorithms/embed_methods/point_charge.rst index 6d74b512..d4b5db44 100644 --- a/docs/source/background/algorithms/embed_methods/point_charge.rst +++ b/docs/source/background/algorithms/embed_methods/point_charge.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + ###################### Point Charge Embedding ###################### diff --git a/docs/source/background/algorithms/frag_methods/dclc.rst b/docs/source/background/algorithms/frag_methods/dclc.rst index 59905f97..54b49ceb 100644 --- a/docs/source/background/algorithms/frag_methods/dclc.rst +++ b/docs/source/background/algorithms/frag_methods/dclc.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + .. _DCLC_fragmentation_method: ######################################################### diff --git a/docs/source/background/algorithms/frag_methods/fea.rst b/docs/source/background/algorithms/frag_methods/fea.rst index 9fe07a09..5dd07842 100644 --- a/docs/source/background/algorithms/frag_methods/fea.rst +++ b/docs/source/background/algorithms/frag_methods/fea.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + .. _fea_frag_method: diff --git a/docs/source/background/algorithms/frag_methods/gebf.rst b/docs/source/background/algorithms/frag_methods/gebf.rst index 26cd326f..c01b32c1 100644 --- a/docs/source/background/algorithms/frag_methods/gebf.rst +++ b/docs/source/background/algorithms/frag_methods/gebf.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + ########################## GEBF Fragmentation Methods ########################## diff --git a/docs/source/background/algorithms/frag_methods/index.rst b/docs/source/background/algorithms/frag_methods/index.rst index 312916f2..e9edd2ea 100644 --- a/docs/source/background/algorithms/frag_methods/index.rst +++ b/docs/source/background/algorithms/frag_methods/index.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + ######################## Fragmentation Algorithms ######################## diff --git a/docs/source/background/algorithms/frag_methods/mfcc.rst b/docs/source/background/algorithms/frag_methods/mfcc.rst index d8d5e3fc..9f1eaa78 100644 --- a/docs/source/background/algorithms/frag_methods/mfcc.rst +++ b/docs/source/background/algorithms/frag_methods/mfcc.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + .. _mfcc_frag_method: ######################### diff --git a/docs/source/background/algorithms/frag_methods/mta.rst b/docs/source/background/algorithms/frag_methods/mta.rst index 2d898a0b..57d46a98 100644 --- a/docs/source/background/algorithms/frag_methods/mta.rst +++ b/docs/source/background/algorithms/frag_methods/mta.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + ########################################## Molecular Tailoring Approach Fragmentation ########################################## diff --git a/docs/source/background/algorithms/frag_methods/other.rst b/docs/source/background/algorithms/frag_methods/other.rst index ab9372c2..577f5252 100644 --- a/docs/source/background/algorithms/frag_methods/other.rst +++ b/docs/source/background/algorithms/frag_methods/other.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + ############################## Other Fragmentation Algorithms ############################## diff --git a/docs/source/background/algorithms/frag_methods/smf.rst b/docs/source/background/algorithms/frag_methods/smf.rst index 421f3a00..d47229bd 100644 --- a/docs/source/background/algorithms/frag_methods/smf.rst +++ b/docs/source/background/algorithms/frag_methods/smf.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + ####################################################### Systematic Molecular Fragmentation Fragmentation Method ####################################################### diff --git a/docs/source/background/algorithms/index.rst b/docs/source/background/algorithms/index.rst index 78e9bd6e..0e8ce1f3 100644 --- a/docs/source/background/algorithms/index.rst +++ b/docs/source/background/algorithms/index.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + ##################################### Algorithms for Fragment-Based Methods ##################################### diff --git a/docs/source/background/algorithms/screening_methods/distance.rst b/docs/source/background/algorithms/screening_methods/distance.rst index 460045cf..07e7dfeb 100644 --- a/docs/source/background/algorithms/screening_methods/distance.rst +++ b/docs/source/background/algorithms/screening_methods/distance.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + ################################### Distance Based Screening Procedures ################################### diff --git a/docs/source/background/algorithms/screening_methods/index.rst b/docs/source/background/algorithms/screening_methods/index.rst index cb75977c..67c75294 100644 --- a/docs/source/background/algorithms/screening_methods/index.rst +++ b/docs/source/background/algorithms/screening_methods/index.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + ################# Screening Methods ################# diff --git a/docs/source/background/algorithms/screening_methods/smf.rst b/docs/source/background/algorithms/screening_methods/smf.rst index d207628b..cc9690d9 100644 --- a/docs/source/background/algorithms/screening_methods/smf.rst +++ b/docs/source/background/algorithms/screening_methods/smf.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + #################### SMF Screening Method #################### diff --git a/docs/source/background/bsse/distance.rst b/docs/source/background/bsse/distance.rst index 78ca88f6..e8c56e9f 100644 --- a/docs/source/background/bsse/distance.rst +++ b/docs/source/background/bsse/distance.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + .. _distance_based_cp: diff --git a/docs/source/background/bsse/history.rst b/docs/source/background/bsse/history.rst index 9f941b25..342b881d 100644 --- a/docs/source/background/bsse/history.rst +++ b/docs/source/background/bsse/history.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + ####### History ####### diff --git a/docs/source/background/bsse/index.rst b/docs/source/background/bsse/index.rst index 48ebc6d6..d023468f 100644 --- a/docs/source/background/bsse/index.rst +++ b/docs/source/background/bsse/index.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + ############################# Basis Set Superposition Error ############################# diff --git a/docs/source/background/established_methods/dclc.rst b/docs/source/background/established_methods/dclc.rst index f4dd8fb6..24138e79 100644 --- a/docs/source/background/established_methods/dclc.rst +++ b/docs/source/background/established_methods/dclc.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + .. _DCLC: ########################################### diff --git a/docs/source/background/established_methods/ecmfcc.rst b/docs/source/background/established_methods/ecmfcc.rst index ea76e305..2f2687b3 100644 --- a/docs/source/background/established_methods/ecmfcc.rst +++ b/docs/source/background/established_methods/ecmfcc.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + .. _ecmfcc: ##################### diff --git a/docs/source/background/established_methods/eembe.rst b/docs/source/background/established_methods/eembe.rst index 4ff6bb68..dd3bf3cf 100644 --- a/docs/source/background/established_methods/eembe.rst +++ b/docs/source/background/established_methods/eembe.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + ###################################################### Electorstatically-Embedded Many-Body Expansion (EE-MB) ###################################################### diff --git a/docs/source/background/established_methods/efamfcc.rst b/docs/source/background/established_methods/efamfcc.rst index 118717e4..d11a62de 100644 --- a/docs/source/background/established_methods/efamfcc.rst +++ b/docs/source/background/established_methods/efamfcc.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + .. _efa_mfcc: ########################################### diff --git a/docs/source/background/established_methods/fea.rst b/docs/source/background/established_methods/fea.rst index ee394f0f..6b7370c9 100644 --- a/docs/source/background/established_methods/fea.rst +++ b/docs/source/background/established_methods/fea.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + .. _fea: ############################### diff --git a/docs/source/background/established_methods/fmo.rst b/docs/source/background/established_methods/fmo.rst index 9e298276..023c8749 100644 --- a/docs/source/background/established_methods/fmo.rst +++ b/docs/source/background/established_methods/fmo.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + ################################# Fragment Molecular Orbital Method ################################# diff --git a/docs/source/background/established_methods/gebf.rst b/docs/source/background/established_methods/gebf.rst index f86bfbdc..a7dd67a6 100644 --- a/docs/source/background/established_methods/gebf.rst +++ b/docs/source/background/established_methods/gebf.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + ############################################# Generalized Energy Based Fragmentation (GEBF) ############################################# diff --git a/docs/source/background/established_methods/index.rst b/docs/source/background/established_methods/index.rst index 5cb5e9ab..f2bb98d2 100644 --- a/docs/source/background/established_methods/index.rst +++ b/docs/source/background/established_methods/index.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + .. _established_fragment_based_methods: ################################## diff --git a/docs/source/background/established_methods/kem.rst b/docs/source/background/established_methods/kem.rst index 212b393e..bb40e782 100644 --- a/docs/source/background/established_methods/kem.rst +++ b/docs/source/background/established_methods/kem.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + .. _kem: ########################## diff --git a/docs/source/background/established_methods/mfcc.rst b/docs/source/background/established_methods/mfcc.rst index a3202722..4c62a87e 100644 --- a/docs/source/background/established_methods/mfcc.rst +++ b/docs/source/background/established_methods/mfcc.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + .. _MFCC: ################################################## diff --git a/docs/source/background/established_methods/mta.rst b/docs/source/background/established_methods/mta.rst index 8975369e..9bc8cd6e 100644 --- a/docs/source/background/established_methods/mta.rst +++ b/docs/source/background/established_methods/mta.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + ################################## Molecular Tailoring Approach (MTA) ################################## diff --git a/docs/source/background/established_methods/overview.rst b/docs/source/background/established_methods/overview.rst index 713de487..f98da97e 100644 --- a/docs/source/background/established_methods/overview.rst +++ b/docs/source/background/established_methods/overview.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + ############################################## Overview of Established Fragment Based Methods ############################################## diff --git a/docs/source/background/established_methods/smf.rst b/docs/source/background/established_methods/smf.rst index 8fe3be29..b628f1cf 100644 --- a/docs/source/background/established_methods/smf.rst +++ b/docs/source/background/established_methods/smf.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + ################################## Systematic Molecular Fragmentation ################################## diff --git a/docs/source/background/established_methods/timeline.rst b/docs/source/background/established_methods/timeline.rst index eb77ad6f..fbe86b1b 100644 --- a/docs/source/background/established_methods/timeline.rst +++ b/docs/source/background/established_methods/timeline.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + ################################# Timeline of Fragmentation Methods ################################# diff --git a/docs/source/background/frag_v_nmer.rst b/docs/source/background/frag_v_nmer.rst index f4fa27e1..e000e5a1 100644 --- a/docs/source/background/frag_v_nmer.rst +++ b/docs/source/background/frag_v_nmer.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + ######################################## Difference between fragments and n-mers? ######################################## diff --git a/docs/source/background/fragment_based_methods.rst b/docs/source/background/fragment_based_methods.rst index 08f9c3c1..01bb04d7 100644 --- a/docs/source/background/fragment_based_methods.rst +++ b/docs/source/background/fragment_based_methods.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + ###################### Fragment Based Methods ###################### diff --git a/docs/source/background/index.rst b/docs/source/background/index.rst index b1392b4b..5a977455 100644 --- a/docs/source/background/index.rst +++ b/docs/source/background/index.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + ###################### Theoretical Background ###################### diff --git a/docs/source/background/mbe/index.rst b/docs/source/background/mbe/index.rst index 97a0e4fe..80afc583 100644 --- a/docs/source/background/mbe/index.rst +++ b/docs/source/background/mbe/index.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + ####################### The Many-Body Expansion ####################### diff --git a/docs/source/background/terminology.rst b/docs/source/background/terminology.rst index 738a43d5..4990febf 100644 --- a/docs/source/background/terminology.rst +++ b/docs/source/background/terminology.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + ######################################### Terminology Used Throughout GhostFragment ######################################### diff --git a/docs/source/bibliography/index.rst b/docs/source/bibliography/index.rst index 06a4fa8f..46808d74 100644 --- a/docs/source/bibliography/index.rst +++ b/docs/source/bibliography/index.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + ########## References ########## diff --git a/docs/source/conf.py b/docs/source/conf.py index 9fb9d7ff..efd9c2c8 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -1,4 +1,18 @@ # -*- coding: utf-8 -*- +# Copyright 2024 GhostFragment +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + import os diff --git a/docs/source/developer/design/fragmented_molecule_driver.rst b/docs/source/developer/design/fragmented_molecule_driver.rst index 5f6b58d4..1e57fa92 100644 --- a/docs/source/developer/design/fragmented_molecule_driver.rst +++ b/docs/source/developer/design/fragmented_molecule_driver.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + .. _gf_designing_fragmented_molecule_driver: ####################################### diff --git a/docs/source/developer/design/fragmented_nuclei_driver.rst b/docs/source/developer/design/fragmented_nuclei_driver.rst index a70f670f..e7b88fba 100644 --- a/docs/source/developer/design/fragmented_nuclei_driver.rst +++ b/docs/source/developer/design/fragmented_nuclei_driver.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + .. _gf_fragmented_nuclei_driver_design: ################################################## diff --git a/docs/source/developer/design/fragmented_system_driver.rst b/docs/source/developer/design/fragmented_system_driver.rst index 9a0adb85..5332f55e 100644 --- a/docs/source/developer/design/fragmented_system_driver.rst +++ b/docs/source/developer/design/fragmented_system_driver.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + .. _gf_fragmented_system_driver_design: ################################################# diff --git a/docs/source/developer/design/gmbe_coefficients.rst b/docs/source/developer/design/gmbe_coefficients.rst index 619eec7e..7d6f1e8e 100644 --- a/docs/source/developer/design/gmbe_coefficients.rst +++ b/docs/source/developer/design/gmbe_coefficients.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + ################# GMBE Coefficients ################# diff --git a/docs/source/developer/design/index.rst b/docs/source/developer/design/index.rst index ac900c2e..056373b4 100644 --- a/docs/source/developer/design/index.rst +++ b/docs/source/developer/design/index.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + ####################### Designing GhostFragment ####################### diff --git a/docs/source/developer/design/input_driver.rst b/docs/source/developer/design/input_driver.rst index fa532025..0363d70a 100644 --- a/docs/source/developer/design/input_driver.rst +++ b/docs/source/developer/design/input_driver.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + .. _gf_input_driver_design: ###################################### diff --git a/docs/source/developer/design/nmers.rst b/docs/source/developer/design/nmers.rst index 54f4df04..bc5da015 100644 --- a/docs/source/developer/design/nmers.rst +++ b/docs/source/developer/design/nmers.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + .. _gf_nmer_driver_design: ######################### diff --git a/docs/source/developer/design/overview.rst b/docs/source/developer/design/overview.rst index a1cb1a05..17bb3fa6 100644 --- a/docs/source/developer/design/overview.rst +++ b/docs/source/developer/design/overview.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + .. _gf_design_overview: ############################# diff --git a/docs/source/developer/development/capping.rst b/docs/source/developer/development/capping.rst index 35d5fe89..59c8cf3d 100644 --- a/docs/source/developer/development/capping.rst +++ b/docs/source/developer/development/capping.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + ############################### How to Add a New Capping Method ############################### diff --git a/docs/source/developer/development/index.rst b/docs/source/developer/development/index.rst index 29664796..ffe22f53 100644 --- a/docs/source/developer/development/index.rst +++ b/docs/source/developer/development/index.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + ################################ GhostFragment Development Topics ################################ diff --git a/docs/source/developer/index.rst b/docs/source/developer/index.rst index c44dd03d..d1625c6e 100644 --- a/docs/source/developer/index.rst +++ b/docs/source/developer/index.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + ####################### Developer Documentation ####################### diff --git a/docs/source/index.rst b/docs/source/index.rst index 1e1adbf5..1ed5021c 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + ############# GhostFragment ############# diff --git a/include/ghostfragment/equation/equation.hpp b/include/ghostfragment/equation/equation.hpp index a6e7f1d5..a26eba03 100644 --- a/include/ghostfragment/equation/equation.hpp +++ b/include/ghostfragment/equation/equation.hpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + // #pragma once // #include // #include diff --git a/include/ghostfragment/equation/expression.hpp b/include/ghostfragment/equation/expression.hpp index e7a8a51a..b86d0aa8 100644 --- a/include/ghostfragment/equation/expression.hpp +++ b/include/ghostfragment/equation/expression.hpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + #pragma once #include #include diff --git a/include/ghostfragment/equation/term.hpp b/include/ghostfragment/equation/term.hpp index 7027803c..2fc1a02d 100644 --- a/include/ghostfragment/equation/term.hpp +++ b/include/ghostfragment/equation/term.hpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + #pragma once #include diff --git a/include/ghostfragment/property_types/charge_multiplicity_assigner.hpp b/include/ghostfragment/property_types/charge_multiplicity_assigner.hpp index 76c0f37a..23e0fad1 100644 --- a/include/ghostfragment/property_types/charge_multiplicity_assigner.hpp +++ b/include/ghostfragment/property_types/charge_multiplicity_assigner.hpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + #pragma once #include #include diff --git a/include/ghostfragment/property_types/expression.hpp b/include/ghostfragment/property_types/expression.hpp index cd4fba91..457e5866 100644 --- a/include/ghostfragment/property_types/expression.hpp +++ b/include/ghostfragment/property_types/expression.hpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + // #pragma once // #include // #include diff --git a/include/ghostfragment/property_types/fragmenting/capped_fragments.hpp b/include/ghostfragment/property_types/fragmenting/capped_fragments.hpp index 2f9d5079..902418b8 100644 --- a/include/ghostfragment/property_types/fragmenting/capped_fragments.hpp +++ b/include/ghostfragment/property_types/fragmenting/capped_fragments.hpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + #pragma once #include #include diff --git a/include/ghostfragment/property_types/fragmenting/fragmented_molecule.hpp b/include/ghostfragment/property_types/fragmenting/fragmented_molecule.hpp index 525153af..b535db5b 100644 --- a/include/ghostfragment/property_types/fragmenting/fragmented_molecule.hpp +++ b/include/ghostfragment/property_types/fragmenting/fragmented_molecule.hpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + #pragma once #include #include diff --git a/include/ghostfragment/property_types/input_queue.hpp b/include/ghostfragment/property_types/input_queue.hpp index 119f02d2..9ae55cd8 100644 --- a/include/ghostfragment/property_types/input_queue.hpp +++ b/include/ghostfragment/property_types/input_queue.hpp @@ -1,16 +1,33 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + // #pragma once // #include // #include // namespace ghostfragment::pt { -// /// Used to conveniently propagate types associated with FragmentedMolecule PT -// struct InputQueueTraits { +// /// Used to conveniently propagate types associated with FragmentedMolecule +// PT struct InputQueueTraits { // /// Expected input type of the molecular system // using system_type = chemist::ChemicalSystem; // /// How the fragmented system is returned. -// using result_type = std::vector>; +// using result_type = std::vector>; // }; // /** @brief Property type for modules which fragment Molecule objects. diff --git a/include/ghostfragment/property_types/nmer_screener.hpp b/include/ghostfragment/property_types/nmer_screener.hpp index a1d08720..a2b8d118 100644 --- a/include/ghostfragment/property_types/nmer_screener.hpp +++ b/include/ghostfragment/property_types/nmer_screener.hpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + // #pragma once // #include // #include diff --git a/include/ghostfragment/property_types/property_types.hpp b/include/ghostfragment/property_types/property_types.hpp index 3a13cdd8..af1c16ef 100644 --- a/include/ghostfragment/property_types/property_types.hpp +++ b/include/ghostfragment/property_types/property_types.hpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + // #pragma once // #include // #include @@ -13,7 +29,8 @@ // /** @brief Namespace collecting all of the property types used throughout // * GhostFragment. // * -// * GhostFragment uses a number of property types. To protect the source code of +// * GhostFragment uses a number of property types. To protect the source code +// of // * GhostFragment from upstream changes to those property types, and for // * consistency, we typedef the property types we use in the pt namespace and // * rely on the typedefs throughout GhostFragment. @@ -30,7 +47,8 @@ // // using FragmentedMolecule = simde::FragmentedMolecule; // /// Traits associated with the PT for NMers -// using nmer_traits = simde::FragmentedTraits; +// using nmer_traits = simde::FragmentedTraits; // /// Property type for a module which computes N-Mers // using NMers = simde::Fragmented; diff --git a/include/ghostfragment/property_types/subset_map.hpp b/include/ghostfragment/property_types/subset_map.hpp index 282d273a..cba1e89f 100644 --- a/include/ghostfragment/property_types/subset_map.hpp +++ b/include/ghostfragment/property_types/subset_map.hpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + // #pragma once // #include diff --git a/include/ghostfragment/property_types/topology/broken_bonds.hpp b/include/ghostfragment/property_types/topology/broken_bonds.hpp index b9b37515..6747578e 100644 --- a/include/ghostfragment/property_types/topology/broken_bonds.hpp +++ b/include/ghostfragment/property_types/topology/broken_bonds.hpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + #pragma once #include #include @@ -11,7 +27,7 @@ struct BrokenBondsTraits { using conns_type = chemist::topology::ConnectivityTable; using size_type = typename fragments_type::size_type; using bond_type = std::pair; - using result_type = std::set; + using result_type = std::set; }; DECLARE_PROPERTY_TYPE(BrokenBonds); diff --git a/include/ghostfragment/property_types/topology/connectivity_table.hpp b/include/ghostfragment/property_types/topology/connectivity_table.hpp index 86c8a934..7d0ff0e7 100644 --- a/include/ghostfragment/property_types/topology/connectivity_table.hpp +++ b/include/ghostfragment/property_types/topology/connectivity_table.hpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + #pragma once #include #include diff --git a/include/ghostfragment/property_types/topology/nuclear_graph.hpp b/include/ghostfragment/property_types/topology/nuclear_graph.hpp index eefebf13..5a914570 100644 --- a/include/ghostfragment/property_types/topology/nuclear_graph.hpp +++ b/include/ghostfragment/property_types/topology/nuclear_graph.hpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + #pragma once #include #include diff --git a/scripts/equations/generate_gmbe.py b/scripts/equations/generate_gmbe.py index d8d6c8c9..848c065d 100644 --- a/scripts/equations/generate_gmbe.py +++ b/scripts/equations/generate_gmbe.py @@ -1,3 +1,17 @@ +# Copyright 2024 GhostFragment +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + from itertools import combinations from union import Union from intersection import Intersection diff --git a/scripts/equations/index.py b/scripts/equations/index.py index 4d8bba46..b0788b76 100644 --- a/scripts/equations/index.py +++ b/scripts/equations/index.py @@ -1,3 +1,17 @@ +# Copyright 2024 GhostFragment +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + class Index: def __init__(self, value): self.value = value diff --git a/scripts/equations/intersection.py b/scripts/equations/intersection.py index fdb22322..41446347 100644 --- a/scripts/equations/intersection.py +++ b/scripts/equations/intersection.py @@ -1,3 +1,17 @@ +# Copyright 2024 GhostFragment +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + from set_base import SetBase from union import Union class Intersection(SetBase): diff --git a/scripts/equations/set_base.py b/scripts/equations/set_base.py index 7eafe5f6..19470d3a 100644 --- a/scripts/equations/set_base.py +++ b/scripts/equations/set_base.py @@ -1,3 +1,17 @@ +# Copyright 2024 GhostFragment +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + class SetBase: def __init__(self, *args): self.terms = [] diff --git a/scripts/equations/tests/test_index.py b/scripts/equations/tests/test_index.py index 5f9c8c2a..5d878110 100644 --- a/scripts/equations/tests/test_index.py +++ b/scripts/equations/tests/test_index.py @@ -1,3 +1,17 @@ +# Copyright 2024 GhostFragment +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + import unittest import sys import os diff --git a/scripts/equations/tests/test_intersection.py b/scripts/equations/tests/test_intersection.py index 57ce1cee..03f4ed41 100644 --- a/scripts/equations/tests/test_intersection.py +++ b/scripts/equations/tests/test_intersection.py @@ -1,3 +1,17 @@ +# Copyright 2024 GhostFragment +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + import unittest import sys import os diff --git a/scripts/equations/tests/test_union.py b/scripts/equations/tests/test_union.py index ac88c107..8d63d3f2 100644 --- a/scripts/equations/tests/test_union.py +++ b/scripts/equations/tests/test_union.py @@ -1,3 +1,17 @@ +# Copyright 2024 GhostFragment +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + import unittest import sys import os diff --git a/scripts/equations/union.py b/scripts/equations/union.py index cac2f217..9aaf6475 100644 --- a/scripts/equations/union.py +++ b/scripts/equations/union.py @@ -1,3 +1,17 @@ +# Copyright 2024 GhostFragment +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + from set_base import SetBase class Union(SetBase): """ Class representing a set which has been formed by taking the symbolic diff --git a/src/ghostfragment/capping/capping.hpp b/src/ghostfragment/capping/capping.hpp index 2bbaff42..c796701a 100644 --- a/src/ghostfragment/capping/capping.hpp +++ b/src/ghostfragment/capping/capping.hpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + #pragma once #include diff --git a/src/ghostfragment/capping/dclc.cpp b/src/ghostfragment/capping/dclc.cpp index 9ea8a4c8..eed7e0ef 100644 --- a/src/ghostfragment/capping/dclc.cpp +++ b/src/ghostfragment/capping/dclc.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + #include "../topology/covalent_radius.hpp" #include "capping.hpp" #include diff --git a/src/ghostfragment/capping/single_atom.cpp b/src/ghostfragment/capping/single_atom.cpp index d4a06217..2ae42f59 100644 --- a/src/ghostfragment/capping/single_atom.cpp +++ b/src/ghostfragment/capping/single_atom.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + #include "capping.hpp" #include diff --git a/src/ghostfragment/capping/weighted_distance.cpp b/src/ghostfragment/capping/weighted_distance.cpp index c28cbcf6..1fc2f332 100644 --- a/src/ghostfragment/capping/weighted_distance.cpp +++ b/src/ghostfragment/capping/weighted_distance.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + #include "../topology/covalent_radius.hpp" #include "capping.hpp" #include diff --git a/src/ghostfragment/drivers/drivers.hpp b/src/ghostfragment/drivers/drivers.hpp index d06771a2..7b6b2bb2 100644 --- a/src/ghostfragment/drivers/drivers.hpp +++ b/src/ghostfragment/drivers/drivers.hpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + #pragma once #include diff --git a/src/ghostfragment/drivers/engine.hpp b/src/ghostfragment/drivers/engine.hpp index 4ec3be2b..f949eb71 100644 --- a/src/ghostfragment/drivers/engine.hpp +++ b/src/ghostfragment/drivers/engine.hpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + // #include // #include diff --git a/src/ghostfragment/drivers/fragment.cpp b/src/ghostfragment/drivers/fragment.cpp index 3127032d..2506aec4 100644 --- a/src/ghostfragment/drivers/fragment.cpp +++ b/src/ghostfragment/drivers/fragment.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + #include "drivers.hpp" #include #include diff --git a/src/ghostfragment/drivers/fragment_based_method.cpp b/src/ghostfragment/drivers/fragment_based_method.cpp index e15719ec..9a0e4c99 100644 --- a/src/ghostfragment/drivers/fragment_based_method.cpp +++ b/src/ghostfragment/drivers/fragment_based_method.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + // #include "drivers.hpp" // #include // #include diff --git a/src/ghostfragment/drivers/fragment_system.cpp b/src/ghostfragment/drivers/fragment_system.cpp index 5fac641c..c09c4481 100644 --- a/src/ghostfragment/drivers/fragment_system.cpp +++ b/src/ghostfragment/drivers/fragment_system.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + #include "drivers.hpp" #include #include diff --git a/src/ghostfragment/drivers/input_queue.cpp b/src/ghostfragment/drivers/input_queue.cpp index 8196a5f3..647a311c 100644 --- a/src/ghostfragment/drivers/input_queue.cpp +++ b/src/ghostfragment/drivers/input_queue.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + // #include "drivers.hpp" // #include diff --git a/src/ghostfragment/drivers/neutral_singlet.cpp b/src/ghostfragment/drivers/neutral_singlet.cpp index af3c84d6..8121f0b5 100644 --- a/src/ghostfragment/drivers/neutral_singlet.cpp +++ b/src/ghostfragment/drivers/neutral_singlet.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + // #include "drivers.hpp" // #include // #include @@ -18,7 +34,8 @@ // This module assigns a charge of zero // and a multiplicity of one to each input fragment. -// The inputs to this module are fragments, a cap set, and the original molecule. +// The inputs to this module are fragments, a cap set, and the original +// molecule. // )"""; // } // end namespace @@ -35,7 +52,6 @@ // charge_result_type charges(frags.size(), 0); // mult_result_type multiplicities; - // // Goes over every fragment and attempts // // to set each one's multiplicity to one. // for(auto frag_i = 0; frag_i < frags.size(); frag_i++) { @@ -62,9 +78,10 @@ // multiplicities.push_back(1); // } -// // With an odd number of electrons, a multiplicity of one is impossible -// else { -// throw std::runtime_error("An odd number of electrons cannot have multiplicity of one"); +// // With an odd number of electrons, a multiplicity of one is +// impossible else { +// throw std::runtime_error("An odd number of electrons cannot have +// multiplicity of one"); // } // } diff --git a/src/ghostfragment/drivers/nmer_system.cpp b/src/ghostfragment/drivers/nmer_system.cpp index b09ab021..b82cbf0f 100644 --- a/src/ghostfragment/drivers/nmer_system.cpp +++ b/src/ghostfragment/drivers/nmer_system.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + // #include "drivers.hpp" // #include diff --git a/src/ghostfragment/equation/detail_/expression_pimpl.hpp b/src/ghostfragment/equation/detail_/expression_pimpl.hpp index b3076b56..c76855a8 100644 --- a/src/ghostfragment/equation/detail_/expression_pimpl.hpp +++ b/src/ghostfragment/equation/detail_/expression_pimpl.hpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + // #pragma once // #include diff --git a/src/ghostfragment/equation/detail_/term_pimpl.hpp b/src/ghostfragment/equation/detail_/term_pimpl.hpp index c850feb7..2813ed6b 100644 --- a/src/ghostfragment/equation/detail_/term_pimpl.hpp +++ b/src/ghostfragment/equation/detail_/term_pimpl.hpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + // #pragma once // #include diff --git a/src/ghostfragment/equation/equation.cpp b/src/ghostfragment/equation/equation.cpp index 8a74ef63..070a8a2b 100644 --- a/src/ghostfragment/equation/equation.cpp +++ b/src/ghostfragment/equation/equation.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + // #include "detail_/term_pimpl.hpp" // #include diff --git a/src/ghostfragment/equation/expression.cpp b/src/ghostfragment/equation/expression.cpp index 42f4c0af..25aed166 100644 --- a/src/ghostfragment/equation/expression.cpp +++ b/src/ghostfragment/equation/expression.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + // #include "detail_/expression_pimpl.hpp" // namespace ghostfragment::equation { @@ -43,7 +59,8 @@ // // -- Utility -// bool Expression::empty() const noexcept { return !static_cast(m_pimpl_); } +// bool Expression::empty() const noexcept { return +// !static_cast(m_pimpl_); } // void Expression::swap(Expression& other) noexcept { // m_pimpl_.swap(other.m_pimpl_); diff --git a/src/ghostfragment/equation/term.cpp b/src/ghostfragment/equation/term.cpp index 8139340d..a4d421bc 100644 --- a/src/ghostfragment/equation/term.cpp +++ b/src/ghostfragment/equation/term.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + // #include "detail_/term_pimpl.hpp" // namespace ghostfragment::equation { @@ -65,7 +81,8 @@ // void Term::assert_pimpl_() const { // if(!empty()) return; -// throw std::runtime_error("Term is empty. Did you default construct it or " +// throw std::runtime_error("Term is empty. Did you default construct it or +// " // "move from it?"); // } diff --git a/src/ghostfragment/expressions/expressions.hpp b/src/ghostfragment/expressions/expressions.hpp index d611d082..949b9a52 100644 --- a/src/ghostfragment/expressions/expressions.hpp +++ b/src/ghostfragment/expressions/expressions.hpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + // #pragma once // #include diff --git a/src/ghostfragment/expressions/mbe.cpp b/src/ghostfragment/expressions/mbe.cpp index 8561c455..f7c0c6a1 100644 --- a/src/ghostfragment/expressions/mbe.cpp +++ b/src/ghostfragment/expressions/mbe.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + // #include "expressions.hpp" // #include // #include diff --git a/src/ghostfragment/fragmenting/ao2atom.cpp b/src/ghostfragment/fragmenting/ao2atom.cpp index 29a72e3e..0abca3d0 100644 --- a/src/ghostfragment/fragmenting/ao2atom.cpp +++ b/src/ghostfragment/fragmenting/ao2atom.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + // #include "fragmenting.hpp" // #include // #include diff --git a/src/ghostfragment/fragmenting/bond_based.cpp b/src/ghostfragment/fragmenting/bond_based.cpp index d45a7f17..f9d19667 100644 --- a/src/ghostfragment/fragmenting/bond_based.cpp +++ b/src/ghostfragment/fragmenting/bond_based.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + #include "fragmenting.hpp" #include #include diff --git a/src/ghostfragment/fragmenting/cluster.cpp b/src/ghostfragment/fragmenting/cluster.cpp index 37bdead4..87208a9c 100644 --- a/src/ghostfragment/fragmenting/cluster.cpp +++ b/src/ghostfragment/fragmenting/cluster.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + #include "fragmenting.hpp" #include #include diff --git a/src/ghostfragment/fragmenting/heavy_atom.cpp b/src/ghostfragment/fragmenting/heavy_atom.cpp index b438a39c..338d1e31 100644 --- a/src/ghostfragment/fragmenting/heavy_atom.cpp +++ b/src/ghostfragment/fragmenting/heavy_atom.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + #include "fragmenting.hpp" #include diff --git a/src/ghostfragment/fragmenting/inter_finder.cpp b/src/ghostfragment/fragmenting/inter_finder.cpp index c08a3c18..9d621a87 100644 --- a/src/ghostfragment/fragmenting/inter_finder.cpp +++ b/src/ghostfragment/fragmenting/inter_finder.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + #include "inter_finder.hpp" // #include // #include diff --git a/src/ghostfragment/fragmenting/inter_finder.hpp b/src/ghostfragment/fragmenting/inter_finder.hpp index 8ed39cd5..1700e280 100644 --- a/src/ghostfragment/fragmenting/inter_finder.hpp +++ b/src/ghostfragment/fragmenting/inter_finder.hpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + #pragma once #include #include diff --git a/src/ghostfragment/fragmenting/nmers.cpp b/src/ghostfragment/fragmenting/nmers.cpp index 0ef921af..49ec7bc3 100644 --- a/src/ghostfragment/fragmenting/nmers.cpp +++ b/src/ghostfragment/fragmenting/nmers.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + #include "fragmenting.hpp" #include #include diff --git a/src/ghostfragment/fragmenting/nuceli_ao.cpp b/src/ghostfragment/fragmenting/nuceli_ao.cpp index 3bcc786a..c9d294fc 100644 --- a/src/ghostfragment/fragmenting/nuceli_ao.cpp +++ b/src/ghostfragment/fragmenting/nuceli_ao.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + // #include "fragmenting.hpp" // #include diff --git a/src/ghostfragment/screening/minimum_distance.cpp b/src/ghostfragment/screening/minimum_distance.cpp index 3ca4c509..2539b30c 100644 --- a/src/ghostfragment/screening/minimum_distance.cpp +++ b/src/ghostfragment/screening/minimum_distance.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + // #include "../connectivity/distance.hpp" // #include "ghostfragment/property_types/property_types.hpp" // #include "screening.hpp" diff --git a/src/ghostfragment/screening/screening.hpp b/src/ghostfragment/screening/screening.hpp index cbea0b5e..cc11f752 100644 --- a/src/ghostfragment/screening/screening.hpp +++ b/src/ghostfragment/screening/screening.hpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + // #pragma once // #include diff --git a/src/ghostfragment/topology/broken_bonds.cpp b/src/ghostfragment/topology/broken_bonds.cpp index 00fd8497..b7cd5afd 100644 --- a/src/ghostfragment/topology/broken_bonds.cpp +++ b/src/ghostfragment/topology/broken_bonds.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + #include "topology.hpp" #include #include diff --git a/src/ghostfragment/topology/covalent_radius.hpp b/src/ghostfragment/topology/covalent_radius.hpp index ed678818..440f4ffb 100644 --- a/src/ghostfragment/topology/covalent_radius.hpp +++ b/src/ghostfragment/topology/covalent_radius.hpp @@ -46,4 +46,4 @@ inline double covalent_radius(std::size_t z) { return cov_radii[z - 1]; } -} // namespace ghostfragment::connectivity +} // namespace ghostfragment::topology diff --git a/src/ghostfragment/topology/distance.hpp b/src/ghostfragment/topology/distance.hpp index dc08f4f0..efe74ad1 100644 --- a/src/ghostfragment/topology/distance.hpp +++ b/src/ghostfragment/topology/distance.hpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + // #include // for std::sqrt // #include diff --git a/src/ghostfragment/topology/nuclear_graph_from_connectivity.cpp b/src/ghostfragment/topology/nuclear_graph_from_connectivity.cpp index 061cdbcc..6696c7d8 100644 --- a/src/ghostfragment/topology/nuclear_graph_from_connectivity.cpp +++ b/src/ghostfragment/topology/nuclear_graph_from_connectivity.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + #include "topology.hpp" #include #include diff --git a/src/python/export_ghostfragment.cpp b/src/python/export_ghostfragment.cpp index 1ecb9936..363ae5bc 100644 --- a/src/python/export_ghostfragment.cpp +++ b/src/python/export_ghostfragment.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + #include #include diff --git a/tests/cxx/unit_tests/ghostfragment/README.rst b/tests/cxx/unit_tests/ghostfragment/README.rst index d60139f8..b29f920c 100644 --- a/tests/cxx/unit_tests/ghostfragment/README.rst +++ b/tests/cxx/unit_tests/ghostfragment/README.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + ################### tests/ghostfragment ################### diff --git a/tests/cxx/unit_tests/ghostfragment/capping/dclc.cpp b/tests/cxx/unit_tests/ghostfragment/capping/dclc.cpp index e8925ed7..4d3ea6b9 100644 --- a/tests/cxx/unit_tests/ghostfragment/capping/dclc.cpp +++ b/tests/cxx/unit_tests/ghostfragment/capping/dclc.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + #include "../test_ghostfragment.hpp" #include "../testing/are_caps_equal.hpp" #include diff --git a/tests/cxx/unit_tests/ghostfragment/capping/single_atom.cpp b/tests/cxx/unit_tests/ghostfragment/capping/single_atom.cpp index 0dc68665..a7e87fb8 100644 --- a/tests/cxx/unit_tests/ghostfragment/capping/single_atom.cpp +++ b/tests/cxx/unit_tests/ghostfragment/capping/single_atom.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + #include "../test_ghostfragment.hpp" #include diff --git a/tests/cxx/unit_tests/ghostfragment/capping/weighted_distance.cpp b/tests/cxx/unit_tests/ghostfragment/capping/weighted_distance.cpp index d96d30d7..39a81c3f 100644 --- a/tests/cxx/unit_tests/ghostfragment/capping/weighted_distance.cpp +++ b/tests/cxx/unit_tests/ghostfragment/capping/weighted_distance.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + #include "../test_ghostfragment.hpp" #include "../testing/are_caps_equal.hpp" #include diff --git a/tests/cxx/unit_tests/ghostfragment/caps.cpp b/tests/cxx/unit_tests/ghostfragment/caps.cpp index 1e8a304e..08ff0725 100644 --- a/tests/cxx/unit_tests/ghostfragment/caps.cpp +++ b/tests/cxx/unit_tests/ghostfragment/caps.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + // #include "test_ghostfragment.hpp" // #include diff --git a/tests/cxx/unit_tests/ghostfragment/drivers/engine.cpp b/tests/cxx/unit_tests/ghostfragment/drivers/engine.cpp index deffd6cf..6c391168 100644 --- a/tests/cxx/unit_tests/ghostfragment/drivers/engine.cpp +++ b/tests/cxx/unit_tests/ghostfragment/drivers/engine.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + // #include "../test_ghostfragment.hpp" // #include "hydrocarbon/hydrocarbon.h" // #include diff --git a/tests/cxx/unit_tests/ghostfragment/drivers/fragment.cpp b/tests/cxx/unit_tests/ghostfragment/drivers/fragment.cpp index 9173821e..e24fa945 100644 --- a/tests/cxx/unit_tests/ghostfragment/drivers/fragment.cpp +++ b/tests/cxx/unit_tests/ghostfragment/drivers/fragment.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + #include "../test_ghostfragment.hpp" #include #include diff --git a/tests/cxx/unit_tests/ghostfragment/drivers/fragment_based_method.cpp b/tests/cxx/unit_tests/ghostfragment/drivers/fragment_based_method.cpp index 083ed45f..1bb5eba6 100644 --- a/tests/cxx/unit_tests/ghostfragment/drivers/fragment_based_method.cpp +++ b/tests/cxx/unit_tests/ghostfragment/drivers/fragment_based_method.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + // #include "../test_ghostfragment.hpp" // #include @@ -13,7 +29,8 @@ // * // * - frag_mod checks that the inputs to the FragmentBasedMethod driver are // * forwarded to it correctly and then returns a set of fragments -// * - nmer_mod makes sure it's given the set of fragments from frag_mod and then +// * - nmer_mod makes sure it's given the set of fragments from frag_mod and +// then // * returns a set of n-mers // * - expr_mod checks that it's given set of n-mers from nmer_mod and then // * creates an expression which depends on the number of fragments and the @@ -39,14 +56,14 @@ // using nmer_sys_pt = pt::NMerSystem; // using expression_pt = pt::Expression; -// // Checks that we pass in the correct system/AO pair, returns a set of fragments -// auto frag_mod(std::size_t n_waters) { +// // Checks that we pass in the correct system/AO pair, returns a set of +// fragments auto frag_mod(std::size_t n_waters) { // return pluginplay::make_lambda([=](auto&& mol_in, // auto&& aos_in) { -// simde::type::chemical_system s(testing::water(n_waters), 10 * n_waters); -// REQUIRE(mol_in == s); -// REQUIRE(aos_in == testing::sto3g(s.molecule())); -// return testing::fragmented_water_system(n_waters); +// simde::type::chemical_system s(testing::water(n_waters), 10 * +// n_waters); REQUIRE(mol_in == s); REQUIRE(aos_in == +// testing::sto3g(s.molecule())); return +// testing::fragmented_water_system(n_waters); // }); // } @@ -104,7 +121,8 @@ // const std::size_t n_waters = n; // auto mol = testing::water(n_waters); // simde::type::chemical_system sys(mol, n_waters * 10); -// auto aos = chemist::orbital_space::AOSpace(testing::sto3g(mol)); +// auto aos = +// chemist::orbital_space::AOSpace(testing::sto3g(mol)); // mod.change_submod("Fragment Maker", frag_mod(n_waters)); // mod.change_submod("N-Mer Maker", nmer_mod(n_waters, m)); diff --git a/tests/cxx/unit_tests/ghostfragment/drivers/fragmented_system.cpp b/tests/cxx/unit_tests/ghostfragment/drivers/fragmented_system.cpp index 8ebb47b4..3b79c96b 100644 --- a/tests/cxx/unit_tests/ghostfragment/drivers/fragmented_system.cpp +++ b/tests/cxx/unit_tests/ghostfragment/drivers/fragmented_system.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + #include "../test_ghostfragment.hpp" #include #include diff --git a/tests/cxx/unit_tests/ghostfragment/drivers/input_queue.cpp b/tests/cxx/unit_tests/ghostfragment/drivers/input_queue.cpp index 094f5c18..d96d9fff 100644 --- a/tests/cxx/unit_tests/ghostfragment/drivers/input_queue.cpp +++ b/tests/cxx/unit_tests/ghostfragment/drivers/input_queue.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + // #include "../test_ghostfragment.hpp" // #include "hydrocarbon/hydrocarbon.h" // #include diff --git a/tests/cxx/unit_tests/ghostfragment/drivers/neutral.cpp b/tests/cxx/unit_tests/ghostfragment/drivers/neutral.cpp index d9a96d89..7ef98763 100644 --- a/tests/cxx/unit_tests/ghostfragment/drivers/neutral.cpp +++ b/tests/cxx/unit_tests/ghostfragment/drivers/neutral.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + // #include "../test_ghostfragment.hpp" // #include // #include @@ -28,7 +44,8 @@ // charge_result_type charge_corr; // mult_result_type mult_corr; -// const auto& [charge_test, mult_test] = mod.run_as(frags, caps, mol); +// const auto& [charge_test, mult_test] = mod.run_as(frags, caps, +// mol); // REQUIRE(charge_test == charge_corr); // REQUIRE(mult_test == mult_corr); @@ -49,7 +66,8 @@ // charge_result_type charge_corr(frags.size(), 0); // mult_result_type mult_corr(frags.size(), 1); -// const auto& [charge_test, mult_test] = mod.run_as(frags, caps, mol); +// const auto& [charge_test, mult_test] = mod.run_as(frags, +// caps, mol); // REQUIRE(charge_test == charge_corr); // REQUIRE(mult_test == mult_corr); @@ -72,7 +90,8 @@ // charge_result_type charge_corr(frags.size(), 0); // mult_result_type mult_corr(frags.size(), 1); -// const auto& [charge_test, mult_test] = mod.run_as(frags, caps, mol); +// const auto& [charge_test, mult_test] = mod.run_as(frags, +// caps, mol); // REQUIRE(charge_test == charge_corr); // REQUIRE(mult_test == mult_corr); @@ -99,7 +118,8 @@ // caps.push_back(cap_set); // } -// REQUIRE_THROWS_AS(mod.run_as(frags, caps, mol), std::runtime_error); +// REQUIRE_THROWS_AS(mod.run_as(frags, caps, mol), +// std::runtime_error); // } // SECTION("Two caps") { @@ -116,7 +136,8 @@ // cap_set2.add_cap(2, 1, Cap2); // caps.push_back(cap_set2); -// REQUIRE_THROWS_AS(mod.run_as(frags, caps, mol), std::runtime_error); +// REQUIRE_THROWS_AS(mod.run_as(frags, caps, mol), +// std::runtime_error); // } // } // } diff --git a/tests/cxx/unit_tests/ghostfragment/drivers/nmer_system.cpp b/tests/cxx/unit_tests/ghostfragment/drivers/nmer_system.cpp index 2116c440..47179fbd 100644 --- a/tests/cxx/unit_tests/ghostfragment/drivers/nmer_system.cpp +++ b/tests/cxx/unit_tests/ghostfragment/drivers/nmer_system.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + // #include "../test_ghostfragment.hpp" // using namespace ghostfragment; diff --git a/tests/cxx/unit_tests/ghostfragment/equation/detail_/expression_pimpl.cpp b/tests/cxx/unit_tests/ghostfragment/equation/detail_/expression_pimpl.cpp index a195d7d0..6a371277 100644 --- a/tests/cxx/unit_tests/ghostfragment/equation/detail_/expression_pimpl.cpp +++ b/tests/cxx/unit_tests/ghostfragment/equation/detail_/expression_pimpl.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + // #include "../../test_ghostfragment.hpp" // #include diff --git a/tests/cxx/unit_tests/ghostfragment/equation/detail_/term_pimpl.cpp b/tests/cxx/unit_tests/ghostfragment/equation/detail_/term_pimpl.cpp index faad73da..25cf6be8 100644 --- a/tests/cxx/unit_tests/ghostfragment/equation/detail_/term_pimpl.cpp +++ b/tests/cxx/unit_tests/ghostfragment/equation/detail_/term_pimpl.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + // #include "../../test_ghostfragment.hpp" // #include diff --git a/tests/cxx/unit_tests/ghostfragment/equation/expression.cpp b/tests/cxx/unit_tests/ghostfragment/equation/expression.cpp index 295932ae..d19722e5 100644 --- a/tests/cxx/unit_tests/ghostfragment/equation/expression.cpp +++ b/tests/cxx/unit_tests/ghostfragment/equation/expression.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + // #include "../test_ghostfragment.hpp" // #include diff --git a/tests/cxx/unit_tests/ghostfragment/equation/term.cpp b/tests/cxx/unit_tests/ghostfragment/equation/term.cpp index 919d1cfd..047e055e 100644 --- a/tests/cxx/unit_tests/ghostfragment/equation/term.cpp +++ b/tests/cxx/unit_tests/ghostfragment/equation/term.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + // #include "../test_ghostfragment.hpp" // #include diff --git a/tests/cxx/unit_tests/ghostfragment/expressions/mbe.cpp b/tests/cxx/unit_tests/ghostfragment/expressions/mbe.cpp index f9a82afe..9e70447a 100644 --- a/tests/cxx/unit_tests/ghostfragment/expressions/mbe.cpp +++ b/tests/cxx/unit_tests/ghostfragment/expressions/mbe.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + // #include "../test_ghostfragment.hpp" // #include diff --git a/tests/cxx/unit_tests/ghostfragment/fragmented_system.cpp b/tests/cxx/unit_tests/ghostfragment/fragmented_system.cpp index 974369ea..89ee31f2 100644 --- a/tests/cxx/unit_tests/ghostfragment/fragmented_system.cpp +++ b/tests/cxx/unit_tests/ghostfragment/fragmented_system.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + // #include "ghostfragment/fragmented_system.hpp" // #include "test_ghostfragment.hpp" diff --git a/tests/cxx/unit_tests/ghostfragment/fragmenting/ao2atom.cpp b/tests/cxx/unit_tests/ghostfragment/fragmenting/ao2atom.cpp index 1a54a892..34fda167 100644 --- a/tests/cxx/unit_tests/ghostfragment/fragmenting/ao2atom.cpp +++ b/tests/cxx/unit_tests/ghostfragment/fragmenting/ao2atom.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + // #include "../test_ghostfragment.hpp" // using return_type = simde::atom_to_center_return_type; @@ -16,8 +32,8 @@ // // Our testing funtions add the centers in order; so atom i's AOs // // are the i-th set of AOs // return_type corr(3 * nwaters); -// for(std::size_t j = 0; j < 3 * nwaters; ++j) corr[j] = set_type{j}; -// REQUIRE(corr == rv); +// for(std::size_t j = 0; j < 3 * nwaters; ++j) corr[j] = +// set_type{j}; REQUIRE(corr == rv); // } // } // } diff --git a/tests/cxx/unit_tests/ghostfragment/fragmenting/bond_based.cpp b/tests/cxx/unit_tests/ghostfragment/fragmenting/bond_based.cpp index b283ea60..c1e1778c 100644 --- a/tests/cxx/unit_tests/ghostfragment/fragmenting/bond_based.cpp +++ b/tests/cxx/unit_tests/ghostfragment/fragmenting/bond_based.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + #include "../test_ghostfragment.hpp" #include using namespace ghostfragment; diff --git a/tests/cxx/unit_tests/ghostfragment/fragmenting/cluster.cpp b/tests/cxx/unit_tests/ghostfragment/fragmenting/cluster.cpp index ac03a81e..374852ef 100644 --- a/tests/cxx/unit_tests/ghostfragment/fragmenting/cluster.cpp +++ b/tests/cxx/unit_tests/ghostfragment/fragmenting/cluster.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + #include "../test_ghostfragment.hpp" #include using namespace ghostfragment; diff --git a/tests/cxx/unit_tests/ghostfragment/fragmenting/heavy_atom.cpp b/tests/cxx/unit_tests/ghostfragment/fragmenting/heavy_atom.cpp index 788ff94e..a574235e 100644 --- a/tests/cxx/unit_tests/ghostfragment/fragmenting/heavy_atom.cpp +++ b/tests/cxx/unit_tests/ghostfragment/fragmenting/heavy_atom.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + #include "../test_ghostfragment.hpp" #include #include diff --git a/tests/cxx/unit_tests/ghostfragment/fragmenting/inter_finder.cpp b/tests/cxx/unit_tests/ghostfragment/fragmenting/inter_finder.cpp index d409f054..77353960 100644 --- a/tests/cxx/unit_tests/ghostfragment/fragmenting/inter_finder.cpp +++ b/tests/cxx/unit_tests/ghostfragment/fragmenting/inter_finder.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + #include "../test_ghostfragment.hpp" #include // #include diff --git a/tests/cxx/unit_tests/ghostfragment/fragmenting/nmers.cpp b/tests/cxx/unit_tests/ghostfragment/fragmenting/nmers.cpp index 4f1fab44..f5c69cf4 100644 --- a/tests/cxx/unit_tests/ghostfragment/fragmenting/nmers.cpp +++ b/tests/cxx/unit_tests/ghostfragment/fragmenting/nmers.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + #include "../test_ghostfragment.hpp" #include diff --git a/tests/cxx/unit_tests/ghostfragment/fragmenting/nuclei_ao.cpp b/tests/cxx/unit_tests/ghostfragment/fragmenting/nuclei_ao.cpp index 83ccf19b..22627a0b 100644 --- a/tests/cxx/unit_tests/ghostfragment/fragmenting/nuclei_ao.cpp +++ b/tests/cxx/unit_tests/ghostfragment/fragmenting/nuclei_ao.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + // #include "../test_ghostfragment.hpp" // using namespace ghostfragment::pt; diff --git a/tests/cxx/unit_tests/ghostfragment/main.cpp b/tests/cxx/unit_tests/ghostfragment/main.cpp index 60c80355..4bad07ef 100644 --- a/tests/cxx/unit_tests/ghostfragment/main.cpp +++ b/tests/cxx/unit_tests/ghostfragment/main.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + #define CATCH_CONFIG_RUNNER #include #include diff --git a/tests/cxx/unit_tests/ghostfragment/nmer_system.cpp b/tests/cxx/unit_tests/ghostfragment/nmer_system.cpp index 2d457777..22de169f 100644 --- a/tests/cxx/unit_tests/ghostfragment/nmer_system.cpp +++ b/tests/cxx/unit_tests/ghostfragment/nmer_system.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + // #include "test_ghostfragment.hpp" // #include @@ -123,20 +139,22 @@ // } // SECTION("n_electrons(nmer)") { -// REQUIRE_THROWS_AS(defaulted.n_electrons(dimers[0]), std::runtime_error); -// REQUIRE(has_value.n_electrons(dimers[0]) == 20); +// REQUIRE_THROWS_AS(defaulted.n_electrons(dimers[0]), +// std::runtime_error); REQUIRE(has_value.n_electrons(dimers[0]) == 20); // REQUIRE(has_value.n_electrons(dimers[1]) == 20); // REQUIRE(has_value.n_electrons(dimers[2]) == 20); -// REQUIRE_THROWS_AS(has_value.n_electrons(trimers[0]), std::out_of_range); +// REQUIRE_THROWS_AS(has_value.n_electrons(trimers[0]), +// std::out_of_range); // } // SECTION("n_electrons(frag)") { // auto bad_water = fragmented_water(4)[0]; -// REQUIRE_THROWS_AS(defaulted.n_electrons(bad_water), std::runtime_error); -// REQUIRE(has_value.n_electrons(frags.fragment(0)) == 10); -// REQUIRE(has_value.n_electrons(frags.fragment(1)) == 10); +// REQUIRE_THROWS_AS(defaulted.n_electrons(bad_water), +// std::runtime_error); REQUIRE(has_value.n_electrons(frags.fragment(0)) +// == 10); REQUIRE(has_value.n_electrons(frags.fragment(1)) == 10); // REQUIRE(has_value.n_electrons(frags.fragment(2)) == 10); -// REQUIRE_THROWS_AS(has_value.n_electrons(bad_water), std::out_of_range); +// REQUIRE_THROWS_AS(has_value.n_electrons(bad_water), +// std::out_of_range); // } // SECTION("Comparisons") { diff --git a/tests/cxx/unit_tests/ghostfragment/nuclear_graph.cpp b/tests/cxx/unit_tests/ghostfragment/nuclear_graph.cpp index 55298fa5..ba3fb636 100644 --- a/tests/cxx/unit_tests/ghostfragment/nuclear_graph.cpp +++ b/tests/cxx/unit_tests/ghostfragment/nuclear_graph.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + #include "test_ghostfragment.hpp" #include namespace ghostfragment { diff --git a/tests/cxx/unit_tests/ghostfragment/screening/distance.cpp b/tests/cxx/unit_tests/ghostfragment/screening/distance.cpp index 73f66f6c..5e219f57 100644 --- a/tests/cxx/unit_tests/ghostfragment/screening/distance.cpp +++ b/tests/cxx/unit_tests/ghostfragment/screening/distance.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + // #include "../test_ghostfragment.hpp" // using my_pt = ghostfragment::pt::NMerScreener; diff --git a/tests/cxx/unit_tests/ghostfragment/testing/README.rst b/tests/cxx/unit_tests/ghostfragment/testing/README.rst index f8b5b2ac..642122eb 100644 --- a/tests/cxx/unit_tests/ghostfragment/testing/README.rst +++ b/tests/cxx/unit_tests/ghostfragment/testing/README.rst @@ -1,3 +1,17 @@ +.. Copyright 2024 GhostFragment +.. +.. Licensed under the Apache License, Version 2.0 (the "License"); +.. you may not use this file except in compliance with the License. +.. You may obtain a copy of the License at +.. +.. http://www.apache.org/licenses/LICENSE-2.0 +.. +.. Unless required by applicable law or agreed to in writing, software +.. distributed under the License is distributed on an "AS IS" BASIS, +.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +.. See the License for the specific language governing permissions and +.. limitations under the License. + ########################### tests/ghostfragment/testing ########################### diff --git a/tests/cxx/unit_tests/ghostfragment/testing/aos.cpp b/tests/cxx/unit_tests/ghostfragment/testing/aos.cpp index 7210f3bc..f38636f7 100644 --- a/tests/cxx/unit_tests/ghostfragment/testing/aos.cpp +++ b/tests/cxx/unit_tests/ghostfragment/testing/aos.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + // #include "aos.hpp" // #include "water.hpp" // #include diff --git a/tests/cxx/unit_tests/ghostfragment/testing/aos.hpp b/tests/cxx/unit_tests/ghostfragment/testing/aos.hpp index 7ceafcf0..d2a19309 100644 --- a/tests/cxx/unit_tests/ghostfragment/testing/aos.hpp +++ b/tests/cxx/unit_tests/ghostfragment/testing/aos.hpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + // #pragma once // #include "sto3g.hpp" // #include diff --git a/tests/cxx/unit_tests/ghostfragment/testing/are_caps_equal.hpp b/tests/cxx/unit_tests/ghostfragment/testing/are_caps_equal.hpp index 2090d345..b4a5fd47 100644 --- a/tests/cxx/unit_tests/ghostfragment/testing/are_caps_equal.hpp +++ b/tests/cxx/unit_tests/ghostfragment/testing/are_caps_equal.hpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + #pragma once #include #include diff --git a/tests/cxx/unit_tests/ghostfragment/testing/hc_fragment.cpp b/tests/cxx/unit_tests/ghostfragment/testing/hc_fragment.cpp index 9367afc6..0e6bdaa5 100644 --- a/tests/cxx/unit_tests/ghostfragment/testing/hc_fragment.cpp +++ b/tests/cxx/unit_tests/ghostfragment/testing/hc_fragment.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + #include "hydrocarbon/hydrocarbon.hpp" #include #include diff --git a/tests/cxx/unit_tests/ghostfragment/testing/hydrocarbon.cpp b/tests/cxx/unit_tests/ghostfragment/testing/hydrocarbon.cpp index 19fc8e2c..e1eb594e 100644 --- a/tests/cxx/unit_tests/ghostfragment/testing/hydrocarbon.cpp +++ b/tests/cxx/unit_tests/ghostfragment/testing/hydrocarbon.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + #include "hydrocarbon/hydrocarbon.hpp" #include diff --git a/tests/cxx/unit_tests/ghostfragment/testing/hydrocarbon/hydrocarbon.cpp b/tests/cxx/unit_tests/ghostfragment/testing/hydrocarbon/hydrocarbon.cpp index 3d0d6f72..681d0334 100644 --- a/tests/cxx/unit_tests/ghostfragment/testing/hydrocarbon/hydrocarbon.cpp +++ b/tests/cxx/unit_tests/ghostfragment/testing/hydrocarbon/hydrocarbon.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + #include "hydrocarbon.hpp" #include "position.hpp" diff --git a/tests/cxx/unit_tests/ghostfragment/testing/hydrocarbon/position.cpp b/tests/cxx/unit_tests/ghostfragment/testing/hydrocarbon/position.cpp index 2a18b0b6..7280696b 100644 --- a/tests/cxx/unit_tests/ghostfragment/testing/hydrocarbon/position.cpp +++ b/tests/cxx/unit_tests/ghostfragment/testing/hydrocarbon/position.cpp @@ -112,4 +112,4 @@ std::array position_hydrogen(const std::vector& source_coords, return coords; } -} +} // namespace testing diff --git a/tests/cxx/unit_tests/ghostfragment/testing/sto3g.cpp b/tests/cxx/unit_tests/ghostfragment/testing/sto3g.cpp index 4bf7b0e5..828aeb0e 100644 --- a/tests/cxx/unit_tests/ghostfragment/testing/sto3g.cpp +++ b/tests/cxx/unit_tests/ghostfragment/testing/sto3g.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + // #include "sto3g.hpp" // #include "water.hpp" // #include diff --git a/tests/cxx/unit_tests/ghostfragment/testing/sto3g.hpp b/tests/cxx/unit_tests/ghostfragment/testing/sto3g.hpp index 066381ba..1d562db0 100644 --- a/tests/cxx/unit_tests/ghostfragment/testing/sto3g.hpp +++ b/tests/cxx/unit_tests/ghostfragment/testing/sto3g.hpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + // #pragma once // #include diff --git a/tests/cxx/unit_tests/ghostfragment/topology/broken_bonds.cpp b/tests/cxx/unit_tests/ghostfragment/topology/broken_bonds.cpp index 069c7e19..3d67f994 100644 --- a/tests/cxx/unit_tests/ghostfragment/topology/broken_bonds.cpp +++ b/tests/cxx/unit_tests/ghostfragment/topology/broken_bonds.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + #include "../test_ghostfragment.hpp" #include #include diff --git a/tests/cxx/unit_tests/ghostfragment/topology/nuclear_graph_from_connectivity.cpp b/tests/cxx/unit_tests/ghostfragment/topology/nuclear_graph_from_connectivity.cpp index 79d04e14..994eb528 100644 --- a/tests/cxx/unit_tests/ghostfragment/topology/nuclear_graph_from_connectivity.cpp +++ b/tests/cxx/unit_tests/ghostfragment/topology/nuclear_graph_from_connectivity.cpp @@ -1,3 +1,19 @@ +/* + * Copyright 2024 GhostFragment + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + #include "../test_ghostfragment.hpp" #include #include diff --git a/tests/python/integration_tests/test_cap.py b/tests/python/integration_tests/test_cap.py index 50c6f489..8eef2956 100644 --- a/tests/python/integration_tests/test_cap.py +++ b/tests/python/integration_tests/test_cap.py @@ -1,3 +1,17 @@ +# Copyright 2024 GhostFragment +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + #import nwchemex as nwx import simde import pluginplay