Merge remote-tracking branch 'upstream/master' into custom-element

Signed-off-by: Adarsh Balasubramanian <[email protected]>

.travis.yml

@@ -7,12 +7,16 @@ language: cpp
 sudo: true
 
 matrix:
+  allow_failures:
+    - os: osx
+
   include:
     - language: python
       sudo: false
       python: 2.7
       env: TASKS="clang-format"
 
+      os: linux
       dist: trusty
       addons:
         apt:
@@ -23,6 +27,7 @@ matrix:
           - clang-format-6.0
 
     - compiler: gcc
+      os: linux
       addons:
         apt:
           sources: ubuntu-toolchain-r-test
@@ -32,6 +37,7 @@ matrix:
         - MATRIX_EVAL="CC=gcc-4.9 && CXX=g++-4.9"
 
     - compiler: gcc
+      os: linux
       addons:
         apt:
           sources: ubuntu-toolchain-r-test
@@ -41,8 +47,12 @@ matrix:
         - MATRIX_EVAL="CC=gcc-6 && CXX=g++-6"
 
     - compiler: clang
+      os: linux
       env: TASKS="ctest clang-3.9"
 
+    - os: osx
+      env: TASKS="Mac clang"
+
 install:
   - . ./scripts/travis/install.sh
 

CMakeLists.txt

@@ -49,6 +49,7 @@ option(USE_VTK "Enable libraries that use VTK" OFF)
 option(USE_LIBARCHIVE "Enable optional Libarchive features" ON)
 option(USE_LIBMSYM "Enable optional features using libmsym" ON)
 option(USE_SPGLIB "Enable optional features using spglib" ON)
+option(USE_MMTF "Enable optional features using mmtf" ON)
 option(USE_PROTOCALL "Enable libraries that use ProtoCall" OFF)
 option(USE_MOLEQUEUE "Enable the MoleQueue dependent functionality" ON)
 option(USE_PYTHON "Use Python to wrap some of our API" OFF)

appveyor.yml

@@ -8,7 +8,7 @@ init:
 environment:
   PATH: '%PATH%;%QTDIR%\bin'
   matrix:
-  - CMAKE_GENERATOR: '"Visual Studio 15 2017 Win64"'
+  - CMAKE_GENERATOR: '"Ninja"'
     QTDIR: C:\Qt\5.6\msvc2015_64
     platform: x64
 build_script:
@@ -29,6 +29,10 @@ build_script:
 
     cd openchemistry-build
 
+    choco install ninja
+
+    call "C:\Program Files (x86)\Microsoft Visual Studio\2017\Community\VC\Auxiliary\Build\vcvarsall.bat" amd64
+
     cmake -G %CMAKE_GENERATOR% ../openchemistry
 
-    cmake --build . --target avogadrolibs --config Release -- /verbosity:detailed
+    cmake --build . --target avogadrolibs --config Release

avogadro/core/atom.h

@@ -163,6 +163,14 @@ class AtomTemplate
   bool selected() const;
   /** @} */
 
+  /**
+   * The force on this atom.
+   * {@
+   */
+  void setForceVector(const Vector3& force);
+  Vector3 forceVector() const;
+  /** @} */
+
 private:
   MoleculeType* m_molecule;
   Index m_index;
@@ -171,14 +179,12 @@ class AtomTemplate
 template <class Molecule_T>
 AtomTemplate<Molecule_T>::AtomTemplate()
   : m_molecule(nullptr), m_index(MaxIndex)
-{
-}
+{}
 
 template <class Molecule_T>
 AtomTemplate<Molecule_T>::AtomTemplate(MoleculeType* m, Index i)
   : m_molecule(m), m_index(i)
-{
-}
+{}
 
 template <class Molecule_T>
 bool AtomTemplate<Molecule_T>::operator==(
@@ -317,7 +323,21 @@ bool AtomTemplate<Molecule_T>::selected() const
   return m_molecule->atomSelected(m_index);
 }
 
-} // end Core namespace
-} // end Avogadro namespace
+template <class Molecule_T>
+void AtomTemplate<Molecule_T>::setForceVector(const Vector3& force)
+{
+  m_molecule->setForceVector(m_index, force);
+}
+
+template <class Molecule_T>
+Vector3 AtomTemplate<Molecule_T>::forceVector() const
+{
+  return m_molecule->forceVectors().size() > 0
+           ? m_molecule->forceVectors()[m_index]
+           : Vector3::Zero();
+}
+
+} // namespace Core
+} // namespace Avogadro
 
 #endif // AVOGADRO_CORE_ATOM_H

avogadro/core/elementdata.h

@@ -151,28 +151,54 @@ double element_covalent[] = {
 };
 
 unsigned char element_color[][3] = {
-  { 17, 127, 178 },  { 255, 255, 255 }, { 216, 255, 255 }, { 204, 127, 255 },
-  { 193, 255, 0 },   { 255, 181, 181 }, { 127, 127, 127 }, { 12, 12, 255 },
-  { 255, 12, 12 },   { 178, 255, 255 }, { 178, 226, 244 }, { 170, 91, 242 },
-  { 137, 255, 0 },   { 191, 165, 165 }, { 127, 153, 153 }, { 255, 127, 0 },
-  { 255, 255, 48 },  { 30, 239, 30 },   { 127, 209, 226 }, { 142, 63, 211 },
-  { 61, 255, 0 },    { 229, 229, 229 }, { 191, 193, 198 }, { 165, 165, 170 },
-  { 137, 153, 198 }, { 155, 122, 198 }, { 127, 122, 198 }, { 112, 122, 198 },
-  { 91, 122, 193 },  { 255, 122, 96 },  { 124, 127, 175 }, { 193, 142, 142 },
-  { 102, 142, 142 }, { 188, 127, 226 }, { 255, 160, 0 },   { 165, 40, 40 },
-  { 91, 183, 209 },  { 112, 45, 175 },  { 0, 255, 0 },     { 147, 255, 255 },
-  { 147, 224, 224 }, { 114, 193, 201 }, { 84, 181, 181 },  { 58, 158, 158 },
-  { 35, 142, 142 },  { 10, 124, 140 },  { 0, 104, 132 },   { 224, 224, 255 },
-  { 255, 216, 142 }, { 165, 117, 114 }, { 102, 127, 127 }, { 158, 99, 181 },
-  { 211, 122, 0 },   { 147, 0, 147 },   { 66, 158, 175 },  { 86, 22, 142 },
-  { 0, 201, 0 },     { 112, 211, 255 }, { 255, 255, 198 }, { 216, 255, 198 },
-  { 198, 255, 198 }, { 163, 255, 198 }, { 142, 255, 198 }, { 96, 255, 198 },
-  { 68, 255, 198 },  { 48, 255, 198 },  { 30, 255, 198 },  { 0, 255, 155 },
-  { 0, 229, 117 },   { 0, 211, 81 },    { 0, 191, 56 },    { 0, 170, 35 },
-  { 76, 193, 255 },  { 76, 165, 255 },  { 33, 147, 214 },  { 38, 124, 170 },
-  { 38, 102, 150 },  { 22, 84, 135 },   { 244, 237, 209 }, { 204, 209, 30 },
-  { 181, 181, 193 }, { 165, 84, 76 },   { 86, 89, 96 },    { 158, 79, 181 },
-  { 170, 91, 0 },    { 117, 79, 68 },   { 66, 130, 150 },  { 66, 0, 102 },
+  // See, for example http://jmol.sourceforge.net/jscolors/index.en.html
+  // Changes - H is not completely white to add contrast on light backgrounds
+  //         - C is slightly darker (i.e. 50% gray - consistent with Avo1)
+  //         - F is bluer to add contrast with Cl (e.g. CFC compounds)
+  // # Du             # H                 # He
+  { 17, 127, 178 },  { 240, 240, 240 }, { 217, 255, 255 }, { 204, 128, 255 },
+  // # Be, B, C, N
+  { 194, 255, 0 },   { 255, 181, 181 }, { 127, 127, 127 }, { 48, 80, 255 },
+  // # O, F, Ne, Na
+  { 255, 13, 13 },   { 178, 255, 255 }, { 178, 227, 245 }, { 171, 91, 242 },
+  // # Mg
+  { 138, 255, 0 },   { 191, 166, 166 }, { 240, 200, 160 }, { 255, 128, 0 },
+  // # S
+  { 255, 255, 48 },  { 31, 240, 31 },   { 128, 209, 227 }, { 143, 64, 212 },
+  // # Ca
+  { 61, 255, 0 },    { 230, 230, 230 }, { 191, 194, 199 }, { 166, 166, 171 },
+  // # Cr
+  { 138, 153, 199 }, { 156, 122, 199 }, { 224, 102, 51 }, { 240, 144, 160 },
+  // # Ni
+  { 80, 208, 80 },  { 200, 128, 51 },  { 125, 128, 176 }, { 194, 143, 143 },
+  // # Ge
+  { 102, 143, 143 }, { 189, 128, 227 }, { 255, 161, 0 },   { 166, 41, 41 },
+  // # Kr
+  { 92, 184, 209 },  { 112, 46, 176 },  { 0, 255, 0 },     { 148, 255, 255 },
+  // # Zr
+  { 148, 224, 224 }, { 115, 194, 201 }, { 84, 181, 181 },  { 59, 158, 158 },
+  // # Ru
+  { 36, 143, 143 },  { 10, 125, 140 },  { 0, 105, 133 },   { 192, 192, 192 },
+  // # Cd
+  { 255, 217, 143 }, { 166, 117, 115 }, { 102, 128, 128 }, { 158, 99, 181 },
+  // # Te
+  { 211, 122, 0 },   { 148, 0, 148 },   { 66, 158, 176 },  { 87, 23, 143 },
+  // # Ba
+  { 0, 201, 0 },     { 112, 212, 255 }, { 255, 255, 199 }, { 217, 255, 199 },
+  // # Nd
+  { 199, 255, 199 }, { 163, 255, 199 }, { 143, 255, 199 }, { 97, 255, 199 },
+  // # Gd
+  { 69, 255, 199 },  { 48, 255, 199 },  { 31, 255, 199 },  { 0, 255, 156 },
+  // # Er
+  { 0, 230, 117 },   { 0, 212, 82 },    { 0, 191, 56 },    { 0, 171, 36 },
+  // # Hf
+  { 77, 194, 255 },  { 77, 166, 255 },  { 33, 148, 214 },  { 38, 102, 150 },
+  // # Os
+  { 38, 102, 150 },  { 23, 84, 135 },   { 208, 208, 224 }, { 255, 209, 35 },
+  // # Hg
+  { 184, 194, 208 }, { 166, 84, 77 },   { 87, 89, 97 },    { 158, 79, 181 },
+  // # Po
+  { 171, 92, 0 },    { 117, 79, 69 },   { 66, 130, 150 },  { 66, 0, 102 },
   { 0, 124, 0 },     { 112, 170, 249 }, { 0, 186, 255 },   { 0, 160, 255 },
   { 0, 142, 255 },   { 0, 127, 255 },   { 0, 107, 255 },   { 84, 91, 242 },
   { 119, 91, 226 },  { 137, 79, 226 },  { 160, 53, 211 },  { 178, 30, 211 },

avogadro/core/gaussianset.cpp

@@ -116,6 +116,47 @@ void GaussianSet::setMolecularOrbitals(const vector<double>& MOs,
       m_moMatrix[index].coeffRef(i, j) = MOs[i + j * m_numMOs];
 }
 
+void GaussianSet::setMolecularOrbitals(const vector<double>& MOs,
+                                       ElectronType type, Index idx)
+{
+  if (!m_numMOs)
+    return;
+
+  size_t index = 0;
+  if (type == Beta)
+    index = 1;
+
+  unsigned int columns = static_cast<unsigned int>(MOs.size()) / m_numMOs;
+
+  MatrixX moMatrix;
+  moMatrix.resize(m_numMOs, columns);
+
+  for (unsigned int j = 0; j < columns; ++j)
+    for (unsigned int i = 0; i < m_numMOs; ++i)
+      moMatrix.coeffRef(i, j) = MOs[i + j * m_numMOs];
+
+  if (idx <= m_moMatrixSet[index].size())
+    m_moMatrixSet[index].resize(idx + 1);
+
+  m_moMatrixSet[index][idx] = moMatrix;
+}
+
+bool GaussianSet::setActiveSetStep(int index)
+{
+  if (index >= static_cast<int>(m_moMatrixSet[0].size()) ||
+      index >= static_cast<int>(m_moMatrixSet[1].size())) {
+    return false;
+  }
+
+  if (index >= m_molecule->coordinate3dCount())
+    return false;
+
+  m_moMatrix[0] = m_moMatrixSet[0][index];
+  m_moMatrix[1] = m_moMatrixSet[1][index];
+  m_molecule->setCoordinate3d(index);
+  return true;
+}
+
 void GaussianSet::setMolecularOrbitalEnergy(const vector<double>& energies,
                                             ElectronType type)
 {

avogadro/core/gaussianset.h

@@ -122,6 +122,27 @@ class AVOGADROCORE_EXPORT GaussianSet : public BasisSet
   void setMolecularOrbitals(const std::vector<double>& MOs,
                             ElectronType type = Paired);
 
+  /**
+   * Set the molecular orbital (MO) coefficients for a given index. Note
+   * that this must be used with coordinate sets to work correctly.
+   * @param MOs Vector containing the MO coefficients for the GaussianSet.
+   * @param type The type of the MOs (Paired, Alpha, Beta).
+   * @param index The index of the MO in the sequence.
+   */
+  void setMolecularOrbitals(const std::vector<double>& MOs, ElectronType type,
+                            Index index);
+
+  /**
+   * Get the number of elements in the set.
+   */
+  int setCount() { return static_cast<int>(m_moMatrixSet[0].size()); }
+
+  /**
+   * Set the active element in the set, this expects a corresponding
+   * coordinate set element, and will change the active MO matrix.
+   */
+  bool setActiveSetStep(int index);
+
   /**
    * @brief Set the molecular orbtial energies, expected in Hartrees.
    * @param energies The vector containing energies for the MOs of type
@@ -314,6 +335,13 @@ class AVOGADROCORE_EXPORT GaussianSet : public BasisSet
    */
   MatrixX m_moMatrix[2]; //! MO coefficient matrix
 
+  /**
+   * @brief If there are a sequence of related MOs, they are stored here, and
+   * set as the active MOs upon demand. Alpha will store Paired or the Alpha,
+   * Beta will store Beta coefficients for the appropriate calculation types.
+   */
+  std::vector<MatrixX> m_moMatrixSet[2];
+
   /**
    * @brief This block stores energies for the molecular orbitals (same
    * convention as the molecular orbital coefficients).

avogadro/core/molecule.cpp

@@ -811,6 +811,16 @@ void Molecule::updateGraph() const
   }
 }
 
+Array<Vector3>& Molecule::forceVectors()
+{
+  return m_forceVectors;
+}
+
+const Array<Vector3>& Molecule::forceVectors() const
+{
+  return m_forceVectors;
+}
+
 Residue& Molecule::addResidue(std::string& name, Index& number, char& id)
 {
   Residue newResidue(name, number, id);
@@ -823,7 +833,7 @@ void Molecule::addResidue(Residue& residue)
   m_residues.push_back(residue);
 }
 
-Residue Molecule::residue(int index)
+Residue& Molecule::residue(int index)
 {
   return m_residues[index];
 }