Added yaehmop with band structure calc

avogadro/core/avospglib.cpp

@@ -31,7 +31,7 @@ extern "C" {
 namespace Avogadro {
 namespace Core {
 
-unsigned short AvoSpglib::getHallNumber(const Molecule& mol, double cartTol)
+unsigned short AvoSpglib::getHallNumber(Molecule& mol, double cartTol)
 {
   if (!mol.unitCell())
     return 0;
@@ -80,6 +80,7 @@ unsigned short AvoSpglib::getHallNumber(const Molecule& mol, double cartTol)
   delete[] positions;
   delete[] types;
 
+  mol.setHallNumber(hallNumber);
   return hallNumber;
 }
 
@@ -175,6 +176,9 @@ bool AvoSpglib::standardizeCell(Molecule& mol, double cartTol, bool toPrimitive,
 
   // Set the new molecule
   mol = newMol;
+
+  // Set the space group in the molecule
+  getHallNumber(mol, cartTol);
   return true;
 }
 

avogadro/core/avospglib.h

@@ -38,18 +38,22 @@ class AVOGADROCORE_EXPORT AvoSpglib
    * Use spglib to find the Hall number for a crystal. If the unit cell does not
    * exist or if the algorithm fails, 0 will be returned.
    *
+   * If the algorithm succeeds, the hall number will be set in the molecule.
+   *
    * @param mol The molecule to be handled.
    * @param cartTol The cartesian tolerance for spglib.
    * @return The Hall number for the crystal.
    */
-  static unsigned short getHallNumber(const Molecule& mol,
+  static unsigned short getHallNumber(Molecule& mol,
                                       double cartTol = 1e-5);
 
   /**
    * Use spglib to reduce the crystal to a primitive cell. Unless the molecule
    * is missing its unit cell, it will be edited by spglib. Positions are
    * not idealized.
    *
+   * If the algorithm succeeds, the hall number will be set in the molecule.
+   *
    * @param mol The molecule to be reduced to its primitive cell.
    * @param cartTol The cartesian tolerance for spglib.
    * @return False if the molecule has no unit cell or if the
@@ -62,6 +66,8 @@ class AVOGADROCORE_EXPORT AvoSpglib
    * molecule is missing its unit cell, it will be edited by spglib. Positions
    * are idealized.
    *
+   * If the algorithm succeeds, the hall number will be set in the molecule.
+   *
    * @param mol The molecule to be conventionalized.
    * @param cartTol The cartesian tolerance for spglib.
    * @return False if the molecule has no unit cell or if the
@@ -74,6 +80,8 @@ class AVOGADROCORE_EXPORT AvoSpglib
    * its unit cell, it will be edited by spglib. It will be reduced
    * to its primitive form, and positions will be idealized.
    *
+   * If the algorithm succeeds, the hall number will be set in the molecule.
+   *
    * @param mol The molecule to be conventionalized.
    * @param cartTol The cartesian tolerance for spglib.
    * @return False if the molecule has no unit cell or if the

avogadro/core/molecule.h

@@ -577,6 +577,15 @@ class AVOGADROCORE_EXPORT Molecule
   const UnitCell* unitCell() const { return m_unitCell; }
   /** @} */
 
+  /**
+   * The space group for this molecule. It is updated after every
+   * space group operation.
+   * @{
+   */
+  void setHallNumber(unsigned short hallNumber) { m_hallNumber = hallNumber; }
+  unsigned short hallNumber() const { return m_hallNumber; }
+  /** @} */
+
   Array<double> vibrationFrequencies() const;
   void setVibrationFrequencies(const Array<double>& freq);
   Array<double> vibrationIntensities() const;
@@ -676,6 +685,9 @@ class AVOGADROCORE_EXPORT Molecule
   UnitCell* m_unitCell;
   Array<Residue> m_residues;
 
+  // This will be stored from the last space group operation
+  unsigned short m_hallNumber = 0;
+
   /** Update the graph to correspond to the current molecule. */
   void updateGraph() const;
 };

avogadro/qtplugins/CMakeLists.txt

@@ -125,10 +125,14 @@ add_subdirectory(surfaces)
 add_subdirectory(spectra)
 add_subdirectory(vrml)
 
+# Plugins that require VTK
 if(USE_VTK)
   add_subdirectory(plotpdf)
   add_subdirectory(plotrmsd)
   add_subdirectory(plotxrd)
+  if(BUILD_YAEHMOP_PLUGIN)
+    add_subdirectory(yaehmop)
+  endif()
   add_subdirectory(coloropacitymap)
 endif()
 

avogadro/qtplugins/yaehmop/CMakeLists.txt

@@ -0,0 +1,22 @@
+
+set(yaehmop_srcs
+  banddialog.cpp
+  specialkpoints.cpp
+  yaehmop.cpp
+  yaehmopout.cpp
+)
+
+set(yaehmop_uis
+  banddialog.ui
+)
+
+avogadro_plugin(Yaehmop
+  "Use yaehmop to perform extended Hückel calculations."
+  ExtensionPlugin
+  yaehmop.h
+  Yaehmop
+  "${yaehmop_srcs}"
+  "${yaehmop_uis}"
+)
+
+target_link_libraries(Yaehmop LINK_PRIVATE AvogadroVtk)

avogadro/qtplugins/yaehmop/banddialog.cpp

@@ -0,0 +1,71 @@
+/******************************************************************************
+
+  This source file is part of the Avogadro project.
+
+  Copyright 2018 Kitware, Inc.
+
+  This source code is released under the New BSD License, (the "License").
+
+  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 "banddialog.h"
+#include "ui_banddialog.h"
+
+#include <QSettings>
+
+namespace Avogadro {
+namespace QtPlugins {
+
+BandDialog::BandDialog(QWidget* aParent, YaehmopSettings& yaehmopSettings)
+  : QDialog(aParent), m_ui(new Ui::BandDialog),
+    m_yaehmopSettings(yaehmopSettings)
+{
+  m_ui->setupUi(this);
+}
+
+BandDialog::~BandDialog() = default;
+
+int BandDialog::exec()
+{
+  // Load the settings then exec
+  m_ui->spin_numKPoints->setValue(m_yaehmopSettings.numBandKPoints);
+  m_ui->edit_specialKPoints->setText(m_yaehmopSettings.specialKPoints);
+  m_ui->cb_displayYaehmopInput->setChecked(
+    m_yaehmopSettings.displayYaehmopInput);
+  m_ui->cb_limitY->setChecked(m_yaehmopSettings.limitY);
+  m_ui->spin_minY->setValue(m_yaehmopSettings.minY);
+  m_ui->spin_maxY->setValue(m_yaehmopSettings.maxY);
+  m_ui->cb_plotFermi->setChecked(m_yaehmopSettings.plotFermi);
+  m_ui->spin_fermi->setValue(m_yaehmopSettings.fermi);
+  m_ui->cb_zeroFermi->setChecked(m_yaehmopSettings.zeroFermi);
+  m_ui->spin_numDim->setValue(m_yaehmopSettings.numDim);
+
+  return QDialog::exec();
+}
+
+void BandDialog::accept()
+{
+  // Save the settings and accept
+  m_yaehmopSettings.numBandKPoints = m_ui->spin_numKPoints->value();
+  m_yaehmopSettings.specialKPoints = m_ui->edit_specialKPoints->toPlainText();
+  m_yaehmopSettings.displayYaehmopInput =
+    m_ui->cb_displayYaehmopInput->isChecked();
+  m_yaehmopSettings.limitY = m_ui->cb_limitY->isChecked();
+  m_yaehmopSettings.minY = m_ui->spin_minY->value();
+  m_yaehmopSettings.maxY = m_ui->spin_maxY->value();
+  m_yaehmopSettings.plotFermi = m_ui->cb_plotFermi->isChecked();
+  m_yaehmopSettings.fermi = m_ui->spin_fermi->value();
+  m_yaehmopSettings.zeroFermi = m_ui->cb_zeroFermi->isChecked();
+  m_yaehmopSettings.numDim = m_ui->spin_numDim->value();
+
+  QDialog::accept();
+}
+
+} // namespace QtPlugins
+} // namespace Avogadro

avogadro/qtplugins/yaehmop/banddialog.h

@@ -0,0 +1,57 @@
+/******************************************************************************
+
+  This source file is part of the Avogadro project.
+
+  Copyright 2018 Kitware, Inc.
+
+  This source code is released under the New BSD License, (the "License").
+
+  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.
+
+******************************************************************************/
+
+#ifndef AVOGADRO_QTPLUGINS_YAEHMOPBANDDIALOG_H
+#define AVOGADRO_QTPLUGINS_YAEHMOPBANDDIALOG_H
+
+#include <memory>
+
+#include <QDialog>
+
+#include "yaehmopsettings.h"
+
+namespace Avogadro {
+namespace QtPlugins {
+
+namespace Ui {
+class BandDialog;
+}
+
+/**
+ * @brief Dialog to perform a band structure calculation with yaehmop.
+ */
+class BandDialog : public QDialog
+{
+  Q_OBJECT
+
+public:
+  explicit BandDialog(QWidget* parent, YaehmopSettings& yaehmopSettings);
+  ~BandDialog();
+
+public slots:
+  int exec() override;
+
+protected slots:
+  void accept() override;
+
+private:
+  std::unique_ptr<Ui::BandDialog> m_ui;
+  YaehmopSettings& m_yaehmopSettings;
+};
+
+} // namespace QtPlugins
+} // namespace Avogadro
+#endif // AVOGADRO_QTPLUGINS_YAEHMOPBANDDIALOG_H