symmetrywidget.cpp

/******************************************************************************
  This source file is part of the Avogadro project.
  This source code is released under the 3-Clause BSD License, (see "LICENSE").
******************************************************************************/

#include "symmetrywidget.h"
#include "richtextdelegate.h"
#include "symmetryutil.h"
#include "ui_symmetrywidget.h"

#include <avogadro/qtgui/molecule.h>

#include <QtCore/QDebug>

#include <QtWidgets/QPlainTextEdit>

using Avogadro::QtGui::Molecule;

using namespace msym;
using namespace Avogadro::QtPlugins::SymmetryUtil;

namespace Avogadro::QtPlugins {

msym_thresholds_t tight_thresholds = { // all defaults
  /*.zero =*/1.0e-3,
  /*.geometry =*/1.0e-3,
  /*.angle =*/1.0e-3,
  /*.equivalence =*/5.0e-4,
  /*.eigfact =*/1.0e-3,
  /*.permutation =*/5.0e-3,
  /*.orthogonalization =*/0.1
};

msym_thresholds_t medium_thresholds = {
  /*.zero =*/1.0e-2,
  /*.geometry =*/1.0e-2,
  /*.angle =*/1.0e-2,
  /*.equivalence =*/6.3e-3,
  /*.eigfact =*/1.0e-3,
  /*.permutation =*/1.58e-2,
  /*.orthogonalization =*/0.1
};

msym_thresholds_t loose_thresholds = {
  /*.zero =*/0.06,
  /*.geometry =*/0.1,
  /*.angle =*/0.06,
  /*.equivalence =*/0.025,
  /*.eigfact =*/1.0e-3,
  /*.permutation =*/1.0e-1,
  /*.orthogonalization =*/0.1
};

msym_thresholds_t sloppy_thresholds = {
  /*.zero =*/0.1,
  /*.geometry =*/0.1,
  /*.angle =*/0.1,
  /*.equivalence =*/0.075,
  /*.eigfact =*/1.0e-3,
  /*.permutation =*/1.0e-1,
  /*.orthogonalization =*/0.1
};

SymmetryWidget::SymmetryWidget(QWidget* parent_)
  : QWidget(parent_)
  , m_ui(new Ui::SymmetryWidget)
  , m_molecule(nullptr)
  , m_equivalenceTreeModel(new QStandardItemModel(this))
  , m_operationsTableModel(new OperationsTableModel(this))
  , m_subgroupsTreeModel(new QStandardItemModel(this))
  , m_es(nullptr)
  , m_sops(nullptr)
  , m_sg(nullptr)
  , m_sopsl(0)
  , m_sgl(0)
  , m_radius(0.0)
{
  setWindowFlags(Qt::Dialog);
  m_ui->setupUi(this);

  m_ui->equivalenceTree->setModel(m_equivalenceTreeModel);

  m_ui->operationsTable->setModel(m_operationsTableModel);
  m_ui->operationsTable->setItemDelegateForColumn(
    OperationsTableModel::ColumnType, new RichTextDelegate(this));

  m_ui->subgroupsTree->setModel(m_subgroupsTreeModel);
  m_ui->subgroupsTree->setItemDelegateForColumn(0, new RichTextDelegate(this));

  connect(
    m_ui->detectSymmetryButton, SIGNAL(clicked()), SIGNAL(detectSymmetry()));
  connect(m_ui->symmetrizeMoleculeButton,
          SIGNAL(clicked()),
          SIGNAL(symmetrizeMolecule()));

  connect(
    m_ui->equivalenceTree->selectionModel(),
    SIGNAL(selectionChanged(const QItemSelection&, const QItemSelection&)),
    SLOT(equivalenceSelectionChanged(const QItemSelection&,
                                     const QItemSelection&)));

  connect(
    m_ui->operationsTable->selectionModel(),
    SIGNAL(selectionChanged(const QItemSelection&, const QItemSelection&)),
    SLOT(operationsSelectionChanged(const QItemSelection&,
                                    const QItemSelection&)));
  connect(
    m_ui->subgroupsTree->selectionModel(),
    SIGNAL(selectionChanged(const QItemSelection&, const QItemSelection&)),
    SLOT(
      subgroupsSelectionChanged(const QItemSelection&, const QItemSelection&)));
}

SymmetryWidget::~SymmetryWidget()
{
  delete m_ui;
}

void SymmetryWidget::setMolecule(QtGui::Molecule* molecule)
{
  if (molecule != m_molecule) {
    if (m_molecule)
      m_molecule->disconnect(this);

    m_molecule = molecule;

    if (m_molecule) {
      connect(m_molecule, SIGNAL(changed(uint)), SLOT(moleculeChanged(uint)));
    }
  }
}

void SymmetryWidget::moleculeChanged(unsigned int changes)
{
  /*
  if (changes & Molecule::UnitCell)
    revert();*/
}

void SymmetryWidget::operationsSelectionChanged(
  const QItemSelection& selected,
  const QItemSelection& deselected)
{

  if (!m_molecule)
    return;
  if (m_ui->tabWidget->currentWidget() != m_ui->subgroupsTab) {
    // qDebug() << "subgroupsTab not selected";
    m_ui->subgroupsTree->selectionModel()->reset();
  }

  QModelIndexList selection =
    m_ui->operationsTable->selectionModel()->selectedRows();

  //  qDebug() << "operations changed";

  // qDebug() << "selection " << selection.size();

  QVariantList reflectionVariantList;
  QVariantList properRotationVariantList;
  QVariantList improperRotationVariantList;

  m_molecule->setProperty("SymmetryOrigo", QVariant());
  m_molecule->setProperty("SymmetryRadius", QVariant());
  m_molecule->setProperty("SymmetryInversion", QVariant());
  m_molecule->setProperty("SymmetryProperRotationVariantList", QVariant());
  m_molecule->setProperty("SymmetryImproperRotationVariantList", QVariant());
  m_molecule->setProperty("SymmetryReflectionVariantList", QVariant());

  // qDebug() << "cleared elements";

  if (m_sopsl > 0 && selection.size() > 0) {
    m_molecule->setProperty("SymmetryOrigo", m_cm);
    m_molecule->setProperty("SymmetryRadius", m_radius);
  }

  foreach (QModelIndex i, selection) {
    unsigned int row = i.row();
    if (!i.isValid() || row >= m_sopsl)
      continue;
    float x = m_sops[row].v[0], y = m_sops[row].v[1], z = m_sops[row].v[2];
    switch (m_sops[row].type) {
      case IDENTITY:
        break;
      case PROPER_ROTATION:
        properRotationVariantList.append(QVector3D(x, y, z));
        break;
      case IMPROPER_ROTATION:
        improperRotationVariantList.append(QVector3D(x, y, z));
        break;
      case REFLECTION:
        reflectionVariantList.append(QVector3D(x, y, z));
        break;
      case INVERSION:
        m_molecule->setProperty("SymmetryInversion", m_cm);
        break;
      default:
        break;
    }
  }
  if (properRotationVariantList.size() > 0)
    m_molecule->setProperty("SymmetryProperRotationVariantList",
                            properRotationVariantList);
  if (improperRotationVariantList.size() > 0)
    m_molecule->setProperty("SymmetryImproperRotationVariantList",
                            improperRotationVariantList);
  if (reflectionVariantList.size() > 0)
    m_molecule->setProperty("SymmetryReflectionVariantList",
                            reflectionVariantList);

  /* A little bit ugly, but it'll do for now */
  m_molecule->emitChanged(QtGui::Molecule::Atoms);
}

void SymmetryWidget::subgroupsSelectionChanged(const QItemSelection& selected,
                                               const QItemSelection& deselected)
{
  // QModelIndexList selection =
  // m_ui->subgroupsTree->selectionModel()->selectedIndexes();
  QModelIndex i =
    m_ui->subgroupsTree->selectionModel()->selectedIndexes().first();
  // qDebug() << "subgroupsSelectionChanged";
  if (!i.isValid())
    return;
  // qDebug() << "valid";
  int sgi = i.data(Qt::UserRole).value<int>();
  // qDebug() << "index " << sgi;
  if (sgi < 0 || sgi >= m_sgl)
    return;
  const msym::msym_subgroup_t* sg = &m_sg[sgi];
  // m_ui->operationsTable->selectionModel()->clear();

  QItemSelectionModel* selectionModel = m_ui->operationsTable->selectionModel();
  // selectionModel->clear();

  QItemSelection selection;

  for (int j = 0; j < sg->order; j++) {
    int row = static_cast<int>(sg->sops[j] - m_sops);
    QModelIndex left = m_operationsTableModel->index(row, 0);
    QModelIndex right = m_operationsTableModel->index(
      row, m_operationsTableModel->columnCount(left) - 1);
    //if (!left.isValid() || !right.isValid())
    //  qDebug() << "invalid index " << j;
    QItemSelection sel(left, right);

    selection.merge(sel, QItemSelectionModel::Select);
  }

  QModelIndexList tmp = selection.indexes();
  //foreach (QModelIndex j, tmp) {
  //  qDebug() << "selecting " << j.row() << " " << j.column();
  //}

  selectionModel->select(selection, QItemSelectionModel::ClearAndSelect);
}

void SymmetryWidget::equivalenceSelectionChanged(
  const QItemSelection& selected,
  const QItemSelection& deselected)
{
  QModelIndex i =
    m_ui->equivalenceTree->selectionModel()->selectedIndexes().first();
  // qDebug() << "equivalenceSelectionChanged";
  if (!i.isValid())
    return;
  int atomInGroup = i.data(Qt::UserRole).value<int>();
  QModelIndex g = i.parent();
  if (!g.isValid())
    return;
  int group = g.data(Qt::UserRole).value<int>();

  // qDebug() << "valid " << group << atomInGroup;
  if (group < 0 || group >= m_esl)
    return;

  // TODO: okay, now we have to find the atoms and select them
  if (!m_molecule)
    return;

  const msym_equivalence_set_t* smes = &m_es[group];
  if (smes == nullptr)
    return;
  const msym_element_t* a = smes->elements[atomInGroup];
  if (a == nullptr)
    return;

  Index length = m_molecule->atomCount();
  // unselect all the atoms
  for (Index iat = 0; iat < length; ++iat) {
    m_molecule->setAtomSelected(iat, false);
  }
  // this is yucky, but libmsym uses <void*> for id
  auto selectedAtom = reinterpret_cast<Index>(a->id);
  m_molecule->setAtomSelected(selectedAtom, true);

  m_molecule->emitChanged(QtGui::Molecule::Atoms);
}

void SymmetryWidget::setRadius(double radius)
{
  m_radius = radius;
}

void SymmetryWidget::setCenterOfMass(double cm[3])
{
  m_cm = QVector3D(cm[0], cm[1], cm[2]);
}

void SymmetryWidget::setPointGroupSymbol(QString pg)
{
  m_ui->pointGroupLabel->setText(pg);
}

void SymmetryWidget::setSymmetryOperations(
  int sopsl,
  const msym::msym_symmetry_operation_t* sops)
{
  m_sops = sops;
  m_sopsl = sopsl;
  m_operationsTableModel->setOperations(sopsl, sops);
  m_molecule->setProperty("SymmetryOrigo", QVariant());
  m_molecule->setProperty("SymmetryRadius", QVariant());
  m_molecule->setProperty("SymmetryInversion", QVariant());
  m_molecule->setProperty("SymmetryProperRotationVariantList", QVariant());
  m_molecule->setProperty("SymmetryImproperRotationVariantList", QVariant());
  m_molecule->setProperty("SymmetryReflectionVariantList", QVariant());
  /* need another change event */
  m_molecule->emitChanged(QtGui::Molecule::Atoms);
}

void SymmetryWidget::setEquivalenceSets(int esl,
                                        const msym::msym_equivalence_set_t* es)
{
  m_esl = esl;
  m_es = es;
  m_equivalenceTreeModel->clear();
  for (int i = 0; i < esl; i++) {
    auto* const parent = new QStandardItem;
    QString label = tr("Group %1").arg(QString::number(i + 1));
    parent->setText(label);
    parent->setData(i, Qt::UserRole);
    m_equivalenceTreeModel->appendRow(parent);
    const msym_equivalence_set_t* smes = &es[i];
    for (int j = 0; j < smes->length; j++) {
      auto* const child = new QStandardItem;
      label =
        tr("%1 %2").arg(smes->elements[j]->name).arg(QString::number(j + 1));
      child->setText(label);
      child->setData(j, Qt::UserRole);
      parent->appendRow(child);
    }
  }
}

void SymmetryWidget::setSubgroups(int sgl, const msym::msym_subgroup_t* sg)
{
  m_sg = sg;
  m_sgl = sgl;
  m_subgroupsTreeModel->clear();
  for (int i = 0; i < sgl; i++) {
    if (sg[i].order <= 2)
      continue;
    auto* const parent = new QStandardItem;
    parent->setText(pointGroupSymbol(sg[i].name));
    parent->setData(i, Qt::UserRole);
    m_subgroupsTreeModel->appendRow(parent);
    for (auto generator : sg[i].generators) {
      if (generator == nullptr)
        continue;
      // qDebug() << "child " << sg[i].generators[j] - m_sg << " "
      //         << sg[i].generators[j] << " " << m_sg;
      auto* const child = new QStandardItem;
      child->setText(pointGroupSymbol(generator->name));

      child->setData(static_cast<int>(generator - m_sg),
                     Qt::UserRole);
      parent->appendRow(child);
    }
  }
}

msym_thresholds_t* SymmetryWidget::getThresholds() const
{
  msym_thresholds_t* thresholds = nullptr;
  switch (m_ui->toleranceCombo->currentIndex()) {
    case 3: // sloppy
      thresholds = &sloppy_thresholds;
      break;
    case 2: // loose
      thresholds = &loose_thresholds;
      break;
    case 1: // normal
      thresholds = &medium_thresholds;
      break;
    case 0: // tight
    default:
      thresholds = &tight_thresholds;
  }
  return thresholds;
}

} // namespace Avogadro