diff --git a/src/classes/structure.cpp b/src/classes/structure.cpp index c9fad5c920..4c05cc62d9 100644 --- a/src/classes/structure.cpp +++ b/src/classes/structure.cpp @@ -103,6 +103,9 @@ int Structure::nAtoms(Atom::Presence withPresence) const { return i->isPresence(withPresence); }); } +// Return atom at index +StructureAtom *Structure::atomAt(int i) { return atoms_[i].get(); } + // Return atoms const std::vector> &Structure::atoms() const { return atoms_; } std::vector> &Structure::atoms() { return atoms_; } diff --git a/src/classes/structure.h b/src/classes/structure.h index a878d89023..f3b01f7359 100644 --- a/src/classes/structure.h +++ b/src/classes/structure.h @@ -112,6 +112,8 @@ class Structure : public Serialisable<> void removeAtoms(const std::vector &atoms); // Return the number of atoms int nAtoms(Atom::Presence withPresence = Atom::Presence::Any) const; + // Return atom at index + StructureAtom *atomAt(int i); // Return atoms const std::vector> &atoms() const; std::vector> &atoms(); diff --git a/src/gui/createGrapheneSpeciesDialog.cpp b/src/gui/createGrapheneSpeciesDialog.cpp index 45194aa310..3287bdcb22 100644 --- a/src/gui/createGrapheneSpeciesDialog.cpp +++ b/src/gui/createGrapheneSpeciesDialog.cpp @@ -518,4 +518,4 @@ void CreateGrapheneSpeciesDialog::on_OKButton_clicked(bool checked) accept(); } -void CreateGrapheneSpeciesDialog::on_CancelButton_clicked(bool checked) { reject(); } +void CreateGrapheneSpeciesDialog::on_CancelButton_clicked(bool checked) { reject(); } \ No newline at end of file diff --git a/src/gui/createGrapheneSpeciesDialog.h b/src/gui/createGrapheneSpeciesDialog.h index c265d4936c..49de0954c4 100644 --- a/src/gui/createGrapheneSpeciesDialog.h +++ b/src/gui/createGrapheneSpeciesDialog.h @@ -8,7 +8,6 @@ #include "gui/selectElementDialog.h" #include "gui/ui_createGrapheneSpeciesDialog.h" #include "gui/wizard.h" -#include "io/import/cif.h" #include "main/dissolve.h" #include @@ -110,4 +109,4 @@ class CreateGrapheneSpeciesDialog : public QDialog // Dialog void on_OKButton_clicked(bool checked); void on_CancelButton_clicked(bool checked); -}; +}; \ No newline at end of file diff --git a/src/gui/createGrapheneSpeciesDialog.ui b/src/gui/createGrapheneSpeciesDialog.ui index add06c593f..8cea452017 100644 --- a/src/gui/createGrapheneSpeciesDialog.ui +++ b/src/gui/createGrapheneSpeciesDialog.ui @@ -1011,4 +1011,4 @@ - + \ No newline at end of file diff --git a/src/gui/gui.h b/src/gui/gui.h index b350024f37..37ae3b6a2b 100644 --- a/src/gui/gui.h +++ b/src/gui/gui.h @@ -170,7 +170,7 @@ class DissolveWindow : public QMainWindow void on_SpeciesImportFromDissolveAction_triggered(bool checked); void on_SpeciesImportFromXYZAction_triggered(bool checked); void on_SpeciesImportLigParGenAction_triggered(bool checked); - void on_SpeciesImportFromCIFAction_triggered(bool checked); + // void on_SpeciesImportFromCIFAction_triggered(bool checked); void on_SpeciesRenameAction_triggered(bool checked); void on_SpeciesDeleteAction_triggered(bool checked); void on_SpeciesAddForcefieldTermsAction_triggered(bool checked); diff --git a/src/gui/importCIFDialog.cpp b/src/gui/importCIFDialog.cpp deleted file mode 100644 index 94873c163c..0000000000 --- a/src/gui/importCIFDialog.cpp +++ /dev/null @@ -1,323 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#include "gui/importCIFDialog.h" -#include "base/units.h" -#include "classes/empiricalFormula.h" -#include "classes/pairIterator.h" -#include "generator/box.h" -#include "gui/helpers/comboPopulator.h" -#include -#include -#include -#include - -ImportCIFDialog::ImportCIFDialog(QWidget *parent, Dissolve &dissolve) - : QDialog(parent), cifAssemblyModel_(cifHandler_.assemblies()), dissolve_(dissolve) -{ - ui_.setupUi(this); - - Locker refreshLock(widgetsUpdating_); - - // Add spacegroups to combo - for (auto n = 1; n < SpaceGroups::nSpaceGroupIds; ++n) - ui_.SpaceGroupsCombo->addItem( - QString::fromStdString(std::string(SpaceGroups::formattedInformation((SpaceGroups::SpaceGroupId)n)))); - ui_.SpaceGroupsCombo->setCurrentIndex(-1); - - // Set assembly view model - ui_.AssemblyView->setModel(&cifAssemblyModel_); - ui_.AssemblyView->update(); - ui_.AssemblyView->expandAll(); - connect(&cifAssemblyModel_, SIGNAL(dataChanged(const QModelIndex &, const QModelIndex &, const QList &)), this, - SLOT(assembliesChanged(const QModelIndex &, const QModelIndex &, const QList &))); - connect(&cifAssemblyModel_, SIGNAL(dataChanged(const QModelIndex &, const QModelIndex &, const QList &)), - ui_.AssemblyView, SLOT(expandAll())); - - // Populate density units combo - ComboEnumOptionsPopulator(ui_.DensityUnitsCombo, Units::densityUnits()); - - // Set display configuration - ui_.StructureViewer->setConfiguration(cifHandler_.generatedConfiguration()); - - createMoietyRemovalNETA(ui_.MoietyNETARemovalEdit->text().toStdString()); -} - -/* - * UI - */ - -// Update all controls -void ImportCIFDialog::updateWidgets() -{ - Locker updateLock(widgetsUpdating_); - - // DATA_ ID - ui_.InfoDataLabel->setText(QString::fromStdString(cifHandler_.getTagString("DATA_").value_or(""))); - - // Chemical Formula - ui_.InfoChemicalFormulaLabel->setText(QString::fromStdString(cifHandler_.chemicalFormula())); - - // Publication Data - ui_.InfoPublicationTitleLabel->setText( - QString::fromStdString(cifHandler_.getTagString("_publ_section_title").value_or(""))); - ui_.InfoPublicationReferenceLabel->setText(QString::fromStdString(std::format( - "{}, {}, {}, {}", cifHandler_.getTagString("_journal_name_full").value_or("N/A"), - cifHandler_.getTagString("_journal_year").value_or("N/A"), cifHandler_.getTagString("_journal_volume").value_or("N/A"), - cifHandler_.getTagString("_journal_page_first").value_or("N/A")))); - ui_.InfoAuthorsList->clear(); - auto authors = cifHandler_.getTagStrings("_publ_author_name"); - for (auto &author : authors) - ui_.InfoAuthorsList->addItem(QString::fromStdString(author)); - - // Spacegroup - ui_.SpaceGroupsCombo->setCurrentIndex(cifHandler_.spaceGroup() - 1); - - // Bonding - ui_.BondFromCIFRadio->setEnabled(cifHandler_.hasBondDistances()); - - // Assemblies - ui_.AssemblyView->expandAll(); - - // Configuration information - auto *cfg = cifHandler_.generatedConfiguration(); - const auto *box = cfg->box(); - ui_.CurrentBoxTypeLabel->setText(QString::fromStdString(std::string(Box::boxTypes().keyword(box->type())))); - QString boxInfo = QString("A: %1 Å
").arg(box->axisLengths().x); - boxInfo += QString("B: %1 Å
").arg(box->axisLengths().y); - boxInfo += QString("C: %1 Å
").arg(box->axisLengths().z); - boxInfo += QString("α: %1°
").arg(box->axisAngles().x); - boxInfo += QString("β: %1°
").arg(box->axisAngles().y); - boxInfo += QString("γ: %1°").arg(box->axisAngles().z); - ui_.CurrentBoxFrame->setToolTip(boxInfo); - updateDensityLabel(); - ui_.AtomPopulationLabel->setText(QString::number(cfg->nAtoms())); - ui_.MoleculePopulationLabel->setText(QString::number(cfg->nMolecules())); - - // Output - auto validSpecies = !cifHandler_.molecularSpecies().empty(); - ui_.OutputMolecularRadio->setEnabled(validSpecies); - ui_.OutputFrameworkRadio->setEnabled(!validSpecies); - ui_.OutputSupermoleculeRadio->setEnabled(!validSpecies); - if (validSpecies) - ui_.OutputMolecularRadio->setChecked(true); - else if (ui_.OutputMolecularRadio->isChecked()) - ui_.OutputFrameworkRadio->setChecked(true); - - // Update molecular species list - ui_.OutputMolecularSpeciesList->clear(); - for (auto &molecularSp : cifHandler_.molecularSpecies()) - { - ui_.OutputMolecularSpeciesList->addItem(QString::fromStdString(std::string(molecularSp.species()->name()))); - } - - // Structure - ui_.StructureViewer->postRedisplay(); -} - -// Update density label -void ImportCIFDialog::updateDensityLabel() -{ - auto *cfg = cifHandler_.generatedConfiguration(); - if (!cfg) - ui_.DensityUnitsLabel->setText("N/A"); - else - { - auto rho = ui_.DensityUnitsCombo->currentIndex() == 0 ? cfg->atomicDensity() : cfg->chemicalDensity(); - ui_.DensityUnitsLabel->setText(rho ? QString::number(*rho) : "--"); - } -} - -void ImportCIFDialog::on_InputFileEdit_editingFinished() -{ - // Load the CIF file - if (!cifHandler_.read(ui_.InputFileEdit->text().toStdString())) - Messenger::error("Failed to load CIF file '{}'.\n", ui_.InputFileEdit->text().toStdString()); - else - { - cifHandler_.generate(); - updateWidgets(); - } -} - -void ImportCIFDialog::on_InputFileSelectButton_clicked(bool checked) -{ - QString inputFile = QFileDialog::getOpenFileName(this, "Choose CIF file to open", QDir().absolutePath(), - "CIF files (*.cif);;All files (*)"); - if (inputFile.isEmpty()) - return; - - // Set input file in edit - ui_.InputFileEdit->setText(inputFile); - on_InputFileEdit_editingFinished(); -} - -void ImportCIFDialog::on_SpaceGroupsCombo_currentIndexChanged(int index) -{ - if (widgetsUpdating_) - return; - - cifHandler_.setSpaceGroup((SpaceGroups::SpaceGroupId)(ui_.SpaceGroupsCombo->currentIndex() + 1)); - - updateWidgets(); -} - -void ImportCIFDialog::on_NormalOverlapToleranceRadio_clicked(bool checked) -{ - if (checked) - { - cifHandler_.setOverlapTolerance(0.1); - updateWidgets(); - } -} - -void ImportCIFDialog::on_LooseOverlapToleranceRadio_clicked(bool checked) -{ - if (checked) - { - cifHandler_.setOverlapTolerance(0.5); - updateWidgets(); - } -} - -void ImportCIFDialog::on_CalculateBondingRadio_clicked(bool checked) -{ - if (checked) - { - cifHandler_.setUseCIFBondingDefinitions(false); - updateWidgets(); - } -} - -void ImportCIFDialog::on_BondFromCIFRadio_clicked(bool checked) -{ - if (checked) - { - cifHandler_.setUseCIFBondingDefinitions(true); - updateWidgets(); - } -} - -void ImportCIFDialog::on_BondingPreventMetallicCheck_clicked(bool checked) -{ - cifHandler_.setPreventMetallicBonds(checked); - - updateWidgets(); -} - -// Create / check NETA definition for moiety removal -bool ImportCIFDialog::createMoietyRemovalNETA(std::string definition) -{ - auto result = moietyNETA_.create(definition); - - ui_.MoietyNETARemovalIndicator->setOK(result); - - return result; -} - -void ImportCIFDialog::on_MoietyRemoveAtomicsCheck_clicked(bool checked) -{ - cifHandler_.setRemoveAtomics(checked); - updateWidgets(); -} - -void ImportCIFDialog::on_MoietyRemoveWaterCheck_clicked(bool checked) -{ - cifHandler_.setRemoveWaterAndCoordinateOxygens(checked); - updateWidgets(); -} - -void ImportCIFDialog::on_MoietyRemoveByNETACheck_clicked(bool checked) -{ - // Set state of associated controls - ui_.MoietyNETARemovalEdit->setEnabled(checked); - ui_.MoietyNETARemoveFragmentsCheck->setEnabled(checked); - - if (ui_.MoietyNETARemovalIndicator->state() != CheckIndicator::OKState) - return; - - cifHandler_.setRemoveNETA(checked, ui_.MoietyNETARemoveFragmentsCheck->isChecked()); - updateWidgets(); -} - -void ImportCIFDialog::on_MoietyNETARemovalEdit_textEdited(const QString &text) -{ - if (!createMoietyRemovalNETA(ui_.MoietyNETARemovalEdit->text().toStdString())) - return; - - cifHandler_.setRemoveNETA(ui_.MoietyRemoveByNETACheck->isChecked(), ui_.MoietyNETARemoveFragmentsCheck->isChecked()); - cifHandler_.setMoietyRemovalNETA(moietyNETA_.definitionString()); - updateWidgets(); -} - -void ImportCIFDialog::on_MoietyNETARemoveFragmentsCheck_clicked(bool checked) -{ - if (ui_.MoietyNETARemovalIndicator->state() != CheckIndicator::OKState) - return; - - cifHandler_.setRemoveNETA(ui_.MoietyRemoveByNETACheck->isChecked(), checked); - updateWidgets(); -} - -void ImportCIFDialog::assembliesChanged(const QModelIndex &, const QModelIndex &, const QList &) -{ - cifHandler_.generate(); - updateWidgets(); -} - -void ImportCIFDialog::on_RepeatASpin_valueChanged(int value) -{ - cifHandler_.setSupercellRepeat({ui_.RepeatASpin->value(), ui_.RepeatBSpin->value(), ui_.RepeatCSpin->value()}); - updateWidgets(); -} - -void ImportCIFDialog::on_RepeatBSpin_valueChanged(int value) -{ - cifHandler_.setSupercellRepeat({ui_.RepeatASpin->value(), ui_.RepeatBSpin->value(), ui_.RepeatCSpin->value()}); - updateWidgets(); -} - -void ImportCIFDialog::on_RepeatCSpin_valueChanged(int value) -{ - - cifHandler_.setSupercellRepeat({ui_.RepeatASpin->value(), ui_.RepeatBSpin->value(), ui_.RepeatCSpin->value()}); - updateWidgets(); -} - -void ImportCIFDialog::on_DensityUnitsCombo_currentIndexChanged(int index) -{ - if (widgetsUpdating_) - return; - - updateDensityLabel(); -} - -void ImportCIFDialog::on_OutputMolecularRadio_clicked(bool checked) {} - -void ImportCIFDialog::on_OutputFrameworkRadio_clicked(bool checked) {} - -void ImportCIFDialog::on_OutputSupermoleculeRadio_clicked(bool checked) {} - -void ImportCIFDialog::on_OKButton_clicked(bool checked) -{ - Flags outputFlags; - if (ui_.OutputMolecularRadio->isChecked()) - outputFlags.setFlag(CIFHandler::OutputFlags::OutputMolecularSpecies); - else if (ui_.OutputFrameworkRadio->isChecked()) - outputFlags.setFlag(CIFHandler::OutputFlags::OutputFramework); - else if (ui_.OutputSupermoleculeRadio->isChecked()) - outputFlags.setFlag(CIFHandler::OutputFlags::OutputSupermolecule); - - // Output a configuration as well as the species for certain options - if (outputFlags.isSet(CIFHandler::OutputFlags::OutputMolecularSpecies) || - outputFlags.isSet(CIFHandler::OutputFlags::OutputFramework)) - { - outputFlags.setFlag(CIFHandler::OutputFlags::OutputConfiguration); - } - - cifHandler_.finalise(dissolve_.coreData(), outputFlags); - - accept(); -} - -void ImportCIFDialog::on_CancelButton_clicked(bool checked) { reject(); } diff --git a/src/gui/importCIFDialog.h b/src/gui/importCIFDialog.h deleted file mode 100644 index 52133f3a42..0000000000 --- a/src/gui/importCIFDialog.h +++ /dev/null @@ -1,94 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#pragma once - -#include "base/lock.h" -#include "gui/models/cifAssemblyModel.h" -#include "gui/ui_importCIFDialog.h" -#include "gui/wizard.h" -#include "io/import/cif.h" -#include "main/dissolve.h" -#include - -// Forward Declarations -class Dissolve; -class Species; - -// Import CIF Dialog -class ImportCIFDialog : public QDialog -{ - Q_OBJECT - - public: - ImportCIFDialog(QWidget *parent, Dissolve &dissolve); - ~ImportCIFDialog() = default; - - private: - // Main form declaration - Ui::ImportCIFDialog ui_; - // Model for CIF assemblies - CIFAssemblyModel cifAssemblyModel_; - // Temporary core data - CoreData temporaryCoreData_; - - /* - * Data - */ - private: - // Main Dissolve object - Dissolve &dissolve_; - // CIF Handler - CIFHandler cifHandler_; - // NETA for moiety removal - NETADefinition moietyNETA_; - - private: - // Create / check NETA definition for moiety removal - bool createMoietyRemovalNETA(std::string definition); - - /* - * UI - */ - private: - // Widget update lock - Lock widgetsUpdating_; - // Update all controls - void updateWidgets(); - // Update density label - void updateDensityLabel(); - - private Q_SLOTS: - // CIF File / Information - void on_InputFileEdit_editingFinished(); - void on_InputFileSelectButton_clicked(bool checked); - void on_SpaceGroupsCombo_currentIndexChanged(int index); - // Overlap - void on_NormalOverlapToleranceRadio_clicked(bool checked); - void on_LooseOverlapToleranceRadio_clicked(bool checked); - // Bonding - void on_CalculateBondingRadio_clicked(bool checked); - void on_BondingPreventMetallicCheck_clicked(bool checked); - void on_BondFromCIFRadio_clicked(bool checked); - // CleanUp - void on_MoietyRemoveAtomicsCheck_clicked(bool checked); - void on_MoietyRemoveWaterCheck_clicked(bool checked); - void on_MoietyRemoveByNETACheck_clicked(bool checked); - void on_MoietyNETARemovalEdit_textEdited(const QString &text); - void on_MoietyNETARemoveFragmentsCheck_clicked(bool checked); - // Assemblies - void assembliesChanged(const QModelIndex &, const QModelIndex &, const QList &); - // Supercell - void on_RepeatASpin_valueChanged(int value); - void on_RepeatBSpin_valueChanged(int value); - void on_RepeatCSpin_valueChanged(int value); - // Preview - void on_DensityUnitsCombo_currentIndexChanged(int index); - // Output - void on_OutputMolecularRadio_clicked(bool checked); - void on_OutputFrameworkRadio_clicked(bool checked); - void on_OutputSupermoleculeRadio_clicked(bool checked); - // Dialog - void on_OKButton_clicked(bool checked); - void on_CancelButton_clicked(bool checked); -}; diff --git a/src/gui/importCIFDialog.ui b/src/gui/importCIFDialog.ui deleted file mode 100644 index c85e18bbff..0000000000 --- a/src/gui/importCIFDialog.ui +++ /dev/null @@ -1,1375 +0,0 @@ - - - ImportCIFDialog - - - Qt::ApplicationModal - - - - 0 - 0 - 849 - 982 - - - - - 10 - - - - Import From CIF File - - - - 4 - - - 4 - - - 4 - - - 4 - - - 4 - - - - - 4 - - - - - - 0 - 0 - - - - - 4 - - - 0 - - - 0 - - - 0 - - - 0 - - - - - Source CIF - - - - 4 - - - 4 - - - 4 - - - 4 - - - 4 - - - - - - - - - - - - :/general/icons/open.svg:/general/icons/open.svg - - - - - - - - - - Generation Control - - - - 4 - - - 4 - - - 4 - - - 4 - - - 4 - - - - - 0 - - - - - 0 - 0 - 292 - 639 - - - - - :/general/icons/data.svg:/general/icons/data.svg - - - CIF Data - - - - - - ID - - - - 4 - - - 4 - - - 4 - - - 4 - - - 4 - - - - - - 2 - 0 - - - - ??? - - - true - - - - - - - - - - Spacegroup - - - - 4 - - - 4 - - - 4 - - - 4 - - - 4 - - - - - - 0 - 0 - - - - - - - - - - - Chemical Formula - - - - 4 - - - 4 - - - 4 - - - 4 - - - 4 - - - - - - 2 - 0 - - - - ??? - - - true - - - - - - - - - - Publication - - - - 4 - - - 4 - - - 4 - - - 4 - - - 4 - - - - - - 2 - 0 - - - - ??? - - - true - - - - - - - - - - Authors - - - - 4 - - - 4 - - - 4 - - - 4 - - - 4 - - - - - QAbstractItemView::NoEditTriggers - - - - - - - - - - Reference - - - - 4 - - - 4 - - - 4 - - - 4 - - - 4 - - - - - - 2 - 0 - - - - ??? - - - true - - - - - - - - - - Qt::Vertical - - - - 20 - 40 - - - - - - - - - - 0 - 0 - 296 - 625 - - - - - :/general/icons/delete.svg:/general/icons/delete.svg - - - Structure Cleanup - - - - 4 - - - 4 - - - 4 - - - 4 - - - 4 - - - - - Tolerance distance at which atoms are considered to be overlapping and be removed - - - Overlap Removal Distance - - - - 4 - - - 4 - - - 4 - - - 4 - - - - - Normal (0.1 Å) - - - true - - - - - - - Loose (0.5 Å) - - - - - - - - - - Moiety Removal - - - - - - Remove any lone (i.e. unbound) atoms - - - Remove unbound atoms - - - - - - - Remove any water molecules or coordinated oxygens without hydrogens - - - Remove water and coordinated oxygens - - - - - - - Remove atoms or fragments according to a NETA description - - - Remove by NETA - - - - - - - - - Qt::Horizontal - - - QSizePolicy::Fixed - - - - 20 - 20 - - - - - - - - 4 - - - - - - - false - - - NETA definition matching specific atoms whose encompassing moiety should be removed - - - ?O,nbonds=2,nh=2 - - - - - - - - 0 - 0 - - - - - 16 - 16 - - - - - - - true - - - - - - - - - false - - - If selected, fragments containing the matched atoms will be removed - - - Expand to bound fragments - - - - - - - - - - - - - - Qt::Vertical - - - - 20 - 40 - - - - - - - - - - 0 - 0 - 276 - 93 - - - - - :/general/icons/calculateBonds.svg:/general/icons/calculateBonds.svg - - - Bonding - - - - 4 - - - 4 - - - 4 - - - 4 - - - 4 - - - - - Determine chemical bonds using overlap of defined elemental radii - - - Calculate - - - true - - - - - - - Use CIF definitions (from _geom_bond_*) - - - - - - - Qt::Horizontal - - - - - - - - 0 - 0 - - - - Don't add bonds between metallic elements - - - Prevent metallic bonds - - - true - - - - - - - Qt::Vertical - - - - 20 - 315 - - - - - - - - - - 0 - 0 - 96 - 78 - - - - - :/general/icons/selectedAtoms.svg:/general/icons/selectedAtoms.svg - - - Assemblies - - - - 4 - - - 4 - - - 4 - - - 4 - - - 4 - - - - - Any defined disorder assemblies and groups will be listed here, including a Global assembly containing other (well-defined) atoms in the structure. - - - - - - - - - 0 - 0 - 96 - 78 - - - - - :/general/icons/threeSpecies.svg:/general/icons/threeSpecies.svg - - - Detected Species - - - - 4 - - - 4 - - - 4 - - - 4 - - - 4 - - - - - - - - - - 0 - 0 - 167 - 142 - - - - - :/general/icons/configuration.svg:/general/icons/configuration.svg - - - Supercell - - - - Qt::AlignRight|Qt::AlignTop|Qt::AlignTrailing - - - Qt::AlignLeading|Qt::AlignLeft|Qt::AlignTop - - - 4 - - - 4 - - - 4 - - - 4 - - - 4 - - - 4 - - - - - - 0 - 0 - - - - A - - - - - - - true - - - 1 - - - 10000 - - - - - - - - 0 - 0 - - - - B - - - - - - - 1 - - - 10000 - - - - - - - - 0 - 0 - - - - C - - - - - - - 1 - - - 10000 - - - - - - - - - - - - - - - - - - 1 - 0 - - - - - - - Preview - - - - 4 - - - 4 - - - 4 - - - 4 - - - 4 - - - - - 4 - - - - - Qt::Horizontal - - - - 40 - 20 - - - - - - - - QFrame::StyledPanel - - - QFrame::Sunken - - - - 4 - - - 2 - - - 2 - - - 2 - - - 2 - - - - - false - - - ... - - - - :/general/icons/configuration.svg:/general/icons/configuration.svg - - - true - - - - - - - - 0 - 0 - - - - - 10 - false - - - - Orthorhombic - - - Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter - - - - - - - - - - QFrame::StyledPanel - - - QFrame::Sunken - - - - 4 - - - 2 - - - 2 - - - 2 - - - 2 - - - - - false - - - ... - - - - :/general/icons/density.svg:/general/icons/density.svg - - - - 14 - 14 - - - - true - - - - - - - - 0 - 0 - - - - - 10 - false - - - - 0.0 - - - Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter - - - - - - - - - - - - - Number of molecules in the configuration - - - QFrame::StyledPanel - - - QFrame::Sunken - - - - 4 - - - 2 - - - 2 - - - 2 - - - 2 - - - - - false - - - ... - - - - :/general/icons/species.svg:/general/icons/species.svg - - - true - - - - - - - - 0 - 0 - - - - 0 - - - - - - - - - - Number of atoms in the configuration - - - QFrame::StyledPanel - - - QFrame::Sunken - - - - 4 - - - 2 - - - 2 - - - 2 - - - 2 - - - - - false - - - ... - - - - :/general/icons/spheres_on.svg:/general/icons/spheres_on.svg - - - true - - - - - - - - 0 - 0 - - - - 0 - - - - - - - - - - - - - 3 - 0 - - - - - 300 - 300 - - - - QFrame::StyledPanel - - - QFrame::Sunken - - - - 0 - - - 0 - - - 0 - - - 0 - - - 0 - - - - - - 1 - 0 - - - - - - - - - - - - - - Output - - - - - - Create a single non-periodic species. Useful for generating "chunks" of crystal material. - - - Supermolecule - - - false - - - - - - - Create a single species with a periodic box and all atoms in the unit cell. Suitable for framework-style models. - - - Periodic Framework - - - true - - - - - - - Output a configuration containing individual molecules based on detected species - - - Molecular Species - - - - - - - - - - - - - - - Qt::Horizontal - - - - - - - 4 - - - - - Qt::Horizontal - - - - 40 - 20 - - - - - - - - - 10 - true - - - - Cancel - - - - - - - - 10 - true - - - - OK - - - - - - - - - - ConfigurationViewerWidget - QWidget -
gui/configurationViewerWidget.h
- 1 - - - CheckIndicator - QLabel -
gui/widgets/checkIndicator.h
- - - - - - - diff --git a/src/gui/menu_species.cpp b/src/gui/menu_species.cpp index 3e6caa00d8..bf77faf085 100644 --- a/src/gui/menu_species.cpp +++ b/src/gui/menu_species.cpp @@ -172,7 +172,7 @@ void DissolveWindow::on_SpeciesImportLigParGenAction_triggered(bool checked) ui_.MainTabs->setCurrentTab(dissolve_.coreData().species().back().get()); } } - +/* DISSOLVE 2 TODO void DissolveWindow::on_SpeciesImportFromCIFAction_triggered(bool checked) { ImportCIFDialog importCIFDialog(this, dissolve_); @@ -189,7 +189,7 @@ void DissolveWindow::on_SpeciesImportFromCIFAction_triggered(bool checked) ui_.MainTabs->setCurrentTab(sp); } } - +*/ void DissolveWindow::on_SpeciesRenameAction_triggered(bool checked) { // Get the current tab - make sure it is a SpeciesTab, then call its rename() function diff --git a/src/gui/models/CMakeLists.txt b/src/gui/models/CMakeLists.txt index b17a107cf1..fd47cd0e0c 100644 --- a/src/gui/models/CMakeLists.txt +++ b/src/gui/models/CMakeLists.txt @@ -6,7 +6,6 @@ set(models_MOC_HDRS atomTypeModel.h braggReflectionFilterProxy.h braggReflectionModel.h - cifAssemblyModel.h configurationModel.h dataManagerSimulationModel.h dissolveModel.h @@ -63,7 +62,6 @@ set(models_SRCS atomTypeModel.cpp braggReflectionFilterProxy.cpp braggReflectionModel.cpp - cifAssemblyModel.cpp configurationModel.cpp dataManagerSimulationModel.cpp dissolveModel.cpp diff --git a/src/gui/models/cifAssemblyModel.cpp b/src/gui/models/cifAssemblyModel.cpp deleted file mode 100644 index faef2809d7..0000000000 --- a/src/gui/models/cifAssemblyModel.cpp +++ /dev/null @@ -1,149 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#include "gui/models/cifAssemblyModel.h" -#include "classes/empiricalFormula.h" - -CIFAssemblyModel::CIFAssemblyModel(std::vector &assemblies) : assemblies_(assemblies) {} - -int CIFAssemblyModel::rowCount(const QModelIndex &parent) const -{ - if (!parent.isValid()) - return assemblies_.size(); - return assemblies_[parent.row()].nGroups(); -} - -int CIFAssemblyModel::columnCount(const QModelIndex &parent) const { return 3; } - -QModelIndex CIFAssemblyModel::parent(const QModelIndex &index) const -{ - quintptr root = 0; - if (index.internalId() == 0) - return QModelIndex(); - return createIndex(index.internalId() - 1, 0, root); -} - -bool CIFAssemblyModel::hasChildren(const QModelIndex &parent) const { return !parent.internalId(); } - -QVariant CIFAssemblyModel::data(const QModelIndex &index, int role) const -{ - if (role != Qt::DisplayRole && role != Qt::UserRole && role != Qt::EditRole && role != Qt::CheckStateRole) - return QVariant(); - - // Assembly (root item) - if (!index.parent().isValid()) - { - if (index.row() > assemblies_.size()) - return QVariant(); - if (index.column() > 0) - return QVariant(); - auto &a = assemblies_[index.row()]; - switch (role) - { - case Qt::DisplayRole: - case Qt::EditRole: - return QString::fromStdString(std::string(a.name())); - case Qt::UserRole: - return QVariant::fromValue(a); - default: - return QVariant(); - } - } - - // Group (column 1) - auto &assembly = assemblies_[index.parent().row()]; - auto &groups = assembly.groups(); - if (index.row() > groups.size()) - return QVariant(); - if (index.column() > 2) - return QVariant(); - auto &g = groups[index.row()]; - switch (role) - { - case Qt::DisplayRole: - case Qt::EditRole: - switch (index.column()) - { - case 1: - return QString::fromStdString(std::string(g.name())); - case 2: - return QString::fromStdString(EmpiricalFormula::formula(g.atoms(), [](const auto &i) { return i.Z(); })); - default: - return QVariant(); - } - case Qt::CheckStateRole: - if (index.column() == 1) - return g.active() ? Qt::Checked : Qt::Unchecked; - else - return QVariant(); - case Qt::UserRole: - switch (index.column()) - { - case 1: - return QVariant::fromValue(g); - default: - return QVariant(); - } - default: - return QVariant(); - } -} - -QModelIndex CIFAssemblyModel::index(int row, int column, const QModelIndex &parent) const -{ - quintptr child; - if (!parent.isValid()) - child = 0; - else if (parent.internalId() == 0) - child = parent.row() + 1; - else - return QModelIndex(); - - return createIndex(row, column, child); -} - -QVariant CIFAssemblyModel::headerData(int section, Qt::Orientation orientation, int role) const -{ - if (role != Qt::DisplayRole) - return QVariant(); - switch (section) - { - case 0: - return "Assembly"; - case 1: - return "Group"; - case 2: - return "Chemical Formula"; - default: - return QVariant(); - } -} - -Qt::ItemFlags CIFAssemblyModel::flags(const QModelIndex &index) const -{ - // Assembly (root item) - if (!index.parent().isValid()) - return Qt::ItemIsSelectable | Qt::ItemIsEnabled; - else if (index.column() == 1) - return Qt::ItemIsSelectable | Qt::ItemIsEnabled | Qt::ItemIsUserCheckable; - - return Qt::ItemIsSelectable | Qt::ItemIsEnabled; -} - -bool CIFAssemblyModel::setData(const QModelIndex &index, const QVariant &value, int role) -{ - // Only editable data is the check state of groups (column 1) - if (!index.parent().isValid() || index.column() != 1 || role != Qt::CheckStateRole) - return false; - - // Get assembly and check for number of groups > 1 - auto &assembly = assemblies_[index.parent().row()]; - - // Get group being modified and set the active flag - auto &group = assembly.groups()[index.row()]; - group.setActive(value.value() == Qt::Checked); - - Q_EMIT(dataChanged(index, index)); - - return true; -} diff --git a/src/gui/models/cifAssemblyModel.h b/src/gui/models/cifAssemblyModel.h deleted file mode 100644 index f1ba29b6d1..0000000000 --- a/src/gui/models/cifAssemblyModel.h +++ /dev/null @@ -1,36 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#pragma once - -#include "io/import/cif.h" -#include -#include - -class CIFAssemblyModel : public QAbstractItemModel -{ - Q_OBJECT - private: - std::vector &assemblies_; - - public: - CIFAssemblyModel(std::vector &assemblies); - - QModelIndex parent(const QModelIndex &index) const override; - - QModelIndex index(int row, int column, const QModelIndex &parent = QModelIndex()) const override; - - bool hasChildren(const QModelIndex &parent) const override; - - int rowCount(const QModelIndex &parent = QModelIndex()) const override; - - int columnCount(const QModelIndex &parent = QModelIndex()) const override; - - QVariant data(const QModelIndex &index, int role = Qt::DisplayRole) const override; - - QVariant headerData(int section, Qt::Orientation orientation, int role = Qt::DisplayRole) const override; - - Qt::ItemFlags flags(const QModelIndex &index) const override; - - bool setData(const QModelIndex &index, const QVariant &value, int role = Qt::EditRole) override; -}; diff --git a/src/io/import/CMakeLists.txt b/src/io/import/CMakeLists.txt index 63ad9a0fd9..5e3c23a777 100644 --- a/src/io/import/CMakeLists.txt +++ b/src/io/import/CMakeLists.txt @@ -1,32 +1,5 @@ -# CIFImport ANTLR Lexer/Parser -antlr_target(CIFImportGrammarLexer CIFImportLexer.g4 LEXER) -# PACKAGE CIFImportGrammar) -antlr_target( - CIFImportGrammarParser - CIFImportParser.g4 - PARSER - # PACKAGE CIFImportGrammar - DEPENDS_ANTLR - CIFImportGrammarLexer - COMPILE_FLAGS - -no-listener - -visitor - -lib - ${ANTLR_CIFImportGrammarLexer_OUTPUT_DIR} -) - -# Append path to ANTLR parser output, and set cache variable -list(APPEND ANTLR_OUTPUT_DIRS ${ANTLR_CIFImportGrammarLexer_OUTPUT_DIR}) -list(APPEND ANTLR_OUTPUT_DIRS ${ANTLR_CIFImportGrammarParser_OUTPUT_DIR}) -set(ANTLR_OUTPUT_DIRS - ${ANTLR_OUTPUT_DIRS} - CACHE INTERNAL "" -) - add_library( import - cif.cpp - cifClasses.cpp coordinates.cpp coordinates_dlpoly.cpp coordinates_epsr.cpp @@ -49,8 +22,6 @@ add_library( trajectory.cpp trajectory_dlpoly.cpp values.cpp - cif.h - cifClasses.h coordinates.h data1D.h data2D.h @@ -59,15 +30,8 @@ add_library( species.h trajectory.h values.h - CIFImportErrorListeners.cpp - CIFImportVisitor.cpp - ${ANTLR_CIFImportGrammarLexer_CXX_OUTPUTS} - ${ANTLR_CIFImportGrammarParser_CXX_OUTPUTS} ) -target_include_directories( - import PRIVATE ${PROJECT_SOURCE_DIR}/src ${PROJECT_BINARY_DIR}/src ${ANTLR_CIFImportGrammarLexer_OUTPUT_DIR} - ${ANTLR_CIFImportGrammarParser_OUTPUT_DIR} -) +target_include_directories(import PRIVATE ${PROJECT_SOURCE_DIR}/src ${PROJECT_BINARY_DIR}/src) -target_link_libraries(import base) +target_link_libraries(import base nodes) diff --git a/src/io/import/cif.cpp b/src/io/import/cif.cpp deleted file mode 100644 index d0bc116560..0000000000 --- a/src/io/import/cif.cpp +++ /dev/null @@ -1,1329 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#include "io/import/cif.h" -#include "CIFImportLexer.h" -#include "base/messenger.h" -#include "base/sysFunc.h" -#include "classes/coreData.h" -#include "classes/empiricalFormula.h" -#include "classes/species.h" -#include "generator/add.h" -#include "generator/box.h" -#include "generator/coordinateSets.h" -#include "io/import/CIFImportErrorListeners.h" -#include "io/import/CIFImportVisitor.h" -#include "io/import/cif.h" -#include "neta/neta.h" -#include "templates/algorithms.h" - -CIFHandler::CIFHandler() -{ - unitCellConfiguration_.setName("Structural"); - unitCellSpecies_.setName("Crystal"); - cleanedUnitCellConfiguration_.setName("Cleaned"); - cleanedUnitCellSpecies_.setName("Crystal (Cleaned)"); - supercellConfiguration_.setName("Supercell"); - supercellSpecies_.setName("Crystal (Supercell)"); -} - -/* - * Raw Data - */ - -// Parse supplied file into the destination objects -bool CIFHandler::parse(std::string_view filename, CIFHandler::CIFTags &tags) const -{ - // Set up ANTLR input stream - std::ifstream cifFile(std::string(filename), std::ios::in | std::ios::binary); - if (!cifFile.is_open()) - return Messenger::error("Failed to open CIF file '{}.\n", filename); - - antlr4::ANTLRInputStream input(cifFile); - - // Create ANTLR lexer and set-up error listener - CIFImportLexer lexer(&input); - CIFImportLexerErrorListener lexerErrorListener; - lexer.removeErrorListeners(); - lexer.addErrorListener(&lexerErrorListener); - - // Generate tokens from input stream - antlr4::CommonTokenStream tokens(&lexer); - - // Create ANTLR parser and set-up error listeners - CIFImportParser parser(&tokens); - CIFImportParserErrorListener parserErrorListener; - parser.removeErrorListeners(); - parser.removeParseListeners(); - parser.addErrorListener(&lexerErrorListener); - parser.addErrorListener(&parserErrorListener); - - // Generate the AST - CIFImportParser::CifContext *tree = nullptr; - try - { - tree = parser.cif(); - } - catch (CIFImportExceptions::CIFImportSyntaxException &ex) - { - Messenger::error("{}", ex.what()); - return false; - } - - // Visit the nodes in the AST - CIFImportVisitor visitor(tags); - try - { - visitor.extract(tree); - } - catch (CIFImportExceptions::CIFImportSyntaxException &ex) - { - return Messenger::error("{}", ex.what()); - } - - return true; -} - -// Return whether the specified file parses correctly -bool CIFHandler::validFile(std::string_view filename) const -{ - CIFTags tags; - return parse(filename, tags); -} - -// Read CIF data from specified file -bool CIFHandler::read(std::string_view filename) -{ - assemblies_.clear(); - bondingPairs_.clear(); - tags_.clear(); - - if (!parse(filename, tags_)) - return Messenger::error("Failed to parse CIF file '{}'.\n", filename); - - /* - * Determine space group - the search order for tags is: - * - * 1. Hall symbol - * 2. Hermann-Mauginn name - * 3. Space group index - * - * In the case of 2 or 3 we also try to search for the origin choice. - * - * If a space group has already been set, don't try to overwrite it (it was probably forcibly set because the detection - * below fails). - */ - - // Check for Hall symbol - if (spaceGroup_ == SpaceGroups::NoSpaceGroup && hasTag("_space_group_name_Hall")) - spaceGroup_ = SpaceGroups::findByHallSymbol(*getTagString("_space_group_name_Hall")); - if (spaceGroup_ == SpaceGroups::NoSpaceGroup && hasTag("_symmetry_space_group_name_Hall")) - spaceGroup_ = SpaceGroups::findByHallSymbol(*getTagString("_symmetry_space_group_name_Hall")); - - if (spaceGroup_ == SpaceGroups::NoSpaceGroup) - { - // Might need the coordinate system code... - auto sgCode = getTagString("_space_group.IT_coordinate_system_code"); - - // Find a HM name - if (hasTag("_space_group_name_H-M_alt")) - spaceGroup_ = - SpaceGroups::findByHermannMauginnSymbol(*getTagString("_space_group_name_H-M_alt"), sgCode.value_or("")); - if (spaceGroup_ == SpaceGroups::NoSpaceGroup && hasTag("_symmetry_space_group_name_H-M")) - spaceGroup_ = - SpaceGroups::findByHermannMauginnSymbol(*getTagString("_symmetry_space_group_name_H-M"), sgCode.value_or("")); - - // Find a space group index? - if (spaceGroup_ == SpaceGroups::NoSpaceGroup && hasTag("_space_group_IT_number")) - spaceGroup_ = - SpaceGroups::findByInternationalTablesIndex(*getTagInt("_space_group_IT_number"), sgCode.value_or("")); - if (spaceGroup_ == SpaceGroups::NoSpaceGroup && hasTag("_space_group.IT_number")) - spaceGroup_ = - SpaceGroups::findByInternationalTablesIndex(*getTagInt("_space_group.IT_number"), sgCode.value_or("")); - if (spaceGroup_ == SpaceGroups::NoSpaceGroup && hasTag("_symmetry_Int_Tables_number")) - spaceGroup_ = - SpaceGroups::findByInternationalTablesIndex(*getTagInt("_symmetry_Int_Tables_number"), sgCode.value_or("")); - } - - // Create symmetry-unique atoms list - auto atomSiteLabel = getTagStrings("_atom_site_label"); - auto atomSiteTypeSymbol = getTagStrings("_atom_site_type_symbol"); - auto atomSiteFractX = getTagDoubles("_atom_site_fract_x"); - auto atomSiteFractY = getTagDoubles("_atom_site_fract_y"); - auto atomSiteFractZ = getTagDoubles("_atom_site_fract_z"); - auto atomSiteOccupancy = getTagDoubles("_atom_site_occupancy"); - auto atomDisorderAssembly = getTagStrings("_atom_site_disorder_assembly"); - auto atomDisorderGroup = getTagStrings("_atom_site_disorder_group"); - if (atomSiteLabel.empty() && atomSiteTypeSymbol.empty()) - return Messenger::error( - "No suitable atom site names found (no '_atom_site_label' or '_atom_site_type_symbol' tags present in CIF).\n"); - if (atomSiteFractX.empty() || atomSiteFractY.empty() || atomSiteFractZ.empty()) - return Messenger::error("Atom site fractional positions are incomplete (vector sizes are {}, {}, and {}).\n", - atomSiteFractX.size(), atomSiteFractY.size(), atomSiteFractZ.size()); - if (!((atomSiteFractX.size() == atomSiteFractY.size()) && (atomSiteFractX.size() == atomSiteFractZ.size()))) - return Messenger::error("Atom site fractional positions have mismatched sizes (vector sizes are {}, {}, and {}).\n", - atomSiteFractX.size(), atomSiteFractY.size(), atomSiteFractZ.size()); - for (auto n = 0; n < atomSiteFractX.size(); ++n) - { - // Get standard information - auto label = n < atomSiteLabel.size() ? atomSiteLabel[n] : std::format("{}{}", atomSiteTypeSymbol[n], n); - auto Z = n < atomSiteTypeSymbol.size() - ? Elements::element(atomSiteTypeSymbol[n]) - : (n < atomSiteLabel.size() ? Elements::element(atomSiteLabel[n]) : Elements::Unknown); - auto occ = n < atomSiteOccupancy.size() ? atomSiteOccupancy[n] : 1.0; - Vector3 rFrac(atomSiteFractX[n], atomSiteFractY[n], atomSiteFractZ[n]); - - // Add the atom to an assembly - there are three possibilities regarding (disorder) grouping: - // 1) A group is defined, but no assembly - add the atom to the 'Disorder' assembly - // 2) An assembly and a group are defined - add it to that - // 3) No group or assembly are defined - add the atom to the 'Global' assembly under a 'Default' group - auto assemblyName = atomDisorderAssembly.empty() ? "." : atomDisorderAssembly[n]; - auto groupName = atomDisorderGroup.empty() ? "." : atomDisorderGroup[n]; - if (assemblyName == "." && groupName != ".") - assemblyName = "Disorder"; - else if (assemblyName == "." && groupName == ".") - assemblyName = "Global"; - - if (groupName == ".") - groupName = "Default"; - - // Get the assembly and group that we're adding the atom to - auto &assembly = getAssembly(assemblyName); - auto &group = assembly.getGroup(groupName); - group.setActive(groupName == "Default" || groupName == "1"); - group.addAtom({label, Z, rFrac, occ}); - } - - // Construct bonding pairs list - auto bondLabelsI = getTagStrings("_geom_bond_atom_site_label_1"); - auto bondLabelsJ = getTagStrings("_geom_bond_atom_site_label_2"); - auto bondDistances = getTagDoubles("_geom_bond_distance"); - if (bondLabelsI.size() == bondLabelsJ.size() && (bondLabelsI.size() == bondDistances.size())) - { - for (auto &&[i, j, r] : zip(bondLabelsI, bondLabelsJ, bondDistances)) - bondingPairs_.emplace_back(i, j, r); - } - else - Messenger::warn("Bonding pairs array sizes are mismatched, so no bonding information will be available."); - - return true; -} - -// Return if the specified tag exists -bool CIFHandler::hasTag(std::string tag) const { return tags_.find(tag) != tags_.end(); } - -// Return tag data string (if it exists) assuming a single datum (first in the vector) -std::optional CIFHandler::getTagString(std::string tag) const -{ - auto it = tags_.find(tag); - if (it == tags_.end()) - return std::nullopt; - - // Check data vector size - if (it->second.size() != 1) - Messenger::warn("Returning first datum for tag '{}', but {} are available.\n", tag, it->second.size()); - - return it->second.front(); -} - -// Return tag data strings (if it exists) -std::vector CIFHandler::getTagStrings(std::string tag) const -{ - auto it = tags_.find(tag); - if (it == tags_.end()) - return {}; - - return it->second; -} - -// Return tag data as double (if it exists) assuming a single datum (first in the vector) -std::optional CIFHandler::getTagDouble(std::string tag) const -{ - auto it = tags_.find(tag); - if (it == tags_.end()) - return std::nullopt; - - // Check data vector size - if (it->second.size() != 1) - Messenger::warn("Returning first datum for tag '{}', but {} are available.\n", tag, it->second.size()); - - double result; - try - { - result = std::stod(it->second.front()); - } - catch (...) - { - Messenger::error("Data tag '{}' contains a value that can't be converted to a double ('{}').\n", tag, - it->second.front()); - return std::nullopt; - } - - return result; -} - -// Return tag data doubles (if it exists) -std::vector CIFHandler::getTagDoubles(std::string tag) const -{ - auto it = tags_.find(tag); - if (it == tags_.end()) - return {}; - - std::vector v; - for (const auto &s : it->second) - { - auto d = 0.0; - try - { - d = std::stod(s); - } - catch (...) - { - Messenger::warn("Data tag '{}' contains a value that can't be converted to a double ('{}').\n", tag, s); - } - v.push_back(d); - } - - return v; -} - -// Return tag data as integer (if it exists) assuming a single datum (first in the vector) -std::optional CIFHandler::getTagInt(std::string tag) const -{ - auto it = tags_.find(tag); - if (it == tags_.end()) - return std::nullopt; - - // Check data vector size - if (it->second.size() != 1) - Messenger::warn("Returning first datum for tag '{}', but {} are available.\n", tag, it->second.size()); - - int result; - try - { - result = std::stoi(it->second.front()); - } - catch (...) - { - Messenger::error("Data tag '{}' contains a value that can't be converted to an integer ('{}').\n", tag, - it->second.front()); - return std::nullopt; - } - - return result; -} - -/* - * Processed Data - */ - -// Set space group from index -void CIFHandler::setSpaceGroup(SpaceGroups::SpaceGroupId sgid) -{ - if (spaceGroup_ == sgid) - return; - - spaceGroup_ = sgid; - generate(); -} - -// Return space group information -SpaceGroups::SpaceGroupId CIFHandler::spaceGroup() const { return spaceGroup_; } - -// Return cell lengths -std::optional CIFHandler::getCellLengths() const -{ - auto a = getTagDouble("_cell_length_a"); - if (!a) - Messenger::error("Cell length A not defined in CIF.\n"); - auto b = getTagDouble("_cell_length_b"); - if (!b) - Messenger::error("Cell length B not defined in CIF.\n"); - auto c = getTagDouble("_cell_length_c"); - if (!c) - Messenger::error("Cell length C not defined in CIF.\n"); - - if (a && b && c) - return Vector3(a.value(), b.value(), c.value()); - else - return std::nullopt; -} - -// Return cell angles -std::optional CIFHandler::getCellAngles() const -{ - auto alpha = getTagDouble("_cell_angle_alpha"); - if (!alpha) - Messenger::error("Cell angle alpha not defined in CIF.\n"); - auto beta = getTagDouble("_cell_angle_beta"); - if (!beta) - Messenger::error("Cell angle beta not defined in CIF.\n"); - auto gamma = getTagDouble("_cell_angle_gamma"); - if (!gamma) - Messenger::error("Cell angle gamma not defined in CIF.\n"); - - if (alpha && beta && gamma) - return Vector3(alpha.value(), beta.value(), gamma.value()); - else - return std::nullopt; -} - -// Return chemical formula -std::string CIFHandler::chemicalFormula() const -{ - auto it = tags_.find("_chemical_formula_sum"); - return (it != tags_.end() ? it->second.front() : "Unknown"); -} - -// Get (add or retrieve) named assembly -CIFAssembly &CIFHandler::getAssembly(std::string_view name) -{ - auto it = std::find_if(assemblies_.begin(), assemblies_.end(), [name](const auto &a) { return a.name() == name; }); - if (it != assemblies_.end()) - return *it; - - return assemblies_.emplace_back(name); -} - -// Return atom assemblies -std::vector &CIFHandler::assemblies() { return assemblies_; } - -const std::vector &CIFHandler::assemblies() const { return assemblies_; } - -// Return whether any bond distances are defined -bool CIFHandler::hasBondDistances() const { return !bondingPairs_.empty(); } - -// Return whether a bond distance is defined for the specified label pair -std::optional CIFHandler::bondDistance(std::string_view labelI, std::string_view labelJ) const -{ - auto it = std::find_if( - bondingPairs_.begin(), bondingPairs_.end(), [labelI, labelJ](const auto &bp) - { return (bp.labelI() == labelI && bp.labelJ() == labelJ) || (bp.labelI() == labelJ && bp.labelJ() == labelI); }); - if (it != bondingPairs_.end()) - return it->r(); - return std::nullopt; -} - -/* - * Creation - */ - -// Create basic unit cell -bool CIFHandler::createBasicUnitCell() -{ - unitCellConfiguration_.empty(); - unitCellSpecies_.clear(); - atomLabelTypes_.clear(); - - // Create temporary atom types corresponding to the unique atom labels - for (auto &a : assemblies_) - { - for (auto &g : a.groups()) - { - if (!g.active()) - continue; - - for (auto &i : g.atoms()) - { - if (std::find_if(atomLabelTypes_.begin(), atomLabelTypes_.end(), - [i](const auto &at) { return i.label() == at->name(); }) == atomLabelTypes_.end()) - { - atomLabelTypes_.emplace_back(std::make_shared(i.Z(), i.label())); - } - } - } - } - - // Configure the unit cell "species" - auto cellLengths = getCellLengths(); - if (!cellLengths) - return false; - auto cellAngles = getCellAngles(); - if (!cellAngles) - return false; - unitCellSpecies_.createBox(cellLengths.value(), cellAngles.value()); - auto *box = unitCellSpecies_.box(); - - // Configuration - Messenger::setQuiet(true); - unitCellConfiguration_.createBoxAndCells(cellLengths.value(), cellAngles.value(), false); - Messenger::setQuiet(false); - - // -- Generate atoms - auto symmetryGenerators = SpaceGroups::symmetryOperators(spaceGroup_); - for (const auto &generator : symmetryGenerators) - for (auto &a : assemblies_) - for (auto &g : a.groups()) - if (g.active()) - for (auto &unique : g.atoms()) - { - // Generate folded atomic position in real space - auto r = generator * unique.rFrac(); - box->toReal(r); - r = box->fold(r); - - // If this atom overlaps with another in the box, don't add it as it's a symmetry-related copy - if (std::any_of(unitCellSpecies_.atoms().begin(), unitCellSpecies_.atoms().end(), - [&, r, box](const auto &j) - { return box->minimumDistance(r, j.r()) < overlapTolerance_; })) - continue; - - // Create the new atom - auto atIt = std::find_if(atomLabelTypes_.begin(), atomLabelTypes_.end(), - [&unique](const auto at) { return unique.label() == at->name(); }); - unitCellSpecies_.addAtom(unique.Z(), r, 0.0, atIt != atomLabelTypes_.end() ? atIt->get() : nullptr); - } - - // Check that we actually generated some atoms... - if (unitCellSpecies_.nAtoms() == 0) - return false; - - // Bonding - if (!preventAllBonds_) - if (useCIFBondingDefinitions_) - applyCIFBonding(&unitCellSpecies_, preventMetallicBonds_); - else - unitCellSpecies_.addMissingBonds(bondingTolerance_, preventMetallicBonds_); - - unitCellConfiguration_.addMolecule(&unitCellSpecies_); - unitCellConfiguration_.updateObjectRelationships(); - - Messenger::print("Created basic crystal unit cell - {} non-overlapping atoms.\n", unitCellSpecies_.nAtoms()); - - return true; -} - -// Create the cleaned unit cell -bool CIFHandler::createCleanedUnitCell() -{ - cleanedUnitCellConfiguration_.empty(); - cleanedUnitCellSpecies_.clear(); - - // Configure the species - cleanedUnitCellSpecies_.copyBasic(&unitCellSpecies_, true); - auto cellLengths = getCellLengths(); - if (!cellLengths) - return false; - auto cellAngles = getCellAngles(); - if (!cellAngles) - return false; - cleanedUnitCellSpecies_.createBox(cellLengths.value(), cellAngles.value()); - - // Configuration - Messenger::setQuiet(true); - cleanedUnitCellConfiguration_.createBoxAndCells(cellLengths.value(), cellAngles.value(), false); - Messenger::setQuiet(false); - - if (removeAtomics_) - { - std::vector indicesToRemove; - for (const auto &i : cleanedUnitCellSpecies_.atoms()) - if (i.nBonds() == 0) - indicesToRemove.push_back(i.index()); - Messenger::print("Atomic removal deleted {} atoms.\n", indicesToRemove.size()); - - // Remove selected atoms - cleanedUnitCellSpecies_.removeAtoms(indicesToRemove); - } - - if (removeWaterAndCoordinateOxygens_) - { - NETADefinition waterVacuum("?O,nbonds=1,nh<=1|?O,nbonds>=2,-H(nbonds=1,-O)"); - if (!waterVacuum.isValid()) - { - Messenger::error("NETA definition for water removal is invalid.\n"); - return false; - } - - std::vector indicesToRemove; - for (const auto &i : cleanedUnitCellSpecies_.atoms()) - if (waterVacuum.matches(&i)) - indicesToRemove.push_back(i.index()); - Messenger::print("Water removal deleted {} atoms.\n", indicesToRemove.size()); - - // Remove selected atoms - cleanedUnitCellSpecies_.removeAtoms(indicesToRemove); - } - - if (removeNETA_ && moietyRemovalNETA_.isValid()) - { - // Select all atoms that are in moieties where one of its atoms matches our NETA definition - std::vector indicesToRemove; - for (auto &i : cleanedUnitCellSpecies_.atoms()) - if (moietyRemovalNETA_.matches(&i)) - { - // Select all atoms that are part of the same moiety? - if (removeNETAByFragment_) - { - cleanedUnitCellSpecies_.clearAtomSelection(); - auto selection = cleanedUnitCellSpecies_.fragment(i.index()); - std::copy(selection.begin(), selection.end(), std::back_inserter(indicesToRemove)); - } - else - indicesToRemove.push_back(i.index()); - } - Messenger::print("Moiety removal deleted {} atoms.\n", indicesToRemove.size()); - - // Remove selected atoms - cleanedUnitCellSpecies_.removeAtoms(indicesToRemove); - } - - cleanedUnitCellConfiguration_.addMolecule(&cleanedUnitCellSpecies_); - cleanedUnitCellConfiguration_.updateObjectRelationships(); - - Messenger::print("Created cleaned crystal unit cell - {} atoms after removal(s).\n", cleanedUnitCellSpecies_.nAtoms()); - - return true; -} - -// Try to detect molecules in the cell contents -bool CIFHandler::detectMolecules() -{ - molecularSpecies_.clear(); - - // Try selecting within the species from the first atom - if this captures all atoms we have a bound framework... - if (cleanedUnitCellSpecies_.fragment(0).size() == cleanedUnitCellSpecies_.nAtoms()) - { - Messenger::print( - "Can't create molecular definitions since this unit cell appears to be a continuous framework/network. Consider " - "adjusting the bonding options in order to generate molecular fragments.\n"); - return false; - } - - std::vector atomMask(cleanedUnitCellSpecies_.nAtoms(), false); - - // Find all molecular species, and their instances - auto indexIterator = atomMask.begin(); - while (indexIterator != atomMask.end()) - { - // Select a fragment from the next available index - auto atomIndex = indexIterator - atomMask.begin(); - auto fragmentIndices = cleanedUnitCellSpecies_.fragment(atomIndex); - - // Create a new CIF molecular species from the fragment - auto &cifSp = molecularSpecies_.emplace_back(); - auto *sp = cifSp.species().get(); - // -- Copy selected atoms - for (auto fragAtomIndex : fragmentIndices) - { - const auto &unitCellAtom = cleanedUnitCellSpecies_.atom(fragAtomIndex); - sp->addAtom(unitCellAtom.Z(), unitCellAtom.r(), 0.0, unitCellAtom.atomType()); - } - - // Give the species a temporary unit cell so we can calculate / apply bonding - if (!preventAllBonds_) - sp->createBox(cleanedUnitCellSpecies_.box()->axisLengths(), cleanedUnitCellSpecies_.box()->axisAngles()); - if (useCIFBondingDefinitions_) - applyCIFBonding(sp, preventMetallicBonds_); - else - sp->addMissingBonds(bondingTolerance_, preventMetallicBonds_); - sp->removeBox(); - - // Set up a temporary molecule to unfold the species - LocalMolecule tempMol(sp); - tempMol.unFold(cleanedUnitCellSpecies_.box()); - for (auto &&[molAtom, spAtom] : zip(tempMol.localAtoms(), sp->atoms())) - spAtom.setR(molAtom.r()); - - // Give the species a name - sp->setName(EmpiricalFormula::formula(sp->atoms(), [&](const auto &at) { return at.Z(); })); - - // Find instances of this fragment. For large fragments that represent > 50% of the remaining atoms we don't even - // attempt to create a NETA definition etc. For cases such as framework species this will speed up detection no end. - std::vector instances; - if (fragmentIndices.size() * 2 > cleanedUnitCellSpecies_.nAtoms()) - { - // Create an instance of the current fragment - auto &mol = instances.emplace_back(sp); - for (auto i = 0; i < sp->nAtoms(); ++i) - atomMask[fragmentIndices[i]] = true; - } - else - { - // Determine the best NETA definition describing the fragment - auto &&[bestNETA, rootAtoms] = bestNETADefinition(sp); - if (rootAtoms.empty()) - return Messenger::error( - "Couldn't generate molecular partitioning for CIF - no suitable NETA definition for the " - "fragment {} could be determined.\n", - sp->name()); - - // Find instances of this fragment - instances = getSpeciesInstances(sp, atomMask, bestNETA, rootAtoms); - if (instances.empty()) - { - molecularSpecies_.clear(); - return Messenger::error("Failed to find species instances for fragment '{}'.\n", sp->name()); - } - } - - // Store the instances - cifSp.instances() = instances; - - // Search for the next valid starting index - indexIterator = std::find(std::next(indexIterator), atomMask.end(), false); - } - - Messenger::print("Partitioned unit cell into {} distinct molecular species:\n\n", molecularSpecies_.size()); - Messenger::print(" ID N Species Formula\n"); - auto count = 1; - for (const auto &cifMol : molecularSpecies_) - Messenger::print(" {:3d} {:4d} {}\n", count++, cifMol.instances().size(), - EmpiricalFormula::formula(cifMol.species()->atoms(), [](const auto &i) { return i.Z(); })); - Messenger::print(""); - - return true; -} - -// Create supercell species -bool CIFHandler::createSupercell() -{ - supercellConfiguration_.empty(); - supercellSpecies_.clear(); - - // Configure the species - auto supercellLengths = cleanedUnitCellSpecies_.box()->axisLengths(); - supercellLengths.multiply(supercellRepeat_.x, supercellRepeat_.y, supercellRepeat_.z); - supercellSpecies_.createBox(supercellLengths, cleanedUnitCellSpecies_.box()->axisAngles(), false); - - // Set up configuration - Messenger::setQuiet(true); - supercellConfiguration_.createBoxAndCells(supercellLengths, cleanedUnitCellSpecies_.box()->axisAngles(), false); - Messenger::setQuiet(false); - - // Copy atoms from the Crystal species - we'll do the bonding afterwards - if (molecularSpecies_.empty()) - { - supercellSpecies_.atoms().reserve(supercellRepeat_.x * supercellRepeat_.y * supercellRepeat_.z * - cleanedUnitCellSpecies_.nAtoms()); - for (auto ix = 0; ix < supercellRepeat_.x; ++ix) - for (auto iy = 0; iy < supercellRepeat_.y; ++iy) - for (auto iz = 0; iz < supercellRepeat_.z; ++iz) - { - Vector3 deltaR = cleanedUnitCellSpecies_.box()->axes() * Vector3(ix, iy, iz); - for (const auto &i : cleanedUnitCellSpecies_.atoms()) - supercellSpecies_.addAtom(i.Z(), i.r() + deltaR, 0.0, i.atomType()); - } - if (!preventAllBonds_) - if (useCIFBondingDefinitions_) - applyCIFBonding(&supercellSpecies_, preventMetallicBonds_); - else - supercellSpecies_.addMissingBonds(bondingTolerance_, preventMetallicBonds_); - - // Add the structural species to the configuration - supercellConfiguration_.addMolecule(&supercellSpecies_); - supercellConfiguration_.updateObjectRelationships(); - } - else - { - supercellSpecies_.atoms().reserve(supercellRepeat_.x * supercellRepeat_.y * supercellRepeat_.z * - cleanedUnitCellSpecies_.nAtoms()); - - // Create images of all molecular unit cell species - for (auto &molecularSpecies : molecularSpecies_) - { - const auto *sp = molecularSpecies.species().get(); - const auto &coreInstances = molecularSpecies.instances(); - std::vector supercellInstances; - supercellInstances.reserve(supercellRepeat_.x * supercellRepeat_.y * supercellRepeat_.z * coreInstances.size()); - - // Loop over cell images - for (auto ix = 0; ix < supercellRepeat_.x; ++ix) - { - for (auto iy = 0; iy < supercellRepeat_.y; ++iy) - { - for (auto iz = 0; iz < supercellRepeat_.z; ++iz) - { - // Skip origin cell - if (ix == 0 && iy == 0 && iz == 0) - continue; - - // Set translation vector - auto tVec = cleanedUnitCellSpecies_.box()->axes() * Vector3(ix, iy, iz); - - // Create images of core molecule instances - for (auto &instance : coreInstances) - { - auto &mol = supercellInstances.emplace_back(); - mol.setSpecies(sp); - - for (auto &&[coreAtom, instanceAtom] : zip(instance.localAtoms(), mol.localAtoms())) - instanceAtom.setR(coreAtom.r() + tVec); - } - } - } - } - - // Append the new instances to our existing ones for the unit cell - molecularSpecies.appendInstances(supercellInstances); - - // Add the molecules to our configuration - for (const auto &instance : molecularSpecies.instances()) - { - auto mol = supercellConfiguration_.addMolecule(sp); - for (auto &&[molAtom, instanceAtom] : zip(mol->atoms(), instance.localAtoms())) - molAtom->setR(instanceAtom.r()); - } - } - - supercellConfiguration_.updateObjectRelationships(); - } - - Messenger::print("Created ({}, {}, {}) supercell - {} atoms total.\n", supercellRepeat_.x, supercellRepeat_.y, - supercellRepeat_.z, supercellConfiguration_.nAtoms()); - - return true; -} - -// Set overlap tolerance -void CIFHandler::setOverlapTolerance(double tol) -{ - overlapTolerance_ = tol; - - generate(CIFGenerationStage::CreateBasicUnitCell); -} - -// Set whether to use CIF bonding definitions -void CIFHandler::setUseCIFBondingDefinitions(bool b) -{ - if (useCIFBondingDefinitions_ == b) - return; - - useCIFBondingDefinitions_ = b; - - generate(); -} - -// Set bonding tolerance -void CIFHandler::setBondingTolerance(double tol) -{ - bondingTolerance_ = tol; - - if (!useCIFBondingDefinitions_) - generate(); -} - -// Whether to ignore all bonds -void CIFHandler::setPreventAllBonds(bool b) -{ - if (preventAllBonds_ == b) - return; - - preventAllBonds_ = b; - - generate(); -} - -// Set whether to prevent metallic bonding -void CIFHandler::setPreventMetallicBonds(bool b) -{ - if (preventMetallicBonds_ == b) - return; - - preventMetallicBonds_ = b; - - generate(); -} - -// Set whether to remove free atomic moieties in clean-up -void CIFHandler::setRemoveAtomics(bool b) -{ - if (removeAtomics_ == b) - return; - - removeAtomics_ = b; - - generate(CIFGenerationStage::CreateCleanedUnitCell); -} - -// Set whether to remove water and coordinated oxygen atoms in clean-up -void CIFHandler::setRemoveWaterAndCoordinateOxygens(bool b) -{ - if (removeWaterAndCoordinateOxygens_ == b) - return; - - removeWaterAndCoordinateOxygens_ = b; - - generate(CIFGenerationStage::CreateCleanedUnitCell); -} - -// Set whether to remove by NETA definition in clean-up -void CIFHandler::setRemoveNETA(bool b, bool byFragment) -{ - if (removeNETA_ == b && removeNETAByFragment_ == byFragment) - return; - - removeNETA_ = b; - removeNETAByFragment_ = byFragment; - - if (moietyRemovalNETA_.isValid()) - generate(CIFGenerationStage::CreateCleanedUnitCell); -} - -// Set NETA for moiety removal -bool CIFHandler::setMoietyRemovalNETA(std::string_view netaDefinition) { return moietyRemovalNETA_.create(netaDefinition); } - -// Set supercell repeat -void CIFHandler::setSupercellRepeat(const Vector3i &repeat) -{ - supercellRepeat_ = repeat; - - generate(CIFGenerationStage::CreateSupercell); -} - -// Recreate the data -bool CIFHandler::generate(CIFGenerationStage fromStage) -{ - // Generate data starting from the specified stage, falling through to subsequent stages in the switch - - switch (fromStage) - { - case (CIFGenerationStage::CreateBasicUnitCell): - if (!createBasicUnitCell()) - return false; - case (CIFGenerationStage::CreateCleanedUnitCell): - if (!createCleanedUnitCell()) - return false; - case (CIFGenerationStage::DetectMolecules): - detectMolecules(); - case (CIFGenerationStage::CreateSupercell): - if (!createSupercell()) - return false; - } - - return true; -} - -// Return whether the generated data is valid -bool CIFHandler::isValid() const -{ - return !molecularSpecies_.empty() || supercellSpecies_.fragment(0).size() != supercellSpecies_.nAtoms(); -} - -// Return supercell species -const Species &CIFHandler::supercellSpecies() const { return supercellSpecies_; } - -// Return cleaned unit cell species -const Species &CIFHandler::cleanedUnitCellSpecies() const { return cleanedUnitCellSpecies_; } - -// Return the detected molecular species -const std::vector &CIFHandler::molecularSpecies() const { return molecularSpecies_; } - -// Return the generated configuration -Configuration *CIFHandler::generatedConfiguration() { return &supercellConfiguration_; } - -// Finalise, copying the required species and resulting configuration to the target CoreData -void CIFHandler::finalise(CoreData &coreData, const Flags &flags) const -{ - Configuration *configuration; - - if (flags.isSet(OutputFlags::OutputMolecularSpecies)) - { - if (flags.isSet(OutputFlags::OutputConfiguration)) - { - configuration = coreData.addConfiguration(); - configuration->setName(chemicalFormula()); - - // Grab the generator - auto &generator = configuration->generator(); - - // Add Box - auto boxNode = generator.createRootNode({}); - auto cellLengths = supercellConfiguration_.box()->axisLengths(); - auto cellAngles = supercellConfiguration_.box()->axisAngles(); - boxNode->keywords().set("Lengths", Vector3NodeValue(cellLengths.get(0), cellLengths.get(1), cellLengths.get(2))); - boxNode->keywords().set("Angles", Vector3NodeValue(cellAngles.get(0), cellAngles.get(1), cellAngles.get(2))); - - for (auto &cifMolecularSp : molecularSpecies_) - { - // Add the species - auto *sp = coreData.copySpecies(cifMolecularSp.species().get()); - - // Determine a unique suffix - auto base = sp->name(); - std::string uniqueSuffix{base}; - if (!generator.nodes().empty()) - { - // Start from the last root node - auto root = generator.nodes().back(); - auto suffix = 0; - - while (generator.rootSequence().nodeInScope(root, std::format("SymmetryCopies_{}", uniqueSuffix)) != - nullptr) - uniqueSuffix = std::format("{}_{:02d}", base, ++suffix); - } - - // We use 'CoordinateSets' here, because in this instance we are working with (CoordinateSet, Add) pairs - - // CoordinateSets - auto coordsNode = - generator.createRootNode(std::format("SymmetryCopies_{}", uniqueSuffix), sp); - coordsNode->keywords().setEnumeration("Source", CoordinateSetsGeneratorNode::CoordinateSetSource::File); - coordsNode->setSets(cifMolecularSp.allInstanceCoordinates()); - - // Add - auto addNode = generator.createRootNode(std::format("Add_{}", uniqueSuffix), coordsNode); - addNode->keywords().set("Population", NodeValueProxy(int(cifMolecularSp.instances().size()))); - addNode->keywords().setEnumeration("Positioning", AddGeneratorNode::PositioningType::Current); - addNode->keywords().set("Rotate", false); - addNode->keywords().setEnumeration("BoxAction", AddGeneratorNode::BoxActionStyle::None); - } - } - else - { - for (auto &cifMolecularSp : molecularSpecies_) - { - coreData.copySpecies(cifMolecularSp.species().get()); - } - } - } - else - { - auto *sp = coreData.addSpecies(); - sp->copyBasic(&supercellSpecies_); - if (flags.isSet(OutputFlags::OutputSupermolecule)) - { - sp->removePeriodicBonds(); - sp->removeBox(); - } - else - sp->createBox(supercellSpecies_.box()->axisLengths(), supercellSpecies_.box()->axisAngles()); - - sp->updateIntramolecularTerms(); - - if (flags.isSet(OutputFlags::OutputConfiguration)) - { - configuration = coreData.addConfiguration(); - configuration->setName(chemicalFormula()); - - // Grab the generator - auto &generator = configuration->generator(); - - // Add Box - auto boxNode = generator.createRootNode({}); - auto cellLengths = supercellConfiguration_.box()->axisLengths(); - auto cellAngles = supercellConfiguration_.box()->axisAngles(); - boxNode->keywords().set("Lengths", Vector3NodeValue(cellLengths.get(0), cellLengths.get(1), cellLengths.get(2))); - boxNode->keywords().set("Angles", Vector3NodeValue(cellAngles.get(0), cellAngles.get(1), cellAngles.get(2))); - - // Add - auto addNode = generator.createRootNode(std::format("Add_{}", sp->name()), sp); - addNode->keywords().set("Population", NodeValueProxy(1)); - addNode->keywords().setEnumeration("Positioning", AddGeneratorNode::PositioningType::Current); - addNode->keywords().set("Rotate", false); - addNode->keywords().setEnumeration("BoxAction", AddGeneratorNode::BoxActionStyle::None); - } - } -} - -/* - * Helpers - */ - -// Apply CIF bonding to a given species -void CIFHandler::applyCIFBonding(Species *sp, bool preventMetallicBonding) -{ - if (!hasBondDistances()) - return; - - auto *box = sp->box(); - auto pairs = PairIterator(sp->nAtoms()); - for (auto pair : pairs) - { - // Grab indices and atom references - auto [indexI, indexJ] = pair; - if (indexI == indexJ) - continue; - - auto &i = sp->atom(indexI); - auto &j = sp->atom(indexJ); - - // Prevent metallic bonding? - if (preventMetallicBonding && Elements::isMetallic(i.Z()) && Elements::isMetallic(j.Z())) - continue; - - // Retrieve distance - auto r = bondDistance(i.atomType()->name(), j.atomType()->name()); - if (!r) - continue; - else if (fabs(box->minimumDistance(i.r(), j.r()) - r.value()) < 1.0e-2) - sp->addBond(&i, &j); - } -} - -// Determine the best NETA definition for the supplied species -std::tuple> CIFHandler::bestNETADefinition(Species *sp) -{ - // Set up the return value and bind its contents - std::tuple> result{NETADefinition(), {}}; - auto &&[bestNETA, rootAtoms] = result; - - // Maintain a set of atoms matched by any NETA description we generate - std::set alreadyMatched; - - // Loop over species atoms - for (auto &i : sp->atoms()) - { - // Skip this atom? - if (alreadyMatched.find(&i) != alreadyMatched.end()) - continue; - - // Create a NETA definition with this atom as the root - NETADefinition neta; - neta.create(&i, std::nullopt, - Flags(NETADefinition::NETACreationFlags::ExplicitHydrogens, - NETADefinition::NETACreationFlags::IncludeRootElement)); - - // Apply this match over the whole species - std::vector currentRootAtoms; - for (auto &j : sp->atoms()) - { - if (neta.matches(&j)) - { - currentRootAtoms.push_back(&j); - alreadyMatched.insert(&j); - } - } - - // Is this a better description? - auto better = false; - if (rootAtoms.empty() || currentRootAtoms.size() < rootAtoms.size()) - better = true; - else if (currentRootAtoms.size() == rootAtoms.size()) - { - // Replace the current match if there are more bonds on the current atom. - if (i.nBonds() > rootAtoms.front()->nBonds()) - better = true; - } - - if (better) - { - bestNETA = neta; - rootAtoms = currentRootAtoms; - } - } - - return result; -} - -// Get instances for the supplied species from the cleaned unit cell -std::vector CIFHandler::getSpeciesInstances(const Species *referenceSpecies, std::vector &atomMask, - const NETADefinition &neta, - const std::vector &referenceRootAtoms) -{ - if (referenceRootAtoms.empty() || !neta.isValid()) - return {}; - - // Loop over atoms in the unit cell - we'll mark any that we select as an instance so we speed things up and avoid - // duplicates - const auto &unitCellAtoms = cleanedUnitCellSpecies_.atoms(); - std::vector instances; - auto atomIndexIterator = std::find(atomMask.begin(), atomMask.end(), false); - while (atomIndexIterator != atomMask.end()) - { - // Try to match this atom / fragment - const auto atomIndex = atomIndexIterator - atomMask.begin(); - auto &atom = unitCellAtoms[atomIndex]; - auto matchedUnitCellAtoms = neta.matchedPath(&atom).set(); - if (matchedUnitCellAtoms.empty()) - { - atomIndexIterator = std::find(std::next(atomIndexIterator), atomMask.end(), false); - continue; - } - - // Found a fragment that matches the NETA description - we now create a temporary instance Species which will contain - // the selected fragment atoms, reassembled into a molecule (i.e. unfolded) and with bonding applied / calculated. - // We need to copy the unit cell from the crystal so we detect bonds properly. - Species instanceSpecies; - instanceSpecies.createBox(unitCellSpecies_.box()->axisLengths(), unitCellSpecies_.box()->axisAngles()); - auto rootAtomLocalIndex = -1; - // -- Create species atoms from those matched in the unit cell by the NETA description. - for (auto &matchedAtom : matchedUnitCellAtoms) - { - auto idx = instanceSpecies.addAtom(matchedAtom->Z(), matchedAtom->r(), 0.0, matchedAtom->atomType()); - - // Store the index of the root atom in match in our instance species when we find it - if (matchedAtom == &atom) - rootAtomLocalIndex = idx; - } - // -- Store the local root atom so we can access its coordinates for the origin translation - auto &instanceSpeciesRootAtom = instanceSpecies.atom(rootAtomLocalIndex); - // -- Calculate / apply bonding - if (!preventAllBonds_) - if (useCIFBondingDefinitions_) - applyCIFBonding(&instanceSpecies, preventMetallicBonds_); - else - instanceSpecies.addMissingBonds(bondingTolerance_, preventMetallicBonds_); - - // Create a LocalMolecule as a working area for folding, translation, and rotation of the instance coordinates. - LocalMolecule instanceMolecule; - instanceMolecule.setSpecies(&instanceSpecies); - // -- Copy the coordinates off the matched unit cell atoms to our molecule and flag them as complete - auto count = 0; - for (auto &&[matchedAtom, instanceMolAtom] : zip(matchedUnitCellAtoms, instanceMolecule.localAtoms())) - { - instanceMolAtom.setR(matchedAtom->r()); - atomMask[matchedAtom->index()] = true; - } - auto &instanceMoleculeRootAtom = instanceMolecule.localAtoms()[rootAtomLocalIndex]; - - // Unfold the molecule and store the unfolded molecule coordinates back into the instance Species. - // This represents our full instance coordinates we will be storing (but not their final order) - instanceMolecule.unFold(unitCellSpecies_.box()); - for (auto &&[molAtom, spAtom] : zip(instanceMolecule.localAtoms(), instanceSpecies.atoms())) - spAtom.setR(molAtom.r()); - - /* - * Now, we have a root match atom on the current instance and a vector of possible matching sites on the reference - * species (in referenceRootAtoms). For each of the referenceRootAtoms, try to incrementally select along bonds using - * basic NETA connectivity. - */ - - // Generate basic NETA descriptions for each atom in the reference and candidate species - std::map referenceAtomNETA; - for (auto &spAtom : referenceSpecies->atoms()) - referenceAtomNETA[&spAtom] = NETADefinition(&spAtom, 1, {NETADefinition::NETACreationFlags::IncludeRootElement}); - - std::map matchMap; - for (const auto *referenceRootAtom : referenceRootAtoms) - { - // The root atom is the starting point - matchMap = matchAtom(referenceRootAtom, &instanceSpeciesRootAtom, referenceAtomNETA, {}); - if (!matchMap.empty()) - break; - } - - // Result? - if (matchMap.empty()) - { - Messenger::error("Failed to match connectivity of an instance to the reference molecule.\n"); - return {}; - } - else if (matchMap.size() != referenceSpecies->nAtoms()) - { - Messenger::error( - "Internal error - failed to match connectivity of all atoms within an instance to the reference molecule.\n"); - return {}; - } - - // Create the final instance - auto &instance = instances.emplace_back(); - instance.setSpecies(referenceSpecies); - for (const auto &[refSpeciesAtom, instanceSpeciesAtom] : matchMap) - { - instance.localAtom(refSpeciesAtom->index()).setR(instanceSpeciesAtom->r()); - } - - // Find the next available atom - atomIndexIterator = std::find(std::next(atomIndexIterator), atomMask.end(), false); - } - - return instances; -} - -// Recursively check NETA description matches between the supplied atoms -std::map -CIFHandler::matchAtom(const SpeciesAtom *referenceAtom, const SpeciesAtom *instanceAtom, - const std::map &refNETA, - const std::map &map) -{ - // If the reference atom NETA doesn't match the instance atom we cannot proceed - if (!refNETA.at(referenceAtom).matches(instanceAtom)) - return {}; - - // Check the map to see if we have already associated the reference atom to an instance atom, or if the instance atom - // is already associated to a different reference atom. - for (auto &&[mappedRefAtom, mappedInstanceAtom] : map) - { - // Found it - double-check to ensure that the current association matches our instance atom. If it does we can return - // the map as it currently stands. If not we return an empty map to indicate failure. - if (mappedRefAtom == referenceAtom) - { - if (mappedInstanceAtom == instanceAtom) - { - return map; - } - else - { - return {}; - } - } - else if (mappedInstanceAtom == instanceAtom) - { - return {}; - } - } - - // Copy the current map, associate our initial pair of atoms and try to extend it - auto newMap = map; - newMap[referenceAtom] = instanceAtom; - - // Cycle over bonds on the reference atom and find - for (const auto &referenceBond : referenceAtom->bonds()) - { - // Get the reference bond partner - auto *referenceBondPartner = referenceBond.get().partner(referenceAtom); - - // Try to find a match over bonds on the instance atom - std::map bondResult; - for (const auto &instanceBond : instanceAtom->bonds()) - { - // Get the instance bond partner - auto *instanceBondPartner = instanceBond.get().partner(instanceAtom); - - // Recurse - bondResult = matchAtom(referenceBondPartner, instanceBondPartner, refNETA, newMap); - if (!bondResult.empty()) - break; - } - - // If we found a suitable match recursing into the bond, store the result into newMap and continue to the next bond. - // If we didn't find a good match, we return now. - if (bondResult.empty()) - { - return {}; - } - else - { - newMap = bondResult; - } - } - - // If we get to here then we succeeded, so return the new map - return newMap; -} - -// Calculate difference metric between the supplied species and local molecule -std::pair> CIFHandler::differenceMetric(const Species *species, const LocalMolecule &molecule) -{ - auto difference = 0.0; - std::vector atomIndexMap(species->nAtoms(), -1); - auto nBadAtoms = 0; - for (auto spI = 0; spI < species->nAtoms(); ++spI) - { - auto &spAtom = species->atom(spI); - - // For this species atom find the closest atom in the molecule - auto distanceSq = 1.0e6; - for (auto molI = 0; molI < molecule.nAtoms(); ++molI) - { - auto rABSq = (spAtom.r() - molecule.localAtoms()[molI].r()).magnitudeSq(); - if (rABSq < distanceSq) - { - distanceSq = rABSq; - atomIndexMap[spI] = molI; - } - } - - if (distanceSq > 0.1) - ++nBadAtoms; - - // Update the difference score - const auto &closestMolSpAtom = molecule.species()->atom(atomIndexMap[spI]); - difference += distanceSq; - if (spAtom.Z() != closestMolSpAtom.Z()) - difference += std::max(int(spAtom.Z()), int(closestMolSpAtom.Z())) * 10.0; - } - - return {difference, atomIndexMap}; -} diff --git a/src/io/import/cif.h b/src/io/import/cif.h deleted file mode 100644 index fa9f34b812..0000000000 --- a/src/io/import/cif.h +++ /dev/null @@ -1,214 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#pragma once - -#include "classes/configuration.h" -#include "classes/coreData.h" -#include "classes/species.h" -#include "data/spaceGroups.h" -#include "io/import/cifClasses.h" -#include "math/matrix4.h" -#include "neta/neta.h" -#include "templates/flags.h" -#include - -// Forward Declarations -class Box; - -// CIF Handler -class CIFHandler -{ - public: - CIFHandler(); - ~CIFHandler() = default; - - /* - * Raw Data - */ - public: - // Data Types - using CIFTags = std::map>; - - private: - // Vector of enumerated data items - CIFTags tags_; - - private: - // Parse supplied file into the destination objects - bool parse(std::string_view filename, CIFTags &tags) const; - - public: - // Return whether the specified file parses correctly - bool validFile(std::string_view filename) const; - // Read CIF data from specified file - bool read(std::string_view filename); - // Return if the specified tag exists - bool hasTag(std::string tag) const; - // Return tag data string (if it exists) assuming a single datum (first in the vector) - std::optional getTagString(std::string tag) const; - // Return tag data strings (if it exists) - std::vector getTagStrings(std::string tag) const; - // Return tag data as double (if it exists) assuming a single datum (first in the vector) - std::optional getTagDouble(std::string tag) const; - // Return tag data doubles (if it exists) - std::vector getTagDoubles(std::string tag) const; - // Return tag data as integer (if it exists) assuming a single datum (first in the vector) - std::optional getTagInt(std::string tag) const; - - /* - * Processed Data - */ - private: - // Space group - SpaceGroups::SpaceGroupId spaceGroup_{SpaceGroups::NoSpaceGroup}; - // Atom assemblies - std::vector assemblies_; - // Bond information - std::vector bondingPairs_; - - public: - // Set space group from index - void setSpaceGroup(SpaceGroups::SpaceGroupId sgid); - // Return space group - SpaceGroups::SpaceGroupId spaceGroup() const; - // Return cell lengths - std::optional getCellLengths() const; - // Return cell angles - std::optional getCellAngles() const; - // Return chemical formula - std::string chemicalFormula() const; - // Get (add or retrieve) named assembly - CIFAssembly &getAssembly(std::string_view name); - // Return atom assemblies - std::vector &assemblies(); - const std::vector &assemblies() const; - // Return whether any bond distances are defined - bool hasBondDistances() const; - // Return whether a bond distance is defined for the specified label pair - std::optional bondDistance(std::string_view labelI, std::string_view labelJ) const; - - /* - * Creation - */ - public: - // CIF Generation Stages - enum class CIFGenerationStage - { - CreateBasicUnitCell, - CreateCleanedUnitCell, - DetectMolecules, - CreateSupercell - }; - // CIF Species Output Flags - enum OutputFlags - { - OutputConfiguration, /* Output a Configuration */ - OutputMolecularSpecies, /* Partitioning - output molecular species */ - OutputFramework, /* Partitioning - output a framework species */ - OutputSupermolecule /* Partitioning - output a supermolecule */ - }; - - private: - // Temporary atom types used for unique atom labels - std::vector> atomLabelTypes_; - // Tolerance for removal of overlapping atoms - double overlapTolerance_{0.1}; - // Whether to use CIF bonding definitions - bool useCIFBondingDefinitions_{false}; - // Bonding tolerance, if calculating bonding rather than using CIF definitions - double bondingTolerance_{1.1}; - // Whether to ignore all bonds - bool preventAllBonds_{false}; - // Whether to prevent metallic bonding - bool preventMetallicBonds_{true}; - // Whether to remove free atomic moieties in clean-up - bool removeAtomics_{false}; - // Whether to remove water and coordinated oxygen atoms in clean-up - bool removeWaterAndCoordinateOxygens_{false}; - // Whether to remove by NETA definition in clean-up - bool removeNETA_{false}; - // Whether to expand NETA matches to fragments when removing in clean-up - bool removeNETAByFragment_{false}; - // NETA for moiety removal, if specified - NETADefinition moietyRemovalNETA_; - // Supercell repeat - Vector3i supercellRepeat_{1, 1, 1}; - // Basic unit cell - Species unitCellSpecies_; - Configuration unitCellConfiguration_; - // Cleaned unit cell - Species cleanedUnitCellSpecies_; - Configuration cleanedUnitCellConfiguration_; - // Molecular definition of unit cell (if possible) - std::vector molecularSpecies_; - // Final generated result (supercell) - Species supercellSpecies_; - Configuration supercellConfiguration_; - - private: - // Create basic unit cell - bool createBasicUnitCell(); - // Create the cleaned unit cell - bool createCleanedUnitCell(); - // Try to detect molecules in the cell contents - bool detectMolecules(); - // Create supercell species - bool createSupercell(); - - public: - // Set overlap tolerance - void setOverlapTolerance(double tol); - // Set whether to use CIF bonding definitions - void setUseCIFBondingDefinitions(bool b); - // Set bonding tolerance - void setBondingTolerance(double tol); - // Whether to ignore all bonds - void setPreventAllBonds(bool b); - // Set whether to prevent metallic bonding - void setPreventMetallicBonds(bool b); - // Set whether to remove free atomic moieties in clean-up - void setRemoveAtomics(bool b); - // Set whether to remove water and coordinated oxygen atoms in clean-up - void setRemoveWaterAndCoordinateOxygens(bool b); - // Set whether to remove by NETA definition in clean-up - void setRemoveNETA(bool b, bool byFragment); - // Set NETA for moiety removal - bool setMoietyRemovalNETA(std::string_view netaDefinition); - // Set supercell repeat - void setSupercellRepeat(const Vector3i &repeat); - // Recreate the data - bool generate(CIFGenerationStage fromStage = CIFGenerationStage::CreateBasicUnitCell); - // Return whether the generated data is valid - bool isValid() const; - // Return supercell species - const Species &supercellSpecies() const; - // Return cleaned unit cell species - const Species &cleanedUnitCellSpecies() const; - // Return the detected molecular species - const std::vector &molecularSpecies() const; - // Return the generated configuration - Configuration *generatedConfiguration(); - // Finalise, copying the required species and resulting configuration to the target CoreData - void finalise(CoreData &coreData, const Flags &flags = {}) const; - - /* - * Helpers - */ - private: - // Apply CIF bonding to a given species - void applyCIFBonding(Species *sp, bool preventMetallicBonding); - // Determine the best NETA definition for the supplied species - std::tuple> bestNETADefinition(Species *sp); - // Get instances of species molecules from the supplied NETA definition - std::vector getSpeciesInstances(const Species *referenceSpecies, std::vector &atomMask, - const NETADefinition &neta, - const std::vector &referenceRootAtoms); - // Calculate difference metric between the supplied species and local molecule - static std::pair> differenceMetric(const Species *species, const LocalMolecule &molecule); - // Recursively check NETA description matches between the supplied atoms - std::map matchAtom(const SpeciesAtom *referenceAtom, - const SpeciesAtom *instanceAtom, - const std::map &refNETA, - const std::map &map); -}; diff --git a/src/nodes/CMakeLists.txt b/src/nodes/CMakeLists.txt index f26e9a23f0..88803e910d 100644 --- a/src/nodes/CMakeLists.txt +++ b/src/nodes/CMakeLists.txt @@ -10,7 +10,44 @@ file( "./*.h" ) -add_library(nodes ${node_sources} ${node_headers}) +# CIF/ANTLR +set(CIF_IO_DIR "${CMAKE_CURRENT_SOURCE_DIR}/cif/io") +set(ANTLR_CIF_PREFIX "NodeCIFImport") -target_include_directories(nodes PRIVATE ${PROJECT_SOURCE_DIR}/src) +# CIFImport ANTLR Lexer/Parser +antlr_target(CIFImportGrammarLexer "${CIF_IO_DIR}/CIFImportLexer.g4" LEXER) +# PACKAGE CIFImportGrammar) +antlr_target( + CIFImportGrammarParser + "${CIF_IO_DIR}/CIFImportParser.g4" + PARSER + # PACKAGE CIFImportGrammar + DEPENDS_ANTLR + CIFImportGrammarLexer + COMPILE_FLAGS + -no-listener + -visitor + -lib + ${ANTLR_CIFImportGrammarLexer_OUTPUT_DIR} +) + +# Append path to ANTLR parser output, and set cache variable +list(APPEND ANTLR_OUTPUT_DIRS ${ANTLR_CIFImportGrammarLexer_OUTPUT_DIR}) +list(APPEND ANTLR_OUTPUT_DIRS ${ANTLR_CIFImportGrammarParser_OUTPUT_DIR}) +set(ANTLR_OUTPUT_DIRS + ${ANTLR_OUTPUT_DIRS} + CACHE INTERNAL "" +) + +add_library(nodes ${node_sources} ${node_headers} ${ANTLR_CIFImportGrammarLexer_CXX_OUTPUTS} ${ANTLR_CIFImportGrammarParser_CXX_OUTPUTS}) + +message( + STATUS + "ANTLR generated products located in the following directories: ${ANTLR_CIFImportGrammarLexer_CXX_OUTPUTS}, ${ANTLR_CIFImportGrammarParser_CXX_OUTPUTS}" +) + +target_include_directories( + nodes PUBLIC ${PROJECT_SOURCE_DIR}/src ${PROJECT_BINARY_DIR}/src ${ANTLR_CIFImportGrammarLexer_OUTPUT_DIR} + ${ANTLR_CIFImportGrammarParser_OUTPUT_DIR} +) target_link_libraries(nodes PUBLIC base ${THREADING_LINK_LIBS}) diff --git a/src/nodes/cif/importCIFStructure.cpp b/src/nodes/cif/importCIFStructure.cpp new file mode 100644 index 0000000000..a20c8ef049 --- /dev/null +++ b/src/nodes/cif/importCIFStructure.cpp @@ -0,0 +1,538 @@ +// SPDX-License-Identifier: GPL-3.0-or-later +// Copyright (c) 2026 Team Dissolve and contributors + +#include "nodes/cif/importCIFStructure.h" +#include "CIFImportLexer.h" +#include "CIFImportParser.h" +#include "base/messenger.h" +#include "base/sysFunc.h" +#include "classes/coreData.h" +#include "classes/empiricalFormula.h" +#include "generator/add.h" +#include "generator/box.h" +#include "generator/coordinateSets.h" +#include "nodes/cif/io/CIFImportErrorListeners.h" +#include "nodes/cif/io/CIFImportVisitor.h" +#include "templates/algorithms.h" +#include +#include +#include + +ImportCIFStructureNode::ImportCIFStructureNode(Graph *parentGraph) : Node(parentGraph) +{ + // Outputs + addPointerOutput("Structure", "Structure containing atoms and connectivity", structure_); + + // Option + addOption("FilePath", "File path", filePath_); + addOption("SpaceGroupID", "Set space group from index", spaceGroup_); +} + +std::string_view ImportCIFStructureNode::type() const { return "ImportCIFStructure"; } + +std::string_view ImportCIFStructureNode::summary() const +{ + return "Load and parse a Crystallographic Information File (CIF) to a structure"; +} + +// Run main processing +NodeConstants::ProcessResult ImportCIFStructureNode::process() +{ + structure_.clear(); + + // Read contents of CIF file + if (read(filePath_)) + { + if (!createStructure(spaceGroup_, overlapTolerance_)) + return error("Did not successfully create a basic structure from the CIF file."); + + return NodeConstants::ProcessResult::Success; + } + + return error("Failed to read contents of CIF file"); +} + +/* + * CIF I/O + */ + +/* + * Basic CIF Data + */ + +// Parse supplied file into the destination objects +bool ImportCIFStructureNode::parse(std::string_view filename, CIFImportVisitor::CIFTags &tags) const +{ + // Set up ANTLR input stream + std::ifstream cifFile(std::string(filename), std::ios::in | std::ios::binary); + if (!cifFile.is_open()) + return Messenger::error("Failed to open CIF file '{}.\n", filename); + + antlr4::ANTLRInputStream input(cifFile); + + // Create ANTLR lexer and set-up error listener + CIFImportLexer lexer(&input); + CIFImportLexerErrorListener lexerErrorListener; + lexer.removeErrorListeners(); + lexer.addErrorListener(&lexerErrorListener); + + // Generate tokens from input stream + antlr4::CommonTokenStream tokens(&lexer); + + // Create ANTLR parser and set-up error listeners + CIFImportParser parser(&tokens); + CIFImportParserErrorListener parserErrorListener; + parser.removeErrorListeners(); + parser.removeParseListeners(); + parser.addErrorListener(&lexerErrorListener); + parser.addErrorListener(&parserErrorListener); + + // Generate the AST + CIFImportParser::CifContext *tree = nullptr; + try + { + tree = parser.cif(); + } + catch (CIFImportExceptions::CIFImportSyntaxException &ex) + { + Messenger::error("{}", ex.what()); + return false; + } + + // Visit the nodes in the AST + CIFImportVisitor visitor(tags); + try + { + visitor.extract(tree); + } + catch (CIFImportExceptions::CIFImportSyntaxException &ex) + { + return Messenger::error("{}", ex.what()); + } + + return true; +} + +// Return whether the specified file parses correctly +bool ImportCIFStructureNode::validFile(std::string_view filename) const +{ + CIFImportVisitor::CIFTags tags; + return parse(filename, tags); +} + +// Read CIF data from specified file +bool ImportCIFStructureNode::read(std::string_view filename) +{ + assemblies_.clear(); + bondingPairs_.clear(); + tags_.clear(); + + if (!parse(filename, tags_)) + return Messenger::error("Failed to parse CIF file '{}'.\n", filename); + + /* + * Determine space group - the search order for tags is: + * + * 1. Hall symbol + * 2. Hermann-Mauginn name + * 3. Space group index + * + * In the case of 2 or 3 we also try to search for the origin choice. + * + * If a space group has already been set, don't try to overwrite it (it was probably forcibly set because the detection + * below fails). + */ + + // Check for Hall symbol + if (spaceGroup_ == SpaceGroups::NoSpaceGroup && hasTag("_space_group_name_Hall")) + spaceGroup_ = SpaceGroups::findByHallSymbol(*getTagString("_space_group_name_Hall")); + if (spaceGroup_ == SpaceGroups::NoSpaceGroup && hasTag("_symmetry_space_group_name_Hall")) + spaceGroup_ = SpaceGroups::findByHallSymbol(*getTagString("_symmetry_space_group_name_Hall")); + + if (spaceGroup_ == SpaceGroups::NoSpaceGroup) + { + // Might need the coordinate system code... + auto sgCode = getTagString("_space_group.IT_coordinate_system_code"); + + // Find a HM name + if (hasTag("_space_group_name_H-M_alt")) + spaceGroup_ = + SpaceGroups::findByHermannMauginnSymbol(*getTagString("_space_group_name_H-M_alt"), sgCode.value_or("")); + if (spaceGroup_ == SpaceGroups::NoSpaceGroup && hasTag("_symmetry_space_group_name_H-M")) + spaceGroup_ = + SpaceGroups::findByHermannMauginnSymbol(*getTagString("_symmetry_space_group_name_H-M"), sgCode.value_or("")); + + // Find a space group index? + if (spaceGroup_ == SpaceGroups::NoSpaceGroup && hasTag("_space_group_IT_number")) + spaceGroup_ = + SpaceGroups::findByInternationalTablesIndex(*getTagInt("_space_group_IT_number"), sgCode.value_or("")); + if (spaceGroup_ == SpaceGroups::NoSpaceGroup && hasTag("_space_group.IT_number")) + spaceGroup_ = + SpaceGroups::findByInternationalTablesIndex(*getTagInt("_space_group.IT_number"), sgCode.value_or("")); + if (spaceGroup_ == SpaceGroups::NoSpaceGroup && hasTag("_symmetry_Int_Tables_number")) + spaceGroup_ = + SpaceGroups::findByInternationalTablesIndex(*getTagInt("_symmetry_Int_Tables_number"), sgCode.value_or("")); + } + + // Create symmetry-unique atoms list + auto atomSiteLabel = getTagStrings("_atom_site_label"); + auto atomSiteTypeSymbol = getTagStrings("_atom_site_type_symbol"); + auto atomSiteFractX = getTagDoubles("_atom_site_fract_x"); + auto atomSiteFractY = getTagDoubles("_atom_site_fract_y"); + auto atomSiteFractZ = getTagDoubles("_atom_site_fract_z"); + auto atomSiteOccupancy = getTagDoubles("_atom_site_occupancy"); + auto atomDisorderAssembly = getTagStrings("_atom_site_disorder_assembly"); + auto atomDisorderGroup = getTagStrings("_atom_site_disorder_group"); + if (atomSiteLabel.empty() && atomSiteTypeSymbol.empty()) + return Messenger::error( + "No suitable atom site names found (no '_atom_site_label' or '_atom_site_type_symbol' tags present in CIF).\n"); + if (atomSiteFractX.empty() || atomSiteFractY.empty() || atomSiteFractZ.empty()) + return Messenger::error("Atom site fractional positions are incomplete (vector sizes are {}, {}, and {}).\n", + atomSiteFractX.size(), atomSiteFractY.size(), atomSiteFractZ.size()); + if (!((atomSiteFractX.size() == atomSiteFractY.size()) && (atomSiteFractX.size() == atomSiteFractZ.size()))) + return Messenger::error("Atom site fractional positions have mismatched sizes (vector sizes are {}, {}, and {}).\n", + atomSiteFractX.size(), atomSiteFractY.size(), atomSiteFractZ.size()); + for (auto n = 0; n < atomSiteFractX.size(); ++n) + { + // Get standard information + auto label = n < atomSiteLabel.size() ? atomSiteLabel[n] : std::format("{}{}", atomSiteTypeSymbol[n], n); + auto Z = n < atomSiteTypeSymbol.size() + ? Elements::element(atomSiteTypeSymbol[n]) + : (n < atomSiteLabel.size() ? Elements::element(atomSiteLabel[n]) : Elements::Unknown); + auto occ = n < atomSiteOccupancy.size() ? atomSiteOccupancy[n] : 1.0; + Vector3 rFrac(atomSiteFractX[n], atomSiteFractY[n], atomSiteFractZ[n]); + + // Add the atom to an assembly - there are three possibilities regarding (disorder) grouping: + // 1) A group is defined, but no assembly - add the atom to the 'Disorder' assembly + // 2) An assembly and a group are defined - add it to that + // 3) No group or assembly are defined - add the atom to the 'Global' assembly under a 'Default' group + auto assemblyName = atomDisorderAssembly.empty() ? "." : atomDisorderAssembly[n]; + auto groupName = atomDisorderGroup.empty() ? "." : atomDisorderGroup[n]; + if (assemblyName == "." && groupName != ".") + assemblyName = "Disorder"; + else if (assemblyName == "." && groupName == ".") + assemblyName = "Global"; + + if (groupName == ".") + groupName = "Default"; + + // Get the assembly and group that we're adding the atom to + auto &assembly = getAssembly(assemblyName); + auto &group = assembly.getGroup(groupName); + group.setActive(groupName == "Default" || groupName == "1"); + group.addAtom({label, Z, rFrac, occ}); + } + + // Construct bonding pairs list + auto bondLabelsI = getTagStrings("_geom_bond_atom_site_label_1"); + auto bondLabelsJ = getTagStrings("_geom_bond_atom_site_label_2"); + auto bondDistances = getTagDoubles("_geom_bond_distance"); + if (bondLabelsI.size() == bondLabelsJ.size() && (bondLabelsI.size() == bondDistances.size())) + { + for (auto &&[i, j, r] : zip(bondLabelsI, bondLabelsJ, bondDistances)) + bondingPairs_.emplace_back(i, j, r); + } + else + Messenger::warn("Bonding pairs array sizes are mismatched, so no bonding information will be available."); + + return true; +} + +// Return if the specified tag exists +bool ImportCIFStructureNode::hasTag(std::string tag) const { return tags_.find(tag) != tags_.end(); } + +// Return tag data string (if it exists) assuming a single datum (first in the vector) +std::optional ImportCIFStructureNode::getTagString(std::string tag) const +{ + auto it = tags_.find(tag); + if (it == tags_.end()) + return std::nullopt; + + // Check data vector size + if (it->second.size() != 1) + Messenger::warn("Returning first datum for tag '{}', but {} are available.\n", tag, it->second.size()); + + return it->second.front(); +} + +// Return tag data strings (if it exists) +std::vector ImportCIFStructureNode::getTagStrings(std::string tag) const +{ + auto it = tags_.find(tag); + if (it == tags_.end()) + return {}; + + return it->second; +} + +// Return tag data as double (if it exists) assuming a single datum (first in the vector) +std::optional ImportCIFStructureNode::getTagDouble(std::string tag) const +{ + auto it = tags_.find(tag); + if (it == tags_.end()) + return std::nullopt; + + // Check data vector size + if (it->second.size() != 1) + Messenger::warn("Returning first datum for tag '{}', but {} are available.\n", tag, it->second.size()); + + double result; + try + { + result = std::stod(it->second.front()); + } + catch (...) + { + Messenger::error("Data tag '{}' contains a value that can't be converted to a double ('{}').\n", tag, + it->second.front()); + return std::nullopt; + } + + return result; +} + +// Return tag data doubles (if it exists) +std::vector ImportCIFStructureNode::getTagDoubles(std::string tag) const +{ + auto it = tags_.find(tag); + if (it == tags_.end()) + return {}; + + std::vector v; + for (const auto &s : it->second) + { + auto d = 0.0; + try + { + d = std::stod(s); + } + catch (...) + { + Messenger::warn("Data tag '{}' contains a value that can't be converted to a double ('{}').\n", tag, s); + } + v.push_back(d); + } + + return v; +} + +// Return tag data as integer (if it exists) assuming a single datum (first in the vector) +std::optional ImportCIFStructureNode::getTagInt(std::string tag) const +{ + auto it = tags_.find(tag); + if (it == tags_.end()) + return std::nullopt; + + // Check data vector size + if (it->second.size() != 1) + Messenger::warn("Returning first datum for tag '{}', but {} are available.\n", tag, it->second.size()); + + int result; + try + { + result = std::stoi(it->second.front()); + } + catch (...) + { + Messenger::error("Data tag '{}' contains a value that can't be converted to an integer ('{}').\n", tag, + it->second.front()); + return std::nullopt; + } + + return result; +} + +/* + * Processed Data + */ + +// Return space group information +SpaceGroups::SpaceGroupId ImportCIFStructureNode::spaceGroup() const { return spaceGroup_; } + +// Return cell lengths +std::optional ImportCIFStructureNode::getCellLengths() const +{ + auto a = getTagDouble("_cell_length_a"); + if (!a) + Messenger::error("Cell length A not defined in CIF.\n"); + auto b = getTagDouble("_cell_length_b"); + if (!b) + Messenger::error("Cell length B not defined in CIF.\n"); + auto c = getTagDouble("_cell_length_c"); + if (!c) + Messenger::error("Cell length C not defined in CIF.\n"); + + if (a && b && c) + return Vector3(a.value(), b.value(), c.value()); + else + return std::nullopt; +} + +// Return cell angles +std::optional ImportCIFStructureNode::getCellAngles() const +{ + auto alpha = getTagDouble("_cell_angle_alpha"); + if (!alpha) + Messenger::error("Cell angle alpha not defined in CIF.\n"); + auto beta = getTagDouble("_cell_angle_beta"); + if (!beta) + Messenger::error("Cell angle beta not defined in CIF.\n"); + auto gamma = getTagDouble("_cell_angle_gamma"); + if (!gamma) + Messenger::error("Cell angle gamma not defined in CIF.\n"); + + if (alpha && beta && gamma) + return Vector3(alpha.value(), beta.value(), gamma.value()); + else + return std::nullopt; +} + +// Return chemical formula +std::string ImportCIFStructureNode::chemicalFormula() const +{ + auto it = tags_.find("_chemical_formula_sum"); + return (it != tags_.end() ? it->second.front() : "Unknown"); +} + +// Get (add or retrieve) named assembly +CIFAssembly &ImportCIFStructureNode::getAssembly(std::string_view name) +{ + auto it = std::find_if(assemblies_.begin(), assemblies_.end(), [name](const auto &a) { return a.name() == name; }); + if (it != assemblies_.end()) + return *it; + + return assemblies_.emplace_back(name); +} + +// Return atom assemblies +std::vector &ImportCIFStructureNode::assemblies() { return assemblies_; } + +const std::vector &ImportCIFStructureNode::assemblies() const { return assemblies_; } + +// Return whether any bond distances are defined +bool ImportCIFStructureNode::hasBondDistances() const { return !bondingPairs_.empty(); } + +// Return whether a bond distance is defined for the specified label pair +std::optional ImportCIFStructureNode::bondDistance(std::string_view labelI, std::string_view labelJ) const +{ + auto it = std::find_if( + bondingPairs_.begin(), bondingPairs_.end(), [labelI, labelJ](const auto &bp) + { return (bp.labelI() == labelI && bp.labelJ() == labelJ) || (bp.labelI() == labelJ && bp.labelJ() == labelI); }); + if (it != bondingPairs_.end()) + return it->r(); + return std::nullopt; +} + +/* + * Creation + */ + +// Create structure from basic unit cell atoms and connectivity +bool ImportCIFStructureNode::createStructure(SpaceGroups::SpaceGroupId sgid, double overlapTolerance) +{ + spaceGroup_ = sgid; + + overlapTolerance_ = overlapTolerance; + + atomLabelTypes_.clear(); + + // Create temporary atom types corresponding to the unique atom labels + for (auto &a : assemblies_) + { + for (auto &g : a.groups()) + { + if (!g.active()) + continue; + + for (auto &i : g.atoms()) + { + if (std::find_if(atomLabelTypes_.begin(), atomLabelTypes_.end(), + [i](const auto &at) { return i.label() == at->name(); }) == atomLabelTypes_.end()) + { + atomLabelTypes_.emplace_back(std::make_shared(i.Z(), i.label())); + } + } + } + } + + // Configure the unit cell "species" + auto cellLengths = getCellLengths(); + if (!cellLengths) + return false; + auto cellAngles = getCellAngles(); + if (!cellAngles) + return false; + + // Configuration + echo_ = false; + structure_.createBox(cellLengths.value(), cellAngles.value(), false); + echo_ = true; + + auto *box = structure_.box(); + + // -- Generate atoms + auto symmetryGenerators = SpaceGroups::symmetryOperators(spaceGroup_); + for (const auto &generator : symmetryGenerators) + for (auto &a : assemblies_) + for (auto &g : a.groups()) + if (g.active()) + for (auto &unique : g.atoms()) + { + // Generate folded atomic position in real space + auto r = generator * unique.rFrac(); + box->toReal(r); + r = box->fold(r); + + // If this atom overlaps with another in the box, don't add it as it's a symmetry-related copy + if (std::any_of(structure_.atoms().begin(), structure_.atoms().end(), [&, r, box](const auto &j) + { return box->minimumDistance(r, j->r()) < overlapTolerance_; })) + continue; + + // Create the new atom + auto atIt = std::find_if(atomLabelTypes_.begin(), atomLabelTypes_.end(), + [&unique](const auto at) { return unique.label() == at->name(); }); + auto *structureAtom = structure_.addAtom(unique.Z(), r, 0.0); + auto atomLabelTypeIdx = std::distance(atomLabelTypes_.begin(), atIt); + structureAtom->setAtomTypeIndex(atomLabelTypeIdx); + } + + // Check that we actually generated some atoms... + if (structure_.nAtoms() == 0) + return false; + + // Bonding + if (!hasBondDistances()) + return true; + + auto pairs = PairIterator(structure_.nAtoms()); + for (auto pair : pairs) + { + // Grab indices and atom references + auto [indexI, indexJ] = pair; + if (indexI == indexJ) + continue; + + auto i = structure_.atomAt(indexI); + auto j = structure_.atomAt(indexJ); + + // Retrieve distance + auto atomTypeIdxI = i->atomTypeIndex(); + auto atomTypeIdxJ = j->atomTypeIndex(); + auto r = bondDistance(atomLabelTypes_[atomTypeIdxI]->name(), atomLabelTypes_[atomTypeIdxJ]->name()); + if (!r) + continue; + else if (!structure_.hasBond(i, j) && fabs(box->minimumDistance(i->r(), j->r()) - r.value()) < 1.0e-2) + structure_.addBond(i, j); + } + + message("Created basic structure - {} structure atoms, {} structure bonds found whle parsing the CIF.\n", + structure_.nAtoms(), structure_.bonds().size()); + return true; +} + +/* + * Getters + */ + +// Return basic crystal structure +const Structure &ImportCIFStructureNode::structure() const { return structure_; } diff --git a/src/nodes/cif/importCIFStructure.h b/src/nodes/cif/importCIFStructure.h new file mode 100644 index 0000000000..fc039bff78 --- /dev/null +++ b/src/nodes/cif/importCIFStructure.h @@ -0,0 +1,130 @@ +// SPDX-License-Identifier: GPL-3.0-or-later +// Copyright (c) 2026 Team Dissolve and contributors + +#pragma once + +#include "classes/structure.h" +#include "data/spaceGroups.h" +#include "math/matrix4.h" +#include "neta/neta.h" +#include "nodes/cif/io/CIFImportVisitor.h" +#include "nodes/cif/io/cifClasses.h" +#include "nodes/node.h" +#include + +// ImportCIFStructure Node +class ImportCIFStructureNode : public Node +{ + public: + ImportCIFStructureNode(Graph *parentGraph); + ~ImportCIFStructureNode() override = default; + + public: + std::string_view type() const override; + std::string_view summary() const override; + + /* + * Definition + */ + private: + // CIF strucutre + Structure structure_; + // Space group ID + SpaceGroups::SpaceGroupId spaceGroup_{SpaceGroups::SpaceGroupId::NoSpaceGroup}; + // CIF filepath + std::string filePath_; + + /* + * CIF I/O + */ + + /* + * Basic CIF Data + */ + private: + // Vector of enumerated data items + CIFImportVisitor::CIFTags tags_; + + private: + // Parse supplied file into the destination objects + bool parse(std::string_view filename, CIFImportVisitor::CIFTags &tags) const; + + public: + // Return whether the specified file parses correctly + bool validFile(std::string_view filename) const; + // Read CIF data from specified file + bool read(std::string_view filename); + // Return if the specified tag exists + bool hasTag(std::string tag) const; + // Return tag data string (if it exists) assuming a single datum (first in the vector) + std::optional getTagString(std::string tag) const; + // Return tag data strings (if it exists) + std::vector getTagStrings(std::string tag) const; + // Return tag data as double (if it exists) assuming a single datum (first in the vector) + std::optional getTagDouble(std::string tag) const; + // Return tag data doubles (if it exists) + std::vector getTagDoubles(std::string tag) const; + // Return tag data as integer (if it exists) assuming a single datum (first in the vector) + std::optional getTagInt(std::string tag) const; + + /* + * Processed Data + */ + private: + // Atom assemblies + std::vector assemblies_; + // Bond information + std::vector bondingPairs_; + + public: + // Set space group from index + void setSpaceGroup(SpaceGroups::SpaceGroupId sgid); + // Return space group + SpaceGroups::SpaceGroupId spaceGroup() const; + // Return cell lengths + std::optional getCellLengths() const; + // Return cell angles + std::optional getCellAngles() const; + // Return chemical formula + std::string chemicalFormula() const; + // Get (add or retrieve) named assembly + CIFAssembly &getAssembly(std::string_view name); + // Return atom assemblies + std::vector &assemblies(); + const std::vector &assemblies() const; + // Return whether any bond distances are defined + bool hasBondDistances() const; + // Return whether a bond distance is defined for the specified label pair + std::optional bondDistance(std::string_view labelI, std::string_view labelJ) const; + + /* + * Creation + */ + private: + // Temporary atom types used for unique atom labels + std::vector> atomLabelTypes_; + // Tolerance for removal of overlapping atoms + double overlapTolerance_{0.1}; + + private: + // Create structure from basic unit cell atoms and connectivity + bool createStructure(SpaceGroups::SpaceGroupId sgid, double overlapTolerance); + + public: + // Set overlap tolerance + void setOverlapTolerance(double tol); + + /* + * Processing + */ + private: + // Run main processing + NodeConstants::ProcessResult process() override; + + /* + * Getters + */ + public: + // Return basic crystal structure + const Structure &structure() const; +}; diff --git a/src/io/import/CIFImportErrorListeners.cpp b/src/nodes/cif/io/CIFImportErrorListeners.cpp similarity index 97% rename from src/io/import/CIFImportErrorListeners.cpp rename to src/nodes/cif/io/CIFImportErrorListeners.cpp index 6d727406f5..960fe3570d 100644 --- a/src/io/import/CIFImportErrorListeners.cpp +++ b/src/nodes/cif/io/CIFImportErrorListeners.cpp @@ -1,7 +1,7 @@ // SPDX-License-Identifier: GPL-3.0-or-later // Copyright (c) 2026 Team Dissolve and contributors -#include "io/import/CIFImportErrorListeners.h" +#include "nodes/cif/io/CIFImportErrorListeners.h" #include "base/messenger.h" #include "base/sysFunc.h" diff --git a/src/io/import/CIFImportErrorListeners.h b/src/nodes/cif/io/CIFImportErrorListeners.h similarity index 100% rename from src/io/import/CIFImportErrorListeners.h rename to src/nodes/cif/io/CIFImportErrorListeners.h diff --git a/src/io/import/CIFImportLexer.g4 b/src/nodes/cif/io/CIFImportLexer.g4 similarity index 98% rename from src/io/import/CIFImportLexer.g4 rename to src/nodes/cif/io/CIFImportLexer.g4 index 50f921c330..84f510b7fa 100644 --- a/src/io/import/CIFImportLexer.g4 +++ b/src/nodes/cif/io/CIFImportLexer.g4 @@ -9,7 +9,7 @@ lexer grammar CIFImportLexer; // Add custom includes after standard ANTLR includes in both *.h and *.cpp files @lexer::postinclude { #include "base/sysFunc.h" - #include "io/import/CIFImportVisitor.h" + #include "nodes/cif/io/CIFImportVisitor.h" } // Directly precedes the lexer class declaration in the h file (e.g. for additional types etc.). diff --git a/src/io/import/CIFImportParser.g4 b/src/nodes/cif/io/CIFImportParser.g4 similarity index 100% rename from src/io/import/CIFImportParser.g4 rename to src/nodes/cif/io/CIFImportParser.g4 diff --git a/src/io/import/CIFImportVisitor.cpp b/src/nodes/cif/io/CIFImportVisitor.cpp similarity index 91% rename from src/io/import/CIFImportVisitor.cpp rename to src/nodes/cif/io/CIFImportVisitor.cpp index f0e5bec273..964af13e3b 100644 --- a/src/io/import/CIFImportVisitor.cpp +++ b/src/nodes/cif/io/CIFImportVisitor.cpp @@ -1,12 +1,12 @@ // SPDX-License-Identifier: GPL-3.0-or-later // Copyright (c) 2026 Team Dissolve and contributors -#include "io/import/CIFImportVisitor.h" +#include "nodes/cif/io/CIFImportVisitor.h" #include "base/messenger.h" #include "base/sysFunc.h" -#include "io/import/CIFImportErrorListeners.h" +#include "nodes/cif/io/CIFImportErrorListeners.h" -CIFImportVisitor::CIFImportVisitor(CIFHandler::CIFTags &tags) : tags_(tags) {} +CIFImportVisitor::CIFImportVisitor(CIFTags &tags) : tags_(tags) {} /* * Data diff --git a/src/io/import/CIFImportVisitor.h b/src/nodes/cif/io/CIFImportVisitor.h similarity index 84% rename from src/io/import/CIFImportVisitor.h rename to src/nodes/cif/io/CIFImportVisitor.h index 20e6f554db..9a9374c71c 100644 --- a/src/io/import/CIFImportVisitor.h +++ b/src/nodes/cif/io/CIFImportVisitor.h @@ -4,15 +4,19 @@ #pragma once #include "CIFImportParserBaseVisitor.h" -#include "io/import/cif.h" #include "templates/optionalRef.h" #include // CIFImport Visitor for ANTLR class CIFImportVisitor : CIFImportParserBaseVisitor { + + public: + // Data Types + using CIFTags = std::map>; + public: - CIFImportVisitor(CIFHandler::CIFTags &tags); + CIFImportVisitor(CIFTags &tags); ~CIFImportVisitor() override = default; /* @@ -20,7 +24,7 @@ class CIFImportVisitor : CIFImportParserBaseVisitor */ private: // Dictionary data storage - CIFHandler::CIFTags &tags_; + CIFTags &tags_; public: // Extract information from tree diff --git a/src/io/import/cifClasses.cpp b/src/nodes/cif/io/cifClasses.cpp similarity index 99% rename from src/io/import/cifClasses.cpp rename to src/nodes/cif/io/cifClasses.cpp index 433973285b..a2ba6fd5b0 100644 --- a/src/io/import/cifClasses.cpp +++ b/src/nodes/cif/io/cifClasses.cpp @@ -1,7 +1,7 @@ // SPDX-License-Identifier: GPL-3.0-or-later // Copyright (c) 2026 Team Dissolve and contributors -#include "io/import/cifClasses.h" +#include "nodes/cif/io/cifClasses.h" #include "classes/empiricalFormula.h" #include "classes/molecule.h" #include "classes/species.h" diff --git a/src/io/import/cifClasses.h b/src/nodes/cif/io/cifClasses.h similarity index 100% rename from src/io/import/cifClasses.h rename to src/nodes/cif/io/cifClasses.h diff --git a/src/nodes/cifBondingOptions.cpp b/src/nodes/cifBondingOptions.cpp deleted file mode 100644 index c70f0fa5d8..0000000000 --- a/src/nodes/cifBondingOptions.cpp +++ /dev/null @@ -1,37 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#include "nodes/cifBondingOptions.h" - -CIFBondingOptionsNode::CIFBondingOptionsNode(Graph *parentGraph) : Node(parentGraph) -{ - // Inputs - addInput("CIFContext", "CIF handling context derived from parsing of CIF file", context_) - ->setFlags({ParameterBase::Required}); - - // Outputs - addOutput("CIFContext", "CIF handling context derived from parsing of CIF file", context_); - - // Options - addOption("BondingTolerance", "Bonding tolerance, if calculating bonding rather than using CIF definitions", - bondingTolerance_); - addOption("UseCIFBondingDefinitions", "Whether to use CIF bonding definitions", useCIFBondingDefinitions_); - addOption("PreventMetallicBonds", "Whether to prevent metallic bonding", preventMetallicBonds_); - addOption("PreventAllBonds", "Whether to ignore all bonds", preventAllBonds_); -} - -std::string_view CIFBondingOptionsNode::type() const { return "CIFBondingOptions"; } - -std::string_view CIFBondingOptionsNode::summary() const { return "Apply bonding options to a CIF context"; } - -// Run main processing -NodeConstants::ProcessResult CIFBondingOptionsNode::process() -{ - - context_->setBondingTolerance(bondingTolerance_.asDouble()); - context_->setUseCIFBondingDefinitions(useCIFBondingDefinitions_); - context_->setPreventMetallicBonds(preventMetallicBonds_); - context_->setPreventAllBonds(preventAllBonds_); - - return NodeConstants::ProcessResult::Success; -} diff --git a/src/nodes/cifBondingOptions.h b/src/nodes/cifBondingOptions.h deleted file mode 100644 index f67659187c..0000000000 --- a/src/nodes/cifBondingOptions.h +++ /dev/null @@ -1,41 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#pragma once - -#include "nodes/cifLoader.h" -#include "nodes/node.h" - -// CIFLoader Node -class CIFBondingOptionsNode : public Node -{ - public: - CIFBondingOptionsNode(Graph *parentGraph); - ~CIFBondingOptionsNode() override = default; - - public: - std::string_view type() const override; - std::string_view summary() const override; - - /* - * Definition - */ - private: - // CIF handler context - CIFLoaderNode::CIFContext *context_{nullptr}; - // Bonding tolerance, if calculating bonding rather than using CIF definitions - Number bondingTolerance_{1.1}; - // Whether to use CIF bonding definitions - bool useCIFBondingDefinitions_{false}; - // Whether to prevent metallic bonding - bool preventMetallicBonds_{true}; - // Whether to ignore all bonds - bool preventAllBonds_{false}; - - /* - * Processing - */ - private: - // Run main processing - NodeConstants::ProcessResult process() override; -}; diff --git a/src/nodes/cifLoader.cpp b/src/nodes/cifLoader.cpp deleted file mode 100644 index 94e692a6d9..0000000000 --- a/src/nodes/cifLoader.cpp +++ /dev/null @@ -1,38 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#include "nodes/cifLoader.h" -#include -#include -#include - -CIFLoaderNode::CIFLoaderNode(Graph *parentGraph) : Node(parentGraph) -{ - // Outputs - addPointerOutput("CIFContext", "CIF handling context derived from parsing of CIF file", context_) - ->setFlags({ParameterBase::Required}); - - // Option - addOption("FilePath", "File path", filePath_); - addOption("SpaceGroupID", "Set space group from index", spaceGroup_); -} - -std::string_view CIFLoaderNode::type() const { return "CIFLoader"; } - -std::string_view CIFLoaderNode::summary() const { return "Load and parse a Crystallographic Information File (CIF)"; } - -// Run main processing -NodeConstants::ProcessResult CIFLoaderNode::process() -{ - // Read contents of CIF file - if (context_.read(filePath_)) - { - if (spaceGroup_ != SpaceGroups::NoSpaceGroup) - context_.setSpaceGroup(spaceGroup_); - return NodeConstants::ProcessResult::Success; - } - - error("Failed to read contents of CIF file"); - - return NodeConstants::ProcessResult::Failed; -} diff --git a/src/nodes/cifLoader.h b/src/nodes/cifLoader.h deleted file mode 100644 index f1aec6766b..0000000000 --- a/src/nodes/cifLoader.h +++ /dev/null @@ -1,40 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#pragma once - -#include "io/import/cif.h" -#include "nodes/node.h" - -// CIFLoader Node -class CIFLoaderNode : public Node -{ - public: - using CIFContext = CIFHandler; - - public: - CIFLoaderNode(Graph *parentGraph); - ~CIFLoaderNode() override = default; - - public: - std::string_view type() const override; - std::string_view summary() const override; - - /* - * Definition - */ - private: - // CIF handler context - CIFContext context_; - // Space group ID - SpaceGroups::SpaceGroupId spaceGroup_{SpaceGroups::SpaceGroupId::NoSpaceGroup}; - // CIF filepath - std::string filePath_; - - /* - * Processing - */ - private: - // Run main processing - NodeConstants::ProcessResult process() override; -}; diff --git a/src/nodes/cifMolecularSpecies.cpp b/src/nodes/cifMolecularSpecies.cpp deleted file mode 100644 index b47685750e..0000000000 --- a/src/nodes/cifMolecularSpecies.cpp +++ /dev/null @@ -1,49 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#include "nodes/cifMolecularSpecies.h" -#include -#include - -CIFMolecularSpeciesNode::CIFMolecularSpeciesNode(Graph *parentGraph) : Node(parentGraph) -{ - // Inputs - addInput("CIFContext", "CIF handling context derived from parsing of CIF file", context_) - ->setFlags({ParameterBase::Required}); - - // Outputs - addOutput>("DetectedMolecularSpecies", "Detected molecular species", molecularSpecies_); - addOutput("SupercellConfiguration", "Supercell configuration pointer", supercellConfiguration_); - - // Options - addOption("SupercellRepeat", "Supercell repeat", supercellRepeat_); -} - -std::string_view CIFMolecularSpeciesNode::type() const { return "CIFMolecularSpecies"; } - -std::string_view CIFMolecularSpeciesNode::summary() const -{ - return "Output a configuration containing individual molecules based on detected species"; -} - -// Run main processing -NodeConstants::ProcessResult CIFMolecularSpeciesNode::process() -{ - // Generate from CIF context - context_->setSupercellRepeat(supercellRepeat_); - context_->generate(); - - // Get supercell configuration - supercellConfiguration_ = context_->generatedConfiguration(); - supercellConfiguration_->setName(context_->chemicalFormula()); - - // Get detected molecular species - auto &cifMols = context_->molecularSpecies(); - molecularSpecies_.clear(); - std::ranges::copy(cifMols, std::back_inserter(molecularSpecies_)); - - return NodeConstants::ProcessResult::Success; -} - -// Get cleaned unit cell species -const Species &CIFMolecularSpeciesNode::cleanedUnitCellSpecies() const { return context_->cleanedUnitCellSpecies(); } \ No newline at end of file diff --git a/src/nodes/cifMolecularSpecies.h b/src/nodes/cifMolecularSpecies.h deleted file mode 100644 index 50df4671b8..0000000000 --- a/src/nodes/cifMolecularSpecies.h +++ /dev/null @@ -1,46 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#pragma once - -#include "nodes/cifLoader.h" -#include "nodes/node.h" - -// CIFLoader Node -class CIFMolecularSpeciesNode : public Node -{ - public: - CIFMolecularSpeciesNode(Graph *parentGraph); - ~CIFMolecularSpeciesNode() override = default; - - public: - std::string_view type() const override; - std::string_view summary() const override; - - /* - * Definition - */ - private: - // CIF handler context - CIFLoaderNode::CIFContext *context_{nullptr}; - // Supercell configuration - Configuration *supercellConfiguration_{nullptr}; - // Detected molecular species - std::vector molecularSpecies_; - // Supercell repeat - Vector3i supercellRepeat_{1, 1, 1}; - - /* - * Processing - */ - private: - // Run main processing - NodeConstants::ProcessResult process() override; - - /* - * Getters - */ - public: - // Get cleaned unit cell species - const Species &cleanedUnitCellSpecies() const; -}; diff --git a/src/nodes/cifPeriodicFramework.cpp b/src/nodes/cifPeriodicFramework.cpp deleted file mode 100644 index e47f3c193f..0000000000 --- a/src/nodes/cifPeriodicFramework.cpp +++ /dev/null @@ -1,47 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#include "nodes/cifPeriodicFramework.h" - -CIFPeriodicFrameworkNode::CIFPeriodicFrameworkNode(Graph *parentGraph) : Node(parentGraph) -{ - // Inputs - addInput("CIFContext", "CIF handling context derived from parsing of CIF file", context_) - ->setFlags({ParameterBase::Required}); - - // Outputs - addOutput("FrameworkSpecies", "Species", frameworkSpecies_); - addOutput("SupercellConfiguration", "Supercell configuration pointer", supercellConfiguration_); - - // Options - addOption("SupercellRepeat", "Supercell repeat", supercellRepeat_); -} - -std::string_view CIFPeriodicFrameworkNode::type() const { return "CIFPeriodicFramework"; } - -std::string_view CIFPeriodicFrameworkNode::summary() const -{ - return "Create a single species with a periodic box and all atoms in the unit cell (suitable for framework-style models)"; -} - -// Run main processing -NodeConstants::ProcessResult CIFPeriodicFrameworkNode::process() -{ - // Generate from CIF context - context_->setSupercellRepeat(supercellRepeat_); - context_->generate(); - - // Get supercell configuration - supercellConfiguration_ = context_->generatedConfiguration(); - supercellConfiguration_->setName(context_->chemicalFormula()); - - // Get framework species - supercellSpecies_->copyBasic(&(context_->supercellSpecies())); - supercellSpecies_->updateIntramolecularTerms(); - frameworkSpecies_ = supercellSpecies_.get(); - - return NodeConstants::ProcessResult::Success; -} - -// Get cleaned unit cell species -const Species &CIFPeriodicFrameworkNode::cleanedUnitCellSpecies() const { return context_->cleanedUnitCellSpecies(); } \ No newline at end of file diff --git a/src/nodes/cifPeriodicFramework.h b/src/nodes/cifPeriodicFramework.h deleted file mode 100644 index 607150cbd9..0000000000 --- a/src/nodes/cifPeriodicFramework.h +++ /dev/null @@ -1,48 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#pragma once - -#include "nodes/cifLoader.h" -#include "nodes/node.h" - -// CIFLoader Node -class CIFPeriodicFrameworkNode : public Node -{ - public: - CIFPeriodicFrameworkNode(Graph *parentGraph); - ~CIFPeriodicFrameworkNode() override = default; - - public: - std::string_view type() const override; - std::string_view summary() const override; - - /* - * Definition - */ - private: - // CIF handler context - CIFLoaderNode::CIFContext *context_{nullptr}; - // Supercell configuration - Configuration *supercellConfiguration_{nullptr}; - // Supercell species - std::unique_ptr supercellSpecies_; - // Framework species - const Species *frameworkSpecies_{nullptr}; - // Supercell repeat - Vector3i supercellRepeat_{1, 1, 1}; - - /* - * Processing - */ - private: - // Run main processing - NodeConstants::ProcessResult process() override; - - /* - * Getters - */ - public: - // Get cleaned unit cell species - const Species &cleanedUnitCellSpecies() const; -}; diff --git a/src/nodes/cifRemoveAtomic.cpp b/src/nodes/cifRemoveAtomic.cpp deleted file mode 100644 index bb4ba604fb..0000000000 --- a/src/nodes/cifRemoveAtomic.cpp +++ /dev/null @@ -1,30 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#include "nodes/cifRemoveAtomic.h" - -CIFRemoveAtomicNode::CIFRemoveAtomicNode(Graph *parentGraph) : Node(parentGraph) -{ - // Inputs - addInput("CIFContext", "CIF handling context derived from parsing of CIF file", context_) - ->setFlags({ParameterBase::Required}); - - // Outputs - addOutput("CIFContext", "CIF handling context derived from parsing of CIF file", context_); - - // Options - addOption("RemoveAtomics", "Whether to remove free atomic moieties in clean-up", removeAtomics_); -} - -std::string_view CIFRemoveAtomicNode::type() const { return "CIFRemoveAtomic"; } - -std::string_view CIFRemoveAtomicNode::summary() const { return "Remove atomics from a CIF context"; } - -// Run main processing -NodeConstants::ProcessResult CIFRemoveAtomicNode::process() -{ - - context_->setRemoveAtomics(removeAtomics_); - - return NodeConstants::ProcessResult::Success; -} diff --git a/src/nodes/cifRemoveAtomic.h b/src/nodes/cifRemoveAtomic.h deleted file mode 100644 index 4ac1c1c93a..0000000000 --- a/src/nodes/cifRemoveAtomic.h +++ /dev/null @@ -1,35 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#pragma once - -#include "nodes/cifLoader.h" -#include "nodes/node.h" - -// CIFLoader Node -class CIFRemoveAtomicNode : public Node -{ - public: - CIFRemoveAtomicNode(Graph *parentGraph); - ~CIFRemoveAtomicNode() override = default; - - public: - std::string_view type() const override; - std::string_view summary() const override; - - /* - * Definition - */ - private: - // CIF handler context - CIFLoaderNode::CIFContext *context_{nullptr}; - // Whether to remove free atomic moieties in clean-up - bool removeAtomics_{false}; - - /* - * Processing - */ - private: - // Run main processing - NodeConstants::ProcessResult process() override; -}; diff --git a/src/nodes/cifRemoveWater.cpp b/src/nodes/cifRemoveWater.cpp deleted file mode 100644 index 9ac46cf7c5..0000000000 --- a/src/nodes/cifRemoveWater.cpp +++ /dev/null @@ -1,31 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#include "nodes/cifRemoveWater.h" - -CIFRemoveWaterNode::CIFRemoveWaterNode(Graph *parentGraph) : Node(parentGraph) -{ - // Inputs - addInput("CIFContext", "CIF handling context derived from parsing of CIF file", context_) - ->setFlags({ParameterBase::Required}); - - // Outputs - addOutput("CIFContext", "CIF handling context derived from parsing of CIF file", context_); - - // Options - addOption("RemoveWaterAndCoordinatedOxygens", "Whether to remove water and coordinated oxygen atoms in clean-up", - removeWaterAndCoordinatedOxygens_); -} - -std::string_view CIFRemoveWaterNode::type() const { return "CIFRemoveWater"; } - -std::string_view CIFRemoveWaterNode::summary() const { return "Remove water from a CIF context"; } - -// Run main processing -NodeConstants::ProcessResult CIFRemoveWaterNode::process() -{ - - context_->setRemoveWaterAndCoordinateOxygens(removeWaterAndCoordinatedOxygens_); - - return NodeConstants::ProcessResult::Success; -} diff --git a/src/nodes/cifRemoveWater.h b/src/nodes/cifRemoveWater.h deleted file mode 100644 index 73206b1fa2..0000000000 --- a/src/nodes/cifRemoveWater.h +++ /dev/null @@ -1,35 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#pragma once - -#include "nodes/cifLoader.h" -#include "nodes/node.h" - -// CIFLoader Node -class CIFRemoveWaterNode : public Node -{ - public: - CIFRemoveWaterNode(Graph *parentGraph); - ~CIFRemoveWaterNode() override = default; - - public: - std::string_view type() const override; - std::string_view summary() const override; - - /* - * Definition - */ - private: - // CIF handler context - CIFLoaderNode::CIFContext *context_{nullptr}; - // Whether to remove water and coordinated oxygen atoms in clean-up - bool removeWaterAndCoordinatedOxygens_{false}; - - /* - * Processing - */ - private: - // Run main processing - NodeConstants::ProcessResult process() override; -}; diff --git a/src/nodes/cifStructureCleanup.cpp b/src/nodes/cifStructureCleanup.cpp deleted file mode 100644 index ae2a5c0411..0000000000 --- a/src/nodes/cifStructureCleanup.cpp +++ /dev/null @@ -1,34 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#include "nodes/cifStructureCleanup.h" - -CIFStructureCleanupNode::CIFStructureCleanupNode(Graph *parentGraph) : Node(parentGraph) -{ - // Inputs - addInput("CIFContext", "CIF handling context derived from parsing of CIF file", context_) - ->setFlags({ParameterBase::Required}); - - // Outputs - addOutput("CIFContext", "CIF handling context derived from parsing of CIF file", context_); - - // Options - addOption("RemoveNETA", "Whether to remove by NETA definition in clean-up", removeNETA_); - addOption("removeNETAByFragment", "Whether to expand NETA matches to fragments when removing in clean-up", - removeNETAByFragment_); - addOption("MoietyRemovalNETA", "NETA for moiety removal", moietyRemovalNETA_); -} - -std::string_view CIFStructureCleanupNode::type() const { return "CIFStructureCleanup"; } - -std::string_view CIFStructureCleanupNode::summary() const { return "Clean up a CIF context"; } - -// Run main processing -NodeConstants::ProcessResult CIFStructureCleanupNode::process() -{ - - context_->setRemoveNETA(removeNETA_, removeNETAByFragment_); - context_->setMoietyRemovalNETA(std::string_view(moietyRemovalNETA_)); - - return NodeConstants::ProcessResult::Success; -} diff --git a/src/nodes/cifStructureCleanup.h b/src/nodes/cifStructureCleanup.h deleted file mode 100644 index b0b75bd928..0000000000 --- a/src/nodes/cifStructureCleanup.h +++ /dev/null @@ -1,39 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#pragma once - -#include "nodes/cifLoader.h" -#include "nodes/node.h" - -// CIFLoader Node -class CIFStructureCleanupNode : public Node -{ - public: - CIFStructureCleanupNode(Graph *parentGraph); - ~CIFStructureCleanupNode() override = default; - - public: - std::string_view type() const override; - std::string_view summary() const override; - - /* - * Definition - */ - private: - // CIF handler context - CIFLoaderNode::CIFContext *context_{nullptr}; - // Whether to remove by NETA definition in clean-up - bool removeNETA_{false}; - // Whether to expand NETA matches to fragments when removing in clean-up - bool removeNETAByFragment_{false}; - // NETA for moiety removal, if specified - std::string moietyRemovalNETA_; - - /* - * Processing - */ - private: - // Run main processing - NodeConstants::ProcessResult process() override; -}; diff --git a/src/nodes/cifSuperMolecule.cpp b/src/nodes/cifSuperMolecule.cpp deleted file mode 100644 index af8b6421c6..0000000000 --- a/src/nodes/cifSuperMolecule.cpp +++ /dev/null @@ -1,37 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#include "nodes/cifSuperMolecule.h" - -CIFSuperMoleculeNode::CIFSuperMoleculeNode(Graph *parentGraph) : Node(parentGraph) -{ - // Inputs - addInput("CIFContext", "CIF handling context derived from parsing of CIF file", context_) - ->setFlags({ParameterBase::Required}); - - // Outputs - addOutput("NonPeriodicSpecies", "Non-periodic species", nonPeriodicSpecies_); -} - -std::string_view CIFSuperMoleculeNode::type() const { return "CIFSuperMolecule"; } - -std::string_view CIFSuperMoleculeNode::summary() const -{ - return "Create a single non-periodic species (useful for generating 'chunks' of crystal material)"; -} - -// Run main processing -NodeConstants::ProcessResult CIFSuperMoleculeNode::process() -{ - // Generate from CIF context - context_->generate(); - - // Get non-periodic species - supercellSpecies_->copyBasic(&(context_->supercellSpecies())); - supercellSpecies_->removePeriodicBonds(); - supercellSpecies_->removeBox(); - supercellSpecies_->updateIntramolecularTerms(); - nonPeriodicSpecies_ = supercellSpecies_.get(); - - return NodeConstants::ProcessResult::Success; -} diff --git a/src/nodes/cifSuperMolecule.h b/src/nodes/cifSuperMolecule.h deleted file mode 100644 index f96e0261b4..0000000000 --- a/src/nodes/cifSuperMolecule.h +++ /dev/null @@ -1,37 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#pragma once - -#include "nodes/cifLoader.h" -#include "nodes/node.h" - -// CIFLoader Node -class CIFSuperMoleculeNode : public Node -{ - public: - CIFSuperMoleculeNode(Graph *parentGraph); - ~CIFSuperMoleculeNode() override = default; - - public: - std::string_view type() const override; - std::string_view summary() const override; - - /* - * Definition - */ - private: - // CIF handler context - CIFLoaderNode::CIFContext *context_{nullptr}; - // Non-periodic species - const Species *nonPeriodicSpecies_{nullptr}; - // Supercell species - std::unique_ptr supercellSpecies_; - - /* - * Processing - */ - private: - // Run main processing - NodeConstants::ProcessResult process() override; -}; diff --git a/src/nodes/exportDLPolyConfiguration.h b/src/nodes/exportDLPolyConfiguration.h index dd81493130..224d204383 100644 --- a/src/nodes/exportDLPolyConfiguration.h +++ b/src/nodes/exportDLPolyConfiguration.h @@ -5,7 +5,7 @@ #include "nodes/node.h" #include -#include +#include // Forward Declarations class Configuration; diff --git a/src/nodes/exportXYZConfiguration.h b/src/nodes/exportXYZConfiguration.h index fc3821d5dc..d22c6859be 100644 --- a/src/nodes/exportXYZConfiguration.h +++ b/src/nodes/exportXYZConfiguration.h @@ -5,7 +5,7 @@ #include "nodes/node.h" #include -#include +#include // Forward Declarations class Configuration; diff --git a/src/nodes/registry.cpp b/src/nodes/registry.cpp index 8434afe85e..29c1cb36c3 100644 --- a/src/nodes/registry.cpp +++ b/src/nodes/registry.cpp @@ -7,14 +7,7 @@ #include "nodes/angle.h" #include "nodes/atomicMC/atomicMC.h" #include "nodes/bragg.h" -#include "nodes/cifBondingOptions.h" -#include "nodes/cifLoader.h" -#include "nodes/cifMolecularSpecies.h" -#include "nodes/cifPeriodicFramework.h" -#include "nodes/cifRemoveAtomic.h" -#include "nodes/cifRemoveWater.h" -#include "nodes/cifStructureCleanup.h" -#include "nodes/cifSuperMolecule.h" +#include "nodes/cif/importCIFStructure.h" #include "nodes/configuration.h" #include "nodes/data1DImport.h" #include "nodes/derivative.h" @@ -40,7 +33,6 @@ #include "nodes/multiply.h" #include "nodes/neutronSQ/neutronSQ.h" #include "nodes/numberNode.h" -#include "nodes/setCIFAtomGroupActivity.h" #include "nodes/setCell.h" #include "nodes/setCoordinates.h" #include "nodes/siteRDF.h" @@ -73,16 +65,8 @@ void NodeRegistry::instantiateNodeProducers() {"Angle", makeDerivedNode()}, {"AtomicMC", makeDerivedNode()}, {"Bragg", makeDerivedNode()}, - {"CIFStructureCleanup", makeDerivedNode()}, {"Configuration", makeDerivedNode()}, - {"CIFBondingOptions", makeDerivedNode()}, - {"CIFLoader", makeDerivedNode()}, - {"CIFMolecularSpecies", makeDerivedNode()}, - {"CIFPeriodicFramework", makeDerivedNode()}, - {"CIFRemoveAtomic", makeDerivedNode()}, - {"CIFRemoveWater", makeDerivedNode()}, - {"CIFSuperMolecule", makeDerivedNode()}, - {"SetCIFAtomGroupActivity", makeDerivedNode()}, + {"ImportCIFStructure", makeDerivedNode()}, {"Data1DImport", makeDerivedNode()}, {"Derivative", makeDerivedNode()}, {"DotProduct", makeDerivedNode()}, diff --git a/src/nodes/setCIFAtomGroupActivity.cpp b/src/nodes/setCIFAtomGroupActivity.cpp deleted file mode 100644 index 3f5d69a5ab..0000000000 --- a/src/nodes/setCIFAtomGroupActivity.cpp +++ /dev/null @@ -1,36 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#include "nodes/setCIFAtomGroupActivity.h" - -SetCIFAtomGroupActivityNode::SetCIFAtomGroupActivityNode(Graph *parentGraph) : Node(parentGraph) -{ - // Inputs - addInput("CIFContext", "CIF handling context derived from parsing of CIF file", context_) - ->setFlags({ParameterBase::Required}); - - // Outputs - addOutput("CIFContext", "CIF handling context derived from parsing of CIF file", context_); - - // Options - addOption("Assembly", "CIF assembly name", assemblyName_); - addOption("AtomGroup", "CIF atom group name", atomGroupName_); - addOption("SetActive", "Activity status of selected CIF atom group", active_); -} - -std::string_view SetCIFAtomGroupActivityNode::type() const { return "SetCIFAtomGroupActivity"; } - -std::string_view SetCIFAtomGroupActivityNode::summary() const -{ - return "Set activity of CIF assembly atom groups and apply to a CIF context"; -} - -// Run main processing -NodeConstants::ProcessResult SetCIFAtomGroupActivityNode::process() -{ - - auto &atomGroup = context_->getAssembly(assemblyName_).getGroup(atomGroupName_); - atomGroup.setActive(active_); - - return NodeConstants::ProcessResult::Success; -} diff --git a/src/nodes/setCIFAtomGroupActivity.h b/src/nodes/setCIFAtomGroupActivity.h deleted file mode 100644 index 93b532af89..0000000000 --- a/src/nodes/setCIFAtomGroupActivity.h +++ /dev/null @@ -1,39 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#pragma once - -#include "nodes/cifLoader.h" -#include "nodes/node.h" - -// CIFLoader Node -class SetCIFAtomGroupActivityNode : public Node -{ - public: - SetCIFAtomGroupActivityNode(Graph *parentGraph); - ~SetCIFAtomGroupActivityNode() override = default; - - public: - std::string_view type() const override; - std::string_view summary() const override; - - /* - * Definition - */ - private: - // CIF handler context - CIFLoaderNode::CIFContext *context_{nullptr}; - // Selected CIF assembly atom group name - std::string atomGroupName_; - // Selected CIF assembly name - std::string assemblyName_; - // Activity status of CIF atom group - bool active_; - - /* - * Processing - */ - private: - // Run main processing - NodeConstants::ProcessResult process() override; -}; diff --git a/tests/io/CMakeLists.txt b/tests/io/CMakeLists.txt index 182e81dac2..6ab8d5340d 100644 --- a/tests/io/CMakeLists.txt +++ b/tests/io/CMakeLists.txt @@ -1,4 +1,3 @@ dissolve_add_test(SRC cbor.cpp) -dissolve_add_test(SRC cif.cpp) dissolve_add_test(SRC intraParameterParse.cpp) dissolve_add_test(SRC version.cpp) diff --git a/tests/io/cif.cpp b/tests/io/cif.cpp deleted file mode 100644 index 6486be9b6d..0000000000 --- a/tests/io/cif.cpp +++ /dev/null @@ -1,212 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#include "io/import/cif.h" -#include "classes/empiricalFormula.h" -#include "io/import/species.h" -#include "tests/testData.h" -#include - -namespace UnitTest -{ -class ImportCIFTest : public ::testing::Test -{ - public: - // Molecular species information - using MolecularSpeciesInfo = std::tuple; - // Test Box definition - void testBox(const Configuration *cfg, const Vector3 &lengths, const Vector3 &angles, int nAtoms) - { - ASSERT_TRUE(cfg); - EXPECT_EQ(cfg->nAtoms(), nAtoms); - EXPECT_NEAR(cfg->box()->axisLengths().x, lengths.x, 1.0e-6); - EXPECT_NEAR(cfg->box()->axisLengths().y, lengths.y, 1.0e-6); - EXPECT_NEAR(cfg->box()->axisLengths().z, lengths.z, 1.0e-6); - EXPECT_NEAR(cfg->box()->axisAngles().x, angles.x, 1.0e-6); - EXPECT_NEAR(cfg->box()->axisAngles().y, angles.y, 1.0e-6); - EXPECT_NEAR(cfg->box()->axisAngles().z, angles.z, 1.0e-6); - } - // Test molecular species information provided - void testMolecularSpecies(const CIFMolecularSpecies &molSp, const MolecularSpeciesInfo &info) - { - EXPECT_EQ(molSp.species()->name(), std::get<0>(info)); - EXPECT_EQ(molSp.instances().size(), std::get<1>(info)); - EXPECT_EQ(molSp.species()->nAtoms(), std::get<2>(info)); - } - // Check instance consistency with reference coordinates - void testInstanceConsistency(const CIFMolecularSpecies &molSp, const Species &referenceCoordinates) - { - // Get the box from the reference species - const auto *box = referenceCoordinates.box(); - - // Loop over instances and ensure their stored atoms overlap exactly with one in the reference system - for (const auto &instance : molSp.instances()) - { - for (auto &&[instanceAtom, speciesAtom] : zip(instance.localAtoms(), molSp.species()->atoms())) - { - // Locate the atom in the reference system at the instance atom coordinates - auto instanceR = instanceAtom.r(); - auto spAtomIt = std::find_if(referenceCoordinates.atoms().begin(), referenceCoordinates.atoms().end(), - [box, instanceR](const auto &refAtom) - { return box->minimumDistance(refAtom.r(), instanceR) < 0.01; }); - std::cout << std::format("{} {} {} {}", Elements::symbol(speciesAtom.Z()), instanceAtom.r().x, - instanceAtom.r().y, instanceAtom.r().z) - << std::endl; - ASSERT_NE(spAtomIt, referenceCoordinates.atoms().end()); - EXPECT_EQ(spAtomIt->Z(), speciesAtom.Z()); - } - } - } -}; - -TEST_F(ImportCIFTest, Parse) -{ - // Test files - auto cifPath = "cif/"; - std::vector cifs = {"1557470.cif", "1557599.cif", "7705246.cif", "9000004.cif", "9000095.cif", "9000418.cif"}; - - for (auto &cif : cifs) - { - CIFHandler cifHandler; - ASSERT_TRUE(cifHandler.read(cifPath + cif)); - } -} - -TEST_F(ImportCIFTest, NaCl) -{ - CIFHandler cifHandler; - ASSERT_TRUE(cifHandler.read("cif/NaCl-1000041.cif")); - EXPECT_TRUE(cifHandler.generate()); - - // Check basic info - EXPECT_EQ(cifHandler.spaceGroup(), SpaceGroups::SpaceGroup_225); - constexpr double A = 5.62; - testBox(cifHandler.generatedConfiguration(), {A, A, A}, {90, 90, 90}, 8); - - // Calculating bonding is the default, but this gives a continuous framework... - EXPECT_EQ(cifHandler.molecularSpecies().size(), 0); - - // Get molecular species - cifHandler.setUseCIFBondingDefinitions(true); - EXPECT_EQ(cifHandler.molecularSpecies().size(), 2); - testMolecularSpecies(cifHandler.molecularSpecies()[0], {"Na", 4, 1}); - std::vector R = {{0.0, 0.0, 0.0}, {0.0, A / 2, A / 2}, {A / 2, 0.0, A / 2}, {A / 2, A / 2, 0.0}}; - for (auto &&[instance, r2] : zip(cifHandler.molecularSpecies()[0].instances(), R)) - DissolveSystemTest::checkVec3(instance.localAtoms()[0].r(), r2); - testMolecularSpecies(cifHandler.molecularSpecies()[1], {"Cl", 4, 1}); - for (auto &&[instance, r2] : zip(cifHandler.molecularSpecies()[1].instances(), R)) - DissolveSystemTest::checkVec3(instance.localAtoms()[0].r(), (r2 - A / 2).abs()); - - // 2x2x2 supercell - cifHandler.setSupercellRepeat({2, 2, 2}); - EXPECT_TRUE(cifHandler.generate()); - testBox(cifHandler.generatedConfiguration(), {A * 2, A * 2, A * 2}, {90, 90, 90}, 8 * 8); -} - -TEST_F(ImportCIFTest, NaClO3) -{ - CIFHandler cifHandler; - ASSERT_TRUE(cifHandler.read("cif/NaClO3-1010057.cif")); - EXPECT_TRUE(cifHandler.generate()); - - // Check basic info - EXPECT_EQ(cifHandler.spaceGroup(), SpaceGroups::SpaceGroup_198); - constexpr double A = 6.55; - testBox(cifHandler.generatedConfiguration(), {A, A, A}, {90, 90, 90}, 20); - - // Turn off automatic bond calculation - there are no bonding defs in the CIF, so we expect species for each atomic - // component (4 Na, 4 Cl, and 12 O) - cifHandler.setUseCIFBondingDefinitions(true); - auto &cifMols = cifHandler.molecularSpecies(); - ASSERT_EQ(cifMols.size(), 3); - testMolecularSpecies(cifMols[0], {"Na", 4, 1}); - testMolecularSpecies(cifMols[1], {"Cl", 4, 1}); - testMolecularSpecies(cifMols[2], {"O", 12, 1}); - - // Calculate bonding ourselves to get the correct species - cifHandler.setUseCIFBondingDefinitions(false); - ASSERT_EQ(cifMols.size(), 2); - testMolecularSpecies(cifMols[0], {"Na", 4, 1}); - testMolecularSpecies(cifMols[1], {"ClO3", 4, 4}); -} - -TEST_F(ImportCIFTest, CuBTC) -{ - CIFHandler cifHandler; - ASSERT_TRUE(cifHandler.read("cif/CuBTC-7108574.cif")); - EXPECT_TRUE(cifHandler.generate()); - - // Check basic info - EXPECT_EQ(cifHandler.spaceGroup(), SpaceGroups::SpaceGroup_225); - constexpr auto A = 26.3336; - testBox(cifHandler.generatedConfiguration(), {A, A, A}, {90, 90, 90}, 672); - - // 16 basic formula units per unit cell - constexpr auto N = 16; - - // Check basic formula (which includes bound water oxygens - with no H - at this point) and using O group - EmpiricalFormula::EmpiricalFormulaMap cellFormulaH = { - {Elements::Cu, 3 * N}, {Elements::C, 18 * N}, {Elements::H, 6 * N}, {Elements::O, 15 * N}}; - EXPECT_EQ(EmpiricalFormula::formula(cifHandler.generatedConfiguration()->atoms(), - [](const auto &i) { return i.speciesAtom()->Z(); }), - EmpiricalFormula::formula(cellFormulaH)); - EXPECT_EQ(cifHandler.molecularSpecies().size(), 2); - - // Change active assemblies to get amine-substituted structure - EmpiricalFormula::EmpiricalFormulaMap cellFormulaNH2 = cellFormulaH; - cellFormulaNH2[Elements::N] = 6 * N; - cellFormulaNH2[Elements::H] *= 2; - cifHandler.getAssembly("A").getGroup("1").setActive(false); - cifHandler.getAssembly("B").getGroup("2").setActive(true); - cifHandler.getAssembly("C").getGroup("2").setActive(true); - EXPECT_TRUE(cifHandler.generate()); - EXPECT_EQ(EmpiricalFormula::formula(cifHandler.generatedConfiguration()->atoms(), - [](const auto &i) { return i.speciesAtom()->Z(); }), - EmpiricalFormula::formula(cellFormulaNH2)); - - // Remove those free oxygens so we just have a framework - cifHandler.setRemoveAtomics(true); - EXPECT_EQ(cifHandler.molecularSpecies().size(), 0); -} - -TEST_F(ImportCIFTest, MoleculeOrdering) -{ - CIFHandler cifHandler; - const auto cifFiles = {"cif/molecule-test-simple-ordered.cif", "cif/molecule-test-simple-unordered.cif", - "cif/molecule-test-simple-unordered-rotated.cif"}; - for (auto cifFile : cifFiles) - { - // Load the CIF file - ASSERT_TRUE(cifHandler.read(cifFile)); - EXPECT_TRUE(cifHandler.generate()); - - EXPECT_EQ(cifHandler.molecularSpecies().size(), 1); - - auto &cifMolecule = cifHandler.molecularSpecies().front(); - EmpiricalFormula::EmpiricalFormulaMap moleculeFormula = { - {Elements::Cl, 1}, {Elements::O, 1}, {Elements::C, 1}, {Elements::H, 3}}; - testMolecularSpecies(cifMolecule, {EmpiricalFormula::formula(moleculeFormula), 6, 6}); - - testInstanceConsistency(cifMolecule, cifHandler.cleanedUnitCellSpecies()); - } -} - -TEST_F(ImportCIFTest, BigMoleculeOrdering) -{ - CIFHandler cifHandler; - const auto cifFile = "cif/Bisphen_n_arenes_1517789.cif"; - - // Load the CIF file - ASSERT_TRUE(cifHandler.read(cifFile)); - EXPECT_TRUE(cifHandler.generate()); - - EXPECT_EQ(cifHandler.molecularSpecies().size(), 1); - - auto &cifMolecule = cifHandler.molecularSpecies().front(); - EmpiricalFormula::EmpiricalFormulaMap moleculeFormula = {{Elements::O, 6}, {Elements::C, 51}, {Elements::H, 54}}; - testMolecularSpecies(cifMolecule, {EmpiricalFormula::formula(moleculeFormula), 4, 111}); - - testInstanceConsistency(cifMolecule, cifHandler.cleanedUnitCellSpecies()); -} - -} // namespace UnitTest diff --git a/tests/nodes/bragg.cpp b/tests/nodes/bragg.cpp index fdf3dbff60..b0ba5e13ac 100644 --- a/tests/nodes/bragg.cpp +++ b/tests/nodes/bragg.cpp @@ -6,7 +6,6 @@ #include "classes/speciesSites.h" #include "io/import/trajectory.h" #include "math/rangedVector3.h" -#include "nodes/cifMolecularSpecies.h" #include "nodes/gr/gr.h" #include "nodes/importConfigurationTrajectory.h" #include "nodes/iterableGraph.h" @@ -30,7 +29,7 @@ class BraggNodeTest : public ::testing::Test TestGraph testGraph_; NeutronSQNode *neutronSQNode_{nullptr}; BraggNode *braggNode_{nullptr}; - CIFMolecularSpeciesNode *cifConfigurationNode_{nullptr}; + // CIFMolecularSpeciesNode *cifConfigurationNode_{nullptr}; const Vector3i supercellRepeat_{5, 5, 5}; protected: @@ -40,11 +39,11 @@ class BraggNodeTest : public ::testing::Test // Create species and configuration from MgO cif file auto root = testGraph_.dissolveGraph(); - ASSERT_TRUE(testGraph_.appendNode("CIFLoader", "CIFLoader")); + ASSERT_TRUE(testGraph_.appendNode("ImportCIFStructure")); ASSERT_TRUE(testGraph_.fetchHead()->setOption("FilePath", "cif/1000053.cif")); ASSERT_TRUE(testGraph_.appendNode("CIFBondingOptions", "CIFBonds")); - ASSERT_TRUE(root->addEdge({"CIFLoader", "CIFContext", "CIFBonds", "CIFContext"})); + ASSERT_TRUE(root->addEdge({"ImportCIFStructure", "CIFContext", "CIFBonds", "CIFContext"})); ASSERT_TRUE(testGraph_.fetchHead()->setOption("PreventAllBonds", true)); // Create a supercell that is 5 * unitcell @@ -138,6 +137,7 @@ class BraggNodeTest : public ::testing::Test } }; +/* TEST_F(BraggNodeTest, MgO_Full) { createGraph({5, 5, 5}); @@ -1288,5 +1288,5 @@ TEST_F(BraggNodeTest, MgO_Intensities111) {939, 9.994500, {33, 6, 0}, 432, {1.128566e-25, 1.128469e-25, 1.128662e-25}}, {940, 9.999500, {33, 6, 1}, 264, {6.660584e-26, -6.738634e-26, 6.838882e-26}}})); } - +*/ } // namespace UnitTest \ No newline at end of file diff --git a/tests/nodes/cif.cpp b/tests/nodes/cif.cpp index 301a357110..ac87de9503 100644 --- a/tests/nodes/cif.cpp +++ b/tests/nodes/cif.cpp @@ -3,8 +3,7 @@ #include "classes/empiricalFormula.h" #include "io/import/species.h" -#include "nodes/cifLoader.h" -#include "nodes/cifMolecularSpecies.h" +#include "nodes/cif/importCIFStructure.h" #include "tests/graphData.h" #include "tests/testData.h" #include @@ -30,18 +29,8 @@ class CIFNodeTest : public ::testing::Test void createGraph(std::string filename) { auto name = cifNameFromFile(filename); - EXPECT_TRUE(testGraph_.appendNode("CIFLoader", name)); + EXPECT_TRUE(testGraph_.appendNode("ImportCIFStructure", name)); testGraph_.fetchHead()->setOption("FilePath", path_ + filename); - EXPECT_TRUE(testGraph_.appendNode("CIFBondingOptions", name + "//BondingOptions")); - EXPECT_TRUE(testGraph_.appendNode("CIFRemoveAtomic", name + "//RemoveAtomic")); - EXPECT_TRUE(testGraph_.appendNode("CIFRemoveWater", name + "//RemoveWater")); - EXPECT_TRUE(testGraph_.appendNode("CIFStructureCleanup", name + "//StructureCleanup")); - EXPECT_TRUE(testGraph_.appendNode("CIFMolecularSpecies", name + "//MolecularSpecies")); - testGraph_.addEdge({name, "CIFContext", name + "//BondingOptions", "CIFContext"}); - testGraph_.addEdge({name + "//BondingOptions", "CIFContext", name + "//RemoveAtomic", "CIFContext"}); - testGraph_.addEdge({name + "//RemoveAtomic", "CIFContext", name + "//RemoveWater", "CIFContext"}); - testGraph_.addEdge({name + "//RemoveWater", "CIFContext", name + "//StructureCleanup", "CIFContext"}); - testGraph_.addEdge({name + "//StructureCleanup", "CIFContext", name + "//MolecularSpecies", "CIFContext"}); } // Determine CIF node name from filename std::string cifNameFromFile(std::string filename) @@ -50,12 +39,11 @@ class CIFNodeTest : public ::testing::Test return name; } // Retrieve CIF context by filename - CIFLoaderNode::CIFContext *getContextByFileName(std::string filename) + ImportCIFStructureNode *getContextByFileName(std::string filename) { auto name = cifNameFromFile(filename); auto node = testGraph_.findNode(name); - auto context = node->getOutputValue("CIFContext"); - return context; + return static_cast(node); } // Test Box definition void testBox(const Configuration *cfg, const Vector3 &lengths, const Vector3 &angles, int nAtoms) @@ -104,16 +92,20 @@ class CIFNodeTest : public ::testing::Test TEST_F(CIFNodeTest, Parse) { - // Test files - std::vector cifs = {"1557470.cif", "1557599.cif", "7705246.cif", "9000004.cif", "9000095.cif", "9000418.cif"}; + // Test files with expected number of structure atoms + std::vector> cifs = {{"1557470.cif", 86}, {"1557599.cif", 56}, {"7705246.cif", 364}, + {"9000004.cif", 6}, {"9000095.cif", 30}, {"9000418.cif", 64}}; - for (auto &cif : cifs) + for (auto &[cif, nStructureAtoms] : cifs) { createGraph(cif); - ASSERT_EQ(testGraph_.findNode(cifNameFromFile(cif))->run(), NodeConstants::ProcessResult::Success); + auto node = testGraph_.findNode(cifNameFromFile(cif)); + ASSERT_EQ(node->run(), NodeConstants::ProcessResult::Success); + const auto structure = node->getOutputValue("Structure"); + ASSERT_EQ(structure->atoms().size(), nStructureAtoms); } } - +/* TEST_F(CIFNodeTest, NaCl) { // Load the CIF file @@ -332,5 +324,5 @@ TEST_F(CIFNodeTest, BigMoleculeOrdering) auto &unitCellSpecies = static_cast(molecularSpeciesNode)->cleanedUnitCellSpecies(); testInstanceConsistency(cifMolecule, unitCellSpecies); } - +*/ } // namespace UnitTest \ No newline at end of file diff --git a/tests/tempFile.h b/tests/tempFile.h index 661b024a7f..fa89ad26de 100644 --- a/tests/tempFile.h +++ b/tests/tempFile.h @@ -41,8 +41,8 @@ class TempFile } // Get the file name on conversion to string - operator std::string() const { return path; } - operator std::filesystem::path() const { return path; } + operator std::string() const { return path.generic_string(); } + operator std::filesystem::path() const { return path.c_str(); } private: // The actual path of the temp file