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Configurable box padding for orbital visualisation
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Useful for observing large / diffuse Rydberg states
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@md-5
md-5 committed Aug 23, 2018
1 parent 79d2216 commit dac38b4
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Showing 7 changed files with 68 additions and 19 deletions.
24 changes: 16 additions & 8 deletions libavogadro/src/extensions/surfaces/orbitalextension.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -396,7 +396,7 @@ namespace Avogadro
void OrbitalExtension::calculateOrbitalFromWidget(unsigned int orbital,
double resolution)
{
addCalculationToQueue(orbital, resolution, m_widget->isovalue(), 0);
addCalculationToQueue(orbital, resolution, m_widget->isovalue(), m_widget->boxPadding(), 0);
checkQueue();
}

Expand Down Expand Up @@ -437,6 +437,7 @@ namespace Avogadro
addCalculationToQueue(i+1, // orbital
OrbitalWidget::OrbitalQualityToDouble(m_widget->defaultQuality()),
m_widget->isovalue(),
m_widget->boxPadding(),
priority);

// Update priority. Stays the same when i = homo.
Expand All @@ -450,13 +451,15 @@ namespace Avogadro
void OrbitalExtension::addCalculationToQueue(unsigned int orbital,
double resolution,
double isovalue,
double boxPadding,
unsigned int priority)
{
// Create new queue entry
calcInfo newCalc;
newCalc.orbital = orbital;
newCalc.resolution = resolution;
newCalc.isovalue = isovalue;
newCalc.boxPadding = boxPadding;
newCalc.priority = priority;
newCalc.state = NotStarted;

Expand Down Expand Up @@ -506,7 +509,8 @@ namespace Avogadro
calcInfo *cI = &m_queue[i];
if (cI->state == Completed &&
cI->orbital == info->orbital &&
cI->resolution == info->resolution) {
cI->resolution == info->resolution &&
cI->boxPadding == info->boxPadding) {
info->cube = cI->cube;
qDebug() << "Reusing cube from calculation " << i << ":\n"
<< "\tOrbital " << cI->orbital << "\n"
Expand All @@ -519,7 +523,7 @@ namespace Avogadro
// Create new cube
Cube *cube = m_molecule->addCube();
info->cube = cube;
cube->setLimits(m_molecule, info->resolution, 2.5);
cube->setLimits(m_molecule, info->resolution, info->boxPadding);

if (m_qube) {
delete m_qube;
Expand Down Expand Up @@ -575,12 +579,14 @@ namespace Avogadro
if (cI->state == Completed &&
cI->orbital == info->orbital &&
cI->resolution == info->resolution &&
cI->isovalue == info->isovalue) {
cI->isovalue == info->isovalue &&
cI->boxPadding == info->boxPadding) {
info->posMesh = cI->posMesh;
qDebug() << "Reusing posMesh from calculation " << i << ":\n"
<< "\tOrbital " << cI->orbital << "\n"
<< "\tResolution " << cI->resolution << "\n"
<< "\tIsovalue " << cI->isovalue;
<< "\tIsovalue " << cI->isovalue << "\n"
<< "\tBoxpadding " << cI->boxPadding;
m_widget->nextProgressStage(info->orbital, 0, 100);
calculateNegMesh();
return;
Expand Down Expand Up @@ -642,12 +648,14 @@ namespace Avogadro
if (cI->state == Completed &&
cI->orbital == info->orbital &&
cI->resolution == info->resolution &&
cI->isovalue == info->isovalue) {
cI->isovalue == info->isovalue &&
cI->boxPadding == info->boxPadding) {
info->negMesh = cI->negMesh;
qDebug() << "Reusing posMesh from calculation " << i << ":\n"
qDebug() << "Reusing negMesh from calculation " << i << ":\n"
<< "\tOrbital " << cI->orbital << "\n"
<< "\tResolution " << cI->resolution << "\n"
<< "\tIsovalue " << cI->isovalue;
<< "\tIsovalue " << cI->isovalue << "\n"
<< "\tBoxpadding " << cI->boxPadding;
m_widget->nextProgressStage(info->orbital, 0, 100);
calculationComplete();
return;
Expand Down
3 changes: 3 additions & 0 deletions libavogadro/src/extensions/surfaces/orbitalextension.h
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Original file line number Diff line number Diff line change
Expand Up @@ -65,6 +65,7 @@ namespace Avogadro
unsigned int orbital;
double resolution;
double isovalue;
double boxPadding;
unsigned int priority;
CalcState state;
};
Expand Down Expand Up @@ -129,11 +130,13 @@ namespace Avogadro
* @param orbital Orbital number
* @param resolution Resolution of grid
* @param isoval Isovalue for surface
* @param boxPadding Box padding for orbital render cube
* @param priority Priority. Default = 0 (user requested)
*/
void addCalculationToQueue(unsigned int orbital,
double resolution,
double isoval,
double boxPadding,
unsigned int priority = 0);
/**
* Check that no calculations are currently running and start the
Expand Down
15 changes: 12 additions & 3 deletions libavogadro/src/extensions/surfaces/orbitalsettingsdialog.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,7 @@ namespace Avogadro {
: QDialog(parent, f),
m_quality(OrbitalWidget::OQ_Low),
m_isoval(0.02),
m_boxPadding(2.5),
m_HOMOFirst(false),
m_limit_precalc(true),
m_precalc_range(10)
Expand All @@ -44,8 +45,8 @@ namespace Avogadro {

connect(this, SIGNAL(calculateAll()),
parent, SIGNAL(calculateAll()));
connect(this, SIGNAL(defaultsUpdated(OrbitalWidget::OrbitalQuality, double, bool)),
parent, SLOT(setDefaults(OrbitalWidget::OrbitalQuality, double, bool)));
connect(this, SIGNAL(defaultsUpdated(OrbitalWidget::OrbitalQuality, double, double, bool)),
parent, SLOT(setDefaults(OrbitalWidget::OrbitalQuality, double, double, bool)));
connect(this, SIGNAL(precalcSettingsUpdated(bool,int)),
parent, SLOT(setPrecalcSettings(bool,int)));
}
Expand All @@ -66,6 +67,12 @@ namespace Avogadro {
m_isoval = i;
}

void OrbitalSettingsDialog::setBoxPadding(double i)
{
ui.spin_boxPadding->setValue(i);
m_boxPadding = i;
}

void OrbitalSettingsDialog::setHOMOFirst(bool HOMOFirst)
{
ui.cb_HOMOFirst->setChecked(HOMOFirst);
Expand All @@ -88,8 +95,9 @@ namespace Avogadro {
{
m_quality = OrbitalWidget::OrbitalQuality(ui.combo_quality->currentIndex());
m_isoval = ui.spin_isoval->value();
m_boxPadding = ui.spin_boxPadding->value();
m_HOMOFirst = ui.cb_HOMOFirst->isChecked();
emit defaultsUpdated(m_quality, m_isoval, m_HOMOFirst);
emit defaultsUpdated(m_quality, m_isoval, m_boxPadding, m_HOMOFirst);
}

void OrbitalSettingsDialog::updatePrecalcSettings()
Expand All @@ -110,6 +118,7 @@ namespace Avogadro {
{
setDefaultQuality(m_quality);
setIsoValue(m_isoval);
setBoxPadding(m_boxPadding);
setHOMOFirst(m_HOMOFirst);
hide();
}
Expand Down
4 changes: 3 additions & 1 deletion libavogadro/src/extensions/surfaces/orbitalsettingsdialog.h
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Original file line number Diff line number Diff line change
Expand Up @@ -44,6 +44,7 @@ namespace Avogadro
public slots:
void setDefaultQuality(OrbitalWidget::OrbitalQuality);
void setIsoValue(double);
void setBoxPadding(double);
void setHOMOFirst(bool);
void setLimitPrecalc(bool);
void setPrecalcRange(int);
Expand All @@ -55,7 +56,7 @@ namespace Avogadro
signals:
void calculateAll();
void defaultsUpdated(OrbitalWidget::OrbitalQuality quality, double isoval,
bool HOMOFirst);
double boxPadding, bool HOMOFirst);
void precalcSettingsUpdated(bool limit, int range);

private slots:
Expand All @@ -65,6 +66,7 @@ namespace Avogadro
Ui::OrbitalSettingsDialog ui;
OrbitalWidget::OrbitalQuality m_quality;
double m_isoval;
double m_boxPadding;
bool m_HOMOFirst;
bool m_limit_precalc;
int m_precalc_range;
Expand Down
30 changes: 25 additions & 5 deletions libavogadro/src/extensions/surfaces/orbitalsettingsdialog.ui
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@
<string>Dialog</string>
</property>
<layout class="QGridLayout" name="gridLayout">
<item row="6" column="0">
<item row="7" column="0">
<widget class="QPushButton" name="push_recalc">
<property name="text">
<string>&amp;Recalculate All</string>
Expand All @@ -41,6 +41,16 @@
</property>
</widget>
</item>
<item row="2" column="0">
<widget class="QLabel" name="label_4">
<property name="text">
<string>&amp;Box Padding:</string>
</property>
<property name="buddy">
<cstring>spin_boxPadding</cstring>
</property>
</widget>
</item>
<item row="0" column="1">
<widget class="QComboBox" name="combo_quality">
<item>
Expand Down Expand Up @@ -75,7 +85,17 @@
</property>
</widget>
</item>
<item row="5" column="0">
<item row="2" column="1">
<widget class="QDoubleSpinBox" name="spin_boxPadding">
<property name="decimals">
<number>1</number>
</property>
<property name="singleStep">
<double>0.1</double>
</property>
</widget>
</item>
<item row="6" column="0">
<spacer name="verticalSpacer">
<property name="orientation">
<enum>Qt::Vertical</enum>
Expand All @@ -88,14 +108,14 @@
</property>
</spacer>
</item>
<item row="2" column="0" colspan="2">
<item row="3" column="0" colspan="2">
<widget class="QCheckBox" name="cb_HOMOFirst">
<property name="text">
<string>Show occupied orbitals first</string>
</property>
</widget>
</item>
<item row="6" column="1">
<item row="7" column="1">
<widget class="QDialogButtonBox" name="buttonBox">
<property name="orientation">
<enum>Qt::Horizontal</enum>
Expand All @@ -105,7 +125,7 @@
</property>
</widget>
</item>
<item row="3" column="0" colspan="2">
<item row="4" column="0" colspan="2">
<layout class="QHBoxLayout" name="horizontalLayout">
<item>
<widget class="QCheckBox" name="cb_limit_precalc">
Expand Down
7 changes: 6 additions & 1 deletion libavogadro/src/extensions/surfaces/orbitalwidget.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -30,6 +30,7 @@ namespace Avogadro {
m_settings(0),
m_quality(OQ_Low),
m_isovalue(0.02),
m_boxPadding(2.5),
m_precalc_limit(true),
m_precalc_range(10),
m_tableModel(new OrbitalTableModel (this)),
Expand Down Expand Up @@ -64,6 +65,7 @@ namespace Avogadro {
settings.beginGroup("orbitals");
m_quality = OrbitalQuality( settings.value("defaultQuality", 0).toInt());
m_isovalue = settings.value("isoValue", 0.02).toDouble();
m_boxPadding = settings.value("boxPadding", 2.5).toDouble();
ui.combo_quality->setCurrentIndex( settings.value("selectedQuality", 0).toInt());
m_sortedTableModel->HOMOFirst( settings.value("HOMOFirst", false).toBool());
m_precalc_limit = settings.value("precalc/limit", true).toBool();
Expand All @@ -77,6 +79,7 @@ namespace Avogadro {
settings.beginGroup("orbitals");
settings.setValue("defaultQuality", m_quality);
settings.setValue("isoValue", m_isovalue);
settings.setValue("boxPadding", m_boxPadding);
settings.setValue("selectedQuality", ui.combo_quality->currentIndex());
settings.setValue("HOMOFirst", m_sortedTableModel->isHOMOFirst());
settings.setValue("precalc/limit", m_precalc_limit);
Expand All @@ -96,6 +99,7 @@ namespace Avogadro {
}
m_settings->setDefaultQuality(m_quality);
m_settings->setIsoValue(m_isovalue);
m_settings->setBoxPadding(m_boxPadding);
m_settings->setHOMOFirst(m_sortedTableModel->isHOMOFirst());
m_settings->setLimitPrecalc(m_precalc_limit);
m_settings->setPrecalcRange(m_precalc_range);
Expand Down Expand Up @@ -195,10 +199,11 @@ namespace Avogadro {
}
}

void OrbitalWidget::setDefaults(OrbitalQuality q, double i, bool HOMOFirst)
void OrbitalWidget::setDefaults(OrbitalQuality q, double i, double bp, bool HOMOFirst)
{
m_quality = q;
m_isovalue = i;
m_boxPadding = bp;
m_sortedTableModel->HOMOFirst(HOMOFirst);
m_sortedTableModel->sort(0, Qt::AscendingOrder);
}
Expand Down
4 changes: 3 additions & 1 deletion libavogadro/src/extensions/surfaces/orbitalwidget.h
View file
Original file line number Diff line number Diff line change
Expand Up @@ -52,6 +52,7 @@ namespace Avogadro {
virtual ~OrbitalWidget();

double isovalue() {return m_isovalue;};
double boxPadding() {return m_boxPadding;};
OrbitalQuality defaultQuality() {return m_quality;};

bool precalcLimit() {return m_precalc_limit;}
Expand All @@ -68,7 +69,7 @@ namespace Avogadro {
void fillTable(QList<Orbital> list);
void setQuality(OrbitalQuality q);
void selectOrbital(unsigned int orbital);
void setDefaults(OrbitalWidget::OrbitalQuality quality, double isovalue, bool HOMOFirst);
void setDefaults(OrbitalWidget::OrbitalQuality quality, double isovalue, double boxPadding, bool HOMOFirst);
void setPrecalcSettings(bool limit, int range);
void initializeProgress(int orbital, int min, int max, int stage, int totalStages);
void nextProgressStage(int orbital, int newmin, int newmax);
Expand All @@ -91,6 +92,7 @@ namespace Avogadro {
OrbitalSettingsDialog *m_settings;
OrbitalQuality m_quality;
double m_isovalue;
double m_boxPadding;

bool m_precalc_limit;
int m_precalc_range;
Expand Down

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