update LAMMPS GUI code with PR 3890 content

doc/src/Howto_lammps_gui.rst

@@ -65,12 +65,13 @@ Running LAMMPS
 ^^^^^^^^^^^^^^
 
 From within the LAMMPS GUI main window LAMMPS can be started either from
-the ``Run`` menu or by the hotkey `Ctrl-Enter` (`Command-Enter` on
-macOS).  LAMMPS is running in a separate thread, so the GUI will stay
-responsive and thus is capable to interact with the calculation and
-access its data.  It is important to note, that LAMMPS is using the
-contents of the input buffer for the run, **not** the file it was read
-from. If there are unsaved changes in the buffer, they *will* be used.
+the ``Run`` menu, by the hotkey `Ctrl-Enter` (`Command-Enter` on macOS),
+or by clicking on the green button in the status bar.  LAMMPS runs in a
+separate thread, so the GUI stays responsive and thus it is able to
+interact with the calculation and access its data.  It is important to
+note, that LAMMPS is using the contents of the input buffer for the run,
+**not** the file it was read from. If there are unsaved changes in the
+buffer, they *will* be used.
 
 .. image:: JPG/lammps-gui-running.png
    :align: center
@@ -82,48 +83,59 @@ contain the selected number of threads, if thread-parallel acceleration
 was selected in the ``Preferences`` dialog.  On the right side, a
 progress bar is shown that displays the estimated progress on the
 current :doc:`run command <run>`.  Additionally, two windows will open:
-the log window with the captured screen output and the chart window
-with a line graph created from the thermodynamic output of the run.
+the log window with the captured screen output and the chart window with
+a line graph created from the thermodynamic output of the run.
 
 The run can be stopped cleanly by using either the ``Stop LAMMPS`` entry
-in the ``Run`` menu or with the hotkey `Ctrl-/` (`Command-/` on macOS).
-This will cause that the running LAMMPS process will complete the
-current iteration and then stop. This is equivalent to the command
-`timer timeout 0 <timer>` and implemented by calling the
-:cpp:func:`lammps_force_timeout()` function of the LAMMPS C-library
-interface.
+in the ``Run`` menu, the hotkey `Ctrl-/` (`Command-/` on macOS), or
+clicking on the red button in the status bar.  This will cause that the
+running LAMMPS process will complete the current iteration and then
+stop.  This is equivalent to the command `timer timeout 0 <timer>` and
+implemented by calling the :cpp:func:`lammps_force_timeout()` function
+of the LAMMPS C-library interface.
 
 
 Viewing Snapshot Images
 ^^^^^^^^^^^^^^^^^^^^^^^
 
-By selecting the ``View Image`` entry in the ``Run`` menu or by hitting
-the `Ctrl-I` (`Command-I` on macOS) hotkey, LAMMPS gui will issue a
+By selecting the ``View Image`` entry in the ``Run`` menu, by hitting
+the `Ctrl-I` (`Command-I` on macOS) hotkey or by clicking on the
+"palette" button in the status bar, LAMMPS GUI will issue a
 :doc:`write_dump image <dump_image>` command and read the resulting
-snapshot image into an image viewer window.
+snapshot image into an image viewer window.  When possible, LAMMPS
+GUI will try to detect which elements the atoms correspond to (via
+their mass) and then colorize them accordingly. Otherwise just some
+predefined sequence of colors are assigned to different atom types.
 
 .. image:: JPG/lammps-gui-image.png
    :align: center
    :scale: 50%
 
-The image size, some default image quality settings, and some colors
-can be changed in the ``Preferences`` dialog window.  From the image
-viewer window further adjustments can be made: high-quality rendering,
-anti-aliasing, display of box or axes, zoom factor. The the image can
-be rotated horizontally and vertically and it is possible to only
-display the atoms within a predefined group (default is "all").
-After each change, the image is rendered again and the display updated.
+The default image size, some default image quality settings, the view
+style and some colors can be changed in the ``Preferences`` dialog
+window.  From the image viewer window further adjustments can be made:
+actual image size, high-quality rendering, anti-aliasing, view style,
+display of box or axes, zoom factor. The the image can be rotated
+horizontally and vertically and it is possible to only display the atoms
+within a predefined group (default is "all").  After each change, the
+image is rendered again and the display updated.  The small palette icon
+on the top left will be colored while LAMMPS is running to render the
+image and it will be grayed out again, when it is done.  When there are
+many items to show and high quality images with anti-aliasing are
+requested, re-rendering can take several seconds.  From the ``File``
+menu, the shown image can be saved to a file permanently or copied into
+the cut-n-paste buffer for pasting into another application.
 
 
 Editor Functions
 ^^^^^^^^^^^^^^^^
 
-The editor has the usual functionality that similar programs have: text
-selection via mouse or with cursor moves while holding the Shift key,
-Cut, Copy, Paste, Undo, Redo.  All of these editing functions are available
-via hotkeys.  When trying to exit the editor with a modified buffer, a
-dialog will pop up asking whether to cancel the quit, or don't save or
-save the buffer's contents to a file.
+The editor has most the usual functionality that similar programs have:
+text selection via mouse or with cursor moves while holding the Shift
+key, Cut, Copy, Paste, Undo, Redo.  All of these editing functions are
+available via hotkeys.  When trying to exit the editor with a modified
+buffer, a dialog will pop up asking whether to cancel the quit, or don't
+save or save the buffer's contents to a file.
 
 Context Specific Help
 ^^^^^^^^^^^^^^^^^^^^^
@@ -285,6 +297,13 @@ General Settings:
 - *Replace image window on new render:* when checked, an existing
   chart window will be replaced when a new snapshot image is requested,
   otherwise each command will create a new image window.
+- *Path to LAMMPS Shared Library File:* this options is only available
+  when LAMMPS GUI was compiled to load the LAMMPS library at run time
+  instead of being linked to it directly.  With the ``Browse..`` button
+  or by changing the text, a different shared library file with a
+  different compilation of LAMMPS with different settings or from a
+  different version can be loaded.  After this setting was changed,
+  LAMMPS GUI needs to be re-launched.
 - *Select Default Font:* Opens a font selection dialog where the type
   and size for the default font (used for everything but the editor and
   log) of the application can be set.
@@ -294,10 +313,10 @@ General Settings:
 Accelerators:
 ^^^^^^^^^^^^^
 
-This tab enables to select accelerator settings and is equivalent to
-using the `-suffix` and `-package` flags on the command line.  Only
-settings supported by the LAMMPS library and local hardware are
-available.  The `Number of threads` field allows to set the maximum
+This tab enables to select which accelerator package is used and is
+equivalent to using the `-suffix` and `-package` flags on the command
+line.  Only settings supported by the LAMMPS library and local hardware
+are available.  The `Number of threads` field allows to set the maximum
 number of threads for the accelerator packages that use threads.
 
 Snapshot Image:
@@ -306,14 +325,16 @@ Snapshot Image:
 This tab allows to set some defaults for the snapshot images displayed
 in the ``Image Viewer`` window, like its dimensions and the zoom factor
 applied.  The *Antialias* switch requests to render images with twice
-the number of pixels for width and height and then uses a bi-cubic
-scaling algorithm to rescale them back to the requested size.  This
-produces higher quality images with smoother edges at the expense of
-requiring more CPU time to render the image.  The *HQ Image mode* option
-turns on using a screen space ambient occlusion mode (SSAO) when
-rendering images.  This is also more time consuming, but produces a more
-'spatial' representation of the system.  Finally there are a couple of
-drop down lists to select the background and box color.
+the number of pixels for width and height and then smoothly scales the
+image back to the requested size.  This produces higher quality images
+with smoother edges at the expense of requiring more CPU time to render
+the image.  The *HQ Image mode* option turns on using a screen space
+ambient occlusion mode (SSAO) when rendering images.  This is also more
+time consuming, but produces a more 'spatial' representation of the
+system.  The *VDW Style* checkbox selects whether atoms are represented
+by space filling spheres when checked or by smaller spheres and stick.
+Finally there are a couple of drop down lists to select the background
+and box color.
 
 
 Hotkeys

tools/lammps-gui/CMakeLists.txt

@@ -1,6 +1,6 @@
 cmake_minimum_required(VERSION 3.16)
 
-project(lammps-gui VERSION 1.2.0 LANGUAGES CXX)
+project(lammps-gui VERSION 1.2.2 LANGUAGES CXX)
 
 set(CMAKE_AUTOUIC ON)
 set(CMAKE_AUTOMOC ON)

tools/lammps-gui/TODO.md

@@ -5,23 +5,17 @@ LAMMPS-GUI TODO list:
 - rewrite syntax highlighting to be line oriented instead of word oriented.
   handle first part of line based on regular expressions, then advance and only highlight strings and numbers.
   handle "&" continuation and multiline strings with """ like C style comments in Qt docs example
-- add CTRL-q hotkey to log windows so you can exit the entire application (add do you really want to? dialog to this)
 - add "syntax check" with enabled "-skiprun" flag
 - need to handle "label" and "jump" commands from within ?
-- switch processing of input to line based commands or?
 - switch input file editor to read-only while loop is running
+- triple quoted heredocs don't work with lammps_commands_string()
 
 # Long term ideas
-- add feature to LAMMPS (to the LAMMPS class) to store current file name and line number, update while reading/parsing
-  use in error messages
-  add API to library interface to query this info and use it for highlighting in text editor
-- rewrite entire application to either use QtCreator for everything or just build the App and its layout manually
+- rewrite entire application to build the App and its layout manually
 - port to Qt6
 - also a rewrite should establish consistent naming conventions. now we have a mix of LAMMPS style, Qt style, and others.
 - add option to attach a debugger to the running program (highly non-portable, need customization support in preferences)
 - write a "wizard" dialog that can be used for beginners to create an input file template for a few typical use scenarios
 - support single stepping, i.e. process input line by line (need to detect continuation chars!) with highlighting active line(s)
-- have command text input file in/above status bar where individual commands can be tested. have insert button to copy line into file at the current point
+- have command text input line in/above status bar where individual commands can be tested. have insert button to copy line into file at the current point
 - support text completion as done with lammps-shell
-- add a "python" mode, where instead of launching LAMMPS, python is loaded where the LAMMPS python module is made available.
-- support multiple tabs and multiple LAMMPS instances?

tools/lammps-gui/highlighter.cpp

@@ -183,7 +183,7 @@ Highlighter::Highlighter(QTextDocument *parent) : QSyntaxHighlighter(parent)
     }
 
     const QString number_keywords[] = {
-        QStringLiteral("(^|\\s+)[0-9]+"),                            // integer
+        QStringLiteral("(^|\\s+)[0-9:*]+"),                          // integer and integer ranges
         QStringLiteral("(^|\\s+)[0-9]+\\.[0-9]*[edED]?[-+]?[0-9]*"), // floating point 1
         QStringLiteral("(^|\\s+)[0-9]*\\.[0-9]+[edED]?[-+]?[0-9]*"), // floating point 2
         QStringLiteral("(^|\\s+)[0-9]+([edED][-+]?[0-9]+)?")         // floating point 3
@@ -207,10 +207,12 @@ Highlighter::Highlighter(QTextDocument *parent) : QSyntaxHighlighter(parent)
 
 void Highlighter::highlightBlock(const QString &text)
 {
+    // clang-format off
     auto style = QRegularExpression("^(fix|compute|dump|set)\\s+(\\w+)\\s+(\\S+)\\s+(\\S+)").match(text);
     auto force = QRegularExpression("^(atom_style|pair_style|bond_style|angle_style|dihedral_style|improper_style|kspace_style)\\s+(\\S+)").match(text);
     auto defs = QRegularExpression("^(group|variable)\\s+(\\S+)\\s+(\\S+)").match(text);
     auto undo = QRegularExpression("^(unfix|uncompute|undump)\\s+(\\w+)").match(text);
+    // clang-format on
     bool do_style = true;
     bool do_force = true;
     bool do_defs  = true;

tools/lammps-gui/imageviewer.cpp

@@ -22,6 +22,7 @@
 #include <QImage>
 #include <QImageReader>
 #include <QLabel>
+#include <QLineEdit>
 #include <QMenuBar>
 #include <QMessageBox>
 #include <QPalette>
@@ -31,11 +32,28 @@
 #include <QScrollArea>
 #include <QScrollBar>
 #include <QSettings>
+#include <QSpinBox>
 #include <QStatusBar>
 #include <QVBoxLayout>
 #include <QWheelEvent>
 #include <QWidgetAction>
 
+#include <cmath>
+
+extern "C" {
+#include "periodic_table.h"
+static int get_pte_from_mass(double mass)
+{
+    int idx = 0;
+    for (int i = 0; i < nr_pte_entries; ++i)
+        if (fabs(mass - pte_mass[i]) < 0.65) idx = i;
+    if ((mass > 0.0) && (mass < 2.2)) idx = 1;
+    // discriminate between Cobalt and Nickel. The loop will detect Nickel
+    if ((mass < 61.24) && (mass > 58.8133)) idx = 27;
+    return idx;
+}
+}
+
 static const QString blank(" ");
 
 ImageViewer::ImageViewer(const QString &fileName, LammpsWrapper *_lammps, QWidget *parent) :
@@ -58,23 +76,63 @@ ImageViewer::ImageViewer(const QString &fileName, LammpsWrapper *_lammps, QWidge
 
     QVBoxLayout *mainLayout = new QVBoxLayout;
 
+    QSettings settings;
+
+    vdwfactor = 0.4;
+    auto *renderstatus = new QLabel(QString());
+    auto pix           = QPixmap(":/emblem-photos.png");
+    renderstatus->setPixmap(pix.scaled(22, 22, Qt::KeepAspectRatio));
+    renderstatus->setEnabled(false);
+    renderstatus->setToolTip("Render status");
+    settings.beginGroup("snapshot");
+    auto *xval = new QSpinBox;
+    xval->setRange(100, 10000);
+    xval->setStepType(QAbstractSpinBox::AdaptiveDecimalStepType);
+    xval->setValue(settings.value("xsize", "800").toInt());
+    xval->setObjectName("xsize");
+    xval->setToolTip("Set rendered image width");
+    auto *yval = new QSpinBox;
+    yval->setRange(100, 10000);
+    yval->setStepType(QAbstractSpinBox::AdaptiveDecimalStepType);
+    yval->setValue(settings.value("ysize", "600").toInt());
+    yval->setObjectName("ysize");
+    yval->setToolTip("Set rendered image height");
+    settings.endGroup();
+    connect(xval, &QAbstractSpinBox::editingFinished, this, &ImageViewer::edit_size);
+    connect(yval, &QAbstractSpinBox::editingFinished, this, &ImageViewer::edit_size);
+
     auto *dossao = new QPushButton(QIcon(":/hd-img.png"), "");
     dossao->setCheckable(true);
+    dossao->setToolTip("Toggle SSAO rendering");
     auto *doanti = new QPushButton(QIcon(":/antialias.png"), "");
     doanti->setCheckable(true);
+    doanti->setToolTip("Toggle anti-aliasing");
+    auto *dovdw = new QPushButton(QIcon(":/vdw-style.png"), "");
+    dovdw->setCheckable(true);
+    dovdw->setToolTip("Toggle VDW style representation");
     auto *dobox = new QPushButton(QIcon(":/system-box.png"), "");
     dobox->setCheckable(true);
+    dobox->setToolTip("Toggle displaying box");
     auto *doaxes = new QPushButton(QIcon(":/axes-img.png"), "");
     doaxes->setCheckable(true);
-    auto *zoomin   = new QPushButton(QIcon(":/gtk-zoom-in.png"), "");
-    auto *zoomout  = new QPushButton(QIcon(":/gtk-zoom-out.png"), "");
-    auto *rotleft  = new QPushButton(QIcon(":/object-rotate-left.png"), "");
+    doaxes->setToolTip("Toggle displaying axes");
+    auto *zoomin = new QPushButton(QIcon(":/gtk-zoom-in.png"), "");
+    zoomin->setToolTip("Zoom in by 10 percent");
+    auto *zoomout = new QPushButton(QIcon(":/gtk-zoom-out.png"), "");
+    zoomout->setToolTip("Zoom out by 10 percent");
+    auto *rotleft = new QPushButton(QIcon(":/object-rotate-left.png"), "");
+    rotleft->setToolTip("Rotate left by 15 degrees");
     auto *rotright = new QPushButton(QIcon(":/object-rotate-right.png"), "");
-    auto *rotup    = new QPushButton(QIcon(":/gtk-go-up.png"), "");
-    auto *rotdown  = new QPushButton(QIcon(":/gtk-go-down.png"), "");
-    auto *reset    = new QPushButton(QIcon(":/gtk-zoom-fit.png"), "");
-    auto *combo    = new QComboBox;
+    rotright->setToolTip("Rotate right by 15 degrees");
+    auto *rotup = new QPushButton(QIcon(":/gtk-go-up.png"), "");
+    rotup->setToolTip("Rotate up by 15 degrees");
+    auto *rotdown = new QPushButton(QIcon(":/gtk-go-down.png"), "");
+    rotdown->setToolTip("Rotate down by 15 degrees");
+    auto *reset = new QPushButton(QIcon(":/gtk-zoom-fit.png"), "");
+    reset->setToolTip("Reset view to defaults");
+    auto *combo = new QComboBox;
     combo->setObjectName("group");
+    combo->setToolTip("Select group to display");
     int ngroup = lammps->id_count("group");
     char gname[64];
     for (int i = 0; i < ngroup; ++i) {
@@ -84,8 +142,14 @@ ImageViewer::ImageViewer(const QString &fileName, LammpsWrapper *_lammps, QWidge
 
     QHBoxLayout *menuLayout = new QHBoxLayout;
     menuLayout->addWidget(menuBar);
+    menuLayout->addWidget(renderstatus);
+    menuLayout->addWidget(new QLabel(" Width: "));
+    menuLayout->addWidget(xval);
+    menuLayout->addWidget(new QLabel(" Height: "));
+    menuLayout->addWidget(yval);
     menuLayout->addWidget(dossao);
     menuLayout->addWidget(doanti);
+    menuLayout->addWidget(dovdw);
     menuLayout->addWidget(dobox);
     menuLayout->addWidget(doaxes);
     menuLayout->addWidget(zoomin);
@@ -100,6 +164,7 @@ ImageViewer::ImageViewer(const QString &fileName, LammpsWrapper *_lammps, QWidge
 
     connect(dossao, &QPushButton::released, this, &ImageViewer::toggle_ssao);
     connect(doanti, &QPushButton::released, this, &ImageViewer::toggle_anti);
+    connect(dovdw, &QPushButton::released, this, &ImageViewer::toggle_vdw);
     connect(dobox, &QPushButton::released, this, &ImageViewer::toggle_box);
     connect(doaxes, &QPushButton::released, this, &ImageViewer::toggle_axes);
     connect(zoomin, &QPushButton::released, this, &ImageViewer::do_zoom_in);
@@ -119,6 +184,7 @@ ImageViewer::ImageViewer(const QString &fileName, LammpsWrapper *_lammps, QWidge
 
     reset_view();
     dobox->setChecked(showbox);
+    dovdw->setChecked(vdwfactor > 1.0);
     doaxes->setChecked(showaxes);
     dossao->setChecked(usessao);
     doanti->setChecked(antialias);
@@ -137,9 +203,12 @@ void ImageViewer::reset_view()
 {
     QSettings settings;
     settings.beginGroup("snapshot");
+    xsize     = settings.value("xsize", "800").toInt();
+    ysize     = settings.value("ysize", "600").toInt();
     zoom      = settings.value("zoom", 1.0).toDouble();
     hrot      = settings.value("hrot", 60).toInt();
     vrot      = settings.value("vrot", 30).toInt();
+    vdwfactor = settings.value("vdwstyle", false).toBool() ? 1.6 : 0.5;
     showbox   = settings.value("box", true).toBool();
     showaxes  = settings.value("axes", false).toBool();
     usessao   = settings.value("ssao", false).toBool();
@@ -151,18 +220,37 @@ void ImageViewer::reset_view()
     if (lo) {
         // grab layout manager for the top bar
         lo = lo->itemAt(0)->layout();
-        // grab the first 4 buttons after the menu bar
-        auto *button = qobject_cast<QPushButton *>(lo->itemAt(1)->widget());
+
+        auto *field = qobject_cast<QSpinBox *>(lo->itemAt(3)->widget());
+        field->setValue(xsize);
+        field = qobject_cast<QSpinBox *>(lo->itemAt(5)->widget());
+        field->setValue(ysize);
+
+        auto *button = qobject_cast<QPushButton *>(lo->itemAt(6)->widget());
         button->setChecked(usessao);
-        button = qobject_cast<QPushButton *>(lo->itemAt(2)->widget());
+        button = qobject_cast<QPushButton *>(lo->itemAt(7)->widget());
         button->setChecked(antialias);
-        button = qobject_cast<QPushButton *>(lo->itemAt(3)->widget());
+        button = qobject_cast<QPushButton *>(lo->itemAt(8)->widget());
+        button->setChecked(vdwfactor > 1.0);
+        button = qobject_cast<QPushButton *>(lo->itemAt(9)->widget());
         button->setChecked(showbox);
-        button = qobject_cast<QPushButton *>(lo->itemAt(4)->widget());
+        button = qobject_cast<QPushButton *>(lo->itemAt(10)->widget());
         button->setChecked(showaxes);
         // grab the last entry -> group selector
         auto *cb = qobject_cast<QComboBox *>(lo->itemAt(lo->count() - 1)->widget());
         cb->setCurrentText("all");
+        this->repaint();
+    }
+    createImage();
+}
+
+void ImageViewer::edit_size()
+{
+    QSpinBox *field = qobject_cast<QSpinBox *>(sender());
+    if (field->objectName() == "xsize") {
+        xsize = field->value();
+    } else if (field->objectName() == "ysize") {
+        ysize = field->value();
     }
     createImage();
 }
@@ -183,6 +271,17 @@ void ImageViewer::toggle_anti()
     createImage();
 }
 
+void ImageViewer::toggle_vdw()
+{
+    QPushButton *button = qobject_cast<QPushButton *>(sender());
+    if (vdwfactor > 1.0)
+        vdwfactor = 0.4;
+    else
+        vdwfactor = 1.6;
+    button->setChecked(vdwfactor > 1.0);
+    createImage();
+}
+
 void ImageViewer::toggle_box()
 {
     QPushButton *button = qobject_cast<QPushButton *>(sender());
@@ -215,28 +314,28 @@ void ImageViewer::do_zoom_out()
 
 void ImageViewer::do_rot_left()
 {
-    vrot -= 15;
+    vrot -= 10;
     if (vrot < -180) vrot += 360;
     createImage();
 }
 
 void ImageViewer::do_rot_right()
 {
-    vrot += 15;
+    vrot += 10;
     if (vrot > 180) vrot -= 360;
     createImage();
 }
 
 void ImageViewer::do_rot_down()
 {
-    hrot -= 15;
+    hrot -= 10;
     if (hrot < 0) hrot += 360;
     createImage();
 }
 
 void ImageViewer::do_rot_up()
 {
-    hrot += 15;
+    hrot += 10;
     if (hrot > 360) hrot -= 360;
     createImage();
 }
@@ -250,6 +349,11 @@ void ImageViewer::change_group(int idx)
 
 void ImageViewer::createImage()
 {
+    auto *lo = layout();
+    if (lo) lo = lo->itemAt(0)->layout();
+    if (lo) qobject_cast<QLabel *>(lo->itemAt(1)->widget())->setEnabled(true);
+    this->repaint();
+
     QSettings settings;
     QString dumpcmd = QString("write_dump ") + group + " image ";
     QDir dumpdir(QDir::tempPath());
@@ -257,16 +361,36 @@ void ImageViewer::createImage()
     dumpcmd += dumpfile.fileName();
 
     settings.beginGroup("snapshot");
-    int aa    = antialias ? 2 : 1;
-    int xsize = settings.value("xsize", 800).toInt() * aa;
-    int ysize = settings.value("ysize", 600).toInt() * aa;
-    int hhrot = (hrot > 180) ? 360 - hrot : hrot;
+    int aa       = antialias ? 2 : 1;
+    int tmpxsize = xsize * aa;
+    int tmpysize = ysize * aa;
+    int hhrot    = (hrot > 180) ? 360 - hrot : hrot;
 
-    dumpcmd += blank + settings.value("color", "type").toString();
+    // determine elements from masses and set their covalent radii
+    int ntypes       = lammps->extract_setting("ntypes");
+    int nbondtypes   = lammps->extract_setting("nbondtypes");
+    double *masses   = (double *)lammps->extract_atom("mass");
+    QString units    = (const char *)lammps->extract_global("units");
+    QString elements = "element ";
+    QString adiams;
+    if ((units == "real") || (units == "metal")) {
+        for (int i = 1; i <= ntypes; ++i) {
+            int idx = get_pte_from_mass(masses[i]);
+            elements += QString(pte_label[idx]) + blank;
+            adiams += QString("adiam %1 %2 ").arg(i).arg(vdwfactor * pte_vdw_radius[idx]);
+        }
+    }
+
+    if (!adiams.isEmpty())
+        dumpcmd += blank + "element";
+    else
+        dumpcmd += blank + settings.value("color", "type").toString();
     dumpcmd += blank + settings.value("diameter", "type").toString();
-    dumpcmd += QString(" size ") + QString::number(xsize) + blank + QString::number(ysize);
+    dumpcmd += QString(" size ") + QString::number(tmpxsize) + blank + QString::number(tmpysize);
     dumpcmd += QString(" zoom ") + QString::number(zoom);
-    lammps->command(dumpcmd.toLocal8Bit());
+    dumpcmd += " shiny 0.5 ";
+    if (nbondtypes > 0) dumpcmd += " bond atom 0.4 ";
+
     if (lammps->extract_setting("dimension") == 3) {
         dumpcmd += QString(" view ") + QString::number(hhrot) + blank + QString::number(vrot);
     }
@@ -277,12 +401,13 @@ void ImageViewer::createImage()
         dumpcmd += QString(" box no 0.0");
 
     if (showaxes)
-        dumpcmd += QString(" axes yes 0.2 0.025");
+        dumpcmd += QString(" axes yes 0.5 0.025");
     else
         dumpcmd += QString(" axes no 0.0 0.0");
 
     dumpcmd += " modify boxcolor " + settings.value("boxcolor", "yellow").toString();
     dumpcmd += " backcolor " + settings.value("background", "black").toString();
+    if (!adiams.isEmpty()) dumpcmd += blank + elements + blank + adiams + blank;
     settings.endGroup();
 
     lammps->command(dumpcmd.toLocal8Bit());
@@ -299,13 +424,12 @@ void ImageViewer::createImage()
     }
     dumpfile.remove();
 
-    settings.beginGroup("snapshot");
-    xsize = settings.value("xsize", 800).toInt();
-    ysize = settings.value("ysize", 600).toInt();
-    settings.endGroup();
     // scale back to achieve antialiasing
     image = newImage.scaled(xsize, ysize, Qt::IgnoreAspectRatio, Qt::SmoothTransformation);
     imageLabel->setPixmap(QPixmap::fromImage(image));
+    imageLabel->adjustSize();
+    if (lo) qobject_cast<QLabel *>(lo->itemAt(1)->widget())->setEnabled(false);
+    this->repaint();
 }
 
 void ImageViewer::saveAs()

tools/lammps-gui/imageviewer.h

@@ -45,9 +45,11 @@ private slots:
     void normalSize();
     void fitToWindow();
 
+    void edit_size();
     void reset_view();
     void toggle_ssao();
     void toggle_anti();
+    void toggle_vdw();
     void toggle_box();
     void toggle_axes();
     void do_zoom_in();
@@ -86,8 +88,9 @@ private:
     LammpsWrapper *lammps;
     QString group;
     QString filename;
+    int xsize, ysize;
     int hrot, vrot;
-    double zoom;
+    double zoom, vdwfactor;
     bool showbox, showaxes, antialias, usessao;
 };
 #endif

tools/lammps-gui/lammpsgui.cpp

@@ -34,6 +34,7 @@
 #include <QPlainTextEdit>
 #include <QProcess>
 #include <QProgressBar>
+#include <QPushButton>
 #include <QSettings>
 #include <QShortcut>
 #include <QStatusBar>
@@ -241,7 +242,22 @@ LammpsGui::LammpsGui(QWidget *parent, const char *filename) :
     auto pix     = QPixmap(":/lammps-icon-128x128.png");
     lammpsstatus->setPixmap(pix.scaled(22, 22, Qt::KeepAspectRatio));
     ui->statusbar->addWidget(lammpsstatus);
+    lammpsstatus->setToolTip("LAMMPS instance is active");
     lammpsstatus->hide();
+
+    auto *lammpsrun   = new QPushButton(QIcon(":/system-run.png"), "");
+    auto *lammpsstop  = new QPushButton(QIcon(":/process-stop.png"), "");
+    auto *lammpsimage = new QPushButton(QIcon(":/emblem-photos.png"), "");
+    lammpsrun->setToolTip("Run LAMMPS on input");
+    lammpsstop->setToolTip("Stop LAMMPS");
+    lammpsimage->setToolTip("Create snapshot image");
+    ui->statusbar->addWidget(lammpsrun);
+    ui->statusbar->addWidget(lammpsstop);
+    ui->statusbar->addWidget(lammpsimage);
+    connect(lammpsrun, &QPushButton::released, this, &LammpsGui::run_buffer);
+    connect(lammpsstop, &QPushButton::released, this, &LammpsGui::stop_run);
+    connect(lammpsimage, &QPushButton::released, this, &LammpsGui::render_image);
+
     status = new QLabel("Ready.");
     status->setFixedWidth(300);
     ui->statusbar->addWidget(status);
@@ -280,6 +296,10 @@ void LammpsGui::new_document()
     current_file.clear();
     ui->textEdit->document()->setPlainText(QString());
 
+    if (lammps.is_running()) {
+        stop_run();
+        runner->wait();
+    }
     lammps.close();
     lammpsstatus->hide();
     setWindowTitle(QString("LAMMPS-GUI - *unknown*"));
@@ -549,6 +569,10 @@ void LammpsGui::save_as()
 
 void LammpsGui::quit()
 {
+    if (lammps.is_running()) {
+        stop_run();
+        runner->wait();
+    }
     lammps.close();
     lammpsstatus->hide();
     lammps.finalize();
@@ -806,7 +830,7 @@ void LammpsGui::run_buffer()
     char *input = mystrdup(ui->textEdit->toPlainText().toStdString() + "\n");
     is_running  = true;
 
-    LammpsRunner *runner = new LammpsRunner(this);
+    runner = new LammpsRunner(this);
     runner->setup_run(&lammps, input);
     connect(runner, &LammpsRunner::resultReady, this, &LammpsGui::run_done);
     connect(runner, &LammpsRunner::finished, runner, &QObject::deleteLater);
@@ -1035,6 +1059,11 @@ void LammpsGui::edit_variables()
     SetVariables vars(newvars);
     if (vars.exec() == QDialog::Accepted) {
         variables = newvars;
+        if (lammps.is_running()) {
+            stop_run();
+            runner->wait();
+            delete runner;
+        }
         lammps.close();
         lammpsstatus->hide();
     }
@@ -1057,6 +1086,11 @@ void LammpsGui::preferences()
             (oldthreads != settings.value("nthreads", 1).toInt()) ||
             (oldecho != settings.value("echo", 0).toInt()) ||
             (oldcite != settings.value("cite", 0).toInt())) {
+            if (lammps.is_running()) {
+                stop_run();
+                runner->wait();
+                delete runner;
+            }
             lammps.close();
             lammpsstatus->hide();
         }

tools/lammps-gui/lammpsgui.h

@@ -26,6 +26,7 @@
 // forward declarations
 
 class GeneralTab;
+class LammpsRunner;
 
 QT_BEGIN_NAMESPACE
 namespace Ui {
@@ -114,6 +115,7 @@ private:
     QList<QPair<QString, QString>> variables;
 
     LammpsWrapper lammps;
+    LammpsRunner *runner;
     std::string plugin_path;
     bool is_running;
     std::vector<char *> lammps_args;

tools/lammps-gui/lammpsgui.qrc

@@ -33,7 +33,7 @@
         <file>help-about.png</file>
         <file>emblem-photos.png</file>
         <file>process-stop.png</file>
-        <file>emblem-default.png</file>
+        <file>system-run.png</file>
         <file>window-close.png</file>
         <file>application-plot.png</file>
         <file>application-calc.png</file>
@@ -43,5 +43,6 @@
         <file>antialias.png</file>
         <file>ovito.png</file>
         <file>vmd.png</file>
+        <file>vdw-style.png</file>
     </qresource>
 </RCC>

tools/lammps-gui/lammpsgui.ui

@@ -212,7 +212,7 @@
   </action>
   <action name="actionRun_Buffer">
    <property name="icon">
-    <iconset theme=":/emblem-default.png"/>
+    <iconset theme=":/system-run.png"/>
    </property>
    <property name="text">
     <string>&amp;Run LAMMPS</string>

tools/lammps-gui/lammpswrapper.cpp

@@ -45,6 +45,32 @@ int LammpsWrapper::extract_setting(const char *keyword)
     return val;
 }
 
+void *LammpsWrapper::extract_global(const char *keyword)
+{
+    void *val = nullptr;
+    if (lammps_handle) {
+#if defined(LAMMPS_GUI_USE_PLUGIN)
+        val = ((liblammpsplugin_t *)plugin_handle)->extract_global(lammps_handle, keyword);
+#else
+        val = lammps_extract_global(lammps_handle, keyword);
+#endif
+    }
+    return val;
+}
+
+void *LammpsWrapper::extract_atom(const char *keyword)
+{
+    void *val = nullptr;
+    if (lammps_handle) {
+#if defined(LAMMPS_GUI_USE_PLUGIN)
+        val = ((liblammpsplugin_t *)plugin_handle)->extract_atom(lammps_handle, keyword);
+#else
+        val = lammps_extract_atom(lammps_handle, keyword);
+#endif
+    }
+    return val;
+}
+
 int LammpsWrapper::id_count(const char *keyword)
 {
     int val = 0;

tools/lammps-gui/lammpswrapper.h

@@ -29,15 +29,21 @@ public:
     void force_timeout();
 
     int extract_setting(const char *keyword);
+    void *extract_global(const char *keyword);
+    void *extract_atom(const char *keyword);
+
     int id_count(const char *idtype);
     int id_name(const char *idtype, int idx, char *buf, int buflen);
 
     double get_thermo(const char *keyword);
     void *last_thermo(const char *keyword, int idx);
+
     bool is_open() const { return lammps_handle != nullptr; }
     bool is_running();
+
     bool has_error() const;
     int get_last_error_message(char *errorbuf, int buflen);
+
     bool config_accelerator(const char *package, const char *category, const char *setting) const;
     bool config_has_package(const char *pkg) const;
     bool has_gpu_device() const;

tools/lammps-gui/periodic_table.h

@@ -0,0 +1,205 @@
+/***************************************************************************
+ * RCS INFORMATION:
+ *
+ *      $RCSfile: periodic_table.h,v $
+ *      $Author: johns $       $Locker:  $             $State: Exp $
+ *      $Revision: 1.12 $       $Date: 2009/01/21 17:45:41 $
+ *
+ ***************************************************************************/
+
+/*
+ * periodic table of elements and helper functions to convert
+ * ordinal numbers to labels and back.
+ * all tables and functions are declared static, so that it
+ * can be safely included by all plugins that may need it.
+ *
+ * 2002-2009 akohlmey@cmm.chem.upenn.edu, vmd@ks.uiuc.edu
+ */
+
+#include <string.h>
+#include <ctype.h>
+
+/* periodic table of elements for translation of ordinal to atom type */
+static const char *pte_label[] = {
+    "X",  "H",  "He", "Li", "Be", "B",  "C",  "N",  "O",  "F",  "Ne",
+    "Na", "Mg", "Al", "Si", "P" , "S",  "Cl", "Ar", "K",  "Ca", "Sc",
+    "Ti", "V",  "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn", "Ga", "Ge",
+    "As", "Se", "Br", "Kr", "Rb", "Sr", "Y",  "Zr", "Nb", "Mo", "Tc",
+    "Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn", "Sb", "Te", "I",  "Xe",
+    "Cs", "Ba", "La", "Ce", "Pr", "Nd", "Pm", "Sm", "Eu", "Gd", "Tb",
+    "Dy", "Ho", "Er", "Tm", "Yb", "Lu", "Hf", "Ta", "W",  "Re", "Os",
+    "Ir", "Pt", "Au", "Hg", "Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr",
+    "Ra", "Ac", "Th", "Pa", "U",  "Np", "Pu", "Am", "Cm", "Bk", "Cf",
+    "Es", "Fm", "Md", "No", "Lr", "Rf", "Db", "Sg", "Bh", "Hs", "Mt",
+    "Ds", "Rg"
+};
+static const int nr_pte_entries = sizeof(pte_label) / sizeof(char *);
+
+/* corresponding table of masses. */
+static const double pte_mass[] = {
+    /* X  */ 0.00000, 1.00794, 4.00260, 6.941, 9.012182, 10.811,
+    /* C  */ 12.0107, 14.0067, 15.9994, 18.9984032, 20.1797,
+    /* Na */ 22.989770, 24.3050, 26.981538, 28.0855, 30.973761,
+    /* S  */ 32.065, 35.453, 39.948, 39.0983, 40.078, 44.955910,
+    /* Ti */ 47.867, 50.9415, 51.9961, 54.938049, 55.845, 58.9332,
+    /* Ni */ 58.6934, 63.546, 65.409, 69.723, 72.64, 74.92160,
+    /* Se */ 78.96, 79.904, 83.798, 85.4678, 87.62, 88.90585,
+    /* Zr */ 91.224, 92.90638, 95.94, 98.0, 101.07, 102.90550,
+    /* Pd */ 106.42, 107.8682, 112.411, 114.818, 118.710, 121.760,
+    /* Te */ 127.60, 126.90447, 131.293, 132.90545, 137.327,
+    /* La */ 138.9055, 140.116, 140.90765, 144.24, 145.0, 150.36,
+    /* Eu */ 151.964, 157.25, 158.92534, 162.500, 164.93032,
+    /* Er */ 167.259, 168.93421, 173.04, 174.967, 178.49, 180.9479,
+    /* W  */ 183.84, 186.207, 190.23, 192.217, 195.078, 196.96655,
+    /* Hg */ 200.59, 204.3833, 207.2, 208.98038, 209.0, 210.0, 222.0,
+    /* Fr */ 223.0, 226.0, 227.0, 232.0381, 231.03588, 238.02891,
+    /* Np */ 237.0, 244.0, 243.0, 247.0, 247.0, 251.0, 252.0, 257.0,
+    /* Md */ 258.0, 259.0, 262.0, 261.0, 262.0, 266.0, 264.0, 269.0,
+    /* Mt */ 268.0, 271.0, 272.0
+};
+
+/*
+ * corresponding table of VDW radii.
+ * van der Waals radii are taken from A. Bondi,
+ * J. Phys. Chem., 68, 441 - 452, 1964,
+ * except the value for H, which is taken from R.S. Rowland & R. Taylor,
+ * J.Phys.Chem., 100, 7384 - 7391, 1996. Radii that are not available in
+ * either of these publications have RvdW = 2.00 \AA
+ * The radii for Ions (Na, K, Cl, Ca, Mg, and Cs are based on the CHARMM27
+ * Rmin/2 parameters for (SOD, POT, CLA, CAL, MG, CES) by default.
+ */
+static const double pte_vdw_radius[] = {
+    /* X  */ 1.5, 1.2, 1.4, 1.82, 2.0, 2.0,
+    /* C  */ 1.7, 1.55, 1.52, 1.47, 1.54,
+    /* Na */ 1.36, 1.18, 2.0, 2.1, 1.8,
+    /* S  */ 1.8, 2.27, 1.88, 1.76, 1.37, 2.0,
+    /* Ti */ 2.0, 2.0, 2.0, 2.0, 2.0, 2.0,
+    /* Ni */ 1.63, 1.4, 1.39, 1.07, 2.0, 1.85,
+    /* Se */ 1.9, 1.85, 2.02, 2.0, 2.0, 2.0,
+    /* Zr */ 2.0, 2.0, 2.0, 2.0, 2.0, 2.0,
+    /* Pd */ 1.63, 1.72, 1.58, 1.93, 2.17, 2.0,
+    /* Te */ 2.06, 1.98, 2.16, 2.1, 2.0,
+    /* La */ 2.0, 2.0, 2.0, 2.0, 2.0, 2.0,
+    /* Eu */ 2.0, 2.0, 2.0, 2.0, 2.0,
+    /* Er */ 2.0, 2.0, 2.0, 2.0, 2.0, 2.0,
+    /* W  */ 2.0, 2.0, 2.0, 2.0, 1.72, 1.66,
+    /* Hg */ 1.55, 1.96, 2.02, 2.0, 2.0, 2.0, 2.0,
+    /* Fr */ 2.0, 2.0, 2.0, 2.0, 2.0, 1.86,
+    /* Np */ 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0,
+    /* Md */ 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0,
+    /* Mt */ 2.0, 2.0, 2.0
+};
+
+/* lookup functions */
+
+static const char *get_pte_label(const int idx)
+{
+    if ((idx < 1) || (idx >= nr_pte_entries)) return pte_label[0];
+
+    return pte_label[idx];
+}
+
+static double get_pte_mass(const int idx)
+{
+    if ((idx < 1) || (idx >= nr_pte_entries)) return pte_mass[0];
+
+    return pte_mass[idx];
+}
+
+static double get_pte_vdw_radius(const int idx)
+{
+    if ((idx < 1) || (idx >= nr_pte_entries)) return pte_vdw_radius[0];
+
+#if 1
+    /* Replace with Hydrogen radius with an "all-atom" radius */
+    if (idx == 1)
+      return 1.0;    /* H  */
+#else
+    /* Replace with old VMD atom radii values */
+    switch (idx) {
+      case  1: return 1.0;    /* H  */
+      case  6: return 1.5;    /* C  */
+      case  7: return 1.4;    /* N  */
+      case  8: return 1.3;    /* O  */
+      case  9: return 1.2;    /* F  */
+      case 15: return 1.5;    /* P  */
+      case 16: return 1.9;    /* S  */
+    }
+#endif
+
+    return pte_vdw_radius[idx];
+}
+
+static int get_pte_idx(const char *label)
+{
+    int i;
+    char atom[3];
+
+    /* zap string */
+    atom[0] = (char) 0;
+    atom[1] = (char) 0;
+    atom[2] = (char) 0;
+    /* if we don't have a null-pointer, there must be at least two
+     * chars, which is all we need. we convert to the capitalization
+     * convention of the table above during assignment. */
+    if (label != NULL) {
+        atom[0] = (char) toupper((int) label[0]);
+        atom[1] = (char) tolower((int) label[1]);
+    }
+    /* discard numbers in atom label */
+    if (isdigit(atom[1])) atom[1] = (char) 0;
+
+    for (i=0; i < nr_pte_entries; ++i) {
+        if ( (pte_label[i][0] == atom[0])
+             && (pte_label[i][1] == atom[1]) ) return i;
+    }
+
+    return 0;
+}
+
+static int get_pte_idx_from_string(const char *label) {
+  int i, ind;
+  char atom[3];
+
+  if (label != NULL) {
+    /* zap string */
+    atom[0] = atom[1] = atom[2] = '\0';
+
+    for (ind=0,i=0; (ind<2) && (label[i]!='\0'); i++) {
+      if (label[i] != ' ') {
+        atom[ind] = toupper(label[i]);
+        ind++;
+      }
+    }
+
+    if (ind < 1)
+      return 0; /* no non-whitespace characters */
+
+    for (i=0; i < nr_pte_entries; ++i) {
+      if ((toupper(pte_label[i][0]) == atom[0]) && (toupper(pte_label[i][1]) == atom[1]))
+        return i;
+    }
+  }
+
+  return 0;
+}
+
+#if 0
+#include <stdio.h>
+
+int main() {
+  int i;
+
+  printf("Periodic table check/dump\n");
+  printf("  Table contains data for %d elements\n", nr_pte_entries);
+  printf("   Mass table size check: %d\n", sizeof(pte_mass) / sizeof(double));
+  printf("    VDW table size check: %d\n", sizeof(pte_vdw_radius) / sizeof(double));
+  printf("\n");
+  printf("Symbol Num    Mass   rVDW\n");
+  for (i=0; i<nr_pte_entries; i++) {
+    printf("   %-2s  %3d  %6.2f  %4.2f\n",
+      get_pte_label(i), i, get_pte_mass(i), get_pte_vdw_radius(i));
+  }
+  return 0;
+}
+#endif

tools/lammps-gui/preferences.cpp

@@ -138,6 +138,8 @@ void Preferences::accept()
     if (box) settings->setValue("box", box->isChecked());
     box = tabWidget->findChild<QCheckBox *>("axes");
     if (box) settings->setValue("axes", box->isChecked());
+    box = tabWidget->findChild<QCheckBox *>("vdwstyle");
+    if (box) settings->setValue("vdwstyle", box->isChecked());
     QComboBox *combo = tabWidget->findChild<QComboBox *>("background");
     if (combo) settings->setValue("background", combo->currentText());
     combo = tabWidget->findChild<QComboBox *>("boxcolor");
@@ -395,6 +397,7 @@ SnapshotTab::SnapshotTab(QSettings *_settings, QWidget *parent) :
     auto *ssao  = new QLabel("HQ Image mode:");
     auto *bbox  = new QLabel("Show Box:");
     auto *axes  = new QLabel("Show Axes:");
+    auto *vdw  = new QLabel("VDW Style:");
     auto *cback = new QLabel("Background Color:");
     auto *cbox  = new QLabel("Box Color:");
     settings->beginGroup("snapshot");
@@ -405,6 +408,7 @@ SnapshotTab::SnapshotTab(QSettings *_settings, QWidget *parent) :
     auto *sval = new QCheckBox;
     auto *bval = new QCheckBox;
     auto *eval = new QCheckBox;
+    auto *vval = new QCheckBox;
     sval->setCheckState(settings->value("ssao", false).toBool() ? Qt::Checked : Qt::Unchecked);
     sval->setObjectName("ssao");
     aval->setCheckState(settings->value("antialias", false).toBool() ? Qt::Checked : Qt::Unchecked);
@@ -413,6 +417,8 @@ SnapshotTab::SnapshotTab(QSettings *_settings, QWidget *parent) :
     bval->setObjectName("box");
     eval->setCheckState(settings->value("axes", false).toBool() ? Qt::Checked : Qt::Unchecked);
     eval->setObjectName("axes");
+    vval->setCheckState(settings->value("vdwstyle", false).toBool() ? Qt::Checked : Qt::Unchecked);
+    vval->setObjectName("vdwstyle");
 
     auto *intval = new QIntValidator(100, 100000, this);
     xval->setValidator(intval);
@@ -442,28 +448,31 @@ SnapshotTab::SnapshotTab(QSettings *_settings, QWidget *parent) :
     boxcolor->setCurrentText(settings->value("boxcolor", "yellow").toString());
     settings->endGroup();
 
-    grid->addWidget(xsize, 0, 0, Qt::AlignTop);
-    grid->addWidget(ysize, 1, 0, Qt::AlignTop);
-    grid->addWidget(zoom, 2, 0, Qt::AlignTop);
-    grid->addWidget(anti, 3, 0, Qt::AlignTop);
-    grid->addWidget(ssao, 4, 0, Qt::AlignTop);
-    grid->addWidget(bbox, 5, 0, Qt::AlignTop);
-    grid->addWidget(axes, 6, 0, Qt::AlignTop);
-    grid->addWidget(cback, 7, 0, Qt::AlignTop);
-    grid->addWidget(cbox, 8, 0, Qt::AlignTop);
-    grid->addWidget(xval, 0, 1, Qt::AlignTop);
-    grid->addWidget(yval, 1, 1, Qt::AlignTop);
-    grid->addWidget(zval, 2, 1, Qt::AlignTop);
-    grid->addWidget(aval, 3, 1, Qt::AlignTop);
-    grid->addWidget(sval, 4, 1, Qt::AlignVCenter);
-    grid->addWidget(bval, 5, 1, Qt::AlignVCenter);
-    grid->addWidget(eval, 6, 1, Qt::AlignVCenter);
-    grid->addWidget(background, 7, 1, Qt::AlignVCenter);
-    grid->addWidget(boxcolor, 8, 1, Qt::AlignVCenter);
+    int i = 0;
+    grid->addWidget(xsize, i, 0, Qt::AlignTop);
+    grid->addWidget(xval, i++, 1, Qt::AlignTop);
+    grid->addWidget(ysize, i, 0, Qt::AlignTop);
+    grid->addWidget(yval, i++, 1, Qt::AlignTop);
+    grid->addWidget(zoom, i, 0, Qt::AlignTop);
+    grid->addWidget(zval, i++, 1, Qt::AlignTop);
+    grid->addWidget(anti, i, 0, Qt::AlignTop);
+    grid->addWidget(aval, i++, 1, Qt::AlignTop);
+    grid->addWidget(ssao, i, 0, Qt::AlignTop);
+    grid->addWidget(sval, i++, 1, Qt::AlignVCenter);
+    grid->addWidget(bbox, i, 0, Qt::AlignTop);
+    grid->addWidget(bval, i++, 1, Qt::AlignVCenter);
+    grid->addWidget(axes, i, 0, Qt::AlignTop);
+    grid->addWidget(eval, i++, 1, Qt::AlignVCenter);
+    grid->addWidget(vdw, i, 0, Qt::AlignTop);
+    grid->addWidget(vval, i++, 1, Qt::AlignVCenter);
+    grid->addWidget(cback, i, 0, Qt::AlignTop);
+    grid->addWidget(background, i++, 1, Qt::AlignVCenter);
+    grid->addWidget(cbox, i, 0, Qt::AlignTop);
+    grid->addWidget(boxcolor, i++, 1, Qt::AlignVCenter);
 
-    grid->addItem(new QSpacerItem(100, 100, QSizePolicy::Minimum, QSizePolicy::Expanding), 9, 0);
-    grid->addItem(new QSpacerItem(100, 100, QSizePolicy::Minimum, QSizePolicy::Expanding), 9, 1);
-    grid->addItem(new QSpacerItem(100, 100, QSizePolicy::Expanding, QSizePolicy::Expanding), 9, 2);
+    grid->addItem(new QSpacerItem(100, 100, QSizePolicy::Minimum, QSizePolicy::Expanding), i, 0);
+    grid->addItem(new QSpacerItem(100, 100, QSizePolicy::Minimum, QSizePolicy::Expanding), i, 1);
+    grid->addItem(new QSpacerItem(100, 100, QSizePolicy::Expanding, QSizePolicy::Expanding), i, 2);
     setLayout(grid);
 }
 

tools/lammps-gui/preferences.h

@@ -34,6 +34,7 @@ private slots:
 
 public:
     bool need_relaunch;
+
 private:
     QTabWidget *tabWidget;
     QDialogButtonBox *buttonBox;