update LAMMPS GUI to version 1.2

cmake/CMakeLists.txt

@@ -1,3 +1,4 @@
+# -*- CMake -*- master configuration file for building LAMMPS
 ########################################
 # CMake build system
 # This file is part of LAMMPS
@@ -888,8 +889,15 @@ else()
 endif()
 include(FeatureSummary)
 feature_summary(DESCRIPTION "The following tools and libraries have been found and configured:" WHAT PACKAGES_FOUND)
+if(GIT_FOUND AND EXISTS ${LAMMPS_DIR}/.git)
+  execute_process(COMMAND ${GIT_EXECUTABLE} describe --dirty=-modified --always
+    OUTPUT_VARIABLE GIT_DESCRIBE
+    ERROR_QUIET
+    WORKING_DIRECTORY ${LAMMPS_DIR}
+    OUTPUT_STRIP_TRAILING_WHITESPACE)
+endif()
 message(STATUS "<<< Build configuration >>>
-   LAMMPS Version:   ${PROJECT_VERSION}
+   LAMMPS Version:   ${PROJECT_VERSION} ${GIT_DESCRIBE}
    Operating System: ${CMAKE_SYSTEM_NAME} ${CMAKE_LINUX_DISTRO} ${CMAKE_DISTRO_VERSION}
    CMake Version:    ${CMAKE_VERSION}
    Build type:       ${LAMMPS_BUILD_TYPE}
@@ -1026,6 +1034,14 @@ endif()
 if(BUILD_LAMMPS_SHELL)
   message(STATUS "<<< Building LAMMPS Shell >>>")
 endif()
+if(BUILD_LAMMPS_GUI)
+  message(STATUS "<<< Building LAMMPS GUI >>>")
+  if(LAMMPS_GUI_USE_PLUGIN)
+    message(STATUS "Loading LAMMPS library as plugin at run time")
+  else()
+    message(STATUS "Linking LAMMPS library at compile time")
+  endif()
+endif()
 if(ENABLE_TESTING)
   message(STATUS "<<< Building Unit Tests >>>")
   if(ENABLE_COVERAGE)

cmake/packaging/build_windows_cross_zip.sh

@@ -1,26 +1,64 @@
-#!/bin/bash -vx
+#!/bin/bash
 
 APP_NAME=lammps-gui
-DESTDIR=${PWD}/../LAMMPS_GUI
+DESTDIR=${PWD}/LAMMPS_GUI
+SYSROOT="$1"
 
 echo "Delete old files, if they exist"
-rm -rvf ${DESTDIR} LAMMPS-Win10-amd64.zip
+rm -rvf ${DESTDIR}/LAMMPS_GUI ${DESTDIR}/LAMMPS-Win10-amd64.zip
 
 echo "Create staging area for deployment and populate"
 DESTDIR=${DESTDIR} cmake --install .  --prefix "/"
 
-echo "Add required dependencies for Qt"
+# no static libs needed
-for dll in Qt5Core.dll Qt5Gui.dll Qt5Widgets.dll
+rm -rvf ${DESTDIR}/lib
+# but the LAMMPS lib
+
+echo "Copying required DLL files"
+for dll in $(objdump -p *.exe *.dll | sed -n -e '/DLL Name:/s/^.*DLL Name: *//p' | sort | uniq)
 do \
-    cp /usr/x86_64-w64-mingw32/sys-root/mingw/bin/${dll} ${DESTDIR}/bin/
+    doskip=0
-done
+    for skip in ADVAPI32 CFGMGR32 GDI32 KERNEL32 MPR NETAPI32 PSAPI SHELL32 USER32 USERENV UxTheme VERSION WS2_32 WSOCK32 d3d11 dwmapi liblammps msvcrt_ole32
-for dir in styles platforms imageformats
+    do \
-do \
+        test ${dll} = ${skip}.dll && doskip=1
-    mkdir -p ${DESTDIR}/${dir}
+    done
-    cp -r /usr/x86_64-w64-mingw32/sys-root/mingw/lib/qt5/plugins/${dir}/*.dll ${DESTDIR}/${dir}
+    test ${doskip} -eq 1 && continue
+    test -f ${DESTDIR}/bin/${dll} || cp -v ${SYSROOT}/bin/${dll} ${DESTDIR}/bin
 done
 
-pushd ..
+echo "Copy required Qt plugins"
-zip -9rv LAMMPS-Win10-amd64.zip LAMMPS_GUI
+mkdir -p ${DESTDIR}/qt5plugins
-popd
+for plugin in imageformats platforms styles
-exit 0
+do \
+    cp -r ${SYSROOT}/lib/qt5/plugins/${plugin} ${DESTDIR}/qt5plugins/
+done
+
+echo "Check dependencies of DLL files"
+for dll in $(objdump -p ${DESTDIR}/bin/*.dll ${DESTDIR}/qt5plugins/*/*.dll | sed -n -e '/DLL Name:/s/^.*DLL Name: *//p' | sort | uniq)
+do \
+    doskip=0
+    for skip in ADVAPI32 CFGMGR32 GDI32 KERNEL32 MPR NETAPI32 PSAPI SHELL32 USER32 USERENV UxTheme VERSION WS2_32 WSOCK32 d3d11 dwmapi liblammps msvcrt_ole32
+    do \
+        test ${dll} = ${skip}.dll && doskip=1
+    done
+    test ${doskip} -eq 1 && continue
+    test -f ${DESTDIR}/bin/${dll} || cp -v ${SYSROOT}/bin/${dll} ${DESTDIR}/bin
+done
+
+for dll in $(objdump -p ${DESTDIR}/bin/*.dll ${DESTDIR}/qt5plugins/*/*.dll | sed -n -e '/DLL Name:/s/^.*DLL Name: *//p' | sort | uniq)
+do \
+    doskip=0
+    for skip in ADVAPI32 CFGMGR32 GDI32 KERNEL32 MPR NETAPI32 PSAPI SHELL32 USER32 USERENV UxTheme VERSION WS2_32 WSOCK32 d3d11 dwmapi liblammps msvcrt_ole32
+    do \
+        test ${dll} = ${skip}.dll && doskip=1
+    done
+    test ${doskip} -eq 1 && continue
+    test -f ${DESTDIR}/bin/${dll} || cp -v ${SYSROOT}/bin/${dll} ${DESTDIR}/bin
+done
+
+cat > ${DESTDIR}/bin/qt.conf <<EOF
+[Paths]
+Plugins = ../qt5plugins
+EOF
+zip -9rvD LAMMPS-Win10-amd64.zip LAMMPS_GUI
+

cmake/packaging/linux_wrapper.sh

@@ -1,6 +1,9 @@
 #!/bin/sh
 # wrapper for bundled executables
 
+# reset locale to avoid problems with decimal numbers
+export LC_ALL=C
+
 BASEDIR=$(dirname "$0")
 EXENAME=$(basename "$0")
 

tools/lammps-gui/CMakeLists.txt

@@ -1,6 +1,6 @@
 cmake_minimum_required(VERSION 3.16)
 
-project(lammps-gui VERSION 1.0.0 LANGUAGES CXX)
+project(lammps-gui VERSION 1.2.0 LANGUAGES CXX)
 
 set(CMAKE_AUTOUIC ON)
 set(CMAKE_AUTOMOC ON)
@@ -16,10 +16,6 @@ mark_as_advanced(LAMMPS_GUI_USE_PLUGIN)
 if(NOT LAMMPS_EXCEPTIONS)
   message(FATAL_ERROR "Must enable LAMMPS_EXCEPTIONS for building the LAMMPS GUI")
 endif()
-if(BUILD_MPI)
-  message(FATAL_ERROR "Must disable BUILD_MPI for building the LAMMPS GUI")
-endif()
-
 # when this file is included as subdirectory in the LAMMPS build, many settings are directly imported
 if(LAMMPS_DIR)
   set(LAMMPS_HEADER_DIR ${LAMMPS_SOURCE_DIR})
@@ -60,12 +56,21 @@ endif()
 
 set(LAMMPS_PLUGINLIB_DIR ${LAMMPS_DIR}/examples/COUPLE/plugin)
 if(LAMMPS_GUI_USE_PLUGIN)
+  if(APPLE)
+    message(FATAL_ERROR "Dynamic loading of the LAMMPS library currently not supported on this platform")
+  endif()
   enable_language(C)
   set(PLUGIN_LOADER_SRC ${LAMMPS_PLUGINLIB_DIR}/liblammpsplugin.c)
 endif()
 
+# include resource compiler to embed icons into the executable on Windows
+if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
+  enable_language(RC)
+  set(ICON_RC_FILE ${CMAKE_CURRENT_SOURCE_DIR}/lmpicons.rc)
+endif()
+
 # we require Qt 5 and at least version 5.12 at that.
-find_package(Qt5 5.12 REQUIRED COMPONENTS Widgets)
+find_package(Qt5 5.12 REQUIRED COMPONENTS Widgets Charts)
 
 set(PROJECT_SOURCES
   main.cpp
@@ -75,6 +80,8 @@ set(PROJECT_SOURCES
   highlighter.h
   imageviewer.cpp
   imageviewer.h
+  chartviewer.cpp
+  chartviewer.h
   lammpsgui.cpp
   lammpsgui.h
   lammpsgui.ui
@@ -82,10 +89,15 @@ set(PROJECT_SOURCES
   lammpswrapper.cpp
   lammpswrapper.h
   linenumberarea.h
+  logwindow.cpp
+  logwindow.h
   preferences.cpp
   preferences.h
+  setvariables.cpp
+  setvariables.h
   stdcapture.cpp
   ${PLUGIN_LOADER_SRC}
+  ${ICON_RC_FILE}
 )
 qt5_add_resources(PROJECT_SOURCES lammpsgui.qrc)
 
@@ -110,7 +122,7 @@ else()
 endif()
 target_include_directories(lammps-gui PRIVATE ${CMAKE_CURRENT_SOURCE_DIR})
 target_compile_definitions(lammps-gui PRIVATE LAMMPS_GUI_VERSION="${PROJECT_VERSION}")
-target_link_libraries(lammps-gui PRIVATE Qt5::Widgets)
+target_link_libraries(lammps-gui PRIVATE Qt5::Widgets Qt5::Charts)
 if(BUILD_OMP)
   find_package(OpenMP COMPONENTS CXX REQUIRED)
   target_link_libraries(lammps-gui PRIVATE OpenMP::OpenMP_CXX)
@@ -172,8 +184,23 @@ elseif(MSVC)
   get_filename_component(QT5_BIN_DIR "${Qt5Core_DIR}/../../../bin" ABSOLUTE)
   get_filename_component(INSTNAME ${CMAKE_INSTALL_PREFIX} NAME)
   install(CODE "execute_process(COMMAND \"${CMAKE_COMMAND}\" -D INSTNAME=${INSTNAME} -D VC_INIT=\"${VC_INIT}\" -D QT5_BIN_DIR=\"${QT5_BIN_DIR}\" -P \"${CMAKE_SOURCE_DIR}/packaging/build_windows_vs.cmake\" WORKING_DIRECTORY \"${CMAKE_INSTALL_PREFIX}/..\" COMMAND_ECHO STDOUT)")
+elseif((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
+  install(TARGETS lammps-gui DESTINATION ${CMAKE_INSTALL_BINDIR})
+  install(FILES $<TARGET_RUNTIME_DLLS:lammps-gui> TYPE BIN)
+  install(FILES $<TARGET_RUNTIME_DLLS:lammps> TYPE BIN)
+  install(FILES $<TARGET_RUNTIME_DLLS:lmp> TYPE BIN)
+  add_custom_target(zip
+    COMMAND sh -vx ${LAMMPS_DIR}/cmake/packaging/build_windows_cross_zip.sh ${CMAKE_INSTALL_PREFIX}
+    DEPENDS lmp lammps-gui
+    COMMENT "Create zip file with windows binaries"
+    BYPRODUCT LAMMPS-Win10-amd64.zip
+    WORKING_DIRECTORY ${CMAKE_BINARY_DIR})
 elseif(CMAKE_SYSTEM_NAME STREQUAL "Linux")
   install(TARGETS lammps-gui DESTINATION ${CMAKE_INSTALL_BINDIR})
+  install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/lammps-gui.desktop DESTINATION ${CMAKE_INSTALL_DATADIR}/applications/)
+  install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/lammps-input.xml DESTINATION ${CMAKE_INSTALL_DATADIR}/mime/packages/)
+  install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/lammps-input.xml DESTINATION ${CMAKE_INSTALL_DATADIR}/mime/text/x-application-lammps.xml)
+  install(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/icons/hicolor DESTINATION ${CMAKE_INSTALL_DATADIR}/icons/)
   install(CODE [[
     file(GET_RUNTIME_DEPENDENCIES
       LIBRARIES $<TARGET_FILE:lammps>

tools/lammps-gui/README.md

@@ -1,104 +1,14 @@
 LAMMPS GUI
 
-# Overview
-
 LAMMPS GUI is essentially a small graphical text editor that is linked
 to the LAMMPS library and thus can run LAMMPS using the contents of the
-text buffer as input. This is similar to what people usually would do
+text buffer as input directly without requiring an additional LAMMPS
-using a text editor to edit the input and then a command line terminal
+executable. It can also capture and show the screen output, a line graph
-window to run the input commands.  The main benefit is that this
+of thermodynamic data and snapshot images in separate windows.
-integrates very well with graphical desktop environments and that it is
-easier to use for beginners in running computations and thus very
-suitable for tutorials on LAMMPS.
 
-# Features
+Detailed documentation about installing and using LAMMPS GUI is in
-
+the LAMMPS manual.
-The main window of the LAMMPS GUI is a text editor window with syntax
-highlighting set up for LAMMPS input files.  It can be used to edit any
-kind of text file, but then trying to run those files will cause errors.
-The output of a run is captured and displayed in a separate window
-dialog.  The log window is updated during the run and a progress bar for
-each run command shown in the main window.  Starting a new run will open
-another log windows.  After the simulation is finished, an image of the
-simulated system can be created and shown in another window.  Ongoing
-runs can be stopped at the next iteration via triggering a timeout.
-
-When opening a file, the editor will determine the directory where the
-file resides and switch its current working directory to that folder.
-Many LAMMPS inputs contain commands that read other files, typically
-from the folder with the input file.  The GUI will show the current
-working directory.  The editor window can also receive (entire) files
-via drag-n-drop from a file manager GUI or a desktop environment.
-
-Almost all commands are accessible via hotkeys. Which those hotkeys are,
-is shown next to the entries in the menu.  Log and image viewer windows
-can be closed with CTRL-W (or Command-W on macOS).  The "About LAMMPS"
-dialog will show the LAMMPS version and the features included into the
-LAMMPS library linked to the LAMMPS GUI.
-
-Due to its nature as a graphical application, it is not possible to use
-the LAMMPS GUI in parallel with MPI, but OpenMP multi-threading is
-available.
-
-# Prerequisites and portability
-
-LAMMPS GUI is programmed using the Qt cross-platform GUI toolkit,
-currently using Qt version 5.15LTS for better compatibility with older
-compilers. It has been successfully compiled and tested on:
-
-- Fedora Linux 38 x86\_64 using GCC 13 and Clang 16
-- Apple macOS 12 (Monterey) and macOS 13 (Ventura) with Xcode on arm64 and x86\_64
-- Windows 10 and 11 x86_64 with Visual Studio 2022 and Visual C++ 14.36
-
-# Compilation
-
-The source for the LAMMPS GUI is included with the LAMMPS source code
-distribution in the folder `tools/lammps-gui` and thus it can be can be
-built as part of a regular LAMMPS compilation.  Using CMake is required.
-To enable its compilation the CMake variable `-D BUILD_LAMMPS_GUI=on`
-must be set when creating the CMake configuration.  All other settings
-(compiler, flags, compile type) for LAMMPS GUI are then inherited from
-the regular LAMMPS build.  If the Qt library is packaged for Linux
-distributions, then its location is typically auto-detected since the
-required CMake configuration files are stored in a location where CMake
-can find them without additional help.  Otherwise, the location of the
-Qt library installation must be indicated by setting `-D
-Qt5_DIR=/path/to/qt5/lib/cmake/Qt5`, which is a path to a folder inside
-the Qt installation that contains the file `Qt5Config.cmake`.
-
-It is also possible to build the LAMMPS GUI as a standalone executable
-(e.g. when LAMMPS has been compiled with traditional make), then the
-CMake configuration needs to be told where to find the LAMMPS headers
-and the LAMMPS library, via `-D LAMMPS_SOURCE_DIR=/path/to/lammps/src`.
-CMake will try to guess a build folder with the LAMMPS library from that
-path, but it can also be set with `-D LAMMPS_LIB_DIR=/path/to/lammps/lib`.
-
-Rather than linking to the LAMMPS library during compilation, it is also
-possible to compile the GUI with a plugin loader library that will load
-the LAMMPS library at runtime during startup of the GUI from a shared
-library; e.g. `liblammps.so` or `liblammps.dylib` or `liblammps.dll`
-depending on the operating system.  This has the advantage that the
-LAMMPS library can be updated LAMMPS without having to recompile the
-GUI.  The ABI of the LAMMPS C-library interface is very stable and
-generally backward compatible.  This feature is enabled by setting
-`-D LAMMPS_GUI_USE_PLUGIN=on` and then
-`-D LAMMPS_PLUGINLIB_DIR=/path/to/lammps/plugin/loader`. Typically, this
-would be the `examples/COUPLE/plugin` folder of the LAMMPS distribution.
-
-# Platform notes
-
-## macOS
-
-When building on macOS, the build procedure will try to manufacture a
-drag-n-drop installer, LAMMPS-macOS-multiarch.dmg.  To build multi-arch
-executables that will run on both, arm64 and x86_64 architectures
-natively, it is necessary to set the CMake variable
-`-D CMAKE_OSX_ARCHITECTURES=arm64;x86_64`.  To achieve wide compatibility
-with different macOS versions, you can also set
-`-D CMAKE_OSX_DEPLOYMENT_TARGET=11.0` which will set compatibility to macOS
-11 (Big Sur) and later, even if you are compiling on a more recent macOS
-version.
 
 --------
 
-updated by Axel Kohlmeyer, 08/1023
+updated by Axel Kohlmeyer, 2023-08-12

tools/lammps-gui/TODO.md

@@ -2,18 +2,26 @@ LAMMPS-GUI TODO list:
 
 # Short term goals
 
+- 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
-- add multi-tab settings dialog where certain properties can be set through customizing the LAMMPS command line
+- need to handle "label" and "jump" commands from within ?
-   + select Font
+- switch processing of input to line based commands or?
-- add list of 5(?) most recently opened/saved files to file dialog (and also write to settings state on exit) (note: must store full path!)
+- switch input file editor to read-only while loop is running
 
 # 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
+- 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
-- use the "lammps_get_last_thermo" function to get access to thermodynamic data during a run and add plot/graph dialog that can plot one or more of those graphs while the simulation is still running
-- possibly also implement a callback interface, so that external programs can be called after thermo data is updated.
 - 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
 - support text completion as done with lammps-shell
-- have context menu for known commands to offer retrieving help by dispatching URL to webbrowser (process index from sphinx for that purpose)
+- add a "python" mode, where instead of launching LAMMPS, python is loaded where the LAMMPS python module is made available.
-- add a "python" mode, where instead of launching LAMMPS, python is loaded that the LAMMPS python module is made available.
+- support multiple tabs and multiple LAMMPS instances?

tools/lammps-gui/chartviewer.cpp

@@ -0,0 +1,248 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   LAMMPS development team: developers@lammps.org
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "chartviewer.h"
+
+#include <QHBoxLayout>
+#include <QLineSeries>
+#include <QSettings>
+#include <QVBoxLayout>
+
+using namespace QtCharts;
+
+ChartWindow::ChartWindow(const QString &_filename, QWidget *parent) :
+    QWidget(parent), menu(new QMenuBar), file(new QMenu("&File")), active_chart(-1),
+    filename(_filename)
+{
+    auto *top = new QHBoxLayout;
+    menu->addMenu(file);
+    menu->setSizePolicy(QSizePolicy::Minimum, QSizePolicy::Preferred);
+
+    columns = new QComboBox;
+    top->addWidget(menu);
+    top->addWidget(columns);
+    saveAsAct = file->addAction("&Save Graph As...", this, &ChartWindow::saveAs);
+    saveAsAct->setIcon(QIcon(":/document-save-as.png"));
+    exportCsvAct = file->addAction("&Export data to CSV...", this, &ChartWindow::exportCsv);
+    exportCsvAct->setIcon(QIcon(":/application-calc.png"));
+    exportDatAct = file->addAction("Export data to &Gnuplot...", this, &ChartWindow::exportDat);
+    exportDatAct->setIcon(QIcon(":/application-plot.png"));
+    file->addSeparator();
+    closeAct = file->addAction("&Close", this, &QWidget::close);
+    closeAct->setIcon(QIcon(":/window-close.png"));
+    auto *layout = new QVBoxLayout;
+    layout->addLayout(top);
+    setLayout(layout);
+
+    connect(columns, SIGNAL(currentIndexChanged(int)), this, SLOT(change_chart(int)));
+    QSettings settings;
+    resize(settings.value("chartx", 500).toInt(), settings.value("charty", 320).toInt());
+}
+
+int ChartWindow::get_step() const
+{
+    if (charts.size() > 0) {
+        auto *v = charts[0];
+        return (int)v->get_step(v->get_count() - 1);
+    } else {
+        return -1;
+    }
+}
+
+void ChartWindow::reset_charts()
+{
+    while (layout()->count() > 1) {
+        auto *item = layout()->takeAt(1);
+        if (item) {
+            layout()->removeItem(item);
+            delete item->widget();
+            delete item;
+        }
+    }
+    charts.clear();
+    columns->clear();
+    active_chart = 0;
+}
+
+void ChartWindow::add_chart(const QString &title, int index)
+{
+    auto *chart = new ChartViewer(title, index);
+    layout()->addWidget(chart);
+    columns->addItem(title, index);
+    columns->show();
+    // hide all but the first chart added
+    if (charts.size() > 0) chart->hide();
+    charts.append(chart);
+    active_chart = 0;
+}
+
+void ChartWindow::add_data(int step, double data, int index)
+{
+    for (auto &c : charts)
+        if (c->get_index() == index) c->add_data(step, data);
+}
+
+void ChartWindow::saveAs()
+{
+    if (charts.empty() || (active_chart < 0)) return;
+    QString defaultname = filename + "." + columns->currentText() + ".png";
+    if (filename.isEmpty()) defaultname = columns->currentText() + ".png";
+    QString fileName = QFileDialog::getSaveFileName(this, "Save Chart as Image", defaultname,
+                                                    "Image Files (*.jpg *.png *.bmp *.ppm)");
+    if (!fileName.isEmpty()) {
+        charts[active_chart]->grab().save(fileName);
+    }
+}
+
+void ChartWindow::exportDat()
+{
+    if (charts.empty() || (active_chart < 0)) return;
+    QString defaultname = filename + ".dat";
+    if (filename.isEmpty()) defaultname = "lammpsdata.dat";
+    QString fileName = QFileDialog::getSaveFileName(this, "Save Chart as Gnuplot data", defaultname,
+                                                    "Image Files (*.dat)");
+    if (!fileName.isEmpty()) {
+        QFile file(fileName);
+        if (file.open(QIODevice::WriteOnly | QIODevice::Text)) {
+
+            file.write("# Thermodynamic data from ");
+            file.write(filename.toLocal8Bit());
+            file.write("\n# Columns:");
+            for (auto &c : charts) {
+                file.write(" ");
+                file.write(c->get_title());
+            }
+            file.write("\n");
+
+            int lines = charts[0]->get_count();
+            for (int i = 0; i < lines; ++i) {
+                // timestep
+                file.write(QString::number(charts[0]->get_step(i)).toLocal8Bit());
+                for (auto &c : charts) {
+                    file.write(" ");
+                    file.write(QString::number(c->get_data(i)).toLocal8Bit());
+                }
+                file.write("\n");
+            }
+            file.close();
+        }
+    }
+}
+
+void ChartWindow::exportCsv()
+{
+    if (charts.empty() || (active_chart < 0)) return;
+    QString defaultname = filename + ".csv";
+    if (filename.isEmpty()) defaultname = "lammpsdata.csv";
+    QString fileName = QFileDialog::getSaveFileName(this, "Save Chart as CSV data", defaultname,
+                                                    "Image Files (*.csv)");
+    if (!fileName.isEmpty()) {
+        QFile file(fileName);
+        if (file.open(QIODevice::WriteOnly | QIODevice::Text)) {
+
+            file.write("Step");
+            for (auto &c : charts) {
+                file.write(",");
+                file.write(c->get_title());
+            }
+            file.write("\n");
+
+            int lines = charts[0]->get_count();
+            for (int i = 0; i < lines; ++i) {
+                // timestep
+                file.write(QString::number(charts[0]->get_step(i)).toLocal8Bit());
+                for (auto &c : charts) {
+                    file.write(",");
+                    file.write(QString::number(c->get_data(i)).toLocal8Bit());
+                }
+                file.write("\n");
+            }
+            file.close();
+        }
+    }
+}
+
+void ChartWindow::change_chart(int index)
+{
+    int choice = columns->currentData().toInt();
+    for (auto &c : charts) {
+        if (choice == c->get_index())
+            c->show();
+        else
+            c->hide();
+    }
+}
+
+void ChartWindow::closeEvent(QCloseEvent *event)
+{
+    QSettings settings;
+    if (!isMaximized()) {
+        settings.setValue("chartx", width());
+        settings.setValue("charty", height());
+    }
+    QWidget::closeEvent(event);
+}
+
+/* -------------------------------------------------------------------- */
+
+ChartViewer::ChartViewer(const QString &title, int _index, QWidget *parent) :
+    QChartView(parent), last_step(-1), index(_index), chart(new QChart), series(new QLineSeries),
+    xaxis(new QValueAxis), yaxis(new QValueAxis)
+{
+    chart->legend()->hide();
+    chart->addAxis(xaxis, Qt::AlignBottom);
+    chart->addAxis(yaxis, Qt::AlignLeft);
+    chart->addSeries(series);
+    series->attachAxis(xaxis);
+    series->attachAxis(yaxis);
+    xaxis->setTitleText("Time step");
+    xaxis->setTickCount(5);
+    xaxis->setLabelFormat("%d");
+    yaxis->setTickCount(5);
+    xaxis->setMinorTickCount(5);
+    yaxis->setMinorTickCount(5);
+    yaxis->setTitleText(title);
+    series->setName(title);
+
+    setRenderHint(QPainter::Antialiasing);
+    setChart(chart);
+    setRubberBand(QChartView::RectangleRubberBand);
+}
+
+/* -------------------------------------------------------------------- */
+
+void ChartViewer::add_data(int step, double data)
+{
+    if (last_step < step) {
+        last_step = step;
+        series->append(step, data);
+        auto points = series->pointsVector();
+
+        qreal xmin = 1.0e100;
+        qreal xmax = -1.0e100;
+        qreal ymin = 1.0e100;
+        qreal ymax = -1.0e100;
+        for (auto &p : points) {
+            xmin = qMin(xmin, p.x());
+            xmax = qMax(xmax, p.x());
+            ymin = qMin(ymin, p.y());
+            ymax = qMax(ymax, p.y());
+        }
+        xaxis->setRange(xmin, xmax);
+        yaxis->setRange(ymin, ymax);
+    }
+}
+
+// Local Variables:
+// c-basic-offset: 4
+// End:

tools/lammps-gui/chartviewer.h

@@ -0,0 +1,94 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   LAMMPS development team: developers@lammps.org
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifndef CHARTVIEWER_H
+#define CHARTVIEWER_H
+
+#include <QList>
+#include <QString>
+#include <QWidget>
+#include <QtCharts>
+
+class QAction;
+class QMenuBar;
+class QMenu;
+class QComboBox;
+class ChartViewer;
+
+class ChartWindow : public QWidget {
+    Q_OBJECT
+
+public:
+    ChartWindow(const QString &filename, QWidget *parent = nullptr);
+
+    int num_charts() const { return charts.size(); }
+    bool has_title(const QString &title, int index) const
+    {
+        return (columns->itemText(index) == title);
+    }
+    int get_step() const;
+    void reset_charts();
+    void add_chart(const QString &title, int index);
+    void add_data(int step, double data, int index);
+
+private slots:
+    void saveAs();
+    void exportDat();
+    void exportCsv();
+
+    void change_chart(int index);
+
+protected:
+    void closeEvent(QCloseEvent *event) override;
+
+private:
+    QMenuBar *menu;
+    QMenu *file;
+    QComboBox *columns;
+    QAction *saveAsAct;
+    QAction *exportCsvAct;
+    QAction *exportDatAct;
+    QAction *closeAct;
+
+    QString filename;
+    int active_chart;
+    QList<ChartViewer *> charts;
+};
+
+/* -------------------------------------------------------------------- */
+
+class ChartViewer : public QtCharts::QChartView {
+    Q_OBJECT
+
+public:
+    explicit ChartViewer(const QString &title, int index, QWidget *parent = nullptr);
+
+    void add_data(int step, double data);
+    int get_index() const { return index; };
+    int get_count() const { return series->count(); }
+    const char *get_title() const { return series->name().toLocal8Bit(); }
+    double get_step(int index) const { return series->at(index).x(); }
+    double get_data(int index) const { return series->at(index).y(); }
+
+private:
+    int last_step, index;
+    QtCharts::QChart *chart;
+    QtCharts::QLineSeries *series;
+    QtCharts::QValueAxis *xaxis;
+    QtCharts::QValueAxis *yaxis;
+};
+#endif
+
+// Local Variables:
+// c-basic-offset: 4
+// End:

tools/lammps-gui/codeeditor.cpp

@@ -15,19 +15,61 @@
 #include "lammpsgui.h"
 #include "linenumberarea.h"
 
+#include <QAction>
+#include <QDesktopServices>
 #include <QDragEnterEvent>
 #include <QDropEvent>
+#include <QIcon>
+#include <QKeySequence>
+#include <QMenu>
 #include <QMimeData>
 #include <QPainter>
+#include <QRegularExpression>
 #include <QTextBlock>
+#include <QUrl>
 
 CodeEditor::CodeEditor(QWidget *parent) : QPlainTextEdit(parent)
 {
-    lineNumberArea = new LineNumberArea(this);
+    help_action = new QShortcut(QKeySequence::fromString("Ctrl+?"), parent);
+    connect(help_action, &QShortcut::activated, this, &CodeEditor::get_help);
 
+    // initialize help system
+    QFile help_index(":/help_index.table");
+    if (help_index.open(QIODevice::ReadOnly | QIODevice::Text)) {
+        while (!help_index.atEnd()) {
+            auto line  = QString(help_index.readLine());
+            auto words = line.trimmed().split(' ');
+            if (words.size() > 2) {
+                if (words.at(1) == "pair_style") {
+                    pair_map[words.at(2)] = words.at(0);
+                } else if (words.at(1) == "bond_style") {
+                    bond_map[words.at(2)] = words.at(0);
+                } else if (words.at(1) == "angle_style") {
+                    angle_map[words.at(2)] = words.at(0);
+                } else if (words.at(1) == "dihedral_style") {
+                    dihedral_map[words.at(2)] = words.at(0);
+                } else if (words.at(1) == "improper_style") {
+                    improper_map[words.at(2)] = words.at(0);
+                } else if (words.at(1) == "fix") {
+                    fix_map[words.at(2)] = words.at(0);
+                } else if (words.at(1) == "compute") {
+                    compute_map[words.at(2)] = words.at(0);
+                } else if (words.at(1) == "kspace_style") {
+                    cmd_map["kspace_style"] = "kspace_style.html";
+                }
+                // ignoring: dump, fix_modify ATC
+            } else if (words.size() == 2) {
+                cmd_map[words.at(1)] = words.at(0);
+            } else {
+                fprintf(stderr, "unhandled: %s", line.toStdString().c_str());
+            }
+        }
+        help_index.close();
+    }
+
+    lineNumberArea = new LineNumberArea(this);
     connect(this, &CodeEditor::blockCountChanged, this, &CodeEditor::updateLineNumberAreaWidth);
     connect(this, &CodeEditor::updateRequest, this, &CodeEditor::updateLineNumberArea);
-
     updateLineNumberAreaWidth(0);
 }
 
@@ -138,6 +180,102 @@ void CodeEditor::lineNumberAreaPaintEvent(QPaintEvent *event)
     }
 }
 
+void CodeEditor::contextMenuEvent(QContextMenuEvent *event)
+{
+    // reposition the cursor here?
+    QString page, help;
+    find_help(page, help);
+
+    // print augmented context menu if an entry was found
+    auto *menu = createStandardContextMenu();
+    if (!page.isEmpty()) {
+        menu->addSeparator();
+        auto action = menu->addAction(QString("View Documentation for '%1'").arg(help));
+        action->setIcon(QIcon(":/system-help.png"));
+        action->setData(page);
+        connect(action, &QAction::triggered, this, &CodeEditor::open_help);
+        // if we link to help with specific styles (fix, compute, pair, bond, ...)
+        // also link to the docs for the primary command
+        auto words = help.split(' ');
+        if (words.size() > 1) {
+            help = words.at(0);
+            page = words.at(0);
+            page += ".html";
+            auto action2 = menu->addAction(QString("View Documentation for '%1'").arg(help));
+            action2->setIcon(QIcon(":/system-help.png"));
+            action2->setData(page);
+            connect(action2, &QAction::triggered, this, &CodeEditor::open_help);
+        }
+    }
+    auto action3 = menu->addAction(QString("LAMMPS Manual"));
+    action3->setIcon(QIcon(":/help-browser.png"));
+    action3->setData(QString());
+    connect(action3, &QAction::triggered, this, &CodeEditor::open_help);
+
+    menu->exec(event->globalPos());
+    delete menu;
+}
+
+void CodeEditor::get_help()
+{
+    QString page, help;
+    find_help(page, help);
+    if (!page.isEmpty())
+        QDesktopServices::openUrl(QUrl(QString("https://docs.lammps.org/%1").arg(page)));
+}
+
+void CodeEditor::find_help(QString &page, QString &help)
+{
+    // process line of text where the cursor is
+    auto text = textCursor().block().text().replace('\t', ' ').trimmed();
+    auto style =
+        QRegularExpression("^(pair|bond|angle|dihedral|improper)_style\\s+(\\S+)").match(text);
+    help.clear();
+    page.clear();
+    if (style.hasMatch()) {
+        if (style.captured(1) == "pair") {
+            page = pair_map.value(style.captured(2), QString());
+            help = QString("pair_style %1").arg(style.captured(2));
+        } else if (style.captured(1) == "bond") {
+            page = bond_map.value(style.captured(2), QString());
+            help = QString("bond_style %1").arg(style.captured(2));
+        } else if (style.captured(1) == "angle") {
+            page = angle_map.value(style.captured(2), QString());
+            help = QString("angle_style %1").arg(style.captured(2));
+        } else if (style.captured(1) == "dihedral") {
+            page = dihedral_map.value(style.captured(2), QString());
+            help = QString("dihedral_style %1").arg(style.captured(2));
+        } else if (style.captured(1) == "improper") {
+            page = improper_map.value(style.captured(2), QString());
+            help = QString("improper_style %1").arg(style.captured(2));
+        }
+    }
+
+    style = QRegularExpression("^(fix|compute)\\s+\\w+\\s+\\w+\\s+(\\S+)").match(text);
+    if (style.hasMatch()) {
+        help = QString("%1 %2").arg(style.captured(1), style.captured(2));
+        if (style.captured(1) == "fix") {
+            page = fix_map.value(style.captured(2), QString());
+        } else if (style.captured(1) == "compute") {
+            page = compute_map.value(style.captured(2), QString());
+        }
+    }
+
+    // could not find a matching "style", now try the plain command
+    if (page.isEmpty() && !text.isEmpty()) {
+        auto cmd = text.split(' ').at(0);
+        help     = cmd;
+        page     = cmd_map.value(cmd, QString());
+    }
+}
+
+void CodeEditor::open_help()
+{
+    QAction *act = qobject_cast<QAction *>(sender());
+    QDesktopServices::openUrl(
+        QUrl(QString("https://docs.lammps.org/%1").arg(act->data().toString())));
+}
+
 // Local Variables:
 // c-basic-offset: 4
 // End:

tools/lammps-gui/codeeditor.h

@@ -14,7 +14,10 @@
 #ifndef CODEEDITOR_H
 #define CODEEDITOR_H
 
+#include <QMap>
 #include <QPlainTextEdit>
+#include <QShortcut>
+#include <QString>
 
 class CodeEditor : public QPlainTextEdit {
     Q_OBJECT
@@ -30,14 +33,29 @@ protected:
     void dragEnterEvent(QDragEnterEvent *event) override;
     bool canInsertFromMimeData(const QMimeData *source) const override;
     void dropEvent(QDropEvent *event) override;
+    void contextMenuEvent(QContextMenuEvent *event) override;
 
 private slots:
     void updateLineNumberAreaWidth(int newBlockCount);
     void highlightCurrentLine();
     void updateLineNumberArea(const QRect &rect, int dy);
+    void get_help();
+    void find_help(QString &page, QString &help);
+    void open_help();
 
 private:
     QWidget *lineNumberArea;
+    QShortcut *help_action;
+
+    QMap<QString, QString> cmd_map;
+    QMap<QString, QString> fix_map;
+    QMap<QString, QString> compute_map;
+    QMap<QString, QString> pair_map;
+    QMap<QString, QString> bond_map;
+    QMap<QString, QString> angle_map;
+    QMap<QString, QString> dihedral_map;
+    QMap<QString, QString> improper_map;
+    QMap<QString, QString> dump_map;
 };
 
 #endif

tools/lammps-gui/highlighter.cpp

@@ -18,18 +18,23 @@ Highlighter::Highlighter(QTextDocument *parent) : QSyntaxHighlighter(parent)
     HighlightingRule rule;
 
     outputFormat.setForeground(Qt::darkYellow);
+    outputFormat.setFontWeight(QFont::Bold);
     readFormat.setForeground(Qt::magenta);
+    readFormat.setFontWeight(QFont::Bold);
     latticeFormat.setForeground(Qt::darkGreen);
+    latticeFormat.setFontWeight(QFont::Bold);
     particleFormat.setForeground(Qt::darkRed);
+    particleFormat.setFontWeight(QFont::Bold);
     setupFormat.setForeground(Qt::darkCyan);
-    runFormat.setForeground(Qt::green);
+    setupFormat.setFontWeight(QFont::Bold);
+    runFormat.setForeground(Qt::darkBlue);
     runFormat.setFontWeight(QFont::Bold);
     defineFormat.setForeground(Qt::darkMagenta);
     defineFormat.setFontWeight(QFont::Bold);
 
     numberFormat.setForeground(Qt::blue);
     commentFormat.setForeground(Qt::red);
-    stringFormat.setForeground(Qt::cyan);
+    stringFormat.setForeground(Qt::darkGreen);
     stringFormat.setFontWeight(QFont::Normal);
 
     const QString output_keywords[] = {
@@ -202,11 +207,44 @@ Highlighter::Highlighter(QTextDocument *parent) : QSyntaxHighlighter(parent)
 
 void Highlighter::highlightBlock(const QString &text)
 {
+    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);
+    bool do_style = true;
+    bool do_force = true;
+    bool do_defs  = true;
+    bool do_undo  = true;
     for (const HighlightingRule &rule : qAsConst(highlightingRules)) {
         QRegularExpressionMatchIterator matchIterator = rule.pattern.globalMatch(text);
         while (matchIterator.hasNext()) {
             QRegularExpressionMatch match = matchIterator.next();
-            setFormat(match.capturedStart(), match.capturedLength(), rule.format);
+            // special treatment for fix/compute/dump styles etc.
+            if (style.hasMatch() && do_style) {
+                setFormat(style.capturedStart(1), style.capturedLength(1), defineFormat);
+                setFormat(style.capturedStart(2), style.capturedLength(2), numberFormat);
+                setFormat(style.capturedStart(3), style.capturedLength(3), stringFormat);
+                setFormat(style.capturedStart(4), style.capturedLength(4), runFormat);
+                do_style = false;
+                // special treatment for force styles styles
+            } else if (force.hasMatch() && do_force) {
+                setFormat(force.capturedStart(1), force.capturedLength(1), particleFormat);
+                setFormat(force.capturedStart(2), force.capturedLength(2), runFormat);
+                do_force = false;
+                // special treatment for undo commands
+            } else if (undo.hasMatch() && do_undo) {
+                setFormat(undo.capturedStart(1), undo.capturedLength(1), defineFormat);
+                setFormat(undo.capturedStart(2), undo.capturedLength(2), stringFormat);
+                do_undo = false;
+                // special treatment for some definitions
+            } else if (defs.hasMatch() && do_defs) {
+                setFormat(defs.capturedStart(1), defs.capturedLength(1), particleFormat);
+                setFormat(defs.capturedStart(2), defs.capturedLength(2), stringFormat);
+                setFormat(defs.capturedStart(3), defs.capturedLength(3), runFormat);
+                do_defs = false;
+            } else {
+                setFormat(match.capturedStart(), match.capturedLength(), rule.format);
+            }
         }
     }
 }

tools/lammps-gui/imageviewer.cpp

@@ -12,6 +12,7 @@
 ------------------------------------------------------------------------- */
 
 #include "imageviewer.h"
+#include "lammpswrapper.h"
 
 #include <QAction>
 #include <QDialogButtonBox>
@@ -25,15 +26,21 @@
 #include <QMessageBox>
 #include <QPalette>
 #include <QPoint>
+#include <QPushButton>
 #include <QScreen>
 #include <QScrollArea>
 #include <QScrollBar>
+#include <QSettings>
 #include <QStatusBar>
 #include <QVBoxLayout>
 #include <QWheelEvent>
+#include <QWidgetAction>
 
-ImageViewer::ImageViewer(const QString &fileName, QWidget *parent) :
+static const QString blank(" ");
-    QDialog(parent), imageLabel(new QLabel), scrollArea(new QScrollArea), menuBar(new QMenuBar)
+
+ImageViewer::ImageViewer(const QString &fileName, LammpsWrapper *_lammps, QWidget *parent) :
+    QDialog(parent), imageLabel(new QLabel), scrollArea(new QScrollArea), menuBar(new QMenuBar),
+    lammps(_lammps), group("all"), filename(fileName)
 {
     imageLabel->setBackgroundRole(QPalette::Base);
     imageLabel->setSizePolicy(QSizePolicy::Ignored, QSizePolicy::Ignored);
@@ -42,8 +49,6 @@ ImageViewer::ImageViewer(const QString &fileName, QWidget *parent) :
 
     scrollArea->setBackgroundRole(QPalette::Dark);
     scrollArea->setWidget(imageLabel);
-    scrollArea->setMouseTracking(true);
-    scrollArea->installEventFilter(this);
     scrollArea->setVisible(false);
 
     buttonBox = new QDialogButtonBox(QDialogButtonBox::Close);
@@ -52,23 +57,72 @@ ImageViewer::ImageViewer(const QString &fileName, QWidget *parent) :
     connect(buttonBox, &QDialogButtonBox::rejected, this, &QDialog::reject);
 
     QVBoxLayout *mainLayout = new QVBoxLayout;
-    mainLayout->addWidget(menuBar);
+
+    auto *dossao = new QPushButton(QIcon(":/hd-img.png"), "");
+    dossao->setCheckable(true);
+    auto *doanti = new QPushButton(QIcon(":/antialias.png"), "");
+    doanti->setCheckable(true);
+    auto *dobox = new QPushButton(QIcon(":/system-box.png"), "");
+    dobox->setCheckable(true);
+    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"), "");
+    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;
+    combo->setObjectName("group");
+    int ngroup = lammps->id_count("group");
+    char gname[64];
+    for (int i = 0; i < ngroup; ++i) {
+        lammps->id_name("group", i, gname, 64);
+        combo->addItem(gname);
+    }
+
+    QHBoxLayout *menuLayout = new QHBoxLayout;
+    menuLayout->addWidget(menuBar);
+    menuLayout->addWidget(dossao);
+    menuLayout->addWidget(doanti);
+    menuLayout->addWidget(dobox);
+    menuLayout->addWidget(doaxes);
+    menuLayout->addWidget(zoomin);
+    menuLayout->addWidget(zoomout);
+    menuLayout->addWidget(rotleft);
+    menuLayout->addWidget(rotright);
+    menuLayout->addWidget(rotup);
+    menuLayout->addWidget(rotdown);
+    menuLayout->addWidget(reset);
+    menuLayout->addWidget(new QLabel(" Group: "));
+    menuLayout->addWidget(combo);
+
+    connect(dossao, &QPushButton::released, this, &ImageViewer::toggle_ssao);
+    connect(doanti, &QPushButton::released, this, &ImageViewer::toggle_anti);
+    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);
+    connect(zoomout, &QPushButton::released, this, &ImageViewer::do_zoom_out);
+    connect(rotleft, &QPushButton::released, this, &ImageViewer::do_rot_left);
+    connect(rotright, &QPushButton::released, this, &ImageViewer::do_rot_right);
+    connect(rotup, &QPushButton::released, this, &ImageViewer::do_rot_up);
+    connect(rotdown, &QPushButton::released, this, &ImageViewer::do_rot_down);
+    connect(reset, &QPushButton::released, this, &ImageViewer::reset_view);
+    connect(combo, SIGNAL(currentIndexChanged(int)), this, SLOT(change_group(int)));
+
+    mainLayout->addLayout(menuLayout);
     mainLayout->addWidget(scrollArea);
     mainLayout->addWidget(buttonBox);
-    setWindowTitle(QString("Image Viewer: ") + QFileInfo(fileName).completeBaseName());
+    setWindowTitle(QString("Image Viewer: ") + QFileInfo(fileName).fileName());
-
     createActions();
 
-    QImageReader reader(fileName);
+    reset_view();
-    reader.setAutoTransform(true);
+    dobox->setChecked(showbox);
-    const QImage newImage = reader.read();
+    doaxes->setChecked(showaxes);
-    if (newImage.isNull()) {
+    dossao->setChecked(usessao);
-        QMessageBox::warning(this, QGuiApplication::applicationDisplayName(),
+    doanti->setChecked(antialias);
-                             tr("Cannot load %1: %2").arg(fileName, reader.errorString()));
+
-        return;
-    }
-    image = newImage;
-    imageLabel->setPixmap(QPixmap::fromImage(image));
     scaleFactor = 1.0;
     resize(image.width() + 20, image.height() + 50);
 
@@ -79,6 +133,181 @@ ImageViewer::ImageViewer(const QString &fileName, QWidget *parent) :
     setLayout(mainLayout);
 }
 
+void ImageViewer::reset_view()
+{
+    QSettings settings;
+    settings.beginGroup("snapshot");
+    zoom      = settings.value("zoom", 1.0).toDouble();
+    hrot      = settings.value("hrot", 60).toInt();
+    vrot      = settings.value("vrot", 30).toInt();
+    showbox   = settings.value("box", true).toBool();
+    showaxes  = settings.value("axes", false).toBool();
+    usessao   = settings.value("ssao", false).toBool();
+    antialias = settings.value("antialias", false).toBool();
+    settings.endGroup();
+
+    // reset state of checkable push buttons and combo box (after main layout is set up)
+    auto *lo = layout();
+    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());
+        button->setChecked(usessao);
+        button = qobject_cast<QPushButton *>(lo->itemAt(2)->widget());
+        button->setChecked(antialias);
+        button = qobject_cast<QPushButton *>(lo->itemAt(3)->widget());
+        button->setChecked(showbox);
+        button = qobject_cast<QPushButton *>(lo->itemAt(4)->widget());
+        button->setChecked(showaxes);
+        // grab the last entry -> group selector
+        auto *cb = qobject_cast<QComboBox *>(lo->itemAt(lo->count() - 1)->widget());
+        cb->setCurrentText("all");
+    }
+    createImage();
+}
+
+void ImageViewer::toggle_ssao()
+{
+    QPushButton *button = qobject_cast<QPushButton *>(sender());
+    usessao             = !usessao;
+    button->setChecked(usessao);
+    createImage();
+}
+
+void ImageViewer::toggle_anti()
+{
+    QPushButton *button = qobject_cast<QPushButton *>(sender());
+    antialias           = !antialias;
+    button->setChecked(antialias);
+    createImage();
+}
+
+void ImageViewer::toggle_box()
+{
+    QPushButton *button = qobject_cast<QPushButton *>(sender());
+    showbox             = !showbox;
+    button->setChecked(showbox);
+    createImage();
+}
+
+void ImageViewer::toggle_axes()
+{
+    QPushButton *button = qobject_cast<QPushButton *>(sender());
+    showaxes            = !showaxes;
+    button->setChecked(showaxes);
+    createImage();
+}
+
+void ImageViewer::do_zoom_in()
+{
+    zoom = zoom * 1.1;
+    if (zoom > 5.0) zoom = 5.0;
+    createImage();
+}
+
+void ImageViewer::do_zoom_out()
+{
+    zoom = zoom / 1.1;
+    if (zoom < 0.5) zoom = 0.5;
+    createImage();
+}
+
+void ImageViewer::do_rot_left()
+{
+    vrot -= 15;
+    if (vrot < -180) vrot += 360;
+    createImage();
+}
+
+void ImageViewer::do_rot_right()
+{
+    vrot += 15;
+    if (vrot > 180) vrot -= 360;
+    createImage();
+}
+
+void ImageViewer::do_rot_down()
+{
+    hrot -= 15;
+    if (hrot < 0) hrot += 360;
+    createImage();
+}
+
+void ImageViewer::do_rot_up()
+{
+    hrot += 15;
+    if (hrot > 360) hrot -= 360;
+    createImage();
+}
+
+void ImageViewer::change_group(int idx)
+{
+    QComboBox *box = findChild<QComboBox *>("group");
+    if (box) group = box->currentText();
+    createImage();
+}
+
+void ImageViewer::createImage()
+{
+    QSettings settings;
+    QString dumpcmd = QString("write_dump ") + group + " image ";
+    QDir dumpdir(QDir::tempPath());
+    QFile dumpfile(dumpdir.absoluteFilePath(filename + ".ppm"));
+    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;
+
+    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(" zoom ") + QString::number(zoom);
+    lammps->command(dumpcmd.toLocal8Bit());
+    if (lammps->extract_setting("dimension") == 3) {
+        dumpcmd += QString(" view ") + QString::number(hhrot) + blank + QString::number(vrot);
+    }
+    if (usessao) dumpcmd += QString(" ssao yes 453983 0.75");
+    if (showbox)
+        dumpcmd += QString(" box yes 0.025");
+    else
+        dumpcmd += QString(" box no 0.0");
+
+    if (showaxes)
+        dumpcmd += QString(" axes yes 0.2 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();
+    settings.endGroup();
+
+    lammps->command(dumpcmd.toLocal8Bit());
+
+    QImageReader reader(dumpfile.fileName());
+    reader.setAutoTransform(true);
+    const QImage newImage = reader.read();
+
+    if (newImage.isNull()) {
+        QMessageBox::warning(
+            this, QGuiApplication::applicationDisplayName(),
+            QString("Cannot load %1: %2").arg(dumpfile.fileName(), reader.errorString()));
+        return;
+    }
+    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));
+}
+
 void ImageViewer::saveAs()
 {
     QString fileName = QFileDialog::getSaveFileName(this, "Save Image File As", QString(),
@@ -90,12 +319,12 @@ void ImageViewer::copy() {}
 
 void ImageViewer::zoomIn()
 {
-    scaleImage(1.1);
+    scaleImage(1.25);
 }
 
 void ImageViewer::zoomOut()
 {
-    scaleImage(0.9);
+    scaleImage(0.8);
 }
 
 void ImageViewer::normalSize()
@@ -119,38 +348,44 @@ void ImageViewer::saveFile(const QString &fileName)
 
 void ImageViewer::createActions()
 {
-    QMenu *fileMenu = menuBar->addMenu(tr("&File"));
+    QMenu *fileMenu = menuBar->addMenu("&File");
 
-    saveAsAct = fileMenu->addAction(tr("&Save As..."), this, &ImageViewer::saveAs);
+    saveAsAct = fileMenu->addAction("&Save As...", this, &ImageViewer::saveAs);
+    saveAsAct->setIcon(QIcon(":/document-save-as.png"));
     saveAsAct->setEnabled(false);
     fileMenu->addSeparator();
-    copyAct = fileMenu->addAction(tr("&Copy"), this, &ImageViewer::copy);
+    copyAct = fileMenu->addAction("&Copy", this, &ImageViewer::copy);
+    copyAct->setIcon(QIcon(":/edit-copy.png"));
     copyAct->setShortcut(QKeySequence::Copy);
     copyAct->setEnabled(false);
     fileMenu->addSeparator();
-    QAction *exitAct = fileMenu->addAction(tr("&Close"), this, &QWidget::close);
+    QAction *exitAct = fileMenu->addAction("&Close", this, &QWidget::close);
-    exitAct->setShortcut(tr("Ctrl+W"));
+    exitAct->setIcon(QIcon(":/window-close.png"));
+    exitAct->setShortcut(QKeySequence::fromString("Ctrl+W"));
 
-    QMenu *viewMenu = menuBar->addMenu(tr("&View"));
+    QMenu *viewMenu = menuBar->addMenu("&View");
 
-    zoomInAct = viewMenu->addAction(tr("Zoom &In (10%)"), this, &ImageViewer::zoomIn);
+    zoomInAct = viewMenu->addAction("Image Zoom &In (25%)", this, &ImageViewer::zoomIn);
     zoomInAct->setShortcut(QKeySequence::ZoomIn);
+    zoomInAct->setIcon(QIcon(":/gtk-zoom-in.png"));
     zoomInAct->setEnabled(false);
 
-    zoomOutAct = viewMenu->addAction(tr("Zoom &Out (10%)"), this, &ImageViewer::zoomOut);
+    zoomOutAct = viewMenu->addAction("Image Zoom &Out (25%)", this, &ImageViewer::zoomOut);
     zoomOutAct->setShortcut(QKeySequence::ZoomOut);
+    zoomOutAct->setIcon(QIcon(":/gtk-zoom-out.png"));
     zoomOutAct->setEnabled(false);
 
-    normalSizeAct = viewMenu->addAction(tr("&Normal Size"), this, &ImageViewer::normalSize);
+    normalSizeAct = viewMenu->addAction("&Reset Image Size", this, &ImageViewer::normalSize);
-    normalSizeAct->setShortcut(tr("Ctrl+S"));
+    normalSizeAct->setShortcut(QKeySequence::fromString("Ctrl+0"));
+    normalSizeAct->setIcon(QIcon(":/gtk-zoom-fit.png"));
     normalSizeAct->setEnabled(false);
 
     viewMenu->addSeparator();
 
-    fitToWindowAct = viewMenu->addAction(tr("&Fit to Window"), this, &ImageViewer::fitToWindow);
+    fitToWindowAct = viewMenu->addAction("&Fit to Window", this, &ImageViewer::fitToWindow);
     fitToWindowAct->setEnabled(false);
     fitToWindowAct->setCheckable(true);
-    fitToWindowAct->setShortcut(tr("Ctrl+F"));
+    fitToWindowAct->setShortcut(QKeySequence::fromString("Ctrl+="));
 }
 
 void ImageViewer::updateActions()
@@ -183,27 +418,6 @@ void ImageViewer::adjustScrollBar(QScrollBar *scrollBar, double factor)
         int(factor * scrollBar->value() + ((factor - 1) * scrollBar->pageStep() / 2)));
 }
 
-bool ImageViewer::eventFilter(QObject *, QEvent *event)
-{
-    if (event->type() == QEvent::Wheel) {
-        wheelEvent((QWheelEvent *)event);
-        return true;
-    }
-    return false;
-}
-
-void ImageViewer::wheelEvent(QWheelEvent *event)
-{
-    QPoint num = event->angleDelta();
-    if (!num.isNull()) {
-        if (num.y() > 0)
-            zoomIn();
-        else
-            zoomOut();
-    }
-    event->accept();
-}
-
 // Local Variables:
 // c-basic-offset: 4
 // End:

tools/lammps-gui/imageviewer.h

@@ -14,8 +14,10 @@
 #ifndef IMAGEVIEWER_H
 #define IMAGEVIEWER_H
 
+#include <QComboBox>
 #include <QDialog>
 #include <QImage>
+#include <QString>
 
 class QAction;
 class QMenuBar;
@@ -25,13 +27,15 @@ class QObject;
 class QScrollArea;
 class QScrollBar;
 class QStatusBar;
-class QWheelEvent;
+class LammpsWrapper;
+class QComboBox;
 
 class ImageViewer : public QDialog {
     Q_OBJECT
 
 public:
-    explicit ImageViewer(const QString &fileName, QWidget *parent = nullptr);
+    explicit ImageViewer(const QString &fileName, LammpsWrapper *_lammps,
+                         QWidget *parent = nullptr);
 
 private slots:
     void saveAs();
@@ -41,14 +45,28 @@ private slots:
     void normalSize();
     void fitToWindow();
 
+    void reset_view();
+    void toggle_ssao();
+    void toggle_anti();
+    void toggle_box();
+    void toggle_axes();
+    void do_zoom_in();
+    void do_zoom_out();
+    void do_rot_left();
+    void do_rot_right();
+    void do_rot_up();
+    void do_rot_down();
+    void change_group(int);
+
+public:
+    void createImage();
+
 private:
     void createActions();
     void updateActions();
     void saveFile(const QString &fileName);
     void scaleImage(double factor);
     void adjustScrollBar(QScrollBar *scrollBar, double factor);
-    bool eventFilter(QObject *object, QEvent *event);
-    void wheelEvent(QWheelEvent *event);
 
 private:
     QImage image;
@@ -64,6 +82,13 @@ private:
     QAction *zoomOutAct;
     QAction *normalSizeAct;
     QAction *fitToWindowAct;
+
+    LammpsWrapper *lammps;
+    QString group;
+    QString filename;
+    int hrot, vrot;
+    double zoom;
+    bool showbox, showaxes, antialias, usessao;
 };
 #endif
 

tools/lammps-gui/lammps-gui.desktop

@@ -0,0 +1,11 @@
+[Desktop Entry]
+Version=1.0
+Type=Application
+Categories=Education;Science
+MimeType=text/x-application-lammps
+Exec=lammps-gui %f
+Name=The LAMMPS GUI
+Terminal=false
+GenericName=LAMMPS MD Simulator GUI
+Keywords=MD Simulation;LAMMPS;Molecular Dynamics;N-Body
+Icon=lammps

tools/lammps-gui/lammps-input.xml

@@ -0,0 +1,8 @@
+<?xml version="1.0"?>
+<mime-info xmlns='http://www.freedesktop.org/standards/shared-mime-info'>
+  <mime-type type="text/x-application-lammps">
+    <comment>LAMMPS input file</comment>
+    <glob pattern="*.lmp"/>
+    <glob pattern="in.*"/>
+  </mime-type>
+</mime-info>

tools/lammps-gui/lammpsgui.h

@@ -17,6 +17,7 @@
 #include <QMainWindow>
 
 #include <QList>
+#include <QPair>
 #include <QString>
 #include <vector>
 
@@ -24,6 +25,8 @@
 
 // forward declarations
 
+class GeneralTab;
+
 QT_BEGIN_NAMESPACE
 namespace Ui {
 class LammpsGui;
@@ -39,11 +42,13 @@ class Highlighter;
 class StdCapture;
 class Preferences;
 class ImageViewer;
+class ChartWindow;
 
 class LammpsGui : public QMainWindow {
     Q_OBJECT
 
     friend class CodeEditor;
+    friend class GeneralTab;
 
 public:
     LammpsGui(QWidget *parent = nullptr, const char *filename = nullptr);
@@ -52,12 +57,16 @@ public:
 protected:
     void open_file(const QString &filename);
     void write_file(const QString &filename);
+    void update_recents(const QString &filename = "");
+    void update_variables();
     void start_lammps();
     void run_done();
 
 private slots:
     void new_document();
     void open();
+    void open_recent();
+    void start_exe();
     void save();
     void save_as();
     void quit();
@@ -69,33 +78,44 @@ private slots:
     void clear();
     void run_buffer();
     void stop_run();
+    void edit_variables();
+    void render_image();
     void view_image();
+    void view_chart();
+    void view_log();
     void about();
     void help();
     void manual();
+    void howto();
     void logupdate();
     void modified();
     void preferences();
     void defaults();
 
-private:
+protected:
     Ui::LammpsGui *ui;
+
+private:
     Highlighter *highlighter;
     StdCapture *capturer;
     QLabel *status;
     QPlainTextEdit *logwindow;
     ImageViewer *imagewindow;
+    ChartWindow *chartwindow;
     QTimer *logupdater;
     QLabel *dirstatus;
     QProgressBar *progress;
     Preferences *prefdialog;
+    QLabel *lammpsstatus;
 
     QString current_file;
     QString current_dir;
+    QList<QString> recent;
+    QList<QPair<QString, QString>> variables;
+
     LammpsWrapper lammps;
     std::string plugin_path;
     bool is_running;
-    QList<QString> recent_files;
     std::vector<char *> lammps_args;
 };
 #endif // LAMMPSGUI_H

tools/lammps-gui/lammpsgui.qrc

@@ -1,6 +1,47 @@
-<!DOCTYPE RCC><RCC version="1.0">
+<RCC>
-<qresource>
+    <qresource prefix="/">
-    <file alias="Monospace.ttf">DejaVuSansMono.ttf</file>
+        <file>lammps-icon-128x128.png</file>
-    <file>lammps-icon-128x128.png</file>
+        <file>help_index.table</file>
-</qresource>
+        <file>system-help.png</file>
+        <file>help-browser.png</file>
+        <file>gtk-zoom-in.png</file>
+        <file>gtk-zoom-out.png</file>
+        <file>gtk-zoom-fit.png</file>
+        <file>edit-delete.png</file>
+        <file>object-rotate-right.png</file>
+        <file>object-rotate-left.png</file>
+        <file>gtk-go-up.png</file>
+        <file>gtk-go-down.png</file>
+        <file>document-save-as.png</file>
+        <file>document-open-recent.png</file>
+        <file>document-open.png</file>
+        <file>document-new.png</file>
+        <file>edit-undo.png</file>
+        <file>edit-redo.png</file>
+        <file>edit-paste.png</file>
+        <file>edit-cut.png</file>
+        <file>edit-copy.png</file>
+        <file>application-exit.png</file>
+        <file>utilities-terminal.png</file>
+        <file>x-office-drawing.png</file>
+        <file>document-save.png</file>
+        <file>document-revert.png</file>
+        <file>preferences-desktop.png</file>
+        <file>preferences-desktop-personal.png</file>
+        <file>preferences-desktop-font.png</file>
+        <file>help-faq.png</file>
+        <file>help-about.png</file>
+        <file>emblem-photos.png</file>
+        <file>process-stop.png</file>
+        <file>emblem-default.png</file>
+        <file>window-close.png</file>
+        <file>application-plot.png</file>
+        <file>application-calc.png</file>
+        <file>system-box.png</file>
+        <file>axes-img.png</file>
+        <file>hd-img.png</file>
+        <file>antialias.png</file>
+        <file>ovito.png</file>
+        <file>vmd.png</file>
+    </qresource>
 </RCC>

tools/lammps-gui/lammpsgui.ui

@@ -13,19 +13,13 @@
   <property name="windowTitle">
    <string>LammpsGui</string>
   </property>
-  <widget class="QWidget" name="centralwidget">
+  <widget class="CodeEditor" name="textEdit">
-   <layout class="QHBoxLayout" name="horizontalLayout">
+   <property name="enabled">
-    <item>
+    <bool>true</bool>
-     <widget class="CodeEditor" name="textEdit">
+   </property>
-      <property name="enabled">
+   <property name="acceptDrops">
-       <bool>true</bool>
+    <bool>true</bool>
-      </property>
+   </property>
-      <property name="acceptDrops">
-       <bool>true</bool>
-      </property>
-     </widget>
-    </item>
-   </layout>
   </widget>
   <widget class="QMenuBar" name="menubar">
    <property name="geometry">
@@ -33,7 +27,7 @@
      <x>0</x>
      <y>0</y>
      <width>600</width>
-     <height>23</height>
+     <height>24</height>
     </rect>
    </property>
    <widget class="QMenu" name="menuFile">
@@ -41,8 +35,15 @@
      <string>&amp;File</string>
     </property>
     <addaction name="actionNew"/>
+    <addaction name="separator"/>
     <addaction name="actionOpen"/>
     <addaction name="separator"/>
+    <addaction name="action_1"/>
+    <addaction name="action_2"/>
+    <addaction name="action_3"/>
+    <addaction name="action_4"/>
+    <addaction name="action_5"/>
+    <addaction name="separator"/>
     <addaction name="actionSave"/>
     <addaction name="actionSave_As"/>
     <addaction name="separator"/>
@@ -69,7 +70,11 @@
     <addaction name="actionRun_Buffer"/>
     <addaction name="actionStop_LAMMPS"/>
     <addaction name="separator"/>
+    <addaction name="actionSet_Variables"/>
+    <addaction name="separator"/>
     <addaction name="actionImage"/>
+    <addaction name="actionView_in_OVITO"/>
+    <addaction name="actionView_in_VMD"/>
    </widget>
    <widget class="QMenu" name="menuAbout">
     <property name="title">
@@ -77,219 +82,162 @@
     </property>
     <addaction name="actionAbout_LAMMPS_GUI"/>
     <addaction name="action_Help"/>
+    <addaction name="actionLAMMPS_GUI_Howto"/>
     <addaction name="actionLAMMPS_Manual"/>
    </widget>
+   <widget class="QMenu" name="menu_View">
+    <property name="title">
+     <string>&amp;View</string>
+    </property>
+    <addaction name="actionView_Log_Window"/>
+    <addaction name="actionView_Graph_Window"/>
+    <addaction name="actionView_Image_Window"/>
+   </widget>
    <addaction name="menuFile"/>
    <addaction name="menuEdit"/>
    <addaction name="menu_Run"/>
+   <addaction name="menu_View"/>
    <addaction name="menuAbout"/>
   </widget>
   <widget class="QStatusBar" name="statusbar"/>
   <action name="actionNew">
    <property name="icon">
-    <iconset theme="document-new">
+    <iconset theme=":/document-new.png"/>
-     <normaloff>.</normaloff>.</iconset>
    </property>
    <property name="text">
     <string>&amp;New</string>
    </property>
-   <property name="toolTip">
-    <string>Start a New Input File</string>
-   </property>
-   <property name="statusTip">
-    <string>Start a New Input File</string>
-   </property>
    <property name="shortcut">
     <string>Ctrl+N</string>
    </property>
   </action>
   <action name="actionOpen">
    <property name="icon">
-    <iconset theme="document-open">
+    <iconset theme=":/document-open.png"/>
-     <normaloff>.</normaloff>.</iconset>
    </property>
    <property name="text">
     <string>&amp;Open</string>
    </property>
-   <property name="toolTip">
-    <string>Open an Input File</string>
-   </property>
-   <property name="statusTip">
-    <string>Open an Input File</string>
-   </property>
    <property name="shortcut">
     <string>Ctrl+O</string>
    </property>
   </action>
   <action name="actionSave">
    <property name="icon">
-    <iconset theme="document-save">
+    <iconset theme=":/document-save.png"/>
-     <normaloff>.</normaloff>.</iconset>
    </property>
    <property name="text">
     <string>&amp;Save</string>
    </property>
-   <property name="toolTip">
-    <string>Save Input File</string>
-   </property>
-   <property name="statusTip">
-    <string>Save Input File</string>
-   </property>
    <property name="shortcut">
     <string>Ctrl+S</string>
    </property>
   </action>
   <action name="actionSave_As">
    <property name="icon">
-    <iconset theme="document-save-as">
+    <iconset theme=":/document-save-as.png"/>
-     <normaloff>.</normaloff>.</iconset>
    </property>
    <property name="text">
     <string>Save &amp;As</string>
    </property>
-   <property name="toolTip">
-    <string>Save Input File As...</string>
-   </property>
-   <property name="statusTip">
-    <string>Save Input File As...</string>
-   </property>
    <property name="shortcut">
     <string>Ctrl+Shift+S</string>
    </property>
   </action>
   <action name="actionQuit">
    <property name="icon">
-    <iconset theme="application-exit">
+    <iconset theme=":/application-exit.png"/>
-     <normaloff>.</normaloff>.</iconset>
    </property>
    <property name="text">
     <string>&amp;Quit</string>
    </property>
-   <property name="toolTip">
-    <string>Quit LAMMPS-GUI</string>
-   </property>
-   <property name="statusTip">
-    <string>Quit LAMMPS-GUI</string>
-   </property>
    <property name="shortcut">
     <string>Ctrl+Q</string>
    </property>
   </action>
   <action name="actionCut">
    <property name="icon">
-    <iconset theme="edit-cut">
+    <iconset theme=":/edit-cut.png"/>
-     <normaloff>.</normaloff>.</iconset>
    </property>
    <property name="text">
     <string>Cu&amp;t</string>
    </property>
-   <property name="statusTip">
-    <string>Cut Selected Text to Clipboard</string>
-   </property>
    <property name="shortcut">
     <string>Ctrl+X</string>
    </property>
   </action>
   <action name="actionCopy">
    <property name="icon">
-    <iconset theme="edit-copy">
+    <iconset theme=":/edit-copy.png"/>
-     <normaloff>.</normaloff>.</iconset>
    </property>
    <property name="text">
     <string>&amp;Copy</string>
    </property>
-   <property name="statusTip">
-    <string>Copy Selected Text to Clipboard</string>
-   </property>
    <property name="shortcut">
     <string>Ctrl+C</string>
    </property>
   </action>
   <action name="actionPaste">
    <property name="icon">
-    <iconset theme="edit-paste">
+    <iconset theme=":/edit-paste.png"/>
-     <normaloff>.</normaloff>.</iconset>
    </property>
    <property name="text">
     <string>&amp;Paste</string>
    </property>
-   <property name="statusTip">
-    <string>Paste Text from Clipboard</string>
-   </property>
    <property name="shortcut">
     <string>Ctrl+V</string>
    </property>
   </action>
   <action name="actionUndo">
    <property name="icon">
-    <iconset theme="edit-undo">
+    <iconset theme=":/edit-undo.png"/>
-     <normaloff>.</normaloff>.</iconset>
    </property>
    <property name="text">
     <string>&amp;Undo</string>
    </property>
-   <property name="statusTip">
-    <string>Undo Edit</string>
-   </property>
    <property name="shortcut">
     <string>Ctrl+Z</string>
    </property>
   </action>
   <action name="actionRedo">
    <property name="icon">
-    <iconset theme="edit-redo">
+    <iconset theme=":/edit-redo.png"/>
-     <normaloff>.</normaloff>.</iconset>
    </property>
    <property name="text">
     <string>&amp;Redo</string>
    </property>
-   <property name="statusTip">
-    <string>Redo Edit</string>
-   </property>
    <property name="shortcut">
     <string>Ctrl+Shift+Z</string>
    </property>
   </action>
   <action name="actionRun_Buffer">
    <property name="icon">
-    <iconset theme="emblem-default">
+    <iconset theme=":/emblem-default.png"/>
-     <normaloff>.</normaloff>.</iconset>
    </property>
    <property name="text">
     <string>&amp;Run LAMMPS</string>
    </property>
-   <property name="toolTip">
-    <string>Run LAMMPS with Input</string>
-   </property>
    <property name="shortcut">
     <string>Ctrl+Return</string>
    </property>
   </action>
   <action name="actionStop_LAMMPS">
    <property name="icon">
-    <iconset theme="process-stop">
+    <iconset theme=":/process-stop.png"/>
-     <normaloff>.</normaloff>.</iconset>
    </property>
    <property name="text">
     <string>&amp;Stop LAMMPS</string>
    </property>
-   <property name="toolTip">
-    <string>Stop LAMMPS Process</string>
-   </property>
    <property name="shortcut">
     <string>Ctrl+/</string>
    </property>
   </action>
   <action name="actionImage">
    <property name="icon">
-    <iconset theme="emblem-photos">
+    <iconset theme=":/emblem-photos.png"/>
-     <normaloff>.</normaloff>.</iconset>
    </property>
    <property name="text">
-    <string>&amp;View Snapshot</string>
+    <string>View &amp;Image</string>
-   </property>
-   <property name="toolTip">
-    <string>View Snapshot of current LAMMPS state</string>
    </property>
    <property name="shortcut">
     <string>Ctrl+I</string>
@@ -297,35 +245,29 @@
   </action>
   <action name="actionAbout_LAMMPS_GUI">
    <property name="icon">
-    <iconset theme="help-about">
+    <iconset theme=":/help-about.png"/>
-     <normaloff>.</normaloff>.</iconset>
    </property>
    <property name="text">
-    <string>&amp;About LAMMPS-GUI</string>
+    <string>&amp;About LAMMPS</string>
    </property>
-   <property name="toolTip">
+   <property name="shortcut">
-    <string>About LAMMPS-GUI</string>
+    <string>Ctrl+Shift+A</string>
    </property>
   </action>
   <action name="action_Help">
    <property name="icon">
-    <iconset theme="help-faq">
+    <iconset theme=":/help-faq.png"/>
-     <normaloff>.</normaloff>.</iconset>
    </property>
    <property name="text">
     <string>Quick &amp;Help</string>
    </property>
-   <property name="toolTip">
-    <string>Quick Help</string>
-   </property>
    <property name="shortcut">
-    <string>Ctrl+Shift+/</string>
+    <string>Ctrl+Shift+H</string>
    </property>
   </action>
   <action name="actionPreferences">
    <property name="icon">
-    <iconset theme="preferences-desktop">
+    <iconset theme=":/preferences-desktop.png"/>
-     <normaloff>.</normaloff>.</iconset>
    </property>
    <property name="text">
     <string>Pre&amp;ferences...</string>
@@ -336,21 +278,140 @@
   </action>
   <action name="actionLAMMPS_Manual">
    <property name="icon">
-    <iconset theme="help-browser">
+    <iconset theme=":/help-browser.png"/>
-     <normaloff>.</normaloff>.</iconset>
    </property>
    <property name="text">
     <string>LAMMPS &amp;Manual</string>
    </property>
+   <property name="shortcut">
+    <string>Ctrl+Shift+M</string>
+   </property>
   </action>
   <action name="actionDefaults">
    <property name="icon">
-    <iconset theme="document-revert"/>
+    <iconset theme=":/document-revert.png"/>
    </property>
    <property name="text">
     <string>Reset to &amp;Defaults</string>
    </property>
   </action>
+  <action name="actionView_in_OVITO">
+   <property name="icon">
+    <iconset theme=":/ovito.png"/>
+   </property>
+   <property name="text">
+    <string>View in &amp;OVITO</string>
+   </property>
+   <property name="shortcut">
+    <string>Ctrl+Shift+O</string>
+   </property>
+  </action>
+  <action name="actionView_in_VMD">
+   <property name="icon">
+    <iconset theme=":/vmd.png"/>
+   </property>
+   <property name="text">
+    <string>View in VM&amp;D</string>
+   </property>
+   <property name="shortcut">
+    <string>Ctrl+Shift+D</string>
+   </property>
+  </action>
+  <action name="actionView_Log_Window">
+   <property name="icon">
+    <iconset theme=":/utilities-terminal.png"/>
+   </property>
+   <property name="text">
+    <string>&amp;Log Window</string>
+   </property>
+   <property name="shortcut">
+    <string>Ctrl+Shift+L</string>
+   </property>
+  </action>
+  <action name="actionView_Graph_Window">
+   <property name="icon">
+    <iconset theme=":/x-office-drawing.png"/>
+   </property>
+   <property name="text">
+    <string>&amp;Chart Window</string>
+   </property>
+   <property name="shortcut">
+    <string>Ctrl+Shift+C</string>
+   </property>
+  </action>
+  <action name="action_1">
+   <property name="icon">
+    <iconset theme=":/document-open-recent.png"/>
+   </property>
+   <property name="text">
+    <string>&amp;1.</string>
+   </property>
+  </action>
+  <action name="action_2">
+   <property name="icon">
+    <iconset theme=":/document-open-recent.png"/>
+   </property>
+   <property name="text">
+    <string>&amp;2.</string>
+   </property>
+  </action>
+  <action name="action_3">
+   <property name="icon">
+    <iconset theme=":/document-open-recent.png"/>
+   </property>
+   <property name="text">
+    <string>&amp;3.</string>
+   </property>
+  </action>
+  <action name="action_4">
+   <property name="icon">
+    <iconset theme=":/document-open-recent.png"/>
+   </property>
+   <property name="text">
+    <string>&amp;4.</string>
+   </property>
+  </action>
+  <action name="action_5">
+   <property name="icon">
+    <iconset theme=":/document-open-recent.png"/>
+   </property>
+   <property name="text">
+    <string>&amp;5.</string>
+   </property>
+  </action>
+  <action name="actionView_Image_Window">
+   <property name="icon">
+    <iconset theme=":/emblem-photos.png"/>
+   </property>
+   <property name="text">
+    <string>&amp;Image Window</string>
+   </property>
+   <property name="shortcut">
+    <string>Ctrl+Shift+I</string>
+   </property>
+  </action>
+  <action name="actionSet_Variables">
+   <property name="icon">
+    <iconset theme=":/preferences-desktop-personal.png"/>
+   </property>
+   <property name="text">
+    <string>Set &amp;Variables...</string>
+   </property>
+   <property name="shortcut">
+    <string>Ctrl+Shift+V</string>
+   </property>
+  </action>
+  <action name="actionLAMMPS_GUI_Howto">
+   <property name="icon">
+    <iconset theme=":/system-help.png"/>
+   </property>
+   <property name="text">
+    <string>LAMMPS GUI Howto</string>
+   </property>
+   <property name="shortcut">
+    <string>Ctrl+Shift+G</string>
+   </property>
+  </action>
  </widget>
  <customwidgets>
   <customwidget>

tools/lammps-gui/lammpsrunner.h

@@ -27,17 +27,17 @@ public:
     // execute LAMMPS in runner thread
     void run() override
     {
-        lammps->command("clear");
         lammps->commands_string(input);
         delete[] input;
         emit resultReady();
     }
 
-    // transfer info to worker thread
+    // transfer info to worker thread and reset LAMMPS instance
     void setup_run(LammpsWrapper *_lammps, const char *_input)
     {
         lammps = _lammps;
         input  = _input;
+        lammps->command("clear");
     }
 
 signals:

tools/lammps-gui/lammpswrapper.cpp

@@ -23,13 +23,13 @@ LammpsWrapper::LammpsWrapper() : lammps_handle(nullptr), plugin_handle(nullptr)
 
 void LammpsWrapper::open(int narg, char **args)
 {
-    if (!lammps_handle) {
+    // since there may only be one LAMMPS instance in LAMMPS GUI we don't open a second
+    if (lammps_handle) return;
 #if defined(LAMMPS_GUI_USE_PLUGIN)
-        lammps_handle = ((liblammpsplugin_t *)plugin_handle)->open_no_mpi(narg, args, nullptr);
+    lammps_handle = ((liblammpsplugin_t *)plugin_handle)->open_no_mpi(narg, args, nullptr);
 #else
-        lammps_handle = lammps_open_no_mpi(narg, args, nullptr);
+    lammps_handle = lammps_open_no_mpi(narg, args, nullptr);
 #endif
-    }
 }
 
 int LammpsWrapper::extract_setting(const char *keyword)
@@ -39,7 +39,33 @@ int LammpsWrapper::extract_setting(const char *keyword)
 #if defined(LAMMPS_GUI_USE_PLUGIN)
         val = ((liblammpsplugin_t *)plugin_handle)->extract_setting(lammps_handle, keyword);
 #else
-        val           = lammps_extract_setting(lammps_handle, keyword);
+        val = lammps_extract_setting(lammps_handle, keyword);
+#endif
+    }
+    return val;
+}
+
+int LammpsWrapper::id_count(const char *keyword)
+{
+    int val = 0;
+    if (lammps_handle) {
+#if defined(LAMMPS_GUI_USE_PLUGIN)
+        val = ((liblammpsplugin_t *)plugin_handle)->id_count(lammps_handle, keyword);
+#else
+        val = lammps_id_count(lammps_handle, keyword);
+#endif
+    }
+    return val;
+}
+
+int LammpsWrapper::id_name(const char *keyword, int idx, char *buf, int len)
+{
+    int val = 0;
+    if (lammps_handle) {
+#if defined(LAMMPS_GUI_USE_PLUGIN)
+        val = ((liblammpsplugin_t *)plugin_handle)->id_name(lammps_handle, keyword, idx, buf, len);
+#else
+        val = lammps_id_name(lammps_handle, keyword, idx, buf, len);
 #endif
     }
     return val;
@@ -52,12 +78,25 @@ double LammpsWrapper::get_thermo(const char *keyword)
 #if defined(LAMMPS_GUI_USE_PLUGIN)
         val = ((liblammpsplugin_t *)plugin_handle)->get_thermo(lammps_handle, keyword);
 #else
-        val           = lammps_get_thermo(lammps_handle, keyword);
+        val = lammps_get_thermo(lammps_handle, keyword);
 #endif
     }
     return val;
 }
 
+void *LammpsWrapper::last_thermo(const char *keyword, int index)
+{
+    void *ptr = nullptr;
+    if (lammps_handle) {
+#if defined(LAMMPS_GUI_USE_PLUGIN)
+        ptr = ((liblammpsplugin_t *)plugin_handle)->last_thermo(lammps_handle, keyword, index);
+#else
+        ptr = lammps_last_thermo(lammps_handle, keyword, index);
+#endif
+    }
+    return ptr;
+}
+
 bool LammpsWrapper::is_running()
 {
     int val = 0;
@@ -65,7 +104,7 @@ bool LammpsWrapper::is_running()
 #if defined(LAMMPS_GUI_USE_PLUGIN)
         val = ((liblammpsplugin_t *)plugin_handle)->is_running(lammps_handle);
 #else
-        val           = lammps_is_running(lammps_handle);
+        val = lammps_is_running(lammps_handle);
 #endif
     }
     return val != 0;
@@ -103,6 +142,7 @@ bool LammpsWrapper::has_error() const
 #endif
 }
 
+// may be called with null handle. returns global error then.
 int LammpsWrapper::get_last_error_message(char *buf, int buflen)
 {
 #if defined(LAMMPS_GUI_USE_PLUGIN)
@@ -115,9 +155,9 @@ int LammpsWrapper::get_last_error_message(char *buf, int buflen)
 void LammpsWrapper::force_timeout()
 {
 #if defined(LAMMPS_GUI_USE_PLUGIN)
-    ((liblammpsplugin_t *)plugin_handle)->force_timeout(lammps_handle);
+    if (lammps_handle) ((liblammpsplugin_t *)plugin_handle)->force_timeout(lammps_handle);
 #else
-    lammps_force_timeout(lammps_handle);
+    if (lammps_handle) lammps_force_timeout(lammps_handle);
 #endif
 }
 
@@ -188,7 +228,10 @@ bool LammpsWrapper::has_plugin() const
 
 bool LammpsWrapper::load_lib(const char *libfile)
 {
-    if (plugin_handle) liblammpsplugin_release((liblammpsplugin_t *)plugin_handle);
+    if (plugin_handle) {
+        close();
+        liblammpsplugin_release((liblammpsplugin_t *)plugin_handle);
+    }
     plugin_handle = liblammpsplugin_load(libfile);
     if (!plugin_handle) return false;
     if (((liblammpsplugin_t *)plugin_handle)->abiversion != LAMMPSPLUGIN_ABI_VERSION) {

tools/lammps-gui/lammpswrapper.h

@@ -29,7 +29,11 @@ public:
     void force_timeout();
 
     int extract_setting(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;

tools/lammps-gui/logwindow.cpp

@@ -0,0 +1,35 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   LAMMPS development team: developers@lammps.org
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "logwindow.h"
+#include <QSettings>
+
+LogWindow::LogWindow(QWidget *parent) : QPlainTextEdit(parent)
+{
+    QSettings settings;
+    resize(settings.value("logx", 500).toInt(), settings.value("logy", 320).toInt());
+}
+
+void LogWindow::closeEvent(QCloseEvent *event)
+{
+    QSettings settings;
+    if (!isMaximized()) {
+        settings.setValue("logx", width());
+        settings.setValue("logy", height());
+    }
+    QPlainTextEdit::closeEvent(event);
+}
+
+// Local Variables:
+// c-basic-offset: 4
+// End:

tools/lammps-gui/logwindow.h

@@ -0,0 +1,32 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   LAMMPS development team: developers@lammps.org
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifndef LOGWINDOW_H
+#define LOGWINDOW_H
+
+#include <QPlainTextEdit>
+
+class LogWindow : public QPlainTextEdit {
+    Q_OBJECT
+
+public:
+    LogWindow(QWidget *parent = nullptr);
+
+protected:
+    void closeEvent(QCloseEvent *event) override;
+};
+
+#endif
+// Local Variables:
+// c-basic-offset: 4
+// End:

tools/lammps-gui/preferences.cpp

@@ -13,16 +13,22 @@
 
 #include "preferences.h"
 
+#include "lammpsgui.h"
 #include "lammpswrapper.h"
+#include "ui_lammpsgui.h"
 
+#include <QApplication>
 #include <QCheckBox>
+#include <QComboBox>
 #include <QCoreApplication>
 #include <QDialogButtonBox>
 #include <QDir>
 #include <QDoubleValidator>
 #include <QFileDialog>
+#include <QFontDialog>
 #include <QGroupBox>
 #include <QHBoxLayout>
+#include <QIcon>
 #include <QIntValidator>
 #include <QLabel>
 #include <QLineEdit>
@@ -38,10 +44,28 @@
 #include <omp.h>
 #endif
 
+#if defined(_WIN32)
+#ifndef WIN32_LEAN_AND_MEAN
+#define WIN32_LEAN_AND_MEAN
+#endif
+#include <process.h>
+#define execl(exe, arg0, arg1) _execl(exe, arg0, arg1)
+#else
+#include <unistd.h>
+#endif
+
+// duplicate string
+static char *mystrdup(const std::string &text)
+{
+    auto tmp = new char[text.size() + 1];
+    memcpy(tmp, text.c_str(), text.size() + 1);
+    return tmp;
+}
+
 Preferences::Preferences(LammpsWrapper *_lammps, QWidget *parent) :
     QDialog(parent), tabWidget(new QTabWidget),
     buttonBox(new QDialogButtonBox(QDialogButtonBox::Ok | QDialogButtonBox::Cancel)),
-    settings(new QSettings), lammps(_lammps)
+    settings(new QSettings), lammps(_lammps), need_relaunch(false)
 {
     tabWidget->addTab(new GeneralTab(settings, lammps), "&General Settings");
     tabWidget->addTab(new AcceleratorTab(settings, lammps), "&Accelerators");
@@ -94,7 +118,7 @@ void Preferences::accept()
     if (field)
         if (field->hasAcceptableInput()) settings->setValue("nthreads", field->text());
 
-    // store image width, height, and zoom
+    // store image width, height, zoom, and rendering settings
 
     settings->beginGroup("snapshot");
     field = tabWidget->findChild<QLineEdit *>("xsize");
@@ -106,14 +130,46 @@ void Preferences::accept()
     field = tabWidget->findChild<QLineEdit *>("zoom");
     if (field)
         if (field->hasAcceptableInput()) settings->setValue("zoom", field->text());
+    QCheckBox *box = tabWidget->findChild<QCheckBox *>("anti");
+    if (box) settings->setValue("antialias", box->isChecked());
+    box = tabWidget->findChild<QCheckBox *>("ssao");
+    if (box) settings->setValue("ssao", box->isChecked());
+    box = tabWidget->findChild<QCheckBox *>("box");
+    if (box) settings->setValue("box", box->isChecked());
+    box = tabWidget->findChild<QCheckBox *>("axes");
+    if (box) settings->setValue("axes", box->isChecked());
+    QComboBox *combo = tabWidget->findChild<QComboBox *>("background");
+    if (combo) settings->setValue("background", combo->currentText());
+    combo = tabWidget->findChild<QComboBox *>("boxcolor");
+    if (combo) settings->setValue("boxcolor", combo->currentText());
     settings->endGroup();
 
     // general settings
-    QCheckBox *box = tabWidget->findChild<QCheckBox *>("echo");
+    box = tabWidget->findChild<QCheckBox *>("echo");
-    if (box) settings->setValue("echo", box->isChecked() ? "1" : "0");
+    if (box) settings->setValue("echo", box->isChecked());
     box = tabWidget->findChild<QCheckBox *>("cite");
-    if (box) settings->setValue("cite", box->isChecked() ? "1" : "0");
+    if (box) settings->setValue("cite", box->isChecked());
+    box = tabWidget->findChild<QCheckBox *>("logreplace");
+    if (box) settings->setValue("logreplace", box->isChecked());
+    box = tabWidget->findChild<QCheckBox *>("chartreplace");
+    if (box) settings->setValue("chartreplace", box->isChecked());
+    box = tabWidget->findChild<QCheckBox *>("imagereplace");
+    if (box) settings->setValue("imagereplace", box->isChecked());
+    box = tabWidget->findChild<QCheckBox *>("viewlog");
+    if (box) settings->setValue("viewlog", box->isChecked());
+    box = tabWidget->findChild<QCheckBox *>("viewchart");
+    if (box) settings->setValue("viewchart", box->isChecked());
 
+    if (need_relaunch) {
+        QMessageBox msg(QMessageBox::Information, QString("Relaunching LAMMPS-GUI"),
+                        QString("LAMMPS library plugin path was changed.\n"
+                                "LAMMPS-GUI must be relaunched."),
+                        QMessageBox::Ok);
+        msg.exec();
+        const char *path = mystrdup(QCoreApplication::applicationFilePath().toStdString());
+        const char *arg0 = mystrdup(QCoreApplication::arguments().at(0).toStdString());
+        execl(path, arg0, (char *)NULL);
+    }
     QDialog::accept();
 }
 
@@ -123,21 +179,29 @@ GeneralTab::GeneralTab(QSettings *_settings, LammpsWrapper *_lammps, QWidget *pa
     auto *layout = new QVBoxLayout;
 
     auto *echo = new QCheckBox("Echo input to log");
-    echo->setCheckState(settings->value("echo", "0").toInt() ? Qt::Checked : Qt::Unchecked);
     echo->setObjectName("echo");
-    auto *cite = new QCheckBox("Include Citations");
+    echo->setCheckState(settings->value("echo", false).toBool() ? Qt::Checked : Qt::Unchecked);
-    cite->setCheckState(settings->value("cite", "0").toInt() ? Qt::Checked : Qt::Unchecked);
+    auto *cite = new QCheckBox("Include citation details");
     cite->setObjectName("cite");
-#if !defined(__APPLE__)
+    cite->setCheckState(settings->value("cite", false).toBool() ? Qt::Checked : Qt::Unchecked);
-    auto *tmplabel  = new QLabel("Scratch Folder:");
+    auto *logv = new QCheckBox("Show log window by default");
-    auto *tmpedit   = new QLineEdit(settings->value("tempdir", ".").toString());
+    logv->setObjectName("viewlog");
-    auto *tmpbrowse = new QPushButton("Browse...");
+    logv->setCheckState(settings->value("viewlog", true).toBool() ? Qt::Checked : Qt::Unchecked);
-    auto *tmplayout = new QHBoxLayout;
+    auto *pltv = new QCheckBox("Show chart window by default");
-    tmpedit->setObjectName("tmpedit");
+    pltv->setObjectName("viewchart");
-    tmplayout->addWidget(tmplabel);
+    pltv->setCheckState(settings->value("viewchart", true).toBool() ? Qt::Checked : Qt::Unchecked);
-    tmplayout->addWidget(tmpedit);
+    auto *logr = new QCheckBox("Replace log window on new run");
-    tmplayout->addWidget(tmpbrowse);
+    logr->setObjectName("logreplace");
-#endif
+    logr->setCheckState(settings->value("logreplace", false).toBool() ? Qt::Checked
+                                                                      : Qt::Unchecked);
+    auto *imgr = new QCheckBox("Replace image window on new render");
+    imgr->setObjectName("imagereplace");
+    imgr->setCheckState(settings->value("imagereplace", false).toBool() ? Qt::Checked
+                                                                        : Qt::Unchecked);
+    auto *pltr = new QCheckBox("Replace chart window on new run");
+    pltr->setObjectName("chartreplace");
+    pltr->setCheckState(settings->value("chartreplace", false).toBool() ? Qt::Checked
+                                                                        : Qt::Unchecked);
 
 #if defined(LAMMPS_GUI_USE_PLUGIN)
     auto *pluginlabel = new QLabel("Path to LAMMPS Shared Library File:");
@@ -151,25 +215,69 @@ GeneralTab::GeneralTab(QSettings *_settings, LammpsWrapper *_lammps, QWidget *pa
 
     connect(pluginbrowse, &QPushButton::released, this, &GeneralTab::pluginpath);
 #endif
+
+    auto *fontlayout = new QHBoxLayout;
+    auto *getallfont =
+        new QPushButton(QIcon(":/preferences-desktop-font.png"), "Select Default Font...");
+    auto *gettextfont =
+        new QPushButton(QIcon(":/preferences-desktop-font.png"), "Select Text Font...");
+    fontlayout->addWidget(getallfont);
+    fontlayout->addWidget(gettextfont);
+    connect(getallfont, &QPushButton::released, this, &GeneralTab::newallfont);
+    connect(gettextfont, &QPushButton::released, this, &GeneralTab::newtextfont);
+
     layout->addWidget(echo);
     layout->addWidget(cite);
-#if !defined(__APPLE__)
+    layout->addWidget(logv);
-    layout->addLayout(tmplayout);
+    layout->addWidget(pltv);
-#endif
+    layout->addWidget(logr);
+    layout->addWidget(pltr);
+    layout->addWidget(imgr);
 #if defined(LAMMPS_GUI_USE_PLUGIN)
     layout->addWidget(pluginlabel);
     layout->addLayout(pluginlayout);
 #endif
+    layout->addLayout(fontlayout);
     layout->addStretch(1);
     setLayout(layout);
 }
 
-void GeneralTab::newtmpfolder()
+void GeneralTab::updatefonts(const QFont &all, const QFont &text)
 {
-    QLineEdit *field = findChild<QLineEdit *>("tmpedit");
+    LammpsGui *main;
-    QString tmpdir =
+    for (QWidget *widget : QApplication::topLevelWidgets())
-        QFileDialog::getExistingDirectory(this, "Find Folder for Temporary Files", field->text());
+        if (widget->objectName() == "LammpsGui") main = dynamic_cast<LammpsGui *>(widget);
-    if (!tmpdir.isEmpty()) field->setText(tmpdir);
+
+    QApplication::setFont(all);
+    main->ui->textEdit->document()->setDefaultFont(text);
+}
+
+void GeneralTab::newallfont()
+{
+    QSettings settings;
+    QFont all, text;
+    all.fromString(settings.value("allfont", "").toString());
+    text.fromString(settings.value("textfont", "").toString());
+
+    bool ok    = false;
+    QFont font = QFontDialog::getFont(&ok, all, this, QString("Select Default Font"));
+    if (ok) updatefonts(font, text);
+
+    settings.setValue("allfont", font.toString());
+}
+
+void GeneralTab::newtextfont()
+{
+    QSettings settings;
+    QFont all, text;
+    all.fromString(settings.value("allfont", "").toString());
+    text.fromString(settings.value("textfont", "").toString());
+
+    bool ok    = false;
+    QFont font = QFontDialog::getFont(&ok, text, this, QString("Select Text Font"));
+    if (ok) updatefonts(all, font);
+
+    settings.setValue("textfont", font.toString());
 }
 
 void GeneralTab::pluginpath()
@@ -179,16 +287,11 @@ void GeneralTab::pluginpath()
         QFileDialog::getOpenFileName(this, "Select Shared LAMMPS Library to Load", field->text(),
                                      "Shared Objects (*.so *.dll *.dylib)");
     if (!pluginfile.isEmpty() && pluginfile.contains("liblammps", Qt::CaseSensitive)) {
-        if (lammps->load_lib(pluginfile.toStdString().c_str())) {
+        auto canonical = QFileInfo(pluginfile).canonicalFilePath();
-            auto canonical = QFileInfo(pluginfile).canonicalFilePath();
+        field->setText(pluginfile);
-            field->setText(pluginfile);
+        settings->setValue("plugin_path", canonical);
-            settings->setValue("plugin_path", canonical);
+        // ugly hack
-        } else {
+        qobject_cast<Preferences *>(parent()->parent()->parent())->need_relaunch = true;
-            // plugin did not load cannot continue
-            settings->remove("plugin_path");
-            QMessageBox::critical(this, "Error", "Cannot open LAMMPS shared library file");
-            QCoreApplication::quit();
-        }
     }
 }
 
@@ -288,11 +391,28 @@ SnapshotTab::SnapshotTab(QSettings *_settings, QWidget *parent) :
     auto *xsize = new QLabel("Image width:");
     auto *ysize = new QLabel("Image height:");
     auto *zoom  = new QLabel("Zoom factor:");
+    auto *anti  = new QLabel("Antialias:");
+    auto *ssao  = new QLabel("HQ Image mode:");
+    auto *bbox  = new QLabel("Show Box:");
+    auto *axes  = new QLabel("Show Axes:");
+    auto *cback = new QLabel("Background Color:");
+    auto *cbox  = new QLabel("Box Color:");
     settings->beginGroup("snapshot");
     auto *xval = new QLineEdit(settings->value("xsize", "800").toString());
     auto *yval = new QLineEdit(settings->value("ysize", "600").toString());
     auto *zval = new QLineEdit(settings->value("zoom", "1.0").toString());
-    settings->endGroup();
+    auto *aval = new QCheckBox;
+    auto *sval = new QCheckBox;
+    auto *bval = new QCheckBox;
+    auto *eval = 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);
+    aval->setObjectName("anti");
+    bval->setCheckState(settings->value("box", true).toBool() ? Qt::Checked : Qt::Unchecked);
+    bval->setObjectName("box");
+    eval->setCheckState(settings->value("axes", false).toBool() ? Qt::Checked : Qt::Unchecked);
+    eval->setObjectName("axes");
 
     auto *intval = new QIntValidator(100, 100000, this);
     xval->setValidator(intval);
@@ -302,15 +422,48 @@ SnapshotTab::SnapshotTab(QSettings *_settings, QWidget *parent) :
     zval->setValidator(new QDoubleValidator(0.01, 100.0, 100, this));
     zval->setObjectName("zoom");
 
+    auto *background = new QComboBox;
+    background->setObjectName("background");
+    background->addItem("black");
+    background->addItem("darkgray");
+    background->addItem("gray");
+    background->addItem("silver");
+    background->addItem("white");
+    background->setCurrentText(settings->value("background", "black").toString());
+
+    auto *boxcolor = new QComboBox;
+    boxcolor->setObjectName("boxcolor");
+    boxcolor->addItem("yellow");
+    boxcolor->addItem("silver");
+    boxcolor->addItem("gray");
+    boxcolor->addItem("darkred");
+    boxcolor->addItem("darkgreen");
+    boxcolor->addItem("darkblue");
+    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->addItem(new QSpacerItem(100, 100, QSizePolicy::Minimum, QSizePolicy::Expanding), 3, 0);
+    grid->addWidget(aval, 3, 1, Qt::AlignTop);
-    grid->addItem(new QSpacerItem(100, 100, QSizePolicy::Minimum, QSizePolicy::Expanding), 3, 1);
+    grid->addWidget(sval, 4, 1, Qt::AlignVCenter);
-    grid->addItem(new QSpacerItem(100, 100, QSizePolicy::Expanding, QSizePolicy::Expanding), 3, 2);
+    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);
+
+    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);
     setLayout(grid);
 }
 

tools/lammps-gui/preferences.h

@@ -17,6 +17,7 @@
 #include <QDialog>
 
 class QDialogButtonBox;
+class QFont;
 class QSettings;
 class QTabWidget;
 class LammpsWrapper;
@@ -31,6 +32,8 @@ public:
 private slots:
     void accept() override;
 
+public:
+    bool need_relaunch;
 private:
     QTabWidget *tabWidget;
     QDialogButtonBox *buttonBox;
@@ -48,9 +51,11 @@ public:
 
 private slots:
     void pluginpath();
-    void newtmpfolder();
+    void newallfont();
+    void newtextfont();
 
 private:
+    void updatefonts(const QFont &all, const QFont &text);
     QSettings *settings;
     LammpsWrapper *lammps;
 };

tools/lammps-gui/setvariables.cpp

@@ -0,0 +1,124 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   LAMMPS development team: developers@lammps.org
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "setvariables.h"
+
+#include <QDialogButtonBox>
+#include <QGridLayout>
+#include <QIcon>
+#include <QLabel>
+#include <QLineEdit>
+#include <QPushButton>
+#include <QSizePolicy>
+
+SetVariables::SetVariables(QList<QPair<QString, QString>> &_vars, QWidget *parent) :
+    QDialog(parent), vars(_vars), layout(new QVBoxLayout)
+{
+    auto *top = new QLabel("Set Variables:");
+    layout->addWidget(top, 0, Qt::AlignHCenter);
+
+    int i = 1;
+    for (const auto &v : vars) {
+        auto *row  = new QHBoxLayout;
+        auto *name = new QLineEdit(v.first);
+        auto *val  = new QLineEdit(v.second);
+        auto *del  = new QPushButton(QIcon(":/edit-delete.png"), "");
+        name->setObjectName("varname");
+        val->setObjectName("varval");
+        del->setObjectName(QString::number(i));
+        connect(del, &QPushButton::released, this, &SetVariables::del_row);
+        row->addWidget(name);
+        row->addWidget(val);
+        row->addWidget(del);
+        layout->addLayout(row);
+        ++i;
+    }
+    layout->addSpacerItem(new QSpacerItem(10, 10, QSizePolicy::Minimum, QSizePolicy::Expanding));
+
+    auto *buttonBox = new QDialogButtonBox(QDialogButtonBox::Ok | QDialogButtonBox::Cancel);
+    auto *add       = new QPushButton("&Add Row");
+    add->setObjectName("add_row");
+    buttonBox->addButton(add, QDialogButtonBox::ActionRole);
+    connect(add, &QPushButton::released, this, &SetVariables::add_row);
+    connect(buttonBox, &QDialogButtonBox::accepted, this, &SetVariables::accept);
+    connect(buttonBox, &QDialogButtonBox::rejected, this, &QDialog::reject);
+
+    layout->addWidget(buttonBox);
+    setLayout(layout);
+    setWindowTitle("LAMMPS-GUI - Set Variables");
+    resize(300, 200);
+}
+
+void SetVariables::accept()
+{
+    // store all data in variables class and then confirm accepting
+    vars.clear();
+    int nrows = layout->count() - 2;
+    for (int i = 1; i < nrows; ++i) {
+        auto *row = layout->itemAt(i)->layout();
+        auto *var = dynamic_cast<QLineEdit *>(row->itemAt(0)->widget());
+        auto *val = dynamic_cast<QLineEdit *>(row->itemAt(1)->widget());
+        if (var && val) vars.append(qMakePair(var->text(), val->text()));
+    }
+
+    QDialog::accept();
+}
+
+void SetVariables::add_row()
+{
+    int nrows  = layout->count();
+    auto *row  = new QHBoxLayout;
+    auto *name = new QLineEdit(QString());
+    auto *val  = new QLineEdit(QString());
+    auto *del  = new QPushButton(QIcon(":/edit-delete.png"), "");
+    name->setObjectName("varname");
+    val->setObjectName("varval");
+    del->setObjectName(QString::number(nrows - 2));
+    connect(del, &QPushButton::released, this, &SetVariables::del_row);
+    row->addWidget(name);
+    row->addWidget(val);
+    row->addWidget(del);
+    layout->insertLayout(nrows - 2, row);
+}
+
+void SetVariables::del_row()
+{
+    int nrows = layout->count();
+    auto *who = sender();
+    if (who) {
+        // figure out which row was deleted and delete its layout and widgets
+        int delrow = who->objectName().toInt();
+        auto *row  = layout->takeAt(delrow);
+        while (row->layout()->count() > 0) {
+            auto *item = row->layout()->takeAt(0);
+            if (item) {
+                row->layout()->removeItem(item);
+                delete item->widget();
+                delete item;
+            }
+        }
+        layout->removeItem(row);
+        delete row->layout();
+
+        // renumber the delete pushbutton names
+        for (int i = delrow; i < nrows - 3; ++i) {
+            auto *row    = layout->itemAt(i)->layout();
+            auto *widget = row->itemAt(2)->widget();
+            widget->setObjectName(QString::number(i));
+        }
+    }
+}
+
+// Local Variables:
+// c-basic-offset: 4
+// End:

tools/lammps-gui/setvariables.h

@@ -0,0 +1,43 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   LAMMPS development team: developers@lammps.org
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifndef SET_VARIABLES_H
+#define SET_VARIABLES_H
+
+#include <QDialog>
+#include <QList>
+#include <QPair>
+#include <QString>
+
+class SetVariables : public QDialog {
+    Q_OBJECT
+
+public:
+    explicit SetVariables(QList<QPair<QString, QString>> &vars, QWidget *parent = nullptr);
+    ~SetVariables() = default;
+
+private slots:
+    void accept() override;
+    void add_row();
+    void del_row();
+
+private:
+    QList<QPair<QString, QString>> &vars;
+    class QVBoxLayout *layout;
+};
+
+#endif
+
+// Local Variables:
+// c-basic-offset: 4
+// End:

tools/lammps-gui/update-help-index.sh

@@ -0,0 +1,4 @@
+#!/bin/sh
+# this updates the help index table
+
+grep '\.\. index::' ../../doc/src/*.rst | sort  | sed -e 's/^.*src\/\([^/]\+\)\.rst:/\1.html /' -e 's/\.\. \+index:: \+//' > help_index.table