Patch 0.2.3 (#10)

* Fixing menu items w.r.t. issue #4

* Fixing issue #8

* Initial commit CLI

* Implementing NEB analysis via CLI

* Updating README.md

* Creating patch file for Qt5

* Fixing compilation instructions

* Fixing compilation instructions

* Fixing bug in info widget

.github/workflows/linux.yml

@@ -0,0 +1,72 @@
+name: linux
+
+on:
+  push:
+    branches: [ "master", "develop" ]
+  pull_request:
+    branches: [ "master", "develop" ]
+
+jobs:
+  #
+  # Ubuntu
+  #
+  build-ubuntu:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - name: Install packages
+      run: |
+        sudo apt update && sudo apt install -y qt6-tools-dev qt6-base-dev libqt6charts6-dev libqt6widgets6 libqt6gui6 libqt6opengl6-dev libgl1-mesa-dev build-essential cmake
+    - name: Configure CMake
+      run: |
+        mkdir build
+        cd build
+        cmake ..
+    - name: Build
+      run: |
+        cd build
+        make -j
+
+  #
+  # Ubuntu 12-Qt5
+  #
+  build-ubuntu-qt5:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - name: Install packages
+      run: |
+        sudo apt update && sudo apt install -y qtbase5-dev libqt5charts5-dev libgl1-mesa-dev build-essential cmake
+    - name: Apply patch
+      run: patch -p1 CMakeLists.txt < qt5.patch
+    - name: Configure CMake
+      run: |
+        mkdir build
+        cd build
+        cmake ..
+    - name: Build
+      run: |
+        cd build
+        make -j
+
+  #
+  # Debian 12
+  #
+  build-debian12:
+    runs-on: ubuntu-latest
+    container:
+      image: debian:12
+    steps:
+    - uses: actions/checkout@v3
+    - name: Install packages
+      run: |
+        apt update && apt install -y qt6-tools-dev qt6-base-dev libqt6charts6-dev libqt6widgets6 libqt6gui6 libqt6opengl6-dev libgl1-mesa-dev build-essential cmake
+    - name: Configure CMake
+      run: |
+        mkdir build
+        cd build
+        cmake ..
+    - name: Build
+      run: |
+        cd build
+        make -j

.github/workflows/build.yml → .github/workflows/windows.yml

@@ -1,4 +1,4 @@
-name: build
+name: windows
 
 on:
   push:
@@ -35,48 +35,6 @@ jobs:
     outputs:
       upload_url: ${{ steps.create_release.outputs.upload_url }}
 
-  #
-  # Ubuntu
-  #
-  build-ubuntu:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v3
-    - name: Install packages
-      run: |
-        sudo apt update && sudo apt install -y qt6-tools-dev qt6-base-dev libqt6charts6-dev libqt6widgets6 libqt6gui6 libqt6opengl6-dev libgl1-mesa-dev build-essential cmake
-    - name: Configure CMake
-      run: |
-        mkdir build
-        cd build
-        cmake ..
-    - name: Build
-      run: |
-        cd build
-        make -j
-
-  #
-  # Debian 12
-  #
-  build-debian12:
-    runs-on: ubuntu-latest
-    container:
-      image: debian:12
-    steps:
-    - uses: actions/checkout@v3
-    - name: Install packages
-      run: |
-        apt update && apt install -y qt6-tools-dev qt6-base-dev libqt6charts6-dev libqt6widgets6 libqt6gui6 libqt6opengl6-dev libgl1-mesa-dev build-essential cmake
-    - name: Configure CMake
-      run: |
-        mkdir build
-        cd build
-        cmake ..
-    - name: Build
-      run: |
-        cd build
-        make -j
-
   #
   # Windows
   #

.gitignore

@@ -53,4 +53,5 @@ glm/*
 .vscode/*
 *.exe
 bin/
-*.zip
+*.zip
+debbuild

README.md

@@ -1,7 +1,8 @@
 # Atom Architect
 
 ![GitHub tag (latest SemVer)](https://img.shields.io/github/v/tag/ifilot/atom-architect?label=version)
-[![build](https://github.com/ifilot/atom-architect/actions/workflows/build.yml/badge.svg)](https://github.com/ifilot/atom-architect/actions/workflows/build.yml)
+[![windows](https://github.com/ifilot/atom-architect/actions/workflows/windows.yml/badge.svg)](https://github.com/ifilot/atom-architect/actions/workflows/windows.yml)
+[![linux](https://github.com/ifilot/atom-architect/actions/workflows/linux.yml/badge.svg)](https://github.com/ifilot/atom-architect/actions/workflows/linux.yml)
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 
 ![Screenshot of Atom Architect](img/atom-architect-screenshot.JPG)
@@ -19,13 +20,17 @@ Latest installer for Window: [here](https://github.com/ifilot/atom-architect/rel
 
 ## Compilation
 
-For Windows, it is recommended to use the installer as shown above. For Linux,
-it is recommended to compile Atom Architect yourself. Please note that Atom
-Architect is only tested for Debian 12 and Ubuntu 22.04. For other
-distributions, you are on your own. 
+### Windows
 
-To compile Atom Architect, please follow the compilation instructions as shown
-below.
+Compilation for Windows is most easily done by installing Qt Creator and loading
+the project file `atom-architect.pro`.
+
+### Linux Debian / Ubuntu
+
+Please note that Atom Architect is only tested for Debian 12 and Ubuntu 22.04.
+For other distributions, you are on your own. 
+
+#### Qt6
 
 Start by installing all the required dependencies
 
@@ -60,11 +65,69 @@ folder the following command.
 sudo cp -v ./atom_architect /usr/local/bin/atom_architect
 ```
 
+#### Qt5
+
+Start by installing all the required dependencies
+
+```bash
+sudo apt update && sudo apt install -y \
+qtbase5-dev \
+libqt5charts5-dev \
+libgl1-mesa-dev \
+build-essential \
+cmake
+```
+
+After having cloned this repository and starting at its root folder, run a patch
+file to change from Qt6 to Qt5.
+
+```bash
+patch -p1 CMakeLists.txt < qt5.patch
+```
+
+Create a new build folder, go to this folder, create the compilation and start
+the compilation.
+
+```bash
+mkdir build
+cd build
+cmake ../
+make -j
+```
+
+This will generate the compilation scripts and compile Atom Architect. You can
+use Atom Architect by running `./atom_architect` in your `build` folder. If
+you wish to install Atom Architect on your system, you can run in your `build`
+folder the following command.
+
+```bash
+sudo cp -v ./atom_architect /usr/local/bin/atom_architect
+```
+
+### Snellius
+
+To compile for the Snellius infrastructure, it is recommended to use the Qt5
+toolchain. To do so, run the following patch file.
+
+```bash
+patch -p1 CMakeLists.txt < qt5.patch
+```
+
 ## Dependencies
 
 Atom Architect depends on [GLM](https://github.com/g-truc/glm) and
 [Eigen3](https://eigen.tuxfamily.org/index.php?title=Main_Page). Both are
 header-only C++ libraries and are for convenience purposes added to this
 repository. This implies that compilation of Atom Architect will not use your
 system-installed version of GLM and Eigen3, but use the one provided in this
-repository.
+repository.
+
+## Common problems
+
+> I have troubles running `Atom Architect` remotely via MobaXterm.
+
+Try to enable direct rendering by setting the following environmental variable:
+
+```bash
+export LIBGL_ALWAYS_INDIRECT=0
+```

assets/themes/darkorange/darkorange.qss

@@ -499,3 +499,11 @@ QHeaderView::section {
     background-color: #222;
     border: 0px;
 }
+
+QTableWidget QTableCornerButton::section {
+    background-color: #323232;
+}
+
+QTableWidget {
+    gridline-color: #fffff8;
+}

qt5.patch

@@ -0,0 +1,22 @@
+--- CMakeLists.txt	2024-09-02 20:58:43.184160900 +0200
++++ CMakeLists-Qt5.txt	2024-09-12 11:33:12.719435600 +0200
+@@ -20,8 +20,8 @@
+ )
+ add_compile_definitions(GIT_HASH="${GIT_HASH}")
+
+-# Find Qt6 packages
+-find_package(Qt6 REQUIRED COMPONENTS Widgets Charts)
++# Find Qt5 packages
++find_package(Qt5 REQUIRED COMPONENTS Widgets Charts)
+
+ add_executable(atom-architect
+     src/main.cpp
+@@ -65,7 +65,7 @@
+ include_directories("src/vendor/eigen-3.4.0"
+                     "src/vendor/glm-1.0.1")
+
+-target_link_libraries(atom-architect PRIVATE Qt6::Core Qt6::Widgets Qt6::Charts)
++target_link_libraries(atom-architect PRIVATE Qt5::Core Qt5::Widgets Qt5::Charts)
+
+ set_target_properties(atom-architect PROPERTIES
+     WIN32_EXECUTABLE ON

src/config.h

@@ -21,4 +21,4 @@
 #pragma once
 
 #define PROGRAM_NAME "Atom Architect"
-#define PROGRAM_VERSION "0.2.2"
+#define PROGRAM_VERSION "0.2.3"

src/data/structure_loader.cpp

@@ -35,9 +35,9 @@ StructureLoader::StructureLoader(){}
 std::shared_ptr<Structure> StructureLoader::load_file(const std::string& filename) {
     QFileInfo qfi(QString(filename.c_str()));
     std::shared_ptr<Structure> structure;
-    if(qfi.fileName() == "POSCAR" || qfi.fileName() == "CONTCAR") {
+    if(qfi.fileName().startsWith("POSCAR") || qfi.fileName().startsWith("CONTCAR")) {
         structure = this->load_poscar(filename);
-    } else if(qfi.fileName() == "OUTCAR") {
+    } else if(qfi.fileName().startsWith("OUTCAR")) {
         structure = this->load_outcar(filename).back();
     } else if(qfi.completeSuffix() == "geo") {
         structure = this->load_geo(filename);
@@ -392,7 +392,7 @@ std::vector<std::shared_ptr<Structure>> StructureLoader::load_outcar(const std::
                 unsigned int version_major = match.captured(2).toUInt();
                 unsigned int version_minor = match.captured(3).toUInt();
 
-                qDebug() << "Detected VASP: " << vasp_version;
+                qDebug() << "Detected VASP: " << vasp_version << "." << version_major << "." << version_minor;
 
                 continue;
             }

src/gui/anaglyph_widget.cpp

@@ -251,10 +251,17 @@ void AnaglyphWidget::mousePressEvent(QMouseEvent *event) {
         emit(signal_selection_message(this->structure->get_selection_string()));
     }
 
-    // custom menu
-    if (event->buttons() & Qt::RightButton && event->modifiers() & Qt::ControlModifier) {
-        this->custom_menu_requested(event->globalPosition().toPoint());
-    }
+    #if QT_VERSION >= QT_VERSION_CHECK(6, 0, 0)
+        // custom menu
+        if (event->buttons() & Qt::RightButton && event->modifiers() & Qt::ControlModifier) {
+            this->custom_menu_requested(event->globalPosition().toPoint());
+        }
+    #else
+        // custom menu
+        if (event->buttons() & Qt::RightButton && event->modifiers() & Qt::ControlModifier) {
+            this->custom_menu_requested(event->globalPos());
+        }
+    #endif
 }
 
 /**
@@ -287,8 +294,14 @@ void AnaglyphWidget::mouseMoveEvent(QMouseEvent *event) {
     if(this->arcball_rotation_flag) { // drag event
         // implementation adapted from
         // https://en.wikibooks.org/wiki/OpenGL_Programming/Modern_OpenGL_Tutorial_Arcball
+
+        #if QT_VERSION >= QT_VERSION_CHECK(6, 0, 0)
         double ex = event->position().x();
         double ey = event->position().y();
+        #else
+        double ex = event->pos().x();
+        double ey = event->pos().y();
+        #endif
         if(ex != this->m_lastPos.x() || ey != this->m_lastPos.y()) {
 
             // calculate arcball vectors

src/gui/anaglyph_widget.h

@@ -33,6 +33,7 @@
 #include <QDebug>
 #include <QTimer>
 #include <QMenu>
+#include <QtGlobal>
 
 #include <QtCore/qmath.h>
 #include <QtCore/qvariant.h>

src/gui/analysis_geometry_optimization.h

@@ -53,7 +53,7 @@ class AnalysisGeometryOptimization : public QWidget {
 public:
     AnalysisGeometryOptimization(QWidget* parent = nullptr);
 
-    inline void set_structures(const std::vector<std::shared_ptr<Structure>> _structures) {
+    inline void set_structures(const std::vector<std::shared_ptr<Structure>>& _structures) {
         this->structures = _structures;
         this->structures.front()->update();
         this->anaglyph_widget->set_structure(this->structures.front());

src/gui/analysis_neb.cpp

@@ -190,23 +190,33 @@ void AnalysisNEB::update_graph() {
  * @brief      Open new OUTCAR file
  */
 void AnalysisNEB::open() {
-    QString filename = QFileDialog::getOpenFileName(this, tr("Open file"), "", tr("VASP NEB binary (nebpack.bin)"));
+    QString filename = QFileDialog::getOpenFileName(this, tr("Open file"), "", tr("VASP NEB binary (*.bin)"));
 
     if(filename.isEmpty()) {
         return;
     }
 
+    this->load_file(filename);
+}
+
+/**
+ * @brief load_file
+ * @param filename
+ */
+void AnalysisNEB::load_file(const QString& filename) {
     StructureLoader sl;
     this->set_structures(sl.load_neb_bin(filename.toStdString()));
 
     // expand anaglyph widgets
-    unsigned int nr_rows = 4;
+    static const unsigned int nr_cols = 4;
+
+    qDebug() << "Loading " << this->structures.size() << " images.";
     for(unsigned int i=0; i<this->structures.size(); i++) {
         this->anaglyph_widgets.push_back(new AnaglyphWidget());
-        this->anaglyph_hypergrid->addWidget(this->anaglyph_widgets.back(), i / nr_rows * 2, i % nr_rows);
+        this->anaglyph_hypergrid->addWidget(this->anaglyph_widgets.back(), (i / nr_cols) * 2, i % nr_cols);
 
         this->image_labels.push_back(new QLabel(tr("Image %1").arg(i+1)));
-        this->anaglyph_hypergrid->addWidget(this->image_labels.back(), i / nr_rows * 2 + 1, i % nr_rows);
+        this->anaglyph_hypergrid->addWidget(this->image_labels.back(), (i / nr_cols) * 2 + 1, i % nr_cols);
 
         this->structures[i].front()->update();
         this->anaglyph_widgets.back()->set_structure(this->structures[i].front());