Merge pull request #71 from ComputationalPhysics/submodule

SimVis as a git submodule

.gitignore

@@ -32,4 +32,7 @@ Makefile*
 
 #QtCtreator Qml
 *.qmlproject.user
-*.qmlproject.user.*
+*.qmlproject.user.*
+
+lammps.pri
+lammps-android.pri

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "SimVis"]
+	path = SimVis
+	url = [email protected]:ComputationalPhysics/SimVis.git

.qmake.conf

@@ -0,0 +1,2 @@
+simvis_srcdir = $$PWD/SimVis
+simvis_builddir = $$shadowed($$PWD)/SimVis

README.md

@@ -1,2 +1,37 @@
-# atomify-lammps
-Atomify - a live LAMMPS visualizer
+# Atomify - a live LAMMPS visualizer #
+
+- Simplifty your workflow significantly.
+- Atomify is a script editor for LAMMPS supporting live visualization of the simulation. Edit your script, just press Run, and you will immediately see the atoms on your screen while LAMMPS is running. There is no need to dump the trajectories to disk and open them in VMD or Ovito anymore. It uses the high performance visualization library **[SimVis](https://github.com/computationalphysics/SimVis)** (based on Qt) allowing live visualization of millions of atoms in a live simulation.
+
+## Why ##
+
+The current workflow for developing LAMMPS scripts is as follows:
+- Edit the script in your favorite text editor
+- Open terminal, run the script and dump trajectories to disk
+- Open VMD, Ovito or some other visualization software to visualize the dumped trajectories
+With Atomify, we solved this problem by combining the script editing and visualizing in the same tool. Atomify runs LAMMPS internally, so there is almost no overhead in visualizing the simulation. 
+
+## Highlights ##
+- Full OpenMP support (MPI support will come later)
+- Also runs on your mobile phone / tablet (both Android and iOS)
+
+## Installation ##
+
+* Atomify is based on the Qt library, so you need to download **[Qt Creator](http://www.qt.io/download-open-source/)** (the open source version is fine). Qt version 5.5.0 or later is required.
+* Download a stable source tarball of the **[LAMMPS source code](http://lammps.sandia.gov/download.html)**
+It is now assumed that <atomify_source_folder> is the folder containing this README.md file. It is also assumed that <lammps_source_folder> is the folder containing the LAMMPS source code. This is for instance '~/Downloads/lammps-10Aug15/src'.
+Once you have downloaded the LAMMPS source code and extracted the contents, you will need to patch the LAMMPS source code with the patch_lammps.py python script:
+- `cd <atomify_source_folder>`
+- `python patch_lammps.py <lammps_source_folder>`
+
+Then, you will need to compile the LAMMPS source code with c++11 support. To do this, open the Makefile you will use (in <lammps_source_folder/MAKE/OPTIONS/Makefile.yourfavorite) and add '-std=c++11' to the CCFLAGS line. For instance, in the Makefile.ompi_g++, you should have the line `CCFLAGS =	-g -O3 -std=c++11`. 
+Now compile LAMMPS as a library. For example, to make the ompi_g++ version of LAMMPS:
+- `cd <lammps_source_folder>`
+- `make ompi_g++ mode=lib`
+
+The last step is to open Atomify in Qt Creator (open <atomify_source_folder>/atomify-lammps.pro). In Qt Creator, open the atomify-lammps.pro file and edit the two lines
+`INCLUDEPATH += /projects/lammps-10Aug15/src`
+`LIBS += -L/projects/lammps-10Aug15/src -llammps_omp`
+to match your <lammps_source_folder> and which version you compiled. For instance, if you compiled the ompi_g++ version, the linking in the last line should be `-llammps_ompi_g++`.
+
+Now, choose Release mode and enjoy Atomify.

atomify-lammps.pro

@@ -1,4 +1,4 @@
 TEMPLATE = subdirs
-SUBDIRS = src atomify-lammps
+SUBDIRS = SimVis atomify-lammps
 CONFIG += ordered
-atomify-lammps.depends = src
+atomify-lammps.depends = SimVis

atomify-lammps/CPcompute.cpp

@@ -30,7 +30,7 @@ CPCompute::CPCompute(QObject *parent) : QObject(parent)
 CPCompute::~CPCompute()
 {
     m_values.clear();
-    m_simulator = NULL;
+    m_simulator = nullptr;
     m_dependencies.clear();
 }
 
@@ -44,7 +44,7 @@ QString CPCompute::command() const
     return m_command;
 }
 
-MySimulator *CPCompute::simulator() const
+AtomifySimulator *CPCompute::simulator() const
 {
     return m_simulator;
 }
@@ -102,7 +102,7 @@ void CPCompute::setCommand(QString command)
     emit commandChanged(command);
 }
 
-void CPCompute::setSimulator(MySimulator *simulator)
+void CPCompute::setSimulator(AtomifySimulator *simulator)
 {
     if (m_simulator == simulator)
         return;

atomify-lammps/CPcompute.h

@@ -2,19 +2,18 @@
 #define COMPUTE_H
 
 #include <QObject>
-#include <QPair>
 #include <QVector>
 #include "lammpsoutput.h"
 
-class MySimulator; class LAMMPSController;
+class AtomifySimulator; class LAMMPSController;
 class CPCompute : public QObject
 {
     Q_OBJECT
     Q_PROPERTY(QString identifier READ identifier WRITE setIdentifier NOTIFY identifierChanged)
     Q_PROPERTY(QString fixIdentifier READ fixIdentifier WRITE setFixIdentifier NOTIFY fixIdentifierChanged)
     Q_PROPERTY(QString fixCommand READ fixCommand WRITE setFixCommand NOTIFY fixCommandChanged)
     Q_PROPERTY(QString command READ command WRITE setCommand NOTIFY commandChanged)
-    Q_PROPERTY(MySimulator* simulator READ simulator WRITE setSimulator NOTIFY simulatorChanged)
+    Q_PROPERTY(AtomifySimulator* simulator READ simulator WRITE setSimulator NOTIFY simulatorChanged)
     Q_PROPERTY(QStringList dependencies READ dependencies WRITE setDependencies NOTIFY dependenciesChanged)
     Q_PROPERTY(bool isVector READ isVector WRITE setIsVector NOTIFY isVectorChanged)
     Q_PROPERTY(double time READ time)
@@ -31,7 +30,7 @@ class CPCompute : public QObject
     QString m_command;
 
     LammpsOutput m_output;
-    MySimulator* m_simulator = NULL;
+    AtomifySimulator* m_simulator = nullptr;
     QStringList m_dependencies;
     QList<double> m_values;
     double m_time = 0;
@@ -43,7 +42,7 @@ class CPCompute : public QObject
 
     QString identifier() const;
     QString command() const;
-    MySimulator* simulator() const;
+    AtomifySimulator* simulator() const;
     QStringList dependencies() const;
     double firstValue() const;
     double secondValue() const;
@@ -59,7 +58,7 @@ class CPCompute : public QObject
 signals:
     void identifierChanged(QString identifier);
     void commandChanged(QString command);
-    void simulatorChanged(MySimulator* simulator);
+    void simulatorChanged(AtomifySimulator* simulator);
     void dependenciesChanged(QStringList dependencies);
     void firstValueChanged(double value);
     void secondValueChanged(double value);
@@ -73,7 +72,7 @@ class CPCompute : public QObject
 public slots:
     void setIdentifier(QString identifier);
     void setCommand(QString command);
-    void setSimulator(MySimulator* simulator);
+    void setSimulator(AtomifySimulator* simulator);
     void setDependencies(QStringList dependencies);
     void setValues(QVector<double> values);
     void setIsVector(bool isVector);