Commit 35f0c21c authored by Michael Sherman's avatar Michael Sherman
Browse files

Reorganized the HelloWaterBox example to look like a clone of the HelloEthane example.

parent 2763eed1
......@@ -16,7 +16,6 @@
#include <cstdio>
#include <string>
#include <vector>
#include <utility>
// -----------------------------------------------------------------------------
// MOCK MD CODE
......@@ -40,8 +39,6 @@ const double SimulationTimeInPs = 100; // total simulation time (ps)
static const bool WantEnergy = true;
// FORCE FIELD DATA
// These data structures are not part of OpenMM; they are a model of the kinds
// of data structures an MD code uses to hold a set of force field parameters.
// For this example we're using a tiny subset of the Amber99 force field.
// We want to keep the data in the original unit system to avoid conversion
// bugs; this requires conversion on the way in and out of OpenMM.
......@@ -220,12 +217,16 @@ namespace OpenMM {
static const double SigmaPerVdwRadius = 1.78179743628068;
}
// This is our opaque "handle" class containing all the OpenMM objects that
// must persist from call to call during a simulation. The main program gets
// a pointer to one of these but sees it as essentially a void* since it
// doesn't know the definition of this class.
struct MyOpenMMData {
MyOpenMMData() : system(0), context(0), integrator(0) {}
~MyOpenMMData() {delete system; delete context; delete integrator;}
~MyOpenMMData() {delete context; delete integrator; delete system;}
OpenMM::System* system;
OpenMM::OpenMMContext* context;
OpenMM::Integrator* integrator;
OpenMM::OpenMMContext* context;
};
......
/* -----------------------------------------------------------------------------
* OpenMM(tm) HelloWaterBox example (May 2009)
* OpenMM(tm) HelloWaterBox example in C++ (June 2009)
* -----------------------------------------------------------------------------
* This is a complete, self-contained "hello world" example demonstrating
* GPU-accelerated simulation of a system with both bonded and nonbonded forces,
* using water (H-O-H) in a periodic box as an example. A multi-frame PDB file is
* written to stdout which can be read by VMD or other visualization tool to
* using water (H-O-H) in a periodic box as an example. This is a constant-
* temperature simulation using an Andersen thermostat. A multi-frame PDB file
* is written to stdout which can be read by VMD or other visualization tool to
* produce an animation of the resulting trajectory.
*
* Pay particular attention to the handling of units in this example. Incorrect
......@@ -13,44 +14,139 @@
* communicating with OpenMM in nanometers and kJoules.
* -------------------------------------------------------------------------- */
// Suppress irrelevant warnings from Microsoft's compiler.
#ifdef _MSC_VER
#pragma warning(disable:4996) // sprintf is unsafe
#pragma warning(disable:4251) // no dll interface for some classes
#endif
#include "OpenMM.h"
#include <cstdio>
#include <cstdlib>
#include <string>
#include <vector>
#include <utility>
using OpenMM::Vec3; // so we can just say "Vec3" below
// -----------------------------------------------------------------------------
// MODELING AND SIMULATION PARAMETERS
// MOCK MD CODE
// -----------------------------------------------------------------------------
// The code starting here and through main() below is meant to represent in
// simplified form some pre-existing molecular dynamics code, which defines its
// own data structures for force fields, the atoms in this simulation, and the
// simulation parameters, and takes care of recording the trajectory. All this
// has nothing to do with OpenMM; the OpenMM-dependent code comes later and is
// clearly marked below.
// -----------------------------------------------------------------------------
// MODELING AND SIMULATION PARAMETERS
const int NumWatersAlongEdge = 10; // Size of box is NxNxN waters.
const double Temperature = 300; // Kelvins
const double FrictionInPerPs = 91.; // collisions per picosecond
const double CutoffDistanceInAng = 10.; // Angstroms
const bool UseConstraints = true; // Should we constrain O-H bonds?
const double StepSizeInFs = 2; // integration step size (fs)
const double ReportIntervalInFs = 100; // how often to generate PDB frame (fs)
const double SimulationTimeInPs = 10; // total simulation time (ps)
static void simulateWaterBox();
static void writePDB(const OpenMM::OpenMMContext&); // PDB file writer; see below.
// FORCE FIELD DATA
// For this example we're using a tiny subset of the Amber99 force field.
// We want to keep the data in the original unit system to avoid conversion
// bugs; this requires conversion on the way in and out of OpenMM.
// Amber reduces nonbonded forces between 1-4 bonded atoms. (These won't be
// used in our all-water simulation.)
const double Coulomb14Scale = 0.5;
const double LennardJones14Scale = 0.5;
// We only need force field parameters for water here.
const double O_mass = 15.9994; // Daltons
const double O_charge = -0.834; // e
const double O_vdwRadInAng = 1.7683; // Angstroms
const double O_vdwEnergyInKcal = 0.1520; // kcal per mole
const double H_mass = 1.00794;
const double H_charge = 0.417;
const double H_vdwRadInAng = 0.0001;
const double H_vdwEnergyInKcal = 0.0000;
// Parameters for the O-H bonds.
const double OH_nominalLengthInAng = 0.9572;
const double OH_stiffnessInKcalPerAng2 = 553.0; // that is, e=k(x-x0)^2
// Parameters for the H-O-H angle.
const double HOH_nominalAngleInDeg = 104.52;
const double HOH_stiffnessInKcalPerRad2 = 100.; // that is e=k(a-a0)^2
// PDB FILE WRITER
// This is a PDB writer that only knows how to write out water molecules. It is
// just here for this example and has nothing to do with OpenMM!
static void
myWritePDBFrame(int frameNum, double timeInPs, const std::vector<double>& atomPosInAng)
{
const char* atomNames[] = {" O ", " H1 ", " H2 "}; // cycle through these
printf("MODEL %d\n", frameNum);
printf("REMARK 250 time=%.3f picoseconds\n", timeInPs);
for (int atom=0; atom < (int)atomPosInAng.size()/3; ++atom)
{
printf("HETATM%5d %4s HOH %4d ", // start of pdb HETATM line
atom+1, atomNames[atom%3], 1 + atom/3); // atom number, name, residue #
printf("%8.3f%8.3f%8.3f", // middle of pdb HETATM line
atomPosInAng[3*atom+0], atomPosInAng[3*atom+1], atomPosInAng[3*atom+2]);
printf(" 1.00 0.00 \n"); // end of pdb HETATM line
}
printf("ENDMDL\n"); // end of trajectory frame
}
// -----------------------------------------------------------------------------
// MAIN PROGRAM
// INTERFACE TO OpenMM
// -----------------------------------------------------------------------------
// These four functions and an opaque structure are used to interface our main
// program with OpenMM without the main program having any direct interaction
// with the OpenMM API. This is a clean approach for interfacing with any MD
// code, although the details of the interface routines will differ. This is
// still just "locally written" code and is not required by OpenMM. Normally
// these would be in another compilation unit but they are defined later in
// this file.
struct MyOpenMMData;
static MyOpenMMData* myInitializeOpenMM(int numWatersAlongEdge,
double temperature,
double frictionInPerPs,
double stepSizeInFs,
std::string& platformName);
static void myStepWithOpenMM(MyOpenMMData*, int numSteps);
static void myGetOpenMMState(MyOpenMMData*, double& time,
std::vector<double>& atomPosInAng);
static void myTerminateOpenMM(MyOpenMMData*);
// -----------------------------------------------------------------------------
// WATER BOX MAIN PROGRAM
// -----------------------------------------------------------------------------
int main() {
// ALWAYS enclose all OpenMM calls with a try/catch block to make sure that
// usage and runtime errors are caught and reported.
try {
// Load all available OpenMM plugins from their default location.
OpenMM::Platform::loadPluginsFromDirectory
(OpenMM::Platform::getDefaultPluginsDirectory());
simulateWaterBox();
std::string platformName;
// Set up OpenMM data structures; return handle and OpenMM Platform name.
MyOpenMMData* omm = myInitializeOpenMM(NumWatersAlongEdge, Temperature,
FrictionInPerPs, StepSizeInFs,
platformName); // output
// Run the simulation:
// (1) Write the first line of the PDB file and the initial configuration.
// (2) Run silently entirely within OpenMM between reporting intervals.
// (3) Write a PDB frame when the time comes.
printf("REMARK Using OpenMM platform %s\n", platformName.c_str());
std::vector<double> atomPositionsInAng; // x,y,z,x,y,z, ...
const int NumSilentSteps = (int)(ReportIntervalInFs / StepSizeInFs + 0.5);
for (int frame=1; ; ++frame) {
double time;
myGetOpenMMState(omm, time, atomPositionsInAng);
myWritePDBFrame(frame, time, atomPositionsInAng);
if (time >= SimulationTimeInPs)
break;
myStepWithOpenMM(omm, NumSilentSteps);
}
// Clean up OpenMM data structures.
myTerminateOpenMM(omm);
return 0; // Normal return from main.
}
......@@ -64,33 +160,76 @@ int main() {
// -----------------------------------------------------------------------------
// FORCE FIELD DATA
// OpenMM-USING CODE
// -----------------------------------------------------------------------------
// The OpenMM API is visible only at this point and below. Normally this would
// be in a separate compilation module; we're including it here for simplicity.
// -----------------------------------------------------------------------------
// These data structures are not part of OpenMM; they are a model of the kinds
// of data structures an MD code uses to hold a set of force field parameters.
// For this example we're using a tiny subset of the Amber99 force field.
// We want to keep the data in the original unit system to avoid conversion
// bugs; this requires conversion on the way in and out of OpenMM.
// Amber reduces nonbonded forces between 1-4 bonded atoms.
const double Coulomb14Scale = 0.5;
const double LennardJones14Scale = 0.5;
// Suppress irrelevant warnings from Microsoft's compiler.
#ifdef _MSC_VER
#pragma warning(disable:4996) // sprintf is unsafe
#pragma warning(disable:4251) // no dll interface for some classes
#endif
#include "OpenMM.h"
using OpenMM::Vec3; // so we can just say "Vec3" below
// Add definition missing from the current version of OpenMM.
namespace OpenMM {
// This conversion factor takes you from a van der Waals radius (defined as 1/2
// the minimum energy separation) to the related Lennard Jones "sigma" parameter
// (defined as the zero crossing separation). The value is 2*pow(2, -1/6).
static const double SigmaPerVdwRadius = 1.78179743628068;
}
// This is our opaque "handle" class containing all the OpenMM objects that
// must persist from call to call during a simulation. The main program gets
// a pointer to one of these but sees it as essentially a void* since it
// doesn't know the definition of this class.
struct MyOpenMMData {
MyOpenMMData() : system(0), context(0), integrator(0) {}
~MyOpenMMData() {delete context; delete integrator; delete system;}
OpenMM::System* system;
OpenMM::Integrator* integrator;
OpenMM::OpenMMContext* context;
};
// This is the conversion factor that takes you from a van der Waals radius
// (defined as 1/2 the minimum energy separation) to the related Lennard Jones
// "sigma" parameter (defined as the zero crossing separation).
static const double SigmaPerVdwRadius = 2*std::pow(2., -1./6.);
// -----------------------------------------------------------------------------
// WATER SIMULATION
// INITIALIZE OpenMM DATA STRUCTURES
// -----------------------------------------------------------------------------
static void simulateWaterBox() {
// -------------------------------------------------------------------------
// We take these actions here:
// (1) Load any available OpenMM plugins, e.g. Cuda and Brook.
// (2) Allocate a MyOpenMMData structure to hang on to OpenMM data structures
// in a manner which is opaque to the caller.
// (3) Fill the OpenMM::System with the force field parameters we want to
// use and the particular set of atoms to be simulated.
// (4) Create an Integrator and a Context associating the Integrator with
// the System.
// (5) Select the OpenMM platform to be used.
// (6) Return the MyOpenMMData struct and the name of the Platform in use.
//
// Note that this function must understand the calling MD code's molecule and
// force field data structures so will need to be customized for each MD code.
static MyOpenMMData*
myInitializeOpenMM( int numWatersAlongEdge,
double temperature,
double frictionInPerPs,
double stepSizeInFs,
std::string& platformName)
{
// Load all available OpenMM plugins from their default location.
OpenMM::Platform::loadPluginsFromDirectory
(OpenMM::Platform::getDefaultPluginsDirectory());
// Allocate space to hold OpenMM objects while we're using them.
MyOpenMMData* omm = new MyOpenMMData();
// Create a System and Force objects within the System. Retain a reference
// to each force object so we can fill in the forces. Note: OpenMM owns
// the objects and will take care of deleting them; don't do it yourself!
// -------------------------------------------------------------------------
OpenMM::System system;
// to each force object so we can fill in the forces. Note: the System owns
// the force objects and will take care of deleting them; don't do it yourself!
OpenMM::System& system = *(omm->system = new OpenMM::System());
OpenMM::NonbondedForce& nonbond = *new OpenMM::NonbondedForce();
system.addForce(&nonbond);
......@@ -102,78 +241,77 @@ static void simulateWaterBox() {
system.addForce(&bondBend);
OpenMM::AndersenThermostat& thermostat = *new OpenMM::AndersenThermostat(
300, // temperature in kelvins
91.0); // collision frequency in 1/picoseconds
// -------------------------------------------------------------------------
// Specify the atoms and their properties:
// (1) System needs to know the masses.
// (2) NonbondedForce needs charges,van der Waals properties (in MD units!).
// (3) Collect default positions for initializing the simulation later.
// -------------------------------------------------------------------------
temperature, // kelvins
frictionInPerPs); // collision frequency in 1/picoseconds
system.addForce(&thermostat);
// Volume of one water is 30 Angstroms cubed;
// Thus length in one dimension is cube-root of 30,
// or 3.107 Angstroms or 0.3107 nanometers
double waterSize = 0.3107; // edge of cube containing one water, in nanometers
// Place 1000 water molecules one at a time in a 10x10x10 rectilinear grid
const int watersPerEdge = 10;
double boxEdgeLength = waterSize * watersPerEdge;
const double WaterSizeInNm = 0.3107; // edge of cube containing one water, in nanometers
// Place water molecules one at a time in an NxNxN rectilinear grid
const double boxEdgeLengthInNm = WaterSizeInNm * numWatersAlongEdge;
// Create periodic box
nonbond.setNonbondedMethod(OpenMM::NonbondedForce::CutoffPeriodic);
nonbond.setCutoffDistance(2);
nonbond.setPeriodicBoxVectors(Vec3(boxEdgeLength,0,0), Vec3(0,boxEdgeLength,0), Vec3(0,0,boxEdgeLength));
nonbond.setCutoffDistance(CutoffDistanceInAng * OpenMM::NmPerAngstrom);
nonbond.setPeriodicBoxVectors(Vec3(boxEdgeLengthInNm,0,0),
Vec3(0,boxEdgeLengthInNm,0),
Vec3(0,0,boxEdgeLengthInNm));
// Specify the atoms and their properties:
// (1) System needs to know the masses and constraints (if any).
// (2) NonbondedForce needs charges,van der Waals properties (in MD units!).
// (3) Collect starting positions for initializing the simulation later.
// Create data structures to hold lists of initial positions and bonds
std::vector<Vec3> initialPositions;
std::vector<Vec3> initialPosInNm;
std::vector< std::pair<int,int> > bondPairs;
// Add water molecules one at a time in the 10x10x10 cubic lattice
for (int latticeX = 0; latticeX < watersPerEdge; ++latticeX)
for (int latticeY = 0; latticeY < watersPerEdge; ++latticeY)
for (int latticeZ = 0; latticeZ < watersPerEdge; ++latticeZ)
for (int latticeX = 0; latticeX < numWatersAlongEdge; ++latticeX)
for (int latticeY = 0; latticeY < numWatersAlongEdge; ++latticeY)
for (int latticeZ = 0; latticeZ < numWatersAlongEdge; ++latticeZ)
{
// Add parameters for one water molecule
// Add atom masses to system
int oIndex = system.addParticle(15.9994); // O
int h1Index = system.addParticle(1.00794); // H1
int h2Index = system.addParticle(1.00794); // H2
int oIndex = system.addParticle(O_mass); // O
int h1Index = system.addParticle(H_mass); // H1
int h2Index = system.addParticle(H_mass); // H2
// Add atom charge, sigma, and stiffness to nonbonded force
nonbond.addParticle( // Oxygen
-0.834, // charge
1.7683 * OpenMM::NmPerAngstrom * SigmaPerVdwRadius,
0.1520 * OpenMM::KJPerKcal);
O_charge,
O_vdwRadInAng * OpenMM::NmPerAngstrom * OpenMM::SigmaPerVdwRadius,
O_vdwEnergyInKcal * OpenMM::KJPerKcal);
nonbond.addParticle( // Hydrogen1
0.417, // charge
0.0001 * OpenMM::NmPerAngstrom * SigmaPerVdwRadius,
0.0000 * OpenMM::KJPerKcal);
H_charge,
H_vdwRadInAng * OpenMM::NmPerAngstrom * OpenMM::SigmaPerVdwRadius,
H_vdwEnergyInKcal * OpenMM::KJPerKcal);
nonbond.addParticle( // Hydrogen2
0.417, // charge
0.0001 * OpenMM::NmPerAngstrom * SigmaPerVdwRadius,
0.0000 * OpenMM::KJPerKcal);
H_charge,
H_vdwRadInAng * OpenMM::NmPerAngstrom * OpenMM::SigmaPerVdwRadius,
H_vdwEnergyInKcal * OpenMM::KJPerKcal);
// constrain O-H bond lengths
// Constrain O-H bond lengths or use harmonic forces.
if (UseConstraints) {
system.addConstraint(oIndex, h1Index,
0.9572 * OpenMM::NmPerAngstrom);
OH_nominalLengthInAng * OpenMM::NmPerAngstrom);
system.addConstraint(oIndex, h2Index,
0.9572 * OpenMM::NmPerAngstrom);
OH_nominalLengthInAng * OpenMM::NmPerAngstrom);
} else {
// Add stretch parameters for two covalent bonds
// Note factor of 2 for stiffness below because Amber specifies the constant
// as it is used in the harmonic energy term kx^2 with force 2kx; OpenMM wants
// it as used in the force term kx, with energy kx^2/2.
bondStretch.addBond(oIndex, h1Index,
0.9572 * OpenMM::NmPerAngstrom,
553.0 * 2 * OpenMM::KJPerKcal
OH_nominalLengthInAng * OpenMM::NmPerAngstrom,
OH_stiffnessInKcalPerAng2 * 2 * OpenMM::KJPerKcal
* OpenMM::AngstromsPerNm * OpenMM::AngstromsPerNm);
bondStretch.addBond(oIndex, h2Index,
0.9572 * OpenMM::NmPerAngstrom,
553.0 * 2 * OpenMM::KJPerKcal
OH_nominalLengthInAng * OpenMM::NmPerAngstrom,
OH_stiffnessInKcalPerAng2 * 2 * OpenMM::KJPerKcal
* OpenMM::AngstromsPerNm * OpenMM::AngstromsPerNm);
}
......@@ -181,93 +319,75 @@ static void simulateWaterBox() {
bondPairs.push_back(std::make_pair(oIndex, h1Index));
bondPairs.push_back(std::make_pair(oIndex, h2Index));
// Add bond bend parameters for one angle
// Add bond bend parameters for one angle.
// See note under bond stretch above regarding the factor of 2 here.
bondBend.addAngle(h1Index, oIndex, h2Index,
104.52 * OpenMM::RadiansPerDegree,
100.00 * 2 * OpenMM::KJPerKcal);
HOH_nominalAngleInDeg * OpenMM::RadiansPerDegree,
HOH_stiffnessInKcalPerRad2 * 2 * OpenMM::KJPerKcal);
// Location of this molecule in the lattice
Vec3 latticeVec(waterSize * latticeX,
waterSize * latticeY,
waterSize * latticeZ);
Vec3 latticeVec(WaterSizeInNm * latticeX,
WaterSizeInNm * latticeY,
WaterSizeInNm * latticeZ);
// flip half the waters to prevent giant dipole
int flip = (rand() % 100) > 49 ? 1 : -1;
// place this water
initialPositions.push_back(Vec3(0,0,0) + latticeVec); // O
initialPositions.push_back(Vec3(0.09572*flip,0,0) + latticeVec); // H1
initialPositions.push_back(Vec3(-0.02397*flip,0.09267*flip,0) + latticeVec); // H2
initialPosInNm.push_back(Vec3(0,0,0) + latticeVec); // O
initialPosInNm.push_back(Vec3(0.09572*flip,0,0) + latticeVec); // H1
initialPosInNm.push_back(Vec3(-0.02397*flip,0.09267*flip,0) + latticeVec); // H2
}
// Populate nonbonded exclusions
nonbond.createExceptionsFromBonds(bondPairs, Coulomb14Scale, LennardJones14Scale);
// -------------------------------------------------------------------------
// Choose an Integrator for advancing time, and a Context connecting the
// System with the Integrator for simulation. Let the Context choose the
// best available Platform. Initialize the configuration from the default
// positions we collected above. Initial velocities will be zero.
// -------------------------------------------------------------------------
OpenMM::VerletIntegrator integrator(
StepSizeInFs * OpenMM::PsPerFs);
OpenMM::OpenMMContext context(system, integrator);
context.setPositions(initialPositions);
omm->integrator = new OpenMM::VerletIntegrator(StepSizeInFs * OpenMM::PsPerFs);
omm->context = new OpenMM::OpenMMContext(*omm->system, *omm->integrator);
omm->context->setPositions(initialPosInNm);
// -------------------------------------------------------------------------
// Run the simulation:
// (1) Write the first line of the PDB file and the initial configuration.
// (2) Run silently entirely within OpenMM between reporting intervals.
// (3) Write a PDB frame when the time comes.
// -------------------------------------------------------------------------
printf("REMARK Using OpenMM platform %s\n", context.getPlatform().getName().c_str() );
writePDB(context);
const int NumSilentSteps = (int)(ReportIntervalInFs / StepSizeInFs + 0.5);
do {
integrator.step(NumSilentSteps);
writePDB(context);
} while (context.getTime() < SimulationTimeInPs);
platformName = omm->context->getPlatform().getName();
return omm;
}
// -----------------------------------------------------------------------------
// PDB FILE WRITER
// COPY STATE BACK TO CPU FROM OPENMM
// -----------------------------------------------------------------------------
static void
writePDB(const OpenMM::OpenMMContext& context) {
myGetOpenMMState(MyOpenMMData* omm, double& timeInPs,
std::vector<double>& atomPositionsInAng)
{
// We don't calculate energy in this example because it would take most of the time
const OpenMM::State state = context.getState(OpenMM::State::Positions);
const std::vector<Vec3>& positions = state.getPositions();
static int modelFrameNumber = 0; // numbering for MODEL records in pdb output
modelFrameNumber++;
printf("MODEL %d\n", modelFrameNumber);
printf("REMARK 250 time=%.3f picoseconds\n", state.getTime());
int residueNumber = 1;
char* atomName = " O ";
for (unsigned int atomIndex=0; atomIndex < positions.size(); ++atomIndex)
{
// cycle through same three atom names
if (0 == atomIndex%3) {
atomName = " O ";
// increment residue number once every three atoms
++residueNumber;
}
else if (1 == atomIndex%3) atomName = " H1 ";
else atomName = " H2 ";
const OpenMM::State state = omm->context->getState(OpenMM::State::Positions);
timeInPs = state.getTime(); // OpenMM time is in ps already
// Copy OpenMM positions into output array and change units from nm to Angstroms.
const std::vector<Vec3>& positionsInNm = state.getPositions();
atomPositionsInAng.resize(3*positionsInNm.size());
for (int i=0; i < (int)positionsInNm.size(); ++i)
for (int j=0; j < 3; ++j)
atomPositionsInAng[3*i+j] = positionsInNm[i][j] * OpenMM::AngstromsPerNm;
}
printf("HETATM%5d %4s HOH %4d ", // start of pdb ATOM line
atomIndex, atomName, residueNumber);
printf("%8.3f%8.3f%8.3f", // middle of pdb ATOM line
positions[atomIndex][0] * OpenMM::AngstromsPerNm, // x
positions[atomIndex][1] * OpenMM::AngstromsPerNm, // y
positions[atomIndex][2] * OpenMM::AngstromsPerNm); // z
printf(" 1.00 0.00 \n"); // end of pdb ATOM line
}
printf("ENDMDL\n"); // end of trajectory frame
// -----------------------------------------------------------------------------
// TAKE MULTIPLE STEPS USING OpenMM
// -----------------------------------------------------------------------------
static void
myStepWithOpenMM(MyOpenMMData* omm, int numSteps) {
omm->integrator->step(numSteps);
}
// -----------------------------------------------------------------------------
// DEALLOCATE OpenMM OBJECTS
// -----------------------------------------------------------------------------
static void
myTerminateOpenMM(MyOpenMMData* omm) {
delete omm;
}
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