int main(int argc,char* argv[])
{
/* Parse the command line: */
SharedJelloServer::Index numAtoms(4,4,8);
SharedJelloServer::Box domain(SharedJelloServer::Box::Point(-60.0,-36.0,0.0),SharedJelloServer::Box::Point(60.0,60.0,96.0));
int listenPortID=-1; // Assign any free port
double updateTime=0.02; // Aim for 50 updates/sec
for(int i=1;i<argc;++i)
{
if(argv[i][0]=='-')
{
if(strcasecmp(argv[i]+1,"numAtoms")==0)
{
/* Read the number of atoms: */
++i;
for(int j=0;j<3&&i<argc;++j,++i)
numAtoms[j]=atoi(argv[i]);
}
else if(strcasecmp(argv[i]+1,"domain")==0)
{
/* Read the simulation domain: */
++i;
for(int j=0;j<3&&i<argc;++j,++i)
domain.min[j]=SharedJelloServer::Box::Scalar(atof(argv[i]));
for(int j=0;j<3&&i<argc;++j,++i)
domain.max[j]=SharedJelloServer::Box::Scalar(atof(argv[i]));
}
else if(strcasecmp(argv[i]+1,"port")==0)
{
/* Read the server listening port: */
++i;
if(i<argc)
listenPortID=atoi(argv[i]);
}
else if(strcasecmp(argv[i]+1,"tick")==0)
{
/* Read the server update time interval: */
++i;
if(i<argc)
updateTime=atof(argv[i]);
}
}
}
/* Ignore SIGPIPE and leave handling of pipe errors to TCP sockets: */
struct sigaction sigPipeAction;
sigPipeAction.sa_handler=SIG_IGN;
sigemptyset(&sigPipeAction.sa_mask);
sigPipeAction.sa_flags=0x0;
sigaction(SIGPIPE,&sigPipeAction,0);
/* Create a shared Jell-O server: */
SharedJelloServer sjs(numAtoms,domain,listenPortID);
std::cout<<"SharedJelloServer::main: Created Jell-O server listening on port "<<sjs.getListenPortID()<<std::endl<<std::flush;
/* Run the simulation loop full speed: */
Misc::Timer timer;
double lastFrameTime=timer.peekTime();
double nextUpdateTime=timer.peekTime()+updateTime;
int numFrames=0;
while(true)
{
/* Calculate the current time step duration: */
double newFrameTime=timer.peekTime();
double timeStep=newFrameTime-lastFrameTime;
lastFrameTime=newFrameTime;
/* Perform a simulation step: */
sjs.simulate(timeStep);
++numFrames;
/* Check if it's time for a state update: */
if(lastFrameTime>=nextUpdateTime)
{
/* Send a state update to all connected clients: */
sjs.sendServerUpdate();
// std::cout<<"\rFrame rate: "<<double(numFrames)/updateTime<<" fps"<<std::flush;
nextUpdateTime+=updateTime;
numFrames=0;
}
}
return 0;
}
void Molecule::addHydrogens(Atom *a,
const QList<unsigned long> &atomIds,
const QList<unsigned long> &bondIds)
{
if (atomIds.size() != bondIds.size()) {
qDebug() << "Error, addHydrogens called with atom & bond id lists of different size!";
}
// Construct an OBMol, call AddHydrogens and translate the changes
OpenBabel::OBMol obmol = OBMol();
if (a) {
OpenBabel::OBAtom *obatom = obmol.GetAtom(a->index()+1);
// Set implicit valence for unusual elements not handled by OpenBabel
// PR#2803076
switch (obatom->GetAtomicNum()) {
case 3:
case 11:
case 19:
case 37:
case 55:
case 85:
case 87:
obatom->SetImplicitValence(1);
obatom->SetHyb(1);
obmol.SetImplicitValencePerceived();
break;
case 4:
case 12:
case 20:
case 38:
case 56:
case 88:
obatom->SetImplicitValence(2);
obatom->SetHyb(2);
obmol.SetImplicitValencePerceived();
break;
case 84: // Po
obatom->SetImplicitValence(2);
obatom->SetHyb(3);
obmol.SetImplicitValencePerceived();
break;
default: // do nothing
break;
}
obmol.AddHydrogens(obatom);
}
else
obmol.AddHydrogens();
// All new atoms in the OBMol must be the additional hydrogens
unsigned int numberAtoms = numAtoms();
int j = 0;
for (unsigned int i = numberAtoms+1; i <= obmol.NumAtoms(); ++i, ++j) {
if (obmol.GetAtom(i)->IsHydrogen()) {
OpenBabel::OBAtom *obatom = obmol.GetAtom(i);
Atom *atom;
if (atomIds.isEmpty())
atom = addAtom();
else if (j < atomIds.size())
atom = addAtom(atomIds.at(j));
else {
qDebug() << "Error - not enough unique ids in addHydrogens.";
break;
}
atom->setOBAtom(obatom);
// Get the neighbor atom
OpenBabel::OBBondIterator iter;
OpenBabel::OBAtom *next = obatom->BeginNbrAtom(iter);
Bond *bond;
if (bondIds.isEmpty())
bond = addBond();
else // Already confirmed by atom ids
bond = addBond(bondIds.at(j));
bond->setEnd(Molecule::atom(atom->index()));
bond->setBegin(Molecule::atom(next->GetIdx()-1));
}
}
for (unsigned int i = 1; i <= numberAtoms; ++i) {
// Warning -- OB atom index off-by-one here
atom(i-1)->setPartialCharge(obmol.GetAtom(i)->GetPartialCharge());
}
}
SharedJello::SharedJello(int& argc,char**& argv,char**& appDefaults)
:Vrui::Application(argc,argv,appDefaults),
pipe(0),
newParameterVersion(1),parameterVersion(1),
lockedIndex(0),mostRecentIndex(1),
nextDraggerID(0),
mainMenu(0),settingsDialog(0)
{
/* Parse the command line: */
const char* serverHostName=0;
int serverPortID=-1;
bool renderDomainBox=true;
for(int i=0;i<argc;++i)
{
if(argv[i][0]=='-')
{
if(strcasecmp(argv[i]+1,"host")==0)
{
++i;
if(i<argc)
serverHostName=argv[i];
else
std::cerr<<"SharedJello::SharedJello: Ignored dangling -host option"<<std::endl;
}
else if(strcasecmp(argv[i]+1,"port")==0)
{
++i;
if(i<argc)
serverPortID=atoi(argv[i]);
else
std::cerr<<"SharedJello::SharedJello: Ignored dangling -port option"<<std::endl;
}
else if(strcasecmp(argv[i]+1,"nobox")==0)
renderDomainBox=false;
}
}
if(serverHostName==0||serverPortID<0)
Misc::throwStdErr("SharedJello::SharedJello: No server host name or port ID provided");
/* Connect to the shared Jell-O server: */
pipe=Cluster::openTCPPipe(Vrui::getClusterMultiplexer(),serverHostName,serverPortID);
pipe->negotiateEndianness();
/* Initiate the connection: */
if(readMessage(*pipe)!=CONNECT_REPLY)
{
/* Bail out: */
pipe=0;
Misc::throwStdErr("SharedJello::SharedJello: Connection refused by shared Jell-O server");
}
/* Read the Jell-O crystal's domain box: */
read(domain,*pipe);
/* Read the number of atoms in the Jell-O crystal: */
Card na[3];
pipe->read(na,3);
JelloCrystal::Index numAtoms(na[0],na[1],na[2]);
/* Wait for the first parameter update message to get the initial simulation parameters: */
if(readMessage(*pipe)!=SERVER_PARAMUPDATE)
{
/* Bail out: */
pipe=0;
Misc::throwStdErr("SharedJello::SharedJello: Connection refused by shared Jell-O server");
}
atomMass=pipe->read<Scalar>();
attenuation=pipe->read<Scalar>();
gravity=pipe->read<Scalar>();
/* Wait for the first server update message to get initial atom positions: */
if(readMessage(*pipe)!=SERVER_UPDATE)
{
/* Bail out: */
pipe=0;
Misc::throwStdErr("SharedJello::SharedJello: Connection refused by shared Jell-O server");
}
/* Create triple buffer of Jell-O crystals: */
for(int i=0;i<3;++i)
crystals[i]=new JelloCrystal(numAtoms);
/* Read the first crystal state: */
crystals[mostRecentIndex]->readAtomStates(*pipe);
/* Calculate the domain box color: */
GLColor<GLfloat,3> domainBoxColor;
for(int i=0;i<3;++i)
domainBoxColor[i]=1.0f-Vrui::getBackgroundColor()[i];
/* Create the triple buffer of Jell-O renderers: */
for(int i=0;i<3;++i)
{
renderers[i]=new JelloRenderer(*crystals[i]);
renderers[i]->setRenderDomainBox(renderDomainBox);
renderers[i]->setDomainBoxColor(domainBoxColor);
}
renderers[mostRecentIndex]->update();
/* Start the server communication thread: */
communicationThread.start(this,&SharedJello::communicationThreadMethod);
/* Create the program's user interface: */
mainMenu=createMainMenu();
Vrui::setMainMenu(mainMenu);
settingsDialog=createSettingsDialog();
/* Initialize the navigation transformation: */
centerDisplayCallback(0);
}
