void init(void) {
int i;
for(i=0;i<numSpheres;i++){
spheres[i][0] = (rand()%600)-300;//XPOS
spheres[i][1] = (rand()%600)-300;//YPOS
spheres[i][2] = rand()%400;//ZPOS
spheres[i][3] = rand()%20;//SIZE
spheres[i][4] = (rand()%20);//SPEED
}
MAXROT = 1.0/6.0*PI;
glClearColor (0.0, 0.0, 0.0, 0.0);
glEnable(GL_DEPTH_TEST);
glShadeModel(GL_SMOOTH);
pmodel = glmReadOBJ("city.obj");
if (!pmodel) fprintf(stderr,"Cannot parse vase.obj");
//glmUnitize(pmodel); // make model to fit in a unit cube
glmFacetNormals(pmodel); // generate normals - is this needed?
glmVertexNormals(pmodel, 90.0); // average joining normals - allow for hard edges.
tmodel = glmReadOBJ("tower.obj");
glmFacetNormals(tmodel); // generate normals - is this needed?
glmVertexNormals(tmodel, 90.0); // average joining normals - allow for hard edges.
readTop();
readFront();
readBack();
readRight();
readLeft();
readFire();
glPixelStorei(GL_UNPACK_ALIGNMENT, 1);
glGenTextures(1, &front);
glGenTextures(1, &top);
glGenTextures(1, &left);
glGenTextures(1, &right);
glGenTextures(1, &back);
glGenTextures(1, &fire);
qsphere = gluNewQuadric();
}
int main(int argc, char * argv[])
{
unsigned numBlock;
float begin, end;
std::string ifile, ofile, tfile;
float time_prec = .01;
TopInfo info;
double refh;
po::options_description desc ("Allow options");
desc.add_options()
("help,h", "print this message")
("begin,b", po::value<float > (&begin)->default_value(0.f), "start time")
("end,e", po::value<float > (&end )->default_value(0.f), "end time")
("block,n", po::value<unsigned > (&numBlock)->default_value(20), "number of block for averaging")
("refh,r", po::value<double > (&refh)->default_value(.1), "size of bin")
("top-file,t",po::value<std::string > (&tfile)->default_value ("mytop"), "topolgy of the system")
("output,o", po::value<std::string > (&ofile)->default_value ("momentum.wave.dat"), "the output of count of h-bond")
("input,f", po::value<std::string > (&ifile)->default_value ("traj.trr"), "the input .xtc file");
po::variables_map vm;
po::store(po::parse_command_line(argc, argv, desc), vm);
po::notify (vm);
if (vm.count("help")) {
std::cout << desc<< "\n";
return 0;
}
if (vm.count("top-file")) {
readTop (tfile, info);
}
std::cout << "###################################################" << std::endl;
std::cout << "# begin->end: " << begin << " " << end << std::endl;
std::cout << "# block: " << numBlock << std::endl;
std::cout << "# top file: " << tfile << std::endl;
std::cout << "###################################################" << std::endl;
TrajLoader_trr tjl (ifile.c_str(), info);
std::vector<std::vector<ValueType > > ch4xx;
std::vector<std::vector<ValueType > > ch4vv;
std::vector<std::vector<ValueType > > ch4ff;
std::vector<std::vector<ValueType > > h2o;
std::vector<std::vector<ValueType > > h2ovv;
std::vector<std::vector<ValueType > > h2off;
std::vector<std::vector<double > > com;
std::vector<double > mass (3);
std::vector<double > moment_r;
mass[info.OIndexH2o] = 16;
mass[info.H1IndexH2o] = 1;
mass[info.H2IndexH2o] = 1;
double totalmass = mass[info.OIndexH2o] + mass[info.H1IndexH2o] + mass[info.H2IndexH2o];
double boxSize[3];
boxSize[0] = tjl.getBox().x;
boxSize[1] = tjl.getBox().y;
boxSize[2] = tjl.getBox().z;
int countread = 0;
MomentumWave dw;
dw.reinit (refh, tjl.getBox());
dw.initFile (ofile.c_str());
while (true == tjl.load()) {
float time = tjl.getTime();
if (end != 0.f) {
if (time < begin - time_prec) {
continue;
}
else if (time > end + time_prec) {
break;
}
}
else {
if (time < begin - time_prec) continue;
}
if (countread++ % 1 == 0) {
// printf ("# load frame at time: %.1f ps\r", time);
fflush (stdout);
}
tjl.formCoords (ch4xx, ch4vv, ch4ff, h2o, h2ovv, h2off);
// cal coms
{
com.resize (h2o.size() / info.numAtomOnH2o);
moment_r.resize (h2o.size() / info.numAtomOnH2o);
for (unsigned ii = 0; ii < h2o.size() / info.numAtomOnH2o; ++ii) {
std::vector<double > composi(3, 0.);
std::vector<double > comvelo(3, 0.);
for (unsigned jj = 1; jj < 3; ++jj) {
for (unsigned dd = 0; dd < 3; ++dd) {
double diff = h2o[info.numAtomOnH2o*ii+jj][dd] - h2o[info.numAtomOnH2o*ii+0][dd];
if (diff > boxSize[dd] * 0.5) {
h2o[info.numAtomOnH2o*ii+jj][dd] -= boxSize[dd];
}
else if (diff < -boxSize[dd] * 0.5) {
h2o[info.numAtomOnH2o*ii+jj][dd] += boxSize[dd];
}
}
}
for (unsigned jj = 0; jj < 3; ++jj) {
for (unsigned dd = 0; dd < 3; ++dd) {
composi[dd] += mass[jj] * h2o[info.numAtomOnH2o*ii+jj][dd];
comvelo[dd] += mass[jj] * h2ovv[info.numAtomOnH2o*ii+jj][dd];
}
}
for (unsigned dd = 0; dd < 3; ++dd) {
composi[dd] /= totalmass;
}
std::vector<double > rr (composi);
for (unsigned dd = 0; dd < 3; ++dd) {
rr[dd] -= boxSize[dd] * 0.5;
}
double dr = rr[0] * rr[0] + rr[1] * rr[1] + rr[2] * rr[2];
dr = sqrt(dr);
rr[0] /= dr;
rr[1] /= dr;
rr[2] /= dr;
com[ii] = composi;
moment_r[ii] = comvelo[0] * rr[0] + comvelo[1] * rr[1] + comvelo[2] * rr[2];
}
}
dw.calculate (time, com, moment_r);
dw.write();
dw.clear ();
}
return 0;
}
