int main(){
cout << "Float size: " << sizeof(flt) << " epsilon: " << std::numeric_limits<flt>::epsilon() << "\n";
assert(std::numeric_limits<flt>::epsilon() < force_max*10);
// new random seed each time, for velocities and placement
seed();
// Volume of the spheres
// Each sphere is σ^d * π/(2d), i.e. π σ^2/4 for 2D, π σ^3/6 for 3D
// Total volume of the spheres takes a constant N out front
const flt Vs = (Ns * pow(sigma, NDIM) + Nl * pow(sigmal, NDIM)) * M_PI_2 / NDIM;
// Initial length of the box is [(volume of spheres) / phi0]^(1/d)
const flt L = pow(Vs / phi0, OVERNDIM);
cout << "Using L = " << L << "\n";
// Create the bounding box (sides of length L), and a "vector" of Natoms atoms
boost::shared_ptr<OriginBox> obox(new OriginBox(L));
// Create a vector of the masses of the atoms
// We just use all mass 1, because this is a packing
boost::shared_ptr<AtomVec> atomptr(new AtomVec(Nl + Ns, 1.0));
AtomVec & atoms = *atomptr;
// Harmonic Interaction
// Its called "Repulsion" for historical reasons
// It takes a pointer to the box, a pointer to the atoms, and a "skin depth" for the NeighborList
boost::shared_ptr<NListed<EpsSigExpAtom, RepulsionPair> >
hertzian(new NListed<EpsSigExpAtom, RepulsionPair>(obox, atomptr, 0.1*sigma));
boost::shared_ptr<NeighborList> nl = hertzian->neighbor_list();
// ^ this is the Interaction
// Note that NListed is a class template; its an Interaction that
// takes various structs as template parameters, and turns them into
// a neighbor Interaction
// See interaction.hpp for a whole bunch of them
// Also note that the NeighborList is not the same as the
// "neighborlisted" Interaction; multiple interactions can use the
// same NeighborList
// Now we run through all the atoms, set their positions / velocities,
// and add them to the Repulsion Interaction (i.e., to the neighbor list)
for (uint i=0; i < atoms.size(); i++){
atoms[i].x = obox->rand_loc(); // random location in the box
atoms[i].v = Vec::Zero(); // A zero-vector
atoms[i].f = Vec::Zero();
atoms[i].a = Vec::Zero();
flt sig = i < Ns ? sigma : sigmal;
// Add it to the Repulsion potential
hertzian->add(EpsSigExpAtom(atoms.get_id(i), epsilon, sig, 2));
// ^ exponent for the harmonic Interaction
}
// force an update the NeighborList, so we can get an accurate energy
nl->update_list(true);
cout << "Starting. Neighborlist contains " << nl->numpairs() << " / " <<
(atoms.size()*(atoms.size()-1))/2 << " pairs\n";
//Now we make our "Collection"
CollectionNLCG collec = CollectionNLCG(obox, atomptr, dt, P0);
// This is very important! Otherwise the NeighborList won't update!
collec.add_tracker(nl);
// And add the Interaction
collec.add_interaction(hertzian);
writefile(atoms, *obox);
//Print out total energy, kinetic_energy energy, and potential energy
cout << "H: " << collec.hamiltonian() << " K: " << collec.kinetic_energy()
<< " U: " << hertzian->energy(*obox) << " phi: " << (Vs/obox->V()) << "\n";
// Run the simulation! And every _ steps, write a frame to the .xyz
// file and print out the energies again
uint i = 0;
for(flt curP=startP; curP>P0; curP/=10){
cout << "P: " << curP << "\n";
collec.set_pressure_goal(curP);
while (true) {
for(uint j=0; j<1000; j++){
collec.timestep();
}
i++;
writefile(atoms, *obox);
flt pdiff = collec.pressure() / curP - 1.0;
flt force_err = 0;
for(uint k=0; k<atoms.size(); k++){
flt fmag = atoms[k].f.norm();
if(fmag > force_err) force_err = fmag;
}
cout.precision(sizeof(flt));
cout << i << " H: " << collec.hamiltonian() << " K: " << collec.kinetic_energy()
<< " U: " << hertzian->energy(*obox) << " phi: " << (Vs/obox->V()) << "\n";
cout.precision(6);
cout << " Pdiff: " << pdiff << " force_err: " << force_err << "\n";
if(abs(pdiff) < P_frac and force_err < force_max){
cout << "Done!\n";
break;
}
}
}
};
int main(){
// new random seed each time, for velocities and placement
seed();
const flt Vs = Natoms * pow(sigma, NDIM) * M_PI_2 / NDIM;
const flt L = pow(Vs / phi, OVERNDIM);
cout << "Using L = " << L << "\n";
// Create the bounding box (sides of length L), and a "vector" of Natoms atoms
boost::shared_ptr<OriginBox> obox(new OriginBox(L));
boost::shared_ptr<AtomVec> atomptr(new AtomVec(Natoms, 1.0));
AtomVec & atoms = *atomptr;
// LJ Interaction
// We'll cut it off at 2.5σ, and have a NeighborList out to 1.4 times that
boost::shared_ptr<NListed<EpsSigCutAtom, LennardJonesCutPair> >
LJ(new NListed<EpsSigCutAtom, LennardJonesCutPair>(obox, atomptr, 0.4*(sigcut*sigma)));
boost::shared_ptr<NeighborList> nl = LJ->neighbor_list();
// ^ this is the Interaction
// Note that NListed is a class template; its an Interaction that
// takes various structs as template parameters, and turns them into
// a neighbor Interaction
// See Interaction.hpp for a whole bunch of them
// Also note that the NeighborList is not the same as the
// "neighborlisted" Interaction; multiple interactions can use the
// same NeighborList
// Now we run through all the atoms, set their positions / velocities,
// and add them to the LJ Interaction (i.e., to the neighbor list)
for (uint i=0; i < atoms.size(); i++){
if((i+1) % 50 == 0) cout << (Natoms - (i+1)) / 50 << ", "; cout.flush();
// we track energy to see if things are overlapping
flt E0 = LJ->energy(*obox);
atoms[i].x = obox->rand_loc(); // random location in the box
atoms[i].v = rand_vec(); // from a Gaussian
atoms[i].f = Vec::Zero();
atoms[i].a = Vec::Zero();
// Add it to the Lennard-Jones potential
LJ->add(EpsSigCutAtom(atoms.get_id(i), epsilon, sigma, sigcut));
// force an update the NeighborList, so we can get an accurate energy
nl->update_list(true);
// If we're overlapping too much, try a new location
while(LJ->energy(*obox) > E0 + epsilon/2.0){
atoms[i].x = obox->rand_loc(); // random location in the box
nl->update_list(true);
}
}
cout << "Starting. Neighborlist contains " << nl->numpairs() << " / " <<
(atoms.size()*(atoms.size()-1))/2 << " pairs.\n";
//Now we make our "Collection"
CollectionVerlet collec = CollectionVerlet(boost::static_pointer_cast<Box>(obox), atomptr, dt);
// This is very important! Otherwise the NeighborList won't update!
collec.add_tracker(nl);
// And add the Interaction
collec.add_interaction(LJ);
// subtract off center of mass velocity, and set a total energy
collec.reset_com_velocity();
collec.scale_velocities_to_energy(Natoms / 4.0);
// We'll put the energies to stdout and the coordinates to a new file.
// VMD is good for 3D visualization purposes, and it can read .xyz files
// see 'writefile' function
ofstream outfile;
outfile.open("LJatoms.xyz", ios::out);
writefile(outfile, atoms, *obox);
//Print out total energy, kinetic_energy energy, and potential energy
cout << "E: " << collec.energy() << " K: " << collec.kinetic_energy()
<< " U: " << LJ->energy(*obox) << "\n";
// Run the simulation! And every _ steps, write a frame to the .xyz
// file and print out the energies again
for(uint i=0; i<500; i++){
for(uint j=0; j<1000; j++){
collec.timestep();
}
writefile(outfile, atoms, *obox);
cout << (500-i) << " E: " << collec.energy() << " K: " << collec.kinetic_energy()
<< " U: " << LJ->energy(*obox) << "\n";
}
// Unnecessary extra:
// Write a "tcl" file with the box boundaries
// the "tcl" file is made specifically for VMD
ofstream pbcfile;
pbcfile.open("LJatoms-pbc.tcl", ios::out);
pbcfile << "set cell [pbc set {";
for(uint j=0; j<NDIM; j++){
pbcfile << obox->box_shape()[j] << " ";
}
pbcfile << "} -all];\n";
pbcfile << "pbc box -toggle -center origin -color red;\n";
// Now you should be able to run "vmd -e LJatoms-pbc.tcl LJatoms.xyz"
// and it will show you the movie and also the bounding box
// if you have .vmdrc in that same directory, you should also be able
// to toggle the box with the "b" button
cout << "Done. Neighborlist contains " << nl->numpairs() << " / " <<
(atoms.size()*(atoms.size()-1))/2 << " pairs.\n";
};
obox obox::transform(const mtx& m) const
{
return obox(x1y1z1 * m, x2y1z1 * m, x1y2z1 * m, x2y2z1 * m, x1y1z2 * m, x1y1z2 * m, x1y2z2 * m, x2y2z2 * m);
}
