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#include "Molmodel.h"
#include <iostream>
#include <exception>
using namespace SimTK;
int main() {
try {
// molecule-specialized simbody System
CompoundSystem system;
SimbodyMatterSubsystem matter(system);
DecorationSubsystem decorations(system);
// molecular force field
DuMMForceFieldSubsystem forceField(system);
// GeneralForceSubsystem forces(system);
// VanderWallSphere boundary(forces, forceField, Vec3(0,0,0), 0.50, 0.2, 0.001);
// Define an atom class for argon
forceField.defineAtomClass_KA(
forceField.getNextUnusedAtomClassIndex(),
"argon",
18,
0,
1.88,
0.0003832
);
forceField.defineChargedAtomType(
forceField.getNextUnusedChargedAtomTypeIndex(),
"argon",
forceField.getAtomClassIndex("argon"),
0.0 // neutral charge
);
if (! Biotype::exists("argon", "argon"))
Biotype::defineBiotype(new Element::Argon(), 0, "argon", "argon");
forceField.setBiotypeChargedAtomType( forceField.getChargedAtomTypeIndex("argon"), Biotype::get("argon", "argon").getIndex() );
forceField.setGbsaGlobalScaleFactor(0);
Argon argonAtom1, argonAtom2; // two argon atoms
// place first argon atom, units are nanometers
system.adoptCompound(argonAtom1, Vec3(-0.3, 0, 0));
// place second argon atom, units are nanometers
system.adoptCompound(argonAtom2, Vec3( 0.3, 0, 0));
// Show me a movie
Visualizer viz(system);
system.addEventReporter( new Visualizer::Reporter(viz, 0.50) );
system.modelCompounds(); // finalize multibody system
State state = system.realizeTopology();
// Simulate it.
VerletIntegrator integ(system);
TimeStepper ts(system, integ);
ts.initialize(state);
ts.stepTo(2000.0);
return 0;
}
catch(const std::exception& e) {
std::cerr << "ERROR: " << e.what() << std::endl;
return 1;
}
catch(...) {
std::cerr << "ERROR: An unknown exception was raised" << std::endl;
return 1;
}
}
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