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Commit 49e0e613 authored by Michael Sherman's avatar Michael Sherman
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Not a good example.

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examples/HelloWorld.cpp deleted 100644 → 0
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// 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 <iostream>
#include <string>
#include <limits>
using namespace OpenMM;
Vec3 operator*(const Vec3& v, double r) {
return Vec3(v[0]*r, v[1]*r, v[2]*r);
}
Vec3 operator*(double r, const Vec3& v) {
return Vec3(r*v[0], r*v[1], r*v[2]);
}
// This is not part of OpenMM; just a struct we can use to collect
// atom parameters for this example. Normally atom parameters would
// come from the force field's parameterization file.
// We're going to use data in Angstrom and Kilocalorie units and
// show how to safely convert to OpenMM's internal unit system
// which uses nanometers and kilojoules.
struct AtomInfo {
char* symbol;
double mass, charge, vdwRadiusAng, vdwEnergyKcal;
Vec3 startPosAng;
};
static AtomInfo atoms[] = {
{"Na+", 22.99, 1, 1.8680, 0.00277, Vec3(-3,0,0)},
{"Cl-", 35.45, -1, 2.4700, 0.1000, Vec3( 3,0,0)},
{""} // end of list
};
static const double Temperature = 100; // Kelvins
static const double FrictionInPerPs = 91.; // collisions per ps
static const double StepSizeFs = 2; // femtoseconds
static const double ReportIntervalFs = 1000;
static const double SimulationTimePs = 1000; // total simulation time (ps)
static const double SigmaPerVdwRadius = 2*std::pow(2., -1./6.);
static double showState(const OpenMMContext&);
int main() {
try {
// Load all available OpenMM plugins from their default location.
Platform::loadPluginsFromDirectory(Platform::getDefaultPluginsDirectory());
// Create a System and a NonbondedForce object within the System.
System system;
NonbondedForce* nonbond = new NonbondedForce();
system.addForce(nonbond);
int numAtoms = 0;
for (; *atoms[numAtoms].symbol; ++numAtoms) {
const AtomInfo& atom = atoms[numAtoms];
system.addParticle(atom.mass);
nonbond->addParticle(atom.charge,
atom.vdwRadiusAng * NmPerAngstrom * SigmaPerVdwRadius,
atom.vdwEnergyKcal * KJPerKcal);
}
// Create an integrator object for advancing time.
//LangevinIntegrator integrator(Temperature, Friction, StepSizeFs * PsPerFs);
VerletIntegrator integrator(StepSizeFs * PsPerFs);
// Create an OpenMM Context for execution; let it choose best platform.
OpenMMContext context(system, integrator);
std::cout << "Will use OpenMM platform " << context.getPlatform().getName() << std::endl;
std::cout << "eps(float)=" << std::numeric_limits<float>::epsilon() << std::endl;
// Fill in a vector of starting positions, one per atom.
std::vector<Vec3> positions(numAtoms);
for (int i=0; i < numAtoms; ++i)
positions[i] = atoms[i].startPosAng * NmPerAngstrom;
// Set the starting positions in the OpenMM context. Velocities will be zero.
context.setPositions(positions);
// Output the initial state.
double time = showState(context);
const int NumSilentSteps = (int)(ReportIntervalFs / StepSizeFs + 0.5);
do {
integrator.step(NumSilentSteps);
time = showState(context);
} while (time < SimulationTimePs);
} catch(const std::exception& e) {
std::cout << "EXCEPTION: " << e.what() << std::endl;
return 1;
}
return 0;
}
static double
showState(const OpenMMContext& context) {
// Caution: at the moment asking for energy requires use of slow reference calculation.
const State state = context.getState( State::Positions | State::Velocities
| State::Forces | State::Energy);
const double energy = state.getPotentialEnergy() + state.getKineticEnergy();
const std::vector<Vec3>& positions = state.getPositions();
const std::vector<Vec3>& forces = state.getForces();
std::cout << "t=" << state.getTime() << " E=" << energy << std::endl;
const double dt = StepSizeFs*PsPerFs;
for (unsigned i=0; i < positions.size(); ++i) {
const Vec3 dq = dt*dt/(2*atoms[i].mass) * forces[i];
std::cout << i << " " << positions[i] * AngstromsPerNm << std::endl;
std::cout << "f=" << forces[i] << " dq=" << dq << std::endl;
}
return state.getTime();
}
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