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Commit 3ec08ba6 authored by Michael Sherman's avatar Michael Sherman
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Added Hello Argon, made some mods to the other examples.

parent 27ff4f1b
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Showing with 88 additions and 24 deletions
examples/HelloArgon.cpp 0 → 100644
View file @ 3ec08ba6
#include "OpenMM.h"
#include <cstdio>
using namespace OpenMM;
void writePdb(const OpenMMContext& context) {
const State state = context.getState(State::Positions);
const std::vector<Vec3>& pos = state.getPositions();
static int modelFrameNumber = 0; // numbering for MODEL records in pdb output
// write out in PDB format
modelFrameNumber++;
printf("MODEL %d\n", modelFrameNumber);
for (int a = 0; a < context.getSystem().getNumParticles(); ++a)
printf("ATOM %5d AR AR 1 %8.3f%8.3f%8.3f 1.00 0.00 AR\n",
a+1, pos[a][0]*10, pos[a][1]*10, pos[a][2]*10);
printf("ENDMDL\n");
}
int main() {
Platform::loadPluginsFromDirectory(Platform::getDefaultPluginsDirectory());
System system;
NonbondedForce* nonbond = new NonbondedForce();
system.addForce(nonbond);
// Create atoms
int numAtoms = 2;
for (int a = 0; a < numAtoms; ++a) {
system.addParticle(39.95); // mass
nonbond->addParticle(0.0, 0.3350, 0.001603); // charge, diameter, well depth
}
// Large step size may be required for stability with small forces
VerletIntegrator integrator(0.002); // step size in picoseconds
// Let OpenMM Context choose best platform.
OpenMMContext context(system, integrator);
printf( "REMARK Using OpenMM platform %s\n", context.getPlatform().getName().c_str() );
// Set the starting positions in the OpenMM context. Velocities will be zero.
std::vector<Vec3> positions(numAtoms);
for (int a = 0; a < numAtoms; ++a)
positions[a] = Vec3(0.5*a,0,0);
context.setPositions(positions);
while(context.getTime() < 500.0) { // picoseconds
writePdb(context);
integrator.step(100); // number of steps between reports
}
writePdb(context);
return 0;
}
examples/HelloSodiumChloride.cpp
View file @ 3ec08ba6
......@@ -27,20 +27,24 @@ struct AtomInfo {
};
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)},
{"NA", 22.99, 1, 1.8680, 0.00277, Vec3(8,0,0)},
{"CL", 35.45, -1, 2.4700, 0.1000, Vec3(-8,0,0)},
{"NA", 22.99, 1, 1.8680, 0.00277, Vec3(0,9,0)},
{"CL", 35.45, -1, 2.4700, 0.1000, Vec3(0,-9,0)},
{"NA", 22.99, 1, 1.8680, 0.00277, Vec3(0,0,-10)},
{"CL", 35.45, -1, 2.4700, 0.1000, Vec3( 0,0,10)},
{""} // end of list
};
static const double Temperature = 100; // Kelvins
static const double Friction = 1./91.; // picoseconds between collisions
static const double StepSizeFs = .1; // femtoseconds
static const double ReportIntervalFs = 1000;
static const double SimulationTimePs = 1000; // total simulation time (ps)
static const double Temperature = 300; // Kelvins
static const double Friction = 1./91.; // picoseconds between collisions
static const double StepSizeFs = 2; // femtoseconds
static const double ReportIntervalFs = 10;
static const double SimulationTimePs = 100; // total simulation time (ps)
static const double SigmaPerVdwRadius = 2*std::pow(2., -1./6.);
static void showState(const OpenMMContext&);
static void writePDB(const OpenMMContext&);
int main() {
try {
......@@ -62,14 +66,14 @@ try {
}
// Create an integrator object for advancing time.
//LangevinIntegrator integrator(Temperature, Friction, StepSizeFs * PsPerFs);
VerletIntegrator integrator(StepSizeFs * PsPerFs);
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);
const std::string platformName = context.getPlatform().getName();
std::cout << "Will use OpenMM platform " << platformName << std::endl;
printf( "REMARK Using OpenMM platform %s\n", context.getPlatform().getName().c_str() );
// Fill in a vector of starting positions, one per atom.
std::vector<Vec3> positions(numAtoms);
......@@ -80,13 +84,13 @@ try {
context.setPositions(positions);
// Output the initial state.
showState(context);
writePDB(context);
const int NumSilentSteps = (int)(ReportIntervalFs / StepSizeFs + 0.5);
do {
integrator.step(NumSilentSteps);
showState(context);
} while (context.getTime() <= SimulationTimePs);
writePDB(context);
} while (context.getTime() < SimulationTimePs);
} catch(const std::exception& e) {
std::cout << "EXCEPTION: " << e.what() << std::endl;
......@@ -97,7 +101,7 @@ try {
}
static void
showState(const OpenMMContext& context) {
writePDB(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::Energy);
const double energy = state.getPotentialEnergy() + state.getKineticEnergy();
......@@ -108,10 +112,11 @@ showState(const OpenMMContext& context) {
modelFrameNumber++;
printf("MODEL %d\n", modelFrameNumber);
printf("REMARK 250 time=%.3f picoseconds; Energy = %.3f kilojoules/mole\n", state.getTime(), energy);
printf("ATOM 1 NA SLT 1 %8.3f%8.3f%8.3f 1.00 0.00 NA\n",
positions[0][0]*AngstromsPerNm, positions[0][1]*AngstromsPerNm, positions[0][2]*AngstromsPerNm);
printf("ATOM 2 CL SLT 1 %8.3f%8.3f%8.3f 1.00 0.00 CL\n",
positions[1][0]*AngstromsPerNm, positions[1][1]*AngstromsPerNm, positions[1][2]*AngstromsPerNm);
for (unsigned i=0; i < positions.size(); ++i) {
const Vec3 pos = positions[i] * AngstromsPerNm;
printf("ATOM %3d %2s SLT 1 %8.3f%8.3f%8.3f 1.00 0.00 %2s\n",
i+1, atoms[i].symbol, pos[0], pos[1], pos[2], atoms[i].symbol);
}
printf("ENDMDL\n");
}
examples/HelloWorld.cpp
View file @ 3ec08ba6
......@@ -2,6 +2,7 @@
#include <iostream>
#include <string>
#include <limits>
using namespace OpenMM;
......@@ -33,7 +34,7 @@ static AtomInfo atoms[] = {
static const double Temperature = 100; // Kelvins
static const double Friction = 1./91.; // picoseconds between collisions
static const double StepSizeFs = 0.1; // femtoseconds
static const double StepSizeFs = 2; // femtoseconds
static const double ReportIntervalFs = 1000;
static const double SimulationTimePs = 1000; // total simulation time (ps)
......@@ -68,6 +69,7 @@ try {
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);
......@@ -84,7 +86,7 @@ try {
do {
integrator.step(NumSilentSteps);
showState(context);
} while (context.getTime() <= SimulationTimePs);
} while (context.getTime() < SimulationTimePs);
} catch(const std::exception& e) {
std::cout << "EXCEPTION: " << e.what() << std::endl;
......@@ -97,11 +99,17 @@ try {
static void
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::Energy);
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;
for (unsigned i=0; i < positions.size(); ++i)
std::cout << i << " " << positions[i] << 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;
}
}
\ No newline at end of file
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