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Commit f23db9f1 authored by Michael Sherman's avatar Michael Sherman
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Chris code-reviewed this so now it is the official HelloEthane example.

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examples/HelloEthane.cpp
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......@@ -3,9 +3,9 @@
* -----------------------------------------------------------------------------
* This is a complete, self-contained "hello world" example demonstrating
* GPU-accelerated simulation of a system with both bonded and nonbonded forces,
* using ethane (H3-C-C-H3) as an example. A multi-frame PDB file is written
* to stdout which can be read by VMD or other visualization tool to produce
* an animation of the resulting trajectory.
* using ethane (H3-C-C-H3) in a vacuum as an example. A multi-frame PDB file is
* written to stdout which can be read by VMD or other visualization tool to
* produce an animation of the resulting trajectory.
*
* Pay particular attention to the handling of units in this example. Incorrect
* handling of units is a very common error; this example shows how you can
......@@ -28,11 +28,40 @@
using namespace OpenMM;
// These are missing from the current version of OpenMM so we're adding them
// temporarily here.
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]);}
static const double SigmaPerVdwRadius = 2*std::pow(2., -1./6.);
// -----------------------------------------------------------------------------
// MODELING AND SIMULATION PARAMETERS
// -----------------------------------------------------------------------------
const bool UseConstraints = false; // Should we constrain C-H bonds?
const double StepSizeInFs = 2; // integration step size (fs)
const double ReportIntervalInFs = 10; // how often to generate PDB frame (fs)
const double SimulationTimeInPs = 100; // total simulation time (ps)
static void simulateEthane();
static void writePDB(const OpenMMContext&); // PDB file writer; see below.
// -----------------------------------------------------------------------------
// MAIN PROGRAM
// -----------------------------------------------------------------------------
int main() {
// ALWAYS enclose all OpenMM calls with a try/catch block to make sure that
// usage and runtime errors are caught and reported.
try {
// Load all available OpenMM plugins from their default location.
Platform::loadPluginsFromDirectory(Platform::getDefaultPluginsDirectory());
simulateEthane();
return 0; // Normal return from main.
}
// Catch and report usage and runtime errors detected by OpenMM and fail.
catch(const std::exception& e) {
printf("EXCEPTION: %s\n", e.what());
return 1;
}
}
// -----------------------------------------------------------------------------
// FORCE FIELD DATA
......@@ -83,61 +112,53 @@ const int HCCH = 0;
// computer do that!
const int EndOfList=-1;
struct AtomInfo {
int type; char* pdbSymbol; Vec3 initPosInAngstroms;
} atoms[] = {/*0*/C, "C1", Vec3( -.765, 0, 0 ),
/*1*/C, "C2", Vec3( .765, 0, 0 ),
/*2*/H, "H1", Vec3(-1.135, 1.03, 0 ), // bonded to C1
/*3*/H, "H2", Vec3(-1.135, -.51, .89),
/*4*/H, "H3", Vec3(-1.135, -.51,-.89),
/*5*/H, "H4", Vec3( 1.135, 1.03, 0 ), // bonded to C2
/*6*/H, "H5", Vec3( 1.135, -.51, .89),
/*7*/H, "H6", Vec3( 1.135, -.51,-.89),
struct AtomInfo
{ int type; char pdb[5]; Vec3 initPosInAngstroms;} atoms[] =
{/*0*/C, " C1 ", Vec3( -.7605, 0, 0 ),
/*1*/C, " C2 ", Vec3( .7605, 0, 0 ),
/*2*/H, "1H1 ", Vec3(-1.135, 1.03, 0 ), // bonded to C1
/*3*/H, "2H1 ", Vec3(-1.135, -.51, .89),
/*4*/H, "3H1 ", Vec3(-1.135, -.51,-.89),
/*5*/H, "1H2 ", Vec3( 1.135, 1.03, 0 ), // bonded to C2
/*6*/H, "2H2 ", Vec3( 1.135, -.51, .89),
/*7*/H, "3H2 ", Vec3( 1.135, -.51,-.89),
EndOfList};
struct {int type; int a[2];} bonds[] = {CC,0,1,CH,0,2,CH,0,3,CH,0,4,
CH,1,5,CH,1,6,CH,1,7,
struct {int type; int atoms[2];} bonds[] =
{CC,0,1,
CH,0,2,CH,0,3,CH,0,4, // C1 methyl
CH,1,5,CH,1,6,CH,1,7, // C2 methyl
EndOfList};
struct {int type; int a[3];} angles[] = {HCC,2,0,1,HCC,3,0,1,HCC,4,0,1,
HCC,5,1,0,HCC,6,1,0,HCC,7,1,0,
struct {int type; int atoms[3];} angles[] =
{HCC,2,0,1,HCC,3,0,1,HCC,4,0,1, // C1 methyl
HCH,2,0,3,HCH,2,0,4,HCH,3,0,4,
HCC,5,1,0,HCC,6,1,0,HCC,7,1,0, // C2 methyl
HCH,5,1,6,HCH,5,1,7,HCH,6,1,7,
EndOfList};
struct {int type; int a[4];} torsions[] = {HCCH,2,0,1,5,HCCH,2,0,1,6,HCCH,2,0,1,7,
struct {int type; int atoms[4];} torsions[] =
{HCCH,2,0,1,5,HCCH,2,0,1,6,HCCH,2,0,1,7,
HCCH,3,0,1,5,HCCH,3,0,1,6,HCCH,3,0,1,7,
HCCH,4,0,1,5,HCCH,4,0,1,6,HCCH,4,0,1,7,
EndOfList};
// -----------------------------------------------------------------------------
// MODELING AND SIMULATION PARAMETERS
// -----------------------------------------------------------------------------
const bool UseConstraints = false; // Should we constrain C-H bonds?
const double Temperature = 300; // bath temperature in Kelvins
const double FrictionInPs = 1./91.; // picoseconds between collisions
const double StepSizeInFs = 2; // integration step size (fs)
const double ReportIntervalInFs = 10; // how often to generate PDB frame (fs)
const double SimulationTimeInPs = 100; // total simulation time (ps)
// PDB file writer; see below.
static void writePDB(const OpenMMContext&);
// Add missing scalar product operators for Vec3.
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 the conversion factor that takes you from a van der Waals radius
// (defined as 1/2 the minimum energy separation) to the related Lennard Jones
// "sigma" parameter (defined as the zero crossing separation).
static const double SigmaPerVdwRadius = 2*std::pow(2., -1./6.);
// -----------------------------------------------------------------------------
// MAIN PROGRAM
// ETHANE SIMULATION
// -----------------------------------------------------------------------------
int main() {
// ALWAYS enclose all OpenMM calls with a try/catch block to make sure that
// usage and runtime errors are caught and reported.
try {
// -------------------------------------------------------------------------
// Load all available OpenMM plugins from their default location.
// -------------------------------------------------------------------------
Platform::loadPluginsFromDirectory(Platform::getDefaultPluginsDirectory());
static void simulateEthane() {
// -------------------------------------------------------------------------
// Create a System and Force objects within the System. Retain a reference
// to each force object so we can fill in the forces.
// to each force object so we can fill in the forces. Note: OpenMM owns
// the objects and will take care of deleting them; don't do it yourself!
// -------------------------------------------------------------------------
System system;
NonbondedForce& nonbond = *new NonbondedForce();
......@@ -173,19 +194,19 @@ int main() {
// -------------------------------------------------------------------------
std::vector< std::pair<int,int> > bondPairs;
for (int i=0; bonds[i].type != EndOfList; ++i) {
const int* atoms = bonds[i].a;
const int* atom = bonds[i].atoms;
const BondType& bond = bondType[bonds[i].type];
// Note factor of 2 for stiffness below because Amber specifies the constant
// as it is used in the harmonic energy term kx^2 with force 2kx; OpenMM wants
// it as used in the force term kx, with energy kx^2/2.
bondStretch.addBond(atoms[0], atoms[1],
bondStretch.addBond(atom[0], atom[1],
bond.nominalLengthInAngstroms * NmPerAngstrom,
bond.stiffnessInKcalPerAngstrom2 * 2 * KJPerKcal * AngstromsPerNm * AngstromsPerNm);
if (UseConstraints && bond.canConstrain)
system.addConstraint(atoms[0], atoms[1],
system.addConstraint(atom[0], atom[1],
bond.nominalLengthInAngstroms * NmPerAngstrom);
bondPairs.push_back(std::make_pair(atoms[0], atoms[1]));
bondPairs.push_back(std::make_pair(atom[0], atom[1]));
}
// Exclude 1-2, 1-3 bonded atoms from nonbonded forces, and scale down 1-4 bonded atoms.
nonbond.createExceptionsFromBonds(bondPairs, Coulomb14Scale, LennardJones14Scale);
......@@ -194,11 +215,11 @@ int main() {
// Create the 1-2-3 bond angle harmonic terms.
// -------------------------------------------------------------------------
for (int i=0; angles[i].type != EndOfList; ++i) {
const int* atoms = angles[i].a;
const int* atom = angles[i].atoms;
const AngleType& angle = angleType[angles[i].type];
// See note under bond stretch above regarding the factor of 2 here.
bondBend.addAngle(atoms[0],atoms[1],atoms[2],
bondBend.addAngle(atom[0],atom[1],atom[2],
angle.nominalAngleInDegrees * RadiansPerDegree,
angle.stiffnessInKcalPerRadian2 * 2 * KJPerKcal);
}
......@@ -207,9 +228,9 @@ int main() {
// Create the 1-2-3-4 bond torsion (dihedral) terms.
// -------------------------------------------------------------------------
for (int i=0; torsions[i].type != EndOfList; ++i) {
const int* atoms = torsions[i].a;
const int* atom = torsions[i].atoms;
const TorsionType& torsion = torsionType[torsions[i].type];
bondTorsion.addTorsion(atoms[0],atoms[1],atoms[2],atoms[3],
bondTorsion.addTorsion(atom[0],atom[1],atom[2],atom[3],
torsion.periodicity,
torsion.phaseInDegrees * RadiansPerDegree,
torsion.amplitudeInKcal * KJPerKcal);
......@@ -221,7 +242,6 @@ int main() {
// best available Platform. Initialize the configuration from the default
// positions we collected above. Initial velocities will be zero.
// -------------------------------------------------------------------------
//LangevinIntegrator integrator(Temperature, FrictionInPs, StepSizeInFs * PsPerFs);
VerletIntegrator integrator(StepSizeInFs * PsPerFs);
OpenMMContext context(system, integrator);
context.setPositions(initialPositions);
......@@ -240,20 +260,10 @@ int main() {
integrator.step(NumSilentSteps);
writePDB(context);
} while (context.getTime() < SimulationTimeInPs);
// -------------------------------------------------------------------------
// Normal return from main.
// -------------------------------------------------------------------------
return 0;
// Catch and report usage and runtime errors detected by OpenMM and fail.
} catch(const std::exception& e) {
printf("EXCEPTION: %s\n", e.what());
return 1;
}
}
// -----------------------------------------------------------------------------
// PDB FILE WRITER
// -----------------------------------------------------------------------------
......@@ -271,8 +281,8 @@ writePDB(const OpenMMContext& context) {
printf("REMARK 250 time=%.3f picoseconds; Energy = %.3f kilojoules/mole\n", state.getTime(), energy);
for (unsigned i=0; i < positions.size(); ++i) {
const Vec3 pos = positions[i] * AngstromsPerNm;
printf("ATOM %5d %2s ETH 1 %8.3f%8.3f%8.3f 1.00 0.00 %2s\n",
i+1, atoms[i].pdbSymbol, pos[0], pos[1], pos[2], atoms[i].pdbSymbol);
printf("ATOM %5d %4s ETH 1 %8.3f%8.3f%8.3f 1.00 0.00 \n",
i+1, atoms[i].pdb, pos[0], pos[1], pos[2]);
}
printf("ENDMDL\n");
}
......
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