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Commit 9c8db8bf authored by Michael Sherman's avatar Michael Sherman
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fix up ugly line endings

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examples/HelloSodiumChloride.cpp
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/* -----------------------------------------------------------------------------
* OpenMM(tm) HelloSodiumChloride example (May 2009)
* -----------------------------------------------------------------------------
* This is a complete, self-contained "hello world" example demonstrating
* GPU-accelerated constant energy simulation of a very simple system with just
* nonbonded forces, consisting of several sodium (Na+) and chloride (Cl-) ions.
* 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
* continue to work with Amber-style units of Angstroms and kCals while correctly
* communicating with OpenMM in nanometers and kJoules.
* -------------------------------------------------------------------------- */
// 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
/* -----------------------------------------------------------------------------
* OpenMM(tm) HelloSodiumChloride example (May 2009)
* -----------------------------------------------------------------------------
* This is a complete, self-contained "hello world" example demonstrating
* GPU-accelerated constant energy simulation of a very simple system with just
* nonbonded forces, consisting of several sodium (Na+) and chloride (Cl-) ions.
* 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
* continue to work with Amber-style units of Angstroms and kCals while correctly
* communicating with OpenMM in nanometers and kJoules.
* -------------------------------------------------------------------------- */
// 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"
......@@ -26,41 +26,41 @@
using OpenMM::Vec3; // so we can just say "Vec3" below
// -----------------------------------------------------------------------------
// MODELING AND SIMULATION PARAMETERS
// -----------------------------------------------------------------------------
const double StepSizeInFs = 2; // integration step size (fs)
const double ReportIntervalInFs = 10; // how often to generate PDB frame (fs)
// MODELING AND SIMULATION PARAMETERS
// -----------------------------------------------------------------------------
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 simulateNaCl();
static void simulateNaCl();
static void writePDB(const OpenMM::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.
OpenMM::Platform::loadPluginsFromDirectory
(OpenMM::Platform::getDefaultPluginsDirectory());
simulateNaCl();
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;
}
// -----------------------------------------------------------------------------
// 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.
OpenMM::Platform::loadPluginsFromDirectory
(OpenMM::Platform::getDefaultPluginsDirectory());
simulateNaCl();
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;
}
}
// -----------------------------------------------------------------------------
// ATOM AND FORCE FIELD DATA
// -----------------------------------------------------------------------------
// ATOM AND FORCE FIELD DATA
// -----------------------------------------------------------------------------
// This is not part of OpenMM; just a struct we can use to collect
// atom parameters for this example. Normally atom parameters would
......@@ -83,22 +83,22 @@ struct AtomInfo {
{""} // end of list
};
// Add missing scalar product operators for OpenMM::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.);
// -----------------------------------------------------------------------------
// NaCl SIMULATION
// Add missing scalar product operators for OpenMM::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.);
// -----------------------------------------------------------------------------
// NaCl SIMULATION
// -----------------------------------------------------------------------------
static void simulateNaCl() {
// -------------------------------------------------------------------------
// Create a System and Force objects within the System. Retain a reference
// 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!
// -------------------------------------------------------------------------
// Create a System and Force objects within the System. Retain a reference
// 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!
// -------------------------------------------------------------------------
OpenMM::System system;
OpenMM::NonbondedForce* nonbond = new OpenMM::NonbondedForce();
......@@ -108,11 +108,11 @@ static void simulateNaCl() {
nonbond->setCutoffDistance(2);
nonbond->setPeriodicBoxVectors(Vec3(5,0,0), Vec3(0,5,0), Vec3(0,0,5));
// -------------------------------------------------------------------------
// Specify the atoms and their properties:
// (1) System needs to know the masses.
// (2) NonbondedForce needs charges,van der Waals properties (in MD units!).
// (3) Collect default positions for initializing the simulation later.
// -------------------------------------------------------------------------
// Specify the atoms and their properties:
// (1) System needs to know the masses.
// (2) NonbondedForce needs charges,van der Waals properties (in MD units!).
// (3) Collect default positions for initializing the simulation later.
// -------------------------------------------------------------------------
std::vector<Vec3> initialPositions;
for (int n=0; *atoms[n].pdb; ++n) {
......@@ -122,25 +122,25 @@ static void simulateNaCl() {
atom.vdwRadiusInAng * OpenMM::NmPerAngstrom
* SigmaPerVdwRadius,
atom.vdwEnergyInKcal * OpenMM::KJPerKcal);
initialPositions.push_back(atoms[n].initPosInAngstroms
* OpenMM::NmPerAngstrom);
initialPositions.push_back(atoms[n].initPosInAngstroms
* OpenMM::NmPerAngstrom);
}
// -------------------------------------------------------------------------
// Choose an Integrator for advancing time, and a Context connecting the
// System with the Integrator for simulation. Let the Context choose the
// best available Platform. Initialize the configuration from the default
// positions we collected above. Initial velocities will be zero.
// -------------------------------------------------------------------------
OpenMM::VerletIntegrator integrator(StepSizeInFs * OpenMM::PsPerFs);
OpenMM::OpenMMContext context(system, integrator);
// -------------------------------------------------------------------------
// Choose an Integrator for advancing time, and a Context connecting the
// System with the Integrator for simulation. Let the Context choose the
// best available Platform. Initialize the configuration from the default
// positions we collected above. Initial velocities will be zero.
// -------------------------------------------------------------------------
OpenMM::VerletIntegrator integrator(StepSizeInFs * OpenMM::PsPerFs);
OpenMM::OpenMMContext context(system, integrator);
context.setPositions(initialPositions);
// -------------------------------------------------------------------------
// Run the simulation:
// (1) Write the first line of the PDB file and the initial configuration.
// (2) Run silently entirely within OpenMM between reporting intervals.
// (3) Write a PDB frame when the time comes.
// -------------------------------------------------------------------------
// Run the simulation:
// (1) Write the first line of the PDB file and the initial configuration.
// (2) Run silently entirely within OpenMM between reporting intervals.
// (3) Write a PDB frame when the time comes.
// -------------------------------------------------------------------------
printf( "REMARK Using OpenMM platform %s\n", context.getPlatform().getName().c_str() );
writePDB(context);
......@@ -152,8 +152,8 @@ static void simulateNaCl() {
} while (context.getTime() < SimulationTimeInPs);
}
// -----------------------------------------------------------------------------
// PDB FILE WRITER
// -----------------------------------------------------------------------------
// PDB FILE WRITER
// -----------------------------------------------------------------------------
static void
writePDB(const OpenMM::OpenMMContext& context) {
......
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