Output Class Reference

#include <Output.h>

List of all members.

Public Member Functions
	Output ()
	~Output ()
void	energy (int, BigReal *)
void	coordinate (int, int, Vector *, FloatVector *, Lattice &)
void	velocity (int, int, Vector *)
Static Public Member Functions
int	coordinateNeeded (int)
int	velocityNeeded (int)

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Constructor & Destructor Documentation

Output::Output (   )

Definition at line 47 of file Output.C. { }

Output::~Output (   )

Definition at line 57 of file Output.C. { }

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Member Function Documentation

void Output::coordinate (  int  , int  , Vector *  , FloatVector *  , Lattice &  )

Definition at line 218 of file Output.C. References SimParameters::dcdFrequency, SimParameters::dcdUnitCell, END_OF_RUN, FILE_OUTPUT, SimParameters::firstTimestep, IMDOutput::gather_coordinates(), Node::getScript(), Node::imd, SimParameters::IMDfreq, SimParameters::IMDon, iout, ScriptTcl::measure(), SimParameters::N, Node::Object(), SimParameters::restartFrequency, Node::simParameters, simParams, and wrap_coor(). Referenced by CollectionMaster::disposePositions(). { SimParameters *simParams = Node::Object()->simParameters; double coor_wrapped = 0; float fcoor_wrapped = 0; if ( timestep >= 0 ) { // Output a DCD trajectory if ( simParams->dcdFrequency && ((timestep % simParams->dcdFrequency) == 0) ) { wrap_coor(fcoor,lattice,&fcoor_wrapped); output_dcdfile(timestep, n, fcoor, simParams->dcdUnitCell ? &lattice : NULL); } // Output a restart file if ( simParams->restartFrequency && ((timestep % simParams->restartFrequency) == 0) ) { iout << "WRITING COORDINATES TO RESTART FILE AT STEP " << timestep << "\n" << endi; wrap_coor(coor,lattice,&coor_wrapped); output_restart_coordinates(coor, n, timestep); iout << "FINISHED WRITING RESTART COORDINATES\n" <<endi; fflush(stdout); } // Interactive MD if ( simParams->IMDon && ( ((timestep % simParams->IMDfreq) == 0) || (timestep == simParams->firstTimestep) ) ) { IMDOutput *imd = Node::Object()->imd; wrap_coor(fcoor,lattice,&fcoor_wrapped); if (imd != NULL) imd->gather_coordinates(timestep, n, fcoor); } } if (timestep == EVAL_MEASURE) { #ifdef NAMD_TCL wrap_coor(coor,lattice,&coor_wrapped); Node::Object()->getScript()->measure(coor); #endif } // Output final coordinates if (timestep == FILE_OUTPUT || timestep == END_OF_RUN) { iout << "WRITING COORDINATES TO OUTPUT FILE AT STEP " << simParams->N << "\n" << endi; fflush(stdout); wrap_coor(coor,lattice,&coor_wrapped); output_final_coordinates(coor, n, simParams->N); } // Close trajectory files if (timestep == END_OF_RUN) { if (simParams->dcdFrequency) output_dcdfile(END_OF_RUN,0,0, simParams->dcdUnitCell ? &lattice : NULL); } }

int Output::coordinateNeeded (  int   )  [static]

Definition at line 77 of file Output.C. References SimParameters::dcdFrequency, END_OF_RUN, FILE_OUTPUT, SimParameters::firstTimestep, SimParameters::IMDfreq, SimParameters::IMDon, Node::Object(), SimParameters::restartFrequency, Node::simParameters, and simParams. Referenced by Controller::enqueueCollections(), and Sequencer::submitCollections(). { SimParameters *simParams = Node::Object()->simParameters; int positionsNeeded = 0; if ( timestep >= 0 ) { // Output a DCD trajectory if ( simParams->dcdFrequency && ((timestep % simParams->dcdFrequency) == 0) ) { positionsNeeded |= 1; } // Output a restart file if ( simParams->restartFrequency && ((timestep % simParams->restartFrequency) == 0) ) { positionsNeeded |= 2; } // Iteractive MD if ( simParams->IMDon && ( ((timestep % simParams->IMDfreq) == 0) || (timestep == simParams->firstTimestep) ) ) { positionsNeeded |= 1; } } // Output final coordinates if (timestep == FILE_OUTPUT || timestep == END_OF_RUN || timestep == EVAL_MEASURE) { positionsNeeded |= 2; } return positionsNeeded; }

void Output::energy (  int  , BigReal *  )

void Output::velocity (  int  , int  , Vector *  )

Definition at line 333 of file Output.C. References END_OF_RUN, FILE_OUTPUT, iout, SimParameters::N, Node::Object(), SimParameters::restartFrequency, Node::simParameters, simParams, and SimParameters::velDcdFrequency. Referenced by CollectionMaster::disposeVelocities(). { SimParameters *simParams = Node::Object()->simParameters; if ( timestep >= 0 ) { // Output velocity DCD trajectory if ( simParams->velDcdFrequency && ((timestep % simParams->velDcdFrequency) == 0) ) { output_veldcdfile(timestep, n, vel); } // Output restart file if ( simParams->restartFrequency && ((timestep % simParams->restartFrequency) == 0) ) { iout << "WRITING VELOCITIES TO RESTART FILE AT STEP " << timestep << "\n" << endi; output_restart_velocities(timestep, n, vel); iout << "FINISHED WRITING RESTART VELOCITIES\n" <<endi; fflush(stdout); } } // Output final velocities if (timestep == FILE_OUTPUT || timestep == END_OF_RUN) { iout << "WRITING VELOCITIES TO OUTPUT FILE AT STEP " << simParams->N << "\n" << endi; fflush(stdout); output_final_velocities(simParams->N, n, vel); } // Close trajectory files if (timestep == END_OF_RUN) { if (simParams->velDcdFrequency) output_veldcdfile(END_OF_RUN,0,0); } }

int Output::velocityNeeded (  int   )  [static]

Definition at line 304 of file Output.C. References FILE_OUTPUT, Node::Object(), SimParameters::restartFrequency, Node::simParameters, simParams, and SimParameters::velDcdFrequency. Referenced by Controller::enqueueCollections(), and Sequencer::submitCollections(). { SimParameters *simParams = Node::Object()->simParameters; int velocitiesNeeded = 0; if ( timestep >= 0 ) { // Output a velocity DCD trajectory if ( simParams->velDcdFrequency && ((timestep % simParams->velDcdFrequency) == 0) ) { velocitiesNeeded |= 1; } // Output a restart file if ( simParams->restartFrequency && ((timestep % simParams->restartFrequency) == 0) ) { velocitiesNeeded |= 2; } } // Output final velocities if (timestep == FILE_OUTPUT || timestep == END_OF_RUN) { velocitiesNeeded |= 2; } return velocitiesNeeded; }

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The documentation for this class was generated from the following files:

• Output.h
• Output.C

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