#include <Output.h>
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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Definition at line 47 of file Output.C. 00047 { }
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Definition at line 57 of file Output.C. 00057 { }
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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(). 00220 {
00221 SimParameters *simParams = Node::Object()->simParameters;
00222 double coor_wrapped = 0;
00223 float fcoor_wrapped = 0;
00224
00225 if ( timestep >= 0 ) {
00226
00227 // Output a DCD trajectory
00228 if ( simParams->dcdFrequency &&
00229 ((timestep % simParams->dcdFrequency) == 0) )
00230 {
00231 wrap_coor(fcoor,lattice,&fcoor_wrapped);
00232 output_dcdfile(timestep, n, fcoor,
00233 simParams->dcdUnitCell ? &lattice : NULL);
00234 }
00235
00236 // Output a restart file
00237 if ( simParams->restartFrequency &&
00238 ((timestep % simParams->restartFrequency) == 0) )
00239 {
00240 iout << "WRITING COORDINATES TO RESTART FILE AT STEP "
00241 << timestep << "\n" << endi;
00242 wrap_coor(coor,lattice,&coor_wrapped);
00243 output_restart_coordinates(coor, n, timestep);
00244 iout << "FINISHED WRITING RESTART COORDINATES\n" <<endi;
00245 fflush(stdout);
00246 }
00247
00248 // Interactive MD
00249 if ( simParams->IMDon &&
00250 ( ((timestep % simParams->IMDfreq) == 0) ||
00251 (timestep == simParams->firstTimestep) ) )
00252 {
00253 IMDOutput *imd = Node::Object()->imd;
00254 wrap_coor(fcoor,lattice,&fcoor_wrapped);
00255 if (imd != NULL) imd->gather_coordinates(timestep, n, fcoor);
00256 }
00257
00258 }
00259
00260 if (timestep == EVAL_MEASURE)
00261 {
00262 #ifdef NAMD_TCL
00263 wrap_coor(coor,lattice,&coor_wrapped);
00264 Node::Object()->getScript()->measure(coor);
00265 #endif
00266 }
00267
00268 // Output final coordinates
00269 if (timestep == FILE_OUTPUT || timestep == END_OF_RUN)
00270 {
00271 iout << "WRITING COORDINATES TO OUTPUT FILE AT STEP "
00272 << simParams->N << "\n" << endi;
00273 fflush(stdout);
00274 wrap_coor(coor,lattice,&coor_wrapped);
00275 output_final_coordinates(coor, n, simParams->N);
00276 }
00277
00278 // Close trajectory files
00279 if (timestep == END_OF_RUN)
00280 {
00281 if (simParams->dcdFrequency) output_dcdfile(END_OF_RUN,0,0,
00282 simParams->dcdUnitCell ? &lattice : NULL);
00283 }
00284
00285 }
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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(). 00078 {
00079 SimParameters *simParams = Node::Object()->simParameters;
00080
00081 int positionsNeeded = 0;
00082
00083 if ( timestep >= 0 ) {
00084
00085 // Output a DCD trajectory
00086 if ( simParams->dcdFrequency &&
00087 ((timestep % simParams->dcdFrequency) == 0) )
00088 { positionsNeeded |= 1; }
00089
00090 // Output a restart file
00091 if ( simParams->restartFrequency &&
00092 ((timestep % simParams->restartFrequency) == 0) )
00093 { positionsNeeded |= 2; }
00094
00095 // Iteractive MD
00096 if ( simParams->IMDon &&
00097 ( ((timestep % simParams->IMDfreq) == 0) ||
00098 (timestep == simParams->firstTimestep) ) )
00099 { positionsNeeded |= 1; }
00100
00101 }
00102
00103 // Output final coordinates
00104 if (timestep == FILE_OUTPUT || timestep == END_OF_RUN ||
00105 timestep == EVAL_MEASURE)
00106 {
00107 positionsNeeded |= 2;
00108 }
00109
00110 return positionsNeeded;
00111 }
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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(). 00334 {
00335 SimParameters *simParams = Node::Object()->simParameters;
00336
00337 if ( timestep >= 0 ) {
00338
00339 // Output velocity DCD trajectory
00340 if ( simParams->velDcdFrequency &&
00341 ((timestep % simParams->velDcdFrequency) == 0) )
00342 {
00343 output_veldcdfile(timestep, n, vel);
00344 }
00345
00346 // Output restart file
00347 if ( simParams->restartFrequency &&
00348 ((timestep % simParams->restartFrequency) == 0) )
00349 {
00350 iout << "WRITING VELOCITIES TO RESTART FILE AT STEP "
00351 << timestep << "\n" << endi;
00352 output_restart_velocities(timestep, n, vel);
00353 iout << "FINISHED WRITING RESTART VELOCITIES\n" <<endi;
00354 fflush(stdout);
00355 }
00356
00357 }
00358
00359 // Output final velocities
00360 if (timestep == FILE_OUTPUT || timestep == END_OF_RUN)
00361 {
00362 iout << "WRITING VELOCITIES TO OUTPUT FILE AT STEP "
00363 << simParams->N << "\n" << endi;
00364 fflush(stdout);
00365 output_final_velocities(simParams->N, n, vel);
00366 }
00367
00368 // Close trajectory files
00369 if (timestep == END_OF_RUN)
00370 {
00371 if (simParams->velDcdFrequency) output_veldcdfile(END_OF_RUN,0,0);
00372 }
00373
00374 }
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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(). 00305 {
00306 SimParameters *simParams = Node::Object()->simParameters;
00307
00308 int velocitiesNeeded = 0;
00309
00310 if ( timestep >= 0 ) {
00311
00312 // Output a velocity DCD trajectory
00313 if ( simParams->velDcdFrequency &&
00314 ((timestep % simParams->velDcdFrequency) == 0) )
00315 { velocitiesNeeded |= 1; }
00316
00317 // Output a restart file
00318 if ( simParams->restartFrequency &&
00319 ((timestep % simParams->restartFrequency) == 0) )
00320 { velocitiesNeeded |= 2; }
00321
00322 }
00323
00324 // Output final velocities
00325 if (timestep == FILE_OUTPUT || timestep == END_OF_RUN)
00326 {
00327 velocitiesNeeded |= 2;
00328 }
00329
00330 return velocitiesNeeded;
00331 }
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1.3.9.1