#include <SimParameters.h>
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Definition at line 813 of file SimParameters.h. 00813 : mgridforcelist() {};
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Definition at line 814 of file SimParameters.h. 00814 : mgridforcelist() { 00815 initialize_config_data(c,cwd); 00816 };
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Definition at line 817 of file SimParameters.h. 00817 {};
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Definition at line 93 of file SimParameters.C. References ParseOptions::check_consistency(), NAMD_die(), and ParseOptions::set(). 00095 {
00096
00097 ParseOptions opts; // Object to check consistency of config file
00098
00099 config_parser(opts);
00100
00102 if (!opts.check_consistency())
00103 {
00104 NAMD_die("Internal error in configuration file parser");
00105 }
00106
00107 // Now, feed the object with the actual configuration options through the
00108 // ParseOptions file and make sure everything is OK
00109 if (!opts.set(*config))
00110 {
00111 NAMD_die("ERROR(S) IN THE CONFIGURATION FILE");
00112 }
00113
00115
00116 check_config(opts,config,cwd);
00117
00118 print_config(opts,config,cwd);
00119
00120 }
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Definition at line 835 of file SimParameters.h. Referenced by Node::startup(). 00835 { return proxyRecvSpanningTree == 1; }
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Definition at line 836 of file SimParameters.h. 00836 { return proxyRecvSpanningTree == -1; }
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Definition at line 833 of file SimParameters.h. Referenced by Node::startup(). 00833 { return proxySendSpanningTree == 1; }
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Definition at line 834 of file SimParameters.h. Referenced by WorkDistrib::savePatchMap(), and WorkDistrib::sendPatchMap(). 00834 { return proxySendSpanningTree == -1; }
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Definition at line 5770 of file SimParameters.C. References binAtomFile, binCoorFile, binVelFile, MGridforceParamsList::clear(), FFTWWisdomString, MIStream::get(), mgridforcelist, tclBCScript, and MGridforceParamsList::unpack_data(). 05772 {
05773 msg->get(sizeof(SimParameters),(char*)this);
05774 if ( FFTWWisdomString ) {
05775 int fftwlen;
05776 msg->get(fftwlen);
05777 FFTWWisdomString = new char[fftwlen];
05778 msg->get(fftwlen,FFTWWisdomString);
05779 #ifdef NAMD_FFTW
05780 #ifdef NAMD_FFTW_3
05781 fftwf_import_wisdom_from_string(FFTWWisdomString);
05782 #else
05783 fftw_import_wisdom_from_string(FFTWWisdomString);
05784 #endif
05785 #endif
05786 }
05787 if ( tclBCScript ) {
05788 int tcllen;
05789 msg->get(tcllen);
05790 tclBCScript = new char[tcllen];
05791 msg->get(tcllen,tclBCScript);
05792 }
05793
05794 #ifdef MEM_OPT_VERSION
05795 int filelen;
05796 msg->get(filelen);
05797 binAtomFile = new char[filelen];
05798 msg->get(filelen, binAtomFile);
05799
05800 msg->get(filelen);
05801 binCoorFile = new char[filelen];
05802 msg->get(filelen, binCoorFile);
05803
05804 if(binVelFile) {
05805 msg->get(filelen);
05806 binVelFile = new char[filelen];
05807 msg->get(filelen, binVelFile);
05808 }
05809 #endif
05810
05811
05812 // The simParameters bit copy above put illegal values in the list pointers
05813 // So this resets everything so that unpacking will work.
05814 mgridforcelist.clear();
05815 mgridforcelist.unpack_data(msg);
05816
05817 delete msg;
05818 }
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Definition at line 134 of file SimParameters.C. References accelMDalpha, accelMDE, accelMDTalpha, accelMDTE, alchEquilSteps, alchFepWCArcut1, alchFepWCArcut2, alchLambda, alchLambda2, atobool(), berendsenPressureCompressibility, berendsenPressureOn, berendsenPressureRelaxationTime, berendsenPressureTarget, commOnly, consForceScaling, constraintScaling, eField, eFieldFreq, eFieldPhase, firstTimestep, fixCellDims, fixCellDimX, fixCellDimY, fixCellDimZ, fixedAtomsOn, initialTemp, langevinPistonDecay, langevinPistonOn, langevinPistonPeriod, langevinPistonTarget, langevinPistonTemp, langevinTemp, loweAndersenTemp, MAX_SCRIPT_PARAM_SIZE, N, NAMD_die(), nonbondedScaling, outputFilename, PRESSUREFACTOR, reassignTemp, rescaleTemp, SCRIPT_PARSE_BOOL, SCRIPT_PARSE_FLOAT, SCRIPT_PARSE_INT, SCRIPT_PARSE_MOD_FLOAT, SCRIPT_PARSE_STRING, SCRIPT_PARSE_VECTOR, scriptArg1, scriptArg2, scriptArg3, scriptArg4, scriptArg5, ComputeNonbondedUtil::select(), stirAxis, stirPivot, surfaceTensionTarget, tclBCArgs, useConstantArea, useConstantRatio, useFlexibleCell, and useGroupPressure. Referenced by Node::scriptParam(). 00134 {
00135
00136 if ( CkMyRank() ) return;
00137
00138 #define MAX_SCRIPT_PARAM_SIZE 128
00139 #define SCRIPT_PARSE_BOOL(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atobool(value); return; } }
00140 #define SCRIPT_PARSE_INT(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atoi(value); return; } }
00141 #define SCRIPT_PARSE_FLOAT(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atof(value); return; } }
00142 #define SCRIPT_PARSE_MOD_FLOAT(NAME,VAR,MOD) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atof(value) MOD; return; } }
00143 #define SCRIPT_PARSE_VECTOR(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR).set(value); return; } }
00144 #define SCRIPT_PARSE_STRING(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { strcpy(VAR,value); return; } }
00145
00146 SCRIPT_PARSE_FLOAT("scriptArg1",scriptArg1)
00147 SCRIPT_PARSE_FLOAT("scriptArg2",scriptArg2)
00148 SCRIPT_PARSE_FLOAT("scriptArg3",scriptArg3)
00149 SCRIPT_PARSE_FLOAT("scriptArg4",scriptArg4)
00150 SCRIPT_PARSE_FLOAT("scriptArg5",scriptArg5)
00151 SCRIPT_PARSE_INT("numsteps",N)
00152 SCRIPT_PARSE_INT("firsttimestep",firstTimestep)
00153 SCRIPT_PARSE_FLOAT("reassignTemp",reassignTemp)
00154 SCRIPT_PARSE_FLOAT("rescaleTemp",rescaleTemp)
00155 // SCRIPT_PARSE_BOOL("Langevin",langevinOn)
00156 SCRIPT_PARSE_FLOAT("langevinTemp",langevinTemp)
00157 SCRIPT_PARSE_FLOAT("loweAndersenTemp",loweAndersenTemp) // BEGIN LA, END LA
00158 SCRIPT_PARSE_FLOAT("initialTemp",initialTemp)
00159 SCRIPT_PARSE_BOOL("useGroupPressure",useGroupPressure)
00160 SCRIPT_PARSE_BOOL("useFlexibleCell",useFlexibleCell)
00161 SCRIPT_PARSE_BOOL("useConstantArea",useConstantArea)
00162 SCRIPT_PARSE_BOOL("fixCellDims",fixCellDims)
00163 SCRIPT_PARSE_BOOL("fixCellDimX",fixCellDimX)
00164 SCRIPT_PARSE_BOOL("fixCellDimY",fixCellDimY)
00165 SCRIPT_PARSE_BOOL("fixCellDimZ",fixCellDimZ)
00166 SCRIPT_PARSE_BOOL("useConstantRatio",useConstantRatio)
00167 SCRIPT_PARSE_BOOL("LangevinPiston",langevinPistonOn)
00168 SCRIPT_PARSE_MOD_FLOAT("LangevinPistonTarget",
00169 langevinPistonTarget,/PRESSUREFACTOR)
00170 SCRIPT_PARSE_FLOAT("LangevinPistonPeriod",langevinPistonPeriod)
00171 SCRIPT_PARSE_FLOAT("LangevinPistonDecay",langevinPistonDecay)
00172 SCRIPT_PARSE_FLOAT("LangevinPistonTemp",langevinPistonTemp)
00173 SCRIPT_PARSE_MOD_FLOAT("SurfaceTensionTarget",
00174 surfaceTensionTarget,*(100.0/PRESSUREFACTOR))
00175 SCRIPT_PARSE_BOOL("BerendsenPressure",berendsenPressureOn)
00176 SCRIPT_PARSE_MOD_FLOAT("BerendsenPressureTarget",
00177 berendsenPressureTarget,/PRESSUREFACTOR)
00178 SCRIPT_PARSE_MOD_FLOAT("BerendsenPressureCompressibility",
00179 berendsenPressureCompressibility,*PRESSUREFACTOR)
00180 SCRIPT_PARSE_FLOAT("BerendsenPressureRelaxationTime",
00181 berendsenPressureRelaxationTime)
00182 SCRIPT_PARSE_FLOAT("constraintScaling",constraintScaling)
00183 SCRIPT_PARSE_FLOAT("consForceScaling",consForceScaling)
00184 SCRIPT_PARSE_STRING("outputname",outputFilename)
00185 SCRIPT_PARSE_STRING("tclBCArgs",tclBCArgs)
00186 SCRIPT_PARSE_VECTOR("eField",eField)
00187 SCRIPT_PARSE_FLOAT("eFieldFreq",eFieldFreq)
00188 SCRIPT_PARSE_FLOAT("eFieldPhase",eFieldPhase)
00189 SCRIPT_PARSE_FLOAT("accelMDE",accelMDE)
00190 SCRIPT_PARSE_FLOAT("accelMDalpha",accelMDalpha)
00191 SCRIPT_PARSE_FLOAT("accelMDTE",accelMDTE)
00192 SCRIPT_PARSE_FLOAT("accelMDTalpha",accelMDTalpha)
00193 SCRIPT_PARSE_VECTOR("stirAxis",stirAxis)
00194 SCRIPT_PARSE_VECTOR("stirPivot",stirPivot)
00195 if ( ! strncasecmp(param,"mgridforcescale",MAX_SCRIPT_PARAM_SIZE) ) {
00196 NAMD_die("Can't yet modify mgridforcescale in a script");
00197 return;
00198 }
00199 if ( ! strncasecmp(param,"mgridforcevoff",MAX_SCRIPT_PARAM_SIZE) ) {
00200 NAMD_die("Can't yet modify mgridforcevoff in a script");
00201 return;
00202 }
00203
00204 if ( ! strncasecmp(param,"fixedatoms",MAX_SCRIPT_PARAM_SIZE) ) {
00205 if ( ! fixedAtomsOn )
00206 NAMD_die("FixedAtoms may not be enabled in a script.");
00207 if ( ! fixedAtomsForces )
00208 NAMD_die("To use fixedAtoms in script first use fixedAtomsForces yes.");
00209 fixedAtomsOn = atobool(value);
00210 return;
00211 }
00212
00213 //Modifications for alchemical fep
00214 SCRIPT_PARSE_INT("alchEquilSteps",alchEquilSteps)
00215
00216 if ( ! strncasecmp(param,"alchFepWCArcut1",MAX_SCRIPT_PARAM_SIZE) ) {
00217 alchFepWCArcut1 = atof(value);
00218 ComputeNonbondedUtil::select();
00219 return;
00220 }
00221
00222 if ( ! strncasecmp(param,"alchFepWCArcut2",MAX_SCRIPT_PARAM_SIZE) ) {
00223 alchFepWCArcut2 = atof(value);
00224 ComputeNonbondedUtil::select();
00225 return;
00226 }
00227
00228 if ( ! strncasecmp(param,"alchLambda",MAX_SCRIPT_PARAM_SIZE) ) {
00229 alchLambda = atof(value);
00230 ComputeNonbondedUtil::select();
00231 return;
00232 }
00233
00234 if ( ! strncasecmp(param,"alchLambda2",MAX_SCRIPT_PARAM_SIZE) ) {
00235 alchLambda2 = atof(value);
00236 ComputeNonbondedUtil::select();
00237 return;
00238 }
00239 //fepe
00240
00241 // REDUNDANT TI BEGINS
00242 // if ( ! strncasecmp(param,"tiLambda",MAX_SCRIPT_PARAM_SIZE) ) {
00243 // alchLambda = atof(value);
00244 // ComputeNonbondedUtil::select();
00245 // return;
00246 // }
00247 // REDUNDANT TI ENDS
00248
00249 if ( ! strncasecmp(param,"nonbondedScaling",MAX_SCRIPT_PARAM_SIZE) ) {
00250 nonbondedScaling = atof(value);
00251 ComputeNonbondedUtil::select();
00252 return;
00253 }
00254 if ( ! strncasecmp(param,"commOnly",MAX_SCRIPT_PARAM_SIZE) ) {
00255 commOnly = atobool(value);
00256 ComputeNonbondedUtil::select();
00257 return;
00258 }
00259
00260 char *error = new char[2 * MAX_SCRIPT_PARAM_SIZE + 100];
00261 sprintf(error,"Setting parameter %s from script failed!\n",param);
00262 NAMD_die(error);
00263
00264 }
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Definition at line 5718 of file SimParameters.C. References binAtomFile, binCoorFile, binVelFile, MOStream::end(), FFTWWisdomString, mgridforcelist, MGridforceParamsList::pack_data(), MOStream::put(), and tclBCScript. 05720 {
05721 /*MOStream *msg = com_obj->newOutputStream(ALLBUTME, SIMPARAMSTAG, BUFSIZE);
05722 if ( msg == NULL )
05723 {
05724 NAMD_die("memory allocation failed in SimParameters::send_SimParameters");
05725 }*/
05726
05727 msg->put(sizeof(SimParameters),(char*)this);
05728 if ( FFTWWisdomString ) {
05729 int fftwlen = strlen(FFTWWisdomString) + 1;
05730 msg->put(fftwlen);
05731 msg->put(fftwlen,FFTWWisdomString);
05732 }
05733 if ( tclBCScript ) {
05734 int tcllen = strlen(tclBCScript) + 1;
05735 msg->put(tcllen);
05736 msg->put(tcllen,tclBCScript);
05737 }
05738
05739 #ifdef MEM_OPT_VERSION
05740 int filelen = strlen(binAtomFile)+1;
05741 msg->put(filelen);
05742 msg->put(filelen, binAtomFile);
05743
05744 filelen = strlen(binCoorFile)+1;
05745 msg->put(filelen);
05746 msg->put(filelen, binCoorFile);
05747
05748 if(binVelFile) {
05749 filelen = strlen(binVelFile)+1;
05750 msg->put(filelen);
05751 msg->put(filelen, binVelFile);
05752 }
05753 #endif
05754
05755 mgridforcelist.pack_data(msg);
05756
05757 msg->end();
05758 }
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Definition at line 746 of file SimParameters.h. |
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Definition at line 489 of file SimParameters.h. Referenced by Controller::rescaleaccelMD(), and scriptSet(). |
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Definition at line 484 of file SimParameters.h. Referenced by Controller::receivePressure(), Controller::rescaleaccelMD(), and ComputeGlobal::saveTotalForces(). |
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Definition at line 482 of file SimParameters.h. Referenced by ComputeHomeTuples< TholeElem, Thole, TholeValue >::ComputeHomeTuples(), Sequencer::integrate(), Sequencer::rescaleaccelMD(), Controller::rescaleaccelMD(), and ComputeGlobal::saveTotalForces(). |
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Definition at line 483 of file SimParameters.h. Referenced by ComputeHomeTuples< TholeElem, Thole, TholeValue >::ComputeHomeTuples(), Sequencer::integrate(), Sequencer::rescaleaccelMD(), and Controller::rescaleaccelMD(). |
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Definition at line 488 of file SimParameters.h. Referenced by Controller::rescaleaccelMD(), and scriptSet(). |
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Definition at line 485 of file SimParameters.h. Referenced by Sequencer::rescaleaccelMD(), and Controller::rescaleaccelMD(). |
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Definition at line 486 of file SimParameters.h. Referenced by Sequencer::rescaleaccelMD(), and Controller::rescaleaccelMD(). |
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Definition at line 487 of file SimParameters.h. Referenced by Controller::receivePressure(), and Controller::rescaleaccelMD(). |
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Definition at line 491 of file SimParameters.h. Referenced by Controller::rescaleaccelMD(), and scriptSet(). |
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Definition at line 490 of file SimParameters.h. Referenced by Controller::rescaleaccelMD(), and scriptSet(). |
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Definition at line 502 of file SimParameters.h. Referenced by Controller::adaptTempInit(). |
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Definition at line 503 of file SimParameters.h. Referenced by Controller::adaptTempInit(). |
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Definition at line 505 of file SimParameters.h. Referenced by Controller::adaptTempInit(). |
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Definition at line 495 of file SimParameters.h. Referenced by Controller::adaptTempUpdate(). |
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Definition at line 504 of file SimParameters.h. Referenced by Controller::adaptTempInit(). |
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Definition at line 496 of file SimParameters.h. Referenced by Sequencer::adaptTempUpdate(), Controller::adaptTempUpdate(), and Controller::rescaleVelocities(). |
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Definition at line 499 of file SimParameters.h. Referenced by Sequencer::adaptTempUpdate(), and Controller::adaptTempUpdate(). |
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Definition at line 508 of file SimParameters.h. Referenced by Controller::adaptTempInit(). |
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Definition at line 506 of file SimParameters.h. Referenced by Sequencer::langevinVelocities(), and Sequencer::langevinVelocitiesBBK2(). |
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Definition at line 497 of file SimParameters.h. Referenced by Sequencer::adaptTempUpdate(), Controller::adaptTempUpdate(), and Controller::rescaleVelocities(). |
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Definition at line 498 of file SimParameters.h. Referenced by Controller::adaptTempUpdate(). |
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Definition at line 511 of file SimParameters.h. Referenced by Controller::adaptTempUpdate(). |
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Definition at line 507 of file SimParameters.h. Referenced by Controller::rescaleVelocities(). |
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Definition at line 509 of file SimParameters.h. Referenced by Controller::adaptTempInit(). |
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Definition at line 510 of file SimParameters.h. Referenced by Controller::adaptTempInit(), and Controller::adaptTempWriteRestart(). |
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Definition at line 501 of file SimParameters.h. Referenced by Controller::adaptTempInit(). |
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Definition at line 500 of file SimParameters.h. Referenced by Controller::adaptTempInit(). |
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Definition at line 391 of file SimParameters.h. Referenced by ComputePme::ComputePme(), ComputePmeMgr::initialize(), and ComputeNonbondedUtil::select(). |
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Definition at line 382 of file SimParameters.h. Referenced by ComputePme::ComputePme(), ComputePmeMgr::initialize(), Controller::outputTiEnergy(), and ComputeNonbondedUtil::select(). |
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Definition at line 377 of file SimParameters.h. Referenced by Controller::outputFepEnergy(), and Controller::writeFepEnergyData(). |
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Definition at line 379 of file SimParameters.h. Referenced by Controller::outputFepEnergy(), Controller::outputTiEnergy(), Controller::printFepMessage(), Controller::printTiMessage(), and scriptSet(). |
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Definition at line 369 of file SimParameters.h. Referenced by ComputeNonbondedUtil::select(). |
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Definition at line 373 of file SimParameters.h. Referenced by scriptSet(), and ComputeNonbondedUtil::select(). |
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Definition at line 374 of file SimParameters.h. Referenced by scriptSet(), and ComputeNonbondedUtil::select(). |
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Definition at line 368 of file SimParameters.h. Referenced by ComputeNonbondedUtil::select(). |
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Definition at line 371 of file SimParameters.h. Referenced by Controller::outputFepEnergy(), Controller::outputTiEnergy(), Controller::printFepMessage(), Controller::printTiMessage(), scriptSet(), ComputeNonbondedUtil::select(), and ComputePme::ungridForces(). |
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Definition at line 372 of file SimParameters.h. Referenced by Controller::outputFepEnergy(), Controller::printFepMessage(), scriptSet(), ComputeNonbondedUtil::select(), and ComputePme::ungridForces(). |
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Definition at line 370 of file SimParameters.h. |
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Definition at line 365 of file SimParameters.h. Referenced by NamdState::configListInit(). |
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Definition at line 378 of file SimParameters.h. Referenced by Controller::outputFepEnergy(), and Controller::outputTiEnergy(). |
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Definition at line 376 of file SimParameters.h. Referenced by Controller::outputFepEnergy(), and Controller::outputTiEnergy(). |
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Definition at line 375 of file SimParameters.h. Referenced by Controller::outputFepEnergy(), Controller::printFepMessage(), Controller::printTiMessage(), and Controller::writeFepEnergyData(). |
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Definition at line 387 of file SimParameters.h. Referenced by Controller::outputTiEnergy(), and ComputeNonbondedUtil::select(). |
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Definition at line 380 of file SimParameters.h. Referenced by ComputeNonbondedUtil::select(). |
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Definition at line 420 of file SimParameters.h. Referenced by ComputeNonbondedSelf::doForce(), ComputeNonbondedPair::doForce(), and ComputeNonbondedCUDA::recvYieldDevice(). |
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Definition at line 421 of file SimParameters.h. Referenced by ComputeNonbondedSelf::doForce(), ComputeNonbondedPair::doForce(), and HomePatch::gbisComputeAfterP1(). |
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Definition at line 765 of file SimParameters.h. Referenced by buildExclusions(), and NamdState::configListInit(). |
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Definition at line 196 of file SimParameters.h. Referenced by CollectionMaster::receiveDataStream(). |
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Definition at line 154 of file SimParameters.h. Referenced by Output::coordinateNeeded(), Output::forceNeeded(), and Output::velocityNeeded(). |
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Definition at line 535 of file SimParameters.h. Referenced by Controller::berendsenPressure(), and scriptSet(). |
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Definition at line 537 of file SimParameters.h. Referenced by Sequencer::berendsenPressure(), and Controller::berendsenPressure(). |
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Definition at line 533 of file SimParameters.h. Referenced by Sequencer::berendsenPressure(), Controller::berendsenPressure(), ComputeGridForce::doForce(), OptPmeMgr::initialize(), and scriptSet(). |
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Definition at line 536 of file SimParameters.h. Referenced by Controller::berendsenPressure(), and scriptSet(). |
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Definition at line 534 of file SimParameters.h. Referenced by Controller::berendsenPressure(), and scriptSet(). |
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Definition at line 212 of file SimParameters.h. |
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Definition at line 210 of file SimParameters.h. |
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Definition at line 799 of file SimParameters.h. Referenced by receive_SimParameters(), and send_SimParameters(). |
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Definition at line 800 of file SimParameters.h. Referenced by receive_SimParameters(), and send_SimParameters(). |
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Definition at line 801 of file SimParameters.h. Referenced by receive_SimParameters(), and send_SimParameters(). |
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Definition at line 116 of file SimParameters.h. |
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Definition at line 117 of file SimParameters.h. |
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Definition at line 118 of file SimParameters.h. |
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Definition at line 119 of file SimParameters.h. |
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Definition at line 469 of file SimParameters.h. |
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Definition at line 471 of file SimParameters.h. |
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Definition at line 472 of file SimParameters.h. |
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Definition at line 450 of file SimParameters.h. Referenced by ComputeMgr::createComputes(), and Sequencer::integrate(). |
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Definition at line 707 of file SimParameters.h. Referenced by ComputeHomeTuples< TholeElem, Thole, TholeValue >::doWork(), Sequencer::integrate(), scriptSet(), ComputeNonbondedUtil::select(), OptPmeCompute::ungridForces(), and ComputePme::ungridForces(). |
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Definition at line 174 of file SimParameters.h. Referenced by ParallelIOMgr::bcastMolInfo(), NamdState::configListInit(), WorkDistrib::createAtomLists(), Molecule::num_deg_freedom(), Molecule::num_group_deg_freedom(), Controller::receivePressure(), ParallelIOMgr::recvMolInfo(), and ParallelIOMgr::updateMolInfo(). |
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Definition at line 807 of file SimParameters.h. Referenced by WorkDistrib::mapComputes(), and ComputeMgr::updateLocalComputes4(). |
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Definition at line 661 of file SimParameters.h. |
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Definition at line 660 of file SimParameters.h. Referenced by NamdState::configListInit(), WorkDistrib::mapComputes(), Molecule::receive_Molecule(), and Molecule::send_Molecule(). |
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Definition at line 662 of file SimParameters.h. Referenced by ComputeConsForce::doForce(), and scriptSet(). |
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Definition at line 319 of file SimParameters.h. |
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Definition at line 317 of file SimParameters.h. |
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Definition at line 321 of file SimParameters.h. Referenced by ComputeConsTorque::doForce(). |
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Definition at line 316 of file SimParameters.h. Referenced by NamdState::configListInit(), WorkDistrib::mapComputes(), Molecule::receive_Molecule(), and Molecule::send_Molecule(). |
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Definition at line 320 of file SimParameters.h. |
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Definition at line 322 of file SimParameters.h. |
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Definition at line 247 of file SimParameters.h. Referenced by ComputeRestraints::ComputeRestraints(). |
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Definition at line 269 of file SimParameters.h. Referenced by ComputeRestraints::doForce(), and scriptSet(). |
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Definition at line 245 of file SimParameters.h. Referenced by NamdState::configListInit(), WorkDistrib::mapComputes(), Molecule::receive_Molecule(), and Molecule::send_Molecule(). |
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Definition at line 265 of file SimParameters.h. Referenced by ComputeRestraints::ComputeRestraints(). |
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Definition at line 265 of file SimParameters.h. Referenced by ComputeRestraints::ComputeRestraints(). |
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Definition at line 265 of file SimParameters.h. Referenced by ComputeRestraints::ComputeRestraints(). |
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Definition at line 439 of file SimParameters.h. Referenced by Parameters::Parameters(). |
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Definition at line 414 of file SimParameters.h. Referenced by ComputeNonbondedSelf::doForce(), ComputeNonbondedPair::doForce(), ComputeGBISser::doWork(), HomePatch::gbisComputeAfterP1(), HomePatch::gbisComputeAfterP2(), ComputeNonbondedCUDA::recvYieldDevice(), and HomePatch::setGBISIntrinsicRadii(). |
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Definition at line 634 of file SimParameters.h. Referenced by ComputeCylindricalBC::ComputeCylindricalBC(). |
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Definition at line 639 of file SimParameters.h. Referenced by ComputeCylindricalBC::ComputeCylindricalBC(). |
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Definition at line 640 of file SimParameters.h. Referenced by ComputeCylindricalBC::ComputeCylindricalBC(). |
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Definition at line 641 of file SimParameters.h. Referenced by ComputeCylindricalBC::ComputeCylindricalBC(). |
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Definition at line 642 of file SimParameters.h. Referenced by ComputeCylindricalBC::ComputeCylindricalBC(). |
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Definition at line 637 of file SimParameters.h. Referenced by ComputeCylindricalBC::ComputeCylindricalBC(). |
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Definition at line 638 of file SimParameters.h. Referenced by ComputeCylindricalBC::ComputeCylindricalBC(). |
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Definition at line 631 of file SimParameters.h. Referenced by WorkDistrib::mapComputes(). |
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Definition at line 635 of file SimParameters.h. Referenced by ComputeCylindricalBC::ComputeCylindricalBC(). |
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Definition at line 636 of file SimParameters.h. Referenced by ComputeCylindricalBC::ComputeCylindricalBC(). |
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Definition at line 633 of file SimParameters.h. Referenced by ComputeCylindricalBC::ComputeCylindricalBC(). |
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Definition at line 753 of file SimParameters.h. |
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Definition at line 753 of file SimParameters.h. |
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Definition at line 753 of file SimParameters.h. |
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Definition at line 197 of file SimParameters.h. |
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Definition at line 187 of file SimParameters.h. Referenced by Output::coordinate(), and Output::coordinateNeeded(). |
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Definition at line 189 of file SimParameters.h. Referenced by Output::coordinate(). |
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Definition at line 749 of file SimParameters.h. |
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Definition at line 749 of file SimParameters.h. |
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Definition at line 749 of file SimParameters.h. |
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Definition at line 181 of file SimParameters.h. Referenced by ComputeMsm::ComputeMsm(), ComputeNonbondedSelf::doForce(), ComputeNonbondedPair::doForce(), HomePatch::gbisComputeAfterP2(), ComputeMsmSerialMgr::recvCoord(), ComputeNonbondedCUDA::recvYieldDevice(), and ComputeNonbondedUtil::select(). |
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Definition at line 468 of file SimParameters.h. |
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Definition at line 746 of file SimParameters.h. |
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Definition at line 746 of file SimParameters.h. |
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Definition at line 431 of file SimParameters.h. Referenced by BondElem::computeForce(). |
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Definition at line 429 of file SimParameters.h. Referenced by BondElem::computeForce(). |
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Definition at line 427 of file SimParameters.h. Referenced by NamdState::configListInit(). |
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Definition at line 432 of file SimParameters.h. Referenced by ComputeNonbondedUtil::select(). |
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Definition at line 426 of file SimParameters.h. Referenced by Sequencer::langevinVelocitiesBBK2(). |
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Definition at line 112 of file SimParameters.h. Referenced by Controller::berendsenPressure(), ComputeEField::doForce(), colvarproxy_namd::dt(), Sequencer::integrate(), Controller::langevinPiston1(), Controller::langevinPiston2(), and Controller::printEnergies(). |
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Definition at line 645 of file SimParameters.h. Referenced by ComputeEField::doForce(), and scriptSet(). |
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Definition at line 646 of file SimParameters.h. Referenced by ComputeEField::doForce(), and scriptSet(). |
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Definition at line 644 of file SimParameters.h. Referenced by WorkDistrib::mapComputes(). |
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Definition at line 647 of file SimParameters.h. Referenced by ComputeEField::doForce(), and scriptSet(). |
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Definition at line 182 of file SimParameters.h. Referenced by buildExclusions(), and ComputeNonbondedUtil::select(). |
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Definition at line 522 of file SimParameters.h. Referenced by NamdState::configListInit(), Molecule::receive_Molecule(), and Molecule::send_Molecule(). |
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Definition at line 404 of file SimParameters.h. Referenced by ComputeExtMgr::recvCoord(). |
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Definition at line 405 of file SimParameters.h. Referenced by ComputeExtMgr::recvCoord(). |
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Definition at line 403 of file SimParameters.h. Referenced by ComputeExtMgr::recvCoord(). |
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Definition at line 402 of file SimParameters.h. Referenced by WorkDistrib::mapComputes(). |
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Definition at line 658 of file SimParameters.h. Referenced by NamdState::configListInit(). |
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Definition at line 600 of file SimParameters.h. Referenced by OptPmeXPencil::fft_init(), OptPmeYPencil::fft_init(), OptPmeZPencil::fft_init(), PmeXPencil::fft_init(), PmeYPencil::fft_init(), PmeZPencil::fft_init(), and ComputePmeMgr::initialize(). |
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Definition at line 601 of file SimParameters.h. Referenced by PmeXPencil::fft_init(), PmeYPencil::fft_init(), PmeZPencil::fft_init(), and ComputePmeMgr::initialize(). |
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Definition at line 602 of file SimParameters.h. |
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Definition at line 603 of file SimParameters.h. |
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Definition at line 604 of file SimParameters.h. Referenced by receive_SimParameters(), and send_SimParameters(). |
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Definition at line 130 of file SimParameters.h. Referenced by LdbCoordinator::initialize(), and Controller::printEnergies(). |
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Definition at line 528 of file SimParameters.h. Referenced by Controller::langevinPiston1(), Controller::langevinPiston2(), Controller::receivePressure(), and scriptSet(). |
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Definition at line 529 of file SimParameters.h. Referenced by Controller::langevinPiston1(), Controller::langevinPiston2(), Controller::receivePressure(), and scriptSet(). |
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Definition at line 530 of file SimParameters.h. Referenced by Controller::langevinPiston1(), Controller::langevinPiston2(), Controller::receivePressure(), and scriptSet(). |
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Definition at line 531 of file SimParameters.h. Referenced by Controller::langevinPiston1(), Controller::langevinPiston2(), Controller::receivePressure(), and scriptSet(). |
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Definition at line 453 of file SimParameters.h. Referenced by ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), HomePatch::positionsReady(), and ComputeNonbondedUtil::select(). |
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Definition at line 565 of file SimParameters.h. |
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Definition at line 564 of file SimParameters.h. |
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Definition at line 562 of file SimParameters.h. |
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Definition at line 563 of file SimParameters.h. |
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Definition at line 561 of file SimParameters.h. Referenced by ComputeGlobal::ComputeGlobal(), WorkDistrib::mapComputes(), WorkDistrib::patchMapInit(), and ComputeNonbondedUtil::select(). |
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Definition at line 126 of file SimParameters.h. |
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Definition at line 199 of file SimParameters.h. |
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Definition at line 192 of file SimParameters.h. Referenced by Output::force(), Output::forceNeeded(), and Output::velocity(). |
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Definition at line 448 of file SimParameters.h. Referenced by ComputeMgr::createComputes(), and ParallelIOMgr::freeMolSpace(). |
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Definition at line 411 of file SimParameters.h. Referenced by ComputeNonbondedSelf::doForce(), ComputeNonbondedPair::doForce(), and ComputeNonbondedCUDA::recvYieldDevice(). |
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Definition at line 567 of file SimParameters.h. Referenced by ComputeGlobal::ComputeGlobal(), WorkDistrib::mapComputes(), and ComputeNonbondedUtil::select(). |
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Definition at line 124 of file SimParameters.h. Referenced by Controller::compareChecksums(), Sequencer::integrate(), Controller::integrate(), Sequencer::minimize(), OptPmeMgr::recvEvir(), and Sequencer::runComputeObjects(). |
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Definition at line 418 of file SimParameters.h. Referenced by ComputeNonbondedSelf::doForce(), ComputeNonbondedPair::doForce(), HomePatch::gbisComputeAfterP1(), and HomePatch::gbisComputeAfterP2(). |
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Definition at line 417 of file SimParameters.h. Referenced by ComputeNonbondedSelf::doForce(), ComputeNonbondedPair::doForce(), HomePatch::gbisComputeAfterP1(), and HomePatch::gbisComputeAfterP2(). |
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Definition at line 419 of file SimParameters.h. Referenced by ComputeNonbondedSelf::doForce(), ComputeNonbondedPair::doForce(), HomePatch::gbisComputeAfterP1(), and HomePatch::gbisComputeAfterP2(). |
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Definition at line 412 of file SimParameters.h. Referenced by ComputeGlobal::ComputeGlobal(), and WorkDistrib::mapComputes(). |
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Definition at line 783 of file SimParameters.h. Referenced by NamdState::configListInit(). |
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Definition at line 440 of file SimParameters.h. Referenced by ComputeMgr::createComputes(), and WorkDistrib::mapComputes(). |
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Definition at line 467 of file SimParameters.h. |
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Definition at line 279 of file SimParameters.h. |
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Definition at line 277 of file SimParameters.h. Referenced by NamdState::configListInit(), Controller::printEnergies(), Molecule::receive_GoMolecule(), ComputeNonbondedUtil::select(), and Molecule::send_GoMolecule(). |
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Definition at line 281 of file SimParameters.h. Referenced by NamdState::configListInit(), Molecule::receive_GoMolecule(), ComputeNonbondedUtil::select(), and Molecule::send_GoMolecule(). |
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Definition at line 278 of file SimParameters.h. |
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Definition at line 253 of file SimParameters.h. |
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Definition at line 254 of file SimParameters.h. |
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Definition at line 255 of file SimParameters.h. |
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Definition at line 257 of file SimParameters.h. |
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Definition at line 250 of file SimParameters.h. |
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Definition at line 252 of file SimParameters.h. |
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Definition at line 256 of file SimParameters.h. |
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Definition at line 251 of file SimParameters.h. |
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Definition at line 770 of file SimParameters.h. Referenced by NamdState::configListInit(). |
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Definition at line 746 of file SimParameters.h. |
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Definition at line 691 of file SimParameters.h. Referenced by HomePatch::doGroupSizeCheck(). |
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Definition at line 134 of file SimParameters.h. Referenced by NamdHybridLB::NamdHybridLB(). |
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Definition at line 736 of file SimParameters.h. |
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Definition at line 758 of file SimParameters.h. Referenced by Output::coordinate(), Output::coordinateNeeded(), and Controller::printEnergies(). |
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Definition at line 761 of file SimParameters.h. Referenced by ComputeMgr::createComputes(), and GlobalMasterIMD::GlobalMasterIMD(). |
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Definition at line 756 of file SimParameters.h. Referenced by Output::coordinate(), Output::coordinateNeeded(), ComputeMgr::createComputes(), and Controller::printEnergies(). |
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Definition at line 757 of file SimParameters.h. Referenced by GlobalMasterIMD::GlobalMasterIMD(). |
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Definition at line 759 of file SimParameters.h. Referenced by GlobalMasterIMD::get_vmd_forces(), and GlobalMasterIMD::GlobalMasterIMD(). |
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Definition at line 172 of file SimParameters.h. Referenced by Controller::adaptTempInit(), Controller::algorithm(), WorkDistrib::createAtomLists(), Sequencer::integrate(), Sequencer::reinitVelocities(), and scriptSet(). |
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Definition at line 416 of file SimParameters.h. |
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Definition at line 415 of file SimParameters.h. Referenced by ComputeNonbondedSelf::doForce(), ComputeNonbondedPair::doForce(), HomePatch::gbisComputeAfterP2(), and ComputeNonbondedCUDA::recvYieldDevice(). |
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Definition at line 457 of file SimParameters.h. Referenced by NamdState::configListInit(). |
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Definition at line 458 of file SimParameters.h. Referenced by NamdState::configListInit(). |
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Definition at line 542 of file SimParameters.h. Referenced by Controller::langevinPiston1(), Controller::langevinPiston2(), and scriptSet(). |
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Definition at line 539 of file SimParameters.h. Referenced by ComputeGridForce::doForce(), OptPmeMgr::initialize(), Sequencer::langevinPiston(), Controller::langevinPiston1(), Controller::langevinPiston2(), scriptSet(), Controller::writeExtendedSystemData(), and Controller::writeExtendedSystemLabels(). |
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Definition at line 541 of file SimParameters.h. Referenced by Controller::langevinPiston1(), Controller::langevinPiston2(), and scriptSet(). |
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Definition at line 540 of file SimParameters.h. Referenced by Controller::langevinPiston1(), Controller::langevinPiston2(), and scriptSet(). |
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Definition at line 543 of file SimParameters.h. Referenced by Controller::langevinPiston1(), Controller::langevinPiston2(), and scriptSet(). |
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Definition at line 456 of file SimParameters.h. Referenced by Controller::adaptTempInit(), Sequencer::adaptTempUpdate(), colvarproxy_namd::colvarproxy_namd(), Sequencer::integrate(), Sequencer::langevinVelocities(), Sequencer::langevinVelocitiesBBK2(), and scriptSet(). |
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Definition at line 132 of file SimParameters.h. Referenced by LdbCoordinator::initialize(). |
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Definition at line 422 of file SimParameters.h. Referenced by Sequencer::integrate(), WorkDistrib::mapComputes(), Sequencer::minimize(), Molecule::Molecule(), WorkDistrib::patchMapInit(), Molecule::receive_Molecule(), Molecule::send_Molecule(), and NamdCentLB::Strategy(). |
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Definition at line 127 of file SimParameters.h. Referenced by LdbCoordinator::createLoadBalancer(), LdbCoordinator::initialize(), and LdbCoordinator::rebalance(). |
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Definition at line 135 of file SimParameters.h. |
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Definition at line 137 of file SimParameters.h. |
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Definition at line 129 of file SimParameters.h. Referenced by LdbCoordinator::initialize(). |
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Definition at line 136 of file SimParameters.h. |
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Definition at line 138 of file SimParameters.h. Referenced by NamdCentLB::Strategy(). |
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Definition at line 128 of file SimParameters.h. Referenced by LdbCoordinator::initialize(), and NamdCentLB::Strategy(). |
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Definition at line 168 of file SimParameters.h. |
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Definition at line 166 of file SimParameters.h. |
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Definition at line 167 of file SimParameters.h. |
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Definition at line 400 of file SimParameters.h. |
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Definition at line 399 of file SimParameters.h. Referenced by Sequencer::langevinVelocities(), Sequencer::langevinVelocitiesBBK2(), Sequencer::reassignVelocities(), and Sequencer::reinitVelocities(). |
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Definition at line 221 of file SimParameters.h. Referenced by ComputeNonbondedUtil::select(). |
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Definition at line 111 of file SimParameters.h. Referenced by Controller::printEnergies(), and Controller::receivePressure(). |
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Definition at line 809 of file SimParameters.h. Referenced by WorkDistrib::mapComputes(). |
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Definition at line 108 of file SimParameters.h. Referenced by Sequencer::integrate(), Sequencer::minimize(), and Sequencer::runComputeObjects(). |
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Definition at line 687 of file SimParameters.h. Referenced by ComputeNonbondedUtil::select(). |
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Definition at line 464 of file SimParameters.h. |
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Definition at line 461 of file SimParameters.h. Referenced by Sequencer::integrate(). |
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Definition at line 463 of file SimParameters.h. |
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Definition at line 462 of file SimParameters.h. Referenced by scriptSet(). |
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Definition at line 787 of file SimParameters.h. Referenced by Node::startup(). |
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Definition at line 215 of file SimParameters.h. Referenced by HomePatch::doMarginCheck(). |
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Definition at line 231 of file SimParameters.h. |
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Definition at line 229 of file SimParameters.h. Referenced by ComputeNonbondedUtil::select(). |
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Definition at line 725 of file SimParameters.h. |
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Definition at line 616 of file SimParameters.h. Referenced by Sequencer::maximumMove(). |
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Definition at line 713 of file SimParameters.h. |
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Definition at line 165 of file SimParameters.h. Referenced by WorkDistrib::patchMapInit(). |
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Definition at line 711 of file SimParameters.h. |
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Definition at line 679 of file SimParameters.h. Referenced by Controller::printEnergies(). |
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Definition at line 260 of file SimParameters.h. Referenced by Molecule::build_gridforce_params(), receive_SimParameters(), Node::reloadGridforceGrid(), and send_SimParameters(). |
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Definition at line 259 of file SimParameters.h. Referenced by NamdState::configListInit(), WorkDistrib::mapComputes(), Molecule::receive_Molecule(), and Molecule::send_Molecule(). |
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Definition at line 723 of file SimParameters.h. Referenced by WorkDistrib::patchMapInit(). |
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Definition at line 613 of file SimParameters.h. Referenced by Controller::minimize(). |
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Definition at line 610 of file SimParameters.h. Referenced by NamdState::configListInit(), and ScriptTcl::run(). |
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Definition at line 615 of file SimParameters.h. Referenced by Sequencer::minimizationQuenchVelocity(). |
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Definition at line 614 of file SimParameters.h. Referenced by Controller::minimize(). |
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Definition at line 612 of file SimParameters.h. Referenced by Controller::minimize(). |
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Definition at line 611 of file SimParameters.h. Referenced by Controller::minimize(). |
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Definition at line 449 of file SimParameters.h. Referenced by ComputeMgr::createComputes(). |
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Definition at line 695 of file SimParameters.h. Referenced by HomePatch::mollyAverage(). |
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Definition at line 693 of file SimParameters.h. Referenced by Controller::compareChecksums(), Sequencer::integrate(), and Sequencer::minimize(). |
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Definition at line 694 of file SimParameters.h. Referenced by HomePatch::mollyAverage(). |
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Definition at line 299 of file SimParameters.h. |
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Definition at line 301 of file SimParameters.h. Referenced by Sequencer::addMovDragToPosition(). |
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Definition at line 298 of file SimParameters.h. Referenced by NamdState::configListInit(), Sequencer::integrate(), Molecule::receive_Molecule(), and Molecule::send_Molecule(). |
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Definition at line 302 of file SimParameters.h. |
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Definition at line 285 of file SimParameters.h. Referenced by ComputeRestraints::ComputeRestraints(). |
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Definition at line 287 of file SimParameters.h. Referenced by ComputeRestraints::ComputeRestraints(). |
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Definition at line 571 of file SimParameters.h. Referenced by ComputeMsmMgr::initialize(), and ComputeMsmSerialMgr::recvCoord(). |
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Definition at line 574 of file SimParameters.h. |
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Definition at line 575 of file SimParameters.h. |
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Definition at line 576 of file SimParameters.h. |
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Definition at line 577 of file SimParameters.h. Referenced by ComputeMsmMgr::initialize(), and ComputeMsmSerialMgr::recvCoord(). |
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Definition at line 573 of file SimParameters.h. Referenced by ComputeMsmMgr::initialize(), and ComputeMsmSerialMgr::recvCoord(). |
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Definition at line 570 of file SimParameters.h. Referenced by WorkDistrib::mapComputes(), WorkDistrib::patchMapInit(), ComputeNonbondedUtil::select(), and Node::startup(). |
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Definition at line 578 of file SimParameters.h. Referenced by ComputeMsmMgr::initialize(), and ComputeMsmSerialMgr::recvCoord(). |
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Definition at line 579 of file SimParameters.h. Referenced by WorkDistrib::mapComputes(), and Node::startup(). |
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Definition at line 572 of file SimParameters.h. Referenced by ComputeMsmMgr::initialize(), ComputeMsmSerialMgr::recvCoord(), and ComputeNonbondedUtil::select(). |
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Definition at line 684 of file SimParameters.h. Referenced by Sequencer::integrate(). |
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Definition at line 122 of file SimParameters.h. Referenced by Sequencer::integrate(), and Controller::integrate(). |
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Definition at line 186 of file SimParameters.h. Referenced by ComputeNonbondedCUDA::recvYieldDevice(), scriptSet(), and ComputeNonbondedUtil::select(). |
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Definition at line 170 of file SimParameters.h. Referenced by WorkDistrib::patchMapInit(). |
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Definition at line 169 of file SimParameters.h. Referenced by WorkDistrib::patchMapInit(). |
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Definition at line 719 of file SimParameters.h. |
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Definition at line 721 of file SimParameters.h. |
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Definition at line 715 of file SimParameters.h. |
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Definition at line 717 of file SimParameters.h. |
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Definition at line 798 of file SimParameters.h. Referenced by NamdState::configListInit(), and ParallelIOMgr::initialize(). |
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Definition at line 805 of file SimParameters.h. Referenced by NamdState::configListInit(), ParallelIOMgr::initialize(), CollectionMaster::startNextRoundOutputForce(), CollectionMaster::startNextRoundOutputPos(), and CollectionMaster::startNextRoundOutputVel(). |
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Definition at line 141 of file SimParameters.h. Referenced by Sequencer::integrate(), and Controller::integrate(). |
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Definition at line 673 of file SimParameters.h. Referenced by ComputeNonbondedCUDA::doWork(), and ComputeNonbondedCUDA::finishWork(). |
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Definition at line 664 of file SimParameters.h. Referenced by Sequencer::integrate(), Controller::printEnergies(), and Controller::printTiming(). |
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Definition at line 201 of file SimParameters.h. Referenced by colvarproxy_namd::colvarproxy_namd(), Controller::outputExtendedSystem(), and scriptSet(). |
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Definition at line 149 of file SimParameters.h. Referenced by Node::outputPatchComputeMaps(). |
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Definition at line 667 of file SimParameters.h. Referenced by Controller::printEnergies(). |
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Definition at line 243 of file SimParameters.h. Referenced by Controller::compareChecksums(), and Controller::printEnergies(). |
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Definition at line 727 of file SimParameters.h. Referenced by WorkDistrib::createAtomLists(). |
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Definition at line 676 of file SimParameters.h. Referenced by Controller::printEnergies(). |
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Definition at line 670 of file SimParameters.h. Referenced by Controller::printTiming(). |
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Definition at line 435 of file SimParameters.h. |
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Definition at line 436 of file SimParameters.h. |
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Definition at line 437 of file SimParameters.h. Referenced by ComputePme::ComputePme(), NamdState::configListInit(), ComputePmeMgr::initialize(), WorkDistrib::mapComputes(), ComputeNonbondedUtil::select(), Sequencer::submitHalfstep(), and Sequencer::submitReductions(). |
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Definition at line 233 of file SimParameters.h. |
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Definition at line 241 of file SimParameters.h. Referenced by HomePatch::doPairlistCheck(). |
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Definition at line 235 of file SimParameters.h. |
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Definition at line 240 of file SimParameters.h. Referenced by HomePatch::doPairlistCheck(). |
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Definition at line 239 of file SimParameters.h. Referenced by Sequencer::runComputeObjects(). |
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Definition at line 242 of file SimParameters.h. Referenced by HomePatch::doPairlistCheck(). |
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Definition at line 273 of file SimParameters.h. Referenced by ParallelIOMgr::bcastHydroBasedCounter(), NamdState::configListInit(), and Parameters::Parameters(). |
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Definition at line 272 of file SimParameters.h. Referenced by ParallelIOMgr::bcastHydroBasedCounter(), NamdState::configListInit(), and Parameters::Parameters(). |
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Definition at line 216 of file SimParameters.h. Referenced by HomePatch::doMarginCheck(), ComputePmeMgr::initialize(), OptPmeMgr::initialize_pencils(), ComputePmeMgr::initialize_pencils(), and WorkDistrib::patchMapInit(). |
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Definition at line 592 of file SimParameters.h. Referenced by ComputePmeMgr::initialize(). |
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Definition at line 583 of file SimParameters.h. Referenced by ComputeNonbondedUtil::select(). |
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Definition at line 585 of file SimParameters.h. Referenced by ComputePme::ComputePme(), ComputePmeMgr::initialize(), and initializePmeGrid(). |
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Definition at line 586 of file SimParameters.h. Referenced by ComputePme::ComputePme(), ComputePmeMgr::initialize(), and initializePmeGrid(). |
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Definition at line 587 of file SimParameters.h. Referenced by ComputePme::ComputePme(), ComputePmeMgr::initialize(), and initializePmeGrid(). |
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Definition at line 588 of file SimParameters.h. |
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Definition at line 584 of file SimParameters.h. Referenced by ComputePme::ComputePme(), ComputePmeMgr::initialize(), and initializePmeGrid(). |
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Definition at line 591 of file SimParameters.h. Referenced by ComputePmeMgr::initialize(), and initializePmeGrid(). |
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Definition at line 590 of file SimParameters.h. Referenced by ComputePmeMgr::initialize(). |
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Definition at line 581 of file SimParameters.h. Referenced by WorkDistrib::assignNodeToPatch(), ComputeGlobal::ComputeGlobal(), WorkDistrib::mapComputes(), ComputeNonbondedUtil::select(), and Node::startup(). |
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Definition at line 593 of file SimParameters.h. Referenced by OptPmeMgr::initialize(), ComputePmeMgr::initialize(), and initializePmeGrid(). |
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Definition at line 589 of file SimParameters.h. Referenced by ComputePmeMgr::initialize(). |
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Definition at line 582 of file SimParameters.h. |
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Definition at line 551 of file SimParameters.h. Referenced by Controller::Controller(), and WorkDistrib::mapComputes(). |
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Definition at line 552 of file SimParameters.h. Referenced by ComputeEwald::ComputeEwald(). |
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Definition at line 553 of file SimParameters.h. Referenced by ComputeEwald::ComputeEwald(). |
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Definition at line 554 of file SimParameters.h. Referenced by ComputeEwald::ComputeEwald(). |
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Definition at line 549 of file SimParameters.h. Referenced by Controller::Controller(), and Controller::printEnergies(). |
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Definition at line 547 of file SimParameters.h. Referenced by ComputeHomeTuples< TholeElem, Thole, TholeValue >::ComputeHomeTuples(), ComputeNonbondedCUDA::ComputeNonbondedCUDA(), Controller::Controller(), ComputeNonbondedUtil::select(), and Sequencer::Sequencer(). |
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Definition at line 407 of file SimParameters.h. Referenced by Sequencer::submitMinimizeReductions(). |
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Definition at line 788 of file SimParameters.h. |
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Definition at line 792 of file SimParameters.h. |
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Definition at line 791 of file SimParameters.h. |
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Definition at line 794 of file SimParameters.h. Referenced by Node::startup(). |
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Definition at line 559 of file SimParameters.h. Referenced by colvarproxy_namd::colvarproxy_namd(), Controller::Controller(), Sequencer::Sequencer(), and Node::startup(). |
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Definition at line 766 of file SimParameters.h. Referenced by buildExclusions(). |
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Definition at line 514 of file SimParameters.h. Referenced by colvarproxy_namd::colvarproxy_namd(), Sequencer::integrate(), Sequencer::reassignVelocities(), and Controller::reassignVelocities(). |
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Definition at line 517 of file SimParameters.h. Referenced by Sequencer::reassignVelocities(), and Controller::reassignVelocities(). |
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Definition at line 516 of file SimParameters.h. Referenced by Sequencer::reassignVelocities(), and Controller::reassignVelocities(). |
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Definition at line 515 of file SimParameters.h. Referenced by colvarproxy_namd::colvarproxy_namd(), Sequencer::reassignVelocities(), Controller::reassignVelocities(), and scriptSet(). |
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Definition at line 478 of file SimParameters.h. Referenced by Controller::adaptTempInit(), colvarproxy_namd::colvarproxy_namd(), Sequencer::integrate(), Sequencer::rescaleVelocities(), and Controller::rescaleVelocities(). |
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Definition at line 479 of file SimParameters.h. Referenced by Controller::adaptTempInit(), colvarproxy_namd::colvarproxy_namd(), Sequencer::integrate(), Controller::rescaleVelocities(), and scriptSet(). |
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Definition at line 206 of file SimParameters.h. Referenced by colvarproxy_namd::colvarproxy_namd(), and Controller::outputExtendedSystem(). |
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Definition at line 207 of file SimParameters.h. Referenced by colvarproxy_namd::colvarproxy_namd(), Output::coordinate(), Output::coordinateNeeded(), Controller::outputExtendedSystem(), Output::velocity(), and Output::velocityNeeded(). |
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Definition at line 209 of file SimParameters.h. Referenced by Controller::outputExtendedSystem(). |
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Definition at line 697 of file SimParameters.h. Referenced by ParallelIOMgr::bcastHydroBasedCounter(), NamdState::configListInit(), WorkDistrib::createAtomLists(), outputCompressedFile(), Sequencer::rattle1(), and Sequencer::rattle2(). |
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Definition at line 702 of file SimParameters.h. Referenced by HomePatch::rattle1(), and HomePatch::rattle2(). |
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Definition at line 701 of file SimParameters.h. Referenced by HomePatch::rattle1(), and HomePatch::rattle2(). |
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Definition at line 700 of file SimParameters.h. Referenced by HomePatch::rattle1(), and HomePatch::rattle2(). |
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Definition at line 292 of file SimParameters.h. Referenced by ComputeRestraints::ComputeRestraints(). |
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Definition at line 293 of file SimParameters.h. Referenced by ComputeRestraints::ComputeRestraints(). |
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Definition at line 290 of file SimParameters.h. Referenced by ComputeRestraints::ComputeRestraints(). |
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Definition at line 294 of file SimParameters.h. Referenced by ComputeRestraints::ComputeRestraints(). |
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Definition at line 309 of file SimParameters.h. |
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Definition at line 307 of file SimParameters.h. |
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Definition at line 311 of file SimParameters.h. Referenced by Sequencer::addRotDragToPosition(). |
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Definition at line 306 of file SimParameters.h. Referenced by NamdState::configListInit(), Sequencer::integrate(), Molecule::receive_Molecule(), and Molecule::send_Molecule(). |
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Definition at line 310 of file SimParameters.h. |
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Definition at line 312 of file SimParameters.h. |
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Definition at line 184 of file SimParameters.h. Referenced by ComputeNonbondedUtil::select(). |
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Definition at line 776 of file SimParameters.h. Referenced by Sequencer::algorithm(), Controller::algorithm(), and scriptSet(). |
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Definition at line 777 of file SimParameters.h. Referenced by scriptSet(). |
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Definition at line 778 of file SimParameters.h. Referenced by scriptSet(). |
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Definition at line 779 of file SimParameters.h. Referenced by scriptSet(). |
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Definition at line 780 of file SimParameters.h. Referenced by scriptSet(). |
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Definition at line 263 of file SimParameters.h. Referenced by ComputeRestraints::ComputeRestraints(). |
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Definition at line 152 of file SimParameters.h. Referenced by Node::outputPatchComputeMaps(), and Node::startup(). |
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Definition at line 151 of file SimParameters.h. Referenced by WorkDistrib::assignNodeToPatch(), Node::outputPatchComputeMaps(), WorkDistrib::patchMapInit(), and Node::startup(). |
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Definition at line 150 of file SimParameters.h. Referenced by WorkDistrib::assignNodeToPatch(), Node::outputPatchComputeMaps(), WorkDistrib::patchMapInit(), and Node::startup(). |
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Definition at line 329 of file SimParameters.h. Referenced by ComputeMgr::createComputes(). |
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Definition at line 332 of file SimParameters.h. Referenced by ComputeMgr::createComputes(). |
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Definition at line 330 of file SimParameters.h. Referenced by ComputeMgr::createComputes(). |
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Definition at line 331 of file SimParameters.h. Referenced by ComputeMgr::createComputes(). |
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Definition at line 327 of file SimParameters.h. Referenced by ComputeMgr::createComputes(). |
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Definition at line 333 of file SimParameters.h. Referenced by ComputeMgr::createComputes(). |
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Definition at line 328 of file SimParameters.h. Referenced by ComputeMgr::createComputes(). |
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Definition at line 413 of file SimParameters.h. Referenced by ComputeNonbondedSelf::doForce(), ComputeNonbondedPair::doForce(), HomePatch::gbisComputeAfterP2(), and ComputeNonbondedCUDA::recvYieldDevice(). |
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Definition at line 628 of file SimParameters.h. Referenced by ComputeSphericalBC::ComputeSphericalBC(). |
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Definition at line 629 of file SimParameters.h. Referenced by ComputeSphericalBC::ComputeSphericalBC(). |
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Definition at line 622 of file SimParameters.h. Referenced by ComputeSphericalBC::ComputeSphericalBC(). |
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Definition at line 624 of file SimParameters.h. Referenced by ComputeSphericalBC::ComputeSphericalBC(). |
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Definition at line 619 of file SimParameters.h. Referenced by WorkDistrib::mapComputes(). |
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Definition at line 626 of file SimParameters.h. Referenced by ComputeSphericalBC::ComputeSphericalBC(). |
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Definition at line 627 of file SimParameters.h. Referenced by ComputeSphericalBC::ComputeSphericalBC(). |
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Definition at line 621 of file SimParameters.h. Referenced by ComputeSphericalBC::ComputeSphericalBC(). |
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Definition at line 690 of file SimParameters.h. |
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Definition at line 728 of file SimParameters.h. Referenced by WorkDistrib::createAtomLists(), WorkDistrib::patchMapInit(), and HomePatch::positionsReady(). |
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Definition at line 708 of file SimParameters.h. Referenced by Sequencer::integrate(), and Controller::integrate(). |
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Definition at line 114 of file SimParameters.h. Referenced by LdbCoordinator::initialize(), Sequencer::integrate(), Controller::integrate(), Sequencer::minimize(), and Sequencer::runComputeObjects(). |
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Definition at line 655 of file SimParameters.h. Referenced by ComputeStir::ComputeStir(), and scriptSet(). |
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Definition at line 650 of file SimParameters.h. |
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Definition at line 654 of file SimParameters.h. Referenced by ComputeStir::doForce(). |
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Definition at line 649 of file SimParameters.h. Referenced by NamdState::configListInit(), WorkDistrib::mapComputes(), Molecule::receive_Molecule(), and Molecule::send_Molecule(). |
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Definition at line 656 of file SimParameters.h. Referenced by ComputeStir::ComputeStir(), and scriptSet(). |
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Definition at line 652 of file SimParameters.h. |
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Definition at line 653 of file SimParameters.h. |
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Definition at line 808 of file SimParameters.h. Referenced by WorkDistrib::mapComputes(), and ComputeMgr::updateLocalComputes4(). |
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Definition at line 556 of file SimParameters.h. Referenced by Controller::Controller(). |
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Definition at line 557 of file SimParameters.h. Referenced by Controller::Controller(). |
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Definition at line 423 of file SimParameters.h. Referenced by ComputeLCPO::ComputeLCPO(). |
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Definition at line 545 of file SimParameters.h. Referenced by Controller::langevinPiston1(), Controller::langevinPiston2(), and scriptSet(). |
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Definition at line 223 of file SimParameters.h. Referenced by ComputeNonbondedSelf::doForce(), ComputeNonbondedPair::doForce(), ComputeNonbondedCUDA::recvYieldDevice(), and ComputeNonbondedUtil::select(). |
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Definition at line 227 of file SimParameters.h. Referenced by ComputeNonbondedCUDA::recvYieldDevice(), and ComputeNonbondedUtil::select(). |
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Definition at line 357 of file SimParameters.h. |
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Definition at line 359 of file SimParameters.h. Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry(). |
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Definition at line 359 of file SimParameters.h. Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry(). |
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Definition at line 355 of file SimParameters.h. Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry(). |
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Definition at line 356 of file SimParameters.h. |
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Definition at line 359 of file SimParameters.h. Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry(). |
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Definition at line 359 of file SimParameters.h. Referenced by ComputeMgr::createComputes(), and GlobalMasterSymmetry::GlobalMasterSymmetry(). |
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Definition at line 358 of file SimParameters.h. |
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Definition at line 354 of file SimParameters.h. Referenced by ComputeMgr::createComputes(). |
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Definition at line 354 of file SimParameters.h. Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry(). |
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Definition at line 340 of file SimParameters.h. Referenced by Parameters::read_ener_table(). |
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Definition at line 342 of file SimParameters.h. Referenced by Parameters::read_ener_table(). |
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Definition at line 338 of file SimParameters.h. Referenced by Parameters::read_ener_table(). |
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Definition at line 341 of file SimParameters.h. Referenced by Parameters::read_ener_table(). |
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Definition at line 337 of file SimParameters.h. Referenced by Parameters::Parameters(), and ComputeNonbondedUtil::select(). |
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Definition at line 339 of file SimParameters.h. Referenced by Parameters::read_ener_table(). |
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Definition at line 447 of file SimParameters.h. Referenced by ComputeTclBC::doWork(), and scriptSet(). |
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Definition at line 445 of file SimParameters.h. Referenced by WorkDistrib::mapComputes(). |
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Definition at line 446 of file SimParameters.h. Referenced by ComputeTclBC::ComputeTclBC(), receive_SimParameters(), and send_SimParameters(). |
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Definition at line 441 of file SimParameters.h. Referenced by ComputeMgr::createComputes(), and Sequencer::integrate(). |
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Definition at line 443 of file SimParameters.h. Referenced by ComputeTclBC::ComputeTclBC(). |
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Definition at line 474 of file SimParameters.h. Referenced by colvarproxy_namd::colvarproxy_namd(), NamdState::configListInit(), Molecule::receive_Molecule(), Molecule::send_Molecule(), Sequencer::tcoupleVelocities(), and Controller::tcoupleVelocities(). |
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Definition at line 476 of file SimParameters.h. Referenced by colvarproxy_namd::colvarproxy_namd(), and Controller::tcoupleVelocities(). |
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Definition at line 706 of file SimParameters.h. |
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Definition at line 346 of file SimParameters.h. Referenced by GlobalMasterTMD::GlobalMasterTMD(). |
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Definition at line 348 of file SimParameters.h. Referenced by GlobalMasterTMD::GlobalMasterTMD(). |
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Definition at line 348 of file SimParameters.h. Referenced by GlobalMasterTMD::GlobalMasterTMD(). |
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Definition at line 351 of file SimParameters.h. Referenced by GlobalMasterTMD::GlobalMasterTMD(). |
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Definition at line 350 of file SimParameters.h. Referenced by GlobalMasterTMD::GlobalMasterTMD(). |
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Definition at line 351 of file SimParameters.h. Referenced by GlobalMasterTMD::GlobalMasterTMD(). |
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Definition at line 347 of file SimParameters.h. Referenced by GlobalMasterTMD::GlobalMasterTMD(). |
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Definition at line 350 of file SimParameters.h. Referenced by GlobalMasterTMD::GlobalMasterTMD(). |
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Definition at line 346 of file SimParameters.h. Referenced by ComputeMgr::createComputes(). |
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Definition at line 349 of file SimParameters.h. Referenced by GlobalMasterTMD::GlobalMasterTMD(). |
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Definition at line 710 of file SimParameters.h. |
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Definition at line 140 of file SimParameters.h. Referenced by Sequencer::integrate(), and Controller::integrate(). |
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Definition at line 162 of file SimParameters.h. Referenced by WorkDistrib::patchMapInit(). |
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Definition at line 163 of file SimParameters.h. Referenced by WorkDistrib::patchMapInit(). |
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Definition at line 164 of file SimParameters.h. Referenced by WorkDistrib::patchMapInit(). |
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Definition at line 739 of file SimParameters.h. |
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Definition at line 782 of file SimParameters.h. Referenced by NamdState::configListInit(), and Molecule::Molecule(). |
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Definition at line 525 of file SimParameters.h. Referenced by Controller::langevinPiston1(), and scriptSet(). |
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Definition at line 526 of file SimParameters.h. Referenced by Controller::Controller(), Controller::langevinPiston1(), Controller::langevinPiston2(), Controller::receivePressure(), and scriptSet(). |
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Definition at line 595 of file SimParameters.h. Referenced by WorkDistrib::mapComputes(). |
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Definition at line 524 of file SimParameters.h. Referenced by Controller::Controller(), Controller::langevinPiston1(), Controller::langevinPiston2(), Controller::receivePressure(), and scriptSet(). |
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Definition at line 519 of file SimParameters.h. Referenced by Sequencer::berendsenPressure(), Sequencer::langevinPiston(), Controller::receivePressure(), scriptSet(), Sequencer::submitHalfstep(), and Sequencer::submitReductions(). |
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Definition at line 597 of file SimParameters.h. Referenced by OptPmeMgr::initialize(). |
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Definition at line 596 of file SimParameters.h. Referenced by WorkDistrib::mapComputes(), and Node::startup(). |
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Definition at line 237 of file SimParameters.h. Referenced by Sequencer::runComputeObjects(), and SELF(). |
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Definition at line 785 of file SimParameters.h. Referenced by NamdState::configListInit(). |
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Definition at line 704 of file SimParameters.h. Referenced by HomePatch::rattle1(), and HomePatch::rattle2(). |
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Definition at line 225 of file SimParameters.h. Referenced by ComputeNonbondedUtil::select(). |
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Definition at line 773 of file SimParameters.h. |
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Definition at line 767 of file SimParameters.h. Referenced by NamdState::configListInit(). |
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Definition at line 198 of file SimParameters.h. |
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Definition at line 190 of file SimParameters.h. Referenced by Output::velocity(), and Output::velocityNeeded(). |
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Definition at line 109 of file SimParameters.h. Referenced by Molecule::num_deg_freedom(), HomePatch::rattle1(), HomePatch::rattle2(), and Sequencer::runComputeObjects(). |
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Definition at line 179 of file SimParameters.h. Referenced by ParallelIOMgr::integrateClusterSize(), ParallelIOMgr::readPerAtomInfo(), ParallelIOMgr::recvFinalClusterCoor(), and wrap_coor_int(). |
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Definition at line 180 of file SimParameters.h. Referenced by ParallelIOMgr::recvFinalClusterCoor(), and wrap_coor_int(). |
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Definition at line 178 of file SimParameters.h. Referenced by ParallelIOMgr::integrateClusterSize(), ParallelIOMgr::readPerAtomInfo(), and wrap_coor_int(). |
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Definition at line 200 of file SimParameters.h. Referenced by Controller::outputExtendedSystem(). |
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Definition at line 194 of file SimParameters.h. Referenced by Controller::outputExtendedSystem(). |
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Definition at line 176 of file SimParameters.h. Referenced by Sequencer::integrate(), and Controller::integrate(). |
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Definition at line 177 of file SimParameters.h. Referenced by Sequencer::correctMomentum(), and Sequencer::submitMomentum(). |
1.3.9.1