#include <SimParameters.h>
Definition at line 100 of file SimParameters.h.
| SimParameters::SimParameters | ( | ) | [inline] |
Definition at line 1055 of file SimParameters.h.
01055 : mgridforcelist(), parseopts(0) {};
| SimParameters::SimParameters | ( | ConfigList * | c, | |
| char *& | cwd | |||
| ) | [inline] |
Definition at line 1056 of file SimParameters.h.
References initialize_config_data().
01056 : mgridforcelist(), parseopts(0) { 01057 initialize_config_data(c,cwd); 01058 };
| SimParameters::~SimParameters | ( | ) | [inline] |
Definition at line 1059 of file SimParameters.h.
| void SimParameters::close_dcdfile | ( | ) |
Definition at line 655 of file Output.C.
References END_OF_RUN, Node::Object(), and Node::output.
Referenced by scriptSet().
00655 { 00656 00657 Output *output = Node::Object()->output; 00658 if ( ! output ) return; 00659 00660 output->output_dcdfile(END_OF_RUN, 0, 0, 0); 00661 00662 }
| void SimParameters::close_veldcdfile | ( | ) |
Definition at line 664 of file Output.C.
References END_OF_RUN, Node::Object(), and Node::output.
Referenced by scriptSet().
00664 { 00665 00666 Output *output = Node::Object()->output; 00667 if ( ! output ) return; 00668 00669 output->output_veldcdfile(END_OF_RUN, 0, 0); 00670 00671 }
Definition at line 7246 of file SimParameters.C.
References alchBondLambdaEnd.
Referenced by Controller::computeAlchWork(), ImproperElem::computeForce(), DihedralElem::computeForce(), CrosstermElem::computeForce(), BondElem::computeForce(), AnisoElem::computeForce(), AngleElem::computeForce(), and Controller::outputTiEnergy().
07246 { 07247 // Convenience function for staggered lambda scaling 07248 return (lambda >= alchBondLambdaEnd ? 1. : lambda / alchBondLambdaEnd); 07249 }
| BigReal SimParameters::getCurrentLambda | ( | const int | step | ) |
Definition at line 7167 of file SimParameters.C.
References alchEquilSteps, alchLambdaFreq, firstTimestep, and getLambdaDelta().
Referenced by Controller::calcPressure(), Controller::computeAlchWork(), TholeElem::computeForce(), ImproperElem::computeForce(), DihedralElem::computeForce(), CrosstermElem::computeForce(), BondElem::computeForce(), AnisoElem::computeForce(), AngleElem::computeForce(), Controller::printEnergies(), and ComputePme::ungridForces().
07167 { 07168 /*Get lambda at the current step. 07169 07170 If alchLambdaFreq = 0, return alchLambda. For positive values of 07171 alchLambdaFreq, apply a linear stepwise schedule from alchLambda to 07172 alchLambda2: 07173 07174 l(t) = l + (l2 - l)*[dn / (N - n0)]*{floor[(n - n0)/dn] + 1} 07175 07176 n - the current time step 07177 n0 - step at which switching begins (default = 0) 07178 N - total steps in the simulation 07179 dn - alchLambdaFreq (increment frequency, in steps) 07180 l/l2 - alchLambda/alchLambda2 07181 07182 Note that each step _begins_ by incrementing alchLambda and then integrates 07183 in time. This means that the first and last switch steps may not behave as 07184 immediately expected - at step 0, alchLambda is NOT evaluated and at step N 07185 no step occurs because alchLambda2 has already been reached. 07186 */ 07187 if ( alchLambdaFreq > 0 && step >= alchEquilSteps ) { 07188 if ( step == N ) { 07189 return alchLambda2; 07190 } 07191 else { 07192 const int timeOrigin = firstTimestep + alchEquilSteps; 07193 const BigReal alchLambdaDelta = getLambdaDelta(); 07194 const BigReal increment = (step - timeOrigin) / BigReal(alchLambdaFreq); 07195 return alchLambda + alchLambdaDelta*(floor(increment) + 1); 07196 } 07197 } 07198 else { 07199 return alchLambda; 07200 } 07201 }
| BigReal SimParameters::getCurrentLambda2 | ( | const int | step | ) |
Definition at line 7129 of file SimParameters.C.
References alchIDWSFreq, and alchLambdaIDWS.
Referenced by TholeElem::computeForce(), ImproperElem::computeForce(), DihedralElem::computeForce(), CrosstermElem::computeForce(), BondElem::computeForce(), AnisoElem::computeForce(), AngleElem::computeForce(), Controller::outputTiEnergy(), Controller::printEnergies(), and ComputePme::ungridForces().
07129 { 07130 if ( alchLambdaIDWS >= 0. ) { 07131 const BigReal lambda2 = ( (step / alchIDWSFreq) % 2 == 1 ) ? alchLambda2 : alchLambdaIDWS; 07132 return lambda2; 07133 } else { 07134 return alchLambda2; 07135 } 07136 }
Definition at line 7209 of file SimParameters.C.
Referenced by Controller::computeAlchWork(), TholeElem::computeForce(), Controller::outputTiEnergy(), ComputePmeMgr::submitReductions(), and ComputePme::ungridForces().
07209 { 07210 // Convenience function for staggered lambda scaling 07211 return (lambda <= alchElecLambdaStart ? 0. 07212 : (lambda - alchElecLambdaStart) / (1. - alchElecLambdaStart)); 07213 }
| char * SimParameters::getfromparseopts | ( | const char * | name, | |
| char * | outbuf | |||
| ) |
Definition at line 104 of file SimParameters.C.
References ParseOptions::getfromptr().
00104 { 00105 if ( parseopts ) return parseopts->getfromptr(name,outbuf); 00106 else return 0; 00107 }
| BigReal SimParameters::getLambdaDelta | ( | void | ) |
Definition at line 7203 of file SimParameters.C.
References alchEquilSteps, alchLambdaFreq, and firstTimestep.
Referenced by getCurrentLambda(), and Controller::outputTiEnergy().
07203 { 07204 // Increment by which Lambda changes. 07205 return ((alchLambda2 - alchLambda)*alchLambdaFreq 07206 / BigReal(N - firstTimestep - alchEquilSteps)); 07207 }
Definition at line 7241 of file SimParameters.C.
References alchRepLambdaEnd.
07241 { 07242 // Convenience function for staggered lambda scaling 07243 return (lambda >= alchRepLambdaEnd ? 1. : lambda / alchRepLambdaEnd); 07244 }
Definition at line 7223 of file SimParameters.C.
References alchRepLambdaEnd, alchVdwLambdaEnd, and alchWCAOn.
Referenced by Controller::computeAlchWork(), and Controller::outputTiEnergy().
07223 { 07224 // Convenience function for staggered lambda scaling 07225 if ( alchWCAOn ) { 07226 // Read this with the alias alchRepLambdaEnd --> alchAttLambdaStart. 07227 // The second condition is needed when attractive interactions are inactive 07228 // for the whole range, otherwise lambda = 0/1 are incorrect. 07229 if ( lambda < alchRepLambdaEnd || alchRepLambdaEnd == 1.0 ) { 07230 return 0.0; 07231 } else if ( lambda >= alchVdwLambdaEnd ) { 07232 return 1.0; 07233 } else { 07234 return (lambda - alchRepLambdaEnd) / (alchVdwLambdaEnd - alchRepLambdaEnd); 07235 } 07236 } else { 07237 return (lambda >= alchVdwLambdaEnd ? 1. : lambda / alchVdwLambdaEnd); 07238 } 07239 }
| void SimParameters::initialize_config_data | ( | ConfigList * | config, | |
| char *& | cwd | |||
| ) |
Definition at line 132 of file SimParameters.C.
References ParseOptions::check_consistency(), NAMD_die(), and ParseOptions::set().
Referenced by SimParameters().
00134 { 00135 00136 parseopts = new ParseOptions; // Object to check consistency of config file 00137 ParseOptions &opts = *parseopts; 00138 00139 config_parser(opts); 00140 00142 if (!opts.check_consistency()) 00143 { 00144 NAMD_die("Internal error in configuration file parser"); 00145 } 00146 00147 // Now, feed the object with the actual configuration options through the 00148 // ParseOptions file and make sure everything is OK 00149 if (!opts.set(*config)) 00150 { 00151 NAMD_die("ERROR(S) IN THE CONFIGURATION FILE"); 00152 } 00153 00155 00156 check_config(opts,config,cwd); 00157 00158 print_config(opts,config,cwd); 00159 00160 }
| int SimParameters::isRecvSpanningTreeOn | ( | ) | [inline] |
Definition at line 1081 of file SimParameters.h.
References proxyRecvSpanningTree.
Referenced by Node::startup().
01081 { return proxyRecvSpanningTree == 1; }
| int SimParameters::isRecvSpanningTreeUnset | ( | ) | [inline] |
Definition at line 1082 of file SimParameters.h.
References proxyRecvSpanningTree.
Referenced by WorkDistrib::savePatchMap(), and WorkDistrib::sendPatchMap().
01082 { return proxyRecvSpanningTree == -1; }
| int SimParameters::isSendSpanningTreeOn | ( | ) | [inline] |
Definition at line 1079 of file SimParameters.h.
References proxySendSpanningTree.
Referenced by Node::startup().
01079 { return proxySendSpanningTree == 1; }
| int SimParameters::isSendSpanningTreeUnset | ( | ) | [inline] |
Definition at line 1080 of file SimParameters.h.
References proxySendSpanningTree.
Referenced by WorkDistrib::savePatchMap(), and WorkDistrib::sendPatchMap().
01080 { return proxySendSpanningTree == -1; }
| int SimParameters::issetinparseopts | ( | const char * | name | ) |
Definition at line 114 of file SimParameters.C.
References ParseOptions::issetfromptr().
00114 { 00115 if ( parseopts ) return parseopts->issetfromptr(name); 00116 else return -1; 00117 }
| int SimParameters::istrueinparseopts | ( | const char * | name | ) |
Definition at line 109 of file SimParameters.C.
References ParseOptions::istruefromptr().
00109 { 00110 if ( parseopts ) return parseopts->istruefromptr(name); 00111 else return -1; 00112 }
| void SimParameters::nonbonded_select | ( | ) | [static] |
Definition at line 397 of file SimParameters.C.
References ComputeNonbondedUtil::select().
Referenced by Node::resendMolecule(), and Node::startup().
00397 { 00398 ComputeNonbondedUtil::select(); 00399 }
| void SimParameters::pme_select | ( | ) | [static] |
Definition at line 401 of file SimParameters.C.
References ComputePmeUtil::select().
Referenced by Node::resendMolecule(), and Node::startup().
00401 { 00402 ComputePmeUtil::select(); 00403 }
| void SimParameters::readExtendedSystem | ( | const char * | filename, | |
| Lattice * | latptr = 0 | |||
| ) |
Definition at line 2330 of file SimParameters.C.
References Lattice::a_p(), Lattice::b_p(), Lattice::c_p(), cellBasisVector1, cellBasisVector2, cellBasisVector3, cellOrigin, endi(), iINFO(), iout, lattice, NAMD_die(), Lattice::set(), strainRate, strainRate2, Vector::x, Vector::y, and Vector::z.
02330 { 02331 02332 if ( ! latptr ) { 02333 iout << iINFO << "EXTENDED SYSTEM FILE " << filename << "\n" << endi; 02334 } 02335 02336 ifstream xscFile(filename); 02337 if ( ! xscFile ) NAMD_die("Unable to open extended system file.\n"); 02338 02339 char labels[1024]; 02340 do { 02341 if ( ! xscFile ) NAMD_die("Error reading extended system file.\n"); 02342 xscFile.getline(labels,1023); 02343 } while ( strncmp(labels,"#$LABELS ",9) ); 02344 02345 int a_x, a_y, a_z, b_x, b_y, b_z, c_x, c_y, c_z; 02346 a_x = a_y = a_z = b_x = b_y = b_z = c_x = c_y = c_z = -1; 02347 int o_x, o_y, o_z, s_u, s_v, s_w, s_x, s_y, s_z; 02348 o_x = o_y = o_z = s_u = s_v = s_w = s_x = s_y = s_z = -1; 02349 02350 int pos = 0; 02351 char *l_i = labels + 8; 02352 while ( *l_i ) { 02353 if ( *l_i == ' ' ) { ++l_i; continue; } 02354 char *l_i2; 02355 for ( l_i2 = l_i; *l_i2 && *l_i2 != ' '; ++l_i2 ); 02356 if ( (l_i2 - l_i) == 3 && (l_i[1] == '_') ) { 02357 if (l_i[0] == 'a' && l_i[2] == 'x') a_x = pos; 02358 if (l_i[0] == 'a' && l_i[2] == 'y') a_y = pos; 02359 if (l_i[0] == 'a' && l_i[2] == 'z') a_z = pos; 02360 if (l_i[0] == 'b' && l_i[2] == 'x') b_x = pos; 02361 if (l_i[0] == 'b' && l_i[2] == 'y') b_y = pos; 02362 if (l_i[0] == 'b' && l_i[2] == 'z') b_z = pos; 02363 if (l_i[0] == 'c' && l_i[2] == 'x') c_x = pos; 02364 if (l_i[0] == 'c' && l_i[2] == 'y') c_y = pos; 02365 if (l_i[0] == 'c' && l_i[2] == 'z') c_z = pos; 02366 if (l_i[0] == 'o' && l_i[2] == 'x') o_x = pos; 02367 if (l_i[0] == 'o' && l_i[2] == 'y') o_y = pos; 02368 if (l_i[0] == 'o' && l_i[2] == 'z') o_z = pos; 02369 if (l_i[0] == 's' && l_i[2] == 'u') s_u = pos; 02370 if (l_i[0] == 's' && l_i[2] == 'v') s_v = pos; 02371 if (l_i[0] == 's' && l_i[2] == 'w') s_w = pos; 02372 if (l_i[0] == 's' && l_i[2] == 'x') s_x = pos; 02373 if (l_i[0] == 's' && l_i[2] == 'y') s_y = pos; 02374 if (l_i[0] == 's' && l_i[2] == 'z') s_z = pos; 02375 } 02376 ++pos; 02377 l_i = l_i2; 02378 } 02379 int numpos = pos; 02380 02381 for ( pos = 0; pos < numpos; ++pos ) { 02382 double tmp; 02383 xscFile >> tmp; 02384 if ( ! xscFile ) NAMD_die("Error reading extended system file.\n"); 02385 if ( pos == a_x ) cellBasisVector1.x = tmp; 02386 if ( pos == a_y ) cellBasisVector1.y = tmp; 02387 if ( pos == a_z ) cellBasisVector1.z = tmp; 02388 if ( pos == b_x ) cellBasisVector2.x = tmp; 02389 if ( pos == b_y ) cellBasisVector2.y = tmp; 02390 if ( pos == b_z ) cellBasisVector2.z = tmp; 02391 if ( pos == c_x ) cellBasisVector3.x = tmp; 02392 if ( pos == c_y ) cellBasisVector3.y = tmp; 02393 if ( pos == c_z ) cellBasisVector3.z = tmp; 02394 if ( pos == o_x ) cellOrigin.x = tmp; 02395 if ( pos == o_y ) cellOrigin.y = tmp; 02396 if ( pos == o_z ) cellOrigin.z = tmp; 02397 if ( pos == s_u ) strainRate2.x = tmp; 02398 if ( pos == s_v ) strainRate2.y = tmp; 02399 if ( pos == s_w ) strainRate2.z = tmp; 02400 if ( pos == s_x ) strainRate.x = tmp; 02401 if ( pos == s_y ) strainRate.y = tmp; 02402 if ( pos == s_z ) strainRate.z = tmp; 02403 } 02404 02405 if ( latptr ) { 02406 Lattice test; 02407 test.set(cellBasisVector1,cellBasisVector2,cellBasisVector3,cellOrigin); 02408 02409 if ( test.a_p() && ! lattice.a_p() ) { 02410 NAMD_die("cellBasisVector1 added during atom reinitialization"); 02411 } 02412 if ( lattice.a_p() && ! test.a_p() ) { 02413 NAMD_die("cellBasisVector1 dropped during atom reinitialization"); 02414 } 02415 if ( test.b_p() && ! lattice.b_p() ) { 02416 NAMD_die("cellBasisVector2 added during atom reinitialization"); 02417 } 02418 if ( lattice.b_p() && ! test.b_p() ) { 02419 NAMD_die("cellBasisVector2 dropped during atom reinitialization"); 02420 } 02421 if ( test.c_p() && ! lattice.c_p() ) { 02422 NAMD_die("cellBasisVector3 added during atom reinitialization"); 02423 } 02424 if ( lattice.c_p() && ! test.c_p() ) { 02425 NAMD_die("cellBasisVector3 dropped during atom reinitialization"); 02426 } 02427 02428 latptr->set(cellBasisVector1,cellBasisVector2,cellBasisVector3,cellOrigin); 02429 } 02430 02431 }
| void SimParameters::receive_SimParameters | ( | MIStream * | msg | ) |
Definition at line 7070 of file SimParameters.C.
References binAtomFile, binCoorFile, binRefFile, binVelFile, MGridforceParamsList::clear(), FFTWWisdomString, MIStream::get(), mgridforcelist, tclBCScript, and MGridforceParamsList::unpack_data().
07072 { 07073 msg->get(sizeof(SimParameters),(char*)this); 07074 if ( FFTWWisdomString ) { 07075 int fftwlen; 07076 msg->get(fftwlen); 07077 FFTWWisdomString = new char[fftwlen]; 07078 msg->get(fftwlen,FFTWWisdomString); 07079 #ifdef NAMD_FFTW 07080 #ifdef NAMD_FFTW_3 07081 fftwf_import_wisdom_from_string(FFTWWisdomString); 07082 #else 07083 fftw_import_wisdom_from_string(FFTWWisdomString); 07084 #endif 07085 #endif 07086 } 07087 if ( tclBCScript ) { 07088 int tcllen; 07089 msg->get(tcllen); 07090 tclBCScript = new char[tcllen]; 07091 msg->get(tcllen,tclBCScript); 07092 } 07093 07094 #ifdef MEM_OPT_VERSION 07095 int filelen; 07096 msg->get(filelen); 07097 binAtomFile = new char[filelen]; 07098 msg->get(filelen, binAtomFile); 07099 07100 msg->get(filelen); 07101 binCoorFile = new char[filelen]; 07102 msg->get(filelen, binCoorFile); 07103 07104 if(binVelFile) { 07105 msg->get(filelen); 07106 binVelFile = new char[filelen]; 07107 msg->get(filelen, binVelFile); 07108 } 07109 07110 if(binRefFile) { 07111 msg->get(filelen); 07112 binRefFile = new char[filelen]; 07113 msg->get(filelen, binRefFile); 07114 } 07115 #endif 07116 07117 07118 // The simParameters bit copy above put illegal values in the list pointers 07119 // So this resets everything so that unpacking will work. 07120 mgridforcelist.clear(); 07121 mgridforcelist.unpack_data(msg); 07122 07123 delete msg; 07124 }
| void SimParameters::scriptSet | ( | const char * | param, | |
| const char * | value | |||
| ) |
Definition at line 174 of file SimParameters.C.
References accelMDalpha, accelMDE, accelMDGRestartFile, accelMDGSigma0D, accelMDGSigma0P, accelMDTalpha, accelMDTE, alchEquilSteps, alchFepOn, alchFepOnAtStartup, alchLambda, alchLambda2, alchLambdaFreq, alchLambdaIDWS, alchOn, alchOnAtStartup, alchThermIntOn, alchThermIntOnAtStartup, atobool(), berendsenPressureCompressibility, berendsenPressureOn, berendsenPressureRelaxationTime, berendsenPressureTarget, close_dcdfile(), close_veldcdfile(), commOnly, consForceScaling, constraintScaling, dcdFilename, dcdFrequency, drudeBondConst, drudeBondLen, drudeHardWallOn, eField, eFieldFreq, eFieldPhase, firstTimestep, fixCellDims, fixCellDimX, fixCellDimY, fixCellDimZ, fixedAtomsForces, fixedAtomsOn, ComputeCUDAMgr::getComputeCUDAMgr(), initialTemp, langevin_useBAOAB, langevinOn, langevinOnAtStartup, langevinPistonDecay, langevinPistonOn, langevinPistonPeriod, langevinPistonTarget, langevinPistonTemp, langevinTemp, loweAndersenTemp, MAX_SCRIPT_PARAM_SIZE, maximumMove, minimizeOn, N, NAMD_die(), nonbondedScaling, outputEnergies, outputFilename, PMEOn, PRESSUREFACTOR, reassignTemp, rescaleTemp, restartFilename, SCRIPT_PARSE_BOOL, SCRIPT_PARSE_FLOAT, SCRIPT_PARSE_INT, SCRIPT_PARSE_MOD_FLOAT, SCRIPT_PARSE_STRING, SCRIPT_PARSE_VECTOR, scriptArg1, scriptArg2, scriptArg3, scriptArg4, scriptArg5, scriptIntArg1, scriptIntArg2, scriptStringArg1, scriptStringArg2, ComputePmeUtil::select(), ComputeNonbondedUtil::select(), setupIDWS(), soluteScalingFactor, soluteScalingFactorCharge, soluteScalingFactorVdw, stirAxis, stirPivot, stochRescaleOn, stochRescaleTemp, surfaceTensionTarget, tclBCArgs, ComputeCUDAMgr::update(), useConstantArea, useConstantRatio, useFlexibleCell, useGroupPressure, and velDcdFilename.
Referenced by Node::scriptParam().
00174 { 00175 00176 if ( CkMyRank() ) return; 00177 00178 #define MAX_SCRIPT_PARAM_SIZE 128 00179 #define SCRIPT_PARSE_BOOL(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atobool(value); return; } } 00180 #define SCRIPT_PARSE_INT(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atoi(value); return; } } 00181 #define SCRIPT_PARSE_FLOAT(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atof(value); return; } } 00182 #define SCRIPT_PARSE_MOD_FLOAT(NAME,VAR,MOD) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atof(value) MOD; return; } } 00183 #define SCRIPT_PARSE_VECTOR(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR).set(value); return; } } 00184 #define SCRIPT_PARSE_STRING(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { strcpy(VAR,value); return; } } 00185 00186 SCRIPT_PARSE_FLOAT("scriptArg1",scriptArg1) 00187 SCRIPT_PARSE_FLOAT("scriptArg2",scriptArg2) 00188 SCRIPT_PARSE_FLOAT("scriptArg3",scriptArg3) 00189 SCRIPT_PARSE_FLOAT("scriptArg4",scriptArg4) 00190 SCRIPT_PARSE_FLOAT("scriptArg5",scriptArg5) 00191 SCRIPT_PARSE_INT("scriptIntArg1",scriptIntArg1) 00192 SCRIPT_PARSE_INT("scriptIntArg2",scriptIntArg2) 00193 SCRIPT_PARSE_STRING("scriptStringArg1",scriptStringArg1) 00194 SCRIPT_PARSE_STRING("scriptStringArg2",scriptStringArg2) 00195 SCRIPT_PARSE_INT("numsteps",N) 00196 if ( ! strncasecmp(param,"firsttimestep",MAX_SCRIPT_PARAM_SIZE) ) { 00197 N = firstTimestep = atoi(value); return; 00198 } 00199 SCRIPT_PARSE_FLOAT("reassignTemp",reassignTemp) 00200 SCRIPT_PARSE_FLOAT("rescaleTemp",rescaleTemp) 00201 SCRIPT_PARSE_BOOL("velocityQuenching",minimizeOn) 00202 SCRIPT_PARSE_BOOL("maximumMove",maximumMove) 00203 // SCRIPT_PARSE_BOOL("Langevin",langevinOn) 00204 if ( ! strncasecmp(param,"Langevin",MAX_SCRIPT_PARAM_SIZE) ) { 00205 langevinOn = atobool(value); 00206 if ( langevinOn && ! langevinOnAtStartup ) { 00207 NAMD_die("Langevin must be enabled at startup to disable and re-enable in script."); 00208 } 00209 return; 00210 } 00211 SCRIPT_PARSE_FLOAT("langevinTemp",langevinTemp) 00212 SCRIPT_PARSE_BOOL("langevinBAOAB",langevin_useBAOAB) // [!!] Use the BAOAB integrator or not 00213 SCRIPT_PARSE_FLOAT("loweAndersenTemp",loweAndersenTemp) // BEGIN LA, END LA 00214 SCRIPT_PARSE_BOOL("stochRescale",stochRescaleOn) 00215 SCRIPT_PARSE_FLOAT("stochRescaleTemp",stochRescaleTemp) 00216 SCRIPT_PARSE_FLOAT("initialTemp",initialTemp) 00217 SCRIPT_PARSE_BOOL("useGroupPressure",useGroupPressure) 00218 SCRIPT_PARSE_BOOL("useFlexibleCell",useFlexibleCell) 00219 SCRIPT_PARSE_BOOL("useConstantArea",useConstantArea) 00220 SCRIPT_PARSE_BOOL("fixCellDims",fixCellDims) 00221 SCRIPT_PARSE_BOOL("fixCellDimX",fixCellDimX) 00222 SCRIPT_PARSE_BOOL("fixCellDimY",fixCellDimY) 00223 SCRIPT_PARSE_BOOL("fixCellDimZ",fixCellDimZ) 00224 SCRIPT_PARSE_BOOL("useConstantRatio",useConstantRatio) 00225 SCRIPT_PARSE_BOOL("LangevinPiston",langevinPistonOn) 00226 SCRIPT_PARSE_MOD_FLOAT("LangevinPistonTarget", 00227 langevinPistonTarget,/PRESSUREFACTOR) 00228 SCRIPT_PARSE_FLOAT("LangevinPistonPeriod",langevinPistonPeriod) 00229 SCRIPT_PARSE_FLOAT("LangevinPistonDecay",langevinPistonDecay) 00230 SCRIPT_PARSE_FLOAT("LangevinPistonTemp",langevinPistonTemp) 00231 SCRIPT_PARSE_MOD_FLOAT("SurfaceTensionTarget", 00232 surfaceTensionTarget,*(100.0/PRESSUREFACTOR)) 00233 SCRIPT_PARSE_BOOL("BerendsenPressure",berendsenPressureOn) 00234 SCRIPT_PARSE_MOD_FLOAT("BerendsenPressureTarget", 00235 berendsenPressureTarget,/PRESSUREFACTOR) 00236 SCRIPT_PARSE_MOD_FLOAT("BerendsenPressureCompressibility", 00237 berendsenPressureCompressibility,*PRESSUREFACTOR) 00238 SCRIPT_PARSE_FLOAT("BerendsenPressureRelaxationTime", 00239 berendsenPressureRelaxationTime) 00240 SCRIPT_PARSE_FLOAT("constraintScaling",constraintScaling) 00241 SCRIPT_PARSE_FLOAT("consForceScaling",consForceScaling) 00242 SCRIPT_PARSE_BOOL("drudeHardWall",drudeHardWallOn) 00243 SCRIPT_PARSE_FLOAT("drudeBondConst",drudeBondConst) 00244 SCRIPT_PARSE_FLOAT("drudeBondLen",drudeBondLen) 00245 SCRIPT_PARSE_STRING("outputname",outputFilename) 00246 SCRIPT_PARSE_INT("outputEnergies",outputEnergies) 00247 SCRIPT_PARSE_STRING("restartname",restartFilename) 00248 SCRIPT_PARSE_INT("DCDfreq",dcdFrequency) 00249 if ( ! strncasecmp(param,"DCDfile",MAX_SCRIPT_PARAM_SIZE) ) { 00250 close_dcdfile(); // *** implemented in Output.C *** 00251 strcpy(dcdFilename,value); 00252 return; 00253 } 00254 if ( ! strncasecmp(param,"velDCDfile",MAX_SCRIPT_PARAM_SIZE) ) { 00255 close_veldcdfile(); // *** implemented in Output.C *** 00256 strcpy(velDcdFilename,value); 00257 return; 00258 } 00259 SCRIPT_PARSE_STRING("tclBCArgs",tclBCArgs) 00260 SCRIPT_PARSE_VECTOR("eField",eField) 00261 SCRIPT_PARSE_FLOAT("eFieldFreq",eFieldFreq) 00262 SCRIPT_PARSE_FLOAT("eFieldPhase",eFieldPhase) 00263 SCRIPT_PARSE_FLOAT("accelMDE",accelMDE) 00264 SCRIPT_PARSE_FLOAT("accelMDalpha",accelMDalpha) 00265 SCRIPT_PARSE_FLOAT("accelMDTE",accelMDTE) 00266 SCRIPT_PARSE_FLOAT("accelMDTalpha",accelMDTalpha) 00267 SCRIPT_PARSE_FLOAT("accelMDGSigma0P",accelMDGSigma0P) 00268 SCRIPT_PARSE_FLOAT("accelMDGSigma0D",accelMDGSigma0D) 00269 SCRIPT_PARSE_STRING("accelMDGRestartFile",accelMDGRestartFile) 00270 SCRIPT_PARSE_VECTOR("stirAxis",stirAxis) 00271 SCRIPT_PARSE_VECTOR("stirPivot",stirPivot) 00272 if ( ! strncasecmp(param,"mgridforcescale",MAX_SCRIPT_PARAM_SIZE) ) { 00273 NAMD_die("Can't yet modify mgridforcescale in a script"); 00274 return; 00275 } 00276 if ( ! strncasecmp(param,"mgridforcevoff",MAX_SCRIPT_PARAM_SIZE) ) { 00277 NAMD_die("Can't yet modify mgridforcevoff in a script"); 00278 return; 00279 } 00280 00281 if ( ! strncasecmp(param,"fixedatoms",MAX_SCRIPT_PARAM_SIZE) ) { 00282 if ( ! fixedAtomsOn ) 00283 NAMD_die("FixedAtoms may not be enabled in a script."); 00284 if ( ! fixedAtomsForces ) 00285 NAMD_die("To use fixedAtoms in script first use fixedAtomsForces yes."); 00286 fixedAtomsOn = atobool(value); 00287 return; 00288 } 00289 00290 //fepb 00291 if ( ! strncasecmp(param,"alch",MAX_SCRIPT_PARAM_SIZE) ) { 00292 alchOn = atobool(value); 00293 if ( alchOn && ! alchOnAtStartup ) { 00294 NAMD_die("Alchemy must be enabled at startup to disable and re-enable in script."); 00295 } 00296 alchFepOn = alchOn && alchFepOnAtStartup; 00297 alchThermIntOn = alchOn && alchThermIntOnAtStartup; 00298 ComputeNonbondedUtil::select(); 00299 if ( PMEOn ) ComputePmeUtil::select(); 00300 return; 00301 } 00302 SCRIPT_PARSE_INT("alchEquilSteps",alchEquilSteps) 00303 00304 if ( ! strncasecmp(param,"alchLambda",MAX_SCRIPT_PARAM_SIZE) ) { 00305 alchLambda = atof(value); 00306 if ( alchLambda < 0.0 || 1.0 < alchLambda ) { 00307 NAMD_die("Alchemical lambda values should be in the range [0.0, 1.0]\n"); 00308 } 00309 ComputeNonbondedUtil::select(); 00310 return; 00311 } 00312 00313 if ( ! strncasecmp(param,"alchLambda2",MAX_SCRIPT_PARAM_SIZE) ) { 00314 alchLambda2 = atof(value); 00315 if ( alchLambda2 < 0.0 || 1.0 < alchLambda2 ) { 00316 NAMD_die("Alchemical lambda values should be in the range [0.0, 1.0]\n"); 00317 } 00318 ComputeNonbondedUtil::select(); 00319 return; 00320 } 00321 00322 if ( ! strncasecmp(param,"alchLambdaIDWS",MAX_SCRIPT_PARAM_SIZE) ) { 00323 alchLambdaIDWS = atof(value); 00324 setupIDWS(); 00325 ComputeNonbondedUtil::select(); 00326 return; 00327 } 00328 00329 if ( ! strncasecmp(param,"alchLambdaFreq",MAX_SCRIPT_PARAM_SIZE) ) { 00330 alchLambdaFreq = atoi(value); 00331 if ( alchLambdaIDWS >= 0 ) { 00332 NAMD_die("alchLambdaIDWS and alchLambdaFreq are not compatible.\n"); 00333 } 00334 ComputeNonbondedUtil::select(); 00335 return; 00336 } 00337 //fepe 00338 00339 if ( ! strncasecmp(param,"nonbondedScaling",MAX_SCRIPT_PARAM_SIZE) ) { 00340 nonbondedScaling = atof(value); 00341 ComputeNonbondedUtil::select(); 00342 return; 00343 } 00344 00345 if ( ! strncasecmp(param,"commOnly",MAX_SCRIPT_PARAM_SIZE) ) { 00346 commOnly = atobool(value); 00347 ComputeNonbondedUtil::select(); 00348 return; 00349 } 00350 00351 // REST2 - We don't have to make any changes to ComputeNonbondedUtil 00352 // other than recalculating the LJTable. Skip doing the other stuff. 00353 if ( ! strncasecmp(param,"soluteScalingFactor",MAX_SCRIPT_PARAM_SIZE)) { 00354 soluteScalingFactor = atof(value); 00355 if (soluteScalingFactor < 0.0) { 00356 NAMD_die("Solute scaling factor should be non-negative\n"); 00357 } 00358 soluteScalingFactorCharge = soluteScalingFactor; 00359 soluteScalingFactorVdw = soluteScalingFactor; 00360 // update LJTable for CPU 00361 ComputeNonbondedUtil::select(); 00362 #ifdef NAMD_CUDA 00363 // update LJTable for GPU, needs CPU update first 00364 ComputeCUDAMgr::getComputeCUDAMgr()->update(); 00365 #endif 00366 return; 00367 } 00368 if ( ! strncasecmp(param,"soluteScalingFactorVdw",MAX_SCRIPT_PARAM_SIZE)) { 00369 soluteScalingFactorVdw = atof(value); 00370 if (soluteScalingFactorVdw < 0.0) { 00371 NAMD_die("Solute scaling factor for van der Waals " 00372 "should be non-negative\n"); 00373 } 00374 // update LJTable for CPU 00375 ComputeNonbondedUtil::select(); 00376 #ifdef NAMD_CUDA 00377 // update LJTable for GPU, needs CPU update first 00378 ComputeCUDAMgr::getComputeCUDAMgr()->update(); 00379 #endif 00380 return; 00381 } 00382 if ( ! strncasecmp(param,"soluteScalingFactorCharge",MAX_SCRIPT_PARAM_SIZE)) { 00383 soluteScalingFactorCharge = atof(value); 00384 if (soluteScalingFactorCharge < 0.0) { 00385 NAMD_die("Solute scaling factor for electrostatics " 00386 "should be non-negative\n"); 00387 } 00388 return; 00389 } 00390 00391 char *error = new char[2 * MAX_SCRIPT_PARAM_SIZE + 100]; 00392 sprintf(error,"Setting parameter %s from script failed!\n",param); 00393 NAMD_die(error); 00394 00395 }
| void SimParameters::send_SimParameters | ( | MOStream * | msg | ) |
Definition at line 7012 of file SimParameters.C.
References binAtomFile, binCoorFile, binRefFile, binVelFile, MOStream::end(), FFTWWisdomString, mgridforcelist, MGridforceParamsList::pack_data(), MOStream::put(), and tclBCScript.
07014 { 07015 /*MOStream *msg = com_obj->newOutputStream(ALLBUTME, SIMPARAMSTAG, BUFSIZE); 07016 if ( msg == NULL ) 07017 { 07018 NAMD_die("memory allocation failed in SimParameters::send_SimParameters"); 07019 }*/ 07020 07021 msg->put(sizeof(SimParameters),(char*)this); 07022 if ( FFTWWisdomString ) { 07023 int fftwlen = strlen(FFTWWisdomString) + 1; 07024 msg->put(fftwlen); 07025 msg->put(fftwlen,FFTWWisdomString); 07026 } 07027 if ( tclBCScript ) { 07028 int tcllen = strlen(tclBCScript) + 1; 07029 msg->put(tcllen); 07030 msg->put(tcllen,tclBCScript); 07031 } 07032 07033 #ifdef MEM_OPT_VERSION 07034 int filelen = strlen(binAtomFile)+1; 07035 msg->put(filelen); 07036 msg->put(filelen, binAtomFile); 07037 07038 filelen = strlen(binCoorFile)+1; 07039 msg->put(filelen); 07040 msg->put(filelen, binCoorFile); 07041 07042 if(binVelFile) { 07043 filelen = strlen(binVelFile)+1; 07044 msg->put(filelen); 07045 msg->put(filelen, binVelFile); 07046 } 07047 07048 if(binRefFile) { 07049 filelen = strlen(binRefFile)+1; 07050 msg->put(filelen); 07051 msg->put(filelen, binRefFile); 07052 } 07053 #endif 07054 07055 mgridforcelist.pack_data(msg); 07056 07057 msg->end(); 07058 }
| int SimParameters::setupIDWS | ( | ) |
Definition at line 7139 of file SimParameters.C.
References alchIDWSFreq, alchLambdaIDWS, alchOutFreq, iout, iWARN(), NAMD_die(), and outputEnergies.
Referenced by scriptSet().
07139 { 07140 if (alchLambdaIDWS < 0.) return 0; 07141 if (alchLambdaIDWS > 1.) { 07142 NAMD_die("alchLambdaIDWS should be either in the range [0.0, 1.0], or negative (disabled).\n"); 07143 } 07144 /* 07145 * The internal parameter alchIDWSFreq determines the number of steps of MD 07146 * before each switch of the value of alchLambda2. At most this occurs every 07147 * time the energy is evaluated and thus the default is the greater of 07148 * fullElectFrequency and nonbondedFrequency. However, this choice fails to 07149 * report alternating values if output is printed less often than every step 07150 * (which is almost certainly true). Thus the frequency is reset to match 07151 * alchOutFreq or, if that is zero, outputEnergies. Note that, if 07152 * alchOutFreq > 0 but != outputEnergies, then the data going to stdout 07153 * are likely not useful since the comparison value is difficult to infer. 07154 */ 07155 alchIDWSFreq = fullElectFrequency > 0 ? fullElectFrequency : nonbondedFrequency; 07156 if ( !alchOutFreq && outputEnergies > alchIDWSFreq ) alchIDWSFreq = outputEnergies; 07157 if ( alchOutFreq > alchIDWSFreq ) alchIDWSFreq = alchOutFreq; 07158 if ( alchOutFreq && alchOutFreq != outputEnergies) { 07159 iout << iWARN << "alchOutFreq and outputEnergies do not match. IDWS ouput" 07160 << " to stdout may not be useful!\n" << endi; 07161 } 07162 return 1; 07163 }
Definition at line 969 of file SimParameters.h.
Definition at line 625 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD(), and scriptSet().
Definition at line 620 of file SimParameters.h.
Referenced by Controller::receivePressure(), Controller::rescaleaccelMD(), and ComputeGlobal::saveTotalForces().
Definition at line 618 of file SimParameters.h.
Referenced by ComputeHomeTuples< TholeElem, Thole, TholeValue >::ComputeHomeTuples(), Sequencer::integrate(), Sequencer::rescaleaccelMD(), Controller::rescaleaccelMD(), and ComputeGlobal::saveTotalForces().
Definition at line 619 of file SimParameters.h.
Referenced by ComputeHomeTuples< TholeElem, Thole, TholeValue >::ComputeHomeTuples(), Sequencer::integrate(), Sequencer::rescaleaccelMD(), and Controller::rescaleaccelMD().
Definition at line 624 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD(), and scriptSet().
Definition at line 621 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD().
Definition at line 629 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD().
Definition at line 633 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD().
Definition at line 631 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD().
Definition at line 634 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD().
Definition at line 632 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD().
Definition at line 630 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD().
Definition at line 640 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD().
Definition at line 638 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD().
| char SimParameters::accelMDGRestartFile[128] |
Definition at line 639 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD(), and scriptSet().
Definition at line 637 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD(), and scriptSet().
Definition at line 636 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD(), and scriptSet().
Definition at line 635 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD().
Definition at line 622 of file SimParameters.h.
Referenced by Sequencer::rescaleaccelMD(), and Controller::rescaleaccelMD().
Definition at line 617 of file SimParameters.h.
Referenced by Controller::calcPressure(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::ComputeHomeTuples(), Controller::Controller(), Sequencer::integrate(), Controller::receivePressure(), Sequencer::rescaleaccelMD(), Controller::rescaleaccelMD(), ComputeNonbondedUtil::select(), and Sequencer::Sequencer().
Definition at line 623 of file SimParameters.h.
Referenced by Controller::receivePressure(), and Controller::rescaleaccelMD().
Definition at line 627 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD(), and scriptSet().
Definition at line 626 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD(), and scriptSet().
Definition at line 651 of file SimParameters.h.
Referenced by Controller::adaptTempInit().
Definition at line 652 of file SimParameters.h.
Referenced by Controller::adaptTempInit().
Definition at line 654 of file SimParameters.h.
Referenced by Controller::adaptTempInit().
Definition at line 644 of file SimParameters.h.
Referenced by Controller::adaptTempUpdate().
Definition at line 653 of file SimParameters.h.
Referenced by Controller::adaptTempInit().
Definition at line 645 of file SimParameters.h.
Referenced by Controller::rescaleVelocities().
Definition at line 648 of file SimParameters.h.
Referenced by Sequencer::adaptTempUpdate(), and Controller::adaptTempUpdate().
| char SimParameters::adaptTempInFile[128] |
Definition at line 657 of file SimParameters.h.
Referenced by Controller::adaptTempInit().
Definition at line 655 of file SimParameters.h.
Referenced by Sequencer::langevinVelocities(), and Sequencer::langevinVelocitiesBBK2().
Definition at line 646 of file SimParameters.h.
Referenced by Sequencer::adaptTempUpdate(), Controller::adaptTempUpdate(), and Controller::rescaleVelocities().
Definition at line 643 of file SimParameters.h.
Referenced by Controller::adaptTempInit(), Sequencer::adaptTempUpdate(), Controller::adaptTempUpdate(), Controller::adaptTempWriteRestart(), Sequencer::integrate(), Sequencer::langevinVelocities(), Sequencer::langevinVelocitiesBBK2(), and Controller::rescaleVelocities().
Definition at line 647 of file SimParameters.h.
Referenced by Controller::adaptTempUpdate().
Definition at line 660 of file SimParameters.h.
Referenced by Controller::adaptTempUpdate().
Definition at line 656 of file SimParameters.h.
Referenced by Controller::rescaleVelocities().
| char SimParameters::adaptTempRestartFile[128] |
Definition at line 658 of file SimParameters.h.
Referenced by Controller::adaptTempInit().
Definition at line 659 of file SimParameters.h.
Referenced by Controller::adaptTempInit(), and Controller::adaptTempWriteRestart().
Definition at line 650 of file SimParameters.h.
Referenced by Controller::adaptTempInit().
Definition at line 649 of file SimParameters.h.
Referenced by Controller::adaptTempInit().
Definition at line 436 of file SimParameters.h.
Referenced by CrosstermElem::computeForce().
Definition at line 430 of file SimParameters.h.
Referenced by getBondLambda().
Definition at line 435 of file SimParameters.h.
Referenced by TholeElem::computeForce(), ComputePmeUtil::select(), and ComputeNonbondedUtil::select().
Definition at line 413 of file SimParameters.h.
Referenced by ComputePmeUtil::select().
Definition at line 408 of file SimParameters.h.
Referenced by Controller::outputFepEnergy(), and Controller::writeFepEnergyData().
Definition at line 410 of file SimParameters.h.
Referenced by getCurrentLambda(), getLambdaDelta(), Controller::outputFepEnergy(), Controller::outputTiEnergy(), Controller::printEnergies(), Controller::printFepMessage(), Controller::printTiMessage(), and scriptSet().
Definition at line 390 of file SimParameters.h.
Referenced by ComputePmeCUDA::initialize(), Controller::outputFepEnergy(), Controller::printEnergies(), Controller::printFepMessage(), scriptSet(), ComputePmeUtil::select(), and ComputeNonbondedUtil::select().
Definition at line 387 of file SimParameters.h.
Referenced by scriptSet().
Definition at line 399 of file SimParameters.h.
Referenced by getCurrentLambda2(), Controller::outputFepEnergy(), setupIDWS(), and Controller::writeFepEnergyData().
Definition at line 396 of file SimParameters.h.
Referenced by ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), Controller::outputFepEnergy(), Controller::outputTiEnergy(), Controller::printFepMessage(), Controller::printTiMessage(), scriptSet(), and Controller::writeFepEnergyData().
Definition at line 397 of file SimParameters.h.
Referenced by Controller::outputFepEnergy(), Controller::printFepMessage(), and scriptSet().
Definition at line 400 of file SimParameters.h.
Referenced by getCurrentLambda(), getLambdaDelta(), Controller::outputTiEnergy(), Controller::printEnergies(), Controller::printFepMessage(), Controller::printTiMessage(), scriptSet(), and Controller::writeTiEnergyData().
Definition at line 398 of file SimParameters.h.
Referenced by getCurrentLambda2(), Controller::outputFepEnergy(), Controller::printFepMessage(), scriptSet(), setupIDWS(), and Controller::writeFepEnergyData().
Definition at line 395 of file SimParameters.h.
Definition at line 389 of file SimParameters.h.
Referenced by TholeElem::computeForce(), ImproperElem::computeForce(), DihedralElem::computeForce(), CrosstermElem::computeForce(), BondElem::computeForce(), AnisoElem::computeForce(), AngleElem::computeForce(), WorkDistrib::createAtomLists(), NamdState::loadStructure(), Controller::outputFepEnergy(), Controller::outputTiEnergy(), Controller::printEnergies(), Controller::printFepMessage(), Controller::printTiMessage(), Molecule::receive_Molecule(), scriptSet(), ComputePmeUtil::select(), and Molecule::send_Molecule().
Definition at line 386 of file SimParameters.h.
Referenced by scriptSet().
| char SimParameters::alchOutFile[128] |
Definition at line 409 of file SimParameters.h.
Referenced by Controller::outputFepEnergy(), and Controller::outputTiEnergy().
Definition at line 407 of file SimParameters.h.
Referenced by Controller::outputFepEnergy(), Controller::outputTiEnergy(), and setupIDWS().
Definition at line 424 of file SimParameters.h.
Referenced by getRepLambda(), and getVdwLambda().
Definition at line 406 of file SimParameters.h.
Referenced by Controller::outputFepEnergy(), Controller::outputTiEnergy(), Controller::printFepMessage(), and Controller::writeFepEnergyData().
Definition at line 393 of file SimParameters.h.
Referenced by ComputePmeCUDA::initialize(), Controller::outputTiEnergy(), Controller::printEnergies(), Controller::printTiMessage(), scriptSet(), ComputePmeUtil::select(), and ComputeNonbondedUtil::select().
Definition at line 388 of file SimParameters.h.
Referenced by scriptSet().
Definition at line 419 of file SimParameters.h.
Referenced by getVdwLambda().
Definition at line 411 of file SimParameters.h.
Referenced by ComputeNonbondedUtil::select().
Definition at line 394 of file SimParameters.h.
Referenced by getVdwLambda(), and ComputeNonbondedUtil::select().
Definition at line 530 of file SimParameters.h.
Referenced by ComputeNonbondedSelf::doForce(), ComputeNonbondedPair::doForce(), and ComputeNonbondedCUDA::recvYieldDevice().
Definition at line 531 of file SimParameters.h.
Referenced by ComputeNonbondedSelf::doForce(), ComputeNonbondedPair::doForce(), and HomePatch::gbisComputeAfterP1().
Definition at line 990 of file SimParameters.h.
Referenced by buildExclusions(), and NamdState::loadStructure().
| char SimParameters::auxFilename[128] |
Definition at line 211 of file SimParameters.h.
Definition at line 167 of file SimParameters.h.
Referenced by Output::coordinateNeeded(), Output::forceNeeded(), and Output::velocityNeeded().
Definition at line 684 of file SimParameters.h.
Referenced by Controller::berendsenPressure(), and scriptSet().
Definition at line 686 of file SimParameters.h.
Referenced by Sequencer::berendsenPressure(), and Controller::berendsenPressure().
Definition at line 682 of file SimParameters.h.
Referenced by Sequencer::berendsenPressure(), Controller::berendsenPressure(), ComputeGridForce::doForce(), and scriptSet().
Definition at line 685 of file SimParameters.h.
Referenced by Controller::berendsenPressure(), and scriptSet().
Definition at line 683 of file SimParameters.h.
Referenced by Controller::berendsenPressure(), and scriptSet().
Definition at line 228 of file SimParameters.h.
Referenced by WorkDistrib::createAtomLists().
Definition at line 226 of file SimParameters.h.
Definition at line 1028 of file SimParameters.h.
Referenced by receive_SimParameters(), and send_SimParameters().
Definition at line 1029 of file SimParameters.h.
Referenced by receive_SimParameters(), and send_SimParameters().
Definition at line 1031 of file SimParameters.h.
Referenced by receive_SimParameters(), and send_SimParameters().
Definition at line 1030 of file SimParameters.h.
Referenced by receive_SimParameters(), and send_SimParameters().
Bitmask for calculating bonded interactions on GPU. Default is 255, with the following bit position settings: 1 -> bonds, 2 -> angles, 4 -> dihedrals, 8 -> impropers, 16 -> exclusions, 32 -> crossterms.
Definition at line 804 of file SimParameters.h.
Referenced by ComputeMgr::createComputes(), LdbCoordinator::initialize(), WorkDistrib::mapComputes(), and Node::startup().
Definition at line 127 of file SimParameters.h.
Referenced by readExtendedSystem().
Definition at line 128 of file SimParameters.h.
Referenced by readExtendedSystem().
Definition at line 129 of file SimParameters.h.
Referenced by readExtendedSystem().
Definition at line 130 of file SimParameters.h.
Referenced by readExtendedSystem().
Definition at line 584 of file SimParameters.h.
Definition at line 586 of file SimParameters.h.
Definition at line 587 of file SimParameters.h.
Definition at line 561 of file SimParameters.h.
Referenced by ComputeGlobal::ComputeGlobal(), ComputeMgr::createComputes(), Sequencer::integrate(), and Sequencer::minimize().
Definition at line 929 of file SimParameters.h.
Referenced by Sequencer::integrate(), scriptSet(), ComputeNonbondedUtil::select(), and ComputePme::ungridForces().
Definition at line 189 of file SimParameters.h.
Referenced by ParallelIOMgr::bcastMolInfo(), WorkDistrib::createAtomLists(), NamdState::loadStructure(), Controller::receivePressure(), ParallelIOMgr::recvMolInfo(), and ParallelIOMgr::updateMolInfo().
| char SimParameters::computeMapFilename[128] |
Definition at line 1037 of file SimParameters.h.
Referenced by WorkDistrib::mapComputes(), and ComputeMgr::updateLocalComputes4().
| char SimParameters::consForceFile[128] |
Definition at line 881 of file SimParameters.h.
Definition at line 880 of file SimParameters.h.
Referenced by NamdState::loadStructure(), WorkDistrib::mapComputes(), Molecule::receive_Molecule(), and Molecule::send_Molecule().
Definition at line 882 of file SimParameters.h.
Referenced by ComputeConsForce::doForce(), and scriptSet().
| char SimParameters::consTorqueAxisFile[128] |
Definition at line 342 of file SimParameters.h.
| char SimParameters::consTorqueFile[128] |
Definition at line 340 of file SimParameters.h.
Definition at line 344 of file SimParameters.h.
Referenced by ComputeConsTorque::doForce().
Definition at line 339 of file SimParameters.h.
Referenced by NamdState::loadStructure(), WorkDistrib::mapComputes(), Molecule::receive_Molecule(), and Molecule::send_Molecule().
| char SimParameters::consTorquePivotFile[128] |
Definition at line 343 of file SimParameters.h.
| char SimParameters::consTorqueValFile[128] |
Definition at line 345 of file SimParameters.h.
Definition at line 263 of file SimParameters.h.
Referenced by ComputeRestraints::ComputeRestraints().
Definition at line 291 of file SimParameters.h.
Referenced by ComputeRestraints::doForce(), and scriptSet().
Definition at line 261 of file SimParameters.h.
Referenced by NamdState::loadStructure(), WorkDistrib::mapComputes(), Molecule::receive_Molecule(), and Molecule::send_Molecule().
Definition at line 282 of file SimParameters.h.
Referenced by ComputeRestraints::ComputeRestraints().
Definition at line 282 of file SimParameters.h.
Referenced by ComputeRestraints::ComputeRestraints().
Definition at line 282 of file SimParameters.h.
Referenced by ComputeRestraints::ComputeRestraints().
Definition at line 550 of file SimParameters.h.
Referenced by Parameters::Parameters().
Definition at line 524 of file SimParameters.h.
Referenced by ComputeNonbondedSelf::doForce(), ComputeNonbondedPair::doForce(), ComputeGBISser::doWork(), HomePatch::gbisComputeAfterP1(), HomePatch::gbisComputeAfterP2(), ComputeNonbondedCUDA::recvYieldDevice(), and HomePatch::setGBISIntrinsicRadii().
Definition at line 230 of file SimParameters.h.
Referenced by GromacsPairElem::computeForce(), ComputeNonbondedSelf::doForce(), ComputeNonbondedPair::doForce(), HomePatch::doMarginCheck(), ComputeQM::initialize(), ComputePmeMgr::initialize(), ComputeMsmMgr::initialize(), ComputePmeMgr::initialize_pencils(), Sequencer::maximumMove(), Parameters::read_ener_table(), ComputeMsmSerialMgr::recvCoord(), ComputeQMMgr::recvPntChrg(), ComputeNonbondedCUDA::recvYieldDevice(), and ComputeNonbondedUtil::select().
Definition at line 851 of file SimParameters.h.
Referenced by ComputeCylindricalBC::ComputeCylindricalBC().
Definition at line 856 of file SimParameters.h.
Referenced by ComputeCylindricalBC::ComputeCylindricalBC().
Definition at line 857 of file SimParameters.h.
Referenced by ComputeCylindricalBC::ComputeCylindricalBC().
Definition at line 858 of file SimParameters.h.
Referenced by ComputeCylindricalBC::ComputeCylindricalBC().
Definition at line 859 of file SimParameters.h.
Referenced by ComputeCylindricalBC::ComputeCylindricalBC().
Definition at line 854 of file SimParameters.h.
Referenced by ComputeCylindricalBC::ComputeCylindricalBC().
Definition at line 855 of file SimParameters.h.
Referenced by ComputeCylindricalBC::ComputeCylindricalBC().
Definition at line 848 of file SimParameters.h.
Referenced by WorkDistrib::mapComputes().
Definition at line 852 of file SimParameters.h.
Referenced by ComputeCylindricalBC::ComputeCylindricalBC().
Definition at line 853 of file SimParameters.h.
Referenced by ComputeCylindricalBC::ComputeCylindricalBC().
Definition at line 850 of file SimParameters.h.
Referenced by ComputeCylindricalBC::ComputeCylindricalBC().
Definition at line 976 of file SimParameters.h.
Definition at line 976 of file SimParameters.h.
Definition at line 976 of file SimParameters.h.
| char SimParameters::dcdFilename[128] |
Definition at line 212 of file SimParameters.h.
Referenced by scriptSet().
Definition at line 202 of file SimParameters.h.
Referenced by Output::coordinate(), Output::coordinateNeeded(), and scriptSet().
Definition at line 204 of file SimParameters.h.
Referenced by Output::coordinate().
Definition at line 972 of file SimParameters.h.
Definition at line 972 of file SimParameters.h.
Definition at line 972 of file SimParameters.h.
Definition at line 196 of file SimParameters.h.
Referenced by ComputeMsm::ComputeMsm(), ComputeNonbondedSelf::doForce(), ComputeNonbondedPair::doForce(), HomePatch::gbisComputeAfterP2(), ComputeMsmSerialMgr::recvCoord(), ComputeFmmSerialMgr::recvCoord(), ComputeQMMgr::recvPntChrg(), ComputeNonbondedCUDA::recvYieldDevice(), and ComputeNonbondedUtil::select().
Definition at line 583 of file SimParameters.h.
Definition at line 164 of file SimParameters.h.
Referenced by recursive_bisect_with_curve().
Definition at line 969 of file SimParameters.h.
Definition at line 969 of file SimParameters.h.
Definition at line 542 of file SimParameters.h.
Referenced by BondElem::computeForce(), and scriptSet().
Definition at line 540 of file SimParameters.h.
Referenced by BondElem::computeForce(), HomePatch::hardWallDrude(), scriptSet(), and Sequencer::submitMinimizeReductions().
Definition at line 538 of file SimParameters.h.
Referenced by NamdState::loadStructure().
Definition at line 536 of file SimParameters.h.
Referenced by BondElem::computeForce(), Sequencer::hardWallDrude(), HomePatch::hardWallDrude(), Sequencer::newMinimizeDirection(), Sequencer::newMinimizePosition(), scriptSet(), and Sequencer::submitMinimizeReductions().
Definition at line 543 of file SimParameters.h.
Referenced by ComputeNonbondedUtil::select().
Definition at line 535 of file SimParameters.h.
Referenced by BondElem::computeForce(), Sequencer::langevinVelocitiesBBK1(), Sequencer::langevinVelocitiesBBK2(), NamdState::loadStructure(), WorkDistrib::mapComputes(), Parameters::Parameters(), Controller::printEnergies(), Controller::receivePressure(), Sequencer::reinitVelocities(), ComputeNonbondedUtil::select(), and Sequencer::submitReductions().
Definition at line 537 of file SimParameters.h.
Referenced by HomePatch::hardWallDrude(), and Sequencer::langevinVelocitiesBBK2().
Definition at line 123 of file SimParameters.h.
Referenced by Controller::berendsenPressure(), Controller::Controller(), ComputeEField::doForce(), colvarproxy_namd::dt(), Sequencer::integrate(), Controller::langevinPiston1(), Controller::langevinPiston2(), Controller::multigratorPressure(), Controller::multigratorTemperature(), Controller::printEnergies(), and ComputeQMMgr::recvPartQM().
Definition at line 863 of file SimParameters.h.
Referenced by ComputeEField::doForce(), and scriptSet().
Definition at line 864 of file SimParameters.h.
Referenced by ComputeEField::doForce(), and scriptSet().
Definition at line 862 of file SimParameters.h.
Referenced by ComputeEField::doForce().
Definition at line 861 of file SimParameters.h.
Referenced by WorkDistrib::mapComputes().
Definition at line 865 of file SimParameters.h.
Referenced by ComputeEField::doForce(), and scriptSet().
Definition at line 197 of file SimParameters.h.
Referenced by buildExclusions(), and ComputeNonbondedUtil::select().
Definition at line 671 of file SimParameters.h.
Referenced by NamdState::loadStructure(), Molecule::receive_Molecule(), and Molecule::send_Molecule().
| char SimParameters::extCoordFilename[128] |
Definition at line 461 of file SimParameters.h.
Referenced by ComputeExtMgr::recvCoord().
| char SimParameters::extForceFilename[128] |
Definition at line 462 of file SimParameters.h.
Referenced by ComputeExtMgr::recvCoord().
| char SimParameters::extForcesCommand[256] |
Definition at line 460 of file SimParameters.h.
Referenced by ComputeExtMgr::recvCoord().
Definition at line 459 of file SimParameters.h.
Referenced by WorkDistrib::mapComputes().
Definition at line 877 of file SimParameters.h.
Definition at line 878 of file SimParameters.h.
Definition at line 876 of file SimParameters.h.
Referenced by Molecule::delete_qm_bonded(), NamdState::loadStructure(), and Molecule::prepare_qm().
Definition at line 817 of file SimParameters.h.
Referenced by PmeXPencil::fft_init(), PmeYPencil::fft_init(), PmeZPencil::fft_init(), and ComputePmeMgr::initialize().
Definition at line 818 of file SimParameters.h.
Referenced by PmeXPencil::fft_init(), PmeYPencil::fft_init(), PmeZPencil::fft_init(), and ComputePmeMgr::initialize().
Definition at line 819 of file SimParameters.h.
| char SimParameters::FFTWWisdomFile[128] |
Definition at line 820 of file SimParameters.h.
Definition at line 821 of file SimParameters.h.
Referenced by receive_SimParameters(), and send_SimParameters().
Definition at line 141 of file SimParameters.h.
Referenced by LdbCoordinator::initialize(), and Controller::printEnergies().
Definition at line 901 of file SimParameters.h.
Referenced by Sequencer::adaptTempUpdate(), Controller::adaptTempUpdate(), Controller::algorithm(), colvarproxy_namd::colvarproxy_namd(), Output::coordinate(), Output::coordinateNeeded(), ComputeMgr::createComputes(), Output::force(), getCurrentLambda(), getLambdaDelta(), GlobalMasterSymmetry::GlobalMasterSymmetry(), GlobalMasterTMD::GlobalMasterTMD(), Sequencer::integrate(), Controller::integrate(), Sequencer::minimize(), Controller::minimize(), Controller::outputExtendedSystem(), Controller::outputFepEnergy(), Controller::outputTiEnergy(), Controller::printEnergies(), Controller::printTiming(), ComputeQMMgr::recvPartQM(), ComputeQMMgr::recvPntChrg(), Controller::rescaleaccelMD(), scriptSet(), Output::velocity(), and Controller::writeFepEnergyData().
Definition at line 677 of file SimParameters.h.
Referenced by Controller::langevinPiston1(), Controller::langevinPiston2(), Controller::receivePressure(), and scriptSet().
Definition at line 678 of file SimParameters.h.
Referenced by Controller::langevinPiston1(), Controller::langevinPiston2(), Controller::receivePressure(), and scriptSet().
Definition at line 679 of file SimParameters.h.
Referenced by Controller::langevinPiston1(), Controller::langevinPiston2(), Controller::receivePressure(), and scriptSet().
Definition at line 680 of file SimParameters.h.
Referenced by Controller::langevinPiston1(), Controller::langevinPiston2(), Controller::receivePressure(), and scriptSet().
Definition at line 565 of file SimParameters.h.
Referenced by CollectionMgr::submitForces().
Definition at line 564 of file SimParameters.h.
Referenced by ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), HomePatch::positionsReady(), scriptSet(), ComputeNonbondedUtil::select(), and ParallelIOMgr::updateMolInfo().
Definition at line 563 of file SimParameters.h.
Referenced by HomePatch::addForceToMomentum(), HomePatch::addForceToMomentum3(), Sequencer::addMovDragToPosition(), Sequencer::addRotDragToPosition(), HomePatch::addVelocityToPosition(), ParallelIOMgr::bcastHydroBasedCounter(), Sequencer::berendsenPressure(), HomePatch::buildRattleList(), ParallelIOMgr::calcAtomsInEachPatch(), Sequencer::calcFixVirial(), Sequencer::correctMomentum(), HomePatch::hardWallDrude(), Sequencer::langevinPiston(), NamdState::loadStructure(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), HomePatch::minimize_rattle2(), Sequencer::minimizeMoveDownhill(), HomePatch::mollyAverage(), HomePatch::mollyMollify(), Sequencer::multigratorPressure(), Sequencer::newMinimizeDirection(), HomePatch::positionsReady(), Molecule::prepare_qm(), HomePatch::rattle1(), HomePatch::rattle1old(), HomePatch::rattle2(), Sequencer::reassignVelocities(), Molecule::receive_Molecule(), Controller::receivePressure(), ParallelIOMgr::recvAtomsCntPerPatch(), Sequencer::reinitVelocities(), ComputeGlobal::saveTotalForces(), Sequencer::scalePositionsVelocities(), scriptSet(), ComputeNonbondedUtil::select(), Molecule::send_Molecule(), Sequencer::submitMinimizeReductions(), and Sequencer::submitReductions().
Definition at line 724 of file SimParameters.h.
Definition at line 723 of file SimParameters.h.
Definition at line 721 of file SimParameters.h.
Definition at line 722 of file SimParameters.h.
Definition at line 720 of file SimParameters.h.
Referenced by ComputeGlobal::ComputeGlobal(), WorkDistrib::mapComputes(), WorkDistrib::patchMapInit(), and ComputeNonbondedUtil::select().
Definition at line 137 of file SimParameters.h.
Definition at line 768 of file SimParameters.h.
Referenced by ComputeFmmSerialMgr::recvCoord().
Definition at line 767 of file SimParameters.h.
Referenced by WorkDistrib::mapComputes(), WorkDistrib::patchMapInit(), and ComputeNonbondedUtil::select().
Definition at line 769 of file SimParameters.h.
Referenced by ComputeFmmSerialMgr::recvCoord().
| char SimParameters::forceDcdFilename[128] |
Definition at line 214 of file SimParameters.h.
Definition at line 207 of file SimParameters.h.
Referenced by Output::force(), Output::forceNeeded(), and Output::velocity().
Definition at line 559 of file SimParameters.h.
Referenced by ComputeMgr::createComputes(), and ParallelIOMgr::freeMolSpace().
Definition at line 521 of file SimParameters.h.
Referenced by ComputeNonbondedSelf::doForce(), ComputeNonbondedPair::doForce(), and ComputeNonbondedCUDA::recvYieldDevice().
Definition at line 726 of file SimParameters.h.
Referenced by ComputeGlobal::ComputeGlobal(), WorkDistrib::mapComputes(), and ComputeNonbondedUtil::select().
Definition at line 135 of file SimParameters.h.
Referenced by Controller::compareChecksums(), Sequencer::integrate(), Controller::integrate(), Sequencer::minimize(), and Sequencer::runComputeObjects().
Definition at line 528 of file SimParameters.h.
Referenced by ComputeNonbondedSelf::doForce(), ComputeNonbondedPair::doForce(), HomePatch::gbisComputeAfterP1(), and HomePatch::gbisComputeAfterP2().
Definition at line 527 of file SimParameters.h.
Referenced by ComputeNonbondedSelf::doForce(), ComputeNonbondedPair::doForce(), HomePatch::gbisComputeAfterP1(), and HomePatch::gbisComputeAfterP2().
Definition at line 529 of file SimParameters.h.
Referenced by ComputeNonbondedSelf::doForce(), ComputeNonbondedPair::doForce(), HomePatch::gbisComputeAfterP1(), and HomePatch::gbisComputeAfterP2().
Definition at line 520 of file SimParameters.h.
Referenced by ComputeGlobal::ComputeGlobal(), ComputeNonbondedCUDA::ComputeNonbondedCUDA(), ComputeCUDAMgr::createCudaComputeNonbonded(), CudaComputeNonbonded::CudaComputeNonbonded(), CudaComputeNonbonded::doWork(), ComputeNonbondedCUDA::doWork(), CudaComputeNonbonded::finishReductions(), ComputeNonbondedCUDA::finishReductions(), ComputeNonbondedCUDA::finishWork(), Sequencer::integrate(), CudaComputeNonbonded::launchWork(), Sequencer::minimize(), ComputeNonbondedCUDA::noWork(), ComputeNonbondedCUDA::recvYieldDevice(), ComputeNonbondedCUDA::registerPatches(), and ComputeNonbondedCUDA::skip().
Definition at line 522 of file SimParameters.h.
Referenced by ComputeGlobal::ComputeGlobal(), and WorkDistrib::mapComputes().
Definition at line 1012 of file SimParameters.h.
Referenced by NamdState::configListInit(), and NamdState::loadStructure().
Definition at line 551 of file SimParameters.h.
Referenced by ComputeMgr::createComputes(), and WorkDistrib::mapComputes().
Definition at line 582 of file SimParameters.h.
| char SimParameters::goCoordinates[128] |
Definition at line 302 of file SimParameters.h.
Definition at line 300 of file SimParameters.h.
Referenced by NamdState::loadStructure(), Controller::printEnergies(), Molecule::receive_GoMolecule(), ComputeNonbondedUtil::select(), and Molecule::send_GoMolecule().
Definition at line 299 of file SimParameters.h.
Referenced by Controller::compareChecksums(), WorkDistrib::mapComputes(), Controller::printEnergies(), Molecule::receive_Molecule(), ComputeNonbondedUtil::select(), and Molecule::send_Molecule().
Definition at line 304 of file SimParameters.h.
Referenced by NamdState::loadStructure(), Molecule::receive_GoMolecule(), ComputeNonbondedUtil::select(), and Molecule::send_GoMolecule().
| char SimParameters::goParameters[128] |
Definition at line 301 of file SimParameters.h.
Definition at line 274 of file SimParameters.h.
Definition at line 269 of file SimParameters.h.
Definition at line 270 of file SimParameters.h.
Definition at line 271 of file SimParameters.h.
Definition at line 273 of file SimParameters.h.
Definition at line 266 of file SimParameters.h.
Definition at line 268 of file SimParameters.h.
Definition at line 272 of file SimParameters.h.
Definition at line 267 of file SimParameters.h.
Definition at line 995 of file SimParameters.h.
Referenced by NamdState::loadStructure().
Definition at line 969 of file SimParameters.h.
Definition at line 913 of file SimParameters.h.
Referenced by HomePatch::doGroupSizeCheck().
Definition at line 145 of file SimParameters.h.
Referenced by NamdHybridLB::NamdHybridLB().
Definition at line 959 of file SimParameters.h.
Definition at line 910 of file SimParameters.h.
Definition at line 981 of file SimParameters.h.
Referenced by Output::coordinate(), Output::coordinateNeeded(), and Controller::printEnergies().
Definition at line 984 of file SimParameters.h.
Referenced by ComputeMgr::createComputes(), and GlobalMasterIMD::GlobalMasterIMD().
Definition at line 986 of file SimParameters.h.
Referenced by ComputeMgr::createComputes(), and GlobalMasterIMD::GlobalMasterIMD().
Definition at line 979 of file SimParameters.h.
Referenced by Output::coordinate(), Output::coordinateNeeded(), ComputeMgr::createComputes(), and Controller::printEnergies().
Definition at line 980 of file SimParameters.h.
Referenced by GlobalMasterIMD::GlobalMasterIMD().
Definition at line 982 of file SimParameters.h.
Referenced by GlobalMasterIMD::get_vmd_forces(), and GlobalMasterIMD::GlobalMasterIMD().
Definition at line 187 of file SimParameters.h.
Referenced by Controller::adaptTempInit(), Controller::algorithm(), WorkDistrib::createAtomLists(), Sequencer::integrate(), Sequencer::reinitVelocities(), and scriptSet().
Definition at line 526 of file SimParameters.h.
Definition at line 525 of file SimParameters.h.
Referenced by ComputeNonbondedSelf::doForce(), ComputeNonbondedPair::doForce(), HomePatch::gbisComputeAfterP2(), and ComputeNonbondedCUDA::recvYieldDevice().
Definition at line 572 of file SimParameters.h.
Referenced by Sequencer::integrate(), Sequencer::langevinVelocities(), Sequencer::langevinVelocitiesBBK1(), Sequencer::langevinVelocitiesBBK2(), and scriptSet().
Definition at line 570 of file SimParameters.h.
Referenced by NamdState::loadStructure().
Definition at line 571 of file SimParameters.h.
Referenced by NamdState::loadStructure().
Definition at line 568 of file SimParameters.h.
Referenced by Controller::adaptTempInit(), Sequencer::adaptTempUpdate(), colvarproxy_namd::colvarproxy_namd(), Sequencer::integrate(), Sequencer::langevinVelocities(), Sequencer::langevinVelocitiesBBK1(), Sequencer::langevinVelocitiesBBK2(), NamdState::loadStructure(), Molecule::receive_Molecule(), Controller::receivePressure(), scriptSet(), and Molecule::send_Molecule().
Definition at line 567 of file SimParameters.h.
Referenced by scriptSet().
Definition at line 689 of file SimParameters.h.
Referenced by Controller::langevinPiston1().
Definition at line 692 of file SimParameters.h.
Referenced by Controller::langevinPiston1(), Controller::langevinPiston2(), and scriptSet().
Definition at line 688 of file SimParameters.h.
Referenced by ComputeGridForce::doForce(), Sequencer::integrate(), Sequencer::langevinPiston(), Controller::langevinPiston1(), Controller::langevinPiston2(), scriptSet(), Controller::writeExtendedSystemData(), and Controller::writeExtendedSystemLabels().
Definition at line 691 of file SimParameters.h.
Referenced by Controller::langevinPiston1(), Controller::langevinPiston2(), and scriptSet().
Definition at line 690 of file SimParameters.h.
Referenced by Controller::langevinPiston1(), Controller::langevinPiston2(), and scriptSet().
Definition at line 693 of file SimParameters.h.
Referenced by Controller::langevinPiston1(), Controller::langevinPiston2(), and scriptSet().
Definition at line 569 of file SimParameters.h.
Referenced by Controller::adaptTempInit(), Sequencer::adaptTempUpdate(), colvarproxy_namd::colvarproxy_namd(), Sequencer::integrate(), Sequencer::langevinVelocities(), Sequencer::langevinVelocitiesBBK2(), and scriptSet().
Definition at line 143 of file SimParameters.h.
Referenced by LdbCoordinator::initialize().
Definition at line 131 of file SimParameters.h.
Referenced by ParallelIOMgr::bcastHydroBasedCounter(), ParallelIOMgr::calcAtomsInEachPatch(), NamdState::configListInit(), WorkDistrib::createAtomLists(), GlobalMasterServer::GlobalMasterServer(), GridforceFullMainGrid::initialize(), ComputePmeMgr::initialize(), ComputeMsmMgr::initialize(), ComputePmeMgr::initialize_pencils(), Patch::Patch(), WorkDistrib::patchMapInit(), readExtendedSystem(), and Node::startup().
Definition at line 532 of file SimParameters.h.
Referenced by Sequencer::integrate(), WorkDistrib::mapComputes(), Sequencer::minimize(), Molecule::Molecule(), WorkDistrib::patchMapInit(), Molecule::receive_Molecule(), Molecule::send_Molecule(), NamdHybridLB::splitComputes(), and NamdCentLB::Strategy().
Definition at line 138 of file SimParameters.h.
Referenced by LdbCoordinator::createLoadBalancer().
Definition at line 146 of file SimParameters.h.
Definition at line 148 of file SimParameters.h.
Definition at line 140 of file SimParameters.h.
Referenced by LdbCoordinator::initialize().
Definition at line 147 of file SimParameters.h.
Definition at line 149 of file SimParameters.h.
Referenced by NamdHybridLB::splitComputes(), and NamdCentLB::Strategy().
Definition at line 139 of file SimParameters.h.
Referenced by NamdCentLB::Strategy().
Definition at line 181 of file SimParameters.h.
Definition at line 182 of file SimParameters.h.
Definition at line 179 of file SimParameters.h.
Definition at line 180 of file SimParameters.h.
Definition at line 441 of file SimParameters.h.
Referenced by Sequencer::langevinVelocities(), Sequencer::langevinVelocitiesBBK2(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), Sequencer::reassignVelocities(), Sequencer::reinitVelocities(), ComputePmeUtil::select(), and ComputeNonbondedUtil::select().
Definition at line 440 of file SimParameters.h.
Referenced by WorkDistrib::createAtomLists(), ComputePmeCUDA::initialize(), Sequencer::langevinVelocities(), Sequencer::langevinVelocitiesBBK2(), NamdState::loadStructure(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), Sequencer::reassignVelocities(), Molecule::receive_Molecule(), Sequencer::reinitVelocities(), ComputePmeUtil::select(), ComputeNonbondedUtil::select(), and Molecule::send_Molecule().
Definition at line 443 of file SimParameters.h.
Definition at line 442 of file SimParameters.h.
Referenced by Sequencer::langevinVelocities(), Sequencer::langevinVelocitiesBBK2(), Sequencer::reassignVelocities(), and Sequencer::reinitVelocities().
Definition at line 237 of file SimParameters.h.
Referenced by ComputeNonbondedUtil::select().
Definition at line 122 of file SimParameters.h.
Referenced by Controller::calcPressure(), NamdState::loadStructure(), Controller::printEnergies(), and Controller::rescaleaccelMD().
Definition at line 1039 of file SimParameters.h.
Referenced by WorkDistrib::mapComputes().
Definition at line 119 of file SimParameters.h.
Referenced by Sequencer::integrate(), and Sequencer::minimize().
Definition at line 907 of file SimParameters.h.
Referenced by ComputeNonbondedUtil::select().
Definition at line 579 of file SimParameters.h.
Definition at line 576 of file SimParameters.h.
Referenced by colvarproxy_namd::colvarproxy_namd(), and Sequencer::integrate().
Definition at line 578 of file SimParameters.h.
Definition at line 577 of file SimParameters.h.
Referenced by colvarproxy_namd::colvarproxy_namd(), and scriptSet().
Definition at line 1016 of file SimParameters.h.
Referenced by Node::startup().
Definition at line 231 of file SimParameters.h.
Referenced by HomePatch::doMarginCheck().
Definition at line 247 of file SimParameters.h.
Definition at line 245 of file SimParameters.h.
Referenced by ComputeNonbondedUtil::select().
Definition at line 947 of file SimParameters.h.
Definition at line 833 of file SimParameters.h.
Referenced by Sequencer::maximumMove(), and scriptSet().
Definition at line 935 of file SimParameters.h.
Definition at line 178 of file SimParameters.h.
Referenced by WorkDistrib::patchMapInit().
Definition at line 933 of file SimParameters.h.
Definition at line 899 of file SimParameters.h.
Referenced by Controller::printEnergies().
Definition at line 277 of file SimParameters.h.
Referenced by Molecule::build_gridforce_params(), receive_SimParameters(), Node::reloadGridforceGrid(), send_SimParameters(), and Node::updateGridScale().
Definition at line 276 of file SimParameters.h.
Referenced by NamdState::loadStructure(), WorkDistrib::mapComputes(), Molecule::receive_Molecule(), and Molecule::send_Molecule().
Definition at line 1047 of file SimParameters.h.
Definition at line 1042 of file SimParameters.h.
Definition at line 1044 of file SimParameters.h.
Definition at line 1045 of file SimParameters.h.
Definition at line 1043 of file SimParameters.h.
Definition at line 1048 of file SimParameters.h.
Definition at line 1046 of file SimParameters.h.
Definition at line 945 of file SimParameters.h.
Referenced by WorkDistrib::patchMapInit().
Definition at line 830 of file SimParameters.h.
Definition at line 827 of file SimParameters.h.
Referenced by NamdState::loadStructure(), and ScriptTcl::run().
Definition at line 832 of file SimParameters.h.
Referenced by Sequencer::minimizationQuenchVelocity(), and scriptSet().
Definition at line 831 of file SimParameters.h.
Referenced by Controller::minimize().
Definition at line 829 of file SimParameters.h.
Definition at line 828 of file SimParameters.h.
Referenced by Controller::minimize().
Definition at line 560 of file SimParameters.h.
Referenced by ComputeMgr::createComputes().
Definition at line 917 of file SimParameters.h.
Referenced by HomePatch::mollyAverage().
Definition at line 915 of file SimParameters.h.
Referenced by Controller::compareChecksums(), Sequencer::integrate(), and Sequencer::minimize().
Definition at line 916 of file SimParameters.h.
Referenced by HomePatch::mollyAverage().
| char SimParameters::movDragFile[128] |
Definition at line 322 of file SimParameters.h.
Definition at line 324 of file SimParameters.h.
Referenced by Sequencer::addMovDragToPosition().
Definition at line 321 of file SimParameters.h.
Referenced by Sequencer::integrate(), NamdState::loadStructure(), Molecule::receive_Molecule(), and Molecule::send_Molecule().
| char SimParameters::movDragVelFile[128] |
Definition at line 325 of file SimParameters.h.
Definition at line 308 of file SimParameters.h.
Referenced by ComputeRestraints::ComputeRestraints().
Definition at line 310 of file SimParameters.h.
Referenced by ComputeRestraints::ComputeRestraints().
Definition at line 736 of file SimParameters.h.
Referenced by ComputeMsmMgr::initialize(), and ComputeMsmSerialMgr::recvCoord().
Definition at line 746 of file SimParameters.h.
Referenced by ComputeMsmMgr::initialize().
Definition at line 747 of file SimParameters.h.
Referenced by ComputeMsmMgr::initialize().
Definition at line 748 of file SimParameters.h.
Referenced by ComputeMsmMgr::initialize().
Definition at line 750 of file SimParameters.h.
Referenced by ComputeMsmMgr::initialize(), and ComputeMsmSerialMgr::recvCoord().
Definition at line 742 of file SimParameters.h.
Referenced by ComputeMsmMgr::initialize(), and ComputeMsmSerialMgr::recvCoord().
Definition at line 729 of file SimParameters.h.
Referenced by WorkDistrib::mapComputes(), WorkDistrib::patchMapInit(), ComputeNonbondedUtil::select(), and Node::startup().
Definition at line 752 of file SimParameters.h.
Referenced by ComputeMsmMgr::initialize(), and ComputeMsmSerialMgr::recvCoord().
Definition at line 732 of file SimParameters.h.
Definition at line 765 of file SimParameters.h.
Referenced by WorkDistrib::mapComputes(), and Node::startup().
Definition at line 739 of file SimParameters.h.
Referenced by ComputeMsmMgr::initialize(), ComputeMsmSerialMgr::recvCoord(), and ComputeNonbondedUtil::select().
Definition at line 759 of file SimParameters.h.
Referenced by ComputeMsmMgr::initialize().
Definition at line 758 of file SimParameters.h.
Referenced by ComputeMsmMgr::initialize().
Definition at line 761 of file SimParameters.h.
Referenced by ComputeMsmMgr::initialize().
Definition at line 760 of file SimParameters.h.
Referenced by ComputeMsmMgr::initialize().
Definition at line 763 of file SimParameters.h.
Referenced by ComputeMsmMgr::initialize().
Definition at line 762 of file SimParameters.h.
Referenced by ComputeMsmMgr::initialize().
Definition at line 904 of file SimParameters.h.
Referenced by Sequencer::integrate().
Definition at line 702 of file SimParameters.h.
Referenced by Controller::Controller(), Controller::multigatorCalcEnthalpy(), and Controller::multigratorTemperature().
Definition at line 695 of file SimParameters.h.
Referenced by Controller::Controller(), LdbCoordinator::initialize(), Sequencer::integrate(), Sequencer::multigratorPressure(), Controller::multigratorPressure(), Sequencer::multigratorTemperature(), Controller::multigratorTemperature(), Controller::printEnergies(), Sequencer::Sequencer(), and Sequencer::submitHalfstep().
Definition at line 698 of file SimParameters.h.
Referenced by LdbCoordinator::initialize(), Sequencer::integrate(), Sequencer::multigratorPressure(), Controller::multigratorPressure(), Sequencer::multigratorTemperature(), and Controller::multigratorTemperature().
Definition at line 697 of file SimParameters.h.
Referenced by Controller::multigatorCalcEnthalpy(), and Controller::multigratorPressure().
Definition at line 696 of file SimParameters.h.
Referenced by Controller::multigatorCalcEnthalpy(), and Controller::multigratorPressure().
Definition at line 701 of file SimParameters.h.
Referenced by Sequencer::integrate(), Sequencer::multigratorTemperature(), and Controller::multigratorTemperature().
Definition at line 700 of file SimParameters.h.
Referenced by Controller::Controller(), and Controller::multigratorTemperature().
Definition at line 699 of file SimParameters.h.
Referenced by Controller::Controller(), Controller::multigatorCalcEnthalpy(), Controller::multigratorPressure(), and Controller::multigratorTemperature().
| int SimParameters::N |
Definition at line 124 of file SimParameters.h.
Referenced by colvarproxy_namd::calculate(), Output::coordinate(), Sequencer::integrate(), Controller::integrate(), Sequencer::minimize(), Controller::minimize(), Sequencer::multigratorPressure(), Controller::outputExtendedSystem(), Controller::outputFepEnergy(), Controller::printEnergies(), Controller::printTiming(), Controller::rescaleaccelMD(), scriptSet(), and Output::velocity().
Definition at line 133 of file SimParameters.h.
Referenced by Sequencer::integrate(), and Controller::integrate().
Definition at line 201 of file SimParameters.h.
Referenced by ComputeQMMgr::recvPntChrg(), ComputeNonbondedCUDA::recvYieldDevice(), scriptSet(), and ComputeNonbondedUtil::select().
Definition at line 185 of file SimParameters.h.
Referenced by WorkDistrib::patchMapInit().
Definition at line 184 of file SimParameters.h.
Referenced by WorkDistrib::patchMapInit().
Definition at line 183 of file SimParameters.h.
Referenced by WorkDistrib::patchMapInit().
Definition at line 941 of file SimParameters.h.
Definition at line 943 of file SimParameters.h.
Definition at line 937 of file SimParameters.h.
Definition at line 939 of file SimParameters.h.
Definition at line 1027 of file SimParameters.h.
Referenced by ParallelIOMgr::initialize(), and NamdState::loadStructure().
Definition at line 1034 of file SimParameters.h.
Referenced by ParallelIOMgr::initialize(), NamdState::loadStructure(), and WorkDistrib::patchMapInit().
Definition at line 1035 of file SimParameters.h.
Referenced by ParallelIOMgr::initialize(), and NamdState::loadStructure().
Definition at line 152 of file SimParameters.h.
Referenced by Sequencer::integrate(), and Controller::integrate().
Definition at line 893 of file SimParameters.h.
Referenced by ComputeNonbondedCUDA::finishReductions().
Definition at line 884 of file SimParameters.h.
Referenced by Sequencer::integrate(), Controller::printEnergies(), Controller::printTiming(), scriptSet(), and setupIDWS().
| char SimParameters::outputFilename[128] |
Definition at line 216 of file SimParameters.h.
Referenced by colvarproxy_namd::colvarproxy_namd(), Controller::outputExtendedSystem(), ComputeQMMgr::recvPartQM(), and scriptSet().
Definition at line 160 of file SimParameters.h.
Referenced by Node::outputPatchComputeMaps().
Definition at line 887 of file SimParameters.h.
Referenced by Sequencer::integrate(), and Controller::printEnergies().
Definition at line 259 of file SimParameters.h.
Referenced by Controller::compareChecksums(), and Controller::printEnergies().
Definition at line 949 of file SimParameters.h.
Referenced by WorkDistrib::createAtomLists().
Definition at line 896 of file SimParameters.h.
Referenced by Sequencer::integrate(), and Controller::printEnergies().
Definition at line 890 of file SimParameters.h.
Referenced by Controller::printTiming().
Definition at line 546 of file SimParameters.h.
Definition at line 547 of file SimParameters.h.
Definition at line 545 of file SimParameters.h.
Referenced by Sequencer::calcKineticEnergy(), WorkDistrib::createAtomLists(), ComputePmeCUDA::initialize(), NamdState::loadStructure(), WorkDistrib::mapComputes(), Sequencer::multigratorPressure(), Controller::printEnergies(), Molecule::receive_Molecule(), Controller::receivePressure(), ComputePmeUtil::select(), ComputeNonbondedUtil::select(), Molecule::send_Molecule(), Sequencer::submitHalfstep(), and Sequencer::submitReductions().
Definition at line 548 of file SimParameters.h.
Referenced by Sequencer::calcKineticEnergy(), NamdState::loadStructure(), WorkDistrib::mapComputes(), Sequencer::multigratorPressure(), ComputePmeUtil::select(), ComputeNonbondedUtil::select(), Sequencer::submitHalfstep(), and Sequencer::submitReductions().
Definition at line 249 of file SimParameters.h.
Definition at line 257 of file SimParameters.h.
Referenced by HomePatch::doPairlistCheck().
Definition at line 251 of file SimParameters.h.
Definition at line 256 of file SimParameters.h.
Referenced by HomePatch::doPairlistCheck().
Definition at line 255 of file SimParameters.h.
Referenced by Sequencer::runComputeObjects().
Definition at line 258 of file SimParameters.h.
Referenced by HomePatch::doPairlistCheck().
Definition at line 295 of file SimParameters.h.
Referenced by ParallelIOMgr::bcastHydroBasedCounter(), NamdState::loadStructure(), and Parameters::Parameters().
Definition at line 294 of file SimParameters.h.
Referenced by ParallelIOMgr::bcastHydroBasedCounter(), NamdState::loadStructure(), and Parameters::Parameters().
Definition at line 232 of file SimParameters.h.
Referenced by HomePatch::doMarginCheck(), ComputePmeMgr::initialize(), ComputePmeMgr::initialize_pencils(), and WorkDistrib::patchMapInit().
Definition at line 782 of file SimParameters.h.
Referenced by ComputePmeMgr::initialize().
Definition at line 773 of file SimParameters.h.
Referenced by ComputeQMMgr::recvPntChrg(), and ComputeNonbondedUtil::select().
Definition at line 775 of file SimParameters.h.
Referenced by ComputePme::ComputePme(), ComputePmeMgr::initialize(), and ComputePmeCUDAMgr::setupPencils().
Definition at line 776 of file SimParameters.h.
Referenced by ComputePme::ComputePme(), ComputePmeMgr::initialize(), and ComputePmeCUDAMgr::setupPencils().
Definition at line 777 of file SimParameters.h.
Referenced by ComputePme::ComputePme(), ComputePmeMgr::initialize(), and ComputePmeCUDAMgr::setupPencils().
Definition at line 778 of file SimParameters.h.
Definition at line 774 of file SimParameters.h.
Referenced by ComputePme::ComputePme(), ComputePmeMgr::initialize(), and ComputePmeCUDAMgr::setupPencils().
Definition at line 781 of file SimParameters.h.
Referenced by ComputePmeMgr::initialize().
Definition at line 780 of file SimParameters.h.
Referenced by ComputePmeMgr::initialize().
Definition at line 790 of file SimParameters.h.
Referenced by ComputeNonbondedCUDA::ComputeNonbondedCUDA(), ComputePme::ComputePme(), ComputePmeMgr::initialize(), PmePencil< CBase_PmeZPencil >::order_init(), and ComputeNonbondedCUDA::recvYieldDevice().
Definition at line 771 of file SimParameters.h.
Referenced by ComputeGlobal::ComputeGlobal(), ComputeNonbondedCUDA::ComputeNonbondedCUDA(), WorkDistrib::mapComputes(), Molecule::prepare_qm(), Controller::printEnergies(), ComputeQMMgr::procQMRes(), HomePatch::qmSwapAtoms(), ComputeQMMgr::recvPntChrg(), ComputeNonbondedCUDA::recvYieldDevice(), Node::resendMolecule(), scriptSet(), ComputeNonbondedUtil::select(), and Node::startup().
Definition at line 783 of file SimParameters.h.
Referenced by ComputePmeMgr::initialize().
Definition at line 784 of file SimParameters.h.
Referenced by ComputePmeMgr::initialize(), and ComputePmeCUDAMgr::setupPencils().
Definition at line 788 of file SimParameters.h.
Referenced by ComputePmeMgr::initialize().
Definition at line 785 of file SimParameters.h.
Referenced by ComputePmeMgr::initialize(), and ComputePmeCUDAMgr::setupPencils().
Definition at line 787 of file SimParameters.h.
Referenced by ComputePmeMgr::initialize().
Definition at line 786 of file SimParameters.h.
Referenced by ComputePmeMgr::initialize(), and ComputePmeCUDAMgr::setupPencils().
Definition at line 779 of file SimParameters.h.
Referenced by ComputePmeMgr::initialize().
Definition at line 789 of file SimParameters.h.
Referenced by ComputePmeMgr::initialize_pencils().
Definition at line 772 of file SimParameters.h.
Definition at line 709 of file SimParameters.h.
Referenced by ComputeEwald::ComputeEwald(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::ComputeHomeTuples(), Controller::Controller(), WorkDistrib::createAtomLists(), NamdState::loadStructure(), ComputeNonbondedUtil::select(), and Sequencer::Sequencer().
Definition at line 710 of file SimParameters.h.
Referenced by Controller::Controller(), and WorkDistrib::mapComputes().
Definition at line 711 of file SimParameters.h.
Referenced by ComputeEwald::ComputeEwald().
Definition at line 712 of file SimParameters.h.
Referenced by ComputeEwald::ComputeEwald().
Definition at line 713 of file SimParameters.h.
Referenced by ComputeEwald::ComputeEwald().
Definition at line 708 of file SimParameters.h.
Referenced by Controller::Controller(), and Controller::printEnergies().
Definition at line 706 of file SimParameters.h.
Referenced by ComputeHomeTuples< TholeElem, Thole, TholeValue >::ComputeHomeTuples(), ComputeNonbondedCUDA::ComputeNonbondedCUDA(), Controller::Controller(), CudaComputeNonbonded::CudaComputeNonbonded(), ComputeNonbondedUtil::select(), and Sequencer::Sequencer().
Definition at line 707 of file SimParameters.h.
Referenced by ComputeEwald::ComputeEwald(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::ComputeHomeTuples(), Controller::Controller(), HomePatch::hardWallDrude(), HomePatch::rattle1old(), ComputeNonbondedUtil::select(), Sequencer::Sequencer(), Sequencer::submitHalfstep(), and Sequencer::submitReductions().
Definition at line 517 of file SimParameters.h.
Referenced by Sequencer::submitMinimizeReductions().
Definition at line 1017 of file SimParameters.h.
Definition at line 1021 of file SimParameters.h.
Referenced by isRecvSpanningTreeOn(), and isRecvSpanningTreeUnset().
Definition at line 1020 of file SimParameters.h.
Referenced by isSendSpanningTreeOn(), and isSendSpanningTreeUnset().
Definition at line 1023 of file SimParameters.h.
Referenced by Node::startup().
| char SimParameters::qmBaseDir[256] |
Definition at line 475 of file SimParameters.h.
Referenced by ComputeQMMgr::recvPntChrg().
| char SimParameters::qmBondColumn[16] |
Definition at line 485 of file SimParameters.h.
Definition at line 486 of file SimParameters.h.
Referenced by Molecule::prepare_qm().
Definition at line 484 of file SimParameters.h.
Referenced by Molecule::prepare_qm().
Definition at line 490 of file SimParameters.h.
Referenced by Molecule::prepare_qm().
| char SimParameters::qmBondSchemeS[16] |
Definition at line 489 of file SimParameters.h.
Definition at line 487 of file SimParameters.h.
Referenced by ComputeQMMgr::recvPartQM().
| char SimParameters::qmBondValueTypeS[16] |
Definition at line 488 of file SimParameters.h.
Definition at line 469 of file SimParameters.h.
Referenced by Molecule::prepare_qm().
Definition at line 473 of file SimParameters.h.
Referenced by ComputeQMMgr::recvPntChrg().
| char SimParameters::qmChrgModeS[16] |
Definition at line 472 of file SimParameters.h.
| char SimParameters::qmColumn[16] |
Definition at line 474 of file SimParameters.h.
Referenced by Molecule::prepare_qm().
Definition at line 510 of file SimParameters.h.
Referenced by Molecule::prepare_qm().
| char SimParameters::qmCSMDFile[128] |
Definition at line 511 of file SimParameters.h.
Definition at line 502 of file SimParameters.h.
Referenced by ComputeQM::initialize(), Molecule::prepare_qm(), and ComputeQMMgr::recvPartQM().
Definition at line 500 of file SimParameters.h.
Referenced by Molecule::prepare_qm().
Definition at line 513 of file SimParameters.h.
Referenced by ComputeQMMgr::storeQMRes().
| char SimParameters::qmExecPath[256] |
Definition at line 470 of file SimParameters.h.
Referenced by ComputeQMMgr::recvPntChrg().
Definition at line 466 of file SimParameters.h.
Referenced by Controller::compareChecksums(), ComputePme::ComputePme(), NamdState::loadStructure(), WorkDistrib::mapComputes(), Controller::printEnergies(), Molecule::receive_Molecule(), ComputeNonbondedUtil::select(), and Molecule::send_Molecule().
Definition at line 480 of file SimParameters.h.
Referenced by Molecule::prepare_qm(), and ComputeQMMgr::recvPntChrg().
Definition at line 505 of file SimParameters.h.
Referenced by Molecule::prepare_qm().
Definition at line 508 of file SimParameters.h.
Referenced by Molecule::prepare_qm().
| char SimParameters::qmLSSModeS[16] |
Definition at line 507 of file SimParameters.h.
Definition at line 504 of file SimParameters.h.
Referenced by HomePatch::positionsReady(), Molecule::prepare_qm(), and ComputeQMMgr::recvPartQM().
| char SimParameters::qmLSSResname[5] |
Definition at line 506 of file SimParameters.h.
Referenced by Molecule::prepare_qm().
Definition at line 482 of file SimParameters.h.
Referenced by Molecule::prepare_qm(), and ComputeQMMgr::recvPntChrg().
Definition at line 499 of file SimParameters.h.
Referenced by Molecule::prepare_qm(), and ComputeQMMgr::recvPartQM().
Definition at line 514 of file SimParameters.h.
Referenced by ComputeQMMgr::procQMRes(), and ComputeQMMgr::recvPartQM().
| char SimParameters::qmParamPDB[128] |
Definition at line 467 of file SimParameters.h.
Referenced by NamdState::loadStructure().
Definition at line 468 of file SimParameters.h.
Referenced by NamdState::loadStructure().
Definition at line 495 of file SimParameters.h.
Referenced by ComputeQMMgr::recvPntChrg().
| char SimParameters::qmPCSchemeS[16] |
Definition at line 494 of file SimParameters.h.
Definition at line 501 of file SimParameters.h.
Referenced by Molecule::prepare_qm().
Definition at line 491 of file SimParameters.h.
Referenced by ComputeQMMgr::recvPntChrg().
Definition at line 493 of file SimParameters.h.
Referenced by ComputeQMMgr::recvPntChrg().
| char SimParameters::qmPCSwitchTypeS[16] |
Definition at line 492 of file SimParameters.h.
Definition at line 515 of file SimParameters.h.
Referenced by ComputeQMMgr::procQMRes(), and ComputeQMMgr::recvPartQM().
| char SimParameters::qmPrepProc[256] |
Definition at line 478 of file SimParameters.h.
Referenced by ComputeQMMgr::recvPntChrg().
Definition at line 479 of file SimParameters.h.
Referenced by ComputeQMMgr::recvPntChrg().
Definition at line 481 of file SimParameters.h.
Referenced by NamdState::loadStructure().
| char SimParameters::qmSecProc[256] |
Definition at line 476 of file SimParameters.h.
Referenced by ComputeQMMgr::recvPntChrg().
Definition at line 477 of file SimParameters.h.
Referenced by ComputeQMMgr::recvPntChrg().
Definition at line 496 of file SimParameters.h.
Referenced by ComputeQMMgr::recvPartQM().
| char SimParameters::qmSoftware[128] |
Definition at line 471 of file SimParameters.h.
Definition at line 498 of file SimParameters.h.
Referenced by Molecule::prepare_qm().
| unsigned int SimParameters::randomSeed |
Definition at line 718 of file SimParameters.h.
Referenced by colvarproxy_namd::colvarproxy_namd(), Controller::Controller(), Sequencer::Sequencer(), and Node::startup().
Definition at line 991 of file SimParameters.h.
Referenced by buildExclusions().
Definition at line 663 of file SimParameters.h.
Referenced by colvarproxy_namd::colvarproxy_namd(), Sequencer::integrate(), Sequencer::reassignVelocities(), and Controller::reassignVelocities().
Definition at line 666 of file SimParameters.h.
Referenced by Sequencer::reassignVelocities(), and Controller::reassignVelocities().
Definition at line 665 of file SimParameters.h.
Referenced by Sequencer::reassignVelocities(), and Controller::reassignVelocities().
Definition at line 664 of file SimParameters.h.
Referenced by colvarproxy_namd::colvarproxy_namd(), Sequencer::reassignVelocities(), Controller::reassignVelocities(), and scriptSet().
Definition at line 951 of file SimParameters.h.
Referenced by WorkDistrib::patchMapInit().
Definition at line 614 of file SimParameters.h.
Referenced by Controller::adaptTempInit(), colvarproxy_namd::colvarproxy_namd(), Sequencer::integrate(), Sequencer::rescaleVelocities(), and Controller::rescaleVelocities().
Definition at line 615 of file SimParameters.h.
Referenced by Controller::adaptTempInit(), colvarproxy_namd::colvarproxy_namd(), Sequencer::integrate(), Controller::rescaleVelocities(), and scriptSet().
| char SimParameters::restartFilename[128] |
Definition at line 221 of file SimParameters.h.
Referenced by colvarproxy_namd::colvarproxy_namd(), Controller::outputExtendedSystem(), and scriptSet().
Definition at line 222 of file SimParameters.h.
Referenced by colvarproxy_namd::colvarproxy_namd(), Output::coordinate(), Output::coordinateNeeded(), Controller::outputExtendedSystem(), Controller::rescaleaccelMD(), Output::velocity(), and Output::velocityNeeded().
Definition at line 224 of file SimParameters.h.
Referenced by Controller::outputExtendedSystem().
Definition at line 225 of file SimParameters.h.
Definition at line 919 of file SimParameters.h.
Referenced by ParallelIOMgr::bcastHydroBasedCounter(), NamdState::configListInit(), WorkDistrib::createAtomLists(), NamdState::loadStructure(), outputCompressedFile(), and Sequencer::rattle1().
Definition at line 924 of file SimParameters.h.
Referenced by HomePatch::hardWallDrude(), HomePatch::minimize_rattle2(), HomePatch::rattle1(), HomePatch::rattle1old(), and HomePatch::rattle2().
Definition at line 923 of file SimParameters.h.
Referenced by HomePatch::minimize_rattle2(), HomePatch::rattle1(), HomePatch::rattle1old(), and HomePatch::rattle2().
Definition at line 922 of file SimParameters.h.
Referenced by HomePatch::minimize_rattle2(), HomePatch::rattle1(), HomePatch::rattle1old(), and HomePatch::rattle2().
Definition at line 315 of file SimParameters.h.
Referenced by ComputeRestraints::ComputeRestraints().
Definition at line 316 of file SimParameters.h.
Referenced by ComputeRestraints::ComputeRestraints().
Definition at line 313 of file SimParameters.h.
Referenced by ComputeRestraints::ComputeRestraints().
Definition at line 317 of file SimParameters.h.
Referenced by ComputeRestraints::ComputeRestraints().
| char SimParameters::rotDragAxisFile[128] |
Definition at line 332 of file SimParameters.h.
| char SimParameters::rotDragFile[128] |
Definition at line 330 of file SimParameters.h.
Definition at line 334 of file SimParameters.h.
Referenced by Sequencer::addRotDragToPosition().
Definition at line 329 of file SimParameters.h.
Referenced by Sequencer::integrate(), NamdState::loadStructure(), Molecule::receive_Molecule(), and Molecule::send_Molecule().
| char SimParameters::rotDragPivotFile[128] |
Definition at line 333 of file SimParameters.h.
| char SimParameters::rotDragVelFile[128] |
Definition at line 335 of file SimParameters.h.
Definition at line 199 of file SimParameters.h.
Referenced by ComputeNonbondedUtil::select().
Definition at line 1001 of file SimParameters.h.
Referenced by Sequencer::algorithm(), Controller::algorithm(), HomePatch::exchangeAtoms(), and scriptSet().
Definition at line 1002 of file SimParameters.h.
Referenced by HomePatch::exchangeAtoms(), and scriptSet().
Definition at line 1003 of file SimParameters.h.
Referenced by scriptSet().
Definition at line 1004 of file SimParameters.h.
Referenced by scriptSet().
Definition at line 1005 of file SimParameters.h.
Referenced by scriptSet().
Definition at line 1006 of file SimParameters.h.
Referenced by Controller::algorithm(), HomePatch::exchangeCheckpoint(), HomePatch::recvCheckpointLoad(), and scriptSet().
Definition at line 1007 of file SimParameters.h.
Referenced by scriptSet().
| char SimParameters::scriptStringArg1[128] |
Definition at line 1008 of file SimParameters.h.
Referenced by Controller::algorithm(), HomePatch::exchangeCheckpoint(), HomePatch::recvCheckpointLoad(), and scriptSet().
| char SimParameters::scriptStringArg2[128] |
Definition at line 1009 of file SimParameters.h.
Referenced by scriptSet().
Definition at line 392 of file SimParameters.h.
Referenced by NamdState::loadStructure(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), Molecule::receive_Molecule(), and Molecule::send_Molecule().
Definition at line 280 of file SimParameters.h.
Referenced by ComputeRestraints::ComputeRestraints().
Definition at line 163 of file SimParameters.h.
Referenced by Node::outputPatchComputeMaps(), and Node::startup().
Definition at line 162 of file SimParameters.h.
Referenced by WorkDistrib::assignNodeToPatch(), Node::outputPatchComputeMaps(), WorkDistrib::patchMapInit(), and Node::startup().
Definition at line 161 of file SimParameters.h.
Referenced by WorkDistrib::assignNodeToPatch(), Node::outputPatchComputeMaps(), WorkDistrib::patchMapInit(), and Node::startup().
Definition at line 391 of file SimParameters.h.
Referenced by ImproperElem::computeForce(), DihedralElem::computeForce(), BondElem::computeForce(), AnisoElem::computeForce(), AngleElem::computeForce(), Sequencer::integrate(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), and Sequencer::minimize().
Definition at line 352 of file SimParameters.h.
Referenced by ComputeMgr::createComputes().
| char SimParameters::SMDFile[128] |
Definition at line 355 of file SimParameters.h.
Referenced by ComputeMgr::createComputes().
Definition at line 353 of file SimParameters.h.
Referenced by ComputeMgr::createComputes().
Definition at line 354 of file SimParameters.h.
Referenced by ComputeMgr::createComputes().
Definition at line 350 of file SimParameters.h.
Referenced by ComputeMgr::createComputes().
Definition at line 356 of file SimParameters.h.
Referenced by ComputeMgr::createComputes().
Definition at line 351 of file SimParameters.h.
Referenced by ComputeMgr::createComputes().
enables scaling for bond and angle terms (default is off)
Definition at line 457 of file SimParameters.h.
Referenced by ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples().
scaling factor for solute interactions
Definition at line 449 of file SimParameters.h.
Referenced by ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), and scriptSet().
optional independent control over scaling factor for electrostatic interactions of solute
Definition at line 451 of file SimParameters.h.
Referenced by Sequencer::algorithm(), scriptSet(), and Sequencer::Sequencer().
optional independent control over scaling factor for van der Waals interactions of solute
Definition at line 454 of file SimParameters.h.
Referenced by scriptSet().
REST2 (replica exchange solute tempering) on?
Definition at line 447 of file SimParameters.h.
Referenced by LJTable::LJTable(), NamdState::loadStructure(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), Molecule::receive_Molecule(), ComputeNonbondedUtil::select(), Molecule::send_Molecule(), and Sequencer::Sequencer().
Definition at line 523 of file SimParameters.h.
Referenced by ComputeNonbondedSelf::doForce(), ComputeNonbondedPair::doForce(), HomePatch::gbisComputeAfterP2(), and ComputeNonbondedCUDA::recvYieldDevice().
Definition at line 845 of file SimParameters.h.
Referenced by ComputeSphericalBC::ComputeSphericalBC().
Definition at line 846 of file SimParameters.h.
Referenced by ComputeSphericalBC::ComputeSphericalBC().
Definition at line 839 of file SimParameters.h.
Referenced by ComputeSphericalBC::ComputeSphericalBC().
Definition at line 841 of file SimParameters.h.
Referenced by ComputeSphericalBC::ComputeSphericalBC().
Definition at line 836 of file SimParameters.h.
Referenced by WorkDistrib::mapComputes().
Definition at line 843 of file SimParameters.h.
Referenced by ComputeSphericalBC::ComputeSphericalBC().
Definition at line 844 of file SimParameters.h.
Referenced by ComputeSphericalBC::ComputeSphericalBC().
Definition at line 838 of file SimParameters.h.
Referenced by ComputeSphericalBC::ComputeSphericalBC().
Definition at line 288 of file SimParameters.h.
Referenced by ComputeRestraints::doForce().
Definition at line 289 of file SimParameters.h.
Referenced by ComputeRestraints::doForce().
Definition at line 912 of file SimParameters.h.
Definition at line 950 of file SimParameters.h.
Referenced by WorkDistrib::createAtomLists(), WorkDistrib::patchMapInit(), and HomePatch::positionsReady().
Definition at line 930 of file SimParameters.h.
Referenced by Sequencer::integrate(), and Controller::integrate().
Definition at line 125 of file SimParameters.h.
Referenced by LdbCoordinator::initialize(), Sequencer::integrate(), Controller::integrate(), Sequencer::minimize(), Sequencer::multigratorPressure(), Molecule::prepare_qm(), and Sequencer::runComputeObjects().
Definition at line 873 of file SimParameters.h.
Referenced by ComputeStir::ComputeStir(), and scriptSet().
| char SimParameters::stirFilename[128] |
Definition at line 868 of file SimParameters.h.
Definition at line 872 of file SimParameters.h.
Referenced by ComputeStir::doForce().
Definition at line 867 of file SimParameters.h.
Referenced by NamdState::loadStructure(), WorkDistrib::mapComputes(), Molecule::receive_Molecule(), and Molecule::send_Molecule().
Definition at line 874 of file SimParameters.h.
Referenced by ComputeStir::ComputeStir(), and scriptSet().
Definition at line 870 of file SimParameters.h.
Definition at line 871 of file SimParameters.h.
How frequently (time steps) stochastic velocity rescaling occurs.
Definition at line 607 of file SimParameters.h.
Referenced by Controller::Controller(), Sequencer::stochRescaleVelocities(), and Controller::stochRescaleVelocities().
Flag TRUE enables calculation and reporting of heat transfer and work. The computation is _cumulative_ from step = firstTimestep.
Definition at line 610 of file SimParameters.h.
Referenced by Controller::printEnergies().
Flag TRUE enables the stochastic velocity rescaling method of Bussi, Donadio, and Parrinello. The method is an extension to the Berendsen thermostat, where a stochastic update to the velocity rescaling produces correct sampling of the NVT ensemble.
Definition at line 594 of file SimParameters.h.
Referenced by colvarproxy_namd::colvarproxy_namd(), Controller::Controller(), Controller::printEnergies(), scriptSet(), Sequencer::stochRescaleVelocities(), and Controller::stochRescaleVelocities().
Timescale (ps) for stochastic velocity rescaling.
Definition at line 604 of file SimParameters.h.
Referenced by Controller::Controller().
Temperature for stochastic velocity rescaling.
Definition at line 601 of file SimParameters.h.
Referenced by colvarproxy_namd::colvarproxy_namd(), scriptSet(), and Controller::stochRescaleCoefficient().
Definition at line 1038 of file SimParameters.h.
Referenced by WorkDistrib::mapComputes(), and ComputeMgr::updateLocalComputes4().
Definition at line 715 of file SimParameters.h.
Referenced by Controller::Controller(), and readExtendedSystem().
Definition at line 716 of file SimParameters.h.
Referenced by Controller::Controller(), and readExtendedSystem().
Definition at line 533 of file SimParameters.h.
Referenced by ComputeLCPO::ComputeLCPO().
Definition at line 704 of file SimParameters.h.
Referenced by Controller::langevinPiston1(), Controller::langevinPiston2(), and scriptSet().
Definition at line 239 of file SimParameters.h.
Referenced by ComputeNonbondedSelf::doForce(), ComputeNonbondedPair::doForce(), ComputeNonbondedCUDA::recvYieldDevice(), and ComputeNonbondedUtil::select().
Definition at line 243 of file SimParameters.h.
Referenced by ComputeQMMgr::recvPntChrg(), ComputeNonbondedCUDA::recvYieldDevice(), and ComputeNonbondedUtil::select().
| char SimParameters::symmetryFile[128] |
Definition at line 380 of file SimParameters.h.
Definition at line 382 of file SimParameters.h.
Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().
Definition at line 382 of file SimParameters.h.
Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().
Definition at line 378 of file SimParameters.h.
Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().
| char SimParameters::symmetrykfile[128] |
Definition at line 379 of file SimParameters.h.
Definition at line 382 of file SimParameters.h.
Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().
Definition at line 382 of file SimParameters.h.
Referenced by ComputeMgr::createComputes(), and GlobalMasterSymmetry::GlobalMasterSymmetry().
| char SimParameters::symmetryMatrixFile[128] |
Definition at line 381 of file SimParameters.h.
Definition at line 377 of file SimParameters.h.
Referenced by ComputeMgr::createComputes().
Definition at line 377 of file SimParameters.h.
Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().
| char SimParameters::tableInterpType[128] |
Definition at line 363 of file SimParameters.h.
Referenced by Parameters::read_ener_table().
Definition at line 365 of file SimParameters.h.
Referenced by Parameters::read_ener_table().
Definition at line 361 of file SimParameters.h.
Referenced by Parameters::read_ener_table().
Definition at line 364 of file SimParameters.h.
Referenced by Parameters::read_ener_table().
Definition at line 360 of file SimParameters.h.
Referenced by Parameters::Parameters(), and ComputeNonbondedUtil::select().
| char SimParameters::tabulatedEnergiesFile[128] |
Definition at line 362 of file SimParameters.h.
Referenced by Parameters::read_ener_table().
| char SimParameters::tclBCArgs[128] |
Definition at line 558 of file SimParameters.h.
Referenced by ComputeTclBC::doWork(), and scriptSet().
Definition at line 556 of file SimParameters.h.
Referenced by WorkDistrib::mapComputes().
Definition at line 557 of file SimParameters.h.
Referenced by ComputeTclBC::ComputeTclBC(), receive_SimParameters(), and send_SimParameters().
Definition at line 552 of file SimParameters.h.
Referenced by ComputeGlobal::ComputeGlobal(), ComputeMgr::createComputes(), Sequencer::integrate(), and Sequencer::minimize().
Definition at line 554 of file SimParameters.h.
Referenced by ComputeTclBC::ComputeTclBC().
Definition at line 589 of file SimParameters.h.
Referenced by colvarproxy_namd::colvarproxy_namd(), NamdState::loadStructure(), Molecule::receive_Molecule(), Molecule::send_Molecule(), Sequencer::tcoupleVelocities(), and Controller::tcoupleVelocities().
Definition at line 591 of file SimParameters.h.
Referenced by colvarproxy_namd::colvarproxy_namd(), and Controller::tcoupleVelocities().
Definition at line 928 of file SimParameters.h.
Definition at line 369 of file SimParameters.h.
Referenced by GlobalMasterTMD::GlobalMasterTMD().
| char SimParameters::TMDFile[128] |
Definition at line 371 of file SimParameters.h.
Referenced by GlobalMasterTMD::GlobalMasterTMD().
| char SimParameters::TMDFile2[128] |
Definition at line 371 of file SimParameters.h.
Referenced by GlobalMasterTMD::GlobalMasterTMD().
Definition at line 374 of file SimParameters.h.
Referenced by GlobalMasterTMD::GlobalMasterTMD().
Definition at line 373 of file SimParameters.h.
Referenced by GlobalMasterTMD::GlobalMasterTMD().
Definition at line 374 of file SimParameters.h.
Referenced by GlobalMasterTMD::GlobalMasterTMD().
Definition at line 370 of file SimParameters.h.
Referenced by GlobalMasterTMD::GlobalMasterTMD().
Definition at line 373 of file SimParameters.h.
Referenced by GlobalMasterTMD::GlobalMasterTMD().
Definition at line 369 of file SimParameters.h.
Referenced by ComputeMgr::createComputes().
Definition at line 372 of file SimParameters.h.
Referenced by GlobalMasterTMD::GlobalMasterTMD().
Definition at line 932 of file SimParameters.h.
Definition at line 151 of file SimParameters.h.
Referenced by Sequencer::integrate(), and Controller::integrate().
Definition at line 175 of file SimParameters.h.
Referenced by WorkDistrib::patchMapInit().
Definition at line 176 of file SimParameters.h.
Referenced by WorkDistrib::patchMapInit().
Definition at line 177 of file SimParameters.h.
Referenced by WorkDistrib::patchMapInit().
Definition at line 962 of file SimParameters.h.
Definition at line 1051 of file SimParameters.h.
Referenced by Patch::positionsReady(), HomePatch::positionsReady(), ProxyPatch::receiveAll(), ProxyPatch::receiveData(), and ComputeNonbondedUtil::select().
Definition at line 173 of file SimParameters.h.
Referenced by PmeZPencil::backward_fft(), PmeYPencil::backward_fft(), PmeXPencil::backward_fft(), PmeXPencil::fft_init(), PmeZPencil::fft_init(), PmeXPencil::forward_fft(), PmeYPencil::forward_fft(), PmeZPencil::forward_fft(), ComputePmeCUDADevice::gatherForceDone(), PmeZPencil::send_all_ungrid(), PmeYPencil::send_trans(), PmeZPencil::send_trans(), PmeYPencil::send_untrans(), PmeXPencil::send_untrans(), ComputePmeMgr::sendTrans(), ComputePmeMgr::sendUngrid(), ComputePmeMgr::sendUntrans(), and Node::startup().
Definition at line 1011 of file SimParameters.h.
Referenced by NamdState::loadStructure(), and Molecule::Molecule().
Definition at line 674 of file SimParameters.h.
Referenced by Controller::langevinPiston1(), and scriptSet().
Definition at line 675 of file SimParameters.h.
Referenced by Controller::calcPressure(), Controller::Controller(), Controller::langevinPiston1(), Controller::langevinPiston2(), and scriptSet().
Flag TRUE to use the second generation nonbonded CUDA kernels developed by Antti-Pekka Hynninen. Default is TRUE.
Definition at line 799 of file SimParameters.h.
Referenced by ComputePmeMgr::chargeGridSubmitted(), ComputeMgr::createComputes(), WorkDistrib::mapComputes(), ComputeNonbondedUtil::select(), and Node::startup().
Flag TRUE to automatically disable individual CUDA kernels that are incompatible with simulation options. Default is TRUE. Specifically, disable CUDA bonds for Drude oscillator simulation and disable CUDA dihedral and CUDA crossterms kernels for accelMDdihe and accelMDdual simulation. Set FALSE to manually control kernel use for development.
Definition at line 810 of file SimParameters.h.
Definition at line 792 of file SimParameters.h.
Referenced by WorkDistrib::mapComputes().
Definition at line 673 of file SimParameters.h.
Referenced by Controller::calcPressure(), Controller::Controller(), Controller::langevinPiston1(), Controller::langevinPiston2(), and scriptSet().
Definition at line 668 of file SimParameters.h.
Referenced by Sequencer::berendsenPressure(), Controller::calcPressure(), Sequencer::langevinPiston(), Sequencer::multigratorPressure(), Sequencer::multigratorTemperature(), Controller::receivePressure(), Sequencer::scalePositionsVelocities(), scriptSet(), Sequencer::submitHalfstep(), and Sequencer::submitReductions().
Definition at line 253 of file SimParameters.h.
Definition at line 1014 of file SimParameters.h.
Referenced by NamdState::loadStructure().
Flag TRUE to use the PME CUDA version. Default is TRUE if running on 4 nodes or less.
Definition at line 795 of file SimParameters.h.
Referenced by ComputeNonbondedCUDA::ComputeNonbondedCUDA(), isPmeProcessor(), WorkDistrib::mapComputes(), ComputeNonbondedCUDA::recvYieldDevice(), and Node::startup().
Definition at line 926 of file SimParameters.h.
Referenced by HomePatch::buildRattleList(), HomePatch::minimize_rattle2(), HomePatch::rattle1(), HomePatch::rattle1old(), and HomePatch::rattle2().
Definition at line 241 of file SimParameters.h.
Referenced by ComputeNonbondedUtil::select().
Definition at line 998 of file SimParameters.h.
Referenced by ComputeNonbondedUtil::select().
Definition at line 992 of file SimParameters.h.
Referenced by NamdState::loadStructure().
| char SimParameters::velDcdFilename[128] |
Definition at line 213 of file SimParameters.h.
Referenced by scriptSet().
Definition at line 205 of file SimParameters.h.
Referenced by Output::velocity(), and Output::velocityNeeded().
Definition at line 165 of file SimParameters.h.
Referenced by recursive_bisect_with_curve().
Definition at line 120 of file SimParameters.h.
Referenced by HomePatch::buildRattleList(), HomePatch::minimize_rattle2(), HomePatch::rattle1(), HomePatch::rattle1old(), and HomePatch::rattle2().
Definition at line 194 of file SimParameters.h.
Referenced by ParallelIOMgr::integrateClusterSize(), ParallelIOMgr::readPerAtomInfo(), ParallelIOMgr::recvFinalClusterCoor(), colvarproxy_namd::setup(), and wrap_coor_int().
Definition at line 195 of file SimParameters.h.
Referenced by ParallelIOMgr::recvFinalClusterCoor(), and wrap_coor_int().
Definition at line 193 of file SimParameters.h.
Referenced by ParallelIOMgr::integrateClusterSize(), ParallelIOMgr::readPerAtomInfo(), and wrap_coor_int().
| char SimParameters::xstFilename[128] |
Definition at line 215 of file SimParameters.h.
Referenced by Controller::outputExtendedSystem().
Definition at line 209 of file SimParameters.h.
Referenced by Controller::outputExtendedSystem().
Definition at line 191 of file SimParameters.h.
Referenced by Sequencer::integrate(), and Controller::integrate().
Definition at line 192 of file SimParameters.h.
Referenced by Sequencer::correctMomentum(), and Sequencer::submitMomentum().
1.6.1