#include <SimParameters.h>
Definition at line 100 of file SimParameters.h.
| SimParameters::SimParameters | ( | ) | [inline] |
Definition at line 1050 of file SimParameters.h.
01050 : mgridforcelist(), parseopts(0) {};
| SimParameters::SimParameters | ( | ConfigList * | c, | |
| char *& | cwd | |||
| ) | [inline] |
Definition at line 1051 of file SimParameters.h.
References initialize_config_data().
01051 : mgridforcelist(), parseopts(0) { 01052 initialize_config_data(c,cwd); 01053 };
| SimParameters::~SimParameters | ( | ) | [inline] |
Definition at line 1054 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 7201 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().
07201 { 07202 // Convenience function for staggered lambda scaling 07203 return (lambda >= alchBondLambdaEnd ? 1. : lambda / alchBondLambdaEnd); 07204 }
| BigReal SimParameters::getCurrentLambda | ( | const int | step | ) |
Definition at line 7122 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().
07122 { 07123 /*Get lambda at the current step. 07124 07125 If alchLambdaFreq = 0, return alchLambda. For positive values of 07126 alchLambdaFreq, apply a linear stepwise schedule from alchLambda to 07127 alchLambda2: 07128 07129 l(t) = l + (l2 - l)*[dn / (N - n0)]*{floor[(n - n0)/dn] + 1} 07130 07131 n - the current time step 07132 n0 - step at which switching begins (default = 0) 07133 N - total steps in the simulation 07134 dn - alchLambdaFreq (increment frequency, in steps) 07135 l/l2 - alchLambda/alchLambda2 07136 07137 Note that each step _begins_ by incrementing alchLambda and then integrates 07138 in time. This means that the first and last switch steps may not behave as 07139 immediately expected - at step 0, alchLambda is NOT evaluated and at step N 07140 no step occurs because alchLambda2 has already been reached. 07141 */ 07142 if ( alchLambdaFreq > 0 && step >= alchEquilSteps ) { 07143 if ( step == N ) { 07144 return alchLambda2; 07145 } 07146 else { 07147 const int timeOrigin = firstTimestep + alchEquilSteps; 07148 const BigReal alchLambdaDelta = getLambdaDelta(); 07149 const BigReal increment = (step - timeOrigin) / BigReal(alchLambdaFreq); 07150 return alchLambda + alchLambdaDelta*(floor(increment) + 1); 07151 } 07152 } 07153 else { 07154 return alchLambda; 07155 } 07156 }
| BigReal SimParameters::getCurrentLambda2 | ( | const int | step | ) |
Definition at line 7084 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().
07084 { 07085 if ( alchLambdaIDWS >= 0. ) { 07086 const BigReal lambda2 = ( (step / alchIDWSFreq) % 2 == 1 ) ? alchLambda2 : alchLambdaIDWS; 07087 return lambda2; 07088 } else { 07089 return alchLambda2; 07090 } 07091 }
Definition at line 7164 of file SimParameters.C.
Referenced by Controller::computeAlchWork(), TholeElem::computeForce(), Controller::outputTiEnergy(), ComputePmeMgr::submitReductions(), and ComputePme::ungridForces().
07164 { 07165 // Convenience function for staggered lambda scaling 07166 return (lambda <= alchElecLambdaStart ? 0. 07167 : (lambda - alchElecLambdaStart) / (1. - alchElecLambdaStart)); 07168 }
| char * SimParameters::getfromparseopts | ( | const char * | name, | |
| char * | outbuf | |||
| ) |
Definition at line 99 of file SimParameters.C.
References ParseOptions::getfromptr().
00099 { 00100 if ( parseopts ) return parseopts->getfromptr(name,outbuf); 00101 else return 0; 00102 }
| BigReal SimParameters::getLambdaDelta | ( | void | ) |
Definition at line 7158 of file SimParameters.C.
References alchEquilSteps, alchLambdaFreq, and firstTimestep.
Referenced by getCurrentLambda(), and Controller::outputTiEnergy().
07158 { 07159 // Increment by which Lambda changes. 07160 return ((alchLambda2 - alchLambda)*alchLambdaFreq 07161 / BigReal(N - firstTimestep - alchEquilSteps)); 07162 }
Definition at line 7196 of file SimParameters.C.
References alchRepLambdaEnd.
07196 { 07197 // Convenience function for staggered lambda scaling 07198 return (lambda >= alchRepLambdaEnd ? 1. : lambda / alchRepLambdaEnd); 07199 }
Definition at line 7178 of file SimParameters.C.
References alchRepLambdaEnd, alchVdwLambdaEnd, and alchWCAOn.
Referenced by Controller::computeAlchWork(), and Controller::outputTiEnergy().
07178 { 07179 // Convenience function for staggered lambda scaling 07180 if ( alchWCAOn ) { 07181 // Read this with the alias alchRepLambdaEnd --> alchAttLambdaStart. 07182 // The second condition is needed when attractive interactions are inactive 07183 // for the whole range, otherwise lambda = 0/1 are incorrect. 07184 if ( lambda < alchRepLambdaEnd || alchRepLambdaEnd == 1.0 ) { 07185 return 0.0; 07186 } else if ( lambda >= alchVdwLambdaEnd ) { 07187 return 1.0; 07188 } else { 07189 return (lambda - alchRepLambdaEnd) / (alchVdwLambdaEnd - alchRepLambdaEnd); 07190 } 07191 } else { 07192 return (lambda >= alchVdwLambdaEnd ? 1. : lambda / alchVdwLambdaEnd); 07193 } 07194 }
| void SimParameters::initialize_config_data | ( | ConfigList * | config, | |
| char *& | cwd | |||
| ) |
Definition at line 127 of file SimParameters.C.
References ParseOptions::check_consistency(), NAMD_die(), and ParseOptions::set().
Referenced by SimParameters().
00129 { 00130 00131 parseopts = new ParseOptions; // Object to check consistency of config file 00132 ParseOptions &opts = *parseopts; 00133 00134 config_parser(opts); 00135 00137 if (!opts.check_consistency()) 00138 { 00139 NAMD_die("Internal error in configuration file parser"); 00140 } 00141 00142 // Now, feed the object with the actual configuration options through the 00143 // ParseOptions file and make sure everything is OK 00144 if (!opts.set(*config)) 00145 { 00146 NAMD_die("ERROR(S) IN THE CONFIGURATION FILE"); 00147 } 00148 00150 00151 check_config(opts,config,cwd); 00152 00153 print_config(opts,config,cwd); 00154 00155 }
| int SimParameters::isRecvSpanningTreeOn | ( | ) | [inline] |
Definition at line 1076 of file SimParameters.h.
References proxyRecvSpanningTree.
Referenced by Node::startup().
01076 { return proxyRecvSpanningTree == 1; }
| int SimParameters::isRecvSpanningTreeUnset | ( | ) | [inline] |
Definition at line 1077 of file SimParameters.h.
References proxyRecvSpanningTree.
Referenced by WorkDistrib::savePatchMap(), and WorkDistrib::sendPatchMap().
01077 { return proxyRecvSpanningTree == -1; }
| int SimParameters::isSendSpanningTreeOn | ( | ) | [inline] |
Definition at line 1074 of file SimParameters.h.
References proxySendSpanningTree.
Referenced by Node::startup().
01074 { return proxySendSpanningTree == 1; }
| int SimParameters::isSendSpanningTreeUnset | ( | ) | [inline] |
Definition at line 1075 of file SimParameters.h.
References proxySendSpanningTree.
Referenced by WorkDistrib::savePatchMap(), and WorkDistrib::sendPatchMap().
01075 { return proxySendSpanningTree == -1; }
| int SimParameters::issetinparseopts | ( | const char * | name | ) |
Definition at line 109 of file SimParameters.C.
References ParseOptions::issetfromptr().
00109 { 00110 if ( parseopts ) return parseopts->issetfromptr(name); 00111 else return -1; 00112 }
| int SimParameters::istrueinparseopts | ( | const char * | name | ) |
Definition at line 104 of file SimParameters.C.
References ParseOptions::istruefromptr().
00104 { 00105 if ( parseopts ) return parseopts->istruefromptr(name); 00106 else return -1; 00107 }
| void SimParameters::nonbonded_select | ( | ) | [static] |
Definition at line 392 of file SimParameters.C.
References ComputeNonbondedUtil::select().
Referenced by Node::resendMolecule(), and Node::startup().
00392 { 00393 ComputeNonbondedUtil::select(); 00394 }
| void SimParameters::pme_select | ( | ) | [static] |
Definition at line 396 of file SimParameters.C.
References ComputePmeUtil::select().
Referenced by Node::resendMolecule(), and Node::startup().
00396 { 00397 ComputePmeUtil::select(); 00398 }
| void SimParameters::readExtendedSystem | ( | const char * | filename, | |
| Lattice * | latptr = 0 | |||
| ) |
Definition at line 2313 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.
02313 { 02314 02315 if ( ! latptr ) { 02316 iout << iINFO << "EXTENDED SYSTEM FILE " << filename << "\n" << endi; 02317 } 02318 02319 ifstream xscFile(filename); 02320 if ( ! xscFile ) NAMD_die("Unable to open extended system file.\n"); 02321 02322 char labels[1024]; 02323 do { 02324 if ( ! xscFile ) NAMD_die("Error reading extended system file.\n"); 02325 xscFile.getline(labels,1023); 02326 } while ( strncmp(labels,"#$LABELS ",9) ); 02327 02328 int a_x, a_y, a_z, b_x, b_y, b_z, c_x, c_y, c_z; 02329 a_x = a_y = a_z = b_x = b_y = b_z = c_x = c_y = c_z = -1; 02330 int o_x, o_y, o_z, s_u, s_v, s_w, s_x, s_y, s_z; 02331 o_x = o_y = o_z = s_u = s_v = s_w = s_x = s_y = s_z = -1; 02332 02333 int pos = 0; 02334 char *l_i = labels + 8; 02335 while ( *l_i ) { 02336 if ( *l_i == ' ' ) { ++l_i; continue; } 02337 char *l_i2; 02338 for ( l_i2 = l_i; *l_i2 && *l_i2 != ' '; ++l_i2 ); 02339 if ( (l_i2 - l_i) == 3 && (l_i[1] == '_') ) { 02340 if (l_i[0] == 'a' && l_i[2] == 'x') a_x = pos; 02341 if (l_i[0] == 'a' && l_i[2] == 'y') a_y = pos; 02342 if (l_i[0] == 'a' && l_i[2] == 'z') a_z = pos; 02343 if (l_i[0] == 'b' && l_i[2] == 'x') b_x = pos; 02344 if (l_i[0] == 'b' && l_i[2] == 'y') b_y = pos; 02345 if (l_i[0] == 'b' && l_i[2] == 'z') b_z = pos; 02346 if (l_i[0] == 'c' && l_i[2] == 'x') c_x = pos; 02347 if (l_i[0] == 'c' && l_i[2] == 'y') c_y = pos; 02348 if (l_i[0] == 'c' && l_i[2] == 'z') c_z = pos; 02349 if (l_i[0] == 'o' && l_i[2] == 'x') o_x = pos; 02350 if (l_i[0] == 'o' && l_i[2] == 'y') o_y = pos; 02351 if (l_i[0] == 'o' && l_i[2] == 'z') o_z = pos; 02352 if (l_i[0] == 's' && l_i[2] == 'u') s_u = pos; 02353 if (l_i[0] == 's' && l_i[2] == 'v') s_v = pos; 02354 if (l_i[0] == 's' && l_i[2] == 'w') s_w = pos; 02355 if (l_i[0] == 's' && l_i[2] == 'x') s_x = pos; 02356 if (l_i[0] == 's' && l_i[2] == 'y') s_y = pos; 02357 if (l_i[0] == 's' && l_i[2] == 'z') s_z = pos; 02358 } 02359 ++pos; 02360 l_i = l_i2; 02361 } 02362 int numpos = pos; 02363 02364 for ( pos = 0; pos < numpos; ++pos ) { 02365 double tmp; 02366 xscFile >> tmp; 02367 if ( ! xscFile ) NAMD_die("Error reading extended system file.\n"); 02368 if ( pos == a_x ) cellBasisVector1.x = tmp; 02369 if ( pos == a_y ) cellBasisVector1.y = tmp; 02370 if ( pos == a_z ) cellBasisVector1.z = tmp; 02371 if ( pos == b_x ) cellBasisVector2.x = tmp; 02372 if ( pos == b_y ) cellBasisVector2.y = tmp; 02373 if ( pos == b_z ) cellBasisVector2.z = tmp; 02374 if ( pos == c_x ) cellBasisVector3.x = tmp; 02375 if ( pos == c_y ) cellBasisVector3.y = tmp; 02376 if ( pos == c_z ) cellBasisVector3.z = tmp; 02377 if ( pos == o_x ) cellOrigin.x = tmp; 02378 if ( pos == o_y ) cellOrigin.y = tmp; 02379 if ( pos == o_z ) cellOrigin.z = tmp; 02380 if ( pos == s_u ) strainRate2.x = tmp; 02381 if ( pos == s_v ) strainRate2.y = tmp; 02382 if ( pos == s_w ) strainRate2.z = tmp; 02383 if ( pos == s_x ) strainRate.x = tmp; 02384 if ( pos == s_y ) strainRate.y = tmp; 02385 if ( pos == s_z ) strainRate.z = tmp; 02386 } 02387 02388 if ( latptr ) { 02389 Lattice test; 02390 test.set(cellBasisVector1,cellBasisVector2,cellBasisVector3,cellOrigin); 02391 02392 if ( test.a_p() && ! lattice.a_p() ) { 02393 NAMD_die("cellBasisVector1 added during atom reinitialization"); 02394 } 02395 if ( lattice.a_p() && ! test.a_p() ) { 02396 NAMD_die("cellBasisVector1 dropped during atom reinitialization"); 02397 } 02398 if ( test.b_p() && ! lattice.b_p() ) { 02399 NAMD_die("cellBasisVector2 added during atom reinitialization"); 02400 } 02401 if ( lattice.b_p() && ! test.b_p() ) { 02402 NAMD_die("cellBasisVector2 dropped during atom reinitialization"); 02403 } 02404 if ( test.c_p() && ! lattice.c_p() ) { 02405 NAMD_die("cellBasisVector3 added during atom reinitialization"); 02406 } 02407 if ( lattice.c_p() && ! test.c_p() ) { 02408 NAMD_die("cellBasisVector3 dropped during atom reinitialization"); 02409 } 02410 02411 latptr->set(cellBasisVector1,cellBasisVector2,cellBasisVector3,cellOrigin); 02412 } 02413 02414 }
| void SimParameters::receive_SimParameters | ( | MIStream * | msg | ) |
Definition at line 7025 of file SimParameters.C.
References binAtomFile, binCoorFile, binRefFile, binVelFile, MGridforceParamsList::clear(), FFTWWisdomString, MIStream::get(), mgridforcelist, tclBCScript, and MGridforceParamsList::unpack_data().
07027 { 07028 msg->get(sizeof(SimParameters),(char*)this); 07029 if ( FFTWWisdomString ) { 07030 int fftwlen; 07031 msg->get(fftwlen); 07032 FFTWWisdomString = new char[fftwlen]; 07033 msg->get(fftwlen,FFTWWisdomString); 07034 #ifdef NAMD_FFTW 07035 #ifdef NAMD_FFTW_3 07036 fftwf_import_wisdom_from_string(FFTWWisdomString); 07037 #else 07038 fftw_import_wisdom_from_string(FFTWWisdomString); 07039 #endif 07040 #endif 07041 } 07042 if ( tclBCScript ) { 07043 int tcllen; 07044 msg->get(tcllen); 07045 tclBCScript = new char[tcllen]; 07046 msg->get(tcllen,tclBCScript); 07047 } 07048 07049 #ifdef MEM_OPT_VERSION 07050 int filelen; 07051 msg->get(filelen); 07052 binAtomFile = new char[filelen]; 07053 msg->get(filelen, binAtomFile); 07054 07055 msg->get(filelen); 07056 binCoorFile = new char[filelen]; 07057 msg->get(filelen, binCoorFile); 07058 07059 if(binVelFile) { 07060 msg->get(filelen); 07061 binVelFile = new char[filelen]; 07062 msg->get(filelen, binVelFile); 07063 } 07064 07065 if(binRefFile) { 07066 msg->get(filelen); 07067 binRefFile = new char[filelen]; 07068 msg->get(filelen, binRefFile); 07069 } 07070 #endif 07071 07072 07073 // The simParameters bit copy above put illegal values in the list pointers 07074 // So this resets everything so that unpacking will work. 07075 mgridforcelist.clear(); 07076 mgridforcelist.unpack_data(msg); 07077 07078 delete msg; 07079 }
| void SimParameters::scriptSet | ( | const char * | param, | |
| const char * | value | |||
| ) |
Definition at line 169 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().
00169 { 00170 00171 if ( CkMyRank() ) return; 00172 00173 #define MAX_SCRIPT_PARAM_SIZE 128 00174 #define SCRIPT_PARSE_BOOL(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atobool(value); return; } } 00175 #define SCRIPT_PARSE_INT(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atoi(value); return; } } 00176 #define SCRIPT_PARSE_FLOAT(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atof(value); return; } } 00177 #define SCRIPT_PARSE_MOD_FLOAT(NAME,VAR,MOD) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atof(value) MOD; return; } } 00178 #define SCRIPT_PARSE_VECTOR(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR).set(value); return; } } 00179 #define SCRIPT_PARSE_STRING(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { strcpy(VAR,value); return; } } 00180 00181 SCRIPT_PARSE_FLOAT("scriptArg1",scriptArg1) 00182 SCRIPT_PARSE_FLOAT("scriptArg2",scriptArg2) 00183 SCRIPT_PARSE_FLOAT("scriptArg3",scriptArg3) 00184 SCRIPT_PARSE_FLOAT("scriptArg4",scriptArg4) 00185 SCRIPT_PARSE_FLOAT("scriptArg5",scriptArg5) 00186 SCRIPT_PARSE_INT("scriptIntArg1",scriptIntArg1) 00187 SCRIPT_PARSE_INT("scriptIntArg2",scriptIntArg2) 00188 SCRIPT_PARSE_STRING("scriptStringArg1",scriptStringArg1) 00189 SCRIPT_PARSE_STRING("scriptStringArg2",scriptStringArg2) 00190 SCRIPT_PARSE_INT("numsteps",N) 00191 if ( ! strncasecmp(param,"firsttimestep",MAX_SCRIPT_PARAM_SIZE) ) { 00192 N = firstTimestep = atoi(value); return; 00193 } 00194 SCRIPT_PARSE_FLOAT("reassignTemp",reassignTemp) 00195 SCRIPT_PARSE_FLOAT("rescaleTemp",rescaleTemp) 00196 SCRIPT_PARSE_BOOL("velocityQuenching",minimizeOn) 00197 SCRIPT_PARSE_BOOL("maximumMove",maximumMove) 00198 // SCRIPT_PARSE_BOOL("Langevin",langevinOn) 00199 if ( ! strncasecmp(param,"Langevin",MAX_SCRIPT_PARAM_SIZE) ) { 00200 langevinOn = atobool(value); 00201 if ( langevinOn && ! langevinOnAtStartup ) { 00202 NAMD_die("Langevin must be enabled at startup to disable and re-enable in script."); 00203 } 00204 return; 00205 } 00206 SCRIPT_PARSE_FLOAT("langevinTemp",langevinTemp) 00207 SCRIPT_PARSE_BOOL("langevinBAOAB",langevin_useBAOAB) // [!!] Use the BAOAB integrator or not 00208 SCRIPT_PARSE_FLOAT("loweAndersenTemp",loweAndersenTemp) // BEGIN LA, END LA 00209 SCRIPT_PARSE_BOOL("stochRescale",stochRescaleOn) 00210 SCRIPT_PARSE_FLOAT("stochRescaleTemp",stochRescaleTemp) 00211 SCRIPT_PARSE_FLOAT("initialTemp",initialTemp) 00212 SCRIPT_PARSE_BOOL("useGroupPressure",useGroupPressure) 00213 SCRIPT_PARSE_BOOL("useFlexibleCell",useFlexibleCell) 00214 SCRIPT_PARSE_BOOL("useConstantArea",useConstantArea) 00215 SCRIPT_PARSE_BOOL("fixCellDims",fixCellDims) 00216 SCRIPT_PARSE_BOOL("fixCellDimX",fixCellDimX) 00217 SCRIPT_PARSE_BOOL("fixCellDimY",fixCellDimY) 00218 SCRIPT_PARSE_BOOL("fixCellDimZ",fixCellDimZ) 00219 SCRIPT_PARSE_BOOL("useConstantRatio",useConstantRatio) 00220 SCRIPT_PARSE_BOOL("LangevinPiston",langevinPistonOn) 00221 SCRIPT_PARSE_MOD_FLOAT("LangevinPistonTarget", 00222 langevinPistonTarget,/PRESSUREFACTOR) 00223 SCRIPT_PARSE_FLOAT("LangevinPistonPeriod",langevinPistonPeriod) 00224 SCRIPT_PARSE_FLOAT("LangevinPistonDecay",langevinPistonDecay) 00225 SCRIPT_PARSE_FLOAT("LangevinPistonTemp",langevinPistonTemp) 00226 SCRIPT_PARSE_MOD_FLOAT("SurfaceTensionTarget", 00227 surfaceTensionTarget,*(100.0/PRESSUREFACTOR)) 00228 SCRIPT_PARSE_BOOL("BerendsenPressure",berendsenPressureOn) 00229 SCRIPT_PARSE_MOD_FLOAT("BerendsenPressureTarget", 00230 berendsenPressureTarget,/PRESSUREFACTOR) 00231 SCRIPT_PARSE_MOD_FLOAT("BerendsenPressureCompressibility", 00232 berendsenPressureCompressibility,*PRESSUREFACTOR) 00233 SCRIPT_PARSE_FLOAT("BerendsenPressureRelaxationTime", 00234 berendsenPressureRelaxationTime) 00235 SCRIPT_PARSE_FLOAT("constraintScaling",constraintScaling) 00236 SCRIPT_PARSE_FLOAT("consForceScaling",consForceScaling) 00237 SCRIPT_PARSE_BOOL("drudeHardWall",drudeHardWallOn) 00238 SCRIPT_PARSE_FLOAT("drudeBondConst",drudeBondConst) 00239 SCRIPT_PARSE_FLOAT("drudeBondLen",drudeBondLen) 00240 SCRIPT_PARSE_STRING("outputname",outputFilename) 00241 SCRIPT_PARSE_INT("outputEnergies",outputEnergies) 00242 SCRIPT_PARSE_STRING("restartname",restartFilename) 00243 SCRIPT_PARSE_INT("DCDfreq",dcdFrequency) 00244 if ( ! strncasecmp(param,"DCDfile",MAX_SCRIPT_PARAM_SIZE) ) { 00245 close_dcdfile(); // *** implemented in Output.C *** 00246 strcpy(dcdFilename,value); 00247 return; 00248 } 00249 if ( ! strncasecmp(param,"velDCDfile",MAX_SCRIPT_PARAM_SIZE) ) { 00250 close_veldcdfile(); // *** implemented in Output.C *** 00251 strcpy(velDcdFilename,value); 00252 return; 00253 } 00254 SCRIPT_PARSE_STRING("tclBCArgs",tclBCArgs) 00255 SCRIPT_PARSE_VECTOR("eField",eField) 00256 SCRIPT_PARSE_FLOAT("eFieldFreq",eFieldFreq) 00257 SCRIPT_PARSE_FLOAT("eFieldPhase",eFieldPhase) 00258 SCRIPT_PARSE_FLOAT("accelMDE",accelMDE) 00259 SCRIPT_PARSE_FLOAT("accelMDalpha",accelMDalpha) 00260 SCRIPT_PARSE_FLOAT("accelMDTE",accelMDTE) 00261 SCRIPT_PARSE_FLOAT("accelMDTalpha",accelMDTalpha) 00262 SCRIPT_PARSE_FLOAT("accelMDGSigma0P",accelMDGSigma0P) 00263 SCRIPT_PARSE_FLOAT("accelMDGSigma0D",accelMDGSigma0D) 00264 SCRIPT_PARSE_STRING("accelMDGRestartFile",accelMDGRestartFile) 00265 SCRIPT_PARSE_VECTOR("stirAxis",stirAxis) 00266 SCRIPT_PARSE_VECTOR("stirPivot",stirPivot) 00267 if ( ! strncasecmp(param,"mgridforcescale",MAX_SCRIPT_PARAM_SIZE) ) { 00268 NAMD_die("Can't yet modify mgridforcescale in a script"); 00269 return; 00270 } 00271 if ( ! strncasecmp(param,"mgridforcevoff",MAX_SCRIPT_PARAM_SIZE) ) { 00272 NAMD_die("Can't yet modify mgridforcevoff in a script"); 00273 return; 00274 } 00275 00276 if ( ! strncasecmp(param,"fixedatoms",MAX_SCRIPT_PARAM_SIZE) ) { 00277 if ( ! fixedAtomsOn ) 00278 NAMD_die("FixedAtoms may not be enabled in a script."); 00279 if ( ! fixedAtomsForces ) 00280 NAMD_die("To use fixedAtoms in script first use fixedAtomsForces yes."); 00281 fixedAtomsOn = atobool(value); 00282 return; 00283 } 00284 00285 //fepb 00286 if ( ! strncasecmp(param,"alch",MAX_SCRIPT_PARAM_SIZE) ) { 00287 alchOn = atobool(value); 00288 if ( alchOn && ! alchOnAtStartup ) { 00289 NAMD_die("Alchemy must be enabled at startup to disable and re-enable in script."); 00290 } 00291 alchFepOn = alchOn && alchFepOnAtStartup; 00292 alchThermIntOn = alchOn && alchThermIntOnAtStartup; 00293 ComputeNonbondedUtil::select(); 00294 if ( PMEOn ) ComputePmeUtil::select(); 00295 return; 00296 } 00297 SCRIPT_PARSE_INT("alchEquilSteps",alchEquilSteps) 00298 00299 if ( ! strncasecmp(param,"alchLambda",MAX_SCRIPT_PARAM_SIZE) ) { 00300 alchLambda = atof(value); 00301 if ( alchLambda < 0.0 || 1.0 < alchLambda ) { 00302 NAMD_die("Alchemical lambda values should be in the range [0.0, 1.0]\n"); 00303 } 00304 ComputeNonbondedUtil::select(); 00305 return; 00306 } 00307 00308 if ( ! strncasecmp(param,"alchLambda2",MAX_SCRIPT_PARAM_SIZE) ) { 00309 alchLambda2 = atof(value); 00310 if ( alchLambda2 < 0.0 || 1.0 < alchLambda2 ) { 00311 NAMD_die("Alchemical lambda values should be in the range [0.0, 1.0]\n"); 00312 } 00313 ComputeNonbondedUtil::select(); 00314 return; 00315 } 00316 00317 if ( ! strncasecmp(param,"alchLambdaIDWS",MAX_SCRIPT_PARAM_SIZE) ) { 00318 alchLambdaIDWS = atof(value); 00319 setupIDWS(); 00320 ComputeNonbondedUtil::select(); 00321 return; 00322 } 00323 00324 if ( ! strncasecmp(param,"alchLambdaFreq",MAX_SCRIPT_PARAM_SIZE) ) { 00325 alchLambdaFreq = atoi(value); 00326 if ( alchLambdaIDWS >= 0 ) { 00327 NAMD_die("alchLambdaIDWS and alchLambdaFreq are not compatible.\n"); 00328 } 00329 ComputeNonbondedUtil::select(); 00330 return; 00331 } 00332 //fepe 00333 00334 if ( ! strncasecmp(param,"nonbondedScaling",MAX_SCRIPT_PARAM_SIZE) ) { 00335 nonbondedScaling = atof(value); 00336 ComputeNonbondedUtil::select(); 00337 return; 00338 } 00339 00340 if ( ! strncasecmp(param,"commOnly",MAX_SCRIPT_PARAM_SIZE) ) { 00341 commOnly = atobool(value); 00342 ComputeNonbondedUtil::select(); 00343 return; 00344 } 00345 00346 // REST2 - We don't have to make any changes to ComputeNonbondedUtil 00347 // other than recalculating the LJTable. Skip doing the other stuff. 00348 if ( ! strncasecmp(param,"soluteScalingFactor",MAX_SCRIPT_PARAM_SIZE)) { 00349 soluteScalingFactor = atof(value); 00350 if (soluteScalingFactor < 0.0) { 00351 NAMD_die("Solute scaling factor should be non-negative\n"); 00352 } 00353 soluteScalingFactorCharge = soluteScalingFactor; 00354 soluteScalingFactorVdw = soluteScalingFactor; 00355 // update LJTable for CPU 00356 ComputeNonbondedUtil::select(); 00357 #ifdef NAMD_CUDA 00358 // update LJTable for GPU, needs CPU update first 00359 ComputeCUDAMgr::getComputeCUDAMgr()->update(); 00360 #endif 00361 return; 00362 } 00363 if ( ! strncasecmp(param,"soluteScalingFactorVdw",MAX_SCRIPT_PARAM_SIZE)) { 00364 soluteScalingFactorVdw = atof(value); 00365 if (soluteScalingFactorVdw < 0.0) { 00366 NAMD_die("Solute scaling factor for van der Waals " 00367 "should be non-negative\n"); 00368 } 00369 // update LJTable for CPU 00370 ComputeNonbondedUtil::select(); 00371 #ifdef NAMD_CUDA 00372 // update LJTable for GPU, needs CPU update first 00373 ComputeCUDAMgr::getComputeCUDAMgr()->update(); 00374 #endif 00375 return; 00376 } 00377 if ( ! strncasecmp(param,"soluteScalingFactorCharge",MAX_SCRIPT_PARAM_SIZE)) { 00378 soluteScalingFactorCharge = atof(value); 00379 if (soluteScalingFactorCharge < 0.0) { 00380 NAMD_die("Solute scaling factor for electrostatics " 00381 "should be non-negative\n"); 00382 } 00383 return; 00384 } 00385 00386 char *error = new char[2 * MAX_SCRIPT_PARAM_SIZE + 100]; 00387 sprintf(error,"Setting parameter %s from script failed!\n",param); 00388 NAMD_die(error); 00389 00390 }
| void SimParameters::send_SimParameters | ( | MOStream * | msg | ) |
Definition at line 6967 of file SimParameters.C.
References binAtomFile, binCoorFile, binRefFile, binVelFile, MOStream::end(), FFTWWisdomString, mgridforcelist, MGridforceParamsList::pack_data(), MOStream::put(), and tclBCScript.
06969 { 06970 /*MOStream *msg = com_obj->newOutputStream(ALLBUTME, SIMPARAMSTAG, BUFSIZE); 06971 if ( msg == NULL ) 06972 { 06973 NAMD_die("memory allocation failed in SimParameters::send_SimParameters"); 06974 }*/ 06975 06976 msg->put(sizeof(SimParameters),(char*)this); 06977 if ( FFTWWisdomString ) { 06978 int fftwlen = strlen(FFTWWisdomString) + 1; 06979 msg->put(fftwlen); 06980 msg->put(fftwlen,FFTWWisdomString); 06981 } 06982 if ( tclBCScript ) { 06983 int tcllen = strlen(tclBCScript) + 1; 06984 msg->put(tcllen); 06985 msg->put(tcllen,tclBCScript); 06986 } 06987 06988 #ifdef MEM_OPT_VERSION 06989 int filelen = strlen(binAtomFile)+1; 06990 msg->put(filelen); 06991 msg->put(filelen, binAtomFile); 06992 06993 filelen = strlen(binCoorFile)+1; 06994 msg->put(filelen); 06995 msg->put(filelen, binCoorFile); 06996 06997 if(binVelFile) { 06998 filelen = strlen(binVelFile)+1; 06999 msg->put(filelen); 07000 msg->put(filelen, binVelFile); 07001 } 07002 07003 if(binRefFile) { 07004 filelen = strlen(binRefFile)+1; 07005 msg->put(filelen); 07006 msg->put(filelen, binRefFile); 07007 } 07008 #endif 07009 07010 mgridforcelist.pack_data(msg); 07011 07012 msg->end(); 07013 }
| int SimParameters::setupIDWS | ( | ) |
Definition at line 7094 of file SimParameters.C.
References alchIDWSFreq, alchLambdaIDWS, alchOutFreq, iout, iWARN(), NAMD_die(), and outputEnergies.
Referenced by scriptSet().
07094 { 07095 if (alchLambdaIDWS < 0.) return 0; 07096 if (alchLambdaIDWS > 1.) { 07097 NAMD_die("alchLambdaIDWS should be either in the range [0.0, 1.0], or negative (disabled).\n"); 07098 } 07099 /* 07100 * The internal parameter alchIDWSFreq determines the number of steps of MD 07101 * before each switch of the value of alchLambda2. At most this occurs every 07102 * time the energy is evaluated and thus the default is the greater of 07103 * fullElectFrequency and nonbondedFrequency. However, this choice fails to 07104 * report alternating values if output is printed less often than every step 07105 * (which is almost certainly true). Thus the frequency is reset to match 07106 * alchOutFreq or, if that is zero, outputEnergies. Note that, if 07107 * alchOutFreq > 0 but != outputEnergies, then the data going to stdout 07108 * are likely not useful since the comparison value is difficult to infer. 07109 */ 07110 alchIDWSFreq = fullElectFrequency > 0 ? fullElectFrequency : nonbondedFrequency; 07111 if ( !alchOutFreq && outputEnergies > alchIDWSFreq ) alchIDWSFreq = outputEnergies; 07112 if ( alchOutFreq > alchIDWSFreq ) alchIDWSFreq = alchOutFreq; 07113 if ( alchOutFreq && alchOutFreq != outputEnergies) { 07114 iout << iWARN << "alchOutFreq and outputEnergies do not match. IDWS ouput" 07115 << " to stdout may not be useful!\n" << endi; 07116 } 07117 return 1; 07118 }
Definition at line 967 of file SimParameters.h.
Definition at line 623 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD(), and scriptSet().
Definition at line 618 of file SimParameters.h.
Referenced by Controller::receivePressure(), Controller::rescaleaccelMD(), and ComputeGlobal::saveTotalForces().
Definition at line 616 of file SimParameters.h.
Referenced by ComputeHomeTuples< TholeElem, Thole, TholeValue >::ComputeHomeTuples(), Sequencer::integrate(), Sequencer::rescaleaccelMD(), Controller::rescaleaccelMD(), and ComputeGlobal::saveTotalForces().
Definition at line 617 of file SimParameters.h.
Referenced by ComputeHomeTuples< TholeElem, Thole, TholeValue >::ComputeHomeTuples(), Sequencer::integrate(), Sequencer::rescaleaccelMD(), and Controller::rescaleaccelMD().
Definition at line 622 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD(), and scriptSet().
Definition at line 619 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD().
Definition at line 627 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD().
Definition at line 631 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD().
Definition at line 629 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 628 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD().
Definition at line 638 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD().
Definition at line 636 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD().
| char SimParameters::accelMDGRestartFile[128] |
Definition at line 637 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD(), and scriptSet().
Definition at line 635 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD(), and scriptSet().
Definition at line 634 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD(), and scriptSet().
Definition at line 633 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD().
Definition at line 620 of file SimParameters.h.
Referenced by Sequencer::rescaleaccelMD(), and Controller::rescaleaccelMD().
Definition at line 615 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 621 of file SimParameters.h.
Referenced by Controller::receivePressure(), and Controller::rescaleaccelMD().
Definition at line 625 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD(), and scriptSet().
Definition at line 624 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD(), and scriptSet().
Definition at line 649 of file SimParameters.h.
Referenced by Controller::adaptTempInit().
Definition at line 650 of file SimParameters.h.
Referenced by Controller::adaptTempInit().
Definition at line 652 of file SimParameters.h.
Referenced by Controller::adaptTempInit().
Definition at line 642 of file SimParameters.h.
Referenced by Controller::adaptTempUpdate().
Definition at line 651 of file SimParameters.h.
Referenced by Controller::adaptTempInit().
Definition at line 643 of file SimParameters.h.
Referenced by Controller::rescaleVelocities().
Definition at line 646 of file SimParameters.h.
Referenced by Sequencer::adaptTempUpdate(), and Controller::adaptTempUpdate().
| char SimParameters::adaptTempInFile[128] |
Definition at line 655 of file SimParameters.h.
Referenced by Controller::adaptTempInit().
Definition at line 653 of file SimParameters.h.
Referenced by Sequencer::langevinVelocities(), and Sequencer::langevinVelocitiesBBK2().
Definition at line 644 of file SimParameters.h.
Referenced by Sequencer::adaptTempUpdate(), Controller::adaptTempUpdate(), and Controller::rescaleVelocities().
Definition at line 641 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 645 of file SimParameters.h.
Referenced by Controller::adaptTempUpdate().
Definition at line 658 of file SimParameters.h.
Referenced by Controller::adaptTempUpdate().
Definition at line 654 of file SimParameters.h.
Referenced by Controller::rescaleVelocities().
| char SimParameters::adaptTempRestartFile[128] |
Definition at line 656 of file SimParameters.h.
Referenced by Controller::adaptTempInit().
Definition at line 657 of file SimParameters.h.
Referenced by Controller::adaptTempInit(), and Controller::adaptTempWriteRestart().
Definition at line 648 of file SimParameters.h.
Referenced by Controller::adaptTempInit().
Definition at line 647 of file SimParameters.h.
Referenced by Controller::adaptTempInit().
Definition at line 434 of file SimParameters.h.
Referenced by CrosstermElem::computeForce().
Definition at line 428 of file SimParameters.h.
Referenced by getBondLambda().
Definition at line 433 of file SimParameters.h.
Referenced by TholeElem::computeForce(), ComputePmeUtil::select(), and ComputeNonbondedUtil::select().
Definition at line 411 of file SimParameters.h.
Referenced by ComputePmeUtil::select().
Definition at line 406 of file SimParameters.h.
Referenced by Controller::outputFepEnergy(), and Controller::writeFepEnergyData().
Definition at line 408 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 397 of file SimParameters.h.
Referenced by getCurrentLambda2(), Controller::outputFepEnergy(), setupIDWS(), and Controller::writeFepEnergyData().
Definition at line 394 of file SimParameters.h.
Referenced by Controller::outputFepEnergy(), Controller::outputTiEnergy(), Controller::printFepMessage(), Controller::printTiMessage(), scriptSet(), and Controller::writeFepEnergyData().
Definition at line 395 of file SimParameters.h.
Referenced by Controller::outputFepEnergy(), Controller::printFepMessage(), and scriptSet().
Definition at line 398 of file SimParameters.h.
Referenced by getCurrentLambda(), getLambdaDelta(), Controller::outputTiEnergy(), Controller::printEnergies(), Controller::printFepMessage(), Controller::printTiMessage(), scriptSet(), and Controller::writeTiEnergyData().
Definition at line 396 of file SimParameters.h.
Referenced by getCurrentLambda2(), Controller::outputFepEnergy(), Controller::printFepMessage(), scriptSet(), setupIDWS(), and Controller::writeFepEnergyData().
Definition at line 393 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 407 of file SimParameters.h.
Referenced by Controller::outputFepEnergy(), and Controller::outputTiEnergy().
Definition at line 405 of file SimParameters.h.
Referenced by Controller::outputFepEnergy(), Controller::outputTiEnergy(), and setupIDWS().
Definition at line 422 of file SimParameters.h.
Referenced by getRepLambda(), and getVdwLambda().
Definition at line 404 of file SimParameters.h.
Referenced by Controller::outputFepEnergy(), Controller::outputTiEnergy(), Controller::printFepMessage(), and Controller::writeFepEnergyData().
Definition at line 391 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 417 of file SimParameters.h.
Referenced by getVdwLambda().
Definition at line 409 of file SimParameters.h.
Referenced by ComputeNonbondedUtil::select().
Definition at line 392 of file SimParameters.h.
Referenced by getVdwLambda(), and ComputeNonbondedUtil::select().
Definition at line 528 of file SimParameters.h.
Referenced by ComputeNonbondedSelf::doForce(), ComputeNonbondedPair::doForce(), and ComputeNonbondedCUDA::recvYieldDevice().
Definition at line 529 of file SimParameters.h.
Referenced by ComputeNonbondedSelf::doForce(), ComputeNonbondedPair::doForce(), and HomePatch::gbisComputeAfterP1().
Definition at line 988 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 682 of file SimParameters.h.
Referenced by Controller::berendsenPressure(), and scriptSet().
Definition at line 684 of file SimParameters.h.
Referenced by Sequencer::berendsenPressure(), and Controller::berendsenPressure().
Definition at line 680 of file SimParameters.h.
Referenced by Sequencer::berendsenPressure(), Controller::berendsenPressure(), ComputeGridForce::doForce(), and scriptSet().
Definition at line 683 of file SimParameters.h.
Referenced by Controller::berendsenPressure(), and scriptSet().
Definition at line 681 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 1026 of file SimParameters.h.
Referenced by receive_SimParameters(), and send_SimParameters().
Definition at line 1027 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 1028 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 802 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 582 of file SimParameters.h.
Definition at line 584 of file SimParameters.h.
Definition at line 585 of file SimParameters.h.
Definition at line 559 of file SimParameters.h.
Referenced by ComputeGlobal::ComputeGlobal(), ComputeMgr::createComputes(), Sequencer::integrate(), and Sequencer::minimize().
Definition at line 927 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 1035 of file SimParameters.h.
Referenced by WorkDistrib::mapComputes(), and ComputeMgr::updateLocalComputes4().
| char SimParameters::consForceFile[128] |
Definition at line 879 of file SimParameters.h.
Definition at line 878 of file SimParameters.h.
Referenced by NamdState::loadStructure(), WorkDistrib::mapComputes(), Molecule::receive_Molecule(), and Molecule::send_Molecule().
Definition at line 880 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 548 of file SimParameters.h.
Referenced by Parameters::Parameters().
Definition at line 522 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 849 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 856 of file SimParameters.h.
Referenced by ComputeCylindricalBC::ComputeCylindricalBC().
Definition at line 857 of file SimParameters.h.
Referenced by ComputeCylindricalBC::ComputeCylindricalBC().
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 846 of file SimParameters.h.
Referenced by WorkDistrib::mapComputes().
Definition at line 850 of file SimParameters.h.
Referenced by ComputeCylindricalBC::ComputeCylindricalBC().
Definition at line 851 of file SimParameters.h.
Referenced by ComputeCylindricalBC::ComputeCylindricalBC().
Definition at line 848 of file SimParameters.h.
Referenced by ComputeCylindricalBC::ComputeCylindricalBC().
Definition at line 974 of file SimParameters.h.
Definition at line 974 of file SimParameters.h.
Definition at line 974 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 970 of file SimParameters.h.
Definition at line 970 of file SimParameters.h.
Definition at line 970 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 581 of file SimParameters.h.
Definition at line 164 of file SimParameters.h.
Referenced by recursive_bisect_with_curve().
Definition at line 967 of file SimParameters.h.
Definition at line 967 of file SimParameters.h.
Definition at line 540 of file SimParameters.h.
Referenced by BondElem::computeForce(), and scriptSet().
Definition at line 538 of file SimParameters.h.
Referenced by BondElem::computeForce(), HomePatch::hardWallDrude(), scriptSet(), and Sequencer::submitMinimizeReductions().
Definition at line 536 of file SimParameters.h.
Referenced by NamdState::loadStructure().
Definition at line 534 of file SimParameters.h.
Referenced by BondElem::computeForce(), Sequencer::hardWallDrude(), HomePatch::hardWallDrude(), Sequencer::newMinimizeDirection(), Sequencer::newMinimizePosition(), scriptSet(), and Sequencer::submitMinimizeReductions().
Definition at line 541 of file SimParameters.h.
Referenced by ComputeNonbondedUtil::select().
Definition at line 533 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 535 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 861 of file SimParameters.h.
Referenced by ComputeEField::doForce(), and scriptSet().
Definition at line 862 of file SimParameters.h.
Referenced by ComputeEField::doForce(), and scriptSet().
Definition at line 860 of file SimParameters.h.
Referenced by ComputeEField::doForce().
Definition at line 859 of file SimParameters.h.
Referenced by WorkDistrib::mapComputes().
Definition at line 863 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 669 of file SimParameters.h.
Referenced by NamdState::loadStructure(), Molecule::receive_Molecule(), and Molecule::send_Molecule().
| char SimParameters::extCoordFilename[128] |
Definition at line 459 of file SimParameters.h.
Referenced by ComputeExtMgr::recvCoord().
| char SimParameters::extForceFilename[128] |
Definition at line 460 of file SimParameters.h.
Referenced by ComputeExtMgr::recvCoord().
| char SimParameters::extForcesCommand[256] |
Definition at line 458 of file SimParameters.h.
Referenced by ComputeExtMgr::recvCoord().
Definition at line 457 of file SimParameters.h.
Referenced by WorkDistrib::mapComputes().
Definition at line 875 of file SimParameters.h.
Definition at line 876 of file SimParameters.h.
Definition at line 874 of file SimParameters.h.
Referenced by Molecule::delete_qm_bonded(), NamdState::loadStructure(), and Molecule::prepare_qm().
Definition at line 815 of file SimParameters.h.
Referenced by PmeXPencil::fft_init(), PmeYPencil::fft_init(), PmeZPencil::fft_init(), and ComputePmeMgr::initialize().
Definition at line 816 of file SimParameters.h.
Referenced by PmeXPencil::fft_init(), PmeYPencil::fft_init(), PmeZPencil::fft_init(), and ComputePmeMgr::initialize().
Definition at line 817 of file SimParameters.h.
| char SimParameters::FFTWWisdomFile[128] |
Definition at line 818 of file SimParameters.h.
Definition at line 819 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 899 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 675 of file SimParameters.h.
Referenced by Controller::langevinPiston1(), Controller::langevinPiston2(), Controller::receivePressure(), and scriptSet().
Definition at line 676 of file SimParameters.h.
Referenced by Controller::langevinPiston1(), Controller::langevinPiston2(), Controller::receivePressure(), and scriptSet().
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 563 of file SimParameters.h.
Referenced by CollectionMgr::submitForces().
Definition at line 562 of file SimParameters.h.
Referenced by ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), HomePatch::positionsReady(), scriptSet(), ComputeNonbondedUtil::select(), and ParallelIOMgr::updateMolInfo().
Definition at line 561 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 722 of file SimParameters.h.
Definition at line 721 of file SimParameters.h.
Definition at line 719 of file SimParameters.h.
Definition at line 720 of file SimParameters.h.
Definition at line 718 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 766 of file SimParameters.h.
Referenced by ComputeFmmSerialMgr::recvCoord().
Definition at line 765 of file SimParameters.h.
Referenced by WorkDistrib::mapComputes(), WorkDistrib::patchMapInit(), and ComputeNonbondedUtil::select().
Definition at line 767 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 557 of file SimParameters.h.
Referenced by ComputeMgr::createComputes(), and ParallelIOMgr::freeMolSpace().
Definition at line 519 of file SimParameters.h.
Referenced by ComputeNonbondedSelf::doForce(), ComputeNonbondedPair::doForce(), and ComputeNonbondedCUDA::recvYieldDevice().
Definition at line 724 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 526 of file SimParameters.h.
Referenced by ComputeNonbondedSelf::doForce(), ComputeNonbondedPair::doForce(), HomePatch::gbisComputeAfterP1(), and HomePatch::gbisComputeAfterP2().
Definition at line 525 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 518 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 520 of file SimParameters.h.
Referenced by ComputeGlobal::ComputeGlobal(), and WorkDistrib::mapComputes().
Definition at line 1010 of file SimParameters.h.
Referenced by NamdState::configListInit(), and NamdState::loadStructure().
Definition at line 549 of file SimParameters.h.
Referenced by ComputeMgr::createComputes(), and WorkDistrib::mapComputes().
Definition at line 580 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 993 of file SimParameters.h.
Referenced by NamdState::loadStructure().
Definition at line 967 of file SimParameters.h.
Definition at line 911 of file SimParameters.h.
Referenced by HomePatch::doGroupSizeCheck().
Definition at line 145 of file SimParameters.h.
Referenced by NamdHybridLB::NamdHybridLB().
Definition at line 957 of file SimParameters.h.
Definition at line 908 of file SimParameters.h.
Definition at line 979 of file SimParameters.h.
Referenced by Output::coordinate(), Output::coordinateNeeded(), and Controller::printEnergies().
Definition at line 982 of file SimParameters.h.
Referenced by ComputeMgr::createComputes(), and GlobalMasterIMD::GlobalMasterIMD().
Definition at line 984 of file SimParameters.h.
Referenced by ComputeMgr::createComputes(), and GlobalMasterIMD::GlobalMasterIMD().
Definition at line 977 of file SimParameters.h.
Referenced by Output::coordinate(), Output::coordinateNeeded(), ComputeMgr::createComputes(), and Controller::printEnergies().
Definition at line 978 of file SimParameters.h.
Referenced by GlobalMasterIMD::GlobalMasterIMD().
Definition at line 980 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 524 of file SimParameters.h.
Definition at line 523 of file SimParameters.h.
Referenced by ComputeNonbondedSelf::doForce(), ComputeNonbondedPair::doForce(), HomePatch::gbisComputeAfterP2(), and ComputeNonbondedCUDA::recvYieldDevice().
Definition at line 570 of file SimParameters.h.
Referenced by Sequencer::integrate(), Sequencer::langevinVelocities(), Sequencer::langevinVelocitiesBBK1(), Sequencer::langevinVelocitiesBBK2(), and scriptSet().
Definition at line 568 of file SimParameters.h.
Referenced by NamdState::loadStructure().
Definition at line 569 of file SimParameters.h.
Referenced by NamdState::loadStructure().
Definition at line 566 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 565 of file SimParameters.h.
Referenced by scriptSet().
Definition at line 687 of file SimParameters.h.
Referenced by Controller::langevinPiston1().
Definition at line 690 of file SimParameters.h.
Referenced by Controller::langevinPiston1(), Controller::langevinPiston2(), and scriptSet().
Definition at line 686 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 689 of file SimParameters.h.
Referenced by Controller::langevinPiston1(), Controller::langevinPiston2(), and scriptSet().
Definition at line 688 of file SimParameters.h.
Referenced by Controller::langevinPiston1(), Controller::langevinPiston2(), and scriptSet().
Definition at line 691 of file SimParameters.h.
Referenced by Controller::langevinPiston1(), Controller::langevinPiston2(), and scriptSet().
Definition at line 567 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 530 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 439 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 438 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 441 of file SimParameters.h.
Definition at line 440 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 1037 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 905 of file SimParameters.h.
Referenced by ComputeNonbondedUtil::select().
Definition at line 577 of file SimParameters.h.
Definition at line 574 of file SimParameters.h.
Referenced by colvarproxy_namd::colvarproxy_namd(), and Sequencer::integrate().
Definition at line 576 of file SimParameters.h.
Definition at line 575 of file SimParameters.h.
Referenced by colvarproxy_namd::colvarproxy_namd(), and scriptSet().
Definition at line 1014 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 945 of file SimParameters.h.
Definition at line 831 of file SimParameters.h.
Referenced by Sequencer::maximumMove(), and scriptSet().
Definition at line 933 of file SimParameters.h.
Definition at line 178 of file SimParameters.h.
Referenced by WorkDistrib::patchMapInit().
Definition at line 931 of file SimParameters.h.
Definition at line 897 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 1045 of file SimParameters.h.
Definition at line 1040 of file SimParameters.h.
Definition at line 1042 of file SimParameters.h.
Definition at line 1043 of file SimParameters.h.
Definition at line 1041 of file SimParameters.h.
Definition at line 1046 of file SimParameters.h.
Definition at line 1044 of file SimParameters.h.
Definition at line 943 of file SimParameters.h.
Referenced by WorkDistrib::patchMapInit().
Definition at line 828 of file SimParameters.h.
Definition at line 825 of file SimParameters.h.
Referenced by NamdState::loadStructure(), and ScriptTcl::run().
Definition at line 830 of file SimParameters.h.
Referenced by Sequencer::minimizationQuenchVelocity(), and scriptSet().
Definition at line 829 of file SimParameters.h.
Referenced by Controller::minimize().
Definition at line 827 of file SimParameters.h.
Definition at line 826 of file SimParameters.h.
Referenced by Controller::minimize().
Definition at line 558 of file SimParameters.h.
Referenced by ComputeMgr::createComputes().
Definition at line 915 of file SimParameters.h.
Referenced by HomePatch::mollyAverage().
Definition at line 913 of file SimParameters.h.
Referenced by Controller::compareChecksums(), Sequencer::integrate(), and Sequencer::minimize().
Definition at line 914 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 734 of file SimParameters.h.
Referenced by ComputeMsmMgr::initialize(), and ComputeMsmSerialMgr::recvCoord().
Definition at line 744 of file SimParameters.h.
Referenced by ComputeMsmMgr::initialize().
Definition at line 745 of file SimParameters.h.
Referenced by ComputeMsmMgr::initialize().
Definition at line 746 of file SimParameters.h.
Referenced by ComputeMsmMgr::initialize().
Definition at line 748 of file SimParameters.h.
Referenced by ComputeMsmMgr::initialize(), and ComputeMsmSerialMgr::recvCoord().
Definition at line 740 of file SimParameters.h.
Referenced by ComputeMsmMgr::initialize(), and ComputeMsmSerialMgr::recvCoord().
Definition at line 727 of file SimParameters.h.
Referenced by WorkDistrib::mapComputes(), WorkDistrib::patchMapInit(), ComputeNonbondedUtil::select(), and Node::startup().
Definition at line 750 of file SimParameters.h.
Referenced by ComputeMsmMgr::initialize(), and ComputeMsmSerialMgr::recvCoord().
Definition at line 730 of file SimParameters.h.
Definition at line 763 of file SimParameters.h.
Referenced by WorkDistrib::mapComputes(), and Node::startup().
Definition at line 737 of file SimParameters.h.
Referenced by ComputeMsmMgr::initialize(), ComputeMsmSerialMgr::recvCoord(), and ComputeNonbondedUtil::select().
Definition at line 757 of file SimParameters.h.
Referenced by ComputeMsmMgr::initialize().
Definition at line 756 of file SimParameters.h.
Referenced by ComputeMsmMgr::initialize().
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 902 of file SimParameters.h.
Referenced by Sequencer::integrate().
Definition at line 700 of file SimParameters.h.
Referenced by Controller::Controller(), Controller::multigatorCalcEnthalpy(), and Controller::multigratorTemperature().
Definition at line 693 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 696 of file SimParameters.h.
Referenced by LdbCoordinator::initialize(), Sequencer::integrate(), Sequencer::multigratorPressure(), Controller::multigratorPressure(), Sequencer::multigratorTemperature(), and Controller::multigratorTemperature().
Definition at line 695 of file SimParameters.h.
Referenced by Controller::multigatorCalcEnthalpy(), and Controller::multigratorPressure().
Definition at line 694 of file SimParameters.h.
Referenced by Controller::multigatorCalcEnthalpy(), and Controller::multigratorPressure().
Definition at line 699 of file SimParameters.h.
Referenced by Sequencer::integrate(), Sequencer::multigratorTemperature(), and Controller::multigratorTemperature().
Definition at line 698 of file SimParameters.h.
Referenced by Controller::Controller(), and Controller::multigratorTemperature().
Definition at line 697 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 939 of file SimParameters.h.
Definition at line 941 of file SimParameters.h.
Definition at line 935 of file SimParameters.h.
Definition at line 937 of file SimParameters.h.
Definition at line 1025 of file SimParameters.h.
Referenced by ParallelIOMgr::initialize(), and NamdState::loadStructure().
Definition at line 1032 of file SimParameters.h.
Referenced by ParallelIOMgr::initialize(), NamdState::loadStructure(), and WorkDistrib::patchMapInit().
Definition at line 1033 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 891 of file SimParameters.h.
Referenced by ComputeNonbondedCUDA::finishReductions().
Definition at line 882 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 885 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 947 of file SimParameters.h.
Referenced by WorkDistrib::createAtomLists().
Definition at line 894 of file SimParameters.h.
Referenced by Sequencer::integrate(), and Controller::printEnergies().
Definition at line 888 of file SimParameters.h.
Referenced by Controller::printTiming().
Definition at line 544 of file SimParameters.h.
Definition at line 545 of file SimParameters.h.
Definition at line 543 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 546 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 780 of file SimParameters.h.
Referenced by ComputePmeMgr::initialize().
Definition at line 771 of file SimParameters.h.
Referenced by ComputeQMMgr::recvPntChrg(), and ComputeNonbondedUtil::select().
Definition at line 773 of file SimParameters.h.
Referenced by ComputePme::ComputePme(), ComputePmeMgr::initialize(), and ComputePmeCUDAMgr::setupPencils().
Definition at line 774 of file SimParameters.h.
Referenced by ComputePme::ComputePme(), ComputePmeMgr::initialize(), and ComputePmeCUDAMgr::setupPencils().
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.
Definition at line 772 of file SimParameters.h.
Referenced by ComputePme::ComputePme(), ComputePmeMgr::initialize(), and ComputePmeCUDAMgr::setupPencils().
Definition at line 779 of file SimParameters.h.
Referenced by ComputePmeMgr::initialize().
Definition at line 778 of file SimParameters.h.
Referenced by ComputePmeMgr::initialize().
Definition at line 788 of file SimParameters.h.
Referenced by ComputeNonbondedCUDA::ComputeNonbondedCUDA(), ComputePme::ComputePme(), ComputePmeMgr::initialize(), PmePencil< CBase_PmeZPencil >::order_init(), and ComputeNonbondedCUDA::recvYieldDevice().
Definition at line 769 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 781 of file SimParameters.h.
Referenced by ComputePmeMgr::initialize().
Definition at line 782 of file SimParameters.h.
Referenced by ComputePmeMgr::initialize(), and ComputePmeCUDAMgr::setupPencils().
Definition at line 786 of file SimParameters.h.
Referenced by ComputePmeMgr::initialize().
Definition at line 783 of file SimParameters.h.
Referenced by ComputePmeMgr::initialize(), and ComputePmeCUDAMgr::setupPencils().
Definition at line 785 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 777 of file SimParameters.h.
Referenced by ComputePmeMgr::initialize().
Definition at line 787 of file SimParameters.h.
Referenced by ComputePmeMgr::initialize_pencils().
Definition at line 770 of file SimParameters.h.
Definition at line 707 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 708 of file SimParameters.h.
Referenced by Controller::Controller(), and WorkDistrib::mapComputes().
Definition at line 709 of file SimParameters.h.
Referenced by ComputeEwald::ComputeEwald().
Definition at line 710 of file SimParameters.h.
Referenced by ComputeEwald::ComputeEwald().
Definition at line 711 of file SimParameters.h.
Referenced by ComputeEwald::ComputeEwald().
Definition at line 706 of file SimParameters.h.
Referenced by Controller::Controller(), and Controller::printEnergies().
Definition at line 704 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 705 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 515 of file SimParameters.h.
Referenced by Sequencer::submitMinimizeReductions().
Definition at line 1015 of file SimParameters.h.
Definition at line 1019 of file SimParameters.h.
Referenced by isRecvSpanningTreeOn(), and isRecvSpanningTreeUnset().
Definition at line 1018 of file SimParameters.h.
Referenced by isSendSpanningTreeOn(), and isSendSpanningTreeUnset().
Definition at line 1021 of file SimParameters.h.
Referenced by Node::startup().
| char SimParameters::qmBaseDir[256] |
Definition at line 473 of file SimParameters.h.
Referenced by ComputeQMMgr::recvPntChrg().
| char SimParameters::qmBondColumn[16] |
Definition at line 483 of file SimParameters.h.
Definition at line 484 of file SimParameters.h.
Referenced by Molecule::prepare_qm().
Definition at line 482 of file SimParameters.h.
Referenced by Molecule::prepare_qm().
Definition at line 488 of file SimParameters.h.
Referenced by Molecule::prepare_qm().
| char SimParameters::qmBondSchemeS[16] |
Definition at line 487 of file SimParameters.h.
Definition at line 485 of file SimParameters.h.
Referenced by ComputeQMMgr::recvPartQM().
| char SimParameters::qmBondValueTypeS[16] |
Definition at line 486 of file SimParameters.h.
Definition at line 467 of file SimParameters.h.
Referenced by Molecule::prepare_qm().
Definition at line 471 of file SimParameters.h.
Referenced by ComputeQMMgr::recvPntChrg().
| char SimParameters::qmChrgModeS[16] |
Definition at line 470 of file SimParameters.h.
| char SimParameters::qmColumn[16] |
Definition at line 472 of file SimParameters.h.
Referenced by Molecule::prepare_qm().
Definition at line 508 of file SimParameters.h.
Referenced by Molecule::prepare_qm().
| char SimParameters::qmCSMDFile[128] |
Definition at line 509 of file SimParameters.h.
Definition at line 500 of file SimParameters.h.
Referenced by ComputeQM::initialize(), Molecule::prepare_qm(), and ComputeQMMgr::recvPartQM().
Definition at line 498 of file SimParameters.h.
Referenced by Molecule::prepare_qm().
Definition at line 511 of file SimParameters.h.
Referenced by ComputeQMMgr::storeQMRes().
| char SimParameters::qmExecPath[256] |
Definition at line 468 of file SimParameters.h.
Referenced by ComputeQMMgr::recvPntChrg().
Definition at line 464 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 478 of file SimParameters.h.
Referenced by Molecule::prepare_qm(), and ComputeQMMgr::recvPntChrg().
Definition at line 503 of file SimParameters.h.
Referenced by Molecule::prepare_qm().
Definition at line 506 of file SimParameters.h.
Referenced by Molecule::prepare_qm().
| char SimParameters::qmLSSModeS[16] |
Definition at line 505 of file SimParameters.h.
Definition at line 502 of file SimParameters.h.
Referenced by HomePatch::positionsReady(), Molecule::prepare_qm(), and ComputeQMMgr::recvPartQM().
| char SimParameters::qmLSSResname[5] |
Definition at line 504 of file SimParameters.h.
Referenced by Molecule::prepare_qm().
Definition at line 480 of file SimParameters.h.
Referenced by Molecule::prepare_qm(), and ComputeQMMgr::recvPntChrg().
Definition at line 497 of file SimParameters.h.
Referenced by Molecule::prepare_qm(), and ComputeQMMgr::recvPartQM().
Definition at line 512 of file SimParameters.h.
Referenced by ComputeQMMgr::procQMRes(), and ComputeQMMgr::recvPartQM().
| char SimParameters::qmParamPDB[128] |
Definition at line 465 of file SimParameters.h.
Referenced by NamdState::loadStructure().
Definition at line 466 of file SimParameters.h.
Referenced by NamdState::loadStructure().
Definition at line 493 of file SimParameters.h.
Referenced by ComputeQMMgr::recvPntChrg().
| char SimParameters::qmPCSchemeS[16] |
Definition at line 492 of file SimParameters.h.
Definition at line 499 of file SimParameters.h.
Referenced by Molecule::prepare_qm().
Definition at line 489 of file SimParameters.h.
Referenced by ComputeQMMgr::recvPntChrg().
Definition at line 491 of file SimParameters.h.
Referenced by ComputeQMMgr::recvPntChrg().
| char SimParameters::qmPCSwitchTypeS[16] |
Definition at line 490 of file SimParameters.h.
Definition at line 513 of file SimParameters.h.
Referenced by ComputeQMMgr::procQMRes(), and ComputeQMMgr::recvPartQM().
| char SimParameters::qmPrepProc[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 479 of file SimParameters.h.
Referenced by NamdState::loadStructure().
| char SimParameters::qmSecProc[256] |
Definition at line 474 of file SimParameters.h.
Referenced by ComputeQMMgr::recvPntChrg().
Definition at line 475 of file SimParameters.h.
Referenced by ComputeQMMgr::recvPntChrg().
Definition at line 494 of file SimParameters.h.
Referenced by ComputeQMMgr::recvPartQM().
| char SimParameters::qmSoftware[128] |
Definition at line 469 of file SimParameters.h.
Definition at line 496 of file SimParameters.h.
Referenced by Molecule::prepare_qm().
| unsigned int SimParameters::randomSeed |
Definition at line 716 of file SimParameters.h.
Referenced by colvarproxy_namd::colvarproxy_namd(), Controller::Controller(), Sequencer::Sequencer(), and Node::startup().
Definition at line 989 of file SimParameters.h.
Referenced by buildExclusions().
Definition at line 661 of file SimParameters.h.
Referenced by colvarproxy_namd::colvarproxy_namd(), Sequencer::integrate(), Sequencer::reassignVelocities(), and Controller::reassignVelocities().
Definition at line 664 of file SimParameters.h.
Referenced by Sequencer::reassignVelocities(), and Controller::reassignVelocities().
Definition at line 663 of file SimParameters.h.
Referenced by Sequencer::reassignVelocities(), and Controller::reassignVelocities().
Definition at line 662 of file SimParameters.h.
Referenced by colvarproxy_namd::colvarproxy_namd(), Sequencer::reassignVelocities(), Controller::reassignVelocities(), and scriptSet().
Definition at line 949 of file SimParameters.h.
Referenced by WorkDistrib::patchMapInit().
Definition at line 612 of file SimParameters.h.
Referenced by Controller::adaptTempInit(), colvarproxy_namd::colvarproxy_namd(), Sequencer::integrate(), Sequencer::rescaleVelocities(), and Controller::rescaleVelocities().
Definition at line 613 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 917 of file SimParameters.h.
Referenced by ParallelIOMgr::bcastHydroBasedCounter(), NamdState::configListInit(), WorkDistrib::createAtomLists(), NamdState::loadStructure(), outputCompressedFile(), and Sequencer::rattle1().
Definition at line 922 of file SimParameters.h.
Referenced by HomePatch::hardWallDrude(), HomePatch::minimize_rattle2(), HomePatch::rattle1(), HomePatch::rattle1old(), and HomePatch::rattle2().
Definition at line 921 of file SimParameters.h.
Referenced by HomePatch::minimize_rattle2(), HomePatch::rattle1(), HomePatch::rattle1old(), and HomePatch::rattle2().
Definition at line 920 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 999 of file SimParameters.h.
Referenced by Sequencer::algorithm(), Controller::algorithm(), HomePatch::exchangeAtoms(), and scriptSet().
Definition at line 1000 of file SimParameters.h.
Referenced by HomePatch::exchangeAtoms(), and scriptSet().
Definition at line 1001 of file SimParameters.h.
Referenced by scriptSet().
Definition at line 1002 of file SimParameters.h.
Referenced by scriptSet().
Definition at line 1003 of file SimParameters.h.
Referenced by scriptSet().
Definition at line 1004 of file SimParameters.h.
Referenced by Controller::algorithm(), HomePatch::exchangeCheckpoint(), HomePatch::recvCheckpointLoad(), and scriptSet().
Definition at line 1005 of file SimParameters.h.
Referenced by scriptSet().
| char SimParameters::scriptStringArg1[128] |
Definition at line 1006 of file SimParameters.h.
Referenced by Controller::algorithm(), HomePatch::exchangeCheckpoint(), HomePatch::recvCheckpointLoad(), and scriptSet().
| char SimParameters::scriptStringArg2[128] |
Definition at line 1007 of file SimParameters.h.
Referenced by scriptSet().
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 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 455 of file SimParameters.h.
Referenced by ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples().
scaling factor for solute interactions
Definition at line 447 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 449 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 452 of file SimParameters.h.
Referenced by scriptSet().
REST2 (replica exchange solute tempering) on?
Definition at line 445 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 521 of file SimParameters.h.
Referenced by ComputeNonbondedSelf::doForce(), ComputeNonbondedPair::doForce(), HomePatch::gbisComputeAfterP2(), and ComputeNonbondedCUDA::recvYieldDevice().
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 837 of file SimParameters.h.
Referenced by ComputeSphericalBC::ComputeSphericalBC().
Definition at line 839 of file SimParameters.h.
Referenced by ComputeSphericalBC::ComputeSphericalBC().
Definition at line 834 of file SimParameters.h.
Referenced by WorkDistrib::mapComputes().
Definition at line 841 of file SimParameters.h.
Referenced by ComputeSphericalBC::ComputeSphericalBC().
Definition at line 842 of file SimParameters.h.
Referenced by ComputeSphericalBC::ComputeSphericalBC().
Definition at line 836 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 910 of file SimParameters.h.
Definition at line 948 of file SimParameters.h.
Referenced by WorkDistrib::createAtomLists(), WorkDistrib::patchMapInit(), and HomePatch::positionsReady().
Definition at line 928 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 871 of file SimParameters.h.
Referenced by ComputeStir::ComputeStir(), and scriptSet().
| char SimParameters::stirFilename[128] |
Definition at line 866 of file SimParameters.h.
Definition at line 870 of file SimParameters.h.
Referenced by ComputeStir::doForce().
Definition at line 865 of file SimParameters.h.
Referenced by NamdState::loadStructure(), WorkDistrib::mapComputes(), Molecule::receive_Molecule(), and Molecule::send_Molecule().
Definition at line 872 of file SimParameters.h.
Referenced by ComputeStir::ComputeStir(), and scriptSet().
Definition at line 868 of file SimParameters.h.
Definition at line 869 of file SimParameters.h.
How frequently (time steps) stochastic velocity rescaling occurs.
Definition at line 605 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 608 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 592 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 602 of file SimParameters.h.
Referenced by Controller::Controller().
Temperature for stochastic velocity rescaling.
Definition at line 599 of file SimParameters.h.
Referenced by colvarproxy_namd::colvarproxy_namd(), scriptSet(), and Controller::stochRescaleCoefficient().
Definition at line 1036 of file SimParameters.h.
Referenced by WorkDistrib::mapComputes(), and ComputeMgr::updateLocalComputes4().
Definition at line 713 of file SimParameters.h.
Referenced by Controller::Controller(), and readExtendedSystem().
Definition at line 714 of file SimParameters.h.
Referenced by Controller::Controller(), and readExtendedSystem().
Definition at line 531 of file SimParameters.h.
Referenced by ComputeLCPO::ComputeLCPO().
Definition at line 702 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 556 of file SimParameters.h.
Referenced by ComputeTclBC::doWork(), and scriptSet().
Definition at line 554 of file SimParameters.h.
Referenced by WorkDistrib::mapComputes().
Definition at line 555 of file SimParameters.h.
Referenced by ComputeTclBC::ComputeTclBC(), receive_SimParameters(), and send_SimParameters().
Definition at line 550 of file SimParameters.h.
Referenced by ComputeGlobal::ComputeGlobal(), ComputeMgr::createComputes(), Sequencer::integrate(), and Sequencer::minimize().
Definition at line 552 of file SimParameters.h.
Referenced by ComputeTclBC::ComputeTclBC().
Definition at line 587 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 589 of file SimParameters.h.
Referenced by colvarproxy_namd::colvarproxy_namd(), and Controller::tcoupleVelocities().
Definition at line 926 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 930 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 960 of file SimParameters.h.
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 1009 of file SimParameters.h.
Referenced by NamdState::loadStructure(), and Molecule::Molecule().
Definition at line 672 of file SimParameters.h.
Referenced by Controller::langevinPiston1(), and scriptSet().
Definition at line 673 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 797 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 808 of file SimParameters.h.
Definition at line 790 of file SimParameters.h.
Referenced by WorkDistrib::mapComputes().
Definition at line 671 of file SimParameters.h.
Referenced by Controller::calcPressure(), Controller::Controller(), Controller::langevinPiston1(), Controller::langevinPiston2(), and scriptSet().
Definition at line 666 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 1012 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 793 of file SimParameters.h.
Referenced by ComputeNonbondedCUDA::ComputeNonbondedCUDA(), isPmeProcessor(), WorkDistrib::mapComputes(), ComputeNonbondedCUDA::recvYieldDevice(), and Node::startup().
Definition at line 924 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 996 of file SimParameters.h.
Definition at line 990 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