#include <SimParameters.h>
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Definition at line 601 of file SimParameters.h. 00601 {};
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Definition at line 602 of file SimParameters.h. 00602 {
00603 initialize_config_data(c,cwd);
00604 };
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Definition at line 605 of file SimParameters.h. 00605 {};
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Definition at line 78 of file SimParameters.C. References ParseOptions::check_consistancy(), NAMD_die(), and ParseOptions::set(). 00080 {
00081
00082 ParseOptions opts; // Object to check consistency of config file
00083
00084 config_parser(opts);
00085
00087 if (!opts.check_consistancy())
00088 {
00089 NAMD_die("Internal error in configuration file parser");
00090 }
00091
00092 // Now, feed the object with the actual configuration options through the
00093 // ParseOptions file and make sure everything is OK
00094 if (!opts.set(*config))
00095 {
00096 NAMD_die("ERROR(S) IN THE CONFIGURATION FILE");
00097 }
00098
00100
00101 check_config(opts,config,cwd);
00102
00103 print_config(opts,config,cwd);
00104
00105 }
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Definition at line 4006 of file SimParameters.C. References FFTWWisdomString, MIStream::get(), and tclBCScript. 04008 {
04009 msg->get(sizeof(SimParameters),(char*)this);
04010 if ( FFTWWisdomString ) {
04011 int fftwlen;
04012 msg->get(fftwlen);
04013 FFTWWisdomString = new char[fftwlen];
04014 msg->get(fftwlen,FFTWWisdomString);
04015 #ifdef NAMD_FFTW
04016 fftw_import_wisdom_from_string(FFTWWisdomString);
04017 #endif
04018 }
04019 if ( tclBCScript ) {
04020 int tcllen;
04021 msg->get(tcllen);
04022 tclBCScript = new char[tcllen];
04023 msg->get(tcllen,tclBCScript);
04024 }
04025
04026 delete msg;
04027 }
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Definition at line 119 of file SimParameters.C. References atobool(), berendsenPressureCompressibility, berendsenPressureOn, berendsenPressureRelaxationTime, berendsenPressureTarget, commOnly, consForceScaling, constraintScaling, eField, eFieldFreq, eFieldPhase, fepEquilSteps, firstTimestep, fixedAtomsOn, gridforceScale, gridforceVOffset, initialTemp, lambda, lambda2, langevinPistonDecay, langevinPistonOn, langevinPistonPeriod, langevinPistonTarget, langevinPistonTemp, langevinTemp, MAX_SCRIPT_PARAM_SIZE, N, NAMD_die(), nonbondedScaling, outputFilename, reassignTemp, rescaleTemp, SCRIPT_PARSE_BOOL, SCRIPT_PARSE_FLOAT, SCRIPT_PARSE_INT, SCRIPT_PARSE_STRING, SCRIPT_PARSE_VECTOR, scriptArg1, scriptArg2, scriptArg3, scriptArg4, scriptArg5, ComputeNonbondedUtil::select(), stirAxis, stirPivot, surfaceTensionTarget, tclBCArgs, useConstantArea, useConstantRatio, useFlexibleCell, and useGroupPressure. Referenced by Node::scriptParam(). 00119 {
00120
00121 #define MAX_SCRIPT_PARAM_SIZE 128
00122 #define SCRIPT_PARSE_BOOL(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atobool(value); return; } }
00123 #define SCRIPT_PARSE_INT(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atoi(value); return; } }
00124 #define SCRIPT_PARSE_FLOAT(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atof(value); return; } }
00125 #define SCRIPT_PARSE_VECTOR(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR).set(value); return; } }
00126 #define SCRIPT_PARSE_STRING(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { strcpy(VAR,value); return; } }
00127
00128 SCRIPT_PARSE_FLOAT("scriptArg1",scriptArg1)
00129 SCRIPT_PARSE_FLOAT("scriptArg2",scriptArg2)
00130 SCRIPT_PARSE_FLOAT("scriptArg3",scriptArg3)
00131 SCRIPT_PARSE_FLOAT("scriptArg4",scriptArg4)
00132 SCRIPT_PARSE_FLOAT("scriptArg5",scriptArg5)
00133 SCRIPT_PARSE_INT("numsteps",N)
00134 SCRIPT_PARSE_INT("firsttimestep",firstTimestep)
00135 SCRIPT_PARSE_FLOAT("reassignTemp",reassignTemp)
00136 SCRIPT_PARSE_FLOAT("rescaleTemp",rescaleTemp)
00137 // SCRIPT_PARSE_BOOL("Langevin",langevinOn)
00138 SCRIPT_PARSE_FLOAT("langevinTemp",langevinTemp)
00139 SCRIPT_PARSE_FLOAT("initialTemp",initialTemp)
00140 SCRIPT_PARSE_BOOL("useGroupPressure",useGroupPressure)
00141 SCRIPT_PARSE_BOOL("useFlexibleCell",useFlexibleCell)
00142 SCRIPT_PARSE_BOOL("useConstantArea",useConstantArea)
00143 SCRIPT_PARSE_BOOL("useConstantRatio",useConstantRatio)
00144 SCRIPT_PARSE_BOOL("LangevinPiston",langevinPistonOn)
00145 SCRIPT_PARSE_FLOAT("LangevinPistonTarget",langevinPistonTarget)
00146 SCRIPT_PARSE_FLOAT("LangevinPistonPeriod",langevinPistonPeriod)
00147 SCRIPT_PARSE_FLOAT("LangevinPistonDecay",langevinPistonDecay)
00148 SCRIPT_PARSE_FLOAT("LangevinPistonTemp",langevinPistonTemp)
00149 SCRIPT_PARSE_FLOAT("SurfaceTensionTarget",surfaceTensionTarget)
00150 SCRIPT_PARSE_BOOL("BerendsenPressure",berendsenPressureOn)
00151 SCRIPT_PARSE_FLOAT("BerendsenPressureTarget",berendsenPressureTarget)
00152 SCRIPT_PARSE_FLOAT("BerendsenPressureCompressibility",
00153 berendsenPressureCompressibility)
00154 SCRIPT_PARSE_FLOAT("BerendsenPressureRelaxationTime",
00155 berendsenPressureRelaxationTime)
00156 SCRIPT_PARSE_FLOAT("constraintScaling",constraintScaling)
00157 SCRIPT_PARSE_FLOAT("consForceScaling",consForceScaling)
00158 SCRIPT_PARSE_STRING("outputname",outputFilename)
00159 SCRIPT_PARSE_STRING("tclBCArgs",tclBCArgs)
00160 SCRIPT_PARSE_VECTOR("eField",eField)
00161 SCRIPT_PARSE_FLOAT("eFieldFreq",eFieldFreq)
00162 SCRIPT_PARSE_FLOAT("eFieldPhase",eFieldPhase)
00163 SCRIPT_PARSE_VECTOR("stirAxis",stirAxis)
00164 SCRIPT_PARSE_VECTOR("stirPivot",stirPivot)
00165 /* BEGIN gf */
00166 SCRIPT_PARSE_VECTOR("gridforcescale",gridforceScale)
00167 SCRIPT_PARSE_VECTOR("gridforcevoff",gridforceVOffset)
00168 /* END gf */
00169
00170 if ( ! strncasecmp(param,"fixedatoms",MAX_SCRIPT_PARAM_SIZE) ) {
00171 if ( ! fixedAtomsOn )
00172 NAMD_die("FixedAtoms may not be enabled in a script.");
00173 if ( ! fixedAtomsForces )
00174 NAMD_die("To use fixedAtoms in script first use fixedAtomsForces yes.");
00175 fixedAtomsOn = atobool(value);
00176 return;
00177 }
00178
00179 //Modifications for alchemical fep
00180 //SD & CC, CNRS - LCTN, Nancy
00181 SCRIPT_PARSE_INT("fepEquilSteps",fepEquilSteps)
00182
00183 if ( ! strncasecmp(param,"lambda",MAX_SCRIPT_PARAM_SIZE) ) {
00184 lambda = atof(value);
00185 ComputeNonbondedUtil::select();
00186 return;
00187 }
00188
00189 if ( ! strncasecmp(param,"lambda2",MAX_SCRIPT_PARAM_SIZE) ) {
00190 lambda2 = atof(value);
00191 ComputeNonbondedUtil::select();
00192 return;
00193 }
00194 //fepe
00195
00196 if ( ! strncasecmp(param,"tiLambda",MAX_SCRIPT_PARAM_SIZE) ) {
00197 lambda = atof(value);
00198 ComputeNonbondedUtil::select();
00199 return;
00200 }
00201
00202 if ( ! strncasecmp(param,"nonbondedScaling",MAX_SCRIPT_PARAM_SIZE) ) {
00203 nonbondedScaling = atof(value);
00204 ComputeNonbondedUtil::select();
00205 return;
00206 }
00207 if ( ! strncasecmp(param,"commOnly",MAX_SCRIPT_PARAM_SIZE) ) {
00208 commOnly = atobool(value);
00209 ComputeNonbondedUtil::select();
00210 return;
00211 }
00212
00213 char *error = new char[2 * MAX_SCRIPT_PARAM_SIZE + 100];
00214 sprintf(error,"Setting parameter %s from script failed!\n",param);
00215 NAMD_die(error);
00216
00217 }
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Definition at line 3972 of file SimParameters.C. References ALLBUTME, BUFSIZE, MOStream::end(), FFTWWisdomString, NAMD_die(), Communicate::newOutputStream(), MOStream::put(), SIMPARAMSTAG, and tclBCScript. 03974 {
03975 MOStream *msg = com_obj->newOutputStream(ALLBUTME, SIMPARAMSTAG, BUFSIZE);
03976 if ( msg == NULL )
03977 {
03978 NAMD_die("memory allocation failed in SimParameters::send_SimParameters");
03979 }
03980
03981 msg->put(sizeof(SimParameters),(char*)this);
03982 if ( FFTWWisdomString ) {
03983 int fftwlen = strlen(FFTWWisdomString) + 1;
03984 msg->put(fftwlen);
03985 msg->put(fftwlen,FFTWWisdomString);
03986 }
03987 if ( tclBCScript ) {
03988 int tcllen = strlen(tclBCScript) + 1;
03989 msg->put(tcllen);
03990 msg->put(tcllen,tclBCScript);
03991 }
03992
03993 msg->end();
03994 }
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Definition at line 557 of file SimParameters.h. |
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Definition at line 576 of file SimParameters.h. Referenced by buildExclusions(), and NamdState::configListInit(). |
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Definition at line 145 of file SimParameters.h. Referenced by CollectionMaster::receiveDataStream(). |
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Definition at line 371 of file SimParameters.h. Referenced by Controller::berendsenPressure(), and scriptSet(). |
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Definition at line 373 of file SimParameters.h. Referenced by Sequencer::berendsenPressure(), and Controller::berendsenPressure(). |
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Definition at line 369 of file SimParameters.h. Referenced by Sequencer::berendsenPressure(), Controller::berendsenPressure(), and scriptSet(). |
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Definition at line 372 of file SimParameters.h. Referenced by Controller::berendsenPressure(), and scriptSet(). |
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Definition at line 370 of file SimParameters.h. Referenced by Controller::berendsenPressure(), and scriptSet(). |
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Definition at line 160 of file SimParameters.h. |
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Definition at line 158 of file SimParameters.h. |
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Definition at line 90 of file SimParameters.h. |
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Definition at line 91 of file SimParameters.h. |
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Definition at line 92 of file SimParameters.h. |
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Definition at line 93 of file SimParameters.h. |
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Definition at line 343 of file SimParameters.h. |
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Definition at line 345 of file SimParameters.h. |
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Definition at line 346 of file SimParameters.h. |
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Definition at line 520 of file SimParameters.h. Referenced by ComputeHomeTuples< BondElem, Bond, BondValue >::doWork(), Sequencer::integrate(), scriptSet(), ComputeNonbondedUtil::select(), and ComputePme::ungridForces(). |
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Definition at line 125 of file SimParameters.h. Referenced by NamdState::configListInit(), WorkDistrib::createAtomLists(), WorkDistrib::initAndSendHomePatch(), and Controller::receivePressure(). |
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Definition at line 477 of file SimParameters.h. |
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Definition at line 476 of file SimParameters.h. Referenced by NamdState::configListInit(), WorkDistrib::mapComputes(), Molecule::receive_Molecule(), and Molecule::send_Molecule(). |
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Definition at line 478 of file SimParameters.h. Referenced by ComputeConsForce::doForce(), and scriptSet(). |
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Definition at line 250 of file SimParameters.h. |
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Definition at line 248 of file SimParameters.h. |
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Definition at line 252 of file SimParameters.h. Referenced by ComputeConsTorque::doForce(). |
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Definition at line 247 of file SimParameters.h. Referenced by NamdState::configListInit(), WorkDistrib::mapComputes(), Molecule::receive_Molecule(), and Molecule::send_Molecule(). |
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Definition at line 251 of file SimParameters.h. |
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Definition at line 253 of file SimParameters.h. |
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Definition at line 189 of file SimParameters.h. Referenced by ComputeRestraints::ComputeRestraints(). |
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Definition at line 208 of file SimParameters.h. Referenced by ComputeRestraints::doForce(), and scriptSet(). |