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#include <cstdlib> |
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#include <iostream> |
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#include <cmath> |
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|
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#include "SimSetup.hpp" |
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#include "parse_me.h" |
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#include "Integrator.hpp" |
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#include "simError.h" |
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|
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#ifdef IS_MPI |
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#include "mpiBASS.h" |
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#include "mpiSimulation.hpp" |
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#endif |
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|
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// some defines for ensemble and Forcefield cases |
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|
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#define NVE_ENS 0 |
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#define NVT_ENS 1 |
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#define NPT_ENS 2 |
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|
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#define FF_DUFF 0 |
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#define FF_LJ 1 |
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|
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|
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SimSetup::SimSetup(){ |
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stamps = new MakeStamps(); |
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globals = new Globals(); |
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|
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#ifdef IS_MPI |
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strcpy( checkPointMsg, "SimSetup creation successful" ); |
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MPIcheckPoint(); |
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#endif // IS_MPI |
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} |
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|
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SimSetup::~SimSetup(){ |
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delete stamps; |
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delete globals; |
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} |
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|
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void SimSetup::parseFile( char* fileName ){ |
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|
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#ifdef IS_MPI |
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if( worldRank == 0 ){ |
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#endif // is_mpi |
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|
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inFileName = fileName; |
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set_interface_stamps( stamps, globals ); |
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|
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#ifdef IS_MPI |
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mpiEventInit(); |
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#endif |
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|
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yacc_BASS( fileName ); |
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|
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#ifdef IS_MPI |
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throwMPIEvent(NULL); |
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} |
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else receiveParse(); |
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#endif |
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|
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} |
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|
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#ifdef IS_MPI |
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void SimSetup::receiveParse(void){ |
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|
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set_interface_stamps( stamps, globals ); |
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mpiEventInit(); |
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MPIcheckPoint(); |
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mpiEventLoop(); |
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|
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} |
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|
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#endif // is_mpi |
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|
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void SimSetup::createSim( void ){ |
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|
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MakeStamps *the_stamps; |
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Globals* the_globals; |
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int i, j, k, globalAtomIndex; |
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|
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int ensembleCase; |
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int ffCase; |
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|
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ensembleCase = -1; |
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ffCase = -1; |
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|
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// get the stamps and globals; |
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the_stamps = stamps; |
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the_globals = globals; |
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|
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// set the easy ones first |
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simnfo->target_temp = the_globals->getTargetTemp(); |
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simnfo->dt = the_globals->getDt(); |
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simnfo->run_time = the_globals->getRunTime(); |
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|
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// get the ones we know are there, yet still may need some work. |
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n_components = the_globals->getNComponents(); |
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strcpy( force_field, the_globals->getForceField() ); |
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|
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if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
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else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
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else{ |
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sprintf( painCave.errMsg, |
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"SimSetup Error. Unrecognized force field -> %s\n", |
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force_field ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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// get the ensemble: |
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strcpy( ensemble, the_globals->getEnsemble() ); |
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|
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if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
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else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
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else if( !strcasecmp( ensemble, "NPT" )) ensembleCase = NPT_ENS; |
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else{ |
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sprintf( painCave.errMsg, |
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"SimSetup Warning. Unrecognized Ensemble -> %s, " |
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"reverting to NVE for this simulation.\n", |
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ensemble ); |
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painCave.isFatal = 0; |
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simError(); |
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strcpy( ensemble, "NVE" ); |
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ensembleCase = NVE_ENS; |
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} |
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strcpy( simnfo->ensemble, ensemble ); |
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|
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|
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// if( !strcasecmp( ensemble, "NPT" ) ) { |
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// the_extendedsystem = new ExtendedSystem( simnfo ); |
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// the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
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// if (the_globals->haveTargetPressure()) |
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// the_extendedsystem->setTargetPressure(the_globals->getTargetPressure()); |
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// else { |
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// sprintf( painCave.errMsg, |
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// "SimSetup error: If you use the constant pressure\n" |
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// " ensemble, you must set targetPressure.\n" |
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// " This was found in the BASS file.\n"); |
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// painCave.isFatal = 1; |
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// simError(); |
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// } |
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|
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// if (the_globals->haveTauThermostat()) |
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// the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
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// else if (the_globals->haveQmass()) |
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// the_extendedsystem->setQmass(the_globals->getQmass()); |
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// else { |
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// sprintf( painCave.errMsg, |
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// "SimSetup error: If you use one of the constant temperature\n" |
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// " ensembles, you must set either tauThermostat or qMass.\n" |
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// " Neither of these was found in the BASS file.\n"); |
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// painCave.isFatal = 1; |
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// simError(); |
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// } |
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|
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// if (the_globals->haveTauBarostat()) |
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// the_extendedsystem->setTauBarostat(the_globals->getTauBarostat()); |
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// else { |
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// sprintf( painCave.errMsg, |
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// "SimSetup error: If you use the constant pressure\n" |
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// " ensemble, you must set tauBarostat.\n" |
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// " This was found in the BASS file.\n"); |
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// painCave.isFatal = 1; |
| 164 |
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// simError(); |
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// } |
| 166 |
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|
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// } else if ( !strcasecmp( ensemble, "NVT") ) { |
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// the_extendedsystem = new ExtendedSystem( simnfo ); |
| 169 |
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// the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
| 170 |
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|
| 171 |
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// if (the_globals->haveTauThermostat()) |
| 172 |
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// the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
| 173 |
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// else if (the_globals->haveQmass()) |
| 174 |
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// the_extendedsystem->setQmass(the_globals->getQmass()); |
| 175 |
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// else { |
| 176 |
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// sprintf( painCave.errMsg, |
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// "SimSetup error: If you use one of the constant temperature\n" |
| 178 |
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// " ensembles, you must set either tauThermostat or qMass.\n" |
| 179 |
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// " Neither of these was found in the BASS file.\n"); |
| 180 |
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// painCave.isFatal = 1; |
| 181 |
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// simError(); |
| 182 |
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// } |
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|
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strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
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simnfo->usePBC = the_globals->getPBC(); |
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|
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int usesDipoles = 0; |
| 188 |
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switch( ffCase ){ |
| 189 |
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|
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case FF_DUFF: |
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the_ff = new DUFF(); |
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usesDipoles = 1; |
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break; |
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|
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case FF_LJ: |
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the_ff = new LJFF(); |
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break; |
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|
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default: |
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sprintf( painCave.errMsg, |
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"SimSetup Error. Unrecognized force field in case statement.\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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#ifdef IS_MPI |
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strcpy( checkPointMsg, "ForceField creation successful" ); |
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MPIcheckPoint(); |
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#endif // is_mpi |
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|
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// get the components and calculate the tot_nMol and indvidual n_mol |
| 212 |
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the_components = the_globals->getComponents(); |
| 213 |
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components_nmol = new int[n_components]; |
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comp_stamps = new MoleculeStamp*[n_components]; |
| 215 |
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|
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if( !the_globals->haveNMol() ){ |
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// we don't have the total number of molecules, so we assume it is |
| 218 |
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// given in each component |
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|
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tot_nmol = 0; |
| 221 |
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for( i=0; i<n_components; i++ ){ |
| 222 |
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|
| 223 |
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if( !the_components[i]->haveNMol() ){ |
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// we have a problem |
| 225 |
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sprintf( painCave.errMsg, |
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"SimSetup Error. No global NMol or component NMol" |
| 227 |
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" given. Cannot calculate the number of atoms.\n" ); |
| 228 |
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painCave.isFatal = 1; |
| 229 |
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simError(); |
| 230 |
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} |
| 231 |
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|
| 232 |
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tot_nmol += the_components[i]->getNMol(); |
| 233 |
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components_nmol[i] = the_components[i]->getNMol(); |
| 234 |
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} |
| 235 |
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} |
| 236 |
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else{ |
| 237 |
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sprintf( painCave.errMsg, |
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"SimSetup error.\n" |
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"\tSorry, the ability to specify total" |
| 240 |
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" nMols and then give molfractions in the components\n" |
| 241 |
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"\tis not currently supported." |
| 242 |
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" Please give nMol in the components.\n" ); |
| 243 |
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painCave.isFatal = 1; |
| 244 |
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simError(); |
| 245 |
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|
| 246 |
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|
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// tot_nmol = the_globals->getNMol(); |
| 248 |
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|
| 249 |
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// //we have the total number of molecules, now we check for molfractions |
| 250 |
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// for( i=0; i<n_components; i++ ){ |
| 251 |
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|
| 252 |
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// if( !the_components[i]->haveMolFraction() ){ |
| 253 |
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|
| 254 |
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// if( !the_components[i]->haveNMol() ){ |
| 255 |
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// //we have a problem |
| 256 |
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// std::cerr << "SimSetup error. Neither molFraction nor " |
| 257 |
< |
// << " nMol was given in component |
| 258 |
< |
|
| 259 |
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} |
| 260 |
< |
|
| 261 |
< |
#ifdef IS_MPI |
| 262 |
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strcpy( checkPointMsg, "Have the number of components" ); |
| 263 |
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MPIcheckPoint(); |
| 264 |
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#endif // is_mpi |
| 265 |
< |
|
| 266 |
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// make an array of molecule stamps that match the components used. |
| 267 |
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// also extract the used stamps out into a separate linked list |
| 268 |
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|
| 269 |
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simnfo->nComponents = n_components; |
| 270 |
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simnfo->componentsNmol = components_nmol; |
| 271 |
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simnfo->compStamps = comp_stamps; |
| 272 |
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simnfo->headStamp = new LinkedMolStamp(); |
| 273 |
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|
| 274 |
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char* id; |
| 275 |
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LinkedMolStamp* headStamp = simnfo->headStamp; |
| 276 |
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LinkedMolStamp* currentStamp = NULL; |
| 277 |
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for( i=0; i<n_components; i++ ){ |
| 278 |
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|
| 279 |
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id = the_components[i]->getType(); |
| 280 |
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comp_stamps[i] = NULL; |
| 281 |
< |
|
| 282 |
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// check to make sure the component isn't already in the list |
| 283 |
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|
| 284 |
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comp_stamps[i] = headStamp->match( id ); |
| 285 |
< |
if( comp_stamps[i] == NULL ){ |
| 286 |
< |
|
| 287 |
< |
// extract the component from the list; |
| 288 |
< |
|
| 289 |
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currentStamp = the_stamps->extractMolStamp( id ); |
| 290 |
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if( currentStamp == NULL ){ |
| 291 |
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sprintf( painCave.errMsg, |
| 292 |
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"SimSetup error: Component \"%s\" was not found in the " |
| 293 |
< |
"list of declared molecules\n", |
| 294 |
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id ); |
| 295 |
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painCave.isFatal = 1; |
| 296 |
< |
simError(); |
| 297 |
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} |
| 298 |
< |
|
| 299 |
< |
headStamp->add( currentStamp ); |
| 300 |
< |
comp_stamps[i] = headStamp->match( id ); |
| 301 |
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} |
| 302 |
< |
} |
| 303 |
< |
|
| 304 |
< |
#ifdef IS_MPI |
| 305 |
< |
strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
| 306 |
< |
MPIcheckPoint(); |
| 307 |
< |
#endif // is_mpi |
| 308 |
< |
|
| 309 |
< |
|
| 310 |
< |
|
| 311 |
< |
|
| 312 |
< |
// caclulate the number of atoms, bonds, bends and torsions |
| 313 |
< |
|
| 314 |
< |
tot_atoms = 0; |
| 315 |
< |
tot_bonds = 0; |
| 316 |
< |
tot_bends = 0; |
| 317 |
< |
tot_torsions = 0; |
| 318 |
< |
for( i=0; i<n_components; i++ ){ |
| 319 |
< |
|
| 320 |
< |
tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
| 321 |
< |
tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
| 322 |
< |
tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
| 323 |
< |
tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
| 324 |
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} |
| 325 |
< |
|
| 326 |
< |
tot_SRI = tot_bonds + tot_bends + tot_torsions; |
| 327 |
< |
|
| 328 |
< |
simnfo->n_atoms = tot_atoms; |
| 329 |
< |
simnfo->n_bonds = tot_bonds; |
| 330 |
< |
simnfo->n_bends = tot_bends; |
| 331 |
< |
simnfo->n_torsions = tot_torsions; |
| 332 |
< |
simnfo->n_SRI = tot_SRI; |
| 333 |
< |
simnfo->n_mol = tot_nmol; |
| 334 |
< |
|
| 335 |
< |
simnfo->molMembershipArray = new int[tot_atoms]; |
| 336 |
< |
|
| 337 |
< |
#ifdef IS_MPI |
| 338 |
< |
|
| 339 |
< |
// divide the molecules among processors here. |
| 340 |
< |
|
| 341 |
< |
mpiSim = new mpiSimulation( simnfo ); |
| 342 |
< |
|
| 343 |
< |
globalIndex = mpiSim->divideLabor(); |
| 344 |
< |
|
| 345 |
< |
// set up the local variables |
| 346 |
< |
|
| 347 |
< |
int localMol, allMol; |
| 348 |
< |
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
| 349 |
< |
|
| 350 |
< |
int* mol2proc = mpiSim->getMolToProcMap(); |
| 351 |
< |
int* molCompType = mpiSim->getMolComponentType(); |
| 352 |
< |
|
| 353 |
< |
allMol = 0; |
| 354 |
< |
localMol = 0; |
| 355 |
< |
local_atoms = 0; |
| 356 |
< |
local_bonds = 0; |
| 357 |
< |
local_bends = 0; |
| 358 |
< |
local_torsions = 0; |
| 359 |
< |
globalAtomIndex = 0; |
| 360 |
< |
|
| 361 |
< |
|
| 362 |
< |
for( i=0; i<n_components; i++ ){ |
| 363 |
< |
|
| 364 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
| 365 |
< |
|
| 366 |
< |
if( mol2proc[allMol] == worldRank ){ |
| 367 |
< |
|
| 368 |
< |
local_atoms += comp_stamps[i]->getNAtoms(); |
| 369 |
< |
local_bonds += comp_stamps[i]->getNBonds(); |
| 370 |
< |
local_bends += comp_stamps[i]->getNBends(); |
| 371 |
< |
local_torsions += comp_stamps[i]->getNTorsions(); |
| 372 |
< |
localMol++; |
| 373 |
< |
} |
| 374 |
< |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
| 375 |
< |
simnfo->molMembershipArray[globalAtomIndex] = allMol; |
| 376 |
< |
globalAtomIndex++; |
| 377 |
< |
} |
| 378 |
< |
|
| 379 |
< |
allMol++; |
| 380 |
< |
} |
| 381 |
< |
} |
| 382 |
< |
local_SRI = local_bonds + local_bends + local_torsions; |
| 383 |
< |
|
| 384 |
< |
simnfo->n_atoms = mpiSim->getMyNlocal(); |
| 385 |
< |
|
| 386 |
< |
if( local_atoms != simnfo->n_atoms ){ |
| 387 |
< |
sprintf( painCave.errMsg, |
| 388 |
< |
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
| 389 |
< |
" localAtom (%d) are not equal.\n", |
| 390 |
< |
simnfo->n_atoms, |
| 391 |
< |
local_atoms ); |
| 392 |
< |
painCave.isFatal = 1; |
| 393 |
< |
simError(); |
| 394 |
< |
} |
| 395 |
< |
|
| 396 |
< |
simnfo->n_bonds = local_bonds; |
| 397 |
< |
simnfo->n_bends = local_bends; |
| 398 |
< |
simnfo->n_torsions = local_torsions; |
| 399 |
< |
simnfo->n_SRI = local_SRI; |
| 400 |
< |
simnfo->n_mol = localMol; |
| 401 |
< |
|
| 402 |
< |
strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
| 403 |
< |
MPIcheckPoint(); |
| 404 |
< |
|
| 405 |
< |
|
| 406 |
< |
#endif // is_mpi |
| 407 |
< |
|
| 408 |
< |
|
| 409 |
< |
// create the atom and short range interaction arrays |
| 410 |
< |
|
| 411 |
< |
Atom::createArrays(simnfo->n_atoms); |
| 412 |
< |
the_atoms = new Atom*[simnfo->n_atoms]; |
| 413 |
< |
the_molecules = new Molecule[simnfo->n_mol]; |
| 414 |
< |
int molIndex; |
| 415 |
< |
|
| 416 |
< |
// initialize the molecule's stampID's |
| 417 |
< |
|
| 418 |
< |
#ifdef IS_MPI |
| 419 |
< |
|
| 420 |
< |
|
| 421 |
< |
molIndex = 0; |
| 422 |
< |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
| 423 |
< |
|
| 424 |
< |
if(mol2proc[i] == worldRank ){ |
| 425 |
< |
the_molecules[molIndex].setStampID( molCompType[i] ); |
| 426 |
< |
the_molecules[molIndex].setMyIndex( molIndex ); |
| 427 |
< |
the_molecules[molIndex].setGlobalIndex( i ); |
| 428 |
< |
molIndex++; |
| 429 |
< |
} |
| 430 |
< |
} |
| 431 |
< |
|
| 432 |
< |
#else // is_mpi |
| 433 |
< |
|
| 434 |
< |
molIndex = 0; |
| 435 |
< |
globalAtomIndex = 0; |
| 436 |
< |
for(i=0; i<n_components; i++){ |
| 437 |
< |
for(j=0; j<components_nmol[i]; j++ ){ |
| 438 |
< |
the_molecules[molIndex].setStampID( i ); |
| 439 |
< |
the_molecules[molIndex].setMyIndex( molIndex ); |
| 440 |
< |
the_molecules[molIndex].setGlobalIndex( molIndex ); |
| 441 |
< |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
| 442 |
< |
simnfo->molMembershipArray[globalAtomIndex] = molIndex; |
| 443 |
< |
globalAtomIndex++; |
| 444 |
< |
} |
| 445 |
< |
molIndex++; |
| 446 |
< |
} |
| 447 |
< |
} |
| 448 |
< |
|
| 449 |
< |
|
| 450 |
< |
#endif // is_mpi |
| 451 |
< |
|
| 452 |
< |
|
| 453 |
< |
if( simnfo->n_SRI ){ |
| 454 |
< |
|
| 455 |
< |
Exclude::createArray(simnfo->n_SRI); |
| 456 |
< |
the_excludes = new Exclude*[simnfo->n_SRI]; |
| 457 |
< |
for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
| 458 |
< |
simnfo->globalExcludes = new int; |
| 459 |
< |
simnfo->n_exclude = simnfo->n_SRI; |
| 460 |
< |
} |
| 461 |
< |
else{ |
| 462 |
< |
|
| 463 |
< |
Exclude::createArray( 1 ); |
| 464 |
< |
the_excludes = new Exclude*; |
| 465 |
< |
the_excludes[0] = new Exclude(0); |
| 466 |
< |
the_excludes[0]->setPair( 0,0 ); |
| 467 |
< |
simnfo->globalExcludes = new int; |
| 468 |
< |
simnfo->globalExcludes[0] = 0; |
| 469 |
< |
simnfo->n_exclude = 0; |
| 470 |
< |
} |
| 471 |
< |
|
| 472 |
< |
// set the arrays into the SimInfo object |
| 473 |
< |
|
| 474 |
< |
simnfo->atoms = the_atoms; |
| 475 |
< |
simnfo->molecules = the_molecules; |
| 476 |
< |
simnfo->nGlobalExcludes = 0; |
| 477 |
< |
simnfo->excludes = the_excludes; |
| 478 |
< |
|
| 479 |
< |
|
| 480 |
< |
// get some of the tricky things that may still be in the globals |
| 481 |
< |
|
| 482 |
< |
double boxVector[3]; |
| 483 |
< |
if( the_globals->haveBox() ){ |
| 484 |
< |
boxVector[0] = the_globals->getBox(); |
| 485 |
< |
boxVector[1] = the_globals->getBox(); |
| 486 |
< |
boxVector[2] = the_globals->getBox(); |
| 487 |
< |
|
| 488 |
< |
simnfo->setBox( boxVector ); |
| 489 |
< |
} |
| 490 |
< |
else if( the_globals->haveDensity() ){ |
| 491 |
< |
|
| 492 |
< |
double vol; |
| 493 |
< |
vol = (double)tot_nmol / the_globals->getDensity(); |
| 494 |
< |
boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
| 495 |
< |
boxVector[1] = boxVector[0]; |
| 496 |
< |
boxVector[2] = boxVector[0]; |
| 497 |
< |
|
| 498 |
< |
simnfo->setBox( boxVector ); |
| 499 |
< |
} |
| 500 |
< |
else{ |
| 501 |
< |
if( !the_globals->haveBoxX() ){ |
| 502 |
< |
sprintf( painCave.errMsg, |
| 503 |
< |
"SimSetup error, no periodic BoxX size given.\n" ); |
| 504 |
< |
painCave.isFatal = 1; |
| 505 |
< |
simError(); |
| 506 |
< |
} |
| 507 |
< |
boxVector[0] = the_globals->getBoxX(); |
| 508 |
< |
|
| 509 |
< |
if( !the_globals->haveBoxY() ){ |
| 510 |
< |
sprintf( painCave.errMsg, |
| 511 |
< |
"SimSetup error, no periodic BoxY size given.\n" ); |
| 512 |
< |
painCave.isFatal = 1; |
| 513 |
< |
simError(); |
| 514 |
< |
} |
| 515 |
< |
boxVector[1] = the_globals->getBoxY(); |
| 516 |
< |
|
| 517 |
< |
if( !the_globals->haveBoxZ() ){ |
| 518 |
< |
sprintf( painCave.errMsg, |
| 519 |
< |
"SimSetup error, no periodic BoxZ size given.\n" ); |
| 520 |
< |
painCave.isFatal = 1; |
| 521 |
< |
simError(); |
| 522 |
< |
} |
| 523 |
< |
boxVector[2] = the_globals->getBoxZ(); |
| 524 |
< |
|
| 525 |
< |
simnfo->setBox( boxVector ); |
| 526 |
< |
} |
| 527 |
< |
|
| 528 |
< |
#ifdef IS_MPI |
| 529 |
< |
strcpy( checkPointMsg, "Box size set up" ); |
| 530 |
< |
MPIcheckPoint(); |
| 531 |
< |
#endif // is_mpi |
| 532 |
< |
|
| 533 |
< |
|
| 534 |
< |
// initialize the arrays |
| 535 |
< |
|
| 536 |
< |
the_ff->setSimInfo( simnfo ); |
| 537 |
< |
|
| 538 |
< |
makeMolecules(); |
| 539 |
< |
simnfo->identArray = new int[simnfo->n_atoms]; |
| 540 |
< |
for(i=0; i<simnfo->n_atoms; i++){ |
| 541 |
< |
simnfo->identArray[i] = the_atoms[i]->getIdent(); |
| 542 |
< |
} |
| 543 |
< |
|
| 544 |
< |
if (the_globals->getUseRF() ) { |
| 545 |
< |
simnfo->useReactionField = 1; |
| 546 |
< |
|
| 547 |
< |
if( !the_globals->haveECR() ){ |
| 548 |
< |
sprintf( painCave.errMsg, |
| 549 |
< |
"SimSetup Warning: using default value of 1/2 the smallest " |
| 550 |
< |
"box length for the electrostaticCutoffRadius.\n" |
| 551 |
< |
"I hope you have a very fast processor!\n"); |
| 552 |
< |
painCave.isFatal = 0; |
| 553 |
< |
simError(); |
| 554 |
< |
double smallest; |
| 555 |
< |
smallest = simnfo->boxLx; |
| 556 |
< |
if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy; |
| 557 |
< |
if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz; |
| 558 |
< |
simnfo->ecr = 0.5 * smallest; |
| 559 |
< |
} else { |
| 560 |
< |
simnfo->ecr = the_globals->getECR(); |
| 561 |
< |
} |
| 562 |
< |
|
| 563 |
< |
if( !the_globals->haveEST() ){ |
| 564 |
< |
sprintf( painCave.errMsg, |
| 565 |
< |
"SimSetup Warning: using default value of 0.05 * the " |
| 566 |
< |
"electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
| 567 |
< |
); |
| 568 |
< |
painCave.isFatal = 0; |
| 569 |
< |
simError(); |
| 570 |
< |
simnfo->est = 0.05 * simnfo->ecr; |
| 571 |
< |
} else { |
| 572 |
< |
simnfo->est = the_globals->getEST(); |
| 573 |
< |
} |
| 574 |
< |
|
| 575 |
< |
if(!the_globals->haveDielectric() ){ |
| 576 |
< |
sprintf( painCave.errMsg, |
| 577 |
< |
"SimSetup Error: You are trying to use Reaction Field without" |
| 578 |
< |
"setting a dielectric constant!\n" |
| 579 |
< |
); |
| 580 |
< |
painCave.isFatal = 1; |
| 581 |
< |
simError(); |
| 582 |
< |
} |
| 583 |
< |
simnfo->dielectric = the_globals->getDielectric(); |
| 584 |
< |
} else { |
| 585 |
< |
if (usesDipoles) { |
| 586 |
< |
|
| 587 |
< |
if( !the_globals->haveECR() ){ |
| 588 |
< |
sprintf( painCave.errMsg, |
| 589 |
< |
"SimSetup Warning: using default value of 1/2 the smallest " |
| 590 |
< |
"box length for the electrostaticCutoffRadius.\n" |
| 591 |
< |
"I hope you have a very fast processor!\n"); |
| 592 |
< |
painCave.isFatal = 0; |
| 593 |
< |
simError(); |
| 594 |
< |
double smallest; |
| 595 |
< |
smallest = simnfo->boxLx; |
| 596 |
< |
if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy; |
| 597 |
< |
if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz; |
| 598 |
< |
simnfo->ecr = 0.5 * smallest; |
| 599 |
< |
} else { |
| 600 |
< |
simnfo->ecr = the_globals->getECR(); |
| 601 |
< |
} |
| 602 |
< |
|
| 603 |
< |
if( !the_globals->haveEST() ){ |
| 604 |
< |
sprintf( painCave.errMsg, |
| 605 |
< |
"SimSetup Warning: using default value of 5%% of the " |
| 606 |
< |
"electrostaticCutoffRadius for the " |
| 607 |
< |
"electrostaticSkinThickness\n" |
| 608 |
< |
); |
| 609 |
< |
painCave.isFatal = 0; |
| 610 |
< |
simError(); |
| 611 |
< |
simnfo->est = 0.05 * simnfo->ecr; |
| 612 |
< |
} else { |
| 613 |
< |
simnfo->est = the_globals->getEST(); |
| 614 |
< |
} |
| 615 |
< |
} |
| 616 |
< |
} |
| 617 |
< |
|
| 618 |
< |
#ifdef IS_MPI |
| 619 |
< |
strcpy( checkPointMsg, "electrostatic parameters check out" ); |
| 620 |
< |
MPIcheckPoint(); |
| 621 |
< |
#endif // is_mpi |
| 622 |
< |
|
| 623 |
< |
if( the_globals->haveInitialConfig() ){ |
| 624 |
< |
|
| 625 |
< |
InitializeFromFile* fileInit; |
| 626 |
< |
#ifdef IS_MPI // is_mpi |
| 627 |
< |
if( worldRank == 0 ){ |
| 628 |
< |
#endif //is_mpi |
| 629 |
< |
fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
| 630 |
< |
#ifdef IS_MPI |
| 631 |
< |
}else fileInit = new InitializeFromFile( NULL ); |
| 632 |
< |
#endif |
| 633 |
< |
fileInit->read_xyz( simnfo ); // default velocities on |
| 634 |
< |
|
| 635 |
< |
delete fileInit; |
| 636 |
< |
} |
| 637 |
< |
else{ |
| 638 |
< |
|
| 639 |
< |
#ifdef IS_MPI |
| 640 |
< |
|
| 641 |
< |
// no init from bass |
| 642 |
< |
|
| 643 |
< |
sprintf( painCave.errMsg, |
| 644 |
< |
"Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
| 645 |
< |
painCave.isFatal; |
| 646 |
< |
simError(); |
| 647 |
< |
|
| 648 |
< |
#else |
| 649 |
< |
|
| 650 |
< |
initFromBass(); |
| 651 |
< |
|
| 652 |
< |
|
| 653 |
< |
#endif |
| 654 |
< |
} |
| 655 |
< |
|
| 656 |
< |
#ifdef IS_MPI |
| 657 |
< |
strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
| 658 |
< |
MPIcheckPoint(); |
| 659 |
< |
#endif // is_mpi |
| 660 |
< |
|
| 661 |
< |
|
| 662 |
< |
|
| 663 |
< |
|
| 664 |
< |
|
| 665 |
< |
|
| 666 |
< |
|
| 667 |
< |
#ifdef IS_MPI |
| 668 |
< |
if( worldRank == 0 ){ |
| 669 |
< |
#endif // is_mpi |
| 670 |
< |
|
| 671 |
< |
if( the_globals->haveFinalConfig() ){ |
| 672 |
< |
strcpy( simnfo->finalName, the_globals->getFinalConfig() ); |
| 673 |
< |
} |
| 674 |
< |
else{ |
| 675 |
< |
strcpy( simnfo->finalName, inFileName ); |
| 676 |
< |
char* endTest; |
| 677 |
< |
int nameLength = strlen( simnfo->finalName ); |
| 678 |
< |
endTest = &(simnfo->finalName[nameLength - 5]); |
| 679 |
< |
if( !strcmp( endTest, ".bass" ) ){ |
| 680 |
< |
strcpy( endTest, ".eor" ); |
| 681 |
< |
} |
| 682 |
< |
else if( !strcmp( endTest, ".BASS" ) ){ |
| 683 |
< |
strcpy( endTest, ".eor" ); |
| 684 |
< |
} |
| 685 |
< |
else{ |
| 686 |
< |
endTest = &(simnfo->finalName[nameLength - 4]); |
| 687 |
< |
if( !strcmp( endTest, ".bss" ) ){ |
| 688 |
< |
strcpy( endTest, ".eor" ); |
| 689 |
< |
} |
| 690 |
< |
else if( !strcmp( endTest, ".mdl" ) ){ |
| 691 |
< |
strcpy( endTest, ".eor" ); |
| 692 |
< |
} |
| 693 |
< |
else{ |
| 694 |
< |
strcat( simnfo->finalName, ".eor" ); |
| 695 |
< |
} |
| 696 |
< |
} |
| 697 |
< |
} |
| 698 |
< |
|
| 699 |
< |
// make the sample and status out names |
| 700 |
< |
|
| 701 |
< |
strcpy( simnfo->sampleName, inFileName ); |
| 702 |
< |
char* endTest; |
| 703 |
< |
int nameLength = strlen( simnfo->sampleName ); |
| 704 |
< |
endTest = &(simnfo->sampleName[nameLength - 5]); |
| 705 |
< |
if( !strcmp( endTest, ".bass" ) ){ |
| 706 |
< |
strcpy( endTest, ".dump" ); |
| 707 |
< |
} |
| 708 |
< |
else if( !strcmp( endTest, ".BASS" ) ){ |
| 709 |
< |
strcpy( endTest, ".dump" ); |
| 710 |
< |
} |
| 711 |
< |
else{ |
| 712 |
< |
endTest = &(simnfo->sampleName[nameLength - 4]); |
| 713 |
< |
if( !strcmp( endTest, ".bss" ) ){ |
| 714 |
< |
strcpy( endTest, ".dump" ); |
| 715 |
< |
} |
| 716 |
< |
else if( !strcmp( endTest, ".mdl" ) ){ |
| 717 |
< |
strcpy( endTest, ".dump" ); |
| 718 |
< |
} |
| 719 |
< |
else{ |
| 720 |
< |
strcat( simnfo->sampleName, ".dump" ); |
| 721 |
< |
} |
| 722 |
< |
} |
| 723 |
< |
|
| 724 |
< |
strcpy( simnfo->statusName, inFileName ); |
| 725 |
< |
nameLength = strlen( simnfo->statusName ); |
| 726 |
< |
endTest = &(simnfo->statusName[nameLength - 5]); |
| 727 |
< |
if( !strcmp( endTest, ".bass" ) ){ |
| 728 |
< |
strcpy( endTest, ".stat" ); |
| 729 |
< |
} |
| 730 |
< |
else if( !strcmp( endTest, ".BASS" ) ){ |
| 731 |
< |
strcpy( endTest, ".stat" ); |
| 732 |
< |
} |
| 733 |
< |
else{ |
| 734 |
< |
endTest = &(simnfo->statusName[nameLength - 4]); |
| 735 |
< |
if( !strcmp( endTest, ".bss" ) ){ |
| 736 |
< |
strcpy( endTest, ".stat" ); |
| 737 |
< |
} |
| 738 |
< |
else if( !strcmp( endTest, ".mdl" ) ){ |
| 739 |
< |
strcpy( endTest, ".stat" ); |
| 740 |
< |
} |
| 741 |
< |
else{ |
| 742 |
< |
strcat( simnfo->statusName, ".stat" ); |
| 743 |
< |
} |
| 744 |
< |
} |
| 745 |
< |
|
| 746 |
< |
#ifdef IS_MPI |
| 747 |
< |
} |
| 748 |
< |
#endif // is_mpi |
| 749 |
< |
|
| 750 |
< |
// set the status, sample, and themal kick times |
| 751 |
< |
|
| 752 |
< |
if( the_globals->haveSampleTime() ){ |
| 753 |
< |
simnfo->sampleTime = the_globals->getSampleTime(); |
| 754 |
< |
simnfo->statusTime = simnfo->sampleTime; |
| 755 |
< |
simnfo->thermalTime = simnfo->sampleTime; |
| 756 |
< |
} |
| 757 |
< |
else{ |
| 758 |
< |
simnfo->sampleTime = the_globals->getRunTime(); |
| 759 |
< |
simnfo->statusTime = simnfo->sampleTime; |
| 760 |
< |
simnfo->thermalTime = simnfo->sampleTime; |
| 761 |
< |
} |
| 762 |
< |
|
| 763 |
< |
if( the_globals->haveStatusTime() ){ |
| 764 |
< |
simnfo->statusTime = the_globals->getStatusTime(); |
| 765 |
< |
} |
| 766 |
< |
|
| 767 |
< |
if( the_globals->haveThermalTime() ){ |
| 768 |
< |
simnfo->thermalTime = the_globals->getThermalTime(); |
| 769 |
< |
} |
| 770 |
< |
|
| 771 |
< |
// check for the temperature set flag |
| 772 |
< |
|
| 773 |
< |
if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
| 774 |
< |
|
| 775 |
< |
|
| 776 |
< |
// make the integrator |
| 777 |
< |
|
| 778 |
< |
|
| 779 |
< |
NVT* myNVT = NULL; |
| 780 |
< |
switch( ensembleCase ){ |
| 781 |
< |
|
| 782 |
< |
case NVE_ENS: |
| 783 |
< |
new NVE( simnfo, the_ff ); |
| 784 |
< |
break; |
| 785 |
< |
|
| 786 |
< |
case NVT_ENS: |
| 787 |
< |
myNVT = new NVT( simnfo, the_ff ); |
| 788 |
< |
myNVT->setTargetTemp(the_globals->getTargetTemp()); |
| 789 |
< |
|
| 790 |
< |
if (the_globals->haveTauThermostat()) |
| 791 |
< |
myNVT->setTauThermostat(the_globals->getTauThermostat()); |
| 792 |
< |
// else if (the_globals->haveQmass()) |
| 793 |
< |
// myNVT->setQmass(the_globals->getQmass()); |
| 794 |
< |
else { |
| 795 |
< |
sprintf( painCave.errMsg, |
| 796 |
< |
"SimSetup error: If you use the NVT\n" |
| 797 |
< |
" ensemble, you must set either tauThermostat or qMass.\n" |
| 798 |
< |
" Neither of these was found in the BASS file.\n"); |
| 799 |
< |
painCave.isFatal = 1; |
| 800 |
< |
simError(); |
| 801 |
< |
} |
| 802 |
< |
break; |
| 803 |
< |
|
| 804 |
< |
default: |
| 805 |
< |
sprintf( painCave.errMsg, |
| 806 |
< |
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
| 807 |
< |
painCave.isFatal = 1; |
| 808 |
< |
simError(); |
| 809 |
< |
} |
| 810 |
< |
|
| 811 |
< |
|
| 812 |
< |
#ifdef IS_MPI |
| 813 |
< |
mpiSim->mpiRefresh(); |
| 814 |
< |
#endif |
| 815 |
< |
|
| 816 |
< |
// initialize the Fortran |
| 817 |
< |
|
| 818 |
< |
|
| 819 |
< |
simnfo->refreshSim(); |
| 820 |
< |
|
| 821 |
< |
if( !strcmp( simnfo->mixingRule, "standard") ){ |
| 822 |
< |
the_ff->initForceField( LB_MIXING_RULE ); |
| 823 |
< |
} |
| 824 |
< |
else if( !strcmp( simnfo->mixingRule, "explicit") ){ |
| 825 |
< |
the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
| 826 |
< |
} |
| 827 |
< |
else{ |
| 828 |
< |
sprintf( painCave.errMsg, |
| 829 |
< |
"SimSetup Error: unknown mixing rule -> \"%s\"\n", |
| 830 |
< |
simnfo->mixingRule ); |
| 831 |
< |
painCave.isFatal = 1; |
| 832 |
< |
simError(); |
| 833 |
< |
} |
| 834 |
< |
|
| 835 |
< |
|
| 836 |
< |
#ifdef IS_MPI |
| 837 |
< |
strcpy( checkPointMsg, |
| 838 |
< |
"Successfully intialized the mixingRule for Fortran." ); |
| 839 |
< |
MPIcheckPoint(); |
| 840 |
< |
#endif // is_mpi |
| 841 |
< |
} |
| 842 |
< |
|
| 843 |
< |
|
| 844 |
< |
void SimSetup::makeMolecules( void ){ |
| 845 |
< |
|
| 846 |
< |
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
| 847 |
< |
molInit info; |
| 848 |
< |
DirectionalAtom* dAtom; |
| 849 |
< |
LinkedAssign* extras; |
| 850 |
< |
LinkedAssign* current_extra; |
| 851 |
< |
AtomStamp* currentAtom; |
| 852 |
< |
BondStamp* currentBond; |
| 853 |
< |
BendStamp* currentBend; |
| 854 |
< |
TorsionStamp* currentTorsion; |
| 855 |
< |
|
| 856 |
< |
bond_pair* theBonds; |
| 857 |
< |
bend_set* theBends; |
| 858 |
< |
torsion_set* theTorsions; |
| 859 |
< |
|
| 860 |
< |
|
| 861 |
< |
//init the forceField paramters |
| 862 |
< |
|
| 863 |
< |
the_ff->readParams(); |
| 864 |
< |
|
| 865 |
< |
|
| 866 |
< |
// init the atoms |
| 867 |
< |
|
| 868 |
< |
double ux, uy, uz, u, uSqr; |
| 869 |
< |
|
| 870 |
< |
atomOffset = 0; |
| 871 |
< |
excludeOffset = 0; |
| 872 |
< |
for(i=0; i<simnfo->n_mol; i++){ |
| 873 |
< |
|
| 874 |
< |
stampID = the_molecules[i].getStampID(); |
| 875 |
< |
|
| 876 |
< |
info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
| 877 |
< |
info.nBonds = comp_stamps[stampID]->getNBonds(); |
| 878 |
< |
info.nBends = comp_stamps[stampID]->getNBends(); |
| 879 |
< |
info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
| 880 |
< |
info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
| 881 |
< |
|
| 882 |
< |
info.myAtoms = &the_atoms[atomOffset]; |
| 883 |
< |
info.myExcludes = &the_excludes[excludeOffset]; |
| 884 |
< |
info.myBonds = new Bond*[info.nBonds]; |
| 885 |
< |
info.myBends = new Bend*[info.nBends]; |
| 886 |
< |
info.myTorsions = new Torsion*[info.nTorsions]; |
| 887 |
< |
|
| 888 |
< |
theBonds = new bond_pair[info.nBonds]; |
| 889 |
< |
theBends = new bend_set[info.nBends]; |
| 890 |
< |
theTorsions = new torsion_set[info.nTorsions]; |
| 891 |
< |
|
| 892 |
< |
// make the Atoms |
| 893 |
< |
|
| 894 |
< |
for(j=0; j<info.nAtoms; j++){ |
| 895 |
< |
|
| 896 |
< |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
| 897 |
< |
if( currentAtom->haveOrientation() ){ |
| 898 |
< |
|
| 899 |
< |
dAtom = new DirectionalAtom(j + atomOffset); |
| 900 |
< |
simnfo->n_oriented++; |
| 901 |
< |
info.myAtoms[j] = dAtom; |
| 902 |
< |
|
| 903 |
< |
ux = currentAtom->getOrntX(); |
| 904 |
< |
uy = currentAtom->getOrntY(); |
| 905 |
< |
uz = currentAtom->getOrntZ(); |
| 906 |
< |
|
| 907 |
< |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
| 908 |
< |
|
| 909 |
< |
u = sqrt( uSqr ); |
| 910 |
< |
ux = ux / u; |
| 911 |
< |
uy = uy / u; |
| 912 |
< |
uz = uz / u; |
| 913 |
< |
|
| 914 |
< |
dAtom->setSUx( ux ); |
| 915 |
< |
dAtom->setSUy( uy ); |
| 916 |
< |
dAtom->setSUz( uz ); |
| 917 |
< |
} |
| 918 |
< |
else{ |
| 919 |
< |
info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
| 920 |
< |
} |
| 921 |
< |
info.myAtoms[j]->setType( currentAtom->getType() ); |
| 922 |
< |
|
| 923 |
< |
#ifdef IS_MPI |
| 924 |
< |
|
| 925 |
< |
info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
| 926 |
< |
|
| 927 |
< |
#endif // is_mpi |
| 928 |
< |
} |
| 929 |
< |
|
| 930 |
< |
// make the bonds |
| 931 |
< |
for(j=0; j<info.nBonds; j++){ |
| 932 |
< |
|
| 933 |
< |
currentBond = comp_stamps[stampID]->getBond( j ); |
| 934 |
< |
theBonds[j].a = currentBond->getA() + atomOffset; |
| 935 |
< |
theBonds[j].b = currentBond->getB() + atomOffset; |
| 936 |
< |
|
| 937 |
< |
exI = theBonds[j].a; |
| 938 |
< |
exJ = theBonds[j].b; |
| 939 |
< |
|
| 940 |
< |
// exclude_I must always be the smaller of the pair |
| 941 |
< |
if( exI > exJ ){ |
| 942 |
< |
tempEx = exI; |
| 943 |
< |
exI = exJ; |
| 944 |
< |
exJ = tempEx; |
| 945 |
< |
} |
| 946 |
< |
#ifdef IS_MPI |
| 947 |
< |
tempEx = exI; |
| 948 |
< |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
| 949 |
< |
tempEx = exJ; |
| 950 |
< |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
| 951 |
< |
|
| 952 |
< |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
| 953 |
< |
#else // isn't MPI |
| 954 |
< |
|
| 955 |
< |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
| 956 |
< |
#endif //is_mpi |
| 957 |
< |
} |
| 958 |
< |
excludeOffset += info.nBonds; |
| 959 |
< |
|
| 960 |
< |
//make the bends |
| 961 |
< |
for(j=0; j<info.nBends; j++){ |
| 962 |
< |
|
| 963 |
< |
currentBend = comp_stamps[stampID]->getBend( j ); |
| 964 |
< |
theBends[j].a = currentBend->getA() + atomOffset; |
| 965 |
< |
theBends[j].b = currentBend->getB() + atomOffset; |
| 966 |
< |
theBends[j].c = currentBend->getC() + atomOffset; |
| 967 |
< |
|
| 968 |
< |
if( currentBend->haveExtras() ){ |
| 969 |
< |
|
| 970 |
< |
extras = currentBend->getExtras(); |
| 971 |
< |
current_extra = extras; |
| 972 |
< |
|
| 973 |
< |
while( current_extra != NULL ){ |
| 974 |
< |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
| 975 |
< |
|
| 976 |
< |
switch( current_extra->getType() ){ |
| 977 |
< |
|
| 978 |
< |
case 0: |
| 979 |
< |
theBends[j].ghost = |
| 980 |
< |
current_extra->getInt() + atomOffset; |
| 981 |
< |
theBends[j].isGhost = 1; |
| 982 |
< |
break; |
| 983 |
< |
|
| 984 |
< |
case 1: |
| 985 |
< |
theBends[j].ghost = |
| 986 |
< |
(int)current_extra->getDouble() + atomOffset; |
| 987 |
< |
theBends[j].isGhost = 1; |
| 988 |
< |
break; |
| 989 |
< |
|
| 990 |
< |
default: |
| 991 |
< |
sprintf( painCave.errMsg, |
| 992 |
< |
"SimSetup Error: ghostVectorSource was neither a " |
| 993 |
< |
"double nor an int.\n" |
| 994 |
< |
"-->Bend[%d] in %s\n", |
| 995 |
< |
j, comp_stamps[stampID]->getID() ); |
| 996 |
< |
painCave.isFatal = 1; |
| 997 |
< |
simError(); |
| 998 |
< |
} |
| 999 |
< |
} |
| 1000 |
< |
|
| 1001 |
< |
else{ |
| 1002 |
< |
|
| 1003 |
< |
sprintf( painCave.errMsg, |
| 1004 |
< |
"SimSetup Error: unhandled bend assignment:\n" |
| 1005 |
< |
" -->%s in Bend[%d] in %s\n", |
| 1006 |
< |
current_extra->getlhs(), |
| 1007 |
< |
j, comp_stamps[stampID]->getID() ); |
| 1008 |
< |
painCave.isFatal = 1; |
| 1009 |
< |
simError(); |
| 1010 |
< |
} |
| 1011 |
< |
|
| 1012 |
< |
current_extra = current_extra->getNext(); |
| 1013 |
< |
} |
| 1014 |
< |
} |
| 1015 |
< |
|
| 1016 |
< |
if( !theBends[j].isGhost ){ |
| 1017 |
< |
|
| 1018 |
< |
exI = theBends[j].a; |
| 1019 |
< |
exJ = theBends[j].c; |
| 1020 |
< |
} |
| 1021 |
< |
else{ |
| 1022 |
< |
|
| 1023 |
< |
exI = theBends[j].a; |
| 1024 |
< |
exJ = theBends[j].b; |
| 1025 |
< |
} |
| 1026 |
< |
|
| 1027 |
< |
// exclude_I must always be the smaller of the pair |
| 1028 |
< |
if( exI > exJ ){ |
| 1029 |
< |
tempEx = exI; |
| 1030 |
< |
exI = exJ; |
| 1031 |
< |
exJ = tempEx; |
| 1032 |
< |
} |
| 1033 |
< |
#ifdef IS_MPI |
| 1034 |
< |
tempEx = exI; |
| 1035 |
< |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
| 1036 |
< |
tempEx = exJ; |
| 1037 |
< |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
| 1038 |
< |
|
| 1039 |
< |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
| 1040 |
< |
#else // isn't MPI |
| 1041 |
< |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
| 1042 |
< |
#endif //is_mpi |
| 1043 |
< |
} |
| 1044 |
< |
excludeOffset += info.nBends; |
| 1045 |
< |
|
| 1046 |
< |
for(j=0; j<info.nTorsions; j++){ |
| 1047 |
< |
|
| 1048 |
< |
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
| 1049 |
< |
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
| 1050 |
< |
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
| 1051 |
< |
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
| 1052 |
< |
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
| 1053 |
< |
|
| 1054 |
< |
exI = theTorsions[j].a; |
| 1055 |
< |
exJ = theTorsions[j].d; |
| 1056 |
< |
|
| 1057 |
< |
// exclude_I must always be the smaller of the pair |
| 1058 |
< |
if( exI > exJ ){ |
| 1059 |
< |
tempEx = exI; |
| 1060 |
< |
exI = exJ; |
| 1061 |
< |
exJ = tempEx; |
| 1062 |
< |
} |
| 1063 |
< |
#ifdef IS_MPI |
| 1064 |
< |
tempEx = exI; |
| 1065 |
< |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
| 1066 |
< |
tempEx = exJ; |
| 1067 |
< |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
| 1068 |
< |
|
| 1069 |
< |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
| 1070 |
< |
#else // isn't MPI |
| 1071 |
< |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
| 1072 |
< |
#endif //is_mpi |
| 1073 |
< |
} |
| 1074 |
< |
excludeOffset += info.nTorsions; |
| 1075 |
< |
|
| 1076 |
< |
|
| 1077 |
< |
// send the arrays off to the forceField for init. |
| 1078 |
< |
|
| 1079 |
< |
the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
| 1080 |
< |
the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
| 1081 |
< |
the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
| 1082 |
< |
the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
| 1083 |
< |
|
| 1084 |
< |
|
| 1085 |
< |
the_molecules[i].initialize( info ); |
| 1086 |
< |
|
| 1087 |
< |
|
| 1088 |
< |
atomOffset += info.nAtoms; |
| 1089 |
< |
delete[] theBonds; |
| 1090 |
< |
delete[] theBends; |
| 1091 |
< |
delete[] theTorsions; |
| 1092 |
< |
} |
| 1093 |
< |
|
| 1094 |
< |
#ifdef IS_MPI |
| 1095 |
< |
sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
| 1096 |
< |
MPIcheckPoint(); |
| 1097 |
< |
#endif // is_mpi |
| 1098 |
< |
|
| 1099 |
< |
// clean up the forcefield |
| 1100 |
< |
the_ff->calcRcut(); |
| 1101 |
< |
the_ff->cleanMe(); |
| 1102 |
< |
|
| 1103 |
< |
} |
| 1104 |
< |
|
| 1105 |
< |
void SimSetup::initFromBass( void ){ |
| 1106 |
< |
|
| 1107 |
< |
int i, j, k; |
| 1108 |
< |
int n_cells; |
| 1109 |
< |
double cellx, celly, cellz; |
| 1110 |
< |
double temp1, temp2, temp3; |
| 1111 |
< |
int n_per_extra; |
| 1112 |
< |
int n_extra; |
| 1113 |
< |
int have_extra, done; |
| 1114 |
< |
|
| 1115 |
< |
temp1 = (double)tot_nmol / 4.0; |
| 1116 |
< |
temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
| 1117 |
< |
temp3 = ceil( temp2 ); |
| 1118 |
< |
|
| 1119 |
< |
have_extra =0; |
| 1120 |
< |
if( temp2 < temp3 ){ // we have a non-complete lattice |
| 1121 |
< |
have_extra =1; |
| 1122 |
< |
|
| 1123 |
< |
n_cells = (int)temp3 - 1; |
| 1124 |
< |
cellx = simnfo->boxLx / temp3; |
| 1125 |
< |
celly = simnfo->boxLy / temp3; |
| 1126 |
< |
cellz = simnfo->boxLz / temp3; |
| 1127 |
< |
n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
| 1128 |
< |
temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
| 1129 |
< |
n_per_extra = (int)ceil( temp1 ); |
| 1130 |
< |
|
| 1131 |
< |
if( n_per_extra > 4){ |
| 1132 |
< |
sprintf( painCave.errMsg, |
| 1133 |
< |
"SimSetup error. There has been an error in constructing" |
| 1134 |
< |
" the non-complete lattice.\n" ); |
| 1135 |
< |
painCave.isFatal = 1; |
| 1136 |
< |
simError(); |
| 1137 |
< |
} |
| 1138 |
< |
} |
| 1139 |
< |
else{ |
| 1140 |
< |
n_cells = (int)temp3; |
| 1141 |
< |
cellx = simnfo->boxLx / temp3; |
| 1142 |
< |
celly = simnfo->boxLy / temp3; |
| 1143 |
< |
cellz = simnfo->boxLz / temp3; |
| 1144 |
< |
} |
| 1145 |
< |
|
| 1146 |
< |
current_mol = 0; |
| 1147 |
< |
current_comp_mol = 0; |
| 1148 |
< |
current_comp = 0; |
| 1149 |
< |
current_atom_ndx = 0; |
| 1150 |
< |
|
| 1151 |
< |
for( i=0; i < n_cells ; i++ ){ |
| 1152 |
< |
for( j=0; j < n_cells; j++ ){ |
| 1153 |
< |
for( k=0; k < n_cells; k++ ){ |
| 1154 |
< |
|
| 1155 |
< |
makeElement( i * cellx, |
| 1156 |
< |
j * celly, |
| 1157 |
< |
k * cellz ); |
| 1158 |
< |
|
| 1159 |
< |
makeElement( i * cellx + 0.5 * cellx, |
| 1160 |
< |
j * celly + 0.5 * celly, |
| 1161 |
< |
k * cellz ); |
| 1162 |
< |
|
| 1163 |
< |
makeElement( i * cellx, |
| 1164 |
< |
j * celly + 0.5 * celly, |
| 1165 |
< |
k * cellz + 0.5 * cellz ); |
| 1166 |
< |
|
| 1167 |
< |
makeElement( i * cellx + 0.5 * cellx, |
| 1168 |
< |
j * celly, |
| 1169 |
< |
k * cellz + 0.5 * cellz ); |
| 1170 |
< |
} |
| 1171 |
< |
} |
| 1172 |
< |
} |
| 1173 |
< |
|
| 1174 |
< |
if( have_extra ){ |
| 1175 |
< |
done = 0; |
| 1176 |
< |
|
| 1177 |
< |
int start_ndx; |
| 1178 |
< |
for( i=0; i < (n_cells+1) && !done; i++ ){ |
| 1179 |
< |
for( j=0; j < (n_cells+1) && !done; j++ ){ |
| 1180 |
< |
|
| 1181 |
< |
if( i < n_cells ){ |
| 1182 |
< |
|
| 1183 |
< |
if( j < n_cells ){ |
| 1184 |
< |
start_ndx = n_cells; |
| 1185 |
< |
} |
| 1186 |
< |
else start_ndx = 0; |
| 1187 |
< |
} |
| 1188 |
< |
else start_ndx = 0; |
| 1189 |
< |
|
| 1190 |
< |
for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
| 1191 |
< |
|
| 1192 |
< |
makeElement( i * cellx, |
| 1193 |
< |
j * celly, |
| 1194 |
< |
k * cellz ); |
| 1195 |
< |
done = ( current_mol >= tot_nmol ); |
| 1196 |
< |
|
| 1197 |
< |
if( !done && n_per_extra > 1 ){ |
| 1198 |
< |
makeElement( i * cellx + 0.5 * cellx, |
| 1199 |
< |
j * celly + 0.5 * celly, |
| 1200 |
< |
k * cellz ); |
| 1201 |
< |
done = ( current_mol >= tot_nmol ); |
| 1202 |
< |
} |
| 1203 |
< |
|
| 1204 |
< |
if( !done && n_per_extra > 2){ |
| 1205 |
< |
makeElement( i * cellx, |
| 1206 |
< |
j * celly + 0.5 * celly, |
| 1207 |
< |
k * cellz + 0.5 * cellz ); |
| 1208 |
< |
done = ( current_mol >= tot_nmol ); |
| 1209 |
< |
} |
| 1210 |
< |
|
| 1211 |
< |
if( !done && n_per_extra > 3){ |
| 1212 |
< |
makeElement( i * cellx + 0.5 * cellx, |
| 1213 |
< |
j * celly, |
| 1214 |
< |
k * cellz + 0.5 * cellz ); |
| 1215 |
< |
done = ( current_mol >= tot_nmol ); |
| 1216 |
< |
} |
| 1217 |
< |
} |
| 1218 |
< |
} |
| 1219 |
< |
} |
| 1220 |
< |
} |
| 1221 |
< |
|
| 1222 |
< |
|
| 1223 |
< |
for( i=0; i<simnfo->n_atoms; i++ ){ |
| 1224 |
< |
simnfo->atoms[i]->set_vx( 0.0 ); |
| 1225 |
< |
simnfo->atoms[i]->set_vy( 0.0 ); |
| 1226 |
< |
simnfo->atoms[i]->set_vz( 0.0 ); |
| 1227 |
< |
} |
| 1228 |
< |
} |
| 1229 |
< |
|
| 1230 |
< |
void SimSetup::makeElement( double x, double y, double z ){ |
| 1231 |
< |
|
| 1232 |
< |
int k; |
| 1233 |
< |
AtomStamp* current_atom; |
| 1234 |
< |
DirectionalAtom* dAtom; |
| 1235 |
< |
double rotMat[3][3]; |
| 1236 |
< |
|
| 1237 |
< |
for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
| 1238 |
< |
|
| 1239 |
< |
current_atom = comp_stamps[current_comp]->getAtom( k ); |
| 1240 |
< |
if( !current_atom->havePosition() ){ |
| 1241 |
< |
sprintf( painCave.errMsg, |
| 1242 |
< |
"SimSetup:initFromBass error.\n" |
| 1243 |
< |
"\tComponent %s, atom %s does not have a position specified.\n" |
| 1244 |
< |
"\tThe initialization routine is unable to give a start" |
| 1245 |
< |
" position.\n", |
| 1246 |
< |
comp_stamps[current_comp]->getID(), |
| 1247 |
< |
current_atom->getType() ); |
| 1248 |
< |
painCave.isFatal = 1; |
| 1249 |
< |
simError(); |
| 1250 |
< |
} |
| 1251 |
< |
|
| 1252 |
< |
the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() ); |
| 1253 |
< |
the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() ); |
| 1254 |
< |
the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() ); |
| 1255 |
< |
|
| 1256 |
< |
if( the_atoms[current_atom_ndx]->isDirectional() ){ |
| 1257 |
< |
|
| 1258 |
< |
dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx]; |
| 1259 |
< |
|
| 1260 |
< |
rotMat[0][0] = 1.0; |
| 1261 |
< |
rotMat[0][1] = 0.0; |
| 1262 |
< |
rotMat[0][2] = 0.0; |
| 1263 |
< |
|
| 1264 |
< |
rotMat[1][0] = 0.0; |
| 1265 |
< |
rotMat[1][1] = 1.0; |
| 1266 |
< |
rotMat[1][2] = 0.0; |
| 1267 |
< |
|
| 1268 |
< |
rotMat[2][0] = 0.0; |
| 1269 |
< |
rotMat[2][1] = 0.0; |
| 1270 |
< |
rotMat[2][2] = 1.0; |
| 1271 |
< |
|
| 1272 |
< |
dAtom->setA( rotMat ); |
| 1273 |
< |
} |
| 1274 |
< |
|
| 1275 |
< |
current_atom_ndx++; |
| 1276 |
< |
} |
| 1277 |
< |
|
| 1278 |
< |
current_mol++; |
| 1279 |
< |
current_comp_mol++; |
| 1280 |
< |
|
| 1281 |
< |
if( current_comp_mol >= components_nmol[current_comp] ){ |
| 1282 |
< |
|
| 1283 |
< |
current_comp_mol = 0; |
| 1284 |
< |
current_comp++; |
| 1285 |
< |
} |
| 1 |
> |
#include <algorithm> |
| 2 |
> |
#include <cstdlib> |
| 3 |
> |
#include <iostream> |
| 4 |
> |
#include <cmath> |
| 5 |
> |
#include <string> |
| 6 |
> |
|
| 7 |
> |
#include "SimSetup.hpp" |
| 8 |
> |
#include "parse_me.h" |
| 9 |
> |
#include "Integrator.hpp" |
| 10 |
> |
#include "simError.h" |
| 11 |
> |
|
| 12 |
> |
#ifdef IS_MPI |
| 13 |
> |
#include "mpiBASS.h" |
| 14 |
> |
#include "mpiSimulation.hpp" |
| 15 |
> |
#endif |
| 16 |
> |
|
| 17 |
> |
// some defines for ensemble and Forcefield cases |
| 18 |
> |
|
| 19 |
> |
#define NVE_ENS 0 |
| 20 |
> |
#define NVT_ENS 1 |
| 21 |
> |
#define NPTi_ENS 2 |
| 22 |
> |
#define NPTf_ENS 3 |
| 23 |
> |
#define NPTim_ENS 4 |
| 24 |
> |
#define NPTfm_ENS 5 |
| 25 |
> |
#define NVEZCONS_ENS 6 |
| 26 |
> |
#define NVTZCONS_ENS 7 |
| 27 |
> |
#define NPTiZCONS_ENS 8 |
| 28 |
> |
#define NPTfZCONS_ENS 9 |
| 29 |
> |
#define NPTimZCONS_ENS 10 |
| 30 |
> |
#define NPTfmZCONS_ENS 11 |
| 31 |
> |
|
| 32 |
> |
#define FF_DUFF 0 |
| 33 |
> |
#define FF_LJ 1 |
| 34 |
> |
#define FF_EAM 2 |
| 35 |
> |
|
| 36 |
> |
using namespace std; |
| 37 |
> |
|
| 38 |
> |
SimSetup::SimSetup(){ |
| 39 |
> |
|
| 40 |
> |
isInfoArray = 0; |
| 41 |
> |
nInfo = 1; |
| 42 |
> |
|
| 43 |
> |
stamps = new MakeStamps(); |
| 44 |
> |
globals = new Globals(); |
| 45 |
> |
|
| 46 |
> |
|
| 47 |
> |
#ifdef IS_MPI |
| 48 |
> |
strcpy( checkPointMsg, "SimSetup creation successful" ); |
| 49 |
> |
MPIcheckPoint(); |
| 50 |
> |
#endif // IS_MPI |
| 51 |
> |
} |
| 52 |
> |
|
| 53 |
> |
SimSetup::~SimSetup(){ |
| 54 |
> |
delete stamps; |
| 55 |
> |
delete globals; |
| 56 |
> |
} |
| 57 |
> |
|
| 58 |
> |
void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) { |
| 59 |
> |
info = the_info; |
| 60 |
> |
nInfo = theNinfo; |
| 61 |
> |
isInfoArray = 1; |
| 62 |
> |
} |
| 63 |
> |
|
| 64 |
> |
|
| 65 |
> |
void SimSetup::parseFile( char* fileName ){ |
| 66 |
> |
|
| 67 |
> |
#ifdef IS_MPI |
| 68 |
> |
if( worldRank == 0 ){ |
| 69 |
> |
#endif // is_mpi |
| 70 |
> |
|
| 71 |
> |
inFileName = fileName; |
| 72 |
> |
set_interface_stamps( stamps, globals ); |
| 73 |
> |
|
| 74 |
> |
#ifdef IS_MPI |
| 75 |
> |
mpiEventInit(); |
| 76 |
> |
#endif |
| 77 |
> |
|
| 78 |
> |
yacc_BASS( fileName ); |
| 79 |
> |
|
| 80 |
> |
#ifdef IS_MPI |
| 81 |
> |
throwMPIEvent(NULL); |
| 82 |
> |
} |
| 83 |
> |
else receiveParse(); |
| 84 |
> |
#endif |
| 85 |
> |
|
| 86 |
> |
} |
| 87 |
> |
|
| 88 |
> |
#ifdef IS_MPI |
| 89 |
> |
void SimSetup::receiveParse(void){ |
| 90 |
> |
|
| 91 |
> |
set_interface_stamps( stamps, globals ); |
| 92 |
> |
mpiEventInit(); |
| 93 |
> |
MPIcheckPoint(); |
| 94 |
> |
mpiEventLoop(); |
| 95 |
> |
|
| 96 |
> |
} |
| 97 |
> |
|
| 98 |
> |
#endif // is_mpi |
| 99 |
> |
|
| 100 |
> |
void SimSetup::createSim( void ){ |
| 101 |
> |
|
| 102 |
> |
int i, j, k, globalAtomIndex; |
| 103 |
> |
|
| 104 |
> |
// gather all of the information from the Bass file |
| 105 |
> |
|
| 106 |
> |
gatherInfo(); |
| 107 |
> |
|
| 108 |
> |
// creation of complex system objects |
| 109 |
> |
|
| 110 |
> |
sysObjectsCreation(); |
| 111 |
> |
|
| 112 |
> |
// check on the post processing info |
| 113 |
> |
|
| 114 |
> |
finalInfoCheck(); |
| 115 |
> |
|
| 116 |
> |
// initialize the system coordinates |
| 117 |
> |
|
| 118 |
> |
initSystemCoords(); |
| 119 |
> |
|
| 120 |
> |
|
| 121 |
> |
// make the output filenames |
| 122 |
> |
|
| 123 |
> |
makeOutNames(); |
| 124 |
> |
|
| 125 |
> |
// make the integrator |
| 126 |
> |
|
| 127 |
> |
makeIntegrator(); |
| 128 |
> |
|
| 129 |
> |
#ifdef IS_MPI |
| 130 |
> |
mpiSim->mpiRefresh(); |
| 131 |
> |
#endif |
| 132 |
> |
|
| 133 |
> |
// initialize the Fortran |
| 134 |
> |
|
| 135 |
> |
initFortran(); |
| 136 |
> |
|
| 137 |
> |
|
| 138 |
> |
|
| 139 |
> |
} |
| 140 |
> |
|
| 141 |
> |
|
| 142 |
> |
void SimSetup::makeMolecules( void ){ |
| 143 |
> |
|
| 144 |
> |
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
| 145 |
> |
molInit molInfo; |
| 146 |
> |
DirectionalAtom* dAtom; |
| 147 |
> |
LinkedAssign* extras; |
| 148 |
> |
LinkedAssign* current_extra; |
| 149 |
> |
AtomStamp* currentAtom; |
| 150 |
> |
BondStamp* currentBond; |
| 151 |
> |
BendStamp* currentBend; |
| 152 |
> |
TorsionStamp* currentTorsion; |
| 153 |
> |
|
| 154 |
> |
bond_pair* theBonds; |
| 155 |
> |
bend_set* theBends; |
| 156 |
> |
torsion_set* theTorsions; |
| 157 |
> |
|
| 158 |
> |
|
| 159 |
> |
//init the forceField paramters |
| 160 |
> |
|
| 161 |
> |
the_ff->readParams(); |
| 162 |
> |
|
| 163 |
> |
|
| 164 |
> |
// init the atoms |
| 165 |
> |
|
| 166 |
> |
double ux, uy, uz, u, uSqr; |
| 167 |
> |
|
| 168 |
> |
atomOffset = 0; |
| 169 |
> |
excludeOffset = 0; |
| 170 |
> |
for(i=0; i<info->n_mol; i++){ |
| 171 |
> |
|
| 172 |
> |
stampID = the_molecules[i].getStampID(); |
| 173 |
> |
|
| 174 |
> |
molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
| 175 |
> |
molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
| 176 |
> |
molInfo.nBends = comp_stamps[stampID]->getNBends(); |
| 177 |
> |
molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
| 178 |
> |
molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
| 179 |
> |
|
| 180 |
> |
molInfo.myAtoms = &the_atoms[atomOffset]; |
| 181 |
> |
molInfo.myExcludes = &the_excludes[excludeOffset]; |
| 182 |
> |
molInfo.myBonds = new Bond*[molInfo.nBonds]; |
| 183 |
> |
molInfo.myBends = new Bend*[molInfo.nBends]; |
| 184 |
> |
molInfo.myTorsions = new Torsion*[molInfo.nTorsions]; |
| 185 |
> |
|
| 186 |
> |
theBonds = new bond_pair[molInfo.nBonds]; |
| 187 |
> |
theBends = new bend_set[molInfo.nBends]; |
| 188 |
> |
theTorsions = new torsion_set[molInfo.nTorsions]; |
| 189 |
> |
|
| 190 |
> |
// make the Atoms |
| 191 |
> |
|
| 192 |
> |
for(j=0; j<molInfo.nAtoms; j++){ |
| 193 |
> |
|
| 194 |
> |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
| 195 |
> |
if( currentAtom->haveOrientation() ){ |
| 196 |
> |
|
| 197 |
> |
dAtom = new DirectionalAtom(j + atomOffset); |
| 198 |
> |
info->n_oriented++; |
| 199 |
> |
molInfo.myAtoms[j] = dAtom; |
| 200 |
> |
|
| 201 |
> |
ux = currentAtom->getOrntX(); |
| 202 |
> |
uy = currentAtom->getOrntY(); |
| 203 |
> |
uz = currentAtom->getOrntZ(); |
| 204 |
> |
|
| 205 |
> |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
| 206 |
> |
|
| 207 |
> |
u = sqrt( uSqr ); |
| 208 |
> |
ux = ux / u; |
| 209 |
> |
uy = uy / u; |
| 210 |
> |
uz = uz / u; |
| 211 |
> |
|
| 212 |
> |
dAtom->setSUx( ux ); |
| 213 |
> |
dAtom->setSUy( uy ); |
| 214 |
> |
dAtom->setSUz( uz ); |
| 215 |
> |
} |
| 216 |
> |
else{ |
| 217 |
> |
molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset); |
| 218 |
> |
} |
| 219 |
> |
molInfo.myAtoms[j]->setType( currentAtom->getType() ); |
| 220 |
> |
|
| 221 |
> |
#ifdef IS_MPI |
| 222 |
> |
|
| 223 |
> |
molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
| 224 |
> |
|
| 225 |
> |
#endif // is_mpi |
| 226 |
> |
} |
| 227 |
> |
|
| 228 |
> |
// make the bonds |
| 229 |
> |
for(j=0; j<molInfo.nBonds; j++){ |
| 230 |
> |
|
| 231 |
> |
currentBond = comp_stamps[stampID]->getBond( j ); |
| 232 |
> |
theBonds[j].a = currentBond->getA() + atomOffset; |
| 233 |
> |
theBonds[j].b = currentBond->getB() + atomOffset; |
| 234 |
> |
|
| 235 |
> |
exI = theBonds[j].a; |
| 236 |
> |
exJ = theBonds[j].b; |
| 237 |
> |
|
| 238 |
> |
// exclude_I must always be the smaller of the pair |
| 239 |
> |
if( exI > exJ ){ |
| 240 |
> |
tempEx = exI; |
| 241 |
> |
exI = exJ; |
| 242 |
> |
exJ = tempEx; |
| 243 |
> |
} |
| 244 |
> |
#ifdef IS_MPI |
| 245 |
> |
tempEx = exI; |
| 246 |
> |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
| 247 |
> |
tempEx = exJ; |
| 248 |
> |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
| 249 |
> |
|
| 250 |
> |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
| 251 |
> |
#else // isn't MPI |
| 252 |
> |
|
| 253 |
> |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
| 254 |
> |
#endif //is_mpi |
| 255 |
> |
} |
| 256 |
> |
excludeOffset += molInfo.nBonds; |
| 257 |
> |
|
| 258 |
> |
//make the bends |
| 259 |
> |
for(j=0; j<molInfo.nBends; j++){ |
| 260 |
> |
|
| 261 |
> |
currentBend = comp_stamps[stampID]->getBend( j ); |
| 262 |
> |
theBends[j].a = currentBend->getA() + atomOffset; |
| 263 |
> |
theBends[j].b = currentBend->getB() + atomOffset; |
| 264 |
> |
theBends[j].c = currentBend->getC() + atomOffset; |
| 265 |
> |
|
| 266 |
> |
if( currentBend->haveExtras() ){ |
| 267 |
> |
|
| 268 |
> |
extras = currentBend->getExtras(); |
| 269 |
> |
current_extra = extras; |
| 270 |
> |
|
| 271 |
> |
while( current_extra != NULL ){ |
| 272 |
> |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
| 273 |
> |
|
| 274 |
> |
switch( current_extra->getType() ){ |
| 275 |
> |
|
| 276 |
> |
case 0: |
| 277 |
> |
theBends[j].ghost = |
| 278 |
> |
current_extra->getInt() + atomOffset; |
| 279 |
> |
theBends[j].isGhost = 1; |
| 280 |
> |
break; |
| 281 |
> |
|
| 282 |
> |
case 1: |
| 283 |
> |
theBends[j].ghost = |
| 284 |
> |
(int)current_extra->getDouble() + atomOffset; |
| 285 |
> |
theBends[j].isGhost = 1; |
| 286 |
> |
break; |
| 287 |
> |
|
| 288 |
> |
default: |
| 289 |
> |
sprintf( painCave.errMsg, |
| 290 |
> |
"SimSetup Error: ghostVectorSource was neither a " |
| 291 |
> |
"double nor an int.\n" |
| 292 |
> |
"-->Bend[%d] in %s\n", |
| 293 |
> |
j, comp_stamps[stampID]->getID() ); |
| 294 |
> |
painCave.isFatal = 1; |
| 295 |
> |
simError(); |
| 296 |
> |
} |
| 297 |
> |
} |
| 298 |
> |
|
| 299 |
> |
else{ |
| 300 |
> |
|
| 301 |
> |
sprintf( painCave.errMsg, |
| 302 |
> |
"SimSetup Error: unhandled bend assignment:\n" |
| 303 |
> |
" -->%s in Bend[%d] in %s\n", |
| 304 |
> |
current_extra->getlhs(), |
| 305 |
> |
j, comp_stamps[stampID]->getID() ); |
| 306 |
> |
painCave.isFatal = 1; |
| 307 |
> |
simError(); |
| 308 |
> |
} |
| 309 |
> |
|
| 310 |
> |
current_extra = current_extra->getNext(); |
| 311 |
> |
} |
| 312 |
> |
} |
| 313 |
> |
|
| 314 |
> |
if( !theBends[j].isGhost ){ |
| 315 |
> |
|
| 316 |
> |
exI = theBends[j].a; |
| 317 |
> |
exJ = theBends[j].c; |
| 318 |
> |
} |
| 319 |
> |
else{ |
| 320 |
> |
|
| 321 |
> |
exI = theBends[j].a; |
| 322 |
> |
exJ = theBends[j].b; |
| 323 |
> |
} |
| 324 |
> |
|
| 325 |
> |
// exclude_I must always be the smaller of the pair |
| 326 |
> |
if( exI > exJ ){ |
| 327 |
> |
tempEx = exI; |
| 328 |
> |
exI = exJ; |
| 329 |
> |
exJ = tempEx; |
| 330 |
> |
} |
| 331 |
> |
#ifdef IS_MPI |
| 332 |
> |
tempEx = exI; |
| 333 |
> |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
| 334 |
> |
tempEx = exJ; |
| 335 |
> |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
| 336 |
> |
|
| 337 |
> |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
| 338 |
> |
#else // isn't MPI |
| 339 |
> |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
| 340 |
> |
#endif //is_mpi |
| 341 |
> |
} |
| 342 |
> |
excludeOffset += molInfo.nBends; |
| 343 |
> |
|
| 344 |
> |
for(j=0; j<molInfo.nTorsions; j++){ |
| 345 |
> |
|
| 346 |
> |
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
| 347 |
> |
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
| 348 |
> |
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
| 349 |
> |
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
| 350 |
> |
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
| 351 |
> |
|
| 352 |
> |
exI = theTorsions[j].a; |
| 353 |
> |
exJ = theTorsions[j].d; |
| 354 |
> |
|
| 355 |
> |
// exclude_I must always be the smaller of the pair |
| 356 |
> |
if( exI > exJ ){ |
| 357 |
> |
tempEx = exI; |
| 358 |
> |
exI = exJ; |
| 359 |
> |
exJ = tempEx; |
| 360 |
> |
} |
| 361 |
> |
#ifdef IS_MPI |
| 362 |
> |
tempEx = exI; |
| 363 |
> |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
| 364 |
> |
tempEx = exJ; |
| 365 |
> |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
| 366 |
> |
|
| 367 |
> |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
| 368 |
> |
#else // isn't MPI |
| 369 |
> |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
| 370 |
> |
#endif //is_mpi |
| 371 |
> |
} |
| 372 |
> |
excludeOffset += molInfo.nTorsions; |
| 373 |
> |
|
| 374 |
> |
|
| 375 |
> |
// send the arrays off to the forceField for init. |
| 376 |
> |
|
| 377 |
> |
the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms ); |
| 378 |
> |
the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds ); |
| 379 |
> |
the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends ); |
| 380 |
> |
the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions ); |
| 381 |
> |
|
| 382 |
> |
|
| 383 |
> |
the_molecules[i].initialize( molInfo ); |
| 384 |
> |
|
| 385 |
> |
|
| 386 |
> |
atomOffset += molInfo.nAtoms; |
| 387 |
> |
delete[] theBonds; |
| 388 |
> |
delete[] theBends; |
| 389 |
> |
delete[] theTorsions; |
| 390 |
> |
} |
| 391 |
> |
|
| 392 |
> |
#ifdef IS_MPI |
| 393 |
> |
sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
| 394 |
> |
MPIcheckPoint(); |
| 395 |
> |
#endif // is_mpi |
| 396 |
> |
|
| 397 |
> |
// clean up the forcefield |
| 398 |
> |
the_ff->calcRcut(); |
| 399 |
> |
the_ff->cleanMe(); |
| 400 |
> |
|
| 401 |
> |
} |
| 402 |
> |
|
| 403 |
> |
void SimSetup::initFromBass( void ){ |
| 404 |
> |
|
| 405 |
> |
int i, j, k; |
| 406 |
> |
int n_cells; |
| 407 |
> |
double cellx, celly, cellz; |
| 408 |
> |
double temp1, temp2, temp3; |
| 409 |
> |
int n_per_extra; |
| 410 |
> |
int n_extra; |
| 411 |
> |
int have_extra, done; |
| 412 |
> |
|
| 413 |
> |
temp1 = (double)tot_nmol / 4.0; |
| 414 |
> |
temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
| 415 |
> |
temp3 = ceil( temp2 ); |
| 416 |
> |
|
| 417 |
> |
have_extra =0; |
| 418 |
> |
if( temp2 < temp3 ){ // we have a non-complete lattice |
| 419 |
> |
have_extra =1; |
| 420 |
> |
|
| 421 |
> |
n_cells = (int)temp3 - 1; |
| 422 |
> |
cellx = info->boxL[0] / temp3; |
| 423 |
> |
celly = info->boxL[1] / temp3; |
| 424 |
> |
cellz = info->boxL[2] / temp3; |
| 425 |
> |
n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
| 426 |
> |
temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
| 427 |
> |
n_per_extra = (int)ceil( temp1 ); |
| 428 |
> |
|
| 429 |
> |
if( n_per_extra > 4){ |
| 430 |
> |
sprintf( painCave.errMsg, |
| 431 |
> |
"SimSetup error. There has been an error in constructing" |
| 432 |
> |
" the non-complete lattice.\n" ); |
| 433 |
> |
painCave.isFatal = 1; |
| 434 |
> |
simError(); |
| 435 |
> |
} |
| 436 |
> |
} |
| 437 |
> |
else{ |
| 438 |
> |
n_cells = (int)temp3; |
| 439 |
> |
cellx = info->boxL[0] / temp3; |
| 440 |
> |
celly = info->boxL[1] / temp3; |
| 441 |
> |
cellz = info->boxL[2] / temp3; |
| 442 |
> |
} |
| 443 |
> |
|
| 444 |
> |
current_mol = 0; |
| 445 |
> |
current_comp_mol = 0; |
| 446 |
> |
current_comp = 0; |
| 447 |
> |
current_atom_ndx = 0; |
| 448 |
> |
|
| 449 |
> |
for( i=0; i < n_cells ; i++ ){ |
| 450 |
> |
for( j=0; j < n_cells; j++ ){ |
| 451 |
> |
for( k=0; k < n_cells; k++ ){ |
| 452 |
> |
|
| 453 |
> |
makeElement( i * cellx, |
| 454 |
> |
j * celly, |
| 455 |
> |
k * cellz ); |
| 456 |
> |
|
| 457 |
> |
makeElement( i * cellx + 0.5 * cellx, |
| 458 |
> |
j * celly + 0.5 * celly, |
| 459 |
> |
k * cellz ); |
| 460 |
> |
|
| 461 |
> |
makeElement( i * cellx, |
| 462 |
> |
j * celly + 0.5 * celly, |
| 463 |
> |
k * cellz + 0.5 * cellz ); |
| 464 |
> |
|
| 465 |
> |
makeElement( i * cellx + 0.5 * cellx, |
| 466 |
> |
j * celly, |
| 467 |
> |
k * cellz + 0.5 * cellz ); |
| 468 |
> |
} |
| 469 |
> |
} |
| 470 |
> |
} |
| 471 |
> |
|
| 472 |
> |
if( have_extra ){ |
| 473 |
> |
done = 0; |
| 474 |
> |
|
| 475 |
> |
int start_ndx; |
| 476 |
> |
for( i=0; i < (n_cells+1) && !done; i++ ){ |
| 477 |
> |
for( j=0; j < (n_cells+1) && !done; j++ ){ |
| 478 |
> |
|
| 479 |
> |
if( i < n_cells ){ |
| 480 |
> |
|
| 481 |
> |
if( j < n_cells ){ |
| 482 |
> |
start_ndx = n_cells; |
| 483 |
> |
} |
| 484 |
> |
else start_ndx = 0; |
| 485 |
> |
} |
| 486 |
> |
else start_ndx = 0; |
| 487 |
> |
|
| 488 |
> |
for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
| 489 |
> |
|
| 490 |
> |
makeElement( i * cellx, |
| 491 |
> |
j * celly, |
| 492 |
> |
k * cellz ); |
| 493 |
> |
done = ( current_mol >= tot_nmol ); |
| 494 |
> |
|
| 495 |
> |
if( !done && n_per_extra > 1 ){ |
| 496 |
> |
makeElement( i * cellx + 0.5 * cellx, |
| 497 |
> |
j * celly + 0.5 * celly, |
| 498 |
> |
k * cellz ); |
| 499 |
> |
done = ( current_mol >= tot_nmol ); |
| 500 |
> |
} |
| 501 |
> |
|
| 502 |
> |
if( !done && n_per_extra > 2){ |
| 503 |
> |
makeElement( i * cellx, |
| 504 |
> |
j * celly + 0.5 * celly, |
| 505 |
> |
k * cellz + 0.5 * cellz ); |
| 506 |
> |
done = ( current_mol >= tot_nmol ); |
| 507 |
> |
} |
| 508 |
> |
|
| 509 |
> |
if( !done && n_per_extra > 3){ |
| 510 |
> |
makeElement( i * cellx + 0.5 * cellx, |
| 511 |
> |
j * celly, |
| 512 |
> |
k * cellz + 0.5 * cellz ); |
| 513 |
> |
done = ( current_mol >= tot_nmol ); |
| 514 |
> |
} |
| 515 |
> |
} |
| 516 |
> |
} |
| 517 |
> |
} |
| 518 |
> |
} |
| 519 |
> |
|
| 520 |
> |
|
| 521 |
> |
for( i=0; i<info->n_atoms; i++ ){ |
| 522 |
> |
info->atoms[i]->set_vx( 0.0 ); |
| 523 |
> |
info->atoms[i]->set_vy( 0.0 ); |
| 524 |
> |
info->atoms[i]->set_vz( 0.0 ); |
| 525 |
> |
} |
| 526 |
> |
} |
| 527 |
> |
|
| 528 |
> |
void SimSetup::makeElement( double x, double y, double z ){ |
| 529 |
> |
|
| 530 |
> |
int k; |
| 531 |
> |
AtomStamp* current_atom; |
| 532 |
> |
DirectionalAtom* dAtom; |
| 533 |
> |
double rotMat[3][3]; |
| 534 |
> |
|
| 535 |
> |
for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
| 536 |
> |
|
| 537 |
> |
current_atom = comp_stamps[current_comp]->getAtom( k ); |
| 538 |
> |
if( !current_atom->havePosition() ){ |
| 539 |
> |
sprintf( painCave.errMsg, |
| 540 |
> |
"SimSetup:initFromBass error.\n" |
| 541 |
> |
"\tComponent %s, atom %s does not have a position specified.\n" |
| 542 |
> |
"\tThe initialization routine is unable to give a start" |
| 543 |
> |
" position.\n", |
| 544 |
> |
comp_stamps[current_comp]->getID(), |
| 545 |
> |
current_atom->getType() ); |
| 546 |
> |
painCave.isFatal = 1; |
| 547 |
> |
simError(); |
| 548 |
> |
} |
| 549 |
> |
|
| 550 |
> |
the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() ); |
| 551 |
> |
the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() ); |
| 552 |
> |
the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() ); |
| 553 |
> |
|
| 554 |
> |
if( the_atoms[current_atom_ndx]->isDirectional() ){ |
| 555 |
> |
|
| 556 |
> |
dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx]; |
| 557 |
> |
|
| 558 |
> |
rotMat[0][0] = 1.0; |
| 559 |
> |
rotMat[0][1] = 0.0; |
| 560 |
> |
rotMat[0][2] = 0.0; |
| 561 |
> |
|
| 562 |
> |
rotMat[1][0] = 0.0; |
| 563 |
> |
rotMat[1][1] = 1.0; |
| 564 |
> |
rotMat[1][2] = 0.0; |
| 565 |
> |
|
| 566 |
> |
rotMat[2][0] = 0.0; |
| 567 |
> |
rotMat[2][1] = 0.0; |
| 568 |
> |
rotMat[2][2] = 1.0; |
| 569 |
> |
|
| 570 |
> |
dAtom->setA( rotMat ); |
| 571 |
> |
} |
| 572 |
> |
|
| 573 |
> |
current_atom_ndx++; |
| 574 |
> |
} |
| 575 |
> |
|
| 576 |
> |
current_mol++; |
| 577 |
> |
current_comp_mol++; |
| 578 |
> |
|
| 579 |
> |
if( current_comp_mol >= components_nmol[current_comp] ){ |
| 580 |
> |
|
| 581 |
> |
current_comp_mol = 0; |
| 582 |
> |
current_comp++; |
| 583 |
> |
} |
| 584 |
> |
} |
| 585 |
> |
|
| 586 |
> |
|
| 587 |
> |
void SimSetup::gatherInfo( void ){ |
| 588 |
> |
int i,j,k; |
| 589 |
> |
|
| 590 |
> |
ensembleCase = -1; |
| 591 |
> |
ffCase = -1; |
| 592 |
> |
|
| 593 |
> |
// get the stamps and globals; |
| 594 |
> |
stamps = stamps; |
| 595 |
> |
globals = globals; |
| 596 |
> |
|
| 597 |
> |
// set the easy ones first |
| 598 |
> |
info->target_temp = globals->getTargetTemp(); |
| 599 |
> |
info->dt = globals->getDt(); |
| 600 |
> |
info->run_time = globals->getRunTime(); |
| 601 |
> |
n_components = globals->getNComponents(); |
| 602 |
> |
|
| 603 |
> |
|
| 604 |
> |
// get the forceField |
| 605 |
> |
|
| 606 |
> |
strcpy( force_field, globals->getForceField() ); |
| 607 |
> |
|
| 608 |
> |
if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
| 609 |
> |
else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
| 610 |
> |
else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM; |
| 611 |
> |
else{ |
| 612 |
> |
sprintf( painCave.errMsg, |
| 613 |
> |
"SimSetup Error. Unrecognized force field -> %s\n", |
| 614 |
> |
force_field ); |
| 615 |
> |
painCave.isFatal = 1; |
| 616 |
> |
simError(); |
| 617 |
> |
} |
| 618 |
> |
|
| 619 |
> |
// get the ensemble |
| 620 |
> |
|
| 621 |
> |
strcpy( ensemble, globals->getEnsemble() ); |
| 622 |
> |
|
| 623 |
> |
if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
| 624 |
> |
else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
| 625 |
> |
else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") ) |
| 626 |
> |
ensembleCase = NPTi_ENS; |
| 627 |
> |
else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; |
| 628 |
> |
else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS; |
| 629 |
> |
else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; |
| 630 |
> |
|
| 631 |
> |
else if( !strcasecmp( ensemble, "NVEZCONS")) ensembleCase = NVEZCONS_ENS; |
| 632 |
> |
else if( !strcasecmp( ensemble, "NVTZCONS")) ensembleCase = NVTZCONS_ENS; |
| 633 |
> |
else if( !strcasecmp( ensemble, "NPTiZCONS") || !strcasecmp( ensemble, "NPT")) |
| 634 |
> |
ensembleCase = NPTiZCONS_ENS; |
| 635 |
> |
else if( !strcasecmp( ensemble, "NPTfCONS")) ensembleCase = NPTfZCONS_ENS; |
| 636 |
> |
else if( !strcasecmp( ensemble, "NPTimZCONS")) ensembleCase = NPTimZCONS_ENS; |
| 637 |
> |
else if( !strcasecmp( ensemble, "NPTfmCONS")) ensembleCase = NPTfmZCONS_ENS; |
| 638 |
> |
|
| 639 |
> |
else{ |
| 640 |
> |
sprintf( painCave.errMsg, |
| 641 |
> |
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
| 642 |
> |
"reverting to NVE for this simulation.\n", |
| 643 |
> |
ensemble ); |
| 644 |
> |
painCave.isFatal = 0; |
| 645 |
> |
simError(); |
| 646 |
> |
strcpy( ensemble, "NVE" ); |
| 647 |
> |
ensembleCase = NVE_ENS; |
| 648 |
> |
} |
| 649 |
> |
strcpy( info->ensemble, ensemble ); |
| 650 |
> |
|
| 651 |
> |
// get the mixing rule |
| 652 |
> |
|
| 653 |
> |
strcpy( info->mixingRule, globals->getMixingRule() ); |
| 654 |
> |
info->usePBC = globals->getPBC(); |
| 655 |
> |
|
| 656 |
> |
|
| 657 |
> |
// get the components and calculate the tot_nMol and indvidual n_mol |
| 658 |
> |
|
| 659 |
> |
the_components = globals->getComponents(); |
| 660 |
> |
components_nmol = new int[n_components]; |
| 661 |
> |
|
| 662 |
> |
|
| 663 |
> |
if( !globals->haveNMol() ){ |
| 664 |
> |
// we don't have the total number of molecules, so we assume it is |
| 665 |
> |
// given in each component |
| 666 |
> |
|
| 667 |
> |
tot_nmol = 0; |
| 668 |
> |
for( i=0; i<n_components; i++ ){ |
| 669 |
> |
|
| 670 |
> |
if( !the_components[i]->haveNMol() ){ |
| 671 |
> |
// we have a problem |
| 672 |
> |
sprintf( painCave.errMsg, |
| 673 |
> |
"SimSetup Error. No global NMol or component NMol" |
| 674 |
> |
" given. Cannot calculate the number of atoms.\n" ); |
| 675 |
> |
painCave.isFatal = 1; |
| 676 |
> |
simError(); |
| 677 |
> |
} |
| 678 |
> |
|
| 679 |
> |
tot_nmol += the_components[i]->getNMol(); |
| 680 |
> |
components_nmol[i] = the_components[i]->getNMol(); |
| 681 |
> |
} |
| 682 |
> |
} |
| 683 |
> |
else{ |
| 684 |
> |
sprintf( painCave.errMsg, |
| 685 |
> |
"SimSetup error.\n" |
| 686 |
> |
"\tSorry, the ability to specify total" |
| 687 |
> |
" nMols and then give molfractions in the components\n" |
| 688 |
> |
"\tis not currently supported." |
| 689 |
> |
" Please give nMol in the components.\n" ); |
| 690 |
> |
painCave.isFatal = 1; |
| 691 |
> |
simError(); |
| 692 |
> |
} |
| 693 |
> |
|
| 694 |
> |
// set the status, sample, and thermal kick times |
| 695 |
> |
|
| 696 |
> |
if( globals->haveSampleTime() ){ |
| 697 |
> |
info->sampleTime = globals->getSampleTime(); |
| 698 |
> |
info->statusTime = info->sampleTime; |
| 699 |
> |
info->thermalTime = info->sampleTime; |
| 700 |
> |
} |
| 701 |
> |
else{ |
| 702 |
> |
info->sampleTime = globals->getRunTime(); |
| 703 |
> |
info->statusTime = info->sampleTime; |
| 704 |
> |
info->thermalTime = info->sampleTime; |
| 705 |
> |
} |
| 706 |
> |
|
| 707 |
> |
if( globals->haveStatusTime() ){ |
| 708 |
> |
info->statusTime = globals->getStatusTime(); |
| 709 |
> |
} |
| 710 |
> |
|
| 711 |
> |
if( globals->haveThermalTime() ){ |
| 712 |
> |
info->thermalTime = globals->getThermalTime(); |
| 713 |
> |
} |
| 714 |
> |
|
| 715 |
> |
// check for the temperature set flag |
| 716 |
> |
|
| 717 |
> |
if( globals->haveTempSet() ) info->setTemp = globals->getTempSet(); |
| 718 |
> |
|
| 719 |
> |
// get some of the tricky things that may still be in the globals |
| 720 |
> |
|
| 721 |
> |
double boxVector[3]; |
| 722 |
> |
if( globals->haveBox() ){ |
| 723 |
> |
boxVector[0] = globals->getBox(); |
| 724 |
> |
boxVector[1] = globals->getBox(); |
| 725 |
> |
boxVector[2] = globals->getBox(); |
| 726 |
> |
|
| 727 |
> |
info->setBox( boxVector ); |
| 728 |
> |
} |
| 729 |
> |
else if( globals->haveDensity() ){ |
| 730 |
> |
|
| 731 |
> |
double vol; |
| 732 |
> |
vol = (double)tot_nmol / globals->getDensity(); |
| 733 |
> |
boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
| 734 |
> |
boxVector[1] = boxVector[0]; |
| 735 |
> |
boxVector[2] = boxVector[0]; |
| 736 |
> |
|
| 737 |
> |
info->setBox( boxVector ); |
| 738 |
> |
} |
| 739 |
> |
else{ |
| 740 |
> |
if( !globals->haveBoxX() ){ |
| 741 |
> |
sprintf( painCave.errMsg, |
| 742 |
> |
"SimSetup error, no periodic BoxX size given.\n" ); |
| 743 |
> |
painCave.isFatal = 1; |
| 744 |
> |
simError(); |
| 745 |
> |
} |
| 746 |
> |
boxVector[0] = globals->getBoxX(); |
| 747 |
> |
|
| 748 |
> |
if( !globals->haveBoxY() ){ |
| 749 |
> |
sprintf( painCave.errMsg, |
| 750 |
> |
"SimSetup error, no periodic BoxY size given.\n" ); |
| 751 |
> |
painCave.isFatal = 1; |
| 752 |
> |
simError(); |
| 753 |
> |
} |
| 754 |
> |
boxVector[1] = globals->getBoxY(); |
| 755 |
> |
|
| 756 |
> |
if( !globals->haveBoxZ() ){ |
| 757 |
> |
sprintf( painCave.errMsg, |
| 758 |
> |
"SimSetup error, no periodic BoxZ size given.\n" ); |
| 759 |
> |
painCave.isFatal = 1; |
| 760 |
> |
simError(); |
| 761 |
> |
} |
| 762 |
> |
boxVector[2] = globals->getBoxZ(); |
| 763 |
> |
|
| 764 |
> |
info->setBox( boxVector ); |
| 765 |
> |
} |
| 766 |
> |
|
| 767 |
> |
|
| 768 |
> |
|
| 769 |
> |
#ifdef IS_MPI |
| 770 |
> |
strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" ); |
| 771 |
> |
MPIcheckPoint(); |
| 772 |
> |
#endif // is_mpi |
| 773 |
> |
|
| 774 |
> |
} |
| 775 |
> |
|
| 776 |
> |
|
| 777 |
> |
void SimSetup::finalInfoCheck( void ){ |
| 778 |
> |
int index; |
| 779 |
> |
int usesDipoles; |
| 780 |
> |
|
| 781 |
> |
|
| 782 |
> |
// check electrostatic parameters |
| 783 |
> |
|
| 784 |
> |
index = 0; |
| 785 |
> |
usesDipoles = 0; |
| 786 |
> |
while( (index < info->n_atoms) && !usesDipoles ){ |
| 787 |
> |
usesDipoles = ((info->atoms)[index])->hasDipole(); |
| 788 |
> |
index++; |
| 789 |
> |
} |
| 790 |
> |
|
| 791 |
> |
#ifdef IS_MPI |
| 792 |
> |
int myUse = usesDipoles; |
| 793 |
> |
MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
| 794 |
> |
#endif //is_mpi |
| 795 |
> |
|
| 796 |
> |
double theEcr, theEst; |
| 797 |
> |
|
| 798 |
> |
if (globals->getUseRF() ) { |
| 799 |
> |
info->useReactionField = 1; |
| 800 |
> |
|
| 801 |
> |
if( !globals->haveECR() ){ |
| 802 |
> |
sprintf( painCave.errMsg, |
| 803 |
> |
"SimSetup Warning: using default value of 1/2 the smallest " |
| 804 |
> |
"box length for the electrostaticCutoffRadius.\n" |
| 805 |
> |
"I hope you have a very fast processor!\n"); |
| 806 |
> |
painCave.isFatal = 0; |
| 807 |
> |
simError(); |
| 808 |
> |
double smallest; |
| 809 |
> |
smallest = info->boxL[0]; |
| 810 |
> |
if (info->boxL[1] <= smallest) smallest = info->boxL[1]; |
| 811 |
> |
if (info->boxL[2] <= smallest) smallest = info->boxL[2]; |
| 812 |
> |
theEcr = 0.5 * smallest; |
| 813 |
> |
} else { |
| 814 |
> |
theEcr = globals->getECR(); |
| 815 |
> |
} |
| 816 |
> |
|
| 817 |
> |
if( !globals->haveEST() ){ |
| 818 |
> |
sprintf( painCave.errMsg, |
| 819 |
> |
"SimSetup Warning: using default value of 0.05 * the " |
| 820 |
> |
"electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
| 821 |
> |
); |
| 822 |
> |
painCave.isFatal = 0; |
| 823 |
> |
simError(); |
| 824 |
> |
theEst = 0.05 * theEcr; |
| 825 |
> |
} else { |
| 826 |
> |
theEst= globals->getEST(); |
| 827 |
> |
} |
| 828 |
> |
|
| 829 |
> |
info->setEcr( theEcr, theEst ); |
| 830 |
> |
|
| 831 |
> |
if(!globals->haveDielectric() ){ |
| 832 |
> |
sprintf( painCave.errMsg, |
| 833 |
> |
"SimSetup Error: You are trying to use Reaction Field without" |
| 834 |
> |
"setting a dielectric constant!\n" |
| 835 |
> |
); |
| 836 |
> |
painCave.isFatal = 1; |
| 837 |
> |
simError(); |
| 838 |
> |
} |
| 839 |
> |
info->dielectric = globals->getDielectric(); |
| 840 |
> |
} |
| 841 |
> |
else { |
| 842 |
> |
if (usesDipoles) { |
| 843 |
> |
|
| 844 |
> |
if( !globals->haveECR() ){ |
| 845 |
> |
sprintf( painCave.errMsg, |
| 846 |
> |
"SimSetup Warning: using default value of 1/2 the smallest " |
| 847 |
> |
"box length for the electrostaticCutoffRadius.\n" |
| 848 |
> |
"I hope you have a very fast processor!\n"); |
| 849 |
> |
painCave.isFatal = 0; |
| 850 |
> |
simError(); |
| 851 |
> |
double smallest; |
| 852 |
> |
smallest = info->boxL[0]; |
| 853 |
> |
if (info->boxL[1] <= smallest) smallest = info->boxL[1]; |
| 854 |
> |
if (info->boxL[2] <= smallest) smallest = info->boxL[2]; |
| 855 |
> |
theEcr = 0.5 * smallest; |
| 856 |
> |
} else { |
| 857 |
> |
theEcr = globals->getECR(); |
| 858 |
> |
} |
| 859 |
> |
|
| 860 |
> |
if( !globals->haveEST() ){ |
| 861 |
> |
sprintf( painCave.errMsg, |
| 862 |
> |
"SimSetup Warning: using default value of 0.05 * the " |
| 863 |
> |
"electrostaticCutoffRadius for the " |
| 864 |
> |
"electrostaticSkinThickness\n" |
| 865 |
> |
); |
| 866 |
> |
painCave.isFatal = 0; |
| 867 |
> |
simError(); |
| 868 |
> |
theEst = 0.05 * theEcr; |
| 869 |
> |
} else { |
| 870 |
> |
theEst= globals->getEST(); |
| 871 |
> |
} |
| 872 |
> |
|
| 873 |
> |
info->setEcr( theEcr, theEst ); |
| 874 |
> |
} |
| 875 |
> |
} |
| 876 |
> |
|
| 877 |
> |
#ifdef IS_MPI |
| 878 |
> |
strcpy( checkPointMsg, "post processing checks out" ); |
| 879 |
> |
MPIcheckPoint(); |
| 880 |
> |
#endif // is_mpi |
| 881 |
> |
|
| 882 |
> |
} |
| 883 |
> |
|
| 884 |
> |
void SimSetup::initSystemCoords( void ){ |
| 885 |
> |
|
| 886 |
> |
if( globals->haveInitialConfig() ){ |
| 887 |
> |
|
| 888 |
> |
InitializeFromFile* fileInit; |
| 889 |
> |
#ifdef IS_MPI // is_mpi |
| 890 |
> |
if( worldRank == 0 ){ |
| 891 |
> |
#endif //is_mpi |
| 892 |
> |
fileInit = new InitializeFromFile( globals->getInitialConfig() ); |
| 893 |
> |
#ifdef IS_MPI |
| 894 |
> |
}else fileInit = new InitializeFromFile( NULL ); |
| 895 |
> |
#endif |
| 896 |
> |
fileInit->readInit( info ); // default velocities on |
| 897 |
> |
|
| 898 |
> |
delete fileInit; |
| 899 |
> |
} |
| 900 |
> |
else{ |
| 901 |
> |
|
| 902 |
> |
#ifdef IS_MPI |
| 903 |
> |
|
| 904 |
> |
// no init from bass |
| 905 |
> |
|
| 906 |
> |
sprintf( painCave.errMsg, |
| 907 |
> |
"Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
| 908 |
> |
painCave.isFatal; |
| 909 |
> |
simError(); |
| 910 |
> |
|
| 911 |
> |
#else |
| 912 |
> |
|
| 913 |
> |
initFromBass(); |
| 914 |
> |
|
| 915 |
> |
|
| 916 |
> |
#endif |
| 917 |
> |
} |
| 918 |
> |
|
| 919 |
> |
#ifdef IS_MPI |
| 920 |
> |
strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
| 921 |
> |
MPIcheckPoint(); |
| 922 |
> |
#endif // is_mpi |
| 923 |
> |
|
| 924 |
> |
} |
| 925 |
> |
|
| 926 |
> |
|
| 927 |
> |
void SimSetup::makeOutNames( void ){ |
| 928 |
> |
|
| 929 |
> |
#ifdef IS_MPI |
| 930 |
> |
if( worldRank == 0 ){ |
| 931 |
> |
#endif // is_mpi |
| 932 |
> |
|
| 933 |
> |
if( globals->haveFinalConfig() ){ |
| 934 |
> |
strcpy( info->finalName, globals->getFinalConfig() ); |
| 935 |
> |
} |
| 936 |
> |
else{ |
| 937 |
> |
strcpy( info->finalName, inFileName ); |
| 938 |
> |
char* endTest; |
| 939 |
> |
int nameLength = strlen( info->finalName ); |
| 940 |
> |
endTest = &(info->finalName[nameLength - 5]); |
| 941 |
> |
if( !strcmp( endTest, ".bass" ) ){ |
| 942 |
> |
strcpy( endTest, ".eor" ); |
| 943 |
> |
} |
| 944 |
> |
else if( !strcmp( endTest, ".BASS" ) ){ |
| 945 |
> |
strcpy( endTest, ".eor" ); |
| 946 |
> |
} |
| 947 |
> |
else{ |
| 948 |
> |
endTest = &(info->finalName[nameLength - 4]); |
| 949 |
> |
if( !strcmp( endTest, ".bss" ) ){ |
| 950 |
> |
strcpy( endTest, ".eor" ); |
| 951 |
> |
} |
| 952 |
> |
else if( !strcmp( endTest, ".mdl" ) ){ |
| 953 |
> |
strcpy( endTest, ".eor" ); |
| 954 |
> |
} |
| 955 |
> |
else{ |
| 956 |
> |
strcat( info->finalName, ".eor" ); |
| 957 |
> |
} |
| 958 |
> |
} |
| 959 |
> |
} |
| 960 |
> |
|
| 961 |
> |
// make the sample and status out names |
| 962 |
> |
|
| 963 |
> |
strcpy( info->sampleName, inFileName ); |
| 964 |
> |
char* endTest; |
| 965 |
> |
int nameLength = strlen( info->sampleName ); |
| 966 |
> |
endTest = &(info->sampleName[nameLength - 5]); |
| 967 |
> |
if( !strcmp( endTest, ".bass" ) ){ |
| 968 |
> |
strcpy( endTest, ".dump" ); |
| 969 |
> |
} |
| 970 |
> |
else if( !strcmp( endTest, ".BASS" ) ){ |
| 971 |
> |
strcpy( endTest, ".dump" ); |
| 972 |
> |
} |
| 973 |
> |
else{ |
| 974 |
> |
endTest = &(info->sampleName[nameLength - 4]); |
| 975 |
> |
if( !strcmp( endTest, ".bss" ) ){ |
| 976 |
> |
strcpy( endTest, ".dump" ); |
| 977 |
> |
} |
| 978 |
> |
else if( !strcmp( endTest, ".mdl" ) ){ |
| 979 |
> |
strcpy( endTest, ".dump" ); |
| 980 |
> |
} |
| 981 |
> |
else{ |
| 982 |
> |
strcat( info->sampleName, ".dump" ); |
| 983 |
> |
} |
| 984 |
> |
} |
| 985 |
> |
|
| 986 |
> |
strcpy( info->statusName, inFileName ); |
| 987 |
> |
nameLength = strlen( info->statusName ); |
| 988 |
> |
endTest = &(info->statusName[nameLength - 5]); |
| 989 |
> |
if( !strcmp( endTest, ".bass" ) ){ |
| 990 |
> |
strcpy( endTest, ".stat" ); |
| 991 |
> |
} |
| 992 |
> |
else if( !strcmp( endTest, ".BASS" ) ){ |
| 993 |
> |
strcpy( endTest, ".stat" ); |
| 994 |
> |
} |
| 995 |
> |
else{ |
| 996 |
> |
endTest = &(info->statusName[nameLength - 4]); |
| 997 |
> |
if( !strcmp( endTest, ".bss" ) ){ |
| 998 |
> |
strcpy( endTest, ".stat" ); |
| 999 |
> |
} |
| 1000 |
> |
else if( !strcmp( endTest, ".mdl" ) ){ |
| 1001 |
> |
strcpy( endTest, ".stat" ); |
| 1002 |
> |
} |
| 1003 |
> |
else{ |
| 1004 |
> |
strcat( info->statusName, ".stat" ); |
| 1005 |
> |
} |
| 1006 |
> |
} |
| 1007 |
> |
|
| 1008 |
> |
#ifdef IS_MPI |
| 1009 |
> |
} |
| 1010 |
> |
#endif // is_mpi |
| 1011 |
> |
|
| 1012 |
> |
} |
| 1013 |
> |
|
| 1014 |
> |
|
| 1015 |
> |
void SimSetup::sysObjectsCreation( void ){ |
| 1016 |
> |
|
| 1017 |
> |
int i; |
| 1018 |
> |
|
| 1019 |
> |
// create the forceField |
| 1020 |
> |
|
| 1021 |
> |
createFF(); |
| 1022 |
> |
|
| 1023 |
> |
// extract componentList |
| 1024 |
> |
|
| 1025 |
> |
compList(); |
| 1026 |
> |
|
| 1027 |
> |
// calc the number of atoms, bond, bends, and torsions |
| 1028 |
> |
|
| 1029 |
> |
calcSysValues(); |
| 1030 |
> |
|
| 1031 |
> |
#ifdef IS_MPI |
| 1032 |
> |
// divide the molecules among the processors |
| 1033 |
> |
|
| 1034 |
> |
mpiMolDivide(); |
| 1035 |
> |
#endif //is_mpi |
| 1036 |
> |
|
| 1037 |
> |
// create the atom and SRI arrays. Also initialize Molecule Stamp ID's |
| 1038 |
> |
|
| 1039 |
> |
makeSysArrays(); |
| 1040 |
> |
|
| 1041 |
> |
// make and initialize the molecules (all but atomic coordinates) |
| 1042 |
> |
|
| 1043 |
> |
makeMolecules(); |
| 1044 |
> |
info->identArray = new int[info->n_atoms]; |
| 1045 |
> |
for(i=0; i<info->n_atoms; i++){ |
| 1046 |
> |
info->identArray[i] = the_atoms[i]->getIdent(); |
| 1047 |
> |
} |
| 1048 |
> |
|
| 1049 |
> |
|
| 1050 |
> |
|
| 1051 |
> |
} |
| 1052 |
> |
|
| 1053 |
> |
|
| 1054 |
> |
void SimSetup::createFF( void ){ |
| 1055 |
> |
|
| 1056 |
> |
switch( ffCase ){ |
| 1057 |
> |
|
| 1058 |
> |
case FF_DUFF: |
| 1059 |
> |
the_ff = new DUFF(); |
| 1060 |
> |
break; |
| 1061 |
> |
|
| 1062 |
> |
case FF_LJ: |
| 1063 |
> |
the_ff = new LJFF(); |
| 1064 |
> |
break; |
| 1065 |
> |
|
| 1066 |
> |
case FF_EAM: |
| 1067 |
> |
the_ff = new EAM_FF(); |
| 1068 |
> |
break; |
| 1069 |
> |
|
| 1070 |
> |
default: |
| 1071 |
> |
sprintf( painCave.errMsg, |
| 1072 |
> |
"SimSetup Error. Unrecognized force field in case statement.\n"); |
| 1073 |
> |
painCave.isFatal = 1; |
| 1074 |
> |
simError(); |
| 1075 |
> |
} |
| 1076 |
> |
|
| 1077 |
> |
#ifdef IS_MPI |
| 1078 |
> |
strcpy( checkPointMsg, "ForceField creation successful" ); |
| 1079 |
> |
MPIcheckPoint(); |
| 1080 |
> |
#endif // is_mpi |
| 1081 |
> |
|
| 1082 |
> |
} |
| 1083 |
> |
|
| 1084 |
> |
|
| 1085 |
> |
void SimSetup::compList( void ){ |
| 1086 |
> |
|
| 1087 |
> |
int i; |
| 1088 |
> |
|
| 1089 |
> |
comp_stamps = new MoleculeStamp*[n_components]; |
| 1090 |
> |
|
| 1091 |
> |
// make an array of molecule stamps that match the components used. |
| 1092 |
> |
// also extract the used stamps out into a separate linked list |
| 1093 |
> |
|
| 1094 |
> |
info->nComponents = n_components; |
| 1095 |
> |
info->componentsNmol = components_nmol; |
| 1096 |
> |
info->compStamps = comp_stamps; |
| 1097 |
> |
info->headStamp = new LinkedMolStamp(); |
| 1098 |
> |
|
| 1099 |
> |
char* id; |
| 1100 |
> |
LinkedMolStamp* headStamp = info->headStamp; |
| 1101 |
> |
LinkedMolStamp* currentStamp = NULL; |
| 1102 |
> |
for( i=0; i<n_components; i++ ){ |
| 1103 |
> |
|
| 1104 |
> |
id = the_components[i]->getType(); |
| 1105 |
> |
comp_stamps[i] = NULL; |
| 1106 |
> |
|
| 1107 |
> |
// check to make sure the component isn't already in the list |
| 1108 |
> |
|
| 1109 |
> |
comp_stamps[i] = headStamp->match( id ); |
| 1110 |
> |
if( comp_stamps[i] == NULL ){ |
| 1111 |
> |
|
| 1112 |
> |
// extract the component from the list; |
| 1113 |
> |
|
| 1114 |
> |
currentStamp = stamps->extractMolStamp( id ); |
| 1115 |
> |
if( currentStamp == NULL ){ |
| 1116 |
> |
sprintf( painCave.errMsg, |
| 1117 |
> |
"SimSetup error: Component \"%s\" was not found in the " |
| 1118 |
> |
"list of declared molecules\n", |
| 1119 |
> |
id ); |
| 1120 |
> |
painCave.isFatal = 1; |
| 1121 |
> |
simError(); |
| 1122 |
> |
} |
| 1123 |
> |
|
| 1124 |
> |
headStamp->add( currentStamp ); |
| 1125 |
> |
comp_stamps[i] = headStamp->match( id ); |
| 1126 |
> |
} |
| 1127 |
> |
} |
| 1128 |
> |
|
| 1129 |
> |
#ifdef IS_MPI |
| 1130 |
> |
strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
| 1131 |
> |
MPIcheckPoint(); |
| 1132 |
> |
#endif // is_mpi |
| 1133 |
> |
|
| 1134 |
> |
|
| 1135 |
> |
} |
| 1136 |
> |
|
| 1137 |
> |
void SimSetup::calcSysValues( void ){ |
| 1138 |
> |
int i, j, k; |
| 1139 |
> |
|
| 1140 |
> |
|
| 1141 |
> |
tot_atoms = 0; |
| 1142 |
> |
tot_bonds = 0; |
| 1143 |
> |
tot_bends = 0; |
| 1144 |
> |
tot_torsions = 0; |
| 1145 |
> |
for( i=0; i<n_components; i++ ){ |
| 1146 |
> |
|
| 1147 |
> |
tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
| 1148 |
> |
tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
| 1149 |
> |
tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
| 1150 |
> |
tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
| 1151 |
> |
} |
| 1152 |
> |
|
| 1153 |
> |
tot_SRI = tot_bonds + tot_bends + tot_torsions; |
| 1154 |
> |
|
| 1155 |
> |
info->n_atoms = tot_atoms; |
| 1156 |
> |
info->n_bonds = tot_bonds; |
| 1157 |
> |
info->n_bends = tot_bends; |
| 1158 |
> |
info->n_torsions = tot_torsions; |
| 1159 |
> |
info->n_SRI = tot_SRI; |
| 1160 |
> |
info->n_mol = tot_nmol; |
| 1161 |
> |
|
| 1162 |
> |
info->molMembershipArray = new int[tot_atoms]; |
| 1163 |
> |
} |
| 1164 |
> |
|
| 1165 |
> |
|
| 1166 |
> |
#ifdef IS_MPI |
| 1167 |
> |
|
| 1168 |
> |
void SimSetup::mpiMolDivide( void ){ |
| 1169 |
> |
|
| 1170 |
> |
int i, j, k; |
| 1171 |
> |
int localMol, allMol; |
| 1172 |
> |
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
| 1173 |
> |
|
| 1174 |
> |
mpiSim = new mpiSimulation( info ); |
| 1175 |
> |
|
| 1176 |
> |
globalIndex = mpiSim->divideLabor(); |
| 1177 |
> |
|
| 1178 |
> |
// set up the local variables |
| 1179 |
> |
|
| 1180 |
> |
mol2proc = mpiSim->getMolToProcMap(); |
| 1181 |
> |
molCompType = mpiSim->getMolComponentType(); |
| 1182 |
> |
|
| 1183 |
> |
allMol = 0; |
| 1184 |
> |
localMol = 0; |
| 1185 |
> |
local_atoms = 0; |
| 1186 |
> |
local_bonds = 0; |
| 1187 |
> |
local_bends = 0; |
| 1188 |
> |
local_torsions = 0; |
| 1189 |
> |
globalAtomIndex = 0; |
| 1190 |
> |
|
| 1191 |
> |
|
| 1192 |
> |
for( i=0; i<n_components; i++ ){ |
| 1193 |
> |
|
| 1194 |
> |
for( j=0; j<components_nmol[i]; j++ ){ |
| 1195 |
> |
|
| 1196 |
> |
if( mol2proc[allMol] == worldRank ){ |
| 1197 |
> |
|
| 1198 |
> |
local_atoms += comp_stamps[i]->getNAtoms(); |
| 1199 |
> |
local_bonds += comp_stamps[i]->getNBonds(); |
| 1200 |
> |
local_bends += comp_stamps[i]->getNBends(); |
| 1201 |
> |
local_torsions += comp_stamps[i]->getNTorsions(); |
| 1202 |
> |
localMol++; |
| 1203 |
> |
} |
| 1204 |
> |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
| 1205 |
> |
info->molMembershipArray[globalAtomIndex] = allMol; |
| 1206 |
> |
globalAtomIndex++; |
| 1207 |
> |
} |
| 1208 |
> |
|
| 1209 |
> |
allMol++; |
| 1210 |
> |
} |
| 1211 |
> |
} |
| 1212 |
> |
local_SRI = local_bonds + local_bends + local_torsions; |
| 1213 |
> |
|
| 1214 |
> |
info->n_atoms = mpiSim->getMyNlocal(); |
| 1215 |
> |
|
| 1216 |
> |
if( local_atoms != info->n_atoms ){ |
| 1217 |
> |
sprintf( painCave.errMsg, |
| 1218 |
> |
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
| 1219 |
> |
" localAtom (%d) are not equal.\n", |
| 1220 |
> |
info->n_atoms, |
| 1221 |
> |
local_atoms ); |
| 1222 |
> |
painCave.isFatal = 1; |
| 1223 |
> |
simError(); |
| 1224 |
> |
} |
| 1225 |
> |
|
| 1226 |
> |
info->n_bonds = local_bonds; |
| 1227 |
> |
info->n_bends = local_bends; |
| 1228 |
> |
info->n_torsions = local_torsions; |
| 1229 |
> |
info->n_SRI = local_SRI; |
| 1230 |
> |
info->n_mol = localMol; |
| 1231 |
> |
|
| 1232 |
> |
strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
| 1233 |
> |
MPIcheckPoint(); |
| 1234 |
> |
} |
| 1235 |
> |
|
| 1236 |
> |
#endif // is_mpi |
| 1237 |
> |
|
| 1238 |
> |
|
| 1239 |
> |
void SimSetup::makeSysArrays( void ){ |
| 1240 |
> |
int i, j, k; |
| 1241 |
> |
|
| 1242 |
> |
|
| 1243 |
> |
// create the atom and short range interaction arrays |
| 1244 |
> |
|
| 1245 |
> |
Atom::createArrays(info->n_atoms); |
| 1246 |
> |
the_atoms = new Atom*[info->n_atoms]; |
| 1247 |
> |
the_molecules = new Molecule[info->n_mol]; |
| 1248 |
> |
int molIndex; |
| 1249 |
> |
|
| 1250 |
> |
// initialize the molecule's stampID's |
| 1251 |
> |
|
| 1252 |
> |
#ifdef IS_MPI |
| 1253 |
> |
|
| 1254 |
> |
|
| 1255 |
> |
molIndex = 0; |
| 1256 |
> |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
| 1257 |
> |
|
| 1258 |
> |
if(mol2proc[i] == worldRank ){ |
| 1259 |
> |
the_molecules[molIndex].setStampID( molCompType[i] ); |
| 1260 |
> |
the_molecules[molIndex].setMyIndex( molIndex ); |
| 1261 |
> |
the_molecules[molIndex].setGlobalIndex( i ); |
| 1262 |
> |
molIndex++; |
| 1263 |
> |
} |
| 1264 |
> |
} |
| 1265 |
> |
|
| 1266 |
> |
#else // is_mpi |
| 1267 |
> |
|
| 1268 |
> |
molIndex = 0; |
| 1269 |
> |
globalAtomIndex = 0; |
| 1270 |
> |
for(i=0; i<n_components; i++){ |
| 1271 |
> |
for(j=0; j<components_nmol[i]; j++ ){ |
| 1272 |
> |
the_molecules[molIndex].setStampID( i ); |
| 1273 |
> |
the_molecules[molIndex].setMyIndex( molIndex ); |
| 1274 |
> |
the_molecules[molIndex].setGlobalIndex( molIndex ); |
| 1275 |
> |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
| 1276 |
> |
info->molMembershipArray[globalAtomIndex] = molIndex; |
| 1277 |
> |
globalAtomIndex++; |
| 1278 |
> |
} |
| 1279 |
> |
molIndex++; |
| 1280 |
> |
} |
| 1281 |
> |
} |
| 1282 |
> |
|
| 1283 |
> |
|
| 1284 |
> |
#endif // is_mpi |
| 1285 |
> |
|
| 1286 |
> |
|
| 1287 |
> |
if( info->n_SRI ){ |
| 1288 |
> |
|
| 1289 |
> |
Exclude::createArray(info->n_SRI); |
| 1290 |
> |
the_excludes = new Exclude*[info->n_SRI]; |
| 1291 |
> |
for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
| 1292 |
> |
info->globalExcludes = new int; |
| 1293 |
> |
info->n_exclude = info->n_SRI; |
| 1294 |
> |
} |
| 1295 |
> |
else{ |
| 1296 |
> |
|
| 1297 |
> |
Exclude::createArray( 1 ); |
| 1298 |
> |
the_excludes = new Exclude*; |
| 1299 |
> |
the_excludes[0] = new Exclude(0); |
| 1300 |
> |
the_excludes[0]->setPair( 0,0 ); |
| 1301 |
> |
info->globalExcludes = new int; |
| 1302 |
> |
info->globalExcludes[0] = 0; |
| 1303 |
> |
info->n_exclude = 0; |
| 1304 |
> |
} |
| 1305 |
> |
|
| 1306 |
> |
// set the arrays into the SimInfo object |
| 1307 |
> |
|
| 1308 |
> |
info->atoms = the_atoms; |
| 1309 |
> |
info->molecules = the_molecules; |
| 1310 |
> |
info->nGlobalExcludes = 0; |
| 1311 |
> |
info->excludes = the_excludes; |
| 1312 |
> |
|
| 1313 |
> |
the_ff->setSimInfo( info ); |
| 1314 |
> |
|
| 1315 |
> |
} |
| 1316 |
> |
|
| 1317 |
> |
void SimSetup::makeIntegrator( void ){ |
| 1318 |
> |
|
| 1319 |
> |
NVT<RealIntegrator>* myNVT = NULL; |
| 1320 |
> |
NPTi<RealIntegrator>* myNPTi = NULL; |
| 1321 |
> |
NPTf<RealIntegrator>* myNPTf = NULL; |
| 1322 |
> |
NPTim<RealIntegrator>* myNPTim = NULL; |
| 1323 |
> |
NPTfm<RealIntegrator>* myNPTfm = NULL; |
| 1324 |
> |
ZConstraint<NVE<RealIntegrator> >* myNVEZCons = NULL; |
| 1325 |
> |
ZConstraint<NVT<RealIntegrator> >* myNVTZCons = NULL; |
| 1326 |
> |
ZConstraint<NPTi<RealIntegrator> >* myNPTiZCons = NULL; |
| 1327 |
> |
ZConstraint<NPTf<RealIntegrator> >* myNPTfZCons = NULL; |
| 1328 |
> |
ZConstraint<NPTim<RealIntegrator> >* myNPTimZCons = NULL; |
| 1329 |
> |
ZConstraint<NPTfm<RealIntegrator> >* myNPTfmZCons = NULL; |
| 1330 |
> |
|
| 1331 |
> |
cerr << "setting integrator" <<endl; |
| 1332 |
> |
|
| 1333 |
> |
switch( ensembleCase ){ |
| 1334 |
> |
|
| 1335 |
> |
case NVE_ENS: |
| 1336 |
> |
new NVE<RealIntegrator>( info, the_ff ); |
| 1337 |
> |
break; |
| 1338 |
> |
|
| 1339 |
> |
case NVT_ENS: |
| 1340 |
> |
myNVT = new NVT<RealIntegrator>( info, the_ff ); |
| 1341 |
> |
myNVT->setTargetTemp(globals->getTargetTemp()); |
| 1342 |
> |
|
| 1343 |
> |
if (globals->haveTauThermostat()) |
| 1344 |
> |
myNVT->setTauThermostat(globals->getTauThermostat()); |
| 1345 |
> |
|
| 1346 |
> |
else { |
| 1347 |
> |
sprintf( painCave.errMsg, |
| 1348 |
> |
"SimSetup error: If you use the NVT\n" |
| 1349 |
> |
" ensemble, you must set tauThermostat.\n"); |
| 1350 |
> |
painCave.isFatal = 1; |
| 1351 |
> |
simError(); |
| 1352 |
> |
} |
| 1353 |
> |
break; |
| 1354 |
> |
|
| 1355 |
> |
case NPTi_ENS: |
| 1356 |
> |
myNPTi = new NPTi<RealIntegrator>( info, the_ff ); |
| 1357 |
> |
myNPTi->setTargetTemp( globals->getTargetTemp() ); |
| 1358 |
> |
|
| 1359 |
> |
if (globals->haveTargetPressure()) |
| 1360 |
> |
myNPTi->setTargetPressure(globals->getTargetPressure()); |
| 1361 |
> |
else { |
| 1362 |
> |
sprintf( painCave.errMsg, |
| 1363 |
> |
"SimSetup error: If you use a constant pressure\n" |
| 1364 |
> |
" ensemble, you must set targetPressure in the BASS file.\n"); |
| 1365 |
> |
painCave.isFatal = 1; |
| 1366 |
> |
simError(); |
| 1367 |
> |
} |
| 1368 |
> |
|
| 1369 |
> |
if( globals->haveTauThermostat() ) |
| 1370 |
> |
myNPTi->setTauThermostat( globals->getTauThermostat() ); |
| 1371 |
> |
else{ |
| 1372 |
> |
sprintf( painCave.errMsg, |
| 1373 |
> |
"SimSetup error: If you use an NPT\n" |
| 1374 |
> |
" ensemble, you must set tauThermostat.\n"); |
| 1375 |
> |
painCave.isFatal = 1; |
| 1376 |
> |
simError(); |
| 1377 |
> |
} |
| 1378 |
> |
|
| 1379 |
> |
if( globals->haveTauBarostat() ) |
| 1380 |
> |
myNPTi->setTauBarostat( globals->getTauBarostat() ); |
| 1381 |
> |
else{ |
| 1382 |
> |
sprintf( painCave.errMsg, |
| 1383 |
> |
"SimSetup error: If you use an NPT\n" |
| 1384 |
> |
" ensemble, you must set tauBarostat.\n"); |
| 1385 |
> |
painCave.isFatal = 1; |
| 1386 |
> |
simError(); |
| 1387 |
> |
} |
| 1388 |
> |
break; |
| 1389 |
> |
|
| 1390 |
> |
case NPTf_ENS: |
| 1391 |
> |
myNPTf = new NPTf<RealIntegrator>( info, the_ff ); |
| 1392 |
> |
myNPTf->setTargetTemp( globals->getTargetTemp()); |
| 1393 |
> |
|
| 1394 |
> |
if (globals->haveTargetPressure()) |
| 1395 |
> |
myNPTf->setTargetPressure(globals->getTargetPressure()); |
| 1396 |
> |
else { |
| 1397 |
> |
sprintf( painCave.errMsg, |
| 1398 |
> |
"SimSetup error: If you use a constant pressure\n" |
| 1399 |
> |
" ensemble, you must set targetPressure in the BASS file.\n"); |
| 1400 |
> |
painCave.isFatal = 1; |
| 1401 |
> |
simError(); |
| 1402 |
> |
} |
| 1403 |
> |
|
| 1404 |
> |
if( globals->haveTauThermostat() ) |
| 1405 |
> |
myNPTf->setTauThermostat( globals->getTauThermostat() ); |
| 1406 |
> |
else{ |
| 1407 |
> |
sprintf( painCave.errMsg, |
| 1408 |
> |
"SimSetup error: If you use an NPT\n" |
| 1409 |
> |
" ensemble, you must set tauThermostat.\n"); |
| 1410 |
> |
painCave.isFatal = 1; |
| 1411 |
> |
simError(); |
| 1412 |
> |
} |
| 1413 |
> |
|
| 1414 |
> |
if( globals->haveTauBarostat() ) |
| 1415 |
> |
myNPTf->setTauBarostat( globals->getTauBarostat() ); |
| 1416 |
> |
else{ |
| 1417 |
> |
sprintf( painCave.errMsg, |
| 1418 |
> |
"SimSetup error: If you use an NPT\n" |
| 1419 |
> |
" ensemble, you must set tauBarostat.\n"); |
| 1420 |
> |
painCave.isFatal = 1; |
| 1421 |
> |
simError(); |
| 1422 |
> |
} |
| 1423 |
> |
break; |
| 1424 |
> |
|
| 1425 |
> |
case NPTim_ENS: |
| 1426 |
> |
myNPTim = new NPTim<RealIntegrator>( info, the_ff ); |
| 1427 |
> |
myNPTim->setTargetTemp( globals->getTargetTemp()); |
| 1428 |
> |
|
| 1429 |
> |
if (globals->haveTargetPressure()) |
| 1430 |
> |
myNPTim->setTargetPressure(globals->getTargetPressure()); |
| 1431 |
> |
else { |
| 1432 |
> |
sprintf( painCave.errMsg, |
| 1433 |
> |
"SimSetup error: If you use a constant pressure\n" |
| 1434 |
> |
" ensemble, you must set targetPressure in the BASS file.\n"); |
| 1435 |
> |
painCave.isFatal = 1; |
| 1436 |
> |
simError(); |
| 1437 |
> |
} |
| 1438 |
> |
|
| 1439 |
> |
if( globals->haveTauThermostat() ) |
| 1440 |
> |
myNPTim->setTauThermostat( globals->getTauThermostat() ); |
| 1441 |
> |
else{ |
| 1442 |
> |
sprintf( painCave.errMsg, |
| 1443 |
> |
"SimSetup error: If you use an NPT\n" |
| 1444 |
> |
" ensemble, you must set tauThermostat.\n"); |
| 1445 |
> |
painCave.isFatal = 1; |
| 1446 |
> |
simError(); |
| 1447 |
> |
} |
| 1448 |
> |
|
| 1449 |
> |
if( globals->haveTauBarostat() ) |
| 1450 |
> |
myNPTim->setTauBarostat( globals->getTauBarostat() ); |
| 1451 |
> |
else{ |
| 1452 |
> |
sprintf( painCave.errMsg, |
| 1453 |
> |
"SimSetup error: If you use an NPT\n" |
| 1454 |
> |
" ensemble, you must set tauBarostat.\n"); |
| 1455 |
> |
painCave.isFatal = 1; |
| 1456 |
> |
simError(); |
| 1457 |
> |
} |
| 1458 |
> |
break; |
| 1459 |
> |
|
| 1460 |
> |
case NPTfm_ENS: |
| 1461 |
> |
myNPTfm = new NPTfm<RealIntegrator>( info, the_ff ); |
| 1462 |
> |
myNPTfm->setTargetTemp( globals->getTargetTemp()); |
| 1463 |
> |
|
| 1464 |
> |
if (globals->haveTargetPressure()) |
| 1465 |
> |
myNPTfm->setTargetPressure(globals->getTargetPressure()); |
| 1466 |
> |
else { |
| 1467 |
> |
sprintf( painCave.errMsg, |
| 1468 |
> |
"SimSetup error: If you use a constant pressure\n" |
| 1469 |
> |
" ensemble, you must set targetPressure in the BASS file.\n"); |
| 1470 |
> |
painCave.isFatal = 1; |
| 1471 |
> |
simError(); |
| 1472 |
> |
} |
| 1473 |
> |
|
| 1474 |
> |
if( globals->haveTauThermostat() ) |
| 1475 |
> |
myNPTfm->setTauThermostat( globals->getTauThermostat() ); |
| 1476 |
> |
else{ |
| 1477 |
> |
sprintf( painCave.errMsg, |
| 1478 |
> |
"SimSetup error: If you use an NPT\n" |
| 1479 |
> |
" ensemble, you must set tauThermostat.\n"); |
| 1480 |
> |
painCave.isFatal = 1; |
| 1481 |
> |
simError(); |
| 1482 |
> |
} |
| 1483 |
> |
|
| 1484 |
> |
if( globals->haveTauBarostat() ) |
| 1485 |
> |
myNPTfm->setTauBarostat( globals->getTauBarostat() ); |
| 1486 |
> |
else{ |
| 1487 |
> |
sprintf( painCave.errMsg, |
| 1488 |
> |
"SimSetup error: If you use an NPT\n" |
| 1489 |
> |
" ensemble, you must set tauBarostat.\n"); |
| 1490 |
> |
painCave.isFatal = 1; |
| 1491 |
> |
simError(); |
| 1492 |
> |
} |
| 1493 |
> |
break; |
| 1494 |
> |
|
| 1495 |
> |
case NVEZCONS_ENS: |
| 1496 |
> |
|
| 1497 |
> |
|
| 1498 |
> |
//setup index of z-constraint molecules, z-constraint sampel time |
| 1499 |
> |
//and z-constraint force output name. These parameter should be known |
| 1500 |
> |
//before constructing the z-constraint integrator |
| 1501 |
> |
setupZConstraint(); |
| 1502 |
> |
|
| 1503 |
> |
myNVEZCons = new ZConstraint<NVE<RealIntegrator> >( info, the_ff ); |
| 1504 |
> |
|
| 1505 |
> |
break; |
| 1506 |
> |
|
| 1507 |
> |
|
| 1508 |
> |
case NVTZCONS_ENS: |
| 1509 |
> |
|
| 1510 |
> |
setupZConstraint(); |
| 1511 |
> |
|
| 1512 |
> |
myNVTZCons = new ZConstraint<NVT<RealIntegrator> >( info, the_ff ); |
| 1513 |
> |
myNVTZCons->setTargetTemp(globals->getTargetTemp()); |
| 1514 |
> |
|
| 1515 |
> |
if (globals->haveTauThermostat()) |
| 1516 |
> |
myNVTZCons->setTauThermostat(globals->getTauThermostat()); |
| 1517 |
> |
|
| 1518 |
> |
else { |
| 1519 |
> |
sprintf( painCave.errMsg, |
| 1520 |
> |
"SimSetup error: If you use the NVT\n" |
| 1521 |
> |
" ensemble, you must set tauThermostat.\n"); |
| 1522 |
> |
painCave.isFatal = 1; |
| 1523 |
> |
simError(); |
| 1524 |
> |
} |
| 1525 |
> |
break; |
| 1526 |
> |
|
| 1527 |
> |
case NPTiZCONS_ENS: |
| 1528 |
> |
|
| 1529 |
> |
setupZConstraint(); |
| 1530 |
> |
|
| 1531 |
> |
myNPTiZCons = new ZConstraint<NPTi<RealIntegrator> >( info, the_ff ); |
| 1532 |
> |
myNPTiZCons->setTargetTemp( globals->getTargetTemp() ); |
| 1533 |
> |
|
| 1534 |
> |
if (globals->haveTargetPressure()) |
| 1535 |
> |
myNPTiZCons->setTargetPressure(globals->getTargetPressure()); |
| 1536 |
> |
else { |
| 1537 |
> |
sprintf( painCave.errMsg, |
| 1538 |
> |
"SimSetup error: If you use a constant pressure\n" |
| 1539 |
> |
" ensemble, you must set targetPressure in the BASS file.\n"); |
| 1540 |
> |
painCave.isFatal = 1; |
| 1541 |
> |
simError(); |
| 1542 |
> |
} |
| 1543 |
> |
|
| 1544 |
> |
if( globals->haveTauThermostat() ) |
| 1545 |
> |
myNPTiZCons->setTauThermostat( globals->getTauThermostat() ); |
| 1546 |
> |
else{ |
| 1547 |
> |
sprintf( painCave.errMsg, |
| 1548 |
> |
"SimSetup error: If you use an NPT\n" |
| 1549 |
> |
" ensemble, you must set tauThermostat.\n"); |
| 1550 |
> |
painCave.isFatal = 1; |
| 1551 |
> |
simError(); |
| 1552 |
> |
} |
| 1553 |
> |
|
| 1554 |
> |
if( globals->haveTauBarostat() ) |
| 1555 |
> |
myNPTiZCons->setTauBarostat( globals->getTauBarostat() ); |
| 1556 |
> |
else{ |
| 1557 |
> |
sprintf( painCave.errMsg, |
| 1558 |
> |
"SimSetup error: If you use an NPT\n" |
| 1559 |
> |
" ensemble, you must set tauBarostat.\n"); |
| 1560 |
> |
painCave.isFatal = 1; |
| 1561 |
> |
simError(); |
| 1562 |
> |
} |
| 1563 |
> |
|
| 1564 |
> |
break; |
| 1565 |
> |
|
| 1566 |
> |
case NPTfZCONS_ENS: |
| 1567 |
> |
|
| 1568 |
> |
setupZConstraint(); |
| 1569 |
> |
|
| 1570 |
> |
myNPTfZCons = new ZConstraint<NPTf<RealIntegrator> >( info, the_ff ); |
| 1571 |
> |
myNPTfZCons->setTargetTemp( globals->getTargetTemp()); |
| 1572 |
> |
|
| 1573 |
> |
if (globals->haveTargetPressure()) |
| 1574 |
> |
myNPTfZCons->setTargetPressure(globals->getTargetPressure()); |
| 1575 |
> |
else { |
| 1576 |
> |
sprintf( painCave.errMsg, |
| 1577 |
> |
"SimSetup error: If you use a constant pressure\n" |
| 1578 |
> |
" ensemble, you must set targetPressure in the BASS file.\n"); |
| 1579 |
> |
painCave.isFatal = 1; |
| 1580 |
> |
simError(); |
| 1581 |
> |
} |
| 1582 |
> |
|
| 1583 |
> |
if( globals->haveTauThermostat() ) |
| 1584 |
> |
myNPTfZCons->setTauThermostat( globals->getTauThermostat() ); |
| 1585 |
> |
else{ |
| 1586 |
> |
sprintf( painCave.errMsg, |
| 1587 |
> |
"SimSetup error: If you use an NPT\n" |
| 1588 |
> |
" ensemble, you must set tauThermostat.\n"); |
| 1589 |
> |
painCave.isFatal = 1; |
| 1590 |
> |
simError(); |
| 1591 |
> |
} |
| 1592 |
> |
|
| 1593 |
> |
if( globals->haveTauBarostat() ) |
| 1594 |
> |
myNPTfZCons->setTauBarostat( globals->getTauBarostat() ); |
| 1595 |
> |
else{ |
| 1596 |
> |
sprintf( painCave.errMsg, |
| 1597 |
> |
"SimSetup error: If you use an NPT\n" |
| 1598 |
> |
" ensemble, you must set tauBarostat.\n"); |
| 1599 |
> |
painCave.isFatal = 1; |
| 1600 |
> |
simError(); |
| 1601 |
> |
} |
| 1602 |
> |
|
| 1603 |
> |
break; |
| 1604 |
> |
|
| 1605 |
> |
case NPTimZCONS_ENS: |
| 1606 |
> |
|
| 1607 |
> |
setupZConstraint(); |
| 1608 |
> |
|
| 1609 |
> |
myNPTimZCons = new ZConstraint<NPTim<RealIntegrator> >( info, the_ff ); |
| 1610 |
> |
myNPTimZCons->setTargetTemp( globals->getTargetTemp()); |
| 1611 |
> |
|
| 1612 |
> |
if (globals->haveTargetPressure()) |
| 1613 |
> |
myNPTimZCons->setTargetPressure(globals->getTargetPressure()); |
| 1614 |
> |
else { |
| 1615 |
> |
sprintf( painCave.errMsg, |
| 1616 |
> |
"SimSetup error: If you use a constant pressure\n" |
| 1617 |
> |
" ensemble, you must set targetPressure in the BASS file.\n"); |
| 1618 |
> |
painCave.isFatal = 1; |
| 1619 |
> |
simError(); |
| 1620 |
> |
} |
| 1621 |
> |
|
| 1622 |
> |
if( globals->haveTauThermostat() ) |
| 1623 |
> |
myNPTimZCons->setTauThermostat( globals->getTauThermostat() ); |
| 1624 |
> |
else{ |
| 1625 |
> |
sprintf( painCave.errMsg, |
| 1626 |
> |
"SimSetup error: If you use an NPT\n" |
| 1627 |
> |
" ensemble, you must set tauThermostat.\n"); |
| 1628 |
> |
painCave.isFatal = 1; |
| 1629 |
> |
simError(); |
| 1630 |
> |
} |
| 1631 |
> |
|
| 1632 |
> |
if( globals->haveTauBarostat() ) |
| 1633 |
> |
myNPTimZCons->setTauBarostat( globals->getTauBarostat() ); |
| 1634 |
> |
else{ |
| 1635 |
> |
sprintf( painCave.errMsg, |
| 1636 |
> |
"SimSetup error: If you use an NPT\n" |
| 1637 |
> |
" ensemble, you must set tauBarostat.\n"); |
| 1638 |
> |
painCave.isFatal = 1; |
| 1639 |
> |
simError(); |
| 1640 |
> |
} |
| 1641 |
> |
|
| 1642 |
> |
break; |
| 1643 |
> |
|
| 1644 |
> |
case NPTfmZCONS_ENS: |
| 1645 |
> |
|
| 1646 |
> |
setupZConstraint(); |
| 1647 |
> |
|
| 1648 |
> |
myNPTfmZCons = new ZConstraint<NPTfm<RealIntegrator> >( info, the_ff ); |
| 1649 |
> |
myNPTfmZCons->setTargetTemp( globals->getTargetTemp()); |
| 1650 |
> |
|
| 1651 |
> |
if (globals->haveTargetPressure()) |
| 1652 |
> |
myNPTfmZCons->setTargetPressure(globals->getTargetPressure()); |
| 1653 |
> |
else { |
| 1654 |
> |
sprintf( painCave.errMsg, |
| 1655 |
> |
"SimSetup error: If you use a constant pressure\n" |
| 1656 |
> |
" ensemble, you must set targetPressure in the BASS file.\n"); |
| 1657 |
> |
painCave.isFatal = 1; |
| 1658 |
> |
simError(); |
| 1659 |
> |
} |
| 1660 |
> |
|
| 1661 |
> |
if( globals->haveTauThermostat() ) |
| 1662 |
> |
myNPTfmZCons->setTauThermostat( globals->getTauThermostat() ); |
| 1663 |
> |
else{ |
| 1664 |
> |
sprintf( painCave.errMsg, |
| 1665 |
> |
"SimSetup error: If you use an NPT\n" |
| 1666 |
> |
" ensemble, you must set tauThermostat.\n"); |
| 1667 |
> |
painCave.isFatal = 1; |
| 1668 |
> |
simError(); |
| 1669 |
> |
} |
| 1670 |
> |
|
| 1671 |
> |
if( globals->haveTauBarostat() ) |
| 1672 |
> |
myNPTfmZCons->setTauBarostat( globals->getTauBarostat() ); |
| 1673 |
> |
else{ |
| 1674 |
> |
sprintf( painCave.errMsg, |
| 1675 |
> |
"SimSetup error: If you use an NPT\n" |
| 1676 |
> |
" ensemble, you must set tauBarostat.\n"); |
| 1677 |
> |
painCave.isFatal = 1; |
| 1678 |
> |
simError(); |
| 1679 |
> |
} |
| 1680 |
> |
break; |
| 1681 |
> |
|
| 1682 |
> |
|
| 1683 |
> |
|
| 1684 |
> |
default: |
| 1685 |
> |
sprintf( painCave.errMsg, |
| 1686 |
> |
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
| 1687 |
> |
painCave.isFatal = 1; |
| 1688 |
> |
simError(); |
| 1689 |
> |
} |
| 1690 |
> |
|
| 1691 |
> |
} |
| 1692 |
> |
|
| 1693 |
> |
void SimSetup::initFortran( void ){ |
| 1694 |
> |
|
| 1695 |
> |
info->refreshSim(); |
| 1696 |
> |
|
| 1697 |
> |
if( !strcmp( info->mixingRule, "standard") ){ |
| 1698 |
> |
the_ff->initForceField( LB_MIXING_RULE ); |
| 1699 |
> |
} |
| 1700 |
> |
else if( !strcmp( info->mixingRule, "explicit") ){ |
| 1701 |
> |
the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
| 1702 |
> |
} |
| 1703 |
> |
else{ |
| 1704 |
> |
sprintf( painCave.errMsg, |
| 1705 |
> |
"SimSetup Error: unknown mixing rule -> \"%s\"\n", |
| 1706 |
> |
info->mixingRule ); |
| 1707 |
> |
painCave.isFatal = 1; |
| 1708 |
> |
simError(); |
| 1709 |
> |
} |
| 1710 |
> |
|
| 1711 |
> |
|
| 1712 |
> |
#ifdef IS_MPI |
| 1713 |
> |
strcpy( checkPointMsg, |
| 1714 |
> |
"Successfully intialized the mixingRule for Fortran." ); |
| 1715 |
> |
MPIcheckPoint(); |
| 1716 |
> |
#endif // is_mpi |
| 1717 |
> |
|
| 1718 |
> |
} |
| 1719 |
> |
|
| 1720 |
> |
void SimSetup::setupZConstraint() |
| 1721 |
> |
{ |
| 1722 |
> |
if(globals->haveZConsTime()){ |
| 1723 |
> |
|
| 1724 |
> |
//add sample time of z-constraint into SimInfo's property list |
| 1725 |
> |
DoubleData* zconsTimeProp = new DoubleData(); |
| 1726 |
> |
zconsTimeProp->setID("zconstime"); |
| 1727 |
> |
zconsTimeProp->setData(globals->getZConsTime()); |
| 1728 |
> |
info->addProperty(zconsTimeProp); |
| 1729 |
> |
} |
| 1730 |
> |
else{ |
| 1731 |
> |
sprintf( painCave.errMsg, |
| 1732 |
> |
"ZConstraint error: If you use an ZConstraint\n" |
| 1733 |
> |
" , you must set sample time.\n"); |
| 1734 |
> |
painCave.isFatal = 1; |
| 1735 |
> |
simError(); |
| 1736 |
> |
} |
| 1737 |
> |
|
| 1738 |
> |
if(globals->haveIndexOfAllZConsMols()){ |
| 1739 |
> |
|
| 1740 |
> |
//add index of z-constraint molecules into SimInfo's property list |
| 1741 |
> |
vector<int> tempIndex = globals->getIndexOfAllZConsMols(); |
| 1742 |
> |
|
| 1743 |
> |
//sort the index |
| 1744 |
> |
sort(tempIndex.begin(), tempIndex.end()); |
| 1745 |
> |
|
| 1746 |
> |
IndexData* zconsIndex = new IndexData(); |
| 1747 |
> |
zconsIndex->setID("zconsindex"); |
| 1748 |
> |
zconsIndex->setIndexData(tempIndex); |
| 1749 |
> |
info->addProperty(zconsIndex); |
| 1750 |
> |
} |
| 1751 |
> |
else{ |
| 1752 |
> |
sprintf( painCave.errMsg, |
| 1753 |
> |
"SimSetup error: If you use an ZConstraint\n" |
| 1754 |
> |
" , you must set index of z-constraint molecules.\n"); |
| 1755 |
> |
painCave.isFatal = 1; |
| 1756 |
> |
simError(); |
| 1757 |
> |
|
| 1758 |
> |
} |
| 1759 |
> |
|
| 1760 |
> |
//Determine the name of ouput file and add it into SimInfo's property list |
| 1761 |
> |
//Be careful, do not use inFileName, since it is a pointer which |
| 1762 |
> |
//point to a string at master node, and slave nodes do not contain that string |
| 1763 |
> |
|
| 1764 |
> |
string zconsOutput(info->finalName); |
| 1765 |
> |
|
| 1766 |
> |
zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
| 1767 |
> |
|
| 1768 |
> |
StringData* zconsFilename = new StringData(); |
| 1769 |
> |
zconsFilename->setID("zconsfilename"); |
| 1770 |
> |
zconsFilename->setData(zconsOutput); |
| 1771 |
> |
|
| 1772 |
> |
info->addProperty(zconsFilename); |
| 1773 |
> |
|
| 1774 |
|
} |
