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mmeineke |
377 |
#include <cstdlib> |
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#include <iostream> |
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#include <cmath> |
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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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#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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mmeineke |
557 |
// some defines for ensemble and Forcefield cases |
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gezelter |
604 |
#define NVE_ENS 0 |
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#define NVT_ENS 1 |
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#define NPTi_ENS 2 |
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#define NPTf_ENS 3 |
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#define NPTim_ENS 4 |
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#define NPTfm_ENS 5 |
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mmeineke |
557 |
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mmeineke |
582 |
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mmeineke |
557 |
#define FF_DUFF 0 |
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#define FF_LJ 1 |
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mmeineke |
377 |
SimSetup::SimSetup(){ |
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stamps = new MakeStamps(); |
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globals = new Globals(); |
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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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SimSetup::~SimSetup(){ |
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delete stamps; |
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delete globals; |
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} |
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void SimSetup::parseFile( char* fileName ){ |
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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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inFileName = fileName; |
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set_interface_stamps( stamps, globals ); |
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#ifdef IS_MPI |
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mpiEventInit(); |
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#endif |
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yacc_BASS( fileName ); |
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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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#ifdef IS_MPI |
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void SimSetup::receiveParse(void){ |
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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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#endif // is_mpi |
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void SimSetup::createSim( void ){ |
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MakeStamps *the_stamps; |
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Globals* the_globals; |
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gezelter |
490 |
int i, j, k, globalAtomIndex; |
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mmeineke |
557 |
|
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int ensembleCase; |
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int ffCase; |
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ensembleCase = -1; |
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ffCase = -1; |
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mmeineke |
377 |
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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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// 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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// 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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gezelter |
466 |
|
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mmeineke |
561 |
if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
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mmeineke |
557 |
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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// get the ensemble: |
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mmeineke |
377 |
strcpy( ensemble, the_globals->getEnsemble() ); |
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gezelter |
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|
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mmeineke |
561 |
if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
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else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
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gezelter |
580 |
else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") ) |
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ensembleCase = NPTi_ENS; |
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else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; |
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gezelter |
604 |
else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS; |
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else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; |
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mmeineke |
557 |
else{ |
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gezelter |
466 |
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" ); |
132 |
mmeineke |
557 |
ensembleCase = NVE_ENS; |
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gezelter |
466 |
} |
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mmeineke |
377 |
strcpy( simnfo->ensemble, ensemble ); |
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mmeineke |
557 |
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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; |
148 |
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// simError(); |
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// } |
150 |
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// if (the_globals->haveTauThermostat()) |
152 |
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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 { |
156 |
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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" |
159 |
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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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// } |
163 |
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164 |
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// if (the_globals->haveTauBarostat()) |
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// the_extendedsystem->setTauBarostat(the_globals->getTauBarostat()); |
166 |
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// else { |
167 |
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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" |
170 |
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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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// } else if ( !strcasecmp( ensemble, "NVT") ) { |
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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->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" |
187 |
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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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// } |
191 |
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192 |
mmeineke |
377 |
strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
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simnfo->usePBC = the_globals->getPBC(); |
194 |
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195 |
mmeineke |
469 |
int usesDipoles = 0; |
196 |
mmeineke |
557 |
switch( ffCase ){ |
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case FF_DUFF: |
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the_ff = new DUFF(); |
200 |
mmeineke |
469 |
usesDipoles = 1; |
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mmeineke |
557 |
break; |
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case FF_LJ: |
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mmeineke |
561 |
the_ff = new LJFF(); |
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mmeineke |
557 |
break; |
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default: |
208 |
mmeineke |
377 |
sprintf( painCave.errMsg, |
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mmeineke |
557 |
"SimSetup Error. Unrecognized force field in case statement.\n"); |
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mmeineke |
377 |
painCave.isFatal = 1; |
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simError(); |
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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 |
218 |
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// get the components and calculate the tot_nMol and indvidual n_mol |
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the_components = the_globals->getComponents(); |
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components_nmol = new int[n_components]; |
222 |
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comp_stamps = new MoleculeStamp*[n_components]; |
223 |
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224 |
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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 |
226 |
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// given in each component |
227 |
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228 |
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tot_nmol = 0; |
229 |
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for( i=0; i<n_components; i++ ){ |
230 |
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if( !the_components[i]->haveNMol() ){ |
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// we have a problem |
233 |
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sprintf( painCave.errMsg, |
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"SimSetup Error. No global NMol or component NMol" |
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" given. Cannot calculate the number of atoms.\n" ); |
236 |
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painCave.isFatal = 1; |
237 |
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simError(); |
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} |
239 |
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240 |
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tot_nmol += the_components[i]->getNMol(); |
241 |
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components_nmol[i] = the_components[i]->getNMol(); |
242 |
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} |
243 |
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} |
244 |
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else{ |
245 |
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sprintf( painCave.errMsg, |
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"SimSetup error.\n" |
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"\tSorry, the ability to specify total" |
248 |
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" nMols and then give molfractions in the components\n" |
249 |
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"\tis not currently supported." |
250 |
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" Please give nMol in the components.\n" ); |
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painCave.isFatal = 1; |
252 |
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simError(); |
253 |
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254 |
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255 |
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// tot_nmol = the_globals->getNMol(); |
256 |
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257 |
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// //we have the total number of molecules, now we check for molfractions |
258 |
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// for( i=0; i<n_components; i++ ){ |
259 |
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260 |
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// if( !the_components[i]->haveMolFraction() ){ |
261 |
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262 |
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// if( !the_components[i]->haveNMol() ){ |
263 |
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// //we have a problem |
264 |
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// std::cerr << "SimSetup error. Neither molFraction nor " |
265 |
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// << " nMol was given in component |
266 |
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267 |
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} |
268 |
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269 |
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#ifdef IS_MPI |
270 |
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strcpy( checkPointMsg, "Have the number of components" ); |
271 |
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MPIcheckPoint(); |
272 |
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#endif // is_mpi |
273 |
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274 |
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// make an array of molecule stamps that match the components used. |
275 |
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// also extract the used stamps out into a separate linked list |
276 |
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277 |
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simnfo->nComponents = n_components; |
278 |
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simnfo->componentsNmol = components_nmol; |
279 |
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simnfo->compStamps = comp_stamps; |
280 |
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simnfo->headStamp = new LinkedMolStamp(); |
281 |
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282 |
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char* id; |
283 |
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LinkedMolStamp* headStamp = simnfo->headStamp; |
284 |
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LinkedMolStamp* currentStamp = NULL; |
285 |
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for( i=0; i<n_components; i++ ){ |
286 |
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287 |
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id = the_components[i]->getType(); |
288 |
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comp_stamps[i] = NULL; |
289 |
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290 |
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// check to make sure the component isn't already in the list |
291 |
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292 |
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comp_stamps[i] = headStamp->match( id ); |
293 |
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if( comp_stamps[i] == NULL ){ |
294 |
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295 |
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// extract the component from the list; |
296 |
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297 |
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currentStamp = the_stamps->extractMolStamp( id ); |
298 |
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if( currentStamp == NULL ){ |
299 |
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sprintf( painCave.errMsg, |
300 |
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"SimSetup error: Component \"%s\" was not found in the " |
301 |
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"list of declared molecules\n", |
302 |
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id ); |
303 |
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painCave.isFatal = 1; |
304 |
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simError(); |
305 |
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} |
306 |
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307 |
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headStamp->add( currentStamp ); |
308 |
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comp_stamps[i] = headStamp->match( id ); |
309 |
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} |
310 |
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} |
311 |
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312 |
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#ifdef IS_MPI |
313 |
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strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
314 |
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MPIcheckPoint(); |
315 |
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#endif // is_mpi |
316 |
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317 |
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318 |
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319 |
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320 |
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// caclulate the number of atoms, bonds, bends and torsions |
321 |
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322 |
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tot_atoms = 0; |
323 |
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tot_bonds = 0; |
324 |
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tot_bends = 0; |
325 |
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tot_torsions = 0; |
326 |
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for( i=0; i<n_components; i++ ){ |
327 |
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328 |
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tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
329 |
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tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
330 |
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tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
331 |
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tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
332 |
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} |
333 |
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334 |
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tot_SRI = tot_bonds + tot_bends + tot_torsions; |
335 |
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336 |
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simnfo->n_atoms = tot_atoms; |
337 |
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simnfo->n_bonds = tot_bonds; |
338 |
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simnfo->n_bends = tot_bends; |
339 |
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simnfo->n_torsions = tot_torsions; |
340 |
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simnfo->n_SRI = tot_SRI; |
341 |
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simnfo->n_mol = tot_nmol; |
342 |
mmeineke |
491 |
|
343 |
gezelter |
490 |
simnfo->molMembershipArray = new int[tot_atoms]; |
344 |
mmeineke |
377 |
|
345 |
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#ifdef IS_MPI |
346 |
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347 |
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// divide the molecules among processors here. |
348 |
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349 |
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mpiSim = new mpiSimulation( simnfo ); |
350 |
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351 |
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globalIndex = mpiSim->divideLabor(); |
352 |
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353 |
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// set up the local variables |
354 |
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355 |
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int localMol, allMol; |
356 |
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int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
357 |
mmeineke |
422 |
|
358 |
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int* mol2proc = mpiSim->getMolToProcMap(); |
359 |
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int* molCompType = mpiSim->getMolComponentType(); |
360 |
mmeineke |
377 |
|
361 |
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allMol = 0; |
362 |
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localMol = 0; |
363 |
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local_atoms = 0; |
364 |
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local_bonds = 0; |
365 |
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local_bends = 0; |
366 |
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local_torsions = 0; |
367 |
gezelter |
490 |
globalAtomIndex = 0; |
368 |
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369 |
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370 |
mmeineke |
377 |
for( i=0; i<n_components; i++ ){ |
371 |
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372 |
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for( j=0; j<components_nmol[i]; j++ ){ |
373 |
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374 |
mmeineke |
487 |
if( mol2proc[allMol] == worldRank ){ |
375 |
mmeineke |
377 |
|
376 |
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local_atoms += comp_stamps[i]->getNAtoms(); |
377 |
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local_bonds += comp_stamps[i]->getNBonds(); |
378 |
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local_bends += comp_stamps[i]->getNBends(); |
379 |
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local_torsions += comp_stamps[i]->getNTorsions(); |
380 |
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localMol++; |
381 |
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} |
382 |
gezelter |
490 |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
383 |
|
|
simnfo->molMembershipArray[globalAtomIndex] = allMol; |
384 |
|
|
globalAtomIndex++; |
385 |
|
|
} |
386 |
|
|
|
387 |
|
|
allMol++; |
388 |
mmeineke |
377 |
} |
389 |
|
|
} |
390 |
|
|
local_SRI = local_bonds + local_bends + local_torsions; |
391 |
|
|
|
392 |
|
|
simnfo->n_atoms = mpiSim->getMyNlocal(); |
393 |
|
|
|
394 |
|
|
if( local_atoms != simnfo->n_atoms ){ |
395 |
|
|
sprintf( painCave.errMsg, |
396 |
|
|
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
397 |
mmeineke |
422 |
" localAtom (%d) are not equal.\n", |
398 |
mmeineke |
377 |
simnfo->n_atoms, |
399 |
|
|
local_atoms ); |
400 |
|
|
painCave.isFatal = 1; |
401 |
|
|
simError(); |
402 |
|
|
} |
403 |
|
|
|
404 |
|
|
simnfo->n_bonds = local_bonds; |
405 |
|
|
simnfo->n_bends = local_bends; |
406 |
|
|
simnfo->n_torsions = local_torsions; |
407 |
|
|
simnfo->n_SRI = local_SRI; |
408 |
|
|
simnfo->n_mol = localMol; |
409 |
|
|
|
410 |
|
|
strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
411 |
|
|
MPIcheckPoint(); |
412 |
|
|
|
413 |
|
|
|
414 |
|
|
#endif // is_mpi |
415 |
|
|
|
416 |
|
|
|
417 |
|
|
// create the atom and short range interaction arrays |
418 |
|
|
|
419 |
|
|
Atom::createArrays(simnfo->n_atoms); |
420 |
|
|
the_atoms = new Atom*[simnfo->n_atoms]; |
421 |
|
|
the_molecules = new Molecule[simnfo->n_mol]; |
422 |
mmeineke |
422 |
int molIndex; |
423 |
mmeineke |
377 |
|
424 |
mmeineke |
422 |
// initialize the molecule's stampID's |
425 |
mmeineke |
377 |
|
426 |
mmeineke |
422 |
#ifdef IS_MPI |
427 |
|
|
|
428 |
|
|
|
429 |
|
|
molIndex = 0; |
430 |
|
|
for(i=0; i<mpiSim->getTotNmol(); i++){ |
431 |
|
|
|
432 |
|
|
if(mol2proc[i] == worldRank ){ |
433 |
|
|
the_molecules[molIndex].setStampID( molCompType[i] ); |
434 |
chuckv |
438 |
the_molecules[molIndex].setMyIndex( molIndex ); |
435 |
mmeineke |
489 |
the_molecules[molIndex].setGlobalIndex( i ); |
436 |
mmeineke |
422 |
molIndex++; |
437 |
|
|
} |
438 |
|
|
} |
439 |
|
|
|
440 |
|
|
#else // is_mpi |
441 |
|
|
|
442 |
|
|
molIndex = 0; |
443 |
gezelter |
490 |
globalAtomIndex = 0; |
444 |
mmeineke |
422 |
for(i=0; i<n_components; i++){ |
445 |
|
|
for(j=0; j<components_nmol[i]; j++ ){ |
446 |
|
|
the_molecules[molIndex].setStampID( i ); |
447 |
chuckv |
438 |
the_molecules[molIndex].setMyIndex( molIndex ); |
448 |
mmeineke |
489 |
the_molecules[molIndex].setGlobalIndex( molIndex ); |
449 |
gezelter |
490 |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
450 |
|
|
simnfo->molMembershipArray[globalAtomIndex] = molIndex; |
451 |
|
|
globalAtomIndex++; |
452 |
|
|
} |
453 |
mmeineke |
422 |
molIndex++; |
454 |
|
|
} |
455 |
|
|
} |
456 |
|
|
|
457 |
|
|
|
458 |
|
|
#endif // is_mpi |
459 |
|
|
|
460 |
|
|
|
461 |
mmeineke |
377 |
if( simnfo->n_SRI ){ |
462 |
mmeineke |
431 |
|
463 |
mmeineke |
412 |
Exclude::createArray(simnfo->n_SRI); |
464 |
|
|
the_excludes = new Exclude*[simnfo->n_SRI]; |
465 |
mmeineke |
431 |
for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
466 |
mmeineke |
377 |
simnfo->globalExcludes = new int; |
467 |
chuckv |
438 |
simnfo->n_exclude = simnfo->n_SRI; |
468 |
mmeineke |
377 |
} |
469 |
|
|
else{ |
470 |
|
|
|
471 |
mmeineke |
412 |
Exclude::createArray( 1 ); |
472 |
|
|
the_excludes = new Exclude*; |
473 |
|
|
the_excludes[0] = new Exclude(0); |
474 |
|
|
the_excludes[0]->setPair( 0,0 ); |
475 |
mmeineke |
377 |
simnfo->globalExcludes = new int; |
476 |
|
|
simnfo->globalExcludes[0] = 0; |
477 |
mmeineke |
412 |
simnfo->n_exclude = 0; |
478 |
mmeineke |
377 |
} |
479 |
|
|
|
480 |
|
|
// set the arrays into the SimInfo object |
481 |
|
|
|
482 |
|
|
simnfo->atoms = the_atoms; |
483 |
mmeineke |
429 |
simnfo->molecules = the_molecules; |
484 |
mmeineke |
377 |
simnfo->nGlobalExcludes = 0; |
485 |
|
|
simnfo->excludes = the_excludes; |
486 |
|
|
|
487 |
|
|
|
488 |
|
|
// get some of the tricky things that may still be in the globals |
489 |
|
|
|
490 |
mmeineke |
572 |
double boxVector[3]; |
491 |
mmeineke |
377 |
if( the_globals->haveBox() ){ |
492 |
mmeineke |
572 |
boxVector[0] = the_globals->getBox(); |
493 |
|
|
boxVector[1] = the_globals->getBox(); |
494 |
|
|
boxVector[2] = the_globals->getBox(); |
495 |
|
|
|
496 |
|
|
simnfo->setBox( boxVector ); |
497 |
mmeineke |
377 |
} |
498 |
|
|
else if( the_globals->haveDensity() ){ |
499 |
|
|
|
500 |
|
|
double vol; |
501 |
|
|
vol = (double)tot_nmol / the_globals->getDensity(); |
502 |
mmeineke |
572 |
boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
503 |
|
|
boxVector[1] = boxVector[0]; |
504 |
|
|
boxVector[2] = boxVector[0]; |
505 |
|
|
|
506 |
|
|
simnfo->setBox( boxVector ); |
507 |
mmeineke |
377 |
} |
508 |
|
|
else{ |
509 |
|
|
if( !the_globals->haveBoxX() ){ |
510 |
|
|
sprintf( painCave.errMsg, |
511 |
|
|
"SimSetup error, no periodic BoxX size given.\n" ); |
512 |
|
|
painCave.isFatal = 1; |
513 |
|
|
simError(); |
514 |
|
|
} |
515 |
mmeineke |
572 |
boxVector[0] = the_globals->getBoxX(); |
516 |
mmeineke |
377 |
|
517 |
|
|
if( !the_globals->haveBoxY() ){ |
518 |
|
|
sprintf( painCave.errMsg, |
519 |
|
|
"SimSetup error, no periodic BoxY size given.\n" ); |
520 |
|
|
painCave.isFatal = 1; |
521 |
|
|
simError(); |
522 |
|
|
} |
523 |
mmeineke |
572 |
boxVector[1] = the_globals->getBoxY(); |
524 |
mmeineke |
377 |
|
525 |
|
|
if( !the_globals->haveBoxZ() ){ |
526 |
|
|
sprintf( painCave.errMsg, |
527 |
|
|
"SimSetup error, no periodic BoxZ size given.\n" ); |
528 |
|
|
painCave.isFatal = 1; |
529 |
|
|
simError(); |
530 |
|
|
} |
531 |
mmeineke |
572 |
boxVector[2] = the_globals->getBoxZ(); |
532 |
|
|
|
533 |
|
|
simnfo->setBox( boxVector ); |
534 |
mmeineke |
377 |
} |
535 |
|
|
|
536 |
|
|
#ifdef IS_MPI |
537 |
|
|
strcpy( checkPointMsg, "Box size set up" ); |
538 |
|
|
MPIcheckPoint(); |
539 |
|
|
#endif // is_mpi |
540 |
|
|
|
541 |
|
|
|
542 |
|
|
// initialize the arrays |
543 |
|
|
|
544 |
|
|
the_ff->setSimInfo( simnfo ); |
545 |
|
|
|
546 |
mmeineke |
422 |
makeMolecules(); |
547 |
mmeineke |
377 |
simnfo->identArray = new int[simnfo->n_atoms]; |
548 |
|
|
for(i=0; i<simnfo->n_atoms; i++){ |
549 |
|
|
simnfo->identArray[i] = the_atoms[i]->getIdent(); |
550 |
|
|
} |
551 |
|
|
|
552 |
gezelter |
394 |
if (the_globals->getUseRF() ) { |
553 |
|
|
simnfo->useReactionField = 1; |
554 |
|
|
|
555 |
|
|
if( !the_globals->haveECR() ){ |
556 |
|
|
sprintf( painCave.errMsg, |
557 |
|
|
"SimSetup Warning: using default value of 1/2 the smallest " |
558 |
|
|
"box length for the electrostaticCutoffRadius.\n" |
559 |
|
|
"I hope you have a very fast processor!\n"); |
560 |
|
|
painCave.isFatal = 0; |
561 |
|
|
simError(); |
562 |
|
|
double smallest; |
563 |
mmeineke |
572 |
smallest = simnfo->boxLx; |
564 |
|
|
if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy; |
565 |
|
|
if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz; |
566 |
gezelter |
394 |
simnfo->ecr = 0.5 * smallest; |
567 |
|
|
} else { |
568 |
|
|
simnfo->ecr = the_globals->getECR(); |
569 |
|
|
} |
570 |
mmeineke |
377 |
|
571 |
gezelter |
394 |
if( !the_globals->haveEST() ){ |
572 |
|
|
sprintf( painCave.errMsg, |
573 |
|
|
"SimSetup Warning: using default value of 0.05 * the " |
574 |
|
|
"electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
575 |
|
|
); |
576 |
|
|
painCave.isFatal = 0; |
577 |
|
|
simError(); |
578 |
|
|
simnfo->est = 0.05 * simnfo->ecr; |
579 |
|
|
} else { |
580 |
|
|
simnfo->est = the_globals->getEST(); |
581 |
|
|
} |
582 |
|
|
|
583 |
|
|
if(!the_globals->haveDielectric() ){ |
584 |
|
|
sprintf( painCave.errMsg, |
585 |
|
|
"SimSetup Error: You are trying to use Reaction Field without" |
586 |
|
|
"setting a dielectric constant!\n" |
587 |
|
|
); |
588 |
|
|
painCave.isFatal = 1; |
589 |
|
|
simError(); |
590 |
|
|
} |
591 |
|
|
simnfo->dielectric = the_globals->getDielectric(); |
592 |
|
|
} else { |
593 |
mmeineke |
469 |
if (usesDipoles) { |
594 |
gezelter |
394 |
|
595 |
|
|
if( !the_globals->haveECR() ){ |
596 |
|
|
sprintf( painCave.errMsg, |
597 |
mmeineke |
469 |
"SimSetup Warning: using default value of 1/2 the smallest " |
598 |
gezelter |
394 |
"box length for the electrostaticCutoffRadius.\n" |
599 |
|
|
"I hope you have a very fast processor!\n"); |
600 |
|
|
painCave.isFatal = 0; |
601 |
|
|
simError(); |
602 |
|
|
double smallest; |
603 |
mmeineke |
572 |
smallest = simnfo->boxLx; |
604 |
|
|
if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy; |
605 |
|
|
if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz; |
606 |
gezelter |
394 |
simnfo->ecr = 0.5 * smallest; |
607 |
|
|
} else { |
608 |
|
|
simnfo->ecr = the_globals->getECR(); |
609 |
|
|
} |
610 |
|
|
|
611 |
|
|
if( !the_globals->haveEST() ){ |
612 |
|
|
sprintf( painCave.errMsg, |
613 |
mmeineke |
469 |
"SimSetup Warning: using default value of 5%% of the " |
614 |
gezelter |
394 |
"electrostaticCutoffRadius for the " |
615 |
|
|
"electrostaticSkinThickness\n" |
616 |
|
|
); |
617 |
|
|
painCave.isFatal = 0; |
618 |
|
|
simError(); |
619 |
|
|
simnfo->est = 0.05 * simnfo->ecr; |
620 |
|
|
} else { |
621 |
|
|
simnfo->est = the_globals->getEST(); |
622 |
|
|
} |
623 |
|
|
} |
624 |
|
|
} |
625 |
mmeineke |
377 |
|
626 |
gezelter |
394 |
#ifdef IS_MPI |
627 |
|
|
strcpy( checkPointMsg, "electrostatic parameters check out" ); |
628 |
|
|
MPIcheckPoint(); |
629 |
|
|
#endif // is_mpi |
630 |
mmeineke |
377 |
|
631 |
|
|
if( the_globals->haveInitialConfig() ){ |
632 |
|
|
|
633 |
|
|
InitializeFromFile* fileInit; |
634 |
|
|
#ifdef IS_MPI // is_mpi |
635 |
|
|
if( worldRank == 0 ){ |
636 |
|
|
#endif //is_mpi |
637 |
|
|
fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
638 |
|
|
#ifdef IS_MPI |
639 |
|
|
}else fileInit = new InitializeFromFile( NULL ); |
640 |
|
|
#endif |
641 |
|
|
fileInit->read_xyz( simnfo ); // default velocities on |
642 |
|
|
|
643 |
|
|
delete fileInit; |
644 |
|
|
} |
645 |
|
|
else{ |
646 |
|
|
|
647 |
|
|
#ifdef IS_MPI |
648 |
|
|
|
649 |
|
|
// no init from bass |
650 |
|
|
|
651 |
|
|
sprintf( painCave.errMsg, |
652 |
|
|
"Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
653 |
|
|
painCave.isFatal; |
654 |
|
|
simError(); |
655 |
|
|
|
656 |
|
|
#else |
657 |
|
|
|
658 |
|
|
initFromBass(); |
659 |
|
|
|
660 |
|
|
|
661 |
|
|
#endif |
662 |
|
|
} |
663 |
|
|
|
664 |
|
|
#ifdef IS_MPI |
665 |
|
|
strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
666 |
|
|
MPIcheckPoint(); |
667 |
|
|
#endif // is_mpi |
668 |
|
|
|
669 |
|
|
|
670 |
|
|
|
671 |
|
|
|
672 |
|
|
|
673 |
|
|
|
674 |
|
|
|
675 |
|
|
#ifdef IS_MPI |
676 |
|
|
if( worldRank == 0 ){ |
677 |
|
|
#endif // is_mpi |
678 |
|
|
|
679 |
|
|
if( the_globals->haveFinalConfig() ){ |
680 |
|
|
strcpy( simnfo->finalName, the_globals->getFinalConfig() ); |
681 |
|
|
} |
682 |
|
|
else{ |
683 |
|
|
strcpy( simnfo->finalName, inFileName ); |
684 |
|
|
char* endTest; |
685 |
|
|
int nameLength = strlen( simnfo->finalName ); |
686 |
|
|
endTest = &(simnfo->finalName[nameLength - 5]); |
687 |
|
|
if( !strcmp( endTest, ".bass" ) ){ |
688 |
|
|
strcpy( endTest, ".eor" ); |
689 |
|
|
} |
690 |
|
|
else if( !strcmp( endTest, ".BASS" ) ){ |
691 |
|
|
strcpy( endTest, ".eor" ); |
692 |
|
|
} |
693 |
|
|
else{ |
694 |
|
|
endTest = &(simnfo->finalName[nameLength - 4]); |
695 |
|
|
if( !strcmp( endTest, ".bss" ) ){ |
696 |
|
|
strcpy( endTest, ".eor" ); |
697 |
|
|
} |
698 |
|
|
else if( !strcmp( endTest, ".mdl" ) ){ |
699 |
|
|
strcpy( endTest, ".eor" ); |
700 |
|
|
} |
701 |
|
|
else{ |
702 |
|
|
strcat( simnfo->finalName, ".eor" ); |
703 |
|
|
} |
704 |
|
|
} |
705 |
|
|
} |
706 |
|
|
|
707 |
|
|
// make the sample and status out names |
708 |
|
|
|
709 |
|
|
strcpy( simnfo->sampleName, inFileName ); |
710 |
|
|
char* endTest; |
711 |
|
|
int nameLength = strlen( simnfo->sampleName ); |
712 |
|
|
endTest = &(simnfo->sampleName[nameLength - 5]); |
713 |
|
|
if( !strcmp( endTest, ".bass" ) ){ |
714 |
|
|
strcpy( endTest, ".dump" ); |
715 |
|
|
} |
716 |
|
|
else if( !strcmp( endTest, ".BASS" ) ){ |
717 |
|
|
strcpy( endTest, ".dump" ); |
718 |
|
|
} |
719 |
|
|
else{ |
720 |
|
|
endTest = &(simnfo->sampleName[nameLength - 4]); |
721 |
|
|
if( !strcmp( endTest, ".bss" ) ){ |
722 |
|
|
strcpy( endTest, ".dump" ); |
723 |
|
|
} |
724 |
|
|
else if( !strcmp( endTest, ".mdl" ) ){ |
725 |
|
|
strcpy( endTest, ".dump" ); |
726 |
|
|
} |
727 |
|
|
else{ |
728 |
|
|
strcat( simnfo->sampleName, ".dump" ); |
729 |
|
|
} |
730 |
|
|
} |
731 |
|
|
|
732 |
|
|
strcpy( simnfo->statusName, inFileName ); |
733 |
|
|
nameLength = strlen( simnfo->statusName ); |
734 |
|
|
endTest = &(simnfo->statusName[nameLength - 5]); |
735 |
|
|
if( !strcmp( endTest, ".bass" ) ){ |
736 |
|
|
strcpy( endTest, ".stat" ); |
737 |
|
|
} |
738 |
|
|
else if( !strcmp( endTest, ".BASS" ) ){ |
739 |
|
|
strcpy( endTest, ".stat" ); |
740 |
|
|
} |
741 |
|
|
else{ |
742 |
|
|
endTest = &(simnfo->statusName[nameLength - 4]); |
743 |
|
|
if( !strcmp( endTest, ".bss" ) ){ |
744 |
|
|
strcpy( endTest, ".stat" ); |
745 |
|
|
} |
746 |
|
|
else if( !strcmp( endTest, ".mdl" ) ){ |
747 |
|
|
strcpy( endTest, ".stat" ); |
748 |
|
|
} |
749 |
|
|
else{ |
750 |
|
|
strcat( simnfo->statusName, ".stat" ); |
751 |
|
|
} |
752 |
|
|
} |
753 |
|
|
|
754 |
|
|
#ifdef IS_MPI |
755 |
|
|
} |
756 |
|
|
#endif // is_mpi |
757 |
|
|
|
758 |
|
|
// set the status, sample, and themal kick times |
759 |
|
|
|
760 |
|
|
if( the_globals->haveSampleTime() ){ |
761 |
|
|
simnfo->sampleTime = the_globals->getSampleTime(); |
762 |
|
|
simnfo->statusTime = simnfo->sampleTime; |
763 |
|
|
simnfo->thermalTime = simnfo->sampleTime; |
764 |
|
|
} |
765 |
|
|
else{ |
766 |
|
|
simnfo->sampleTime = the_globals->getRunTime(); |
767 |
|
|
simnfo->statusTime = simnfo->sampleTime; |
768 |
|
|
simnfo->thermalTime = simnfo->sampleTime; |
769 |
|
|
} |
770 |
|
|
|
771 |
|
|
if( the_globals->haveStatusTime() ){ |
772 |
|
|
simnfo->statusTime = the_globals->getStatusTime(); |
773 |
|
|
} |
774 |
|
|
|
775 |
|
|
if( the_globals->haveThermalTime() ){ |
776 |
|
|
simnfo->thermalTime = the_globals->getThermalTime(); |
777 |
|
|
} |
778 |
|
|
|
779 |
|
|
// check for the temperature set flag |
780 |
|
|
|
781 |
|
|
if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
782 |
|
|
|
783 |
|
|
|
784 |
mmeineke |
555 |
// make the integrator |
785 |
mmeineke |
561 |
|
786 |
|
|
|
787 |
mmeineke |
586 |
NVT* myNVT = NULL; |
788 |
|
|
NPTi* myNPTi = NULL; |
789 |
|
|
NPTf* myNPTf = NULL; |
790 |
gezelter |
604 |
NPTim* myNPTim = NULL; |
791 |
|
|
|
792 |
mmeineke |
558 |
switch( ensembleCase ){ |
793 |
mmeineke |
377 |
|
794 |
mmeineke |
558 |
case NVE_ENS: |
795 |
|
|
new NVE( simnfo, the_ff ); |
796 |
|
|
break; |
797 |
|
|
|
798 |
mmeineke |
561 |
case NVT_ENS: |
799 |
|
|
myNVT = new NVT( simnfo, the_ff ); |
800 |
|
|
myNVT->setTargetTemp(the_globals->getTargetTemp()); |
801 |
|
|
|
802 |
|
|
if (the_globals->haveTauThermostat()) |
803 |
|
|
myNVT->setTauThermostat(the_globals->getTauThermostat()); |
804 |
mmeineke |
586 |
|
805 |
mmeineke |
561 |
else { |
806 |
|
|
sprintf( painCave.errMsg, |
807 |
|
|
"SimSetup error: If you use the NVT\n" |
808 |
mmeineke |
586 |
" ensemble, you must set tauThermostat.\n"); |
809 |
mmeineke |
561 |
painCave.isFatal = 1; |
810 |
|
|
simError(); |
811 |
|
|
} |
812 |
|
|
break; |
813 |
|
|
|
814 |
mmeineke |
586 |
case NPTi_ENS: |
815 |
|
|
myNPTi = new NPTi( simnfo, the_ff ); |
816 |
|
|
myNPTi->setTargetTemp( the_globals->getTargetTemp()); |
817 |
|
|
|
818 |
|
|
if (the_globals->haveTargetPressure()) |
819 |
|
|
myNPTi->setTargetPressure(the_globals->getTargetPressure()); |
820 |
|
|
else { |
821 |
|
|
sprintf( painCave.errMsg, |
822 |
|
|
"SimSetup error: If you use a constant pressure\n" |
823 |
|
|
" ensemble, you must set targetPressure in the BASS file.\n"); |
824 |
|
|
painCave.isFatal = 1; |
825 |
|
|
simError(); |
826 |
|
|
} |
827 |
|
|
|
828 |
|
|
if( the_globals->haveTauThermostat() ) |
829 |
|
|
myNPTi->setTauThermostat( the_globals->getTauThermostat() ); |
830 |
|
|
else{ |
831 |
|
|
sprintf( painCave.errMsg, |
832 |
|
|
"SimSetup error: If you use an NPT\n" |
833 |
|
|
" ensemble, you must set tauThermostat.\n"); |
834 |
|
|
painCave.isFatal = 1; |
835 |
|
|
simError(); |
836 |
|
|
} |
837 |
|
|
|
838 |
|
|
if( the_globals->haveTauBarostat() ) |
839 |
|
|
myNPTi->setTauBarostat( the_globals->getTauBarostat() ); |
840 |
|
|
else{ |
841 |
|
|
sprintf( painCave.errMsg, |
842 |
|
|
"SimSetup error: If you use an NPT\n" |
843 |
|
|
" ensemble, you must set tauBarostat.\n"); |
844 |
|
|
painCave.isFatal = 1; |
845 |
|
|
simError(); |
846 |
|
|
} |
847 |
|
|
break; |
848 |
|
|
|
849 |
|
|
case NPTf_ENS: |
850 |
|
|
myNPTf = new NPTf( simnfo, the_ff ); |
851 |
|
|
myNPTf->setTargetTemp( the_globals->getTargetTemp()); |
852 |
|
|
|
853 |
|
|
if (the_globals->haveTargetPressure()) |
854 |
|
|
myNPTf->setTargetPressure(the_globals->getTargetPressure()); |
855 |
|
|
else { |
856 |
|
|
sprintf( painCave.errMsg, |
857 |
|
|
"SimSetup error: If you use a constant pressure\n" |
858 |
|
|
" ensemble, you must set targetPressure in the BASS file.\n"); |
859 |
|
|
painCave.isFatal = 1; |
860 |
|
|
simError(); |
861 |
|
|
} |
862 |
|
|
|
863 |
|
|
if( the_globals->haveTauThermostat() ) |
864 |
|
|
myNPTf->setTauThermostat( the_globals->getTauThermostat() ); |
865 |
|
|
else{ |
866 |
|
|
sprintf( painCave.errMsg, |
867 |
|
|
"SimSetup error: If you use an NPT\n" |
868 |
|
|
" ensemble, you must set tauThermostat.\n"); |
869 |
|
|
painCave.isFatal = 1; |
870 |
|
|
simError(); |
871 |
|
|
} |
872 |
|
|
|
873 |
|
|
if( the_globals->haveTauBarostat() ) |
874 |
|
|
myNPTf->setTauBarostat( the_globals->getTauBarostat() ); |
875 |
|
|
else{ |
876 |
|
|
sprintf( painCave.errMsg, |
877 |
|
|
"SimSetup error: If you use an NPT\n" |
878 |
|
|
" ensemble, you must set tauBarostat.\n"); |
879 |
|
|
painCave.isFatal = 1; |
880 |
|
|
simError(); |
881 |
|
|
} |
882 |
|
|
break; |
883 |
|
|
|
884 |
gezelter |
604 |
case NPTim_ENS: |
885 |
|
|
myNPTim = new NPTim( simnfo, the_ff ); |
886 |
|
|
myNPTim->setTargetTemp( the_globals->getTargetTemp()); |
887 |
|
|
|
888 |
|
|
if (the_globals->haveTargetPressure()) |
889 |
|
|
myNPTim->setTargetPressure(the_globals->getTargetPressure()); |
890 |
|
|
else { |
891 |
|
|
sprintf( painCave.errMsg, |
892 |
|
|
"SimSetup error: If you use a constant pressure\n" |
893 |
|
|
" ensemble, you must set targetPressure in the BASS file.\n"); |
894 |
|
|
painCave.isFatal = 1; |
895 |
|
|
simError(); |
896 |
|
|
} |
897 |
mmeineke |
586 |
|
898 |
gezelter |
604 |
if( the_globals->haveTauThermostat() ) |
899 |
|
|
myNPTim->setTauThermostat( the_globals->getTauThermostat() ); |
900 |
|
|
else{ |
901 |
|
|
sprintf( painCave.errMsg, |
902 |
|
|
"SimSetup error: If you use an NPT\n" |
903 |
|
|
" ensemble, you must set tauThermostat.\n"); |
904 |
|
|
painCave.isFatal = 1; |
905 |
|
|
simError(); |
906 |
|
|
} |
907 |
mmeineke |
586 |
|
908 |
gezelter |
604 |
if( the_globals->haveTauBarostat() ) |
909 |
|
|
myNPTim->setTauBarostat( the_globals->getTauBarostat() ); |
910 |
|
|
else{ |
911 |
|
|
sprintf( painCave.errMsg, |
912 |
|
|
"SimSetup error: If you use an NPT\n" |
913 |
|
|
" ensemble, you must set tauBarostat.\n"); |
914 |
|
|
painCave.isFatal = 1; |
915 |
|
|
simError(); |
916 |
|
|
} |
917 |
|
|
break; |
918 |
|
|
|
919 |
|
|
|
920 |
|
|
|
921 |
mmeineke |
558 |
default: |
922 |
|
|
sprintf( painCave.errMsg, |
923 |
|
|
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
924 |
|
|
painCave.isFatal = 1; |
925 |
|
|
simError(); |
926 |
mmeineke |
469 |
} |
927 |
mmeineke |
504 |
|
928 |
mmeineke |
558 |
|
929 |
chuckv |
432 |
#ifdef IS_MPI |
930 |
|
|
mpiSim->mpiRefresh(); |
931 |
|
|
#endif |
932 |
mmeineke |
377 |
|
933 |
chuckv |
432 |
// initialize the Fortran |
934 |
mmeineke |
377 |
|
935 |
chuckv |
432 |
|
936 |
mmeineke |
377 |
simnfo->refreshSim(); |
937 |
|
|
|
938 |
|
|
if( !strcmp( simnfo->mixingRule, "standard") ){ |
939 |
|
|
the_ff->initForceField( LB_MIXING_RULE ); |
940 |
|
|
} |
941 |
|
|
else if( !strcmp( simnfo->mixingRule, "explicit") ){ |
942 |
|
|
the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
943 |
|
|
} |
944 |
|
|
else{ |
945 |
|
|
sprintf( painCave.errMsg, |
946 |
|
|
"SimSetup Error: unknown mixing rule -> \"%s\"\n", |
947 |
|
|
simnfo->mixingRule ); |
948 |
|
|
painCave.isFatal = 1; |
949 |
|
|
simError(); |
950 |
|
|
} |
951 |
|
|
|
952 |
|
|
|
953 |
|
|
#ifdef IS_MPI |
954 |
|
|
strcpy( checkPointMsg, |
955 |
|
|
"Successfully intialized the mixingRule for Fortran." ); |
956 |
|
|
MPIcheckPoint(); |
957 |
|
|
#endif // is_mpi |
958 |
|
|
} |
959 |
|
|
|
960 |
mmeineke |
407 |
|
961 |
|
|
void SimSetup::makeMolecules( void ){ |
962 |
|
|
|
963 |
mmeineke |
412 |
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
964 |
mmeineke |
407 |
molInit info; |
965 |
|
|
DirectionalAtom* dAtom; |
966 |
mmeineke |
412 |
LinkedAssign* extras; |
967 |
|
|
LinkedAssign* current_extra; |
968 |
mmeineke |
407 |
AtomStamp* currentAtom; |
969 |
|
|
BondStamp* currentBond; |
970 |
|
|
BendStamp* currentBend; |
971 |
|
|
TorsionStamp* currentTorsion; |
972 |
mmeineke |
427 |
|
973 |
|
|
bond_pair* theBonds; |
974 |
|
|
bend_set* theBends; |
975 |
|
|
torsion_set* theTorsions; |
976 |
|
|
|
977 |
mmeineke |
407 |
|
978 |
|
|
//init the forceField paramters |
979 |
|
|
|
980 |
|
|
the_ff->readParams(); |
981 |
|
|
|
982 |
|
|
|
983 |
mmeineke |
427 |
// init the atoms |
984 |
mmeineke |
407 |
|
985 |
mmeineke |
427 |
double ux, uy, uz, u, uSqr; |
986 |
|
|
|
987 |
mmeineke |
407 |
atomOffset = 0; |
988 |
mmeineke |
412 |
excludeOffset = 0; |
989 |
mmeineke |
407 |
for(i=0; i<simnfo->n_mol; i++){ |
990 |
|
|
|
991 |
|
|
stampID = the_molecules[i].getStampID(); |
992 |
|
|
|
993 |
|
|
info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
994 |
|
|
info.nBonds = comp_stamps[stampID]->getNBonds(); |
995 |
|
|
info.nBends = comp_stamps[stampID]->getNBends(); |
996 |
|
|
info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
997 |
mmeineke |
412 |
info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
998 |
|
|
|
999 |
mmeineke |
407 |
info.myAtoms = &the_atoms[atomOffset]; |
1000 |
mmeineke |
412 |
info.myExcludes = &the_excludes[excludeOffset]; |
1001 |
mmeineke |
407 |
info.myBonds = new Bond*[info.nBonds]; |
1002 |
|
|
info.myBends = new Bend*[info.nBends]; |
1003 |
mmeineke |
427 |
info.myTorsions = new Torsion*[info.nTorsions]; |
1004 |
mmeineke |
407 |
|
1005 |
|
|
theBonds = new bond_pair[info.nBonds]; |
1006 |
|
|
theBends = new bend_set[info.nBends]; |
1007 |
|
|
theTorsions = new torsion_set[info.nTorsions]; |
1008 |
|
|
|
1009 |
|
|
// make the Atoms |
1010 |
|
|
|
1011 |
|
|
for(j=0; j<info.nAtoms; j++){ |
1012 |
|
|
|
1013 |
mmeineke |
427 |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
1014 |
mmeineke |
407 |
if( currentAtom->haveOrientation() ){ |
1015 |
|
|
|
1016 |
|
|
dAtom = new DirectionalAtom(j + atomOffset); |
1017 |
|
|
simnfo->n_oriented++; |
1018 |
|
|
info.myAtoms[j] = dAtom; |
1019 |
|
|
|
1020 |
|
|
ux = currentAtom->getOrntX(); |
1021 |
|
|
uy = currentAtom->getOrntY(); |
1022 |
|
|
uz = currentAtom->getOrntZ(); |
1023 |
|
|
|
1024 |
|
|
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
1025 |
|
|
|
1026 |
|
|
u = sqrt( uSqr ); |
1027 |
|
|
ux = ux / u; |
1028 |
|
|
uy = uy / u; |
1029 |
|
|
uz = uz / u; |
1030 |
|
|
|
1031 |
|
|
dAtom->setSUx( ux ); |
1032 |
|
|
dAtom->setSUy( uy ); |
1033 |
|
|
dAtom->setSUz( uz ); |
1034 |
|
|
} |
1035 |
|
|
else{ |
1036 |
|
|
info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
1037 |
|
|
} |
1038 |
|
|
info.myAtoms[j]->setType( currentAtom->getType() ); |
1039 |
|
|
|
1040 |
|
|
#ifdef IS_MPI |
1041 |
|
|
|
1042 |
|
|
info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
1043 |
|
|
|
1044 |
|
|
#endif // is_mpi |
1045 |
|
|
} |
1046 |
|
|
|
1047 |
|
|
// make the bonds |
1048 |
mmeineke |
412 |
for(j=0; j<info.nBonds; j++){ |
1049 |
mmeineke |
407 |
|
1050 |
|
|
currentBond = comp_stamps[stampID]->getBond( j ); |
1051 |
|
|
theBonds[j].a = currentBond->getA() + atomOffset; |
1052 |
|
|
theBonds[j].b = currentBond->getB() + atomOffset; |
1053 |
|
|
|
1054 |
mmeineke |
435 |
exI = theBonds[j].a; |
1055 |
|
|
exJ = theBonds[j].b; |
1056 |
mmeineke |
407 |
|
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 |
mmeineke |
412 |
tempEx = exI; |
1065 |
|
|
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
1066 |
|
|
tempEx = exJ; |
1067 |
|
|
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1068 |
mmeineke |
407 |
|
1069 |
mmeineke |
412 |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1070 |
|
|
#else // isn't MPI |
1071 |
mmeineke |
435 |
|
1072 |
mmeineke |
412 |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1073 |
|
|
#endif //is_mpi |
1074 |
|
|
} |
1075 |
|
|
excludeOffset += info.nBonds; |
1076 |
|
|
|
1077 |
|
|
//make the bends |
1078 |
|
|
for(j=0; j<info.nBends; j++){ |
1079 |
mmeineke |
407 |
|
1080 |
mmeineke |
412 |
currentBend = comp_stamps[stampID]->getBend( j ); |
1081 |
|
|
theBends[j].a = currentBend->getA() + atomOffset; |
1082 |
|
|
theBends[j].b = currentBend->getB() + atomOffset; |
1083 |
|
|
theBends[j].c = currentBend->getC() + atomOffset; |
1084 |
|
|
|
1085 |
|
|
if( currentBend->haveExtras() ){ |
1086 |
|
|
|
1087 |
mmeineke |
427 |
extras = currentBend->getExtras(); |
1088 |
mmeineke |
412 |
current_extra = extras; |
1089 |
|
|
|
1090 |
|
|
while( current_extra != NULL ){ |
1091 |
|
|
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
1092 |
|
|
|
1093 |
|
|
switch( current_extra->getType() ){ |
1094 |
|
|
|
1095 |
|
|
case 0: |
1096 |
|
|
theBends[j].ghost = |
1097 |
|
|
current_extra->getInt() + atomOffset; |
1098 |
|
|
theBends[j].isGhost = 1; |
1099 |
|
|
break; |
1100 |
|
|
|
1101 |
|
|
case 1: |
1102 |
|
|
theBends[j].ghost = |
1103 |
|
|
(int)current_extra->getDouble() + atomOffset; |
1104 |
|
|
theBends[j].isGhost = 1; |
1105 |
|
|
break; |
1106 |
|
|
|
1107 |
|
|
default: |
1108 |
|
|
sprintf( painCave.errMsg, |
1109 |
chuckv |
434 |
"SimSetup Error: ghostVectorSource was neither a " |
1110 |
mmeineke |
412 |
"double nor an int.\n" |
1111 |
|
|
"-->Bend[%d] in %s\n", |
1112 |
|
|
j, comp_stamps[stampID]->getID() ); |
1113 |
|
|
painCave.isFatal = 1; |
1114 |
|
|
simError(); |
1115 |
|
|
} |
1116 |
|
|
} |
1117 |
|
|
|
1118 |
|
|
else{ |
1119 |
|
|
|
1120 |
|
|
sprintf( painCave.errMsg, |
1121 |
|
|
"SimSetup Error: unhandled bend assignment:\n" |
1122 |
|
|
" -->%s in Bend[%d] in %s\n", |
1123 |
|
|
current_extra->getlhs(), |
1124 |
|
|
j, comp_stamps[stampID]->getID() ); |
1125 |
|
|
painCave.isFatal = 1; |
1126 |
|
|
simError(); |
1127 |
|
|
} |
1128 |
|
|
|
1129 |
|
|
current_extra = current_extra->getNext(); |
1130 |
|
|
} |
1131 |
|
|
} |
1132 |
|
|
|
1133 |
|
|
if( !theBends[j].isGhost ){ |
1134 |
|
|
|
1135 |
|
|
exI = theBends[j].a; |
1136 |
|
|
exJ = theBends[j].c; |
1137 |
|
|
} |
1138 |
|
|
else{ |
1139 |
|
|
|
1140 |
|
|
exI = theBends[j].a; |
1141 |
|
|
exJ = theBends[j].b; |
1142 |
|
|
} |
1143 |
|
|
|
1144 |
|
|
// exclude_I must always be the smaller of the pair |
1145 |
|
|
if( exI > exJ ){ |
1146 |
|
|
tempEx = exI; |
1147 |
|
|
exI = exJ; |
1148 |
|
|
exJ = tempEx; |
1149 |
|
|
} |
1150 |
|
|
#ifdef IS_MPI |
1151 |
|
|
tempEx = exI; |
1152 |
|
|
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
1153 |
|
|
tempEx = exJ; |
1154 |
|
|
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1155 |
|
|
|
1156 |
|
|
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1157 |
mmeineke |
407 |
#else // isn't MPI |
1158 |
mmeineke |
412 |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1159 |
|
|
#endif //is_mpi |
1160 |
|
|
} |
1161 |
|
|
excludeOffset += info.nBends; |
1162 |
|
|
|
1163 |
|
|
for(j=0; j<info.nTorsions; j++){ |
1164 |
mmeineke |
407 |
|
1165 |
mmeineke |
412 |
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
1166 |
|
|
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
1167 |
|
|
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
1168 |
|
|
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
1169 |
|
|
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
1170 |
|
|
|
1171 |
|
|
exI = theTorsions[j].a; |
1172 |
|
|
exJ = theTorsions[j].d; |
1173 |
mmeineke |
407 |
|
1174 |
mmeineke |
412 |
// exclude_I must always be the smaller of the pair |
1175 |
|
|
if( exI > exJ ){ |
1176 |
|
|
tempEx = exI; |
1177 |
|
|
exI = exJ; |
1178 |
|
|
exJ = tempEx; |
1179 |
|
|
} |
1180 |
|
|
#ifdef IS_MPI |
1181 |
|
|
tempEx = exI; |
1182 |
|
|
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
1183 |
|
|
tempEx = exJ; |
1184 |
|
|
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1185 |
|
|
|
1186 |
|
|
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1187 |
|
|
#else // isn't MPI |
1188 |
|
|
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1189 |
mmeineke |
407 |
#endif //is_mpi |
1190 |
mmeineke |
412 |
} |
1191 |
|
|
excludeOffset += info.nTorsions; |
1192 |
|
|
|
1193 |
mmeineke |
407 |
|
1194 |
mmeineke |
414 |
// send the arrays off to the forceField for init. |
1195 |
mmeineke |
407 |
|
1196 |
mmeineke |
414 |
the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
1197 |
|
|
the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
1198 |
|
|
the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
1199 |
|
|
the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
1200 |
mmeineke |
407 |
|
1201 |
|
|
|
1202 |
mmeineke |
414 |
the_molecules[i].initialize( info ); |
1203 |
chuckv |
438 |
|
1204 |
|
|
|
1205 |
mmeineke |
414 |
atomOffset += info.nAtoms; |
1206 |
mmeineke |
427 |
delete[] theBonds; |
1207 |
|
|
delete[] theBends; |
1208 |
|
|
delete[] theTorsions; |
1209 |
mmeineke |
414 |
} |
1210 |
mmeineke |
407 |
|
1211 |
chuckv |
434 |
#ifdef IS_MPI |
1212 |
|
|
sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
1213 |
|
|
MPIcheckPoint(); |
1214 |
|
|
#endif // is_mpi |
1215 |
|
|
|
1216 |
mmeineke |
414 |
// clean up the forcefield |
1217 |
mmeineke |
420 |
the_ff->calcRcut(); |
1218 |
mmeineke |
414 |
the_ff->cleanMe(); |
1219 |
chuckv |
434 |
|
1220 |
mmeineke |
414 |
} |
1221 |
mmeineke |
407 |
|
1222 |
mmeineke |
377 |
void SimSetup::initFromBass( void ){ |
1223 |
|
|
|
1224 |
|
|
int i, j, k; |
1225 |
|
|
int n_cells; |
1226 |
|
|
double cellx, celly, cellz; |
1227 |
|
|
double temp1, temp2, temp3; |
1228 |
|
|
int n_per_extra; |
1229 |
|
|
int n_extra; |
1230 |
|
|
int have_extra, done; |
1231 |
|
|
|
1232 |
|
|
temp1 = (double)tot_nmol / 4.0; |
1233 |
|
|
temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
1234 |
|
|
temp3 = ceil( temp2 ); |
1235 |
|
|
|
1236 |
|
|
have_extra =0; |
1237 |
|
|
if( temp2 < temp3 ){ // we have a non-complete lattice |
1238 |
|
|
have_extra =1; |
1239 |
|
|
|
1240 |
|
|
n_cells = (int)temp3 - 1; |
1241 |
mmeineke |
572 |
cellx = simnfo->boxLx / temp3; |
1242 |
|
|
celly = simnfo->boxLy / temp3; |
1243 |
|
|
cellz = simnfo->boxLz / temp3; |
1244 |
mmeineke |
377 |
n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
1245 |
|
|
temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
1246 |
|
|
n_per_extra = (int)ceil( temp1 ); |
1247 |
|
|
|
1248 |
|
|
if( n_per_extra > 4){ |
1249 |
|
|
sprintf( painCave.errMsg, |
1250 |
|
|
"SimSetup error. There has been an error in constructing" |
1251 |
|
|
" the non-complete lattice.\n" ); |
1252 |
|
|
painCave.isFatal = 1; |
1253 |
|
|
simError(); |
1254 |
|
|
} |
1255 |
|
|
} |
1256 |
|
|
else{ |
1257 |
|
|
n_cells = (int)temp3; |
1258 |
mmeineke |
572 |
cellx = simnfo->boxLx / temp3; |
1259 |
|
|
celly = simnfo->boxLy / temp3; |
1260 |
|
|
cellz = simnfo->boxLz / temp3; |
1261 |
mmeineke |
377 |
} |
1262 |
|
|
|
1263 |
|
|
current_mol = 0; |
1264 |
|
|
current_comp_mol = 0; |
1265 |
|
|
current_comp = 0; |
1266 |
|
|
current_atom_ndx = 0; |
1267 |
|
|
|
1268 |
|
|
for( i=0; i < n_cells ; i++ ){ |
1269 |
|
|
for( j=0; j < n_cells; j++ ){ |
1270 |
|
|
for( k=0; k < n_cells; k++ ){ |
1271 |
|
|
|
1272 |
|
|
makeElement( i * cellx, |
1273 |
|
|
j * celly, |
1274 |
|
|
k * cellz ); |
1275 |
|
|
|
1276 |
|
|
makeElement( i * cellx + 0.5 * cellx, |
1277 |
|
|
j * celly + 0.5 * celly, |
1278 |
|
|
k * cellz ); |
1279 |
|
|
|
1280 |
|
|
makeElement( i * cellx, |
1281 |
|
|
j * celly + 0.5 * celly, |
1282 |
|
|
k * cellz + 0.5 * cellz ); |
1283 |
|
|
|
1284 |
|
|
makeElement( i * cellx + 0.5 * cellx, |
1285 |
|
|
j * celly, |
1286 |
|
|
k * cellz + 0.5 * cellz ); |
1287 |
|
|
} |
1288 |
|
|
} |
1289 |
|
|
} |
1290 |
|
|
|
1291 |
|
|
if( have_extra ){ |
1292 |
|
|
done = 0; |
1293 |
|
|
|
1294 |
|
|
int start_ndx; |
1295 |
|
|
for( i=0; i < (n_cells+1) && !done; i++ ){ |
1296 |
|
|
for( j=0; j < (n_cells+1) && !done; j++ ){ |
1297 |
|
|
|
1298 |
|
|
if( i < n_cells ){ |
1299 |
|
|
|
1300 |
|
|
if( j < n_cells ){ |
1301 |
|
|
start_ndx = n_cells; |
1302 |
|
|
} |
1303 |
|
|
else start_ndx = 0; |
1304 |
|
|
} |
1305 |
|
|
else start_ndx = 0; |
1306 |
|
|
|
1307 |
|
|
for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
1308 |
|
|
|
1309 |
|
|
makeElement( i * cellx, |
1310 |
|
|
j * celly, |
1311 |
|
|
k * cellz ); |
1312 |
|
|
done = ( current_mol >= tot_nmol ); |
1313 |
|
|
|
1314 |
|
|
if( !done && n_per_extra > 1 ){ |
1315 |
|
|
makeElement( i * cellx + 0.5 * cellx, |
1316 |
|
|
j * celly + 0.5 * celly, |
1317 |
|
|
k * cellz ); |
1318 |
|
|
done = ( current_mol >= tot_nmol ); |
1319 |
|
|
} |
1320 |
|
|
|
1321 |
|
|
if( !done && n_per_extra > 2){ |
1322 |
|
|
makeElement( i * cellx, |
1323 |
|
|
j * celly + 0.5 * celly, |
1324 |
|
|
k * cellz + 0.5 * cellz ); |
1325 |
|
|
done = ( current_mol >= tot_nmol ); |
1326 |
|
|
} |
1327 |
|
|
|
1328 |
|
|
if( !done && n_per_extra > 3){ |
1329 |
|
|
makeElement( i * cellx + 0.5 * cellx, |
1330 |
|
|
j * celly, |
1331 |
|
|
k * cellz + 0.5 * cellz ); |
1332 |
|
|
done = ( current_mol >= tot_nmol ); |
1333 |
|
|
} |
1334 |
|
|
} |
1335 |
|
|
} |
1336 |
|
|
} |
1337 |
|
|
} |
1338 |
|
|
|
1339 |
|
|
|
1340 |
|
|
for( i=0; i<simnfo->n_atoms; i++ ){ |
1341 |
|
|
simnfo->atoms[i]->set_vx( 0.0 ); |
1342 |
|
|
simnfo->atoms[i]->set_vy( 0.0 ); |
1343 |
|
|
simnfo->atoms[i]->set_vz( 0.0 ); |
1344 |
|
|
} |
1345 |
|
|
} |
1346 |
|
|
|
1347 |
|
|
void SimSetup::makeElement( double x, double y, double z ){ |
1348 |
|
|
|
1349 |
|
|
int k; |
1350 |
|
|
AtomStamp* current_atom; |
1351 |
|
|
DirectionalAtom* dAtom; |
1352 |
|
|
double rotMat[3][3]; |
1353 |
|
|
|
1354 |
|
|
for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
1355 |
|
|
|
1356 |
|
|
current_atom = comp_stamps[current_comp]->getAtom( k ); |
1357 |
|
|
if( !current_atom->havePosition() ){ |
1358 |
|
|
sprintf( painCave.errMsg, |
1359 |
|
|
"SimSetup:initFromBass error.\n" |
1360 |
|
|
"\tComponent %s, atom %s does not have a position specified.\n" |
1361 |
|
|
"\tThe initialization routine is unable to give a start" |
1362 |
|
|
" position.\n", |
1363 |
|
|
comp_stamps[current_comp]->getID(), |
1364 |
|
|
current_atom->getType() ); |
1365 |
|
|
painCave.isFatal = 1; |
1366 |
|
|
simError(); |
1367 |
|
|
} |
1368 |
|
|
|
1369 |
|
|
the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() ); |
1370 |
|
|
the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() ); |
1371 |
|
|
the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() ); |
1372 |
|
|
|
1373 |
|
|
if( the_atoms[current_atom_ndx]->isDirectional() ){ |
1374 |
|
|
|
1375 |
|
|
dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx]; |
1376 |
|
|
|
1377 |
|
|
rotMat[0][0] = 1.0; |
1378 |
|
|
rotMat[0][1] = 0.0; |
1379 |
|
|
rotMat[0][2] = 0.0; |
1380 |
|
|
|
1381 |
|
|
rotMat[1][0] = 0.0; |
1382 |
|
|
rotMat[1][1] = 1.0; |
1383 |
|
|
rotMat[1][2] = 0.0; |
1384 |
|
|
|
1385 |
|
|
rotMat[2][0] = 0.0; |
1386 |
|
|
rotMat[2][1] = 0.0; |
1387 |
|
|
rotMat[2][2] = 1.0; |
1388 |
|
|
|
1389 |
|
|
dAtom->setA( rotMat ); |
1390 |
|
|
} |
1391 |
|
|
|
1392 |
|
|
current_atom_ndx++; |
1393 |
|
|
} |
1394 |
|
|
|
1395 |
|
|
current_mol++; |
1396 |
|
|
current_comp_mol++; |
1397 |
|
|
|
1398 |
|
|
if( current_comp_mol >= components_nmol[current_comp] ){ |
1399 |
|
|
|
1400 |
|
|
current_comp_mol = 0; |
1401 |
|
|
current_comp++; |
1402 |
|
|
} |
1403 |
|
|
} |