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mmeineke |
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#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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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 |
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ExtendedSystem* the_extendedsystem; |
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mmeineke |
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int i, j; |
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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 |
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// get the ensemble and set up an extended system if we need it: |
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mmeineke |
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strcpy( ensemble, the_globals->getEnsemble() ); |
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gezelter |
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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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the_extendedsystem->setTargetPressure(the_globals->getTargetPressure()); |
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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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} else if ( !strcasecmp( ensemble, "NVE") ) { |
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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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} |
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mmeineke |
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strcpy( simnfo->ensemble, ensemble ); |
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strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
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simnfo->usePBC = the_globals->getPBC(); |
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mmeineke |
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if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
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gezelter |
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else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
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mmeineke |
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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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#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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// 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]; |
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comp_stamps = new MoleculeStamp*[n_components]; |
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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 |
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// given in each component |
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tot_nmol = 0; |
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for( i=0; i<n_components; i++ ){ |
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if( !the_components[i]->haveNMol() ){ |
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// we have a problem |
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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" ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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tot_nmol += the_components[i]->getNMol(); |
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components_nmol[i] = the_components[i]->getNMol(); |
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} |
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} |
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else{ |
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sprintf( painCave.errMsg, |
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"SimSetup error.\n" |
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"\tSorry, the ability to specify total" |
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" nMols and then give molfractions in the components\n" |
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"\tis not currently supported." |
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" Please give nMol in the components.\n" ); |
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painCave.isFatal = 1; |
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simError(); |
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// tot_nmol = the_globals->getNMol(); |
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// //we have the total number of molecules, now we check for molfractions |
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// for( i=0; i<n_components; i++ ){ |
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// if( !the_components[i]->haveMolFraction() ){ |
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// if( !the_components[i]->haveNMol() ){ |
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// //we have a problem |
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// std::cerr << "SimSetup error. Neither molFraction nor " |
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// << " nMol was given in component |
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} |
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#ifdef IS_MPI |
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strcpy( checkPointMsg, "Have the number of components" ); |
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MPIcheckPoint(); |
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#endif // is_mpi |
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// make an array of molecule stamps that match the components used. |
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// also extract the used stamps out into a separate linked list |
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simnfo->nComponents = n_components; |
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simnfo->componentsNmol = components_nmol; |
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simnfo->compStamps = comp_stamps; |
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simnfo->headStamp = new LinkedMolStamp(); |
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char* id; |
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LinkedMolStamp* headStamp = simnfo->headStamp; |
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LinkedMolStamp* currentStamp = NULL; |
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for( i=0; i<n_components; i++ ){ |
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id = the_components[i]->getType(); |
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comp_stamps[i] = NULL; |
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// check to make sure the component isn't already in the list |
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comp_stamps[i] = headStamp->match( id ); |
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if( comp_stamps[i] == NULL ){ |
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// extract the component from the list; |
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currentStamp = the_stamps->extractMolStamp( id ); |
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if( currentStamp == NULL ){ |
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sprintf( painCave.errMsg, |
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"SimSetup error: Component \"%s\" was not found in the " |
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"list of declared molecules\n", |
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id ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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headStamp->add( currentStamp ); |
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comp_stamps[i] = headStamp->match( id ); |
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} |
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} |
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#ifdef IS_MPI |
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strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
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MPIcheckPoint(); |
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#endif // is_mpi |
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// caclulate the number of atoms, bonds, bends and torsions |
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tot_atoms = 0; |
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tot_bonds = 0; |
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tot_bends = 0; |
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tot_torsions = 0; |
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for( i=0; i<n_components; i++ ){ |
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tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
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tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
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tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
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tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
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} |
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tot_SRI = tot_bonds + tot_bends + tot_torsions; |
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simnfo->n_atoms = tot_atoms; |
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simnfo->n_bonds = tot_bonds; |
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simnfo->n_bends = tot_bends; |
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simnfo->n_torsions = tot_torsions; |
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simnfo->n_SRI = tot_SRI; |
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simnfo->n_mol = tot_nmol; |
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#ifdef IS_MPI |
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// divide the molecules among processors here. |
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mpiSim = new mpiSimulation( simnfo ); |
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globalIndex = mpiSim->divideLabor(); |
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// set up the local variables |
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int localMol, allMol; |
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int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
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mmeineke |
422 |
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int* mol2proc = mpiSim->getMolToProcMap(); |
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int* molCompType = mpiSim->getMolComponentType(); |
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mmeineke |
377 |
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allMol = 0; |
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localMol = 0; |
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local_atoms = 0; |
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local_bonds = 0; |
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local_bends = 0; |
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local_torsions = 0; |
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for( i=0; i<n_components; i++ ){ |
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for( j=0; j<components_nmol[i]; j++ ){ |
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mmeineke |
422 |
if( mol2proc[j] == worldRank ){ |
280 |
mmeineke |
377 |
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local_atoms += comp_stamps[i]->getNAtoms(); |
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local_bonds += comp_stamps[i]->getNBonds(); |
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local_bends += comp_stamps[i]->getNBends(); |
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local_torsions += comp_stamps[i]->getNTorsions(); |
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localMol++; |
286 |
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} |
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allMol++; |
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} |
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} |
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local_SRI = local_bonds + local_bends + local_torsions; |
291 |
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293 |
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simnfo->n_atoms = mpiSim->getMyNlocal(); |
294 |
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if( local_atoms != simnfo->n_atoms ){ |
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sprintf( painCave.errMsg, |
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"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
298 |
mmeineke |
422 |
" localAtom (%d) are not equal.\n", |
299 |
mmeineke |
377 |
simnfo->n_atoms, |
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local_atoms ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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simnfo->n_bonds = local_bonds; |
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simnfo->n_bends = local_bends; |
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simnfo->n_torsions = local_torsions; |
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simnfo->n_SRI = local_SRI; |
309 |
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simnfo->n_mol = localMol; |
310 |
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strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
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MPIcheckPoint(); |
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#endif // is_mpi |
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318 |
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// create the atom and short range interaction arrays |
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320 |
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Atom::createArrays(simnfo->n_atoms); |
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the_atoms = new Atom*[simnfo->n_atoms]; |
322 |
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the_molecules = new Molecule[simnfo->n_mol]; |
323 |
mmeineke |
422 |
int molIndex; |
324 |
mmeineke |
377 |
|
325 |
mmeineke |
422 |
// initialize the molecule's stampID's |
326 |
mmeineke |
377 |
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327 |
mmeineke |
422 |
#ifdef IS_MPI |
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329 |
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molIndex = 0; |
331 |
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for(i=0; i<mpiSim->getTotNmol(); i++){ |
332 |
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333 |
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if(mol2proc[i] == worldRank ){ |
334 |
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the_molecules[molIndex].setStampID( molCompType[i] ); |
335 |
chuckv |
438 |
the_molecules[molIndex].setMyIndex( molIndex ); |
336 |
mmeineke |
422 |
molIndex++; |
337 |
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} |
338 |
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} |
339 |
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340 |
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#else // is_mpi |
341 |
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342 |
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molIndex = 0; |
343 |
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for(i=0; i<n_components; i++){ |
344 |
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for(j=0; j<components_nmol[i]; j++ ){ |
345 |
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the_molecules[molIndex].setStampID( i ); |
346 |
chuckv |
438 |
the_molecules[molIndex].setMyIndex( molIndex ); |
347 |
mmeineke |
422 |
molIndex++; |
348 |
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} |
349 |
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} |
350 |
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351 |
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352 |
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#endif // is_mpi |
353 |
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354 |
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355 |
mmeineke |
377 |
if( simnfo->n_SRI ){ |
356 |
mmeineke |
431 |
|
357 |
mmeineke |
412 |
Exclude::createArray(simnfo->n_SRI); |
358 |
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the_excludes = new Exclude*[simnfo->n_SRI]; |
359 |
mmeineke |
431 |
for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
360 |
mmeineke |
377 |
simnfo->globalExcludes = new int; |
361 |
chuckv |
438 |
simnfo->n_exclude = simnfo->n_SRI; |
362 |
mmeineke |
377 |
} |
363 |
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else{ |
364 |
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365 |
mmeineke |
412 |
Exclude::createArray( 1 ); |
366 |
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the_excludes = new Exclude*; |
367 |
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the_excludes[0] = new Exclude(0); |
368 |
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the_excludes[0]->setPair( 0,0 ); |
369 |
mmeineke |
377 |
simnfo->globalExcludes = new int; |
370 |
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simnfo->globalExcludes[0] = 0; |
371 |
mmeineke |
412 |
simnfo->n_exclude = 0; |
372 |
mmeineke |
377 |
} |
373 |
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374 |
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// set the arrays into the SimInfo object |
375 |
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376 |
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simnfo->atoms = the_atoms; |
377 |
mmeineke |
429 |
simnfo->molecules = the_molecules; |
378 |
mmeineke |
377 |
simnfo->nGlobalExcludes = 0; |
379 |
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simnfo->excludes = the_excludes; |
380 |
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381 |
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382 |
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// get some of the tricky things that may still be in the globals |
383 |
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384 |
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385 |
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if( the_globals->haveBox() ){ |
386 |
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simnfo->box_x = the_globals->getBox(); |
387 |
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simnfo->box_y = the_globals->getBox(); |
388 |
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simnfo->box_z = the_globals->getBox(); |
389 |
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|
} |
390 |
|
|
else if( the_globals->haveDensity() ){ |
391 |
|
|
|
392 |
|
|
double vol; |
393 |
|
|
vol = (double)tot_nmol / the_globals->getDensity(); |
394 |
|
|
simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) ); |
395 |
|
|
simnfo->box_y = simnfo->box_x; |
396 |
|
|
simnfo->box_z = simnfo->box_x; |
397 |
|
|
} |
398 |
|
|
else{ |
399 |
|
|
if( !the_globals->haveBoxX() ){ |
400 |
|
|
sprintf( painCave.errMsg, |
401 |
|
|
"SimSetup error, no periodic BoxX size given.\n" ); |
402 |
|
|
painCave.isFatal = 1; |
403 |
|
|
simError(); |
404 |
|
|
} |
405 |
|
|
simnfo->box_x = the_globals->getBoxX(); |
406 |
|
|
|
407 |
|
|
if( !the_globals->haveBoxY() ){ |
408 |
|
|
sprintf( painCave.errMsg, |
409 |
|
|
"SimSetup error, no periodic BoxY size given.\n" ); |
410 |
|
|
painCave.isFatal = 1; |
411 |
|
|
simError(); |
412 |
|
|
} |
413 |
|
|
simnfo->box_y = the_globals->getBoxY(); |
414 |
|
|
|
415 |
|
|
if( !the_globals->haveBoxZ() ){ |
416 |
|
|
sprintf( painCave.errMsg, |
417 |
|
|
"SimSetup error, no periodic BoxZ size given.\n" ); |
418 |
|
|
painCave.isFatal = 1; |
419 |
|
|
simError(); |
420 |
|
|
} |
421 |
|
|
simnfo->box_z = the_globals->getBoxZ(); |
422 |
|
|
} |
423 |
|
|
|
424 |
|
|
#ifdef IS_MPI |
425 |
|
|
strcpy( checkPointMsg, "Box size set up" ); |
426 |
|
|
MPIcheckPoint(); |
427 |
|
|
#endif // is_mpi |
428 |
|
|
|
429 |
|
|
|
430 |
|
|
// initialize the arrays |
431 |
|
|
|
432 |
|
|
the_ff->setSimInfo( simnfo ); |
433 |
|
|
|
434 |
mmeineke |
422 |
makeMolecules(); |
435 |
mmeineke |
377 |
simnfo->identArray = new int[simnfo->n_atoms]; |
436 |
|
|
for(i=0; i<simnfo->n_atoms; i++){ |
437 |
|
|
simnfo->identArray[i] = the_atoms[i]->getIdent(); |
438 |
|
|
} |
439 |
|
|
|
440 |
gezelter |
394 |
if (the_globals->getUseRF() ) { |
441 |
|
|
simnfo->useReactionField = 1; |
442 |
|
|
|
443 |
|
|
if( !the_globals->haveECR() ){ |
444 |
|
|
sprintf( painCave.errMsg, |
445 |
|
|
"SimSetup Warning: using default value of 1/2 the smallest " |
446 |
|
|
"box length for the electrostaticCutoffRadius.\n" |
447 |
|
|
"I hope you have a very fast processor!\n"); |
448 |
|
|
painCave.isFatal = 0; |
449 |
|
|
simError(); |
450 |
|
|
double smallest; |
451 |
|
|
smallest = simnfo->box_x; |
452 |
|
|
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
453 |
|
|
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
454 |
|
|
simnfo->ecr = 0.5 * smallest; |
455 |
|
|
} else { |
456 |
|
|
simnfo->ecr = the_globals->getECR(); |
457 |
|
|
} |
458 |
mmeineke |
377 |
|
459 |
gezelter |
394 |
if( !the_globals->haveEST() ){ |
460 |
|
|
sprintf( painCave.errMsg, |
461 |
|
|
"SimSetup Warning: using default value of 0.05 * the " |
462 |
|
|
"electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
463 |
|
|
); |
464 |
|
|
painCave.isFatal = 0; |
465 |
|
|
simError(); |
466 |
|
|
simnfo->est = 0.05 * simnfo->ecr; |
467 |
|
|
} else { |
468 |
|
|
simnfo->est = the_globals->getEST(); |
469 |
|
|
} |
470 |
|
|
|
471 |
|
|
if(!the_globals->haveDielectric() ){ |
472 |
|
|
sprintf( painCave.errMsg, |
473 |
|
|
"SimSetup Error: You are trying to use Reaction Field without" |
474 |
|
|
"setting a dielectric constant!\n" |
475 |
|
|
); |
476 |
|
|
painCave.isFatal = 1; |
477 |
|
|
simError(); |
478 |
|
|
} |
479 |
|
|
simnfo->dielectric = the_globals->getDielectric(); |
480 |
|
|
} else { |
481 |
|
|
if (simnfo->n_dipoles) { |
482 |
|
|
|
483 |
|
|
if( !the_globals->haveECR() ){ |
484 |
|
|
sprintf( painCave.errMsg, |
485 |
|
|
"SimSetup Warning: using default value of 1/2 the smallest" |
486 |
|
|
"box length for the electrostaticCutoffRadius.\n" |
487 |
|
|
"I hope you have a very fast processor!\n"); |
488 |
|
|
painCave.isFatal = 0; |
489 |
|
|
simError(); |
490 |
|
|
double smallest; |
491 |
|
|
smallest = simnfo->box_x; |
492 |
|
|
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
493 |
|
|
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
494 |
|
|
simnfo->ecr = 0.5 * smallest; |
495 |
|
|
} else { |
496 |
|
|
simnfo->ecr = the_globals->getECR(); |
497 |
|
|
} |
498 |
|
|
|
499 |
|
|
if( !the_globals->haveEST() ){ |
500 |
|
|
sprintf( painCave.errMsg, |
501 |
|
|
"SimSetup Warning: using default value of 5% of the" |
502 |
|
|
"electrostaticCutoffRadius for the " |
503 |
|
|
"electrostaticSkinThickness\n" |
504 |
|
|
); |
505 |
|
|
painCave.isFatal = 0; |
506 |
|
|
simError(); |
507 |
|
|
simnfo->est = 0.05 * simnfo->ecr; |
508 |
|
|
} else { |
509 |
|
|
simnfo->est = the_globals->getEST(); |
510 |
|
|
} |
511 |
|
|
} |
512 |
|
|
} |
513 |
mmeineke |
377 |
|
514 |
gezelter |
394 |
#ifdef IS_MPI |
515 |
|
|
strcpy( checkPointMsg, "electrostatic parameters check out" ); |
516 |
|
|
MPIcheckPoint(); |
517 |
|
|
#endif // is_mpi |
518 |
mmeineke |
377 |
|
519 |
|
|
if( the_globals->haveInitialConfig() ){ |
520 |
|
|
|
521 |
|
|
InitializeFromFile* fileInit; |
522 |
|
|
#ifdef IS_MPI // is_mpi |
523 |
|
|
if( worldRank == 0 ){ |
524 |
|
|
#endif //is_mpi |
525 |
|
|
fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
526 |
|
|
#ifdef IS_MPI |
527 |
|
|
}else fileInit = new InitializeFromFile( NULL ); |
528 |
|
|
#endif |
529 |
|
|
fileInit->read_xyz( simnfo ); // default velocities on |
530 |
|
|
|
531 |
|
|
delete fileInit; |
532 |
|
|
} |
533 |
|
|
else{ |
534 |
|
|
|
535 |
|
|
#ifdef IS_MPI |
536 |
|
|
|
537 |
|
|
// no init from bass |
538 |
|
|
|
539 |
|
|
sprintf( painCave.errMsg, |
540 |
|
|
"Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
541 |
|
|
painCave.isFatal; |
542 |
|
|
simError(); |
543 |
|
|
|
544 |
|
|
#else |
545 |
|
|
|
546 |
|
|
initFromBass(); |
547 |
|
|
|
548 |
|
|
|
549 |
|
|
#endif |
550 |
|
|
} |
551 |
|
|
|
552 |
|
|
#ifdef IS_MPI |
553 |
|
|
strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
554 |
|
|
MPIcheckPoint(); |
555 |
|
|
#endif // is_mpi |
556 |
|
|
|
557 |
|
|
|
558 |
|
|
|
559 |
|
|
|
560 |
|
|
|
561 |
|
|
|
562 |
|
|
|
563 |
|
|
#ifdef IS_MPI |
564 |
|
|
if( worldRank == 0 ){ |
565 |
|
|
#endif // is_mpi |
566 |
|
|
|
567 |
|
|
if( the_globals->haveFinalConfig() ){ |
568 |
|
|
strcpy( simnfo->finalName, the_globals->getFinalConfig() ); |
569 |
|
|
} |
570 |
|
|
else{ |
571 |
|
|
strcpy( simnfo->finalName, inFileName ); |
572 |
|
|
char* endTest; |
573 |
|
|
int nameLength = strlen( simnfo->finalName ); |
574 |
|
|
endTest = &(simnfo->finalName[nameLength - 5]); |
575 |
|
|
if( !strcmp( endTest, ".bass" ) ){ |
576 |
|
|
strcpy( endTest, ".eor" ); |
577 |
|
|
} |
578 |
|
|
else if( !strcmp( endTest, ".BASS" ) ){ |
579 |
|
|
strcpy( endTest, ".eor" ); |
580 |
|
|
} |
581 |
|
|
else{ |
582 |
|
|
endTest = &(simnfo->finalName[nameLength - 4]); |
583 |
|
|
if( !strcmp( endTest, ".bss" ) ){ |
584 |
|
|
strcpy( endTest, ".eor" ); |
585 |
|
|
} |
586 |
|
|
else if( !strcmp( endTest, ".mdl" ) ){ |
587 |
|
|
strcpy( endTest, ".eor" ); |
588 |
|
|
} |
589 |
|
|
else{ |
590 |
|
|
strcat( simnfo->finalName, ".eor" ); |
591 |
|
|
} |
592 |
|
|
} |
593 |
|
|
} |
594 |
|
|
|
595 |
|
|
// make the sample and status out names |
596 |
|
|
|
597 |
|
|
strcpy( simnfo->sampleName, inFileName ); |
598 |
|
|
char* endTest; |
599 |
|
|
int nameLength = strlen( simnfo->sampleName ); |
600 |
|
|
endTest = &(simnfo->sampleName[nameLength - 5]); |
601 |
|
|
if( !strcmp( endTest, ".bass" ) ){ |
602 |
|
|
strcpy( endTest, ".dump" ); |
603 |
|
|
} |
604 |
|
|
else if( !strcmp( endTest, ".BASS" ) ){ |
605 |
|
|
strcpy( endTest, ".dump" ); |
606 |
|
|
} |
607 |
|
|
else{ |
608 |
|
|
endTest = &(simnfo->sampleName[nameLength - 4]); |
609 |
|
|
if( !strcmp( endTest, ".bss" ) ){ |
610 |
|
|
strcpy( endTest, ".dump" ); |
611 |
|
|
} |
612 |
|
|
else if( !strcmp( endTest, ".mdl" ) ){ |
613 |
|
|
strcpy( endTest, ".dump" ); |
614 |
|
|
} |
615 |
|
|
else{ |
616 |
|
|
strcat( simnfo->sampleName, ".dump" ); |
617 |
|
|
} |
618 |
|
|
} |
619 |
|
|
|
620 |
|
|
strcpy( simnfo->statusName, inFileName ); |
621 |
|
|
nameLength = strlen( simnfo->statusName ); |
622 |
|
|
endTest = &(simnfo->statusName[nameLength - 5]); |
623 |
|
|
if( !strcmp( endTest, ".bass" ) ){ |
624 |
|
|
strcpy( endTest, ".stat" ); |
625 |
|
|
} |
626 |
|
|
else if( !strcmp( endTest, ".BASS" ) ){ |
627 |
|
|
strcpy( endTest, ".stat" ); |
628 |
|
|
} |
629 |
|
|
else{ |
630 |
|
|
endTest = &(simnfo->statusName[nameLength - 4]); |
631 |
|
|
if( !strcmp( endTest, ".bss" ) ){ |
632 |
|
|
strcpy( endTest, ".stat" ); |
633 |
|
|
} |
634 |
|
|
else if( !strcmp( endTest, ".mdl" ) ){ |
635 |
|
|
strcpy( endTest, ".stat" ); |
636 |
|
|
} |
637 |
|
|
else{ |
638 |
|
|
strcat( simnfo->statusName, ".stat" ); |
639 |
|
|
} |
640 |
|
|
} |
641 |
|
|
|
642 |
|
|
#ifdef IS_MPI |
643 |
|
|
} |
644 |
|
|
#endif // is_mpi |
645 |
|
|
|
646 |
|
|
// set the status, sample, and themal kick times |
647 |
|
|
|
648 |
|
|
if( the_globals->haveSampleTime() ){ |
649 |
|
|
simnfo->sampleTime = the_globals->getSampleTime(); |
650 |
|
|
simnfo->statusTime = simnfo->sampleTime; |
651 |
|
|
simnfo->thermalTime = simnfo->sampleTime; |
652 |
|
|
} |
653 |
|
|
else{ |
654 |
|
|
simnfo->sampleTime = the_globals->getRunTime(); |
655 |
|
|
simnfo->statusTime = simnfo->sampleTime; |
656 |
|
|
simnfo->thermalTime = simnfo->sampleTime; |
657 |
|
|
} |
658 |
|
|
|
659 |
|
|
if( the_globals->haveStatusTime() ){ |
660 |
|
|
simnfo->statusTime = the_globals->getStatusTime(); |
661 |
|
|
} |
662 |
|
|
|
663 |
|
|
if( the_globals->haveThermalTime() ){ |
664 |
|
|
simnfo->thermalTime = the_globals->getThermalTime(); |
665 |
|
|
} |
666 |
|
|
|
667 |
|
|
// check for the temperature set flag |
668 |
|
|
|
669 |
|
|
if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
670 |
|
|
|
671 |
|
|
|
672 |
|
|
// // make the longe range forces and the integrator |
673 |
|
|
|
674 |
|
|
// new AllLong( simnfo ); |
675 |
|
|
|
676 |
gezelter |
466 |
if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic(simnfo, |
677 |
|
|
the_ff, |
678 |
|
|
the_extendedsystem); |
679 |
|
|
if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, |
680 |
|
|
the_ff, |
681 |
|
|
the_extendedsystem ); |
682 |
mmeineke |
377 |
|
683 |
chuckv |
432 |
#ifdef IS_MPI |
684 |
|
|
mpiSim->mpiRefresh(); |
685 |
|
|
#endif |
686 |
mmeineke |
377 |
|
687 |
chuckv |
432 |
// initialize the Fortran |
688 |
mmeineke |
377 |
|
689 |
chuckv |
432 |
|
690 |
mmeineke |
377 |
simnfo->refreshSim(); |
691 |
|
|
|
692 |
|
|
if( !strcmp( simnfo->mixingRule, "standard") ){ |
693 |
|
|
the_ff->initForceField( LB_MIXING_RULE ); |
694 |
|
|
} |
695 |
|
|
else if( !strcmp( simnfo->mixingRule, "explicit") ){ |
696 |
|
|
the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
697 |
|
|
} |
698 |
|
|
else{ |
699 |
|
|
sprintf( painCave.errMsg, |
700 |
|
|
"SimSetup Error: unknown mixing rule -> \"%s\"\n", |
701 |
|
|
simnfo->mixingRule ); |
702 |
|
|
painCave.isFatal = 1; |
703 |
|
|
simError(); |
704 |
|
|
} |
705 |
|
|
|
706 |
|
|
|
707 |
|
|
#ifdef IS_MPI |
708 |
|
|
strcpy( checkPointMsg, |
709 |
|
|
"Successfully intialized the mixingRule for Fortran." ); |
710 |
|
|
MPIcheckPoint(); |
711 |
|
|
#endif // is_mpi |
712 |
|
|
} |
713 |
|
|
|
714 |
mmeineke |
407 |
|
715 |
|
|
void SimSetup::makeMolecules( void ){ |
716 |
|
|
|
717 |
mmeineke |
412 |
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
718 |
mmeineke |
407 |
molInit info; |
719 |
|
|
DirectionalAtom* dAtom; |
720 |
mmeineke |
412 |
LinkedAssign* extras; |
721 |
|
|
LinkedAssign* current_extra; |
722 |
mmeineke |
407 |
AtomStamp* currentAtom; |
723 |
|
|
BondStamp* currentBond; |
724 |
|
|
BendStamp* currentBend; |
725 |
|
|
TorsionStamp* currentTorsion; |
726 |
mmeineke |
427 |
|
727 |
|
|
bond_pair* theBonds; |
728 |
|
|
bend_set* theBends; |
729 |
|
|
torsion_set* theTorsions; |
730 |
|
|
|
731 |
mmeineke |
407 |
|
732 |
|
|
//init the forceField paramters |
733 |
|
|
|
734 |
|
|
the_ff->readParams(); |
735 |
|
|
|
736 |
|
|
|
737 |
mmeineke |
427 |
// init the atoms |
738 |
mmeineke |
407 |
|
739 |
mmeineke |
427 |
double ux, uy, uz, u, uSqr; |
740 |
|
|
|
741 |
mmeineke |
407 |
atomOffset = 0; |
742 |
mmeineke |
412 |
excludeOffset = 0; |
743 |
mmeineke |
407 |
for(i=0; i<simnfo->n_mol; i++){ |
744 |
|
|
|
745 |
|
|
stampID = the_molecules[i].getStampID(); |
746 |
|
|
|
747 |
|
|
info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
748 |
|
|
info.nBonds = comp_stamps[stampID]->getNBonds(); |
749 |
|
|
info.nBends = comp_stamps[stampID]->getNBends(); |
750 |
|
|
info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
751 |
mmeineke |
412 |
info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
752 |
|
|
|
753 |
mmeineke |
407 |
info.myAtoms = &the_atoms[atomOffset]; |
754 |
mmeineke |
412 |
info.myExcludes = &the_excludes[excludeOffset]; |
755 |
mmeineke |
407 |
info.myBonds = new Bond*[info.nBonds]; |
756 |
|
|
info.myBends = new Bend*[info.nBends]; |
757 |
mmeineke |
427 |
info.myTorsions = new Torsion*[info.nTorsions]; |
758 |
mmeineke |
407 |
|
759 |
|
|
theBonds = new bond_pair[info.nBonds]; |
760 |
|
|
theBends = new bend_set[info.nBends]; |
761 |
|
|
theTorsions = new torsion_set[info.nTorsions]; |
762 |
|
|
|
763 |
|
|
// make the Atoms |
764 |
|
|
|
765 |
|
|
for(j=0; j<info.nAtoms; j++){ |
766 |
|
|
|
767 |
mmeineke |
427 |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
768 |
mmeineke |
407 |
if( currentAtom->haveOrientation() ){ |
769 |
|
|
|
770 |
|
|
dAtom = new DirectionalAtom(j + atomOffset); |
771 |
|
|
simnfo->n_oriented++; |
772 |
|
|
info.myAtoms[j] = dAtom; |
773 |
|
|
|
774 |
|
|
ux = currentAtom->getOrntX(); |
775 |
|
|
uy = currentAtom->getOrntY(); |
776 |
|
|
uz = currentAtom->getOrntZ(); |
777 |
|
|
|
778 |
|
|
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
779 |
|
|
|
780 |
|
|
u = sqrt( uSqr ); |
781 |
|
|
ux = ux / u; |
782 |
|
|
uy = uy / u; |
783 |
|
|
uz = uz / u; |
784 |
|
|
|
785 |
|
|
dAtom->setSUx( ux ); |
786 |
|
|
dAtom->setSUy( uy ); |
787 |
|
|
dAtom->setSUz( uz ); |
788 |
|
|
} |
789 |
|
|
else{ |
790 |
|
|
info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
791 |
|
|
} |
792 |
|
|
info.myAtoms[j]->setType( currentAtom->getType() ); |
793 |
|
|
|
794 |
|
|
#ifdef IS_MPI |
795 |
|
|
|
796 |
|
|
info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
797 |
|
|
|
798 |
|
|
#endif // is_mpi |
799 |
|
|
} |
800 |
|
|
|
801 |
|
|
// make the bonds |
802 |
mmeineke |
412 |
for(j=0; j<info.nBonds; j++){ |
803 |
mmeineke |
407 |
|
804 |
|
|
currentBond = comp_stamps[stampID]->getBond( j ); |
805 |
|
|
theBonds[j].a = currentBond->getA() + atomOffset; |
806 |
|
|
theBonds[j].b = currentBond->getB() + atomOffset; |
807 |
|
|
|
808 |
mmeineke |
435 |
exI = theBonds[j].a; |
809 |
|
|
exJ = theBonds[j].b; |
810 |
mmeineke |
407 |
|
811 |
|
|
// exclude_I must always be the smaller of the pair |
812 |
|
|
if( exI > exJ ){ |
813 |
|
|
tempEx = exI; |
814 |
|
|
exI = exJ; |
815 |
|
|
exJ = tempEx; |
816 |
|
|
} |
817 |
|
|
#ifdef IS_MPI |
818 |
mmeineke |
412 |
tempEx = exI; |
819 |
|
|
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
820 |
|
|
tempEx = exJ; |
821 |
|
|
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
822 |
mmeineke |
407 |
|
823 |
mmeineke |
412 |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
824 |
|
|
#else // isn't MPI |
825 |
mmeineke |
435 |
|
826 |
mmeineke |
412 |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
827 |
|
|
#endif //is_mpi |
828 |
|
|
} |
829 |
|
|
excludeOffset += info.nBonds; |
830 |
|
|
|
831 |
|
|
//make the bends |
832 |
|
|
for(j=0; j<info.nBends; j++){ |
833 |
mmeineke |
407 |
|
834 |
mmeineke |
412 |
currentBend = comp_stamps[stampID]->getBend( j ); |
835 |
|
|
theBends[j].a = currentBend->getA() + atomOffset; |
836 |
|
|
theBends[j].b = currentBend->getB() + atomOffset; |
837 |
|
|
theBends[j].c = currentBend->getC() + atomOffset; |
838 |
|
|
|
839 |
|
|
if( currentBend->haveExtras() ){ |
840 |
|
|
|
841 |
mmeineke |
427 |
extras = currentBend->getExtras(); |
842 |
mmeineke |
412 |
current_extra = extras; |
843 |
|
|
|
844 |
|
|
while( current_extra != NULL ){ |
845 |
|
|
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
846 |
|
|
|
847 |
|
|
switch( current_extra->getType() ){ |
848 |
|
|
|
849 |
|
|
case 0: |
850 |
|
|
theBends[j].ghost = |
851 |
|
|
current_extra->getInt() + atomOffset; |
852 |
|
|
theBends[j].isGhost = 1; |
853 |
|
|
break; |
854 |
|
|
|
855 |
|
|
case 1: |
856 |
|
|
theBends[j].ghost = |
857 |
|
|
(int)current_extra->getDouble() + atomOffset; |
858 |
|
|
theBends[j].isGhost = 1; |
859 |
|
|
break; |
860 |
|
|
|
861 |
|
|
default: |
862 |
|
|
sprintf( painCave.errMsg, |
863 |
chuckv |
434 |
"SimSetup Error: ghostVectorSource was neither a " |
864 |
mmeineke |
412 |
"double nor an int.\n" |
865 |
|
|
"-->Bend[%d] in %s\n", |
866 |
|
|
j, comp_stamps[stampID]->getID() ); |
867 |
|
|
painCave.isFatal = 1; |
868 |
|
|
simError(); |
869 |
|
|
} |
870 |
|
|
} |
871 |
|
|
|
872 |
|
|
else{ |
873 |
|
|
|
874 |
|
|
sprintf( painCave.errMsg, |
875 |
|
|
"SimSetup Error: unhandled bend assignment:\n" |
876 |
|
|
" -->%s in Bend[%d] in %s\n", |
877 |
|
|
current_extra->getlhs(), |
878 |
|
|
j, comp_stamps[stampID]->getID() ); |
879 |
|
|
painCave.isFatal = 1; |
880 |
|
|
simError(); |
881 |
|
|
} |
882 |
|
|
|
883 |
|
|
current_extra = current_extra->getNext(); |
884 |
|
|
} |
885 |
|
|
} |
886 |
|
|
|
887 |
|
|
if( !theBends[j].isGhost ){ |
888 |
|
|
|
889 |
|
|
exI = theBends[j].a; |
890 |
|
|
exJ = theBends[j].c; |
891 |
|
|
} |
892 |
|
|
else{ |
893 |
|
|
|
894 |
|
|
exI = theBends[j].a; |
895 |
|
|
exJ = theBends[j].b; |
896 |
|
|
} |
897 |
|
|
|
898 |
|
|
// exclude_I must always be the smaller of the pair |
899 |
|
|
if( exI > exJ ){ |
900 |
|
|
tempEx = exI; |
901 |
|
|
exI = exJ; |
902 |
|
|
exJ = tempEx; |
903 |
|
|
} |
904 |
|
|
#ifdef IS_MPI |
905 |
|
|
tempEx = exI; |
906 |
|
|
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
907 |
|
|
tempEx = exJ; |
908 |
|
|
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
909 |
|
|
|
910 |
|
|
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
911 |
mmeineke |
407 |
#else // isn't MPI |
912 |
mmeineke |
412 |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
913 |
|
|
#endif //is_mpi |
914 |
|
|
} |
915 |
|
|
excludeOffset += info.nBends; |
916 |
|
|
|
917 |
|
|
for(j=0; j<info.nTorsions; j++){ |
918 |
mmeineke |
407 |
|
919 |
mmeineke |
412 |
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
920 |
|
|
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
921 |
|
|
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
922 |
|
|
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
923 |
|
|
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
924 |
|
|
|
925 |
|
|
exI = theTorsions[j].a; |
926 |
|
|
exJ = theTorsions[j].d; |
927 |
mmeineke |
407 |
|
928 |
mmeineke |
412 |
// exclude_I must always be the smaller of the pair |
929 |
|
|
if( exI > exJ ){ |
930 |
|
|
tempEx = exI; |
931 |
|
|
exI = exJ; |
932 |
|
|
exJ = tempEx; |
933 |
|
|
} |
934 |
|
|
#ifdef IS_MPI |
935 |
|
|
tempEx = exI; |
936 |
|
|
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
937 |
|
|
tempEx = exJ; |
938 |
|
|
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
939 |
|
|
|
940 |
|
|
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
941 |
|
|
#else // isn't MPI |
942 |
|
|
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
943 |
mmeineke |
407 |
#endif //is_mpi |
944 |
mmeineke |
412 |
} |
945 |
|
|
excludeOffset += info.nTorsions; |
946 |
|
|
|
947 |
mmeineke |
407 |
|
948 |
mmeineke |
414 |
// send the arrays off to the forceField for init. |
949 |
mmeineke |
407 |
|
950 |
mmeineke |
414 |
the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
951 |
|
|
the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
952 |
|
|
the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
953 |
|
|
the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
954 |
mmeineke |
407 |
|
955 |
|
|
|
956 |
mmeineke |
414 |
the_molecules[i].initialize( info ); |
957 |
chuckv |
438 |
|
958 |
|
|
|
959 |
mmeineke |
414 |
atomOffset += info.nAtoms; |
960 |
mmeineke |
427 |
delete[] theBonds; |
961 |
|
|
delete[] theBends; |
962 |
|
|
delete[] theTorsions; |
963 |
mmeineke |
414 |
} |
964 |
mmeineke |
407 |
|
965 |
chuckv |
434 |
#ifdef IS_MPI |
966 |
|
|
sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
967 |
|
|
MPIcheckPoint(); |
968 |
|
|
#endif // is_mpi |
969 |
|
|
|
970 |
mmeineke |
414 |
// clean up the forcefield |
971 |
mmeineke |
420 |
the_ff->calcRcut(); |
972 |
mmeineke |
414 |
the_ff->cleanMe(); |
973 |
chuckv |
434 |
|
974 |
mmeineke |
414 |
} |
975 |
mmeineke |
407 |
|
976 |
mmeineke |
377 |
void SimSetup::initFromBass( void ){ |
977 |
|
|
|
978 |
|
|
int i, j, k; |
979 |
|
|
int n_cells; |
980 |
|
|
double cellx, celly, cellz; |
981 |
|
|
double temp1, temp2, temp3; |
982 |
|
|
int n_per_extra; |
983 |
|
|
int n_extra; |
984 |
|
|
int have_extra, done; |
985 |
|
|
|
986 |
|
|
temp1 = (double)tot_nmol / 4.0; |
987 |
|
|
temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
988 |
|
|
temp3 = ceil( temp2 ); |
989 |
|
|
|
990 |
|
|
have_extra =0; |
991 |
|
|
if( temp2 < temp3 ){ // we have a non-complete lattice |
992 |
|
|
have_extra =1; |
993 |
|
|
|
994 |
|
|
n_cells = (int)temp3 - 1; |
995 |
|
|
cellx = simnfo->box_x / temp3; |
996 |
|
|
celly = simnfo->box_y / temp3; |
997 |
|
|
cellz = simnfo->box_z / temp3; |
998 |
|
|
n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
999 |
|
|
temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
1000 |
|
|
n_per_extra = (int)ceil( temp1 ); |
1001 |
|
|
|
1002 |
|
|
if( n_per_extra > 4){ |
1003 |
|
|
sprintf( painCave.errMsg, |
1004 |
|
|
"SimSetup error. There has been an error in constructing" |
1005 |
|
|
" the non-complete lattice.\n" ); |
1006 |
|
|
painCave.isFatal = 1; |
1007 |
|
|
simError(); |
1008 |
|
|
} |
1009 |
|
|
} |
1010 |
|
|
else{ |
1011 |
|
|
n_cells = (int)temp3; |
1012 |
|
|
cellx = simnfo->box_x / temp3; |
1013 |
|
|
celly = simnfo->box_y / temp3; |
1014 |
|
|
cellz = simnfo->box_z / temp3; |
1015 |
|
|
} |
1016 |
|
|
|
1017 |
|
|
current_mol = 0; |
1018 |
|
|
current_comp_mol = 0; |
1019 |
|
|
current_comp = 0; |
1020 |
|
|
current_atom_ndx = 0; |
1021 |
|
|
|
1022 |
|
|
for( i=0; i < n_cells ; i++ ){ |
1023 |
|
|
for( j=0; j < n_cells; j++ ){ |
1024 |
|
|
for( k=0; k < n_cells; k++ ){ |
1025 |
|
|
|
1026 |
|
|
makeElement( i * cellx, |
1027 |
|
|
j * celly, |
1028 |
|
|
k * cellz ); |
1029 |
|
|
|
1030 |
|
|
makeElement( i * cellx + 0.5 * cellx, |
1031 |
|
|
j * celly + 0.5 * celly, |
1032 |
|
|
k * cellz ); |
1033 |
|
|
|
1034 |
|
|
makeElement( i * cellx, |
1035 |
|
|
j * celly + 0.5 * celly, |
1036 |
|
|
k * cellz + 0.5 * cellz ); |
1037 |
|
|
|
1038 |
|
|
makeElement( i * cellx + 0.5 * cellx, |
1039 |
|
|
j * celly, |
1040 |
|
|
k * cellz + 0.5 * cellz ); |
1041 |
|
|
} |
1042 |
|
|
} |
1043 |
|
|
} |
1044 |
|
|
|
1045 |
|
|
if( have_extra ){ |
1046 |
|
|
done = 0; |
1047 |
|
|
|
1048 |
|
|
int start_ndx; |
1049 |
|
|
for( i=0; i < (n_cells+1) && !done; i++ ){ |
1050 |
|
|
for( j=0; j < (n_cells+1) && !done; j++ ){ |
1051 |
|
|
|
1052 |
|
|
if( i < n_cells ){ |
1053 |
|
|
|
1054 |
|
|
if( j < n_cells ){ |
1055 |
|
|
start_ndx = n_cells; |
1056 |
|
|
} |
1057 |
|
|
else start_ndx = 0; |
1058 |
|
|
} |
1059 |
|
|
else start_ndx = 0; |
1060 |
|
|
|
1061 |
|
|
for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
1062 |
|
|
|
1063 |
|
|
makeElement( i * cellx, |
1064 |
|
|
j * celly, |
1065 |
|
|
k * cellz ); |
1066 |
|
|
done = ( current_mol >= tot_nmol ); |
1067 |
|
|
|
1068 |
|
|
if( !done && n_per_extra > 1 ){ |
1069 |
|
|
makeElement( i * cellx + 0.5 * cellx, |
1070 |
|
|
j * celly + 0.5 * celly, |
1071 |
|
|
k * cellz ); |
1072 |
|
|
done = ( current_mol >= tot_nmol ); |
1073 |
|
|
} |
1074 |
|
|
|
1075 |
|
|
if( !done && n_per_extra > 2){ |
1076 |
|
|
makeElement( i * cellx, |
1077 |
|
|
j * celly + 0.5 * celly, |
1078 |
|
|
k * cellz + 0.5 * cellz ); |
1079 |
|
|
done = ( current_mol >= tot_nmol ); |
1080 |
|
|
} |
1081 |
|
|
|
1082 |
|
|
if( !done && n_per_extra > 3){ |
1083 |
|
|
makeElement( i * cellx + 0.5 * cellx, |
1084 |
|
|
j * celly, |
1085 |
|
|
k * cellz + 0.5 * cellz ); |
1086 |
|
|
done = ( current_mol >= tot_nmol ); |
1087 |
|
|
} |
1088 |
|
|
} |
1089 |
|
|
} |
1090 |
|
|
} |
1091 |
|
|
} |
1092 |
|
|
|
1093 |
|
|
|
1094 |
|
|
for( i=0; i<simnfo->n_atoms; i++ ){ |
1095 |
|
|
simnfo->atoms[i]->set_vx( 0.0 ); |
1096 |
|
|
simnfo->atoms[i]->set_vy( 0.0 ); |
1097 |
|
|
simnfo->atoms[i]->set_vz( 0.0 ); |
1098 |
|
|
} |
1099 |
|
|
} |
1100 |
|
|
|
1101 |
|
|
void SimSetup::makeElement( double x, double y, double z ){ |
1102 |
|
|
|
1103 |
|
|
int k; |
1104 |
|
|
AtomStamp* current_atom; |
1105 |
|
|
DirectionalAtom* dAtom; |
1106 |
|
|
double rotMat[3][3]; |
1107 |
|
|
|
1108 |
|
|
for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
1109 |
|
|
|
1110 |
|
|
current_atom = comp_stamps[current_comp]->getAtom( k ); |
1111 |
|
|
if( !current_atom->havePosition() ){ |
1112 |
|
|
sprintf( painCave.errMsg, |
1113 |
|
|
"SimSetup:initFromBass error.\n" |
1114 |
|
|
"\tComponent %s, atom %s does not have a position specified.\n" |
1115 |
|
|
"\tThe initialization routine is unable to give a start" |
1116 |
|
|
" position.\n", |
1117 |
|
|
comp_stamps[current_comp]->getID(), |
1118 |
|
|
current_atom->getType() ); |
1119 |
|
|
painCave.isFatal = 1; |
1120 |
|
|
simError(); |
1121 |
|
|
} |
1122 |
|
|
|
1123 |
|
|
the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() ); |
1124 |
|
|
the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() ); |
1125 |
|
|
the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() ); |
1126 |
|
|
|
1127 |
|
|
if( the_atoms[current_atom_ndx]->isDirectional() ){ |
1128 |
|
|
|
1129 |
|
|
dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx]; |
1130 |
|
|
|
1131 |
|
|
rotMat[0][0] = 1.0; |
1132 |
|
|
rotMat[0][1] = 0.0; |
1133 |
|
|
rotMat[0][2] = 0.0; |
1134 |
|
|
|
1135 |
|
|
rotMat[1][0] = 0.0; |
1136 |
|
|
rotMat[1][1] = 1.0; |
1137 |
|
|
rotMat[1][2] = 0.0; |
1138 |
|
|
|
1139 |
|
|
rotMat[2][0] = 0.0; |
1140 |
|
|
rotMat[2][1] = 0.0; |
1141 |
|
|
rotMat[2][2] = 1.0; |
1142 |
|
|
|
1143 |
|
|
dAtom->setA( rotMat ); |
1144 |
|
|
} |
1145 |
|
|
|
1146 |
|
|
current_atom_ndx++; |
1147 |
|
|
} |
1148 |
|
|
|
1149 |
|
|
current_mol++; |
1150 |
|
|
current_comp_mol++; |
1151 |
|
|
|
1152 |
|
|
if( current_comp_mol >= components_nmol[current_comp] ){ |
1153 |
|
|
|
1154 |
|
|
current_comp_mol = 0; |
1155 |
|
|
current_comp++; |
1156 |
|
|
} |
1157 |
|
|
} |