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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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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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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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strcpy( ensemble, the_globals->getEnsemble() ); |
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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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if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF(); |
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else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF(); |
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else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
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else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
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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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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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if( mpiSim->getMyMolStart() <= allMol && |
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allMol <= mpiSim->getMyMolEnd() ){ |
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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++; |
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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; |
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simnfo->n_atoms = mpiSim->getMyNlocal(); |
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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" |
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" localAtom (%d) are note equal.\n", |
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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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} |
288 |
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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; |
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simnfo->n_mol = localMol; |
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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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// create the atom and short range interaction arrays |
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Atom::createArrays(simnfo->n_atoms); |
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the_atoms = new Atom*[simnfo->n_atoms]; |
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the_molecules = new Molecule[simnfo->n_mol]; |
307 |
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308 |
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309 |
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if( simnfo->n_SRI ){ |
310 |
mmeineke |
412 |
Exclude::createArray(simnfo->n_SRI); |
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the_excludes = new Exclude*[simnfo->n_SRI]; |
312 |
mmeineke |
377 |
simnfo->globalExcludes = new int; |
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simnfo->n_exclude = tot_SRI; |
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} |
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else{ |
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mmeineke |
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Exclude::createArray( 1 ); |
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the_excludes = new Exclude*; |
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the_excludes[0] = new Exclude(0); |
320 |
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the_excludes[0]->setPair( 0,0 ); |
321 |
mmeineke |
377 |
simnfo->globalExcludes = new int; |
322 |
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simnfo->globalExcludes[0] = 0; |
323 |
mmeineke |
412 |
simnfo->n_exclude = 0; |
324 |
mmeineke |
377 |
} |
325 |
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// set the arrays into the SimInfo object |
327 |
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328 |
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simnfo->atoms = the_atoms; |
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simnfo->sr_interactions = the_sris; |
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simnfo->nGlobalExcludes = 0; |
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simnfo->excludes = the_excludes; |
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333 |
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// get some of the tricky things that may still be in the globals |
335 |
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337 |
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if( the_globals->haveBox() ){ |
338 |
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simnfo->box_x = the_globals->getBox(); |
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simnfo->box_y = the_globals->getBox(); |
340 |
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simnfo->box_z = the_globals->getBox(); |
341 |
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} |
342 |
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else if( the_globals->haveDensity() ){ |
343 |
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344 |
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double vol; |
345 |
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vol = (double)tot_nmol / the_globals->getDensity(); |
346 |
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simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) ); |
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simnfo->box_y = simnfo->box_x; |
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simnfo->box_z = simnfo->box_x; |
349 |
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} |
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else{ |
351 |
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if( !the_globals->haveBoxX() ){ |
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sprintf( painCave.errMsg, |
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"SimSetup error, no periodic BoxX size given.\n" ); |
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painCave.isFatal = 1; |
355 |
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simError(); |
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} |
357 |
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simnfo->box_x = the_globals->getBoxX(); |
358 |
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359 |
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if( !the_globals->haveBoxY() ){ |
360 |
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sprintf( painCave.errMsg, |
361 |
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"SimSetup error, no periodic BoxY size given.\n" ); |
362 |
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painCave.isFatal = 1; |
363 |
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simError(); |
364 |
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} |
365 |
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simnfo->box_y = the_globals->getBoxY(); |
366 |
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367 |
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if( !the_globals->haveBoxZ() ){ |
368 |
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sprintf( painCave.errMsg, |
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"SimSetup error, no periodic BoxZ size given.\n" ); |
370 |
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painCave.isFatal = 1; |
371 |
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simError(); |
372 |
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} |
373 |
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simnfo->box_z = the_globals->getBoxZ(); |
374 |
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} |
375 |
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376 |
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#ifdef IS_MPI |
377 |
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strcpy( checkPointMsg, "Box size set up" ); |
378 |
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MPIcheckPoint(); |
379 |
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#endif // is_mpi |
380 |
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381 |
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382 |
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// initialize the arrays |
383 |
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384 |
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the_ff->setSimInfo( simnfo ); |
385 |
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386 |
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makeAtoms(); |
387 |
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simnfo->identArray = new int[simnfo->n_atoms]; |
388 |
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for(i=0; i<simnfo->n_atoms; i++){ |
389 |
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simnfo->identArray[i] = the_atoms[i]->getIdent(); |
390 |
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} |
391 |
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392 |
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if( tot_bonds ){ |
393 |
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makeBonds(); |
394 |
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} |
395 |
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396 |
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if( tot_bends ){ |
397 |
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|
makeBends(); |
398 |
|
|
} |
399 |
|
|
|
400 |
|
|
if( tot_torsions ){ |
401 |
|
|
makeTorsions(); |
402 |
|
|
} |
403 |
|
|
|
404 |
|
|
|
405 |
gezelter |
394 |
if (the_globals->getUseRF() ) { |
406 |
|
|
simnfo->useReactionField = 1; |
407 |
|
|
|
408 |
|
|
if( !the_globals->haveECR() ){ |
409 |
|
|
sprintf( painCave.errMsg, |
410 |
|
|
"SimSetup Warning: using default value of 1/2 the smallest " |
411 |
|
|
"box length for the electrostaticCutoffRadius.\n" |
412 |
|
|
"I hope you have a very fast processor!\n"); |
413 |
|
|
painCave.isFatal = 0; |
414 |
|
|
simError(); |
415 |
|
|
double smallest; |
416 |
|
|
smallest = simnfo->box_x; |
417 |
|
|
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
418 |
|
|
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
419 |
|
|
simnfo->ecr = 0.5 * smallest; |
420 |
|
|
} else { |
421 |
|
|
simnfo->ecr = the_globals->getECR(); |
422 |
|
|
} |
423 |
mmeineke |
377 |
|
424 |
gezelter |
394 |
if( !the_globals->haveEST() ){ |
425 |
|
|
sprintf( painCave.errMsg, |
426 |
|
|
"SimSetup Warning: using default value of 0.05 * the " |
427 |
|
|
"electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
428 |
|
|
); |
429 |
|
|
painCave.isFatal = 0; |
430 |
|
|
simError(); |
431 |
|
|
simnfo->est = 0.05 * simnfo->ecr; |
432 |
|
|
} else { |
433 |
|
|
simnfo->est = the_globals->getEST(); |
434 |
|
|
} |
435 |
|
|
|
436 |
|
|
if(!the_globals->haveDielectric() ){ |
437 |
|
|
sprintf( painCave.errMsg, |
438 |
|
|
"SimSetup Error: You are trying to use Reaction Field without" |
439 |
|
|
"setting a dielectric constant!\n" |
440 |
|
|
); |
441 |
|
|
painCave.isFatal = 1; |
442 |
|
|
simError(); |
443 |
|
|
} |
444 |
|
|
simnfo->dielectric = the_globals->getDielectric(); |
445 |
|
|
} else { |
446 |
|
|
if (simnfo->n_dipoles) { |
447 |
|
|
|
448 |
|
|
if( !the_globals->haveECR() ){ |
449 |
|
|
sprintf( painCave.errMsg, |
450 |
|
|
"SimSetup Warning: using default value of 1/2 the smallest" |
451 |
|
|
"box length for the electrostaticCutoffRadius.\n" |
452 |
|
|
"I hope you have a very fast processor!\n"); |
453 |
|
|
painCave.isFatal = 0; |
454 |
|
|
simError(); |
455 |
|
|
double smallest; |
456 |
|
|
smallest = simnfo->box_x; |
457 |
|
|
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
458 |
|
|
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
459 |
|
|
simnfo->ecr = 0.5 * smallest; |
460 |
|
|
} else { |
461 |
|
|
simnfo->ecr = the_globals->getECR(); |
462 |
|
|
} |
463 |
|
|
|
464 |
|
|
if( !the_globals->haveEST() ){ |
465 |
|
|
sprintf( painCave.errMsg, |
466 |
|
|
"SimSetup Warning: using default value of 5% of the" |
467 |
|
|
"electrostaticCutoffRadius for the " |
468 |
|
|
"electrostaticSkinThickness\n" |
469 |
|
|
); |
470 |
|
|
painCave.isFatal = 0; |
471 |
|
|
simError(); |
472 |
|
|
simnfo->est = 0.05 * simnfo->ecr; |
473 |
|
|
} else { |
474 |
|
|
simnfo->est = the_globals->getEST(); |
475 |
|
|
} |
476 |
|
|
} |
477 |
|
|
} |
478 |
mmeineke |
377 |
|
479 |
gezelter |
394 |
#ifdef IS_MPI |
480 |
|
|
strcpy( checkPointMsg, "electrostatic parameters check out" ); |
481 |
|
|
MPIcheckPoint(); |
482 |
|
|
#endif // is_mpi |
483 |
mmeineke |
377 |
|
484 |
|
|
if( the_globals->haveInitialConfig() ){ |
485 |
|
|
|
486 |
|
|
InitializeFromFile* fileInit; |
487 |
|
|
#ifdef IS_MPI // is_mpi |
488 |
|
|
if( worldRank == 0 ){ |
489 |
|
|
#endif //is_mpi |
490 |
|
|
fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
491 |
|
|
#ifdef IS_MPI |
492 |
|
|
}else fileInit = new InitializeFromFile( NULL ); |
493 |
|
|
#endif |
494 |
|
|
fileInit->read_xyz( simnfo ); // default velocities on |
495 |
|
|
|
496 |
|
|
delete fileInit; |
497 |
|
|
} |
498 |
|
|
else{ |
499 |
|
|
|
500 |
|
|
#ifdef IS_MPI |
501 |
|
|
|
502 |
|
|
// no init from bass |
503 |
|
|
|
504 |
|
|
sprintf( painCave.errMsg, |
505 |
|
|
"Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
506 |
|
|
painCave.isFatal; |
507 |
|
|
simError(); |
508 |
|
|
|
509 |
|
|
#else |
510 |
|
|
|
511 |
|
|
initFromBass(); |
512 |
|
|
|
513 |
|
|
|
514 |
|
|
#endif |
515 |
|
|
} |
516 |
|
|
|
517 |
|
|
#ifdef IS_MPI |
518 |
|
|
strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
519 |
|
|
MPIcheckPoint(); |
520 |
|
|
#endif // is_mpi |
521 |
|
|
|
522 |
|
|
|
523 |
|
|
|
524 |
|
|
|
525 |
|
|
|
526 |
|
|
|
527 |
|
|
|
528 |
|
|
#ifdef IS_MPI |
529 |
|
|
if( worldRank == 0 ){ |
530 |
|
|
#endif // is_mpi |
531 |
|
|
|
532 |
|
|
if( the_globals->haveFinalConfig() ){ |
533 |
|
|
strcpy( simnfo->finalName, the_globals->getFinalConfig() ); |
534 |
|
|
} |
535 |
|
|
else{ |
536 |
|
|
strcpy( simnfo->finalName, inFileName ); |
537 |
|
|
char* endTest; |
538 |
|
|
int nameLength = strlen( simnfo->finalName ); |
539 |
|
|
endTest = &(simnfo->finalName[nameLength - 5]); |
540 |
|
|
if( !strcmp( endTest, ".bass" ) ){ |
541 |
|
|
strcpy( endTest, ".eor" ); |
542 |
|
|
} |
543 |
|
|
else if( !strcmp( endTest, ".BASS" ) ){ |
544 |
|
|
strcpy( endTest, ".eor" ); |
545 |
|
|
} |
546 |
|
|
else{ |
547 |
|
|
endTest = &(simnfo->finalName[nameLength - 4]); |
548 |
|
|
if( !strcmp( endTest, ".bss" ) ){ |
549 |
|
|
strcpy( endTest, ".eor" ); |
550 |
|
|
} |
551 |
|
|
else if( !strcmp( endTest, ".mdl" ) ){ |
552 |
|
|
strcpy( endTest, ".eor" ); |
553 |
|
|
} |
554 |
|
|
else{ |
555 |
|
|
strcat( simnfo->finalName, ".eor" ); |
556 |
|
|
} |
557 |
|
|
} |
558 |
|
|
} |
559 |
|
|
|
560 |
|
|
// make the sample and status out names |
561 |
|
|
|
562 |
|
|
strcpy( simnfo->sampleName, inFileName ); |
563 |
|
|
char* endTest; |
564 |
|
|
int nameLength = strlen( simnfo->sampleName ); |
565 |
|
|
endTest = &(simnfo->sampleName[nameLength - 5]); |
566 |
|
|
if( !strcmp( endTest, ".bass" ) ){ |
567 |
|
|
strcpy( endTest, ".dump" ); |
568 |
|
|
} |
569 |
|
|
else if( !strcmp( endTest, ".BASS" ) ){ |
570 |
|
|
strcpy( endTest, ".dump" ); |
571 |
|
|
} |
572 |
|
|
else{ |
573 |
|
|
endTest = &(simnfo->sampleName[nameLength - 4]); |
574 |
|
|
if( !strcmp( endTest, ".bss" ) ){ |
575 |
|
|
strcpy( endTest, ".dump" ); |
576 |
|
|
} |
577 |
|
|
else if( !strcmp( endTest, ".mdl" ) ){ |
578 |
|
|
strcpy( endTest, ".dump" ); |
579 |
|
|
} |
580 |
|
|
else{ |
581 |
|
|
strcat( simnfo->sampleName, ".dump" ); |
582 |
|
|
} |
583 |
|
|
} |
584 |
|
|
|
585 |
|
|
strcpy( simnfo->statusName, inFileName ); |
586 |
|
|
nameLength = strlen( simnfo->statusName ); |
587 |
|
|
endTest = &(simnfo->statusName[nameLength - 5]); |
588 |
|
|
if( !strcmp( endTest, ".bass" ) ){ |
589 |
|
|
strcpy( endTest, ".stat" ); |
590 |
|
|
} |
591 |
|
|
else if( !strcmp( endTest, ".BASS" ) ){ |
592 |
|
|
strcpy( endTest, ".stat" ); |
593 |
|
|
} |
594 |
|
|
else{ |
595 |
|
|
endTest = &(simnfo->statusName[nameLength - 4]); |
596 |
|
|
if( !strcmp( endTest, ".bss" ) ){ |
597 |
|
|
strcpy( endTest, ".stat" ); |
598 |
|
|
} |
599 |
|
|
else if( !strcmp( endTest, ".mdl" ) ){ |
600 |
|
|
strcpy( endTest, ".stat" ); |
601 |
|
|
} |
602 |
|
|
else{ |
603 |
|
|
strcat( simnfo->statusName, ".stat" ); |
604 |
|
|
} |
605 |
|
|
} |
606 |
|
|
|
607 |
|
|
#ifdef IS_MPI |
608 |
|
|
} |
609 |
|
|
#endif // is_mpi |
610 |
|
|
|
611 |
|
|
// set the status, sample, and themal kick times |
612 |
|
|
|
613 |
|
|
if( the_globals->haveSampleTime() ){ |
614 |
|
|
simnfo->sampleTime = the_globals->getSampleTime(); |
615 |
|
|
simnfo->statusTime = simnfo->sampleTime; |
616 |
|
|
simnfo->thermalTime = simnfo->sampleTime; |
617 |
|
|
} |
618 |
|
|
else{ |
619 |
|
|
simnfo->sampleTime = the_globals->getRunTime(); |
620 |
|
|
simnfo->statusTime = simnfo->sampleTime; |
621 |
|
|
simnfo->thermalTime = simnfo->sampleTime; |
622 |
|
|
} |
623 |
|
|
|
624 |
|
|
if( the_globals->haveStatusTime() ){ |
625 |
|
|
simnfo->statusTime = the_globals->getStatusTime(); |
626 |
|
|
} |
627 |
|
|
|
628 |
|
|
if( the_globals->haveThermalTime() ){ |
629 |
|
|
simnfo->thermalTime = the_globals->getThermalTime(); |
630 |
|
|
} |
631 |
|
|
|
632 |
|
|
// check for the temperature set flag |
633 |
|
|
|
634 |
|
|
if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
635 |
|
|
|
636 |
|
|
|
637 |
|
|
// // make the longe range forces and the integrator |
638 |
|
|
|
639 |
|
|
// new AllLong( simnfo ); |
640 |
|
|
|
641 |
|
|
if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff ); |
642 |
|
|
if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff ); |
643 |
|
|
if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); |
644 |
|
|
if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
645 |
|
|
|
646 |
|
|
|
647 |
|
|
|
648 |
|
|
// initialize the Fortran |
649 |
|
|
|
650 |
|
|
simnfo->refreshSim(); |
651 |
|
|
|
652 |
|
|
if( !strcmp( simnfo->mixingRule, "standard") ){ |
653 |
|
|
the_ff->initForceField( LB_MIXING_RULE ); |
654 |
|
|
} |
655 |
|
|
else if( !strcmp( simnfo->mixingRule, "explicit") ){ |
656 |
|
|
the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
657 |
|
|
} |
658 |
|
|
else{ |
659 |
|
|
sprintf( painCave.errMsg, |
660 |
|
|
"SimSetup Error: unknown mixing rule -> \"%s\"\n", |
661 |
|
|
simnfo->mixingRule ); |
662 |
|
|
painCave.isFatal = 1; |
663 |
|
|
simError(); |
664 |
|
|
} |
665 |
|
|
|
666 |
|
|
|
667 |
|
|
#ifdef IS_MPI |
668 |
|
|
strcpy( checkPointMsg, |
669 |
|
|
"Successfully intialized the mixingRule for Fortran." ); |
670 |
|
|
MPIcheckPoint(); |
671 |
|
|
#endif // is_mpi |
672 |
|
|
} |
673 |
|
|
|
674 |
mmeineke |
407 |
|
675 |
|
|
void SimSetup::makeMolecules( void ){ |
676 |
|
|
|
677 |
mmeineke |
412 |
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
678 |
mmeineke |
407 |
molInit info; |
679 |
|
|
DirectionalAtom* dAtom; |
680 |
mmeineke |
412 |
LinkedAssign* extras; |
681 |
|
|
LinkedAssign* current_extra; |
682 |
mmeineke |
407 |
AtomStamp* currentAtom; |
683 |
|
|
BondStamp* currentBond; |
684 |
|
|
BendStamp* currentBend; |
685 |
|
|
TorsionStamp* currentTorsion; |
686 |
|
|
|
687 |
|
|
//init the forceField paramters |
688 |
|
|
|
689 |
|
|
the_ff->readParams(); |
690 |
|
|
|
691 |
|
|
|
692 |
|
|
// init the molecules |
693 |
|
|
|
694 |
|
|
atomOffset = 0; |
695 |
mmeineke |
412 |
excludeOffset = 0; |
696 |
mmeineke |
407 |
for(i=0; i<simnfo->n_mol; i++){ |
697 |
|
|
|
698 |
|
|
stampID = the_molecules[i].getStampID(); |
699 |
|
|
|
700 |
|
|
info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
701 |
|
|
info.nBonds = comp_stamps[stampID]->getNBonds(); |
702 |
|
|
info.nBends = comp_stamps[stampID]->getNBends(); |
703 |
|
|
info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
704 |
mmeineke |
412 |
info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
705 |
|
|
|
706 |
mmeineke |
407 |
info.myAtoms = &the_atoms[atomOffset]; |
707 |
mmeineke |
412 |
info.myExcludes = &the_excludes[excludeOffset]; |
708 |
mmeineke |
407 |
info.myBonds = new Bond*[info.nBonds]; |
709 |
|
|
info.myBends = new Bend*[info.nBends]; |
710 |
|
|
info.myTorsions = new Torsions*[info.nTorsions]; |
711 |
|
|
|
712 |
|
|
theBonds = new bond_pair[info.nBonds]; |
713 |
|
|
theBends = new bend_set[info.nBends]; |
714 |
|
|
theTorsions = new torsion_set[info.nTorsions]; |
715 |
|
|
|
716 |
|
|
// make the Atoms |
717 |
|
|
|
718 |
|
|
for(j=0; j<info.nAtoms; j++){ |
719 |
|
|
|
720 |
|
|
currentAtom = theComponents[stampID]->getAtom( j ); |
721 |
|
|
if( currentAtom->haveOrientation() ){ |
722 |
|
|
|
723 |
|
|
dAtom = new DirectionalAtom(j + atomOffset); |
724 |
|
|
simnfo->n_oriented++; |
725 |
|
|
info.myAtoms[j] = dAtom; |
726 |
|
|
|
727 |
|
|
ux = currentAtom->getOrntX(); |
728 |
|
|
uy = currentAtom->getOrntY(); |
729 |
|
|
uz = currentAtom->getOrntZ(); |
730 |
|
|
|
731 |
|
|
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
732 |
|
|
|
733 |
|
|
u = sqrt( uSqr ); |
734 |
|
|
ux = ux / u; |
735 |
|
|
uy = uy / u; |
736 |
|
|
uz = uz / u; |
737 |
|
|
|
738 |
|
|
dAtom->setSUx( ux ); |
739 |
|
|
dAtom->setSUy( uy ); |
740 |
|
|
dAtom->setSUz( uz ); |
741 |
|
|
} |
742 |
|
|
else{ |
743 |
|
|
info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
744 |
|
|
} |
745 |
|
|
info.myAtoms[j]->setType( currentAtom->getType() ); |
746 |
|
|
|
747 |
|
|
#ifdef IS_MPI |
748 |
|
|
|
749 |
|
|
info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
750 |
|
|
|
751 |
|
|
#endif // is_mpi |
752 |
|
|
} |
753 |
|
|
|
754 |
|
|
// make the bonds |
755 |
mmeineke |
412 |
for(j=0; j<info.nBonds; j++){ |
756 |
mmeineke |
407 |
|
757 |
|
|
currentBond = comp_stamps[stampID]->getBond( j ); |
758 |
|
|
theBonds[j].a = currentBond->getA() + atomOffset; |
759 |
|
|
theBonds[j].b = currentBond->getB() + atomOffset; |
760 |
|
|
|
761 |
|
|
exI = theBonds[i].a; |
762 |
|
|
exJ = theBonds[i].b; |
763 |
|
|
|
764 |
|
|
// exclude_I must always be the smaller of the pair |
765 |
|
|
if( exI > exJ ){ |
766 |
|
|
tempEx = exI; |
767 |
|
|
exI = exJ; |
768 |
|
|
exJ = tempEx; |
769 |
|
|
} |
770 |
|
|
#ifdef IS_MPI |
771 |
mmeineke |
412 |
tempEx = exI; |
772 |
|
|
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
773 |
|
|
tempEx = exJ; |
774 |
|
|
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
775 |
mmeineke |
407 |
|
776 |
mmeineke |
412 |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
777 |
|
|
#else // isn't MPI |
778 |
|
|
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
779 |
|
|
#endif //is_mpi |
780 |
|
|
} |
781 |
|
|
excludeOffset += info.nBonds; |
782 |
|
|
|
783 |
|
|
//make the bends |
784 |
|
|
for(j=0; j<info.nBends; j++){ |
785 |
mmeineke |
407 |
|
786 |
mmeineke |
412 |
currentBend = comp_stamps[stampID]->getBend( j ); |
787 |
|
|
theBends[j].a = currentBend->getA() + atomOffset; |
788 |
|
|
theBends[j].b = currentBend->getB() + atomOffset; |
789 |
|
|
theBends[j].c = currentBend->getC() + atomOffset; |
790 |
|
|
|
791 |
|
|
if( currentBend->haveExtras() ){ |
792 |
|
|
|
793 |
|
|
extras = current_bend->getExtras(); |
794 |
|
|
current_extra = extras; |
795 |
|
|
|
796 |
|
|
while( current_extra != NULL ){ |
797 |
|
|
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
798 |
|
|
|
799 |
|
|
switch( current_extra->getType() ){ |
800 |
|
|
|
801 |
|
|
case 0: |
802 |
|
|
theBends[j].ghost = |
803 |
|
|
current_extra->getInt() + atomOffset; |
804 |
|
|
theBends[j].isGhost = 1; |
805 |
|
|
break; |
806 |
|
|
|
807 |
|
|
case 1: |
808 |
|
|
theBends[j].ghost = |
809 |
|
|
(int)current_extra->getDouble() + atomOffset; |
810 |
|
|
theBends[j].isGhost = 1; |
811 |
|
|
break; |
812 |
|
|
|
813 |
|
|
default: |
814 |
|
|
sprintf( painCave.errMsg, |
815 |
|
|
"SimSetup Error: ghostVectorSource was neiter a " |
816 |
|
|
"double nor an int.\n" |
817 |
|
|
"-->Bend[%d] in %s\n", |
818 |
|
|
j, comp_stamps[stampID]->getID() ); |
819 |
|
|
painCave.isFatal = 1; |
820 |
|
|
simError(); |
821 |
|
|
} |
822 |
|
|
} |
823 |
|
|
|
824 |
|
|
else{ |
825 |
|
|
|
826 |
|
|
sprintf( painCave.errMsg, |
827 |
|
|
"SimSetup Error: unhandled bend assignment:\n" |
828 |
|
|
" -->%s in Bend[%d] in %s\n", |
829 |
|
|
current_extra->getlhs(), |
830 |
|
|
j, comp_stamps[stampID]->getID() ); |
831 |
|
|
painCave.isFatal = 1; |
832 |
|
|
simError(); |
833 |
|
|
} |
834 |
|
|
|
835 |
|
|
current_extra = current_extra->getNext(); |
836 |
|
|
} |
837 |
|
|
} |
838 |
|
|
|
839 |
|
|
if( !theBends[j].isGhost ){ |
840 |
|
|
|
841 |
|
|
exI = theBends[j].a; |
842 |
|
|
exJ = theBends[j].c; |
843 |
|
|
} |
844 |
|
|
else{ |
845 |
|
|
|
846 |
|
|
exI = theBends[j].a; |
847 |
|
|
exJ = theBends[j].b; |
848 |
|
|
} |
849 |
|
|
|
850 |
|
|
// exclude_I must always be the smaller of the pair |
851 |
|
|
if( exI > exJ ){ |
852 |
|
|
tempEx = exI; |
853 |
|
|
exI = exJ; |
854 |
|
|
exJ = tempEx; |
855 |
|
|
} |
856 |
|
|
#ifdef IS_MPI |
857 |
|
|
tempEx = exI; |
858 |
|
|
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
859 |
|
|
tempEx = exJ; |
860 |
|
|
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
861 |
|
|
|
862 |
|
|
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
863 |
mmeineke |
407 |
#else // isn't MPI |
864 |
mmeineke |
412 |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
865 |
|
|
#endif //is_mpi |
866 |
|
|
} |
867 |
|
|
excludeOffset += info.nBends; |
868 |
|
|
|
869 |
|
|
for(j=0; j<info.nTorsions; j++){ |
870 |
mmeineke |
407 |
|
871 |
mmeineke |
412 |
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
872 |
|
|
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
873 |
|
|
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
874 |
|
|
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
875 |
|
|
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
876 |
|
|
|
877 |
|
|
exI = theTorsions[j].a; |
878 |
|
|
exJ = theTorsions[j].d; |
879 |
mmeineke |
407 |
|
880 |
mmeineke |
412 |
// exclude_I must always be the smaller of the pair |
881 |
|
|
if( exI > exJ ){ |
882 |
|
|
tempEx = exI; |
883 |
|
|
exI = exJ; |
884 |
|
|
exJ = tempEx; |
885 |
|
|
} |
886 |
|
|
#ifdef IS_MPI |
887 |
|
|
tempEx = exI; |
888 |
|
|
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
889 |
|
|
tempEx = exJ; |
890 |
|
|
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
891 |
|
|
|
892 |
|
|
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
893 |
|
|
#else // isn't MPI |
894 |
|
|
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
895 |
mmeineke |
407 |
#endif //is_mpi |
896 |
mmeineke |
412 |
} |
897 |
|
|
excludeOffset += info.nTorsions; |
898 |
|
|
|
899 |
mmeineke |
407 |
|
900 |
mmeineke |
414 |
// send the arrays off to the forceField for init. |
901 |
mmeineke |
407 |
|
902 |
mmeineke |
414 |
the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
903 |
|
|
the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
904 |
|
|
the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
905 |
|
|
the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
906 |
mmeineke |
407 |
|
907 |
|
|
|
908 |
mmeineke |
414 |
the_molecules[i].initialize( info ); |
909 |
|
|
atomOffset += info.nAtoms; |
910 |
|
|
} |
911 |
mmeineke |
407 |
|
912 |
mmeineke |
414 |
// clean up the forcefield |
913 |
mmeineke |
420 |
the_ff->calcRcut(); |
914 |
mmeineke |
414 |
the_ff->cleanMe(); |
915 |
|
|
} |
916 |
mmeineke |
407 |
|
917 |
mmeineke |
377 |
void SimSetup::initFromBass( void ){ |
918 |
|
|
|
919 |
|
|
int i, j, k; |
920 |
|
|
int n_cells; |
921 |
|
|
double cellx, celly, cellz; |
922 |
|
|
double temp1, temp2, temp3; |
923 |
|
|
int n_per_extra; |
924 |
|
|
int n_extra; |
925 |
|
|
int have_extra, done; |
926 |
|
|
|
927 |
|
|
temp1 = (double)tot_nmol / 4.0; |
928 |
|
|
temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
929 |
|
|
temp3 = ceil( temp2 ); |
930 |
|
|
|
931 |
|
|
have_extra =0; |
932 |
|
|
if( temp2 < temp3 ){ // we have a non-complete lattice |
933 |
|
|
have_extra =1; |
934 |
|
|
|
935 |
|
|
n_cells = (int)temp3 - 1; |
936 |
|
|
cellx = simnfo->box_x / temp3; |
937 |
|
|
celly = simnfo->box_y / temp3; |
938 |
|
|
cellz = simnfo->box_z / temp3; |
939 |
|
|
n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
940 |
|
|
temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
941 |
|
|
n_per_extra = (int)ceil( temp1 ); |
942 |
|
|
|
943 |
|
|
if( n_per_extra > 4){ |
944 |
|
|
sprintf( painCave.errMsg, |
945 |
|
|
"SimSetup error. There has been an error in constructing" |
946 |
|
|
" the non-complete lattice.\n" ); |
947 |
|
|
painCave.isFatal = 1; |
948 |
|
|
simError(); |
949 |
|
|
} |
950 |
|
|
} |
951 |
|
|
else{ |
952 |
|
|
n_cells = (int)temp3; |
953 |
|
|
cellx = simnfo->box_x / temp3; |
954 |
|
|
celly = simnfo->box_y / temp3; |
955 |
|
|
cellz = simnfo->box_z / temp3; |
956 |
|
|
} |
957 |
|
|
|
958 |
|
|
current_mol = 0; |
959 |
|
|
current_comp_mol = 0; |
960 |
|
|
current_comp = 0; |
961 |
|
|
current_atom_ndx = 0; |
962 |
|
|
|
963 |
|
|
for( i=0; i < n_cells ; i++ ){ |
964 |
|
|
for( j=0; j < n_cells; j++ ){ |
965 |
|
|
for( k=0; k < n_cells; k++ ){ |
966 |
|
|
|
967 |
|
|
makeElement( i * cellx, |
968 |
|
|
j * celly, |
969 |
|
|
k * cellz ); |
970 |
|
|
|
971 |
|
|
makeElement( i * cellx + 0.5 * cellx, |
972 |
|
|
j * celly + 0.5 * celly, |
973 |
|
|
k * cellz ); |
974 |
|
|
|
975 |
|
|
makeElement( i * cellx, |
976 |
|
|
j * celly + 0.5 * celly, |
977 |
|
|
k * cellz + 0.5 * cellz ); |
978 |
|
|
|
979 |
|
|
makeElement( i * cellx + 0.5 * cellx, |
980 |
|
|
j * celly, |
981 |
|
|
k * cellz + 0.5 * cellz ); |
982 |
|
|
} |
983 |
|
|
} |
984 |
|
|
} |
985 |
|
|
|
986 |
|
|
if( have_extra ){ |
987 |
|
|
done = 0; |
988 |
|
|
|
989 |
|
|
int start_ndx; |
990 |
|
|
for( i=0; i < (n_cells+1) && !done; i++ ){ |
991 |
|
|
for( j=0; j < (n_cells+1) && !done; j++ ){ |
992 |
|
|
|
993 |
|
|
if( i < n_cells ){ |
994 |
|
|
|
995 |
|
|
if( j < n_cells ){ |
996 |
|
|
start_ndx = n_cells; |
997 |
|
|
} |
998 |
|
|
else start_ndx = 0; |
999 |
|
|
} |
1000 |
|
|
else start_ndx = 0; |
1001 |
|
|
|
1002 |
|
|
for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
1003 |
|
|
|
1004 |
|
|
makeElement( i * cellx, |
1005 |
|
|
j * celly, |
1006 |
|
|
k * cellz ); |
1007 |
|
|
done = ( current_mol >= tot_nmol ); |
1008 |
|
|
|
1009 |
|
|
if( !done && n_per_extra > 1 ){ |
1010 |
|
|
makeElement( i * cellx + 0.5 * cellx, |
1011 |
|
|
j * celly + 0.5 * celly, |
1012 |
|
|
k * cellz ); |
1013 |
|
|
done = ( current_mol >= tot_nmol ); |
1014 |
|
|
} |
1015 |
|
|
|
1016 |
|
|
if( !done && n_per_extra > 2){ |
1017 |
|
|
makeElement( i * cellx, |
1018 |
|
|
j * celly + 0.5 * celly, |
1019 |
|
|
k * cellz + 0.5 * cellz ); |
1020 |
|
|
done = ( current_mol >= tot_nmol ); |
1021 |
|
|
} |
1022 |
|
|
|
1023 |
|
|
if( !done && n_per_extra > 3){ |
1024 |
|
|
makeElement( i * cellx + 0.5 * cellx, |
1025 |
|
|
j * celly, |
1026 |
|
|
k * cellz + 0.5 * cellz ); |
1027 |
|
|
done = ( current_mol >= tot_nmol ); |
1028 |
|
|
} |
1029 |
|
|
} |
1030 |
|
|
} |
1031 |
|
|
} |
1032 |
|
|
} |
1033 |
|
|
|
1034 |
|
|
|
1035 |
|
|
for( i=0; i<simnfo->n_atoms; i++ ){ |
1036 |
|
|
simnfo->atoms[i]->set_vx( 0.0 ); |
1037 |
|
|
simnfo->atoms[i]->set_vy( 0.0 ); |
1038 |
|
|
simnfo->atoms[i]->set_vz( 0.0 ); |
1039 |
|
|
} |
1040 |
|
|
} |
1041 |
|
|
|
1042 |
|
|
void SimSetup::makeElement( double x, double y, double z ){ |
1043 |
|
|
|
1044 |
|
|
int k; |
1045 |
|
|
AtomStamp* current_atom; |
1046 |
|
|
DirectionalAtom* dAtom; |
1047 |
|
|
double rotMat[3][3]; |
1048 |
|
|
|
1049 |
|
|
for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
1050 |
|
|
|
1051 |
|
|
current_atom = comp_stamps[current_comp]->getAtom( k ); |
1052 |
|
|
if( !current_atom->havePosition() ){ |
1053 |
|
|
sprintf( painCave.errMsg, |
1054 |
|
|
"SimSetup:initFromBass error.\n" |
1055 |
|
|
"\tComponent %s, atom %s does not have a position specified.\n" |
1056 |
|
|
"\tThe initialization routine is unable to give a start" |
1057 |
|
|
" position.\n", |
1058 |
|
|
comp_stamps[current_comp]->getID(), |
1059 |
|
|
current_atom->getType() ); |
1060 |
|
|
painCave.isFatal = 1; |
1061 |
|
|
simError(); |
1062 |
|
|
} |
1063 |
|
|
|
1064 |
|
|
the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() ); |
1065 |
|
|
the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() ); |
1066 |
|
|
the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() ); |
1067 |
|
|
|
1068 |
|
|
if( the_atoms[current_atom_ndx]->isDirectional() ){ |
1069 |
|
|
|
1070 |
|
|
dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx]; |
1071 |
|
|
|
1072 |
|
|
rotMat[0][0] = 1.0; |
1073 |
|
|
rotMat[0][1] = 0.0; |
1074 |
|
|
rotMat[0][2] = 0.0; |
1075 |
|
|
|
1076 |
|
|
rotMat[1][0] = 0.0; |
1077 |
|
|
rotMat[1][1] = 1.0; |
1078 |
|
|
rotMat[1][2] = 0.0; |
1079 |
|
|
|
1080 |
|
|
rotMat[2][0] = 0.0; |
1081 |
|
|
rotMat[2][1] = 0.0; |
1082 |
|
|
rotMat[2][2] = 1.0; |
1083 |
|
|
|
1084 |
|
|
dAtom->setA( rotMat ); |
1085 |
|
|
} |
1086 |
|
|
|
1087 |
|
|
current_atom_ndx++; |
1088 |
|
|
} |
1089 |
|
|
|
1090 |
|
|
current_mol++; |
1091 |
|
|
current_comp_mol++; |
1092 |
|
|
|
1093 |
|
|
if( current_comp_mol >= components_nmol[current_comp] ){ |
1094 |
|
|
|
1095 |
|
|
current_comp_mol = 0; |
1096 |
|
|
current_comp++; |
1097 |
|
|
} |
1098 |
|
|
} |