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#include <cmath> |
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#include "simError.h" |
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#include "parse_me.h" |
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#include "MakeStamps.hpp" |
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#include "Globals.hpp" |
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#include "SimInfo.hpp" |
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#include "ReadWrite.hpp" |
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#include "MoLocator.hpp" |
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#include "sysBuild.hpp" |
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#include "bilayerSys.hpp" |
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// this routine is defined in BASS_interface.cpp |
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extern void set_interface_stamps( MakeStamps* ms, Globals* g ); |
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int buildRandomBilayer( void ); |
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void buildRandomBilayer( sysBuildInfo info ); |
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void getRandomRot( double rot[3][3] ); |
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void buildBilayer( sysBuildInfo info ){ |
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int buildBilayer( int isRandom ){ |
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if( info.isRandom ){ |
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buildRandomBilayer( info ); |
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if( isRandom ){ |
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return buildRandomBilayer(); |
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} |
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else{ |
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|
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sprintf( painCave.errMsg, |
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"Cannot currently create a non-random bilayer.\n" ); |
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painCave.isFatal = 1; |
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simError(); |
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return 0; |
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} |
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} |
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void buildRandomBilayer( sysBuildInfo info ){ |
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int buildRandomBilayer( void ){ |
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MakeStamps* the_stamps; |
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Globals* the_globals; |
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int i,j,k; |
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int nAtoms, atomIndex; |
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int* molSeq; |
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int* molMap; |
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int* cardDeck; |
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int deckSize; |
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int rSite, rCard; |
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double cell; |
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int nCells, nSites, siteIndex; |
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double rot[3][3]; |
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double pos[3]; |
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|
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Atom** atoms; |
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SimInfo* simnfo; |
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bwMolLinked bwInfo; |
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DumpWriter* writer; |
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MoLocator** locate; |
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|
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// initialize functions and variables |
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// init the bwInfo |
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srand48( RAND_SEED ); |
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molSeq = NULL; |
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molMap = NULL; |
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cardDeck = NULL; |
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atoms = NULL; |
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locate = NULL; |
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simnfo = NULL; |
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writer = NULL; |
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|
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// calculate the number of cells in the fcc box |
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|
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nCells = 0; |
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nSites = 0; |
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while( nSites < bsInfo.totNmol ){ |
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nCells++; |
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nSites = 4 * pow( nCells, 3 ); |
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} |
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// create the molMap and cardDeck arrays |
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bwinfo.components = NULL; |
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molMap = new int[nSites]; |
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cardDeck = new int[nSites]; |
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bwInfo.havePressure = 0; |
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bwInfo.haveTauBarrostat = 0; |
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bwInfo.haveTauTemp = 0; |
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bwInfo.haveQmass = 0; |
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for(i=0; i<nSites; i++){ |
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molMap[i] = -1; |
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cardDeck[i] = i; |
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} |
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|
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// randomly place the molecules on the sites |
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deckSize = nSites; |
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for(i=0; i<bsInfo.totNmol; i++){ |
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rCard = (int)( deckSize * drand48() ); |
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rSite = cardDeck[rCard]; |
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molMap[rSite] = i; |
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// book keep the card deck; |
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|
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deckSize--; |
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cardDeck[rCard] = cardDeck[deckSize]; |
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} |
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// create parser and read the Bas file |
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simnfo = new SimInfo(); |
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the_stamps = new MakeStamps(); |
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the_globals = new Globals(); |
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set_interface_stamps( the_stamps, the_globals ); |
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// create the MoLocator and Atom arrays |
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nAtoms = 0; |
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molIndex = 0; |
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locate = new MoLocator*[bsInfo.nComponents]; |
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molSeq = new int[bsInfo.totNmol]; |
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for(i=0; i<bsInfo.nComponents; i++){ |
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locate[i] = new MoLocator( bsInfo.compStamps[i] ); |
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for(j=0; j<bsInfo.componentsNmol[i]; j++){ |
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molSeq[molIndex] = i; |
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molIndex++; |
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nAtoms += bsInfo.compStamp[i]->getNAtoms(); |
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} |
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} |
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Atom::createArrays( nAtoms ); |
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atoms = new Atom*[nAtoms]; |
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// place the molecules at each FCC site |
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cell = 5.0; |
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for(i=0; i<bsInfo.nComponents; i++){ |
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if(cell < locate[i]->getMaxLength() ) cell = locate[i]->getMaxLength(); |
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} |
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cell *= M_SQRT_2; |
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yacc_BASS( info.in_name ); |
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siteIndex = 0; |
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atomIndex = 0; |
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for(i=0; i<nCells; i++){ |
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for(j=0; j<nCells; j++){ |
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for(k=0; k<nCells; k++){ |
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|
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if( molMap[siteIndex] >= 0 ){ |
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pos[0] = i * cell; |
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pos[1] = j * cell; |
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pos[2] = k * cell; |
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getRandomRot( rot ); |
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molID = molSeq[molMap[siteIndex]]; |
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locate[molID]->placeMol( pos, rot, &atoms[atomIndex] ); |
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atomIndex += bsInfo.compStamps[molID]->getNatoms(); |
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} |
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siteIndex++; |
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if( molMap[siteIndex] >= 0 ){ |
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pos[0] = i * cell + (0.5 * cell); |
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pos[1] = j * cell; |
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pos[2] = k * cell + (0.5 * cell); |
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|
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getRandomRot( rot ); |
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molID = molSeq[molMap[siteIndex]]; |
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locate[molID]->placeMol( pos, rot, &atoms[atomIndex] ); |
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atomIndex += bsInfo.compStamps[molID]->getNatoms(); |
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} |
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siteIndex++; |
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if( molMap[siteIndex] >= 0 ){ |
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pos[0] = i * cell + (0.5 * cell); |
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pos[1] = j * cell + (0.5 * cell); |
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pos[2] = k * cell; |
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|
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getRandomRot( rot ); |
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molID = molSeq[molMap[siteIndex]]; |
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locate[molID]->placeMol( pos, rot, &atoms[atomIndex] ); |
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atomIndex += bsInfo.compStamps[molID]->getNatoms(); |
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} |
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siteIndex++; |
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// set the easy ones first |
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bwInfo.targetTemp = the_globals->getTargetTemp(); |
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bwInfo.dt = the_globals->getDt(); |
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bwInfo.runTime = the_globals->getRunTime(); |
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if( molMap[siteIndex] >= 0 ){ |
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pos[0] = i * cell; |
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pos[1] = j * cell + (0.5 * cell); |
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pos[2] = k * cell + (0.5 * cell); |
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getRandomRot( rot ); |
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molID = molSeq[molMap[siteIndex]]; |
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locate[molID]->placeMol( pos, rot, &atoms[atomIndex] ); |
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atomIndex += bsInfo.compStamps[molID]->getNatoms(); |
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} |
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siteIndex++; |
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} |
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} |
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} |
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// get the ones we know are there, yet still may need some work. |
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bwInfo.nComponents = the_globals->getNComponents(); |
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strcpy( bwInfo.forceField, the_globals->getForceField() ); |
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// get the ensemble: |
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strcpy( bwInfo.ensemble, the_globals->getEnsemble() ); |
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if( !strcasecmp( bwInfo.ensemble, "NPT" ) ) { |
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> |
// set up the SimInfo object |
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|
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bsInfo.boxX = nCells * cell; |
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bsInfo.boxY = nCells * cell; |
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> |
bsInfo.boxZ = nCells * cell; |
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simnfo = new SimInfo(); |
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simnfo.n_atoms = nAtoms; |
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simnfo.box_x = bsInfo.boxX; |
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simnfo.box_y = bsInfo.boxY; |
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simnfo.box_z = bsInfo.boxZ; |
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|
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sprintf( simnfo.statusName, "%s.dump", bsInfo.outPrefix ); |
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> |
sprintf( simnfo.finalName, "%s.init", bsInfo.outPrefix ); |
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> |
|
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> |
simnfo.atoms = atoms; |
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> |
|
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> |
// set up the writer and write out |
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|
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writer = new DumpWriter( &simnfo ); |
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writer->writeFinal(); |
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< |
if (the_globals->haveTargetPressure()){ |
| 210 |
< |
bwInfo.targetPressure = the_globals->getTargetPressure(); |
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< |
bwInfo.havePressure = 1; |
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> |
// clean up the memory |
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> |
|
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> |
if( molMap != NULL ) delete[] molMap; |
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> |
if( cardDeck != NULL ) delete[] cardDeck; |
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> |
if( locate != NULL ){ |
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> |
for(i=0; i<bsInfo.nComponents; i++){ |
| 215 |
> |
delete locate[i]; |
| 216 |
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} |
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< |
else { |
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< |
sprintf( painCave.errMsg, |
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< |
"buildBilayer error: If you use the constant pressure\n" |
| 220 |
< |
" ensemble, you must set targetPressure.\n" |
| 221 |
< |
" This was found in the BASS file.\n"); |
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< |
painCave.isFatal = 1; |
| 90 |
< |
simError(); |
| 217 |
> |
delete[] locate; |
| 218 |
> |
} |
| 219 |
> |
if( atoms != NULL ){ |
| 220 |
> |
for(i=0; i<nAtoms; i++){ |
| 221 |
> |
delete atoms[i]; |
| 222 |
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} |
| 223 |
+ |
Atom::destroyArrays(); |
| 224 |
+ |
delete[] atoms; |
| 225 |
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} |
| 226 |
+ |
if( molSeq != NULL ) delete[] molSeq; |
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+ |
if( simnfo != NULL ) delete simnfo; |
| 228 |
+ |
if( writer != NULL ) delete writer; |
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< |
if (the_globals->haveTauThermostat()){ |
| 231 |
< |
bwInfo.tauThermostat = the_globals->getTauThermostat(); |
| 95 |
< |
bwInfo.haveTauThermostat = 1;; |
| 96 |
< |
} |
| 97 |
< |
else if (the_globals->haveQmass()){ |
| 98 |
< |
bwinfo.Qmass = the_globals->getQmass(); |
| 99 |
< |
bwInfo.haveQmass = 1; |
| 100 |
< |
} |
| 101 |
< |
else { |
| 102 |
< |
sprintf( painCave.errMsg, |
| 103 |
< |
"buildBilayer error: If you use one of the constant temperature\n" |
| 104 |
< |
" ensembles, you must set either tauThermostat or qMass.\n" |
| 105 |
< |
" Neither of these was found in the BASS file.\n"); |
| 106 |
< |
painCave.isFatal = 1; |
| 107 |
< |
simError(); |
| 108 |
< |
} |
| 230 |
> |
return 1; |
| 231 |
> |
} |
| 232 |
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| 110 |
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if (the_globals->haveTauBarostat()){ |
| 111 |
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bwInfo.tauBarostat = the_globals->getTauBarostat(); |
| 112 |
– |
bwInfo.haveTauBarostat = 1; |
| 113 |
– |
} |
| 114 |
– |
else { |
| 115 |
– |
sprintf( painCave.errMsg, |
| 116 |
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"SimSetup error: If you use the constant pressure\n" |
| 117 |
– |
" ensemble, you must set tauBarostat.\n" |
| 118 |
– |
" This was found in the BASS file.\n"); |
| 119 |
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painCave.isFatal = 1; |
| 120 |
– |
simError(); |
| 121 |
– |
} |
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|
| 234 |
< |
} else if ( !strcasecmp( ensemble, "NVT") ) { |
| 124 |
< |
the_extendedsystem = new ExtendedSystem( simnfo ); |
| 125 |
< |
the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
| 234 |
> |
void getRandomRot( double rot[3][3] ){ |
| 235 |
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|
| 236 |
< |
if (the_globals->haveTauThermostat()) |
| 237 |
< |
the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
| 129 |
< |
else if (the_globals->haveQmass()) |
| 130 |
< |
the_extendedsystem->setQmass(the_globals->getQmass()); |
| 131 |
< |
else { |
| 132 |
< |
sprintf( painCave.errMsg, |
| 133 |
< |
"SimSetup error: If you use one of the constant temperature\n" |
| 134 |
< |
" ensembles, you must set either tauThermostat or qMass.\n" |
| 135 |
< |
" Neither of these was found in the BASS file.\n"); |
| 136 |
< |
painCave.isFatal = 1; |
| 137 |
< |
simError(); |
| 138 |
< |
} |
| 236 |
> |
double theta, phi, psi; |
| 237 |
> |
double cosTheta; |
| 238 |
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|
| 239 |
< |
} else if ( !strcasecmp( ensemble, "NVE") ) { |
| 141 |
< |
} else { |
| 142 |
< |
sprintf( painCave.errMsg, |
| 143 |
< |
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
| 144 |
< |
"reverting to NVE for this simulation.\n", |
| 145 |
< |
ensemble ); |
| 146 |
< |
painCave.isFatal = 0; |
| 147 |
< |
simError(); |
| 148 |
< |
strcpy( ensemble, "NVE" ); |
| 149 |
< |
} |
| 150 |
< |
strcpy( simnfo->ensemble, ensemble ); |
| 239 |
> |
// select random phi, psi, and cosTheta |
| 240 |
|
|
| 241 |
+ |
phi = 2.0 * M_PI * drand48(); |
| 242 |
+ |
psi = 2.0 * M_PI * drand48(); |
| 243 |
+ |
cosTheta = (2.0 * drand48()) - 1.0; // sample cos -1 to 1 |
| 244 |
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|
| 245 |
+ |
theta = acos( cosTheta ); |
| 246 |
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|
| 247 |
< |
delete stamps; |
| 248 |
< |
delete globals; |
| 247 |
> |
rot[0][0] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi)); |
| 248 |
> |
rot[0][1] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi)); |
| 249 |
> |
rot[0][2[ = sin(theta) * sin(psi); |
| 250 |
> |
|
| 251 |
> |
rot[1][0] = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi)); |
| 252 |
> |
rot[1][1] = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi)); |
| 253 |
> |
rot[1][2] = sin(theta) * cos(psi); |
| 254 |
> |
|
| 255 |
> |
rot[2][0] = sin(phi) * sin(theta); |
| 256 |
> |
rot[2][1] = -cos(phi) * sin(theta); |
| 257 |
> |
rot[2][2] = cos(theta); |
| 258 |
|
} |
| 259 |
+ |
|
