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#include <iostream> |
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|
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#include <cstdlib> |
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#include <cstring> |
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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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|
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void buildRandomBilayer( sysBuildInfo info ); |
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void map( double &x, double &y, double &z, |
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double boxX, double boxY, double boxZ ); |
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int buildRandomBilayer( void ); |
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void buildBilayer( sysBuildInfo info ){ |
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void getRandomRot( double rot[3][3] ); |
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|
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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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int buildRandomBilayer( void ){ |
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void buildRandomBilayer( sysBuildInfo info ){ |
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typedef struct{ |
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double rot[3][3]; |
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double pos[3]; |
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} coord; |
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MakeStamps* the_stamps; |
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Globals* the_globals; |
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|
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const double waterRho = 0.0334; // number density per cubic angstrom |
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const double waterVol = 4.0 / waterRho; // volume occupied by 4 waters |
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const double waterCell = 4.929; // fcc unit cell length |
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|
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const double water_padding = 2.5; |
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const double lipid_spaceing = 5.0; |
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|
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|
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int i,j,k, l; |
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int nAtoms, atomIndex, molIndex, molID; |
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int* molSeq; |
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int* molMap; |
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int* molStart; |
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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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|
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coord testSite; |
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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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|
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MoleculeStamp* lipidStamp; |
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MoleculeStamp* waterStamp; |
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MoLocator *lipidLocate; |
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MoLocator *waterLocate; |
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int foundLipid, foundWater; |
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int nLipids, lipidNatoms, nWaters, waterNatoms; |
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double testBox, maxLength; |
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// init the bwInfo |
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srand48( RAND_SEED ); |
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|
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|
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// set the the lipidStamp |
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|
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foundLipid = 0; |
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foundWater = 0; |
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for(i=0; i<bsInfo.nComponents; i++){ |
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if( !strcmp( bsInfo.compStamps[i]->getID(), bsInfo.lipidName ) ){ |
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|
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foundLipid = 1; |
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lipidStamp = bsInfo.compStamps[i]; |
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nLipids = bsInfo.componentsNmol[i]; |
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} |
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if( !strcmp( bsInfo.compStamps[i]->getID(), bsInfo.waterName ) ){ |
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|
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foundWater = 1; |
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|
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waterStamp = bsInfo.compStamps[i]; |
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nWaters = bsInfo.componentsNmol[i]; |
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} |
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} |
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if( !foundLipid ){ |
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sprintf(painCave.errMsg, |
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"Could not find lipid \"%s\" in the bass file.\n", |
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bsInfo.lipidName ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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if( !foundWater ){ |
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sprintf(painCave.errMsg, |
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"Could not find solvent \"%s\" in the bass file.\n", |
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bsInfo.waterName ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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bwinfo.components = NULL; |
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//create the temp Molocator and atom Arrays |
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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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lipidLocate = new MoLocator( lipidStamp ); |
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lipidNatoms = lipidStamp->getNAtoms(); |
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maxLength = lipidLocate->getMaxLength(); |
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|
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waterLocate = new MoLocator( waterStamp ); |
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waterNatoms = waterStamp->getNAtoms(); |
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nAtoms = nLipids * lipidNatoms; |
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|
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Atom::createArrays( nAtoms ); |
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atoms = new Atom*[nAtoms]; |
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|
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// create the test box for initial water displacement |
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|
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testBox = maxLength + waterCell * 4.0; // pad with 4 cells |
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nCells = (int)( testBox / waterCell + 1.0 ); |
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int testWaters = 4 * nCells * nCells * nCells; |
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// create parser and read the Bas file |
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double* waterX = new double[testWaters]; |
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double* waterY = new double[testWaters]; |
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double* waterZ = new double[testWaters]; |
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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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double x0 = 0.0 - ( testBox * 0.5 ); |
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double y0 = 0.0 - ( testBox * 0.5 ); |
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> |
double z0 = 0.0 - ( testBox * 0.5 ); |
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|
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yacc_BASS( info.in_name ); |
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// create an fcc lattice in the water box. |
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int ndx = 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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waterX[ndx] = i * waterCell + x0; |
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waterY[ndx] = j * waterCell + y0; |
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waterZ[ndx] = k * waterCell + z0; |
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ndx++; |
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|
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waterX[ndx] = i * waterCell + 0.5 * waterCell + x0; |
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waterY[ndx] = j * waterCell + 0.5 * waterCell + y0; |
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waterZ[ndx] = k * waterCell + z0; |
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ndx++; |
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|
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waterX[ndx] = i * waterCell + x0; |
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waterY[ndx] = j * waterCell + 0.5 * waterCell + y0; |
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waterZ[ndx] = k * waterCell + 0.5 * waterCell + z0; |
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ndx++; |
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|
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waterX[ndx] = i * waterCell + 0.5 * waterCell + x0; |
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waterY[ndx] = j * waterCell + y0; |
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waterZ[ndx] = k * waterCell + 0.5 * waterCell + z0; |
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ndx++; |
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} |
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} |
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} |
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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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// calculate the number of water's displaced by our lipid. |
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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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> |
testSite.rot[0][0] = 1.0; |
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testSite.rot[0][1] = 0.0; |
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testSite.rot[0][2] = 0.0; |
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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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|
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if (the_globals->haveTargetPressure()){ |
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bwInfo.targetPressure = the_globals->getTargetPressure(); |
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bwInfo.havePressure = 1; |
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> |
testSite.rot[1][0] = 0.0; |
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> |
testSite.rot[1][1] = 1.0; |
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> |
testSite.rot[1][2] = 0.0; |
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> |
|
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> |
testSite.rot[2][0] = 0.0; |
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> |
testSite.rot[2][1] = 0.0; |
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> |
testSite.rot[2][2] = 1.0; |
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> |
|
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testSite.pos[0] = 0.0; |
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> |
testSite.pos[1] = 0.0; |
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testSite.pos[2] = 0.0; |
| 193 |
> |
|
| 194 |
> |
lipidLocate->placeMol( testSite.pos, testSite.rot, atoms, 0 ); |
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> |
|
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> |
int *isActive = new int[testWaters]; |
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> |
for(i=0; i<testWaters; i++) isActive[i] = 1; |
| 198 |
> |
|
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> |
int n_deleted = 0; |
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> |
double dx, dy, dz; |
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> |
double dx2, dy2, dz2, dSqr; |
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> |
double rCutSqr = water_padding * water_padding; |
| 203 |
> |
|
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> |
for(i=0; ( (i<testWaters) && isActive[i] ); i++){ |
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> |
for(j=0; ( (j<lipidNatoms) && isActive[i] ); j++){ |
| 206 |
> |
|
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> |
dx = waterX[i] - atoms[j]->getX(); |
| 208 |
> |
dy = waterY[i] - atoms[j]->getY(); |
| 209 |
> |
dz = waterZ[i] - atoms[j]->getZ(); |
| 210 |
> |
|
| 211 |
> |
map( dx, dy, dz, testBox, testBox, testBox ); |
| 212 |
> |
|
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> |
dx2 = dx * dx; |
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> |
dy2 = dy * dy; |
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> |
dz2 = dz * dz; |
| 216 |
> |
|
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> |
dSqr = dx2 + dy2 + dz2; |
| 218 |
> |
if( dSqr < rCutSqr ){ |
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> |
isActive[i] = 0; |
| 220 |
> |
n_deleted++; |
| 221 |
> |
} |
| 222 |
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} |
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< |
else { |
| 224 |
< |
sprintf( painCave.errMsg, |
| 225 |
< |
"buildBilayer error: If you use the constant pressure\n" |
| 87 |
< |
" ensemble, you must set targetPressure.\n" |
| 88 |
< |
" This was found in the BASS file.\n"); |
| 89 |
< |
painCave.isFatal = 1; |
| 90 |
< |
simError(); |
| 91 |
< |
} |
| 223 |
> |
} |
| 224 |
> |
|
| 225 |
> |
int targetWaters = nWaters + n_deleted * nLipids; |
| 226 |
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|
| 227 |
< |
if (the_globals->haveTauThermostat()){ |
| 228 |
< |
bwInfo.tauThermostat = the_globals->getTauThermostat(); |
| 229 |
< |
bwInfo.haveTauThermostat = 1;; |
| 227 |
> |
// find the best box size for the sim |
| 228 |
> |
|
| 229 |
> |
int testTot; |
| 230 |
> |
int done = 0; |
| 231 |
> |
ndx = 0; |
| 232 |
> |
while( !done ){ |
| 233 |
> |
|
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ndx++; |
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> |
testTot = 4 * ndx * ndx * ndx; |
| 236 |
> |
|
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> |
if( testTot >= targetWaters ) done = 1; |
| 238 |
> |
} |
| 239 |
> |
|
| 240 |
> |
nCells = ndx; |
| 241 |
> |
|
| 242 |
> |
|
| 243 |
> |
// create the new water box to the new specifications |
| 244 |
> |
|
| 245 |
> |
int newWaters = nCells * nCells * nCells * 4; |
| 246 |
> |
|
| 247 |
> |
delete[] waterX; |
| 248 |
> |
delete[] waterY; |
| 249 |
> |
delete[] waterZ; |
| 250 |
> |
|
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> |
coord* waterSites = new coord[newWaters]; |
| 252 |
> |
|
| 253 |
> |
double box_x = waterCell * nCells; |
| 254 |
> |
double box_y = waterCell * nCells; |
| 255 |
> |
double box_z = waterCell * nCells; |
| 256 |
> |
|
| 257 |
> |
// create an fcc lattice in the water box. |
| 258 |
> |
|
| 259 |
> |
ndx = 0; |
| 260 |
> |
for( i=0; i < nCells; i++ ){ |
| 261 |
> |
for( j=0; j < nCells; j++ ){ |
| 262 |
> |
for( k=0; k < nCells; k++ ){ |
| 263 |
> |
|
| 264 |
> |
waterSites[ndx].pos[0] = i * waterCell; |
| 265 |
> |
waterSites[ndx].pos[1] = j * waterCell; |
| 266 |
> |
waterSites[ndx].pos[2] = k * waterCell; |
| 267 |
> |
ndx++; |
| 268 |
> |
|
| 269 |
> |
waterSites[ndx].pos[0] = i * waterCell + 0.5 * waterCell; |
| 270 |
> |
waterSites[ndx].pos[1] = j * waterCell + 0.5 * waterCell; |
| 271 |
> |
waterSites[ndx].pos[2] = k * waterCell; |
| 272 |
> |
ndx++; |
| 273 |
> |
|
| 274 |
> |
waterSites[ndx].pos[0] = i * waterCell; |
| 275 |
> |
waterSites[ndx].pos[1] = j * waterCell + 0.5 * waterCell; |
| 276 |
> |
waterSites[ndx].pos[2] = k * waterCell + 0.5 * waterCell; |
| 277 |
> |
ndx++; |
| 278 |
> |
|
| 279 |
> |
waterSites[ndx].pos[0] = i * waterCell + 0.5 * waterCell; |
| 280 |
> |
waterSites[ndx].pos[1] = j * waterCell; |
| 281 |
> |
waterSites[ndx].pos[2] = k * waterCell + 0.5 * waterCell; |
| 282 |
> |
ndx++; |
| 283 |
> |
} |
| 284 |
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} |
| 285 |
< |
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 |
< |
} |
| 285 |
> |
} |
| 286 |
|
|
| 287 |
< |
if (the_globals->haveTauBarostat()){ |
| 288 |
< |
bwInfo.tauBarostat = the_globals->getTauBarostat(); |
| 289 |
< |
bwInfo.haveTauBarostat = 1; |
| 290 |
< |
} |
| 291 |
< |
else { |
| 292 |
< |
sprintf( painCave.errMsg, |
| 293 |
< |
"SimSetup error: If you use the constant pressure\n" |
| 294 |
< |
" ensemble, you must set tauBarostat.\n" |
| 295 |
< |
" This was found in the BASS file.\n"); |
| 296 |
< |
painCave.isFatal = 1; |
| 297 |
< |
simError(); |
| 287 |
> |
|
| 288 |
> |
// clear up memory from the test box |
| 289 |
> |
|
| 290 |
> |
for(i=0; i<lipidNatoms; i++ ) delete atoms[i]; |
| 291 |
> |
|
| 292 |
> |
coord* lipidSites = new coord[nLipids]; |
| 293 |
> |
|
| 294 |
> |
// start a 3D RSA for the for the lipid placements |
| 295 |
> |
|
| 296 |
> |
|
| 297 |
> |
int reject; |
| 298 |
> |
int testDX, acceptedDX; |
| 299 |
> |
|
| 300 |
> |
rCutSqr = lipid_spaceing * lipid_spaceing; |
| 301 |
> |
|
| 302 |
> |
for(i=0; i<nLipids; i++ ){ |
| 303 |
> |
done = 0; |
| 304 |
> |
while( !done ){ |
| 305 |
> |
|
| 306 |
> |
lipidSites[i].pos[0] = drand48() * box_x; |
| 307 |
> |
lipidSites[i].pos[1] = drand48() * box_y; |
| 308 |
> |
lipidSites[i].pos[2] = drand48() * box_z; |
| 309 |
> |
|
| 310 |
> |
getRandomRot( lipidSites[i].rot ); |
| 311 |
> |
|
| 312 |
> |
ndx = i * lipidNatoms; |
| 313 |
> |
|
| 314 |
> |
lipidLocate->placeMol( lipidSites[i].pos, lipidSites[i].rot, atoms, |
| 315 |
> |
ndx ); |
| 316 |
> |
|
| 317 |
> |
reject = 0; |
| 318 |
> |
for( j=0; !reject && j<i; j++){ |
| 319 |
> |
for(k=0; !reject && k<lipidNatoms; k++){ |
| 320 |
> |
|
| 321 |
> |
acceptedDX = j*lipidNatoms + k; |
| 322 |
> |
for(l=0; !reject && l<lipidNatoms; l++){ |
| 323 |
> |
|
| 324 |
> |
testDX = ndx + l; |
| 325 |
> |
|
| 326 |
> |
dx = atoms[testDX]->getX() - atoms[acceptedDX]->getX(); |
| 327 |
> |
dy = atoms[testDX]->getY() - atoms[acceptedDX]->getY(); |
| 328 |
> |
dz = atoms[testDX]->getZ() - atoms[acceptedDX]->getZ(); |
| 329 |
> |
|
| 330 |
> |
map( dx, dy, dz, box_x, box_y, box_z ); |
| 331 |
> |
|
| 332 |
> |
dx2 = dx * dx; |
| 333 |
> |
dy2 = dy * dy; |
| 334 |
> |
dz2 = dz * dz; |
| 335 |
> |
|
| 336 |
> |
dSqr = dx2 + dy2 + dz2; |
| 337 |
> |
if( dSqr < rCutSqr ) reject = 1; |
| 338 |
> |
} |
| 339 |
> |
} |
| 340 |
> |
} |
| 341 |
> |
|
| 342 |
> |
if( reject ){ |
| 343 |
> |
|
| 344 |
> |
for(j=0; j< lipidNatoms; j++) delete atoms[ndx+j]; |
| 345 |
> |
} |
| 346 |
> |
else{ |
| 347 |
> |
done = 1; |
| 348 |
> |
std::cout << i << " has been accepted\n"; |
| 349 |
> |
} |
| 350 |
|
} |
| 351 |
+ |
} |
| 352 |
+ |
|
| 353 |
+ |
// cut out the waters that overlap with the lipids. |
| 354 |
+ |
|
| 355 |
+ |
delete[] isActive; |
| 356 |
+ |
isActive = new int[newWaters]; |
| 357 |
+ |
for(i=0; i<newWaters; i++) isActive[i] = 1; |
| 358 |
+ |
int n_active = newWaters; |
| 359 |
+ |
rCutSqr = water_padding * water_padding; |
| 360 |
+ |
|
| 361 |
+ |
for(i=0; ( (i<newWaters) && isActive[i] ); i++){ |
| 362 |
+ |
for(j=0; ( (j<nAtoms) && isActive[i] ); j++){ |
| 363 |
|
|
| 364 |
< |
} else if ( !strcasecmp( ensemble, "NVT") ) { |
| 365 |
< |
the_extendedsystem = new ExtendedSystem( simnfo ); |
| 366 |
< |
the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
| 364 |
> |
dx = waterSites[i].pos[0] - atoms[j]->getX(); |
| 365 |
> |
dy = waterSites[i].pos[1] - atoms[j]->getY(); |
| 366 |
> |
dz = waterSites[i].pos[2] - atoms[j]->getZ(); |
| 367 |
|
|
| 368 |
< |
if (the_globals->haveTauThermostat()) |
| 369 |
< |
the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
| 370 |
< |
else if (the_globals->haveQmass()) |
| 371 |
< |
the_extendedsystem->setQmass(the_globals->getQmass()); |
| 372 |
< |
else { |
| 373 |
< |
sprintf( painCave.errMsg, |
| 374 |
< |
"SimSetup error: If you use one of the constant temperature\n" |
| 375 |
< |
" ensembles, you must set either tauThermostat or qMass.\n" |
| 376 |
< |
" Neither of these was found in the BASS file.\n"); |
| 377 |
< |
painCave.isFatal = 1; |
| 378 |
< |
simError(); |
| 368 |
> |
map( dx, dy, dz, box_x, box_y, box_z ); |
| 369 |
> |
|
| 370 |
> |
dx2 = dx * dx; |
| 371 |
> |
dy2 = dy * dy; |
| 372 |
> |
dz2 = dz * dz; |
| 373 |
> |
|
| 374 |
> |
dSqr = dx2 + dy2 + dz2; |
| 375 |
> |
if( dSqr < rCutSqr ){ |
| 376 |
> |
isActive[i] = 0; |
| 377 |
> |
n_active--; |
| 378 |
> |
} |
| 379 |
|
} |
| 380 |
+ |
} |
| 381 |
|
|
| 382 |
< |
} else if ( !strcasecmp( ensemble, "NVE") ) { |
| 383 |
< |
} else { |
| 382 |
> |
if( n_active < nWaters ){ |
| 383 |
> |
|
| 384 |
|
sprintf( painCave.errMsg, |
| 385 |
< |
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
| 386 |
< |
"reverting to NVE for this simulation.\n", |
| 387 |
< |
ensemble ); |
| 146 |
< |
painCave.isFatal = 0; |
| 385 |
> |
"Too many waters were removed, edit code and try again.\n" ); |
| 386 |
> |
|
| 387 |
> |
painCave.isFatal = 1; |
| 388 |
|
simError(); |
| 389 |
< |
strcpy( ensemble, "NVE" ); |
| 389 |
> |
} |
| 390 |
> |
|
| 391 |
> |
int quickKill; |
| 392 |
> |
while( n_active > nWaters ){ |
| 393 |
> |
|
| 394 |
> |
quickKill = (int)(drand48()*newWaters); |
| 395 |
> |
|
| 396 |
> |
if( isActive[quickKill] ){ |
| 397 |
> |
isActive[quickKill] = 0; |
| 398 |
> |
n_active--; |
| 399 |
> |
} |
| 400 |
> |
} |
| 401 |
> |
|
| 402 |
> |
if( n_active != nWaters ){ |
| 403 |
> |
|
| 404 |
> |
sprintf( painCave.errMsg, |
| 405 |
> |
"QuickKill didn't work right. n_active = %d, and nWaters = %d\n", |
| 406 |
> |
n_active, nWaters ); |
| 407 |
> |
painCave.isFatal = 1; |
| 408 |
> |
simError(); |
| 409 |
> |
} |
| 410 |
> |
|
| 411 |
> |
// clean up our messes before building the final system. |
| 412 |
> |
|
| 413 |
> |
for(i=0; i<nAtoms; i++){ |
| 414 |
> |
|
| 415 |
> |
delete atoms[i]; |
| 416 |
> |
} |
| 417 |
> |
Atom::destroyArrays(); |
| 418 |
> |
|
| 419 |
> |
|
| 420 |
> |
// create the real Atom arrays |
| 421 |
> |
|
| 422 |
> |
nAtoms = 0; |
| 423 |
> |
molIndex = 0; |
| 424 |
> |
molStart = new int[nLipids + nWaters]; |
| 425 |
> |
|
| 426 |
> |
for(j=0; j<nLipids; j++){ |
| 427 |
> |
molStart[molIndex] = nAtoms; |
| 428 |
> |
molIndex++; |
| 429 |
> |
nAtoms += lipidNatoms; |
| 430 |
> |
} |
| 431 |
> |
|
| 432 |
> |
for(j=0; j<nWaters; j++){ |
| 433 |
> |
molStart[molIndex] = nAtoms; |
| 434 |
> |
molIndex++; |
| 435 |
> |
nAtoms += waterNatoms; |
| 436 |
> |
} |
| 437 |
> |
|
| 438 |
> |
|
| 439 |
> |
Atom::createArrays( nAtoms ); |
| 440 |
> |
atoms = new Atom*[nAtoms]; |
| 441 |
> |
|
| 442 |
> |
|
| 443 |
> |
// initialize lipid positions |
| 444 |
> |
|
| 445 |
> |
molIndex = 0; |
| 446 |
> |
for(i=0; i<nLipids; i++ ){ |
| 447 |
> |
lipidLocate->placeMol( lipidSites[i].pos, lipidSites[i].rot, atoms, |
| 448 |
> |
molStart[molIndex] ); |
| 449 |
> |
molIndex++; |
| 450 |
> |
} |
| 451 |
> |
|
| 452 |
> |
// initialize the water positions |
| 453 |
> |
|
| 454 |
> |
for(i=0; i<newWaters; i++){ |
| 455 |
> |
|
| 456 |
> |
if( isActive[i] ){ |
| 457 |
> |
|
| 458 |
> |
getRandomRot( waterSites[i].rot ); |
| 459 |
> |
waterLocate->placeMol( waterSites[i].pos, waterSites[i].rot, atoms, |
| 460 |
> |
molStart[molIndex] ); |
| 461 |
> |
molIndex++; |
| 462 |
> |
} |
| 463 |
|
} |
| 150 |
– |
strcpy( simnfo->ensemble, ensemble ); |
| 464 |
|
|
| 465 |
+ |
// set up the SimInfo object |
| 466 |
+ |
|
| 467 |
+ |
bsInfo.boxX = box_x; |
| 468 |
+ |
bsInfo.boxY = box_y; |
| 469 |
+ |
bsInfo.boxZ = box_z; |
| 470 |
+ |
|
| 471 |
+ |
simnfo = new SimInfo(); |
| 472 |
+ |
simnfo->n_atoms = nAtoms; |
| 473 |
+ |
simnfo->box_x = bsInfo.boxX; |
| 474 |
+ |
simnfo->box_y = bsInfo.boxY; |
| 475 |
+ |
simnfo->box_z = bsInfo.boxZ; |
| 476 |
+ |
|
| 477 |
+ |
sprintf( simnfo->sampleName, "%s.dump", bsInfo.outPrefix ); |
| 478 |
+ |
sprintf( simnfo->finalName, "%s.init", bsInfo.outPrefix ); |
| 479 |
|
|
| 480 |
+ |
simnfo->atoms = atoms; |
| 481 |
+ |
|
| 482 |
+ |
// set up the writer and write out |
| 483 |
+ |
|
| 484 |
+ |
writer = new DumpWriter( simnfo ); |
| 485 |
+ |
writer->writeFinal(); |
| 486 |
+ |
|
| 487 |
+ |
// clean up the memory |
| 488 |
+ |
|
| 489 |
+ |
// if( molMap != NULL ) delete[] molMap; |
| 490 |
+ |
// if( cardDeck != NULL ) delete[] cardDeck; |
| 491 |
+ |
// if( locate != NULL ){ |
| 492 |
+ |
// for(i=0; i<bsInfo.nComponents; i++){ |
| 493 |
+ |
// delete locate[i]; |
| 494 |
+ |
// } |
| 495 |
+ |
// delete[] locate; |
| 496 |
+ |
// } |
| 497 |
+ |
// if( atoms != NULL ){ |
| 498 |
+ |
// for(i=0; i<nAtoms; i++){ |
| 499 |
+ |
// delete atoms[i]; |
| 500 |
+ |
// } |
| 501 |
+ |
// Atom::destroyArrays(); |
| 502 |
+ |
// delete[] atoms; |
| 503 |
+ |
// } |
| 504 |
+ |
// if( molSeq != NULL ) delete[] molSeq; |
| 505 |
+ |
// if( simnfo != NULL ) delete simnfo; |
| 506 |
+ |
// if( writer != NULL ) delete writer; |
| 507 |
|
|
| 508 |
< |
delete stamps; |
| 155 |
< |
delete globals; |
| 508 |
> |
return 1; |
| 509 |
|
} |
| 510 |
+ |
|
| 511 |
+ |
|
| 512 |
+ |
|
| 513 |
+ |
int Old_buildRandomBilayer( void ){ |
| 514 |
+ |
|
| 515 |
+ |
int i,j,k; |
| 516 |
+ |
int nAtoms, atomIndex, molIndex, molID; |
| 517 |
+ |
int* molSeq; |
| 518 |
+ |
int* molMap; |
| 519 |
+ |
int* molStart; |
| 520 |
+ |
int* cardDeck; |
| 521 |
+ |
int deckSize; |
| 522 |
+ |
int rSite, rCard; |
| 523 |
+ |
double cell; |
| 524 |
+ |
int nCells, nSites, siteIndex; |
| 525 |
+ |
double rot[3][3]; |
| 526 |
+ |
double pos[3]; |
| 527 |
+ |
|
| 528 |
+ |
Atom** atoms; |
| 529 |
+ |
SimInfo* simnfo; |
| 530 |
+ |
DumpWriter* writer; |
| 531 |
+ |
MoLocator** locate; |
| 532 |
+ |
|
| 533 |
+ |
// initialize functions and variables |
| 534 |
+ |
|
| 535 |
+ |
srand48( RAND_SEED ); |
| 536 |
+ |
molSeq = NULL; |
| 537 |
+ |
molStart = NULL; |
| 538 |
+ |
molMap = NULL; |
| 539 |
+ |
cardDeck = NULL; |
| 540 |
+ |
atoms = NULL; |
| 541 |
+ |
locate = NULL; |
| 542 |
+ |
simnfo = NULL; |
| 543 |
+ |
writer = NULL; |
| 544 |
+ |
|
| 545 |
+ |
// calculate the number of cells in the fcc box |
| 546 |
+ |
|
| 547 |
+ |
nCells = 0; |
| 548 |
+ |
nSites = 0; |
| 549 |
+ |
while( nSites < bsInfo.totNmol ){ |
| 550 |
+ |
nCells++; |
| 551 |
+ |
nSites = 4.0 * pow( (double)nCells, 3.0 ); |
| 552 |
+ |
} |
| 553 |
+ |
|
| 554 |
+ |
|
| 555 |
+ |
// create the molMap and cardDeck arrays |
| 556 |
+ |
|
| 557 |
+ |
molMap = new int[nSites]; |
| 558 |
+ |
cardDeck = new int[nSites]; |
| 559 |
+ |
|
| 560 |
+ |
for(i=0; i<nSites; i++){ |
| 561 |
+ |
molMap[i] = -1; |
| 562 |
+ |
cardDeck[i] = i; |
| 563 |
+ |
} |
| 564 |
+ |
|
| 565 |
+ |
// randomly place the molecules on the sites |
| 566 |
+ |
|
| 567 |
+ |
deckSize = nSites; |
| 568 |
+ |
for(i=0; i<bsInfo.totNmol; i++){ |
| 569 |
+ |
rCard = (int)( deckSize * drand48() ); |
| 570 |
+ |
rSite = cardDeck[rCard]; |
| 571 |
+ |
molMap[rSite] = i; |
| 572 |
+ |
|
| 573 |
+ |
// book keep the card deck; |
| 574 |
+ |
|
| 575 |
+ |
deckSize--; |
| 576 |
+ |
cardDeck[rCard] = cardDeck[deckSize]; |
| 577 |
+ |
} |
| 578 |
+ |
|
| 579 |
+ |
|
| 580 |
+ |
// create the MoLocator and Atom arrays |
| 581 |
+ |
|
| 582 |
+ |
nAtoms = 0; |
| 583 |
+ |
molIndex = 0; |
| 584 |
+ |
locate = new MoLocator*[bsInfo.nComponents]; |
| 585 |
+ |
molSeq = new int[bsInfo.totNmol]; |
| 586 |
+ |
molStart = new int[bsInfo.totNmol]; |
| 587 |
+ |
for(i=0; i<bsInfo.nComponents; i++){ |
| 588 |
+ |
locate[i] = new MoLocator( bsInfo.compStamps[i] ); |
| 589 |
+ |
for(j=0; j<bsInfo.componentsNmol[i]; j++){ |
| 590 |
+ |
molSeq[molIndex] = i; |
| 591 |
+ |
molStart[molIndex] = nAtoms; |
| 592 |
+ |
molIndex++; |
| 593 |
+ |
nAtoms += bsInfo.compStamps[i]->getNAtoms(); |
| 594 |
+ |
} |
| 595 |
+ |
} |
| 596 |
+ |
|
| 597 |
+ |
Atom::createArrays( nAtoms ); |
| 598 |
+ |
atoms = new Atom*[nAtoms]; |
| 599 |
+ |
|
| 600 |
+ |
|
| 601 |
+ |
// place the molecules at each FCC site |
| 602 |
+ |
|
| 603 |
+ |
cell = 5.0; |
| 604 |
+ |
for(i=0; i<bsInfo.nComponents; i++){ |
| 605 |
+ |
if(cell < locate[i]->getMaxLength() ) cell = locate[i]->getMaxLength(); |
| 606 |
+ |
} |
| 607 |
+ |
cell *= 1.2; // add a little buffer |
| 608 |
+ |
|
| 609 |
+ |
cell *= M_SQRT2; |
| 610 |
+ |
|
| 611 |
+ |
siteIndex = 0; |
| 612 |
+ |
for(i=0; i<nCells; i++){ |
| 613 |
+ |
for(j=0; j<nCells; j++){ |
| 614 |
+ |
for(k=0; k<nCells; k++){ |
| 615 |
+ |
|
| 616 |
+ |
if( molMap[siteIndex] >= 0 ){ |
| 617 |
+ |
pos[0] = i * cell; |
| 618 |
+ |
pos[1] = j * cell; |
| 619 |
+ |
pos[2] = k * cell; |
| 620 |
+ |
|
| 621 |
+ |
getRandomRot( rot ); |
| 622 |
+ |
molID = molSeq[molMap[siteIndex]]; |
| 623 |
+ |
atomIndex = molStart[ molMap[siteIndex] ]; |
| 624 |
+ |
locate[molID]->placeMol( pos, rot, atoms, atomIndex ); |
| 625 |
+ |
} |
| 626 |
+ |
siteIndex++; |
| 627 |
+ |
|
| 628 |
+ |
if( molMap[siteIndex] >= 0 ){ |
| 629 |
+ |
pos[0] = i * cell + (0.5 * cell); |
| 630 |
+ |
pos[1] = j * cell; |
| 631 |
+ |
pos[2] = k * cell + (0.5 * cell); |
| 632 |
+ |
|
| 633 |
+ |
getRandomRot( rot ); |
| 634 |
+ |
molID = molSeq[molMap[siteIndex]]; |
| 635 |
+ |
atomIndex = molStart[ molMap[siteIndex] ]; |
| 636 |
+ |
locate[molID]->placeMol( pos, rot, atoms, atomIndex ); |
| 637 |
+ |
} |
| 638 |
+ |
siteIndex++; |
| 639 |
+ |
|
| 640 |
+ |
if( molMap[siteIndex] >= 0 ){ |
| 641 |
+ |
pos[0] = i * cell + (0.5 * cell); |
| 642 |
+ |
pos[1] = j * cell + (0.5 * cell); |
| 643 |
+ |
pos[2] = k * cell; |
| 644 |
+ |
|
| 645 |
+ |
getRandomRot( rot ); |
| 646 |
+ |
molID = molSeq[molMap[siteIndex]]; |
| 647 |
+ |
atomIndex = molStart[ molMap[siteIndex] ]; |
| 648 |
+ |
locate[molID]->placeMol( pos, rot, atoms, atomIndex ); |
| 649 |
+ |
} |
| 650 |
+ |
siteIndex++; |
| 651 |
+ |
|
| 652 |
+ |
if( molMap[siteIndex] >= 0 ){ |
| 653 |
+ |
pos[0] = i * cell; |
| 654 |
+ |
pos[1] = j * cell + (0.5 * cell); |
| 655 |
+ |
pos[2] = k * cell + (0.5 * cell); |
| 656 |
+ |
|
| 657 |
+ |
getRandomRot( rot ); |
| 658 |
+ |
molID = molSeq[molMap[siteIndex]]; |
| 659 |
+ |
atomIndex = molStart[ molMap[siteIndex] ]; |
| 660 |
+ |
locate[molID]->placeMol( pos, rot, atoms, atomIndex ); |
| 661 |
+ |
} |
| 662 |
+ |
siteIndex++; |
| 663 |
+ |
} |
| 664 |
+ |
} |
| 665 |
+ |
} |
| 666 |
+ |
|
| 667 |
+ |
// set up the SimInfo object |
| 668 |
+ |
|
| 669 |
+ |
bsInfo.boxX = nCells * cell; |
| 670 |
+ |
bsInfo.boxY = nCells * cell; |
| 671 |
+ |
bsInfo.boxZ = nCells * cell; |
| 672 |
+ |
|
| 673 |
+ |
simnfo = new SimInfo(); |
| 674 |
+ |
simnfo->n_atoms = nAtoms; |
| 675 |
+ |
simnfo->box_x = bsInfo.boxX; |
| 676 |
+ |
simnfo->box_y = bsInfo.boxY; |
| 677 |
+ |
simnfo->box_z = bsInfo.boxZ; |
| 678 |
+ |
|
| 679 |
+ |
sprintf( simnfo->sampleName, "%s.dump", bsInfo.outPrefix ); |
| 680 |
+ |
sprintf( simnfo->finalName, "%s.init", bsInfo.outPrefix ); |
| 681 |
+ |
|
| 682 |
+ |
simnfo->atoms = atoms; |
| 683 |
+ |
|
| 684 |
+ |
// set up the writer and write out |
| 685 |
+ |
|
| 686 |
+ |
writer = new DumpWriter( simnfo ); |
| 687 |
+ |
writer->writeFinal(); |
| 688 |
+ |
|
| 689 |
+ |
// clean up the memory |
| 690 |
+ |
|
| 691 |
+ |
if( molMap != NULL ) delete[] molMap; |
| 692 |
+ |
if( cardDeck != NULL ) delete[] cardDeck; |
| 693 |
+ |
if( locate != NULL ){ |
| 694 |
+ |
for(i=0; i<bsInfo.nComponents; i++){ |
| 695 |
+ |
delete locate[i]; |
| 696 |
+ |
} |
| 697 |
+ |
delete[] locate; |
| 698 |
+ |
} |
| 699 |
+ |
if( atoms != NULL ){ |
| 700 |
+ |
for(i=0; i<nAtoms; i++){ |
| 701 |
+ |
delete atoms[i]; |
| 702 |
+ |
} |
| 703 |
+ |
Atom::destroyArrays(); |
| 704 |
+ |
delete[] atoms; |
| 705 |
+ |
} |
| 706 |
+ |
if( molSeq != NULL ) delete[] molSeq; |
| 707 |
+ |
if( simnfo != NULL ) delete simnfo; |
| 708 |
+ |
if( writer != NULL ) delete writer; |
| 709 |
+ |
|
| 710 |
+ |
return 1; |
| 711 |
+ |
} |
| 712 |
+ |
|
| 713 |
+ |
|
| 714 |
+ |
void getRandomRot( double rot[3][3] ){ |
| 715 |
+ |
|
| 716 |
+ |
double theta, phi, psi; |
| 717 |
+ |
double cosTheta; |
| 718 |
+ |
|
| 719 |
+ |
// select random phi, psi, and cosTheta |
| 720 |
+ |
|
| 721 |
+ |
phi = 2.0 * M_PI * drand48(); |
| 722 |
+ |
psi = 2.0 * M_PI * drand48(); |
| 723 |
+ |
cosTheta = (2.0 * drand48()) - 1.0; // sample cos -1 to 1 |
| 724 |
+ |
|
| 725 |
+ |
theta = acos( cosTheta ); |
| 726 |
+ |
|
| 727 |
+ |
rot[0][0] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi)); |
| 728 |
+ |
rot[0][1] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi)); |
| 729 |
+ |
rot[0][2] = sin(theta) * sin(psi); |
| 730 |
+ |
|
| 731 |
+ |
rot[1][0] = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi)); |
| 732 |
+ |
rot[1][1] = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi)); |
| 733 |
+ |
rot[1][2] = sin(theta) * cos(psi); |
| 734 |
+ |
|
| 735 |
+ |
rot[2][0] = sin(phi) * sin(theta); |
| 736 |
+ |
rot[2][1] = -cos(phi) * sin(theta); |
| 737 |
+ |
rot[2][2] = cos(theta); |
| 738 |
+ |
} |
| 739 |
+ |
|
| 740 |
+ |
|
| 741 |
+ |
|
| 742 |
+ |
void map( double &x, double &y, double &z, |
| 743 |
+ |
double boxX, double boxY, double boxZ ){ |
| 744 |
+ |
|
| 745 |
+ |
if(x < 0) x -= boxX * (double)( (int)( (x / boxX) - 0.5 ) ); |
| 746 |
+ |
else x -= boxX * (double)( (int)( (x / boxX ) + 0.5)); |
| 747 |
+ |
|
| 748 |
+ |
if(y < 0) y -= boxY * (double)( (int)( (y / boxY) - 0.5 ) ); |
| 749 |
+ |
else y -= boxY * (double)( (int)( (y / boxY ) + 0.5)); |
| 750 |
+ |
|
| 751 |
+ |
if(z < 0) z -= boxZ * (double)( (int)( (z / boxZ) - 0.5 ) ); |
| 752 |
+ |
else z -= boxZ * (double)( (int)( (z / boxZ ) + 0.5)); |
| 753 |
+ |
} |
