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#include <algorithm> |
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#include <cstdlib> |
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#include <iostream> |
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#include <cmath> |
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#include <string> |
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#include "SimSetup.hpp" |
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#include "ReadWrite.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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|
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// some defines for ensemble and Forcefield cases |
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|
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#define NVE_ENS 0 |
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#define NVT_ENS 1 |
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#define NPTi_ENS 2 |
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< |
#define NPTf_ENS 3 |
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#define NPTim_ENS 4 |
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#define NPTfm_ENS 5 |
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#define NVE_ENS 0 |
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#define NVT_ENS 1 |
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#define NPTi_ENS 2 |
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#define NPTf_ENS 3 |
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#define NPTim_ENS 4 |
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#define NPTfm_ENS 5 |
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|
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|
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#define FF_DUFF 0 |
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#define FF_LJ 1 |
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#define FF_EAM 2 |
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|
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using namespace std; |
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|
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SimSetup::SimSetup(){ |
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|
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isInfoArray = 0; |
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nInfo = 1; |
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|
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stamps = new MakeStamps(); |
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globals = new Globals(); |
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|
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|
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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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delete globals; |
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} |
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|
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void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) { |
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info = the_info; |
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nInfo = theNinfo; |
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isInfoArray = 1; |
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} |
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|
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|
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void SimSetup::parseFile( char* fileName ){ |
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|
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#ifdef IS_MPI |
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|
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#endif // is_mpi |
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|
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void SimSetup::createSim( void ){ |
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void SimSetup::createSim(void){ |
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|
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MakeStamps *the_stamps; |
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Globals* the_globals; |
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int i, j, k, globalAtomIndex; |
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|
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int ensembleCase; |
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int ffCase; |
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// gather all of the information from the Bass file |
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|
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gatherInfo(); |
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|
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// creation of complex system objects |
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|
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sysObjectsCreation(); |
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|
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// check on the post processing info |
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|
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finalInfoCheck(); |
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|
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// initialize the system coordinates |
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|
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if( !isInfoArray ) initSystemCoords(); |
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|
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// make the output filenames |
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|
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makeOutNames(); |
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|
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// make the integrator |
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|
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ensembleCase = -1; |
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ffCase = -1; |
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makeIntegrator(); |
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|
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#ifdef IS_MPI |
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mpiSim->mpiRefresh(); |
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#endif |
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|
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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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// initialize the Fortran |
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|
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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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initFortran(); |
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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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n_components = the_globals->getNComponents(); |
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strcpy( force_field, the_globals->getForceField() ); |
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|
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|
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} |
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|
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|
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void SimSetup::makeMolecules( void ){ |
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|
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int k,l; |
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int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
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molInit molInfo; |
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DirectionalAtom* dAtom; |
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LinkedAssign* extras; |
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LinkedAssign* current_extra; |
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AtomStamp* currentAtom; |
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BondStamp* currentBond; |
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BendStamp* currentBend; |
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TorsionStamp* currentTorsion; |
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|
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bond_pair* theBonds; |
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bend_set* theBends; |
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torsion_set* theTorsions; |
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|
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|
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//init the forceField paramters |
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|
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the_ff->readParams(); |
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|
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|
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// init the atoms |
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|
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double ux, uy, uz, u, uSqr; |
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|
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for(k=0; k<nInfo; k++){ |
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|
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the_ff->setSimInfo( &(info[k]) ); |
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|
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atomOffset = 0; |
168 |
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excludeOffset = 0; |
169 |
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for(i=0; i<info[k].n_mol; i++){ |
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|
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stampID = info[k].molecules[i].getStampID(); |
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|
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molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
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molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
175 |
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molInfo.nBends = comp_stamps[stampID]->getNBends(); |
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molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
177 |
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molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
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|
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molInfo.myAtoms = &(info[k].atoms[atomOffset]); |
180 |
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molInfo.myExcludes = &(info[k].excludes[excludeOffset]); |
181 |
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molInfo.myBonds = new Bond*[molInfo.nBonds]; |
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molInfo.myBends = new Bend*[molInfo.nBends]; |
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molInfo.myTorsions = new Torsion*[molInfo.nTorsions]; |
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|
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theBonds = new bond_pair[molInfo.nBonds]; |
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theBends = new bend_set[molInfo.nBends]; |
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theTorsions = new torsion_set[molInfo.nTorsions]; |
188 |
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|
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// make the Atoms |
190 |
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|
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for(j=0; j<molInfo.nAtoms; j++){ |
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|
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currentAtom = comp_stamps[stampID]->getAtom( j ); |
194 |
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if( currentAtom->haveOrientation() ){ |
195 |
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|
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dAtom = new DirectionalAtom( (j + atomOffset), |
197 |
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info[k].getConfiguration() ); |
198 |
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info[k].n_oriented++; |
199 |
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molInfo.myAtoms[j] = dAtom; |
200 |
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|
201 |
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ux = currentAtom->getOrntX(); |
202 |
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uy = currentAtom->getOrntY(); |
203 |
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uz = currentAtom->getOrntZ(); |
204 |
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|
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uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
206 |
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|
207 |
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u = sqrt( uSqr ); |
208 |
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ux = ux / u; |
209 |
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uy = uy / u; |
210 |
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uz = uz / u; |
211 |
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|
212 |
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dAtom->setSUx( ux ); |
213 |
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dAtom->setSUy( uy ); |
214 |
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dAtom->setSUz( uz ); |
215 |
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} |
216 |
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else{ |
217 |
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molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset), |
218 |
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info[k].getConfiguration() ); |
219 |
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} |
220 |
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molInfo.myAtoms[j]->setType( currentAtom->getType() ); |
221 |
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|
222 |
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#ifdef IS_MPI |
223 |
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|
224 |
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molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
225 |
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|
226 |
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#endif // is_mpi |
227 |
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} |
228 |
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|
229 |
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// make the bonds |
230 |
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for(j=0; j<molInfo.nBonds; j++){ |
231 |
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|
232 |
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currentBond = comp_stamps[stampID]->getBond( j ); |
233 |
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theBonds[j].a = currentBond->getA() + atomOffset; |
234 |
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theBonds[j].b = currentBond->getB() + atomOffset; |
235 |
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|
236 |
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exI = theBonds[j].a; |
237 |
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exJ = theBonds[j].b; |
238 |
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|
239 |
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// exclude_I must always be the smaller of the pair |
240 |
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if( exI > exJ ){ |
241 |
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tempEx = exI; |
242 |
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exI = exJ; |
243 |
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exJ = tempEx; |
244 |
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} |
245 |
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#ifdef IS_MPI |
246 |
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tempEx = exI; |
247 |
+ |
exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
248 |
+ |
tempEx = exJ; |
249 |
+ |
exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
250 |
+ |
|
251 |
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info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
252 |
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#else // isn't MPI |
253 |
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|
254 |
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info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
255 |
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#endif //is_mpi |
256 |
+ |
} |
257 |
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excludeOffset += molInfo.nBonds; |
258 |
+ |
|
259 |
+ |
//make the bends |
260 |
+ |
for(j=0; j<molInfo.nBends; j++){ |
261 |
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|
262 |
+ |
currentBend = comp_stamps[stampID]->getBend( j ); |
263 |
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theBends[j].a = currentBend->getA() + atomOffset; |
264 |
+ |
theBends[j].b = currentBend->getB() + atomOffset; |
265 |
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theBends[j].c = currentBend->getC() + atomOffset; |
266 |
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|
267 |
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if( currentBend->haveExtras() ){ |
268 |
+ |
|
269 |
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extras = currentBend->getExtras(); |
270 |
+ |
current_extra = extras; |
271 |
+ |
|
272 |
+ |
while( current_extra != NULL ){ |
273 |
+ |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
274 |
+ |
|
275 |
+ |
switch( current_extra->getType() ){ |
276 |
+ |
|
277 |
+ |
case 0: |
278 |
+ |
theBends[j].ghost = |
279 |
+ |
current_extra->getInt() + atomOffset; |
280 |
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theBends[j].isGhost = 1; |
281 |
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break; |
282 |
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|
283 |
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case 1: |
284 |
+ |
theBends[j].ghost = |
285 |
+ |
(int)current_extra->getDouble() + atomOffset; |
286 |
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theBends[j].isGhost = 1; |
287 |
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break; |
288 |
+ |
|
289 |
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default: |
290 |
+ |
sprintf( painCave.errMsg, |
291 |
+ |
"SimSetup Error: ghostVectorSource was neither a " |
292 |
+ |
"double nor an int.\n" |
293 |
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"-->Bend[%d] in %s\n", |
294 |
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j, comp_stamps[stampID]->getID() ); |
295 |
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painCave.isFatal = 1; |
296 |
+ |
simError(); |
297 |
+ |
} |
298 |
+ |
} |
299 |
+ |
|
300 |
+ |
else{ |
301 |
+ |
|
302 |
+ |
sprintf( painCave.errMsg, |
303 |
+ |
"SimSetup Error: unhandled bend assignment:\n" |
304 |
+ |
" -->%s in Bend[%d] in %s\n", |
305 |
+ |
current_extra->getlhs(), |
306 |
+ |
j, comp_stamps[stampID]->getID() ); |
307 |
+ |
painCave.isFatal = 1; |
308 |
+ |
simError(); |
309 |
+ |
} |
310 |
+ |
|
311 |
+ |
current_extra = current_extra->getNext(); |
312 |
+ |
} |
313 |
+ |
} |
314 |
+ |
|
315 |
+ |
if( !theBends[j].isGhost ){ |
316 |
+ |
|
317 |
+ |
exI = theBends[j].a; |
318 |
+ |
exJ = theBends[j].c; |
319 |
+ |
} |
320 |
+ |
else{ |
321 |
+ |
|
322 |
+ |
exI = theBends[j].a; |
323 |
+ |
exJ = theBends[j].b; |
324 |
+ |
} |
325 |
+ |
|
326 |
+ |
// exclude_I must always be the smaller of the pair |
327 |
+ |
if( exI > exJ ){ |
328 |
+ |
tempEx = exI; |
329 |
+ |
exI = exJ; |
330 |
+ |
exJ = tempEx; |
331 |
+ |
} |
332 |
+ |
#ifdef IS_MPI |
333 |
+ |
tempEx = exI; |
334 |
+ |
exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
335 |
+ |
tempEx = exJ; |
336 |
+ |
exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
337 |
+ |
|
338 |
+ |
info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
339 |
+ |
#else // isn't MPI |
340 |
+ |
info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
341 |
+ |
#endif //is_mpi |
342 |
+ |
} |
343 |
+ |
excludeOffset += molInfo.nBends; |
344 |
+ |
|
345 |
+ |
for(j=0; j<molInfo.nTorsions; j++){ |
346 |
+ |
|
347 |
+ |
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
348 |
+ |
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
349 |
+ |
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
350 |
+ |
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
351 |
+ |
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
352 |
+ |
|
353 |
+ |
exI = theTorsions[j].a; |
354 |
+ |
exJ = theTorsions[j].d; |
355 |
+ |
|
356 |
+ |
// exclude_I must always be the smaller of the pair |
357 |
+ |
if( exI > exJ ){ |
358 |
+ |
tempEx = exI; |
359 |
+ |
exI = exJ; |
360 |
+ |
exJ = tempEx; |
361 |
+ |
} |
362 |
+ |
#ifdef IS_MPI |
363 |
+ |
tempEx = exI; |
364 |
+ |
exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
365 |
+ |
tempEx = exJ; |
366 |
+ |
exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
367 |
+ |
|
368 |
+ |
info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
369 |
+ |
#else // isn't MPI |
370 |
+ |
info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
371 |
+ |
#endif //is_mpi |
372 |
+ |
} |
373 |
+ |
excludeOffset += molInfo.nTorsions; |
374 |
+ |
|
375 |
+ |
|
376 |
+ |
// send the arrays off to the forceField for init. |
377 |
+ |
|
378 |
+ |
the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms ); |
379 |
+ |
the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds ); |
380 |
+ |
the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends ); |
381 |
+ |
the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions ); |
382 |
+ |
|
383 |
+ |
|
384 |
+ |
info[k].molecules[i].initialize( molInfo ); |
385 |
+ |
|
386 |
+ |
|
387 |
+ |
atomOffset += molInfo.nAtoms; |
388 |
+ |
delete[] theBonds; |
389 |
+ |
delete[] theBends; |
390 |
+ |
delete[] theTorsions; |
391 |
+ |
} |
392 |
+ |
} |
393 |
+ |
|
394 |
+ |
#ifdef IS_MPI |
395 |
+ |
sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
396 |
+ |
MPIcheckPoint(); |
397 |
+ |
#endif // is_mpi |
398 |
+ |
|
399 |
+ |
// clean up the forcefield |
400 |
+ |
|
401 |
+ |
the_ff->calcRcut(); |
402 |
+ |
the_ff->cleanMe(); |
403 |
+ |
|
404 |
+ |
} |
405 |
+ |
|
406 |
+ |
void SimSetup::initFromBass( void ){ |
407 |
+ |
|
408 |
+ |
int i, j, k; |
409 |
+ |
int n_cells; |
410 |
+ |
double cellx, celly, cellz; |
411 |
+ |
double temp1, temp2, temp3; |
412 |
+ |
int n_per_extra; |
413 |
+ |
int n_extra; |
414 |
+ |
int have_extra, done; |
415 |
+ |
|
416 |
+ |
double vel[3]; |
417 |
+ |
vel[0] = 0.0; |
418 |
+ |
vel[1] = 0.0; |
419 |
+ |
vel[2] = 0.0; |
420 |
+ |
|
421 |
+ |
temp1 = (double)tot_nmol / 4.0; |
422 |
+ |
temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
423 |
+ |
temp3 = ceil( temp2 ); |
424 |
+ |
|
425 |
+ |
have_extra =0; |
426 |
+ |
if( temp2 < temp3 ){ // we have a non-complete lattice |
427 |
+ |
have_extra =1; |
428 |
+ |
|
429 |
+ |
n_cells = (int)temp3 - 1; |
430 |
+ |
cellx = info[0].boxL[0] / temp3; |
431 |
+ |
celly = info[0].boxL[1] / temp3; |
432 |
+ |
cellz = info[0].boxL[2] / temp3; |
433 |
+ |
n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
434 |
+ |
temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
435 |
+ |
n_per_extra = (int)ceil( temp1 ); |
436 |
+ |
|
437 |
+ |
if( n_per_extra > 4){ |
438 |
+ |
sprintf( painCave.errMsg, |
439 |
+ |
"SimSetup error. There has been an error in constructing" |
440 |
+ |
" the non-complete lattice.\n" ); |
441 |
+ |
painCave.isFatal = 1; |
442 |
+ |
simError(); |
443 |
+ |
} |
444 |
+ |
} |
445 |
+ |
else{ |
446 |
+ |
n_cells = (int)temp3; |
447 |
+ |
cellx = info[0].boxL[0] / temp3; |
448 |
+ |
celly = info[0].boxL[1] / temp3; |
449 |
+ |
cellz = info[0].boxL[2] / temp3; |
450 |
+ |
} |
451 |
+ |
|
452 |
+ |
current_mol = 0; |
453 |
+ |
current_comp_mol = 0; |
454 |
+ |
current_comp = 0; |
455 |
+ |
current_atom_ndx = 0; |
456 |
+ |
|
457 |
+ |
for( i=0; i < n_cells ; i++ ){ |
458 |
+ |
for( j=0; j < n_cells; j++ ){ |
459 |
+ |
for( k=0; k < n_cells; k++ ){ |
460 |
+ |
|
461 |
+ |
makeElement( i * cellx, |
462 |
+ |
j * celly, |
463 |
+ |
k * cellz ); |
464 |
+ |
|
465 |
+ |
makeElement( i * cellx + 0.5 * cellx, |
466 |
+ |
j * celly + 0.5 * celly, |
467 |
+ |
k * cellz ); |
468 |
+ |
|
469 |
+ |
makeElement( i * cellx, |
470 |
+ |
j * celly + 0.5 * celly, |
471 |
+ |
k * cellz + 0.5 * cellz ); |
472 |
+ |
|
473 |
+ |
makeElement( i * cellx + 0.5 * cellx, |
474 |
+ |
j * celly, |
475 |
+ |
k * cellz + 0.5 * cellz ); |
476 |
+ |
} |
477 |
+ |
} |
478 |
+ |
} |
479 |
+ |
|
480 |
+ |
if( have_extra ){ |
481 |
+ |
done = 0; |
482 |
+ |
|
483 |
+ |
int start_ndx; |
484 |
+ |
for( i=0; i < (n_cells+1) && !done; i++ ){ |
485 |
+ |
for( j=0; j < (n_cells+1) && !done; j++ ){ |
486 |
+ |
|
487 |
+ |
if( i < n_cells ){ |
488 |
+ |
|
489 |
+ |
if( j < n_cells ){ |
490 |
+ |
start_ndx = n_cells; |
491 |
+ |
} |
492 |
+ |
else start_ndx = 0; |
493 |
+ |
} |
494 |
+ |
else start_ndx = 0; |
495 |
+ |
|
496 |
+ |
for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
497 |
+ |
|
498 |
+ |
makeElement( i * cellx, |
499 |
+ |
j * celly, |
500 |
+ |
k * cellz ); |
501 |
+ |
done = ( current_mol >= tot_nmol ); |
502 |
+ |
|
503 |
+ |
if( !done && n_per_extra > 1 ){ |
504 |
+ |
makeElement( i * cellx + 0.5 * cellx, |
505 |
+ |
j * celly + 0.5 * celly, |
506 |
+ |
k * cellz ); |
507 |
+ |
done = ( current_mol >= tot_nmol ); |
508 |
+ |
} |
509 |
+ |
|
510 |
+ |
if( !done && n_per_extra > 2){ |
511 |
+ |
makeElement( i * cellx, |
512 |
+ |
j * celly + 0.5 * celly, |
513 |
+ |
k * cellz + 0.5 * cellz ); |
514 |
+ |
done = ( current_mol >= tot_nmol ); |
515 |
+ |
} |
516 |
+ |
|
517 |
+ |
if( !done && n_per_extra > 3){ |
518 |
+ |
makeElement( i * cellx + 0.5 * cellx, |
519 |
+ |
j * celly, |
520 |
+ |
k * cellz + 0.5 * cellz ); |
521 |
+ |
done = ( current_mol >= tot_nmol ); |
522 |
+ |
} |
523 |
+ |
} |
524 |
+ |
} |
525 |
+ |
} |
526 |
+ |
} |
527 |
+ |
|
528 |
+ |
for( i=0; i<info[0].n_atoms; i++ ){ |
529 |
+ |
info[0].atoms[i]->setVel( vel ); |
530 |
+ |
} |
531 |
+ |
} |
532 |
+ |
|
533 |
+ |
void SimSetup::makeElement( double x, double y, double z ){ |
534 |
+ |
|
535 |
+ |
int k; |
536 |
+ |
AtomStamp* current_atom; |
537 |
+ |
DirectionalAtom* dAtom; |
538 |
+ |
double rotMat[3][3]; |
539 |
+ |
double pos[3]; |
540 |
+ |
|
541 |
+ |
for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
542 |
+ |
|
543 |
+ |
current_atom = comp_stamps[current_comp]->getAtom( k ); |
544 |
+ |
if( !current_atom->havePosition() ){ |
545 |
+ |
sprintf( painCave.errMsg, |
546 |
+ |
"SimSetup:initFromBass error.\n" |
547 |
+ |
"\tComponent %s, atom %s does not have a position specified.\n" |
548 |
+ |
"\tThe initialization routine is unable to give a start" |
549 |
+ |
" position.\n", |
550 |
+ |
comp_stamps[current_comp]->getID(), |
551 |
+ |
current_atom->getType() ); |
552 |
+ |
painCave.isFatal = 1; |
553 |
+ |
simError(); |
554 |
+ |
} |
555 |
+ |
|
556 |
+ |
pos[0] = x + current_atom->getPosX(); |
557 |
+ |
pos[1] = y + current_atom->getPosY(); |
558 |
+ |
pos[2] = z + current_atom->getPosZ(); |
559 |
+ |
|
560 |
+ |
info[0].atoms[current_atom_ndx]->setPos( pos ); |
561 |
+ |
|
562 |
+ |
if( info[0].atoms[current_atom_ndx]->isDirectional() ){ |
563 |
+ |
|
564 |
+ |
dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx]; |
565 |
+ |
|
566 |
+ |
rotMat[0][0] = 1.0; |
567 |
+ |
rotMat[0][1] = 0.0; |
568 |
+ |
rotMat[0][2] = 0.0; |
569 |
+ |
|
570 |
+ |
rotMat[1][0] = 0.0; |
571 |
+ |
rotMat[1][1] = 1.0; |
572 |
+ |
rotMat[1][2] = 0.0; |
573 |
+ |
|
574 |
+ |
rotMat[2][0] = 0.0; |
575 |
+ |
rotMat[2][1] = 0.0; |
576 |
+ |
rotMat[2][2] = 1.0; |
577 |
+ |
|
578 |
+ |
dAtom->setA( rotMat ); |
579 |
+ |
} |
580 |
+ |
|
581 |
+ |
current_atom_ndx++; |
582 |
+ |
} |
583 |
+ |
|
584 |
+ |
current_mol++; |
585 |
+ |
current_comp_mol++; |
586 |
+ |
|
587 |
+ |
if( current_comp_mol >= components_nmol[current_comp] ){ |
588 |
+ |
|
589 |
+ |
current_comp_mol = 0; |
590 |
+ |
current_comp++; |
591 |
+ |
} |
592 |
+ |
} |
593 |
+ |
|
594 |
+ |
|
595 |
+ |
void SimSetup::gatherInfo( void ){ |
596 |
+ |
int i,j,k; |
597 |
+ |
|
598 |
+ |
ensembleCase = -1; |
599 |
+ |
ffCase = -1; |
600 |
+ |
|
601 |
+ |
// set the easy ones first |
602 |
+ |
|
603 |
+ |
for( i=0; i<nInfo; i++){ |
604 |
+ |
info[i].target_temp = globals->getTargetTemp(); |
605 |
+ |
info[i].dt = globals->getDt(); |
606 |
+ |
info[i].run_time = globals->getRunTime(); |
607 |
+ |
} |
608 |
+ |
n_components = globals->getNComponents(); |
609 |
+ |
|
610 |
+ |
|
611 |
+ |
// get the forceField |
612 |
+ |
|
613 |
+ |
strcpy( force_field, globals->getForceField() ); |
614 |
+ |
|
615 |
|
if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
616 |
|
else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
617 |
+ |
else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM; |
618 |
|
else{ |
619 |
|
sprintf( painCave.errMsg, |
620 |
|
"SimSetup Error. Unrecognized force field -> %s\n", |
623 |
|
simError(); |
624 |
|
} |
625 |
|
|
626 |
< |
// get the ensemble: |
115 |
< |
strcpy( ensemble, the_globals->getEnsemble() ); |
626 |
> |
// get the ensemble |
627 |
|
|
628 |
+ |
strcpy( ensemble, globals->getEnsemble() ); |
629 |
+ |
|
630 |
|
if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
631 |
|
else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
632 |
|
else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") ) |
644 |
|
strcpy( ensemble, "NVE" ); |
645 |
|
ensembleCase = NVE_ENS; |
646 |
|
} |
647 |
< |
strcpy( simnfo->ensemble, ensemble ); |
647 |
> |
|
648 |
> |
for(i=0; i<nInfo; i++){ |
649 |
> |
|
650 |
> |
strcpy( info[i].ensemble, ensemble ); |
651 |
|
|
652 |
+ |
// get the mixing rule |
653 |
|
|
654 |
< |
// if( !strcasecmp( ensemble, "NPT" ) ) { |
655 |
< |
// the_extendedsystem = new ExtendedSystem( simnfo ); |
139 |
< |
// the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
140 |
< |
// if (the_globals->haveTargetPressure()) |
141 |
< |
// the_extendedsystem->setTargetPressure(the_globals->getTargetPressure()); |
142 |
< |
// else { |
143 |
< |
// sprintf( painCave.errMsg, |
144 |
< |
// "SimSetup error: If you use the constant pressure\n" |
145 |
< |
// " ensemble, you must set targetPressure.\n" |
146 |
< |
// " This was found in the BASS file.\n"); |
147 |
< |
// painCave.isFatal = 1; |
148 |
< |
// simError(); |
149 |
< |
// } |
150 |
< |
|
151 |
< |
// if (the_globals->haveTauThermostat()) |
152 |
< |
// the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
153 |
< |
// else if (the_globals->haveQmass()) |
154 |
< |
// the_extendedsystem->setQmass(the_globals->getQmass()); |
155 |
< |
// else { |
156 |
< |
// sprintf( painCave.errMsg, |
157 |
< |
// "SimSetup error: If you use one of the constant temperature\n" |
158 |
< |
// " ensembles, you must set either tauThermostat or qMass.\n" |
159 |
< |
// " Neither of these was found in the BASS file.\n"); |
160 |
< |
// painCave.isFatal = 1; |
161 |
< |
// simError(); |
162 |
< |
// } |
163 |
< |
|
164 |
< |
// if (the_globals->haveTauBarostat()) |
165 |
< |
// the_extendedsystem->setTauBarostat(the_globals->getTauBarostat()); |
166 |
< |
// else { |
167 |
< |
// sprintf( painCave.errMsg, |
168 |
< |
// "SimSetup error: If you use the constant pressure\n" |
169 |
< |
// " ensemble, you must set tauBarostat.\n" |
170 |
< |
// " This was found in the BASS file.\n"); |
171 |
< |
// painCave.isFatal = 1; |
172 |
< |
// simError(); |
173 |
< |
// } |
174 |
< |
|
175 |
< |
// } else if ( !strcasecmp( ensemble, "NVT") ) { |
176 |
< |
// the_extendedsystem = new ExtendedSystem( simnfo ); |
177 |
< |
// the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
178 |
< |
|
179 |
< |
// if (the_globals->haveTauThermostat()) |
180 |
< |
// the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
181 |
< |
// else if (the_globals->haveQmass()) |
182 |
< |
// the_extendedsystem->setQmass(the_globals->getQmass()); |
183 |
< |
// else { |
184 |
< |
// sprintf( painCave.errMsg, |
185 |
< |
// "SimSetup error: If you use one of the constant temperature\n" |
186 |
< |
// " ensembles, you must set either tauThermostat or qMass.\n" |
187 |
< |
// " Neither of these was found in the BASS file.\n"); |
188 |
< |
// painCave.isFatal = 1; |
189 |
< |
// simError(); |
190 |
< |
// } |
191 |
< |
|
192 |
< |
strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
193 |
< |
simnfo->usePBC = the_globals->getPBC(); |
194 |
< |
|
195 |
< |
int usesDipoles = 0; |
196 |
< |
switch( ffCase ){ |
197 |
< |
|
198 |
< |
case FF_DUFF: |
199 |
< |
the_ff = new DUFF(); |
200 |
< |
usesDipoles = 1; |
201 |
< |
break; |
202 |
< |
|
203 |
< |
case FF_LJ: |
204 |
< |
the_ff = new LJFF(); |
205 |
< |
break; |
206 |
< |
|
207 |
< |
default: |
208 |
< |
sprintf( painCave.errMsg, |
209 |
< |
"SimSetup Error. Unrecognized force field in case statement.\n"); |
210 |
< |
painCave.isFatal = 1; |
211 |
< |
simError(); |
654 |
> |
strcpy( info[i].mixingRule, globals->getMixingRule() ); |
655 |
> |
info[i].usePBC = globals->getPBC(); |
656 |
|
} |
657 |
< |
|
214 |
< |
#ifdef IS_MPI |
215 |
< |
strcpy( checkPointMsg, "ForceField creation successful" ); |
216 |
< |
MPIcheckPoint(); |
217 |
< |
#endif // is_mpi |
218 |
< |
|
657 |
> |
|
658 |
|
// get the components and calculate the tot_nMol and indvidual n_mol |
659 |
< |
the_components = the_globals->getComponents(); |
659 |
> |
|
660 |
> |
the_components = globals->getComponents(); |
661 |
|
components_nmol = new int[n_components]; |
222 |
– |
comp_stamps = new MoleculeStamp*[n_components]; |
662 |
|
|
663 |
< |
if( !the_globals->haveNMol() ){ |
663 |
> |
|
664 |
> |
if( !globals->haveNMol() ){ |
665 |
|
// we don't have the total number of molecules, so we assume it is |
666 |
|
// given in each component |
667 |
|
|
690 |
|
" Please give nMol in the components.\n" ); |
691 |
|
painCave.isFatal = 1; |
692 |
|
simError(); |
253 |
– |
|
254 |
– |
|
255 |
– |
// tot_nmol = the_globals->getNMol(); |
256 |
– |
|
257 |
– |
// //we have the total number of molecules, now we check for molfractions |
258 |
– |
// for( i=0; i<n_components; i++ ){ |
259 |
– |
|
260 |
– |
// if( !the_components[i]->haveMolFraction() ){ |
261 |
– |
|
262 |
– |
// if( !the_components[i]->haveNMol() ){ |
263 |
– |
// //we have a problem |
264 |
– |
// std::cerr << "SimSetup error. Neither molFraction nor " |
265 |
– |
// << " nMol was given in component |
266 |
– |
|
693 |
|
} |
694 |
|
|
695 |
< |
#ifdef IS_MPI |
270 |
< |
strcpy( checkPointMsg, "Have the number of components" ); |
271 |
< |
MPIcheckPoint(); |
272 |
< |
#endif // is_mpi |
273 |
< |
|
274 |
< |
// make an array of molecule stamps that match the components used. |
275 |
< |
// also extract the used stamps out into a separate linked list |
276 |
< |
|
277 |
< |
simnfo->nComponents = n_components; |
278 |
< |
simnfo->componentsNmol = components_nmol; |
279 |
< |
simnfo->compStamps = comp_stamps; |
280 |
< |
simnfo->headStamp = new LinkedMolStamp(); |
695 |
> |
// set the status, sample, and thermal kick times |
696 |
|
|
697 |
< |
char* id; |
283 |
< |
LinkedMolStamp* headStamp = simnfo->headStamp; |
284 |
< |
LinkedMolStamp* currentStamp = NULL; |
285 |
< |
for( i=0; i<n_components; i++ ){ |
697 |
> |
for(i=0; i<nInfo; i++){ |
698 |
|
|
699 |
< |
id = the_components[i]->getType(); |
700 |
< |
comp_stamps[i] = NULL; |
699 |
> |
if( globals->haveSampleTime() ){ |
700 |
> |
info[i].sampleTime = globals->getSampleTime(); |
701 |
> |
info[i].statusTime = info[i].sampleTime; |
702 |
> |
info[i].thermalTime = info[i].sampleTime; |
703 |
> |
} |
704 |
> |
else{ |
705 |
> |
info[i].sampleTime = globals->getRunTime(); |
706 |
> |
info[i].statusTime = info[i].sampleTime; |
707 |
> |
info[i].thermalTime = info[i].sampleTime; |
708 |
> |
} |
709 |
|
|
710 |
< |
// check to make sure the component isn't already in the list |
710 |
> |
if( globals->haveStatusTime() ){ |
711 |
> |
info[i].statusTime = globals->getStatusTime(); |
712 |
> |
} |
713 |
> |
|
714 |
> |
if( globals->haveThermalTime() ){ |
715 |
> |
info[i].thermalTime = globals->getThermalTime(); |
716 |
> |
} |
717 |
|
|
718 |
< |
comp_stamps[i] = headStamp->match( id ); |
719 |
< |
if( comp_stamps[i] == NULL ){ |
718 |
> |
// check for the temperature set flag |
719 |
> |
|
720 |
> |
if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet(); |
721 |
> |
|
722 |
> |
// get some of the tricky things that may still be in the globals |
723 |
> |
|
724 |
> |
double boxVector[3]; |
725 |
> |
if( globals->haveBox() ){ |
726 |
> |
boxVector[0] = globals->getBox(); |
727 |
> |
boxVector[1] = globals->getBox(); |
728 |
> |
boxVector[2] = globals->getBox(); |
729 |
|
|
730 |
< |
// extract the component from the list; |
730 |
> |
info[i].setBox( boxVector ); |
731 |
> |
} |
732 |
> |
else if( globals->haveDensity() ){ |
733 |
|
|
734 |
< |
currentStamp = the_stamps->extractMolStamp( id ); |
735 |
< |
if( currentStamp == NULL ){ |
734 |
> |
double vol; |
735 |
> |
vol = (double)tot_nmol / globals->getDensity(); |
736 |
> |
boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
737 |
> |
boxVector[1] = boxVector[0]; |
738 |
> |
boxVector[2] = boxVector[0]; |
739 |
> |
|
740 |
> |
info[i].setBox( boxVector ); |
741 |
> |
} |
742 |
> |
else{ |
743 |
> |
if( !globals->haveBoxX() ){ |
744 |
|
sprintf( painCave.errMsg, |
745 |
< |
"SimSetup error: Component \"%s\" was not found in the " |
301 |
< |
"list of declared molecules\n", |
302 |
< |
id ); |
745 |
> |
"SimSetup error, no periodic BoxX size given.\n" ); |
746 |
|
painCave.isFatal = 1; |
747 |
|
simError(); |
748 |
|
} |
749 |
+ |
boxVector[0] = globals->getBoxX(); |
750 |
|
|
751 |
< |
headStamp->add( currentStamp ); |
752 |
< |
comp_stamps[i] = headStamp->match( id ); |
751 |
> |
if( !globals->haveBoxY() ){ |
752 |
> |
sprintf( painCave.errMsg, |
753 |
> |
"SimSetup error, no periodic BoxY size given.\n" ); |
754 |
> |
painCave.isFatal = 1; |
755 |
> |
simError(); |
756 |
> |
} |
757 |
> |
boxVector[1] = globals->getBoxY(); |
758 |
> |
|
759 |
> |
if( !globals->haveBoxZ() ){ |
760 |
> |
sprintf( painCave.errMsg, |
761 |
> |
"SimSetup error, no periodic BoxZ size given.\n" ); |
762 |
> |
painCave.isFatal = 1; |
763 |
> |
simError(); |
764 |
> |
} |
765 |
> |
boxVector[2] = globals->getBoxZ(); |
766 |
> |
|
767 |
> |
info[i].setBox( boxVector ); |
768 |
|
} |
310 |
– |
} |
769 |
|
|
770 |
+ |
} |
771 |
+ |
|
772 |
|
#ifdef IS_MPI |
773 |
< |
strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
773 |
> |
strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" ); |
774 |
|
MPIcheckPoint(); |
775 |
|
#endif // is_mpi |
316 |
– |
|
776 |
|
|
777 |
+ |
} |
778 |
|
|
779 |
|
|
780 |
< |
// caclulate the number of atoms, bonds, bends and torsions |
780 |
> |
void SimSetup::finalInfoCheck( void ){ |
781 |
> |
int index; |
782 |
> |
int usesDipoles; |
783 |
> |
int i; |
784 |
|
|
785 |
< |
tot_atoms = 0; |
786 |
< |
tot_bonds = 0; |
324 |
< |
tot_bends = 0; |
325 |
< |
tot_torsions = 0; |
326 |
< |
for( i=0; i<n_components; i++ ){ |
785 |
> |
for(i=0; i<nInfo; i++){ |
786 |
> |
// check electrostatic parameters |
787 |
|
|
788 |
< |
tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
789 |
< |
tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
790 |
< |
tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
791 |
< |
tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
792 |
< |
} |
793 |
< |
|
794 |
< |
tot_SRI = tot_bonds + tot_bends + tot_torsions; |
795 |
< |
|
796 |
< |
simnfo->n_atoms = tot_atoms; |
797 |
< |
simnfo->n_bonds = tot_bonds; |
798 |
< |
simnfo->n_bends = tot_bends; |
799 |
< |
simnfo->n_torsions = tot_torsions; |
800 |
< |
simnfo->n_SRI = tot_SRI; |
341 |
< |
simnfo->n_mol = tot_nmol; |
788 |
> |
index = 0; |
789 |
> |
usesDipoles = 0; |
790 |
> |
while( (index < info[i].n_atoms) && !usesDipoles ){ |
791 |
> |
usesDipoles = (info[i].atoms[index])->hasDipole(); |
792 |
> |
index++; |
793 |
> |
} |
794 |
> |
|
795 |
> |
#ifdef IS_MPI |
796 |
> |
int myUse = usesDipoles; |
797 |
> |
MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
798 |
> |
#endif //is_mpi |
799 |
> |
|
800 |
> |
double theEcr, theEst; |
801 |
|
|
802 |
< |
simnfo->molMembershipArray = new int[tot_atoms]; |
802 |
> |
if (globals->getUseRF() ) { |
803 |
> |
info[i].useReactionField = 1; |
804 |
> |
|
805 |
> |
if( !globals->haveECR() ){ |
806 |
> |
sprintf( painCave.errMsg, |
807 |
> |
"SimSetup Warning: using default value of 1/2 the smallest " |
808 |
> |
"box length for the electrostaticCutoffRadius.\n" |
809 |
> |
"I hope you have a very fast processor!\n"); |
810 |
> |
painCave.isFatal = 0; |
811 |
> |
simError(); |
812 |
> |
double smallest; |
813 |
> |
smallest = info[i].boxL[0]; |
814 |
> |
if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
815 |
> |
if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
816 |
> |
theEcr = 0.5 * smallest; |
817 |
> |
} else { |
818 |
> |
theEcr = globals->getECR(); |
819 |
> |
} |
820 |
> |
|
821 |
> |
if( !globals->haveEST() ){ |
822 |
> |
sprintf( painCave.errMsg, |
823 |
> |
"SimSetup Warning: using default value of 0.05 * the " |
824 |
> |
"electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
825 |
> |
); |
826 |
> |
painCave.isFatal = 0; |
827 |
> |
simError(); |
828 |
> |
theEst = 0.05 * theEcr; |
829 |
> |
} else { |
830 |
> |
theEst= globals->getEST(); |
831 |
> |
} |
832 |
> |
|
833 |
> |
info[i].setEcr( theEcr, theEst ); |
834 |
> |
|
835 |
> |
if(!globals->haveDielectric() ){ |
836 |
> |
sprintf( painCave.errMsg, |
837 |
> |
"SimSetup Error: You are trying to use Reaction Field without" |
838 |
> |
"setting a dielectric constant!\n" |
839 |
> |
); |
840 |
> |
painCave.isFatal = 1; |
841 |
> |
simError(); |
842 |
> |
} |
843 |
> |
info[i].dielectric = globals->getDielectric(); |
844 |
> |
} |
845 |
> |
else { |
846 |
> |
if (usesDipoles) { |
847 |
> |
|
848 |
> |
if( !globals->haveECR() ){ |
849 |
> |
sprintf( painCave.errMsg, |
850 |
> |
"SimSetup Warning: using default value of 1/2 the smallest " |
851 |
> |
"box length for the electrostaticCutoffRadius.\n" |
852 |
> |
"I hope you have a very fast processor!\n"); |
853 |
> |
painCave.isFatal = 0; |
854 |
> |
simError(); |
855 |
> |
double smallest; |
856 |
> |
smallest = info[i].boxL[0]; |
857 |
> |
if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
858 |
> |
if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
859 |
> |
theEcr = 0.5 * smallest; |
860 |
> |
} else { |
861 |
> |
theEcr = globals->getECR(); |
862 |
> |
} |
863 |
> |
|
864 |
> |
if( !globals->haveEST() ){ |
865 |
> |
sprintf( painCave.errMsg, |
866 |
> |
"SimSetup Warning: using default value of 0.05 * the " |
867 |
> |
"electrostaticCutoffRadius for the " |
868 |
> |
"electrostaticSkinThickness\n" |
869 |
> |
); |
870 |
> |
painCave.isFatal = 0; |
871 |
> |
simError(); |
872 |
> |
theEst = 0.05 * theEcr; |
873 |
> |
} else { |
874 |
> |
theEst= globals->getEST(); |
875 |
> |
} |
876 |
> |
|
877 |
> |
info[i].setEcr( theEcr, theEst ); |
878 |
> |
} |
879 |
> |
} |
880 |
> |
} |
881 |
|
|
882 |
|
#ifdef IS_MPI |
883 |
+ |
strcpy( checkPointMsg, "post processing checks out" ); |
884 |
+ |
MPIcheckPoint(); |
885 |
+ |
#endif // is_mpi |
886 |
|
|
887 |
< |
// divide the molecules among processors here. |
348 |
< |
|
349 |
< |
mpiSim = new mpiSimulation( simnfo ); |
350 |
< |
|
351 |
< |
globalIndex = mpiSim->divideLabor(); |
887 |
> |
} |
888 |
|
|
889 |
< |
// set up the local variables |
889 |
> |
void SimSetup::initSystemCoords( void ){ |
890 |
> |
int i; |
891 |
|
|
892 |
< |
int localMol, allMol; |
356 |
< |
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
892 |
> |
char* inName; |
893 |
|
|
358 |
– |
int* mol2proc = mpiSim->getMolToProcMap(); |
359 |
– |
int* molCompType = mpiSim->getMolComponentType(); |
360 |
– |
|
361 |
– |
allMol = 0; |
362 |
– |
localMol = 0; |
363 |
– |
local_atoms = 0; |
364 |
– |
local_bonds = 0; |
365 |
– |
local_bends = 0; |
366 |
– |
local_torsions = 0; |
367 |
– |
globalAtomIndex = 0; |
894 |
|
|
895 |
< |
|
370 |
< |
for( i=0; i<n_components; i++ ){ |
371 |
< |
|
372 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
373 |
< |
|
374 |
< |
if( mol2proc[allMol] == worldRank ){ |
375 |
< |
|
376 |
< |
local_atoms += comp_stamps[i]->getNAtoms(); |
377 |
< |
local_bonds += comp_stamps[i]->getNBonds(); |
378 |
< |
local_bends += comp_stamps[i]->getNBends(); |
379 |
< |
local_torsions += comp_stamps[i]->getNTorsions(); |
380 |
< |
localMol++; |
381 |
< |
} |
382 |
< |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
383 |
< |
simnfo->molMembershipArray[globalAtomIndex] = allMol; |
384 |
< |
globalAtomIndex++; |
385 |
< |
} |
386 |
< |
|
387 |
< |
allMol++; |
388 |
< |
} |
389 |
< |
} |
390 |
< |
local_SRI = local_bonds + local_bends + local_torsions; |
895 |
> |
(info[0].getConfiguration())->createArrays( info[0].n_atoms ); |
896 |
|
|
897 |
< |
simnfo->n_atoms = mpiSim->getMyNlocal(); |
897 |
> |
for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords(); |
898 |
|
|
899 |
< |
if( local_atoms != simnfo->n_atoms ){ |
899 |
> |
if( globals->haveInitialConfig() ){ |
900 |
> |
|
901 |
> |
InitializeFromFile* fileInit; |
902 |
> |
#ifdef IS_MPI // is_mpi |
903 |
> |
if( worldRank == 0 ){ |
904 |
> |
#endif //is_mpi |
905 |
> |
inName = globals->getInitialConfig(); |
906 |
> |
fileInit = new InitializeFromFile( inName ); |
907 |
> |
#ifdef IS_MPI |
908 |
> |
}else fileInit = new InitializeFromFile( NULL ); |
909 |
> |
#endif |
910 |
> |
fileInit->readInit( info ); // default velocities on |
911 |
> |
|
912 |
> |
delete fileInit; |
913 |
> |
} |
914 |
> |
else{ |
915 |
> |
|
916 |
> |
#ifdef IS_MPI |
917 |
> |
|
918 |
> |
// no init from bass |
919 |
> |
|
920 |
|
sprintf( painCave.errMsg, |
921 |
< |
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
922 |
< |
" localAtom (%d) are not equal.\n", |
398 |
< |
simnfo->n_atoms, |
399 |
< |
local_atoms ); |
400 |
< |
painCave.isFatal = 1; |
921 |
> |
"Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
922 |
> |
painCave.isFatal; |
923 |
|
simError(); |
924 |
+ |
|
925 |
+ |
#else |
926 |
+ |
|
927 |
+ |
initFromBass(); |
928 |
+ |
|
929 |
+ |
|
930 |
+ |
#endif |
931 |
|
} |
403 |
– |
|
404 |
– |
simnfo->n_bonds = local_bonds; |
405 |
– |
simnfo->n_bends = local_bends; |
406 |
– |
simnfo->n_torsions = local_torsions; |
407 |
– |
simnfo->n_SRI = local_SRI; |
408 |
– |
simnfo->n_mol = localMol; |
409 |
– |
|
410 |
– |
strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
411 |
– |
MPIcheckPoint(); |
932 |
|
|
933 |
< |
|
933 |
> |
#ifdef IS_MPI |
934 |
> |
strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
935 |
> |
MPIcheckPoint(); |
936 |
|
#endif // is_mpi |
937 |
|
|
938 |
+ |
} |
939 |
|
|
417 |
– |
// create the atom and short range interaction arrays |
940 |
|
|
941 |
< |
Atom::createArrays(simnfo->n_atoms); |
420 |
< |
the_atoms = new Atom*[simnfo->n_atoms]; |
421 |
< |
the_molecules = new Molecule[simnfo->n_mol]; |
422 |
< |
int molIndex; |
423 |
< |
|
424 |
< |
// initialize the molecule's stampID's |
425 |
< |
|
426 |
< |
#ifdef IS_MPI |
941 |
> |
void SimSetup::makeOutNames( void ){ |
942 |
|
|
943 |
+ |
int k; |
944 |
|
|
429 |
– |
molIndex = 0; |
430 |
– |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
431 |
– |
|
432 |
– |
if(mol2proc[i] == worldRank ){ |
433 |
– |
the_molecules[molIndex].setStampID( molCompType[i] ); |
434 |
– |
the_molecules[molIndex].setMyIndex( molIndex ); |
435 |
– |
the_molecules[molIndex].setGlobalIndex( i ); |
436 |
– |
molIndex++; |
437 |
– |
} |
438 |
– |
} |
439 |
– |
|
440 |
– |
#else // is_mpi |
945 |
|
|
946 |
< |
molIndex = 0; |
443 |
< |
globalAtomIndex = 0; |
444 |
< |
for(i=0; i<n_components; i++){ |
445 |
< |
for(j=0; j<components_nmol[i]; j++ ){ |
446 |
< |
the_molecules[molIndex].setStampID( i ); |
447 |
< |
the_molecules[molIndex].setMyIndex( molIndex ); |
448 |
< |
the_molecules[molIndex].setGlobalIndex( molIndex ); |
449 |
< |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
450 |
< |
simnfo->molMembershipArray[globalAtomIndex] = molIndex; |
451 |
< |
globalAtomIndex++; |
452 |
< |
} |
453 |
< |
molIndex++; |
454 |
< |
} |
455 |
< |
} |
456 |
< |
|
946 |
> |
for(k=0; k<nInfo; k++){ |
947 |
|
|
948 |
+ |
#ifdef IS_MPI |
949 |
+ |
if( worldRank == 0 ){ |
950 |
|
#endif // is_mpi |
951 |
+ |
|
952 |
+ |
if( globals->haveFinalConfig() ){ |
953 |
+ |
strcpy( info[k].finalName, globals->getFinalConfig() ); |
954 |
+ |
} |
955 |
+ |
else{ |
956 |
+ |
strcpy( info[k].finalName, inFileName ); |
957 |
+ |
char* endTest; |
958 |
+ |
int nameLength = strlen( info[k].finalName ); |
959 |
+ |
endTest = &(info[k].finalName[nameLength - 5]); |
960 |
+ |
if( !strcmp( endTest, ".bass" ) ){ |
961 |
+ |
strcpy( endTest, ".eor" ); |
962 |
+ |
} |
963 |
+ |
else if( !strcmp( endTest, ".BASS" ) ){ |
964 |
+ |
strcpy( endTest, ".eor" ); |
965 |
+ |
} |
966 |
+ |
else{ |
967 |
+ |
endTest = &(info[k].finalName[nameLength - 4]); |
968 |
+ |
if( !strcmp( endTest, ".bss" ) ){ |
969 |
+ |
strcpy( endTest, ".eor" ); |
970 |
+ |
} |
971 |
+ |
else if( !strcmp( endTest, ".mdl" ) ){ |
972 |
+ |
strcpy( endTest, ".eor" ); |
973 |
+ |
} |
974 |
+ |
else{ |
975 |
+ |
strcat( info[k].finalName, ".eor" ); |
976 |
+ |
} |
977 |
+ |
} |
978 |
+ |
} |
979 |
+ |
|
980 |
+ |
// make the sample and status out names |
981 |
+ |
|
982 |
+ |
strcpy( info[k].sampleName, inFileName ); |
983 |
+ |
char* endTest; |
984 |
+ |
int nameLength = strlen( info[k].sampleName ); |
985 |
+ |
endTest = &(info[k].sampleName[nameLength - 5]); |
986 |
+ |
if( !strcmp( endTest, ".bass" ) ){ |
987 |
+ |
strcpy( endTest, ".dump" ); |
988 |
+ |
} |
989 |
+ |
else if( !strcmp( endTest, ".BASS" ) ){ |
990 |
+ |
strcpy( endTest, ".dump" ); |
991 |
+ |
} |
992 |
+ |
else{ |
993 |
+ |
endTest = &(info[k].sampleName[nameLength - 4]); |
994 |
+ |
if( !strcmp( endTest, ".bss" ) ){ |
995 |
+ |
strcpy( endTest, ".dump" ); |
996 |
+ |
} |
997 |
+ |
else if( !strcmp( endTest, ".mdl" ) ){ |
998 |
+ |
strcpy( endTest, ".dump" ); |
999 |
+ |
} |
1000 |
+ |
else{ |
1001 |
+ |
strcat( info[k].sampleName, ".dump" ); |
1002 |
+ |
} |
1003 |
+ |
} |
1004 |
+ |
|
1005 |
+ |
strcpy( info[k].statusName, inFileName ); |
1006 |
+ |
nameLength = strlen( info[k].statusName ); |
1007 |
+ |
endTest = &(info[k].statusName[nameLength - 5]); |
1008 |
+ |
if( !strcmp( endTest, ".bass" ) ){ |
1009 |
+ |
strcpy( endTest, ".stat" ); |
1010 |
+ |
} |
1011 |
+ |
else if( !strcmp( endTest, ".BASS" ) ){ |
1012 |
+ |
strcpy( endTest, ".stat" ); |
1013 |
+ |
} |
1014 |
+ |
else{ |
1015 |
+ |
endTest = &(info[k].statusName[nameLength - 4]); |
1016 |
+ |
if( !strcmp( endTest, ".bss" ) ){ |
1017 |
+ |
strcpy( endTest, ".stat" ); |
1018 |
+ |
} |
1019 |
+ |
else if( !strcmp( endTest, ".mdl" ) ){ |
1020 |
+ |
strcpy( endTest, ".stat" ); |
1021 |
+ |
} |
1022 |
+ |
else{ |
1023 |
+ |
strcat( info[k].statusName, ".stat" ); |
1024 |
+ |
} |
1025 |
+ |
} |
1026 |
+ |
|
1027 |
+ |
#ifdef IS_MPI |
1028 |
+ |
} |
1029 |
+ |
#endif // is_mpi |
1030 |
+ |
} |
1031 |
+ |
} |
1032 |
|
|
1033 |
|
|
1034 |
< |
if( simnfo->n_SRI ){ |
1035 |
< |
|
1036 |
< |
Exclude::createArray(simnfo->n_SRI); |
1037 |
< |
the_excludes = new Exclude*[simnfo->n_SRI]; |
1038 |
< |
for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
466 |
< |
simnfo->globalExcludes = new int; |
467 |
< |
simnfo->n_exclude = simnfo->n_SRI; |
468 |
< |
} |
469 |
< |
else{ |
470 |
< |
|
471 |
< |
Exclude::createArray( 1 ); |
472 |
< |
the_excludes = new Exclude*; |
473 |
< |
the_excludes[0] = new Exclude(0); |
474 |
< |
the_excludes[0]->setPair( 0,0 ); |
475 |
< |
simnfo->globalExcludes = new int; |
476 |
< |
simnfo->globalExcludes[0] = 0; |
477 |
< |
simnfo->n_exclude = 0; |
478 |
< |
} |
1034 |
> |
void SimSetup::sysObjectsCreation( void ){ |
1035 |
> |
|
1036 |
> |
int i,k; |
1037 |
> |
|
1038 |
> |
// create the forceField |
1039 |
|
|
1040 |
< |
// set the arrays into the SimInfo object |
1040 |
> |
createFF(); |
1041 |
|
|
1042 |
< |
simnfo->atoms = the_atoms; |
483 |
< |
simnfo->molecules = the_molecules; |
484 |
< |
simnfo->nGlobalExcludes = 0; |
485 |
< |
simnfo->excludes = the_excludes; |
1042 |
> |
// extract componentList |
1043 |
|
|
1044 |
+ |
compList(); |
1045 |
|
|
1046 |
< |
// get some of the tricky things that may still be in the globals |
1046 |
> |
// calc the number of atoms, bond, bends, and torsions |
1047 |
|
|
1048 |
< |
double boxVector[3]; |
491 |
< |
if( the_globals->haveBox() ){ |
492 |
< |
boxVector[0] = the_globals->getBox(); |
493 |
< |
boxVector[1] = the_globals->getBox(); |
494 |
< |
boxVector[2] = the_globals->getBox(); |
495 |
< |
|
496 |
< |
simnfo->setBox( boxVector ); |
497 |
< |
} |
498 |
< |
else if( the_globals->haveDensity() ){ |
1048 |
> |
calcSysValues(); |
1049 |
|
|
1050 |
< |
double vol; |
1051 |
< |
vol = (double)tot_nmol / the_globals->getDensity(); |
1052 |
< |
boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
1053 |
< |
boxVector[1] = boxVector[0]; |
1054 |
< |
boxVector[2] = boxVector[0]; |
1050 |
> |
#ifdef IS_MPI |
1051 |
> |
// divide the molecules among the processors |
1052 |
> |
|
1053 |
> |
mpiMolDivide(); |
1054 |
> |
#endif //is_mpi |
1055 |
> |
|
1056 |
> |
// create the atom and SRI arrays. Also initialize Molecule Stamp ID's |
1057 |
> |
|
1058 |
> |
makeSysArrays(); |
1059 |
|
|
1060 |
< |
simnfo->setBox( boxVector ); |
1061 |
< |
} |
1062 |
< |
else{ |
1063 |
< |
if( !the_globals->haveBoxX() ){ |
1064 |
< |
sprintf( painCave.errMsg, |
1065 |
< |
"SimSetup error, no periodic BoxX size given.\n" ); |
1066 |
< |
painCave.isFatal = 1; |
1067 |
< |
simError(); |
1060 |
> |
// make and initialize the molecules (all but atomic coordinates) |
1061 |
> |
|
1062 |
> |
makeMolecules(); |
1063 |
> |
|
1064 |
> |
for(k=0; k<nInfo; k++){ |
1065 |
> |
info[k].identArray = new int[info[k].n_atoms]; |
1066 |
> |
for(i=0; i<info[k].n_atoms; i++){ |
1067 |
> |
info[k].identArray[i] = info[k].atoms[i]->getIdent(); |
1068 |
|
} |
1069 |
< |
boxVector[0] = the_globals->getBoxX(); |
1069 |
> |
} |
1070 |
> |
} |
1071 |
|
|
517 |
– |
if( !the_globals->haveBoxY() ){ |
518 |
– |
sprintf( painCave.errMsg, |
519 |
– |
"SimSetup error, no periodic BoxY size given.\n" ); |
520 |
– |
painCave.isFatal = 1; |
521 |
– |
simError(); |
522 |
– |
} |
523 |
– |
boxVector[1] = the_globals->getBoxY(); |
1072 |
|
|
1073 |
< |
if( !the_globals->haveBoxZ() ){ |
526 |
< |
sprintf( painCave.errMsg, |
527 |
< |
"SimSetup error, no periodic BoxZ size given.\n" ); |
528 |
< |
painCave.isFatal = 1; |
529 |
< |
simError(); |
530 |
< |
} |
531 |
< |
boxVector[2] = the_globals->getBoxZ(); |
1073 |
> |
void SimSetup::createFF( void ){ |
1074 |
|
|
1075 |
< |
simnfo->setBox( boxVector ); |
1075 |
> |
switch( ffCase ){ |
1076 |
> |
|
1077 |
> |
case FF_DUFF: |
1078 |
> |
the_ff = new DUFF(); |
1079 |
> |
break; |
1080 |
> |
|
1081 |
> |
case FF_LJ: |
1082 |
> |
the_ff = new LJFF(); |
1083 |
> |
break; |
1084 |
> |
|
1085 |
> |
case FF_EAM: |
1086 |
> |
the_ff = new EAM_FF(); |
1087 |
> |
break; |
1088 |
> |
|
1089 |
> |
default: |
1090 |
> |
sprintf( painCave.errMsg, |
1091 |
> |
"SimSetup Error. Unrecognized force field in case statement.\n"); |
1092 |
> |
painCave.isFatal = 1; |
1093 |
> |
simError(); |
1094 |
|
} |
1095 |
|
|
1096 |
|
#ifdef IS_MPI |
1097 |
< |
strcpy( checkPointMsg, "Box size set up" ); |
1097 |
> |
strcpy( checkPointMsg, "ForceField creation successful" ); |
1098 |
|
MPIcheckPoint(); |
1099 |
|
#endif // is_mpi |
1100 |
|
|
1101 |
+ |
} |
1102 |
|
|
542 |
– |
// initialize the arrays |
1103 |
|
|
1104 |
< |
the_ff->setSimInfo( simnfo ); |
1104 |
> |
void SimSetup::compList( void ){ |
1105 |
|
|
1106 |
< |
makeMolecules(); |
1107 |
< |
simnfo->identArray = new int[simnfo->n_atoms]; |
1108 |
< |
for(i=0; i<simnfo->n_atoms; i++){ |
1109 |
< |
simnfo->identArray[i] = the_atoms[i]->getIdent(); |
1110 |
< |
} |
1106 |
> |
int i; |
1107 |
> |
char* id; |
1108 |
> |
LinkedMolStamp* headStamp = new LinkedMolStamp(); |
1109 |
> |
LinkedMolStamp* currentStamp = NULL; |
1110 |
> |
comp_stamps = new MoleculeStamp*[n_components]; |
1111 |
|
|
1112 |
< |
if (the_globals->getUseRF() ) { |
1113 |
< |
simnfo->useReactionField = 1; |
1112 |
> |
// make an array of molecule stamps that match the components used. |
1113 |
> |
// also extract the used stamps out into a separate linked list |
1114 |
|
|
1115 |
< |
if( !the_globals->haveECR() ){ |
1116 |
< |
sprintf( painCave.errMsg, |
1117 |
< |
"SimSetup Warning: using default value of 1/2 the smallest " |
1118 |
< |
"box length for the electrostaticCutoffRadius.\n" |
1119 |
< |
"I hope you have a very fast processor!\n"); |
1120 |
< |
painCave.isFatal = 0; |
1121 |
< |
simError(); |
562 |
< |
double smallest; |
563 |
< |
smallest = simnfo->boxLx; |
564 |
< |
if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy; |
565 |
< |
if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz; |
566 |
< |
simnfo->ecr = 0.5 * smallest; |
567 |
< |
} else { |
568 |
< |
simnfo->ecr = the_globals->getECR(); |
569 |
< |
} |
1115 |
> |
for(i=0; i<nInfo; i++){ |
1116 |
> |
info[i].nComponents = n_components; |
1117 |
> |
info[i].componentsNmol = components_nmol; |
1118 |
> |
info[i].compStamps = comp_stamps; |
1119 |
> |
info[i].headStamp = headStamp; |
1120 |
> |
} |
1121 |
> |
|
1122 |
|
|
1123 |
< |
if( !the_globals->haveEST() ){ |
1124 |
< |
sprintf( painCave.errMsg, |
1125 |
< |
"SimSetup Warning: using default value of 0.05 * the " |
1126 |
< |
"electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
575 |
< |
); |
576 |
< |
painCave.isFatal = 0; |
577 |
< |
simError(); |
578 |
< |
simnfo->est = 0.05 * simnfo->ecr; |
579 |
< |
} else { |
580 |
< |
simnfo->est = the_globals->getEST(); |
581 |
< |
} |
1123 |
> |
for( i=0; i<n_components; i++ ){ |
1124 |
> |
|
1125 |
> |
id = the_components[i]->getType(); |
1126 |
> |
comp_stamps[i] = NULL; |
1127 |
|
|
1128 |
< |
if(!the_globals->haveDielectric() ){ |
1129 |
< |
sprintf( painCave.errMsg, |
1130 |
< |
"SimSetup Error: You are trying to use Reaction Field without" |
1131 |
< |
"setting a dielectric constant!\n" |
587 |
< |
); |
588 |
< |
painCave.isFatal = 1; |
589 |
< |
simError(); |
590 |
< |
} |
591 |
< |
simnfo->dielectric = the_globals->getDielectric(); |
592 |
< |
} else { |
593 |
< |
if (usesDipoles) { |
1128 |
> |
// check to make sure the component isn't already in the list |
1129 |
> |
|
1130 |
> |
comp_stamps[i] = headStamp->match( id ); |
1131 |
> |
if( comp_stamps[i] == NULL ){ |
1132 |
|
|
1133 |
< |
if( !the_globals->haveECR() ){ |
596 |
< |
sprintf( painCave.errMsg, |
597 |
< |
"SimSetup Warning: using default value of 1/2 the smallest " |
598 |
< |
"box length for the electrostaticCutoffRadius.\n" |
599 |
< |
"I hope you have a very fast processor!\n"); |
600 |
< |
painCave.isFatal = 0; |
601 |
< |
simError(); |
602 |
< |
double smallest; |
603 |
< |
smallest = simnfo->boxLx; |
604 |
< |
if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy; |
605 |
< |
if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz; |
606 |
< |
simnfo->ecr = 0.5 * smallest; |
607 |
< |
} else { |
608 |
< |
simnfo->ecr = the_globals->getECR(); |
609 |
< |
} |
1133 |
> |
// extract the component from the list; |
1134 |
|
|
1135 |
< |
if( !the_globals->haveEST() ){ |
1136 |
< |
sprintf( painCave.errMsg, |
1137 |
< |
"SimSetup Warning: using default value of 5%% of the " |
1138 |
< |
"electrostaticCutoffRadius for the " |
1139 |
< |
"electrostaticSkinThickness\n" |
1140 |
< |
); |
1141 |
< |
painCave.isFatal = 0; |
1142 |
< |
simError(); |
619 |
< |
simnfo->est = 0.05 * simnfo->ecr; |
620 |
< |
} else { |
621 |
< |
simnfo->est = the_globals->getEST(); |
1135 |
> |
currentStamp = stamps->extractMolStamp( id ); |
1136 |
> |
if( currentStamp == NULL ){ |
1137 |
> |
sprintf( painCave.errMsg, |
1138 |
> |
"SimSetup error: Component \"%s\" was not found in the " |
1139 |
> |
"list of declared molecules\n", |
1140 |
> |
id ); |
1141 |
> |
painCave.isFatal = 1; |
1142 |
> |
simError(); |
1143 |
|
} |
1144 |
+ |
|
1145 |
+ |
headStamp->add( currentStamp ); |
1146 |
+ |
comp_stamps[i] = headStamp->match( id ); |
1147 |
|
} |
1148 |
< |
} |
1148 |
> |
} |
1149 |
|
|
1150 |
|
#ifdef IS_MPI |
1151 |
< |
strcpy( checkPointMsg, "electrostatic parameters check out" ); |
1151 |
> |
strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
1152 |
|
MPIcheckPoint(); |
1153 |
|
#endif // is_mpi |
1154 |
|
|
631 |
– |
if( the_globals->haveInitialConfig() ){ |
632 |
– |
|
633 |
– |
InitializeFromFile* fileInit; |
634 |
– |
#ifdef IS_MPI // is_mpi |
635 |
– |
if( worldRank == 0 ){ |
636 |
– |
#endif //is_mpi |
637 |
– |
fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
638 |
– |
#ifdef IS_MPI |
639 |
– |
}else fileInit = new InitializeFromFile( NULL ); |
640 |
– |
#endif |
641 |
– |
fileInit->read_xyz( simnfo ); // default velocities on |
1155 |
|
|
1156 |
< |
delete fileInit; |
644 |
< |
} |
645 |
< |
else{ |
1156 |
> |
} |
1157 |
|
|
1158 |
< |
#ifdef IS_MPI |
1159 |
< |
|
649 |
< |
// no init from bass |
1158 |
> |
void SimSetup::calcSysValues( void ){ |
1159 |
> |
int i, j, k; |
1160 |
|
|
1161 |
< |
sprintf( painCave.errMsg, |
652 |
< |
"Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
653 |
< |
painCave.isFatal; |
654 |
< |
simError(); |
1161 |
> |
int *molMembershipArray; |
1162 |
|
|
1163 |
< |
#else |
1163 |
> |
tot_atoms = 0; |
1164 |
> |
tot_bonds = 0; |
1165 |
> |
tot_bends = 0; |
1166 |
> |
tot_torsions = 0; |
1167 |
> |
for( i=0; i<n_components; i++ ){ |
1168 |
> |
|
1169 |
> |
tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1170 |
> |
tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1171 |
> |
tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1172 |
> |
tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
1173 |
> |
} |
1174 |
> |
|
1175 |
> |
tot_SRI = tot_bonds + tot_bends + tot_torsions; |
1176 |
> |
molMembershipArray = new int[tot_atoms]; |
1177 |
> |
|
1178 |
> |
for(i=0; i<nInfo; i++){ |
1179 |
> |
info[i].n_atoms = tot_atoms; |
1180 |
> |
info[i].n_bonds = tot_bonds; |
1181 |
> |
info[i].n_bends = tot_bends; |
1182 |
> |
info[i].n_torsions = tot_torsions; |
1183 |
> |
info[i].n_SRI = tot_SRI; |
1184 |
> |
info[i].n_mol = tot_nmol; |
1185 |
> |
|
1186 |
> |
info[i].molMembershipArray = molMembershipArray; |
1187 |
> |
} |
1188 |
> |
} |
1189 |
|
|
1190 |
< |
initFromBass(); |
1190 |
> |
#ifdef IS_MPI |
1191 |
|
|
1192 |
+ |
void SimSetup::mpiMolDivide( void ){ |
1193 |
+ |
|
1194 |
+ |
int i, j, k; |
1195 |
+ |
int localMol, allMol; |
1196 |
+ |
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
1197 |
|
|
1198 |
< |
#endif |
1199 |
< |
} |
1200 |
< |
|
1201 |
< |
#ifdef IS_MPI |
1202 |
< |
strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
1198 |
> |
mpiSim = new mpiSimulation( info ); |
1199 |
> |
|
1200 |
> |
globalIndex = mpiSim->divideLabor(); |
1201 |
> |
|
1202 |
> |
// set up the local variables |
1203 |
> |
|
1204 |
> |
mol2proc = mpiSim->getMolToProcMap(); |
1205 |
> |
molCompType = mpiSim->getMolComponentType(); |
1206 |
> |
|
1207 |
> |
allMol = 0; |
1208 |
> |
localMol = 0; |
1209 |
> |
local_atoms = 0; |
1210 |
> |
local_bonds = 0; |
1211 |
> |
local_bends = 0; |
1212 |
> |
local_torsions = 0; |
1213 |
> |
globalAtomIndex = 0; |
1214 |
> |
|
1215 |
> |
|
1216 |
> |
for( i=0; i<n_components; i++ ){ |
1217 |
> |
|
1218 |
> |
for( j=0; j<components_nmol[i]; j++ ){ |
1219 |
> |
|
1220 |
> |
if( mol2proc[allMol] == worldRank ){ |
1221 |
> |
|
1222 |
> |
local_atoms += comp_stamps[i]->getNAtoms(); |
1223 |
> |
local_bonds += comp_stamps[i]->getNBonds(); |
1224 |
> |
local_bends += comp_stamps[i]->getNBends(); |
1225 |
> |
local_torsions += comp_stamps[i]->getNTorsions(); |
1226 |
> |
localMol++; |
1227 |
> |
} |
1228 |
> |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1229 |
> |
info[0].molMembershipArray[globalAtomIndex] = allMol; |
1230 |
> |
globalAtomIndex++; |
1231 |
> |
} |
1232 |
> |
|
1233 |
> |
allMol++; |
1234 |
> |
} |
1235 |
> |
} |
1236 |
> |
local_SRI = local_bonds + local_bends + local_torsions; |
1237 |
> |
|
1238 |
> |
info[0].n_atoms = mpiSim->getMyNlocal(); |
1239 |
> |
|
1240 |
> |
if( local_atoms != info[0].n_atoms ){ |
1241 |
> |
sprintf( painCave.errMsg, |
1242 |
> |
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1243 |
> |
" localAtom (%d) are not equal.\n", |
1244 |
> |
info[0].n_atoms, |
1245 |
> |
local_atoms ); |
1246 |
> |
painCave.isFatal = 1; |
1247 |
> |
simError(); |
1248 |
> |
} |
1249 |
> |
|
1250 |
> |
info[0].n_bonds = local_bonds; |
1251 |
> |
info[0].n_bends = local_bends; |
1252 |
> |
info[0].n_torsions = local_torsions; |
1253 |
> |
info[0].n_SRI = local_SRI; |
1254 |
> |
info[0].n_mol = localMol; |
1255 |
> |
|
1256 |
> |
strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
1257 |
|
MPIcheckPoint(); |
1258 |
+ |
} |
1259 |
+ |
|
1260 |
|
#endif // is_mpi |
1261 |
|
|
1262 |
|
|
1263 |
< |
|
1264 |
< |
|
672 |
< |
|
1263 |
> |
void SimSetup::makeSysArrays( void ){ |
1264 |
> |
int i, j, k, l; |
1265 |
|
|
1266 |
+ |
Atom** the_atoms; |
1267 |
+ |
Molecule* the_molecules; |
1268 |
+ |
Exclude** the_excludes; |
1269 |
+ |
|
1270 |
|
|
1271 |
+ |
for(l=0; l<nInfo; l++){ |
1272 |
+ |
|
1273 |
+ |
// create the atom and short range interaction arrays |
1274 |
+ |
|
1275 |
+ |
the_atoms = new Atom*[info[l].n_atoms]; |
1276 |
+ |
the_molecules = new Molecule[info[l].n_mol]; |
1277 |
+ |
int molIndex; |
1278 |
+ |
|
1279 |
+ |
// initialize the molecule's stampID's |
1280 |
+ |
|
1281 |
|
#ifdef IS_MPI |
676 |
– |
if( worldRank == 0 ){ |
677 |
– |
#endif // is_mpi |
1282 |
|
|
679 |
– |
if( the_globals->haveFinalConfig() ){ |
680 |
– |
strcpy( simnfo->finalName, the_globals->getFinalConfig() ); |
681 |
– |
} |
682 |
– |
else{ |
683 |
– |
strcpy( simnfo->finalName, inFileName ); |
684 |
– |
char* endTest; |
685 |
– |
int nameLength = strlen( simnfo->finalName ); |
686 |
– |
endTest = &(simnfo->finalName[nameLength - 5]); |
687 |
– |
if( !strcmp( endTest, ".bass" ) ){ |
688 |
– |
strcpy( endTest, ".eor" ); |
689 |
– |
} |
690 |
– |
else if( !strcmp( endTest, ".BASS" ) ){ |
691 |
– |
strcpy( endTest, ".eor" ); |
692 |
– |
} |
693 |
– |
else{ |
694 |
– |
endTest = &(simnfo->finalName[nameLength - 4]); |
695 |
– |
if( !strcmp( endTest, ".bss" ) ){ |
696 |
– |
strcpy( endTest, ".eor" ); |
697 |
– |
} |
698 |
– |
else if( !strcmp( endTest, ".mdl" ) ){ |
699 |
– |
strcpy( endTest, ".eor" ); |
700 |
– |
} |
701 |
– |
else{ |
702 |
– |
strcat( simnfo->finalName, ".eor" ); |
703 |
– |
} |
704 |
– |
} |
705 |
– |
} |
1283 |
|
|
1284 |
< |
// make the sample and status out names |
1284 |
> |
molIndex = 0; |
1285 |
> |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
1286 |
|
|
1287 |
< |
strcpy( simnfo->sampleName, inFileName ); |
1288 |
< |
char* endTest; |
1289 |
< |
int nameLength = strlen( simnfo->sampleName ); |
1290 |
< |
endTest = &(simnfo->sampleName[nameLength - 5]); |
1291 |
< |
if( !strcmp( endTest, ".bass" ) ){ |
714 |
< |
strcpy( endTest, ".dump" ); |
715 |
< |
} |
716 |
< |
else if( !strcmp( endTest, ".BASS" ) ){ |
717 |
< |
strcpy( endTest, ".dump" ); |
718 |
< |
} |
719 |
< |
else{ |
720 |
< |
endTest = &(simnfo->sampleName[nameLength - 4]); |
721 |
< |
if( !strcmp( endTest, ".bss" ) ){ |
722 |
< |
strcpy( endTest, ".dump" ); |
1287 |
> |
if(mol2proc[i] == worldRank ){ |
1288 |
> |
the_molecules[molIndex].setStampID( molCompType[i] ); |
1289 |
> |
the_molecules[molIndex].setMyIndex( molIndex ); |
1290 |
> |
the_molecules[molIndex].setGlobalIndex( i ); |
1291 |
> |
molIndex++; |
1292 |
|
} |
724 |
– |
else if( !strcmp( endTest, ".mdl" ) ){ |
725 |
– |
strcpy( endTest, ".dump" ); |
726 |
– |
} |
727 |
– |
else{ |
728 |
– |
strcat( simnfo->sampleName, ".dump" ); |
729 |
– |
} |
1293 |
|
} |
1294 |
|
|
1295 |
< |
strcpy( simnfo->statusName, inFileName ); |
1296 |
< |
nameLength = strlen( simnfo->statusName ); |
1297 |
< |
endTest = &(simnfo->statusName[nameLength - 5]); |
1298 |
< |
if( !strcmp( endTest, ".bass" ) ){ |
1299 |
< |
strcpy( endTest, ".stat" ); |
1300 |
< |
} |
1301 |
< |
else if( !strcmp( endTest, ".BASS" ) ){ |
1302 |
< |
strcpy( endTest, ".stat" ); |
1303 |
< |
} |
1304 |
< |
else{ |
1305 |
< |
endTest = &(simnfo->statusName[nameLength - 4]); |
1306 |
< |
if( !strcmp( endTest, ".bss" ) ){ |
1307 |
< |
strcpy( endTest, ".stat" ); |
1295 |
> |
#else // is_mpi |
1296 |
> |
|
1297 |
> |
molIndex = 0; |
1298 |
> |
globalAtomIndex = 0; |
1299 |
> |
for(i=0; i<n_components; i++){ |
1300 |
> |
for(j=0; j<components_nmol[i]; j++ ){ |
1301 |
> |
the_molecules[molIndex].setStampID( i ); |
1302 |
> |
the_molecules[molIndex].setMyIndex( molIndex ); |
1303 |
> |
the_molecules[molIndex].setGlobalIndex( molIndex ); |
1304 |
> |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1305 |
> |
info[l].molMembershipArray[globalAtomIndex] = molIndex; |
1306 |
> |
globalAtomIndex++; |
1307 |
> |
} |
1308 |
> |
molIndex++; |
1309 |
|
} |
746 |
– |
else if( !strcmp( endTest, ".mdl" ) ){ |
747 |
– |
strcpy( endTest, ".stat" ); |
748 |
– |
} |
749 |
– |
else{ |
750 |
– |
strcat( simnfo->statusName, ".stat" ); |
751 |
– |
} |
1310 |
|
} |
1311 |
|
|
1312 |
< |
#ifdef IS_MPI |
755 |
< |
} |
1312 |
> |
|
1313 |
|
#endif // is_mpi |
757 |
– |
|
758 |
– |
// set the status, sample, and themal kick times |
759 |
– |
|
760 |
– |
if( the_globals->haveSampleTime() ){ |
761 |
– |
simnfo->sampleTime = the_globals->getSampleTime(); |
762 |
– |
simnfo->statusTime = simnfo->sampleTime; |
763 |
– |
simnfo->thermalTime = simnfo->sampleTime; |
764 |
– |
} |
765 |
– |
else{ |
766 |
– |
simnfo->sampleTime = the_globals->getRunTime(); |
767 |
– |
simnfo->statusTime = simnfo->sampleTime; |
768 |
– |
simnfo->thermalTime = simnfo->sampleTime; |
769 |
– |
} |
1314 |
|
|
771 |
– |
if( the_globals->haveStatusTime() ){ |
772 |
– |
simnfo->statusTime = the_globals->getStatusTime(); |
773 |
– |
} |
1315 |
|
|
1316 |
< |
if( the_globals->haveThermalTime() ){ |
1317 |
< |
simnfo->thermalTime = the_globals->getThermalTime(); |
1318 |
< |
} |
1316 |
> |
if( info[l].n_SRI ){ |
1317 |
> |
|
1318 |
> |
Exclude::createArray(info[l].n_SRI); |
1319 |
> |
the_excludes = new Exclude*[info[l].n_SRI]; |
1320 |
> |
for( int ex=0; ex<info[l].n_SRI; ex++){ |
1321 |
> |
the_excludes[ex] = new Exclude(ex); |
1322 |
> |
} |
1323 |
> |
info[l].globalExcludes = new int; |
1324 |
> |
info[l].n_exclude = info[l].n_SRI; |
1325 |
> |
} |
1326 |
> |
else{ |
1327 |
> |
|
1328 |
> |
Exclude::createArray( 1 ); |
1329 |
> |
the_excludes = new Exclude*; |
1330 |
> |
the_excludes[0] = new Exclude(0); |
1331 |
> |
the_excludes[0]->setPair( 0,0 ); |
1332 |
> |
info[l].globalExcludes = new int; |
1333 |
> |
info[l].globalExcludes[0] = 0; |
1334 |
> |
info[l].n_exclude = 0; |
1335 |
> |
} |
1336 |
|
|
1337 |
< |
// check for the temperature set flag |
1337 |
> |
// set the arrays into the SimInfo object |
1338 |
|
|
1339 |
< |
if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
1339 |
> |
info[l].atoms = the_atoms; |
1340 |
> |
info[l].molecules = the_molecules; |
1341 |
> |
info[l].nGlobalExcludes = 0; |
1342 |
> |
info[l].excludes = the_excludes; |
1343 |
|
|
1344 |
+ |
the_ff->setSimInfo( info ); |
1345 |
+ |
|
1346 |
+ |
} |
1347 |
+ |
} |
1348 |
|
|
1349 |
< |
// make the integrator |
785 |
< |
|
786 |
< |
|
787 |
< |
NVT* myNVT = NULL; |
788 |
< |
NPTi* myNPTi = NULL; |
789 |
< |
NPTf* myNPTf = NULL; |
790 |
< |
NPTim* myNPTim = NULL; |
1349 |
> |
void SimSetup::makeIntegrator( void ){ |
1350 |
|
|
1351 |
< |
switch( ensembleCase ){ |
1351 |
> |
int k; |
1352 |
|
|
1353 |
< |
case NVE_ENS: |
1354 |
< |
new NVE( simnfo, the_ff ); |
1355 |
< |
break; |
1356 |
< |
|
1357 |
< |
case NVT_ENS: |
1358 |
< |
myNVT = new NVT( simnfo, the_ff ); |
1359 |
< |
myNVT->setTargetTemp(the_globals->getTargetTemp()); |
801 |
< |
|
802 |
< |
if (the_globals->haveTauThermostat()) |
803 |
< |
myNVT->setTauThermostat(the_globals->getTauThermostat()); |
804 |
< |
|
805 |
< |
else { |
806 |
< |
sprintf( painCave.errMsg, |
807 |
< |
"SimSetup error: If you use the NVT\n" |
808 |
< |
" ensemble, you must set tauThermostat.\n"); |
809 |
< |
painCave.isFatal = 1; |
810 |
< |
simError(); |
811 |
< |
} |
812 |
< |
break; |
813 |
< |
|
814 |
< |
case NPTi_ENS: |
815 |
< |
myNPTi = new NPTi( simnfo, the_ff ); |
816 |
< |
myNPTi->setTargetTemp( the_globals->getTargetTemp()); |
817 |
< |
|
818 |
< |
if (the_globals->haveTargetPressure()) |
819 |
< |
myNPTi->setTargetPressure(the_globals->getTargetPressure()); |
820 |
< |
else { |
821 |
< |
sprintf( painCave.errMsg, |
822 |
< |
"SimSetup error: If you use a constant pressure\n" |
823 |
< |
" ensemble, you must set targetPressure in the BASS file.\n"); |
824 |
< |
painCave.isFatal = 1; |
825 |
< |
simError(); |
826 |
< |
} |
1353 |
> |
NVT<RealIntegrator>* myNVT = NULL; |
1354 |
> |
NPTi<RealIntegrator>* myNPTi = NULL; |
1355 |
> |
NPTf<RealIntegrator>* myNPTf = NULL; |
1356 |
> |
NPTim<RealIntegrator>* myNPTim = NULL; |
1357 |
> |
NPTfm<RealIntegrator>* myNPTfm = NULL; |
1358 |
> |
|
1359 |
> |
for(k=0; k<nInfo; k++){ |
1360 |
|
|
1361 |
< |
if( the_globals->haveTauThermostat() ) |
1362 |
< |
myNPTi->setTauThermostat( the_globals->getTauThermostat() ); |
1363 |
< |
else{ |
1364 |
< |
sprintf( painCave.errMsg, |
1365 |
< |
"SimSetup error: If you use an NPT\n" |
1366 |
< |
" ensemble, you must set tauThermostat.\n"); |
1367 |
< |
painCave.isFatal = 1; |
835 |
< |
simError(); |
836 |
< |
} |
1361 |
> |
switch( ensembleCase ){ |
1362 |
> |
|
1363 |
> |
case NVE_ENS: |
1364 |
> |
if (globals->haveZconstraints()){ |
1365 |
> |
setupZConstraint(info[k]); |
1366 |
> |
new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff ); |
1367 |
> |
} |
1368 |
|
|
1369 |
< |
if( the_globals->haveTauBarostat() ) |
1370 |
< |
myNPTi->setTauBarostat( the_globals->getTauBarostat() ); |
1371 |
< |
else{ |
1372 |
< |
sprintf( painCave.errMsg, |
1373 |
< |
"SimSetup error: If you use an NPT\n" |
1374 |
< |
" ensemble, you must set tauBarostat.\n"); |
1375 |
< |
painCave.isFatal = 1; |
1376 |
< |
simError(); |
1377 |
< |
} |
1378 |
< |
break; |
1369 |
> |
else |
1370 |
> |
new NVE<RealIntegrator>( &(info[k]), the_ff ); |
1371 |
> |
break; |
1372 |
> |
|
1373 |
> |
case NVT_ENS: |
1374 |
> |
if (globals->haveZconstraints()){ |
1375 |
> |
setupZConstraint(info[k]); |
1376 |
> |
myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff ); |
1377 |
> |
} |
1378 |
> |
else |
1379 |
> |
myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff ); |
1380 |
|
|
1381 |
< |
case NPTf_ENS: |
1382 |
< |
myNPTf = new NPTf( simnfo, the_ff ); |
1383 |
< |
myNPTf->setTargetTemp( the_globals->getTargetTemp()); |
1381 |
> |
myNVT->setTargetTemp(globals->getTargetTemp()); |
1382 |
> |
|
1383 |
> |
if (globals->haveTauThermostat()) |
1384 |
> |
myNVT->setTauThermostat(globals->getTauThermostat()); |
1385 |
> |
|
1386 |
> |
else { |
1387 |
> |
sprintf( painCave.errMsg, |
1388 |
> |
"SimSetup error: If you use the NVT\n" |
1389 |
> |
" ensemble, you must set tauThermostat.\n"); |
1390 |
> |
painCave.isFatal = 1; |
1391 |
> |
simError(); |
1392 |
> |
} |
1393 |
> |
break; |
1394 |
> |
|
1395 |
> |
case NPTi_ENS: |
1396 |
> |
if (globals->haveZconstraints()){ |
1397 |
> |
setupZConstraint(info[k]); |
1398 |
> |
myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff ); |
1399 |
> |
} |
1400 |
> |
else |
1401 |
> |
myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff ); |
1402 |
|
|
1403 |
< |
if (the_globals->haveTargetPressure()) |
1404 |
< |
myNPTf->setTargetPressure(the_globals->getTargetPressure()); |
1405 |
< |
else { |
1406 |
< |
sprintf( painCave.errMsg, |
1407 |
< |
"SimSetup error: If you use a constant pressure\n" |
1408 |
< |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1409 |
< |
painCave.isFatal = 1; |
1410 |
< |
simError(); |
1411 |
< |
} |
1412 |
< |
|
1413 |
< |
if( the_globals->haveTauThermostat() ) |
1414 |
< |
myNPTf->setTauThermostat( the_globals->getTauThermostat() ); |
1415 |
< |
else{ |
1416 |
< |
sprintf( painCave.errMsg, |
1417 |
< |
"SimSetup error: If you use an NPT\n" |
1418 |
< |
" ensemble, you must set tauThermostat.\n"); |
1419 |
< |
painCave.isFatal = 1; |
1420 |
< |
simError(); |
1421 |
< |
} |
1403 |
> |
myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1404 |
> |
|
1405 |
> |
if (globals->haveTargetPressure()) |
1406 |
> |
myNPTi->setTargetPressure(globals->getTargetPressure()); |
1407 |
> |
else { |
1408 |
> |
sprintf( painCave.errMsg, |
1409 |
> |
"SimSetup error: If you use a constant pressure\n" |
1410 |
> |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1411 |
> |
painCave.isFatal = 1; |
1412 |
> |
simError(); |
1413 |
> |
} |
1414 |
> |
|
1415 |
> |
if( globals->haveTauThermostat() ) |
1416 |
> |
myNPTi->setTauThermostat( globals->getTauThermostat() ); |
1417 |
> |
else{ |
1418 |
> |
sprintf( painCave.errMsg, |
1419 |
> |
"SimSetup error: If you use an NPT\n" |
1420 |
> |
" ensemble, you must set tauThermostat.\n"); |
1421 |
> |
painCave.isFatal = 1; |
1422 |
> |
simError(); |
1423 |
> |
} |
1424 |
> |
|
1425 |
> |
if( globals->haveTauBarostat() ) |
1426 |
> |
myNPTi->setTauBarostat( globals->getTauBarostat() ); |
1427 |
> |
else{ |
1428 |
> |
sprintf( painCave.errMsg, |
1429 |
> |
"SimSetup error: If you use an NPT\n" |
1430 |
> |
" ensemble, you must set tauBarostat.\n"); |
1431 |
> |
painCave.isFatal = 1; |
1432 |
> |
simError(); |
1433 |
> |
} |
1434 |
> |
break; |
1435 |
> |
|
1436 |
> |
case NPTf_ENS: |
1437 |
> |
if (globals->haveZconstraints()){ |
1438 |
> |
setupZConstraint(info[k]); |
1439 |
> |
myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff ); |
1440 |
> |
} |
1441 |
> |
else |
1442 |
> |
myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff ); |
1443 |
|
|
1444 |
< |
if( the_globals->haveTauBarostat() ) |
1445 |
< |
myNPTf->setTauBarostat( the_globals->getTauBarostat() ); |
1446 |
< |
else{ |
1444 |
> |
myNPTf->setTargetTemp( globals->getTargetTemp()); |
1445 |
> |
|
1446 |
> |
if (globals->haveTargetPressure()) |
1447 |
> |
myNPTf->setTargetPressure(globals->getTargetPressure()); |
1448 |
> |
else { |
1449 |
> |
sprintf( painCave.errMsg, |
1450 |
> |
"SimSetup error: If you use a constant pressure\n" |
1451 |
> |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1452 |
> |
painCave.isFatal = 1; |
1453 |
> |
simError(); |
1454 |
> |
} |
1455 |
> |
|
1456 |
> |
if( globals->haveTauThermostat() ) |
1457 |
> |
myNPTf->setTauThermostat( globals->getTauThermostat() ); |
1458 |
> |
else{ |
1459 |
> |
sprintf( painCave.errMsg, |
1460 |
> |
"SimSetup error: If you use an NPT\n" |
1461 |
> |
" ensemble, you must set tauThermostat.\n"); |
1462 |
> |
painCave.isFatal = 1; |
1463 |
> |
simError(); |
1464 |
> |
} |
1465 |
> |
|
1466 |
> |
if( globals->haveTauBarostat() ) |
1467 |
> |
myNPTf->setTauBarostat( globals->getTauBarostat() ); |
1468 |
> |
else{ |
1469 |
> |
sprintf( painCave.errMsg, |
1470 |
> |
"SimSetup error: If you use an NPT\n" |
1471 |
> |
" ensemble, you must set tauBarostat.\n"); |
1472 |
> |
painCave.isFatal = 1; |
1473 |
> |
simError(); |
1474 |
> |
} |
1475 |
> |
break; |
1476 |
> |
|
1477 |
> |
case NPTim_ENS: |
1478 |
> |
if (globals->haveZconstraints()){ |
1479 |
> |
setupZConstraint(info[k]); |
1480 |
> |
myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff ); |
1481 |
> |
} |
1482 |
> |
else |
1483 |
> |
myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff ); |
1484 |
> |
|
1485 |
> |
myNPTim->setTargetTemp( globals->getTargetTemp()); |
1486 |
> |
|
1487 |
> |
if (globals->haveTargetPressure()) |
1488 |
> |
myNPTim->setTargetPressure(globals->getTargetPressure()); |
1489 |
> |
else { |
1490 |
> |
sprintf( painCave.errMsg, |
1491 |
> |
"SimSetup error: If you use a constant pressure\n" |
1492 |
> |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1493 |
> |
painCave.isFatal = 1; |
1494 |
> |
simError(); |
1495 |
> |
} |
1496 |
> |
|
1497 |
> |
if( globals->haveTauThermostat() ) |
1498 |
> |
myNPTim->setTauThermostat( globals->getTauThermostat() ); |
1499 |
> |
else{ |
1500 |
> |
sprintf( painCave.errMsg, |
1501 |
> |
"SimSetup error: If you use an NPT\n" |
1502 |
> |
" ensemble, you must set tauThermostat.\n"); |
1503 |
> |
painCave.isFatal = 1; |
1504 |
> |
simError(); |
1505 |
> |
} |
1506 |
> |
|
1507 |
> |
if( globals->haveTauBarostat() ) |
1508 |
> |
myNPTim->setTauBarostat( globals->getTauBarostat() ); |
1509 |
> |
else{ |
1510 |
|
sprintf( painCave.errMsg, |
1511 |
|
"SimSetup error: If you use an NPT\n" |
1512 |
|
" ensemble, you must set tauBarostat.\n"); |
1513 |
|
painCave.isFatal = 1; |
1514 |
|
simError(); |
1515 |
< |
} |
1516 |
< |
break; |
1517 |
< |
|
1518 |
< |
case NPTim_ENS: |
1519 |
< |
myNPTim = new NPTim( simnfo, the_ff ); |
1520 |
< |
myNPTim->setTargetTemp( the_globals->getTargetTemp()); |
1515 |
> |
} |
1516 |
> |
break; |
1517 |
> |
|
1518 |
> |
case NPTfm_ENS: |
1519 |
> |
if (globals->haveZconstraints()){ |
1520 |
> |
setupZConstraint(info[k]); |
1521 |
> |
myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff ); |
1522 |
> |
} |
1523 |
> |
else |
1524 |
> |
myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff ); |
1525 |
|
|
1526 |
< |
if (the_globals->haveTargetPressure()) |
1527 |
< |
myNPTim->setTargetPressure(the_globals->getTargetPressure()); |
1528 |
< |
else { |
1526 |
> |
myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1527 |
> |
|
1528 |
> |
if (globals->haveTargetPressure()) |
1529 |
> |
myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1530 |
> |
else { |
1531 |
> |
sprintf( painCave.errMsg, |
1532 |
> |
"SimSetup error: If you use a constant pressure\n" |
1533 |
> |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1534 |
> |
painCave.isFatal = 1; |
1535 |
> |
simError(); |
1536 |
> |
} |
1537 |
> |
|
1538 |
> |
if( globals->haveTauThermostat() ) |
1539 |
> |
myNPTfm->setTauThermostat( globals->getTauThermostat() ); |
1540 |
> |
else{ |
1541 |
> |
sprintf( painCave.errMsg, |
1542 |
> |
"SimSetup error: If you use an NPT\n" |
1543 |
> |
" ensemble, you must set tauThermostat.\n"); |
1544 |
> |
painCave.isFatal = 1; |
1545 |
> |
simError(); |
1546 |
> |
} |
1547 |
> |
|
1548 |
> |
if( globals->haveTauBarostat() ) |
1549 |
> |
myNPTfm->setTauBarostat( globals->getTauBarostat() ); |
1550 |
> |
else{ |
1551 |
> |
sprintf( painCave.errMsg, |
1552 |
> |
"SimSetup error: If you use an NPT\n" |
1553 |
> |
" ensemble, you must set tauBarostat.\n"); |
1554 |
> |
painCave.isFatal = 1; |
1555 |
> |
simError(); |
1556 |
> |
} |
1557 |
> |
break; |
1558 |
> |
|
1559 |
> |
default: |
1560 |
|
sprintf( painCave.errMsg, |
1561 |
< |
"SimSetup error: If you use a constant pressure\n" |
893 |
< |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1561 |
> |
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1562 |
|
painCave.isFatal = 1; |
1563 |
|
simError(); |
1564 |
|
} |
897 |
– |
|
898 |
– |
if( the_globals->haveTauThermostat() ) |
899 |
– |
myNPTim->setTauThermostat( the_globals->getTauThermostat() ); |
900 |
– |
else{ |
901 |
– |
sprintf( painCave.errMsg, |
902 |
– |
"SimSetup error: If you use an NPT\n" |
903 |
– |
" ensemble, you must set tauThermostat.\n"); |
904 |
– |
painCave.isFatal = 1; |
905 |
– |
simError(); |
906 |
– |
} |
907 |
– |
|
908 |
– |
if( the_globals->haveTauBarostat() ) |
909 |
– |
myNPTim->setTauBarostat( the_globals->getTauBarostat() ); |
910 |
– |
else{ |
911 |
– |
sprintf( painCave.errMsg, |
912 |
– |
"SimSetup error: If you use an NPT\n" |
913 |
– |
" ensemble, you must set tauBarostat.\n"); |
914 |
– |
painCave.isFatal = 1; |
915 |
– |
simError(); |
916 |
– |
} |
917 |
– |
break; |
918 |
– |
|
919 |
– |
|
920 |
– |
|
921 |
– |
default: |
922 |
– |
sprintf( painCave.errMsg, |
923 |
– |
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
924 |
– |
painCave.isFatal = 1; |
925 |
– |
simError(); |
1565 |
|
} |
1566 |
+ |
} |
1567 |
|
|
1568 |
+ |
void SimSetup::initFortran( void ){ |
1569 |
|
|
1570 |
< |
#ifdef IS_MPI |
930 |
< |
mpiSim->mpiRefresh(); |
931 |
< |
#endif |
932 |
< |
|
933 |
< |
// initialize the Fortran |
934 |
< |
|
935 |
< |
|
936 |
< |
simnfo->refreshSim(); |
1570 |
> |
info[0].refreshSim(); |
1571 |
|
|
1572 |
< |
if( !strcmp( simnfo->mixingRule, "standard") ){ |
1572 |
> |
if( !strcmp( info[0].mixingRule, "standard") ){ |
1573 |
|
the_ff->initForceField( LB_MIXING_RULE ); |
1574 |
|
} |
1575 |
< |
else if( !strcmp( simnfo->mixingRule, "explicit") ){ |
1575 |
> |
else if( !strcmp( info[0].mixingRule, "explicit") ){ |
1576 |
|
the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
1577 |
|
} |
1578 |
|
else{ |
1579 |
|
sprintf( painCave.errMsg, |
1580 |
|
"SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1581 |
< |
simnfo->mixingRule ); |
1581 |
> |
info[0].mixingRule ); |
1582 |
|
painCave.isFatal = 1; |
1583 |
|
simError(); |
1584 |
|
} |
1589 |
|
"Successfully intialized the mixingRule for Fortran." ); |
1590 |
|
MPIcheckPoint(); |
1591 |
|
#endif // is_mpi |
1592 |
+ |
|
1593 |
|
} |
1594 |
|
|
1595 |
+ |
void SimSetup::setupZConstraint(SimInfo& theInfo) |
1596 |
+ |
{ |
1597 |
+ |
int nZConstraints; |
1598 |
+ |
ZconStamp** zconStamp; |
1599 |
+ |
|
1600 |
+ |
if(globals->haveZconstraintTime()){ |
1601 |
+ |
|
1602 |
+ |
//add sample time of z-constraint into SimInfo's property list |
1603 |
+ |
DoubleData* zconsTimeProp = new DoubleData(); |
1604 |
+ |
zconsTimeProp->setID(ZCONSTIME_ID); |
1605 |
+ |
zconsTimeProp->setData(globals->getZconsTime()); |
1606 |
+ |
theInfo.addProperty(zconsTimeProp); |
1607 |
+ |
} |
1608 |
+ |
else{ |
1609 |
+ |
sprintf( painCave.errMsg, |
1610 |
+ |
"ZConstraint error: If you use an ZConstraint\n" |
1611 |
+ |
" , you must set sample time.\n"); |
1612 |
+ |
painCave.isFatal = 1; |
1613 |
+ |
simError(); |
1614 |
+ |
} |
1615 |
|
|
1616 |
< |
void SimSetup::makeMolecules( void ){ |
1616 |
> |
// |
1617 |
> |
nZConstraints = globals->getNzConstraints(); |
1618 |
> |
zconStamp = globals->getZconStamp(); |
1619 |
> |
ZConsParaItem tempParaItem; |
1620 |
|
|
1621 |
< |
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
1622 |
< |
molInit info; |
1623 |
< |
DirectionalAtom* dAtom; |
1624 |
< |
LinkedAssign* extras; |
1625 |
< |
LinkedAssign* current_extra; |
1626 |
< |
AtomStamp* currentAtom; |
1627 |
< |
BondStamp* currentBond; |
1628 |
< |
BendStamp* currentBend; |
971 |
< |
TorsionStamp* currentTorsion; |
1621 |
> |
ZConsParaData* zconsParaData = new ZConsParaData(); |
1622 |
> |
zconsParaData->setID(ZCONSPARADATA_ID); |
1623 |
> |
|
1624 |
> |
for(int i = 0; i < nZConstraints; i++){ |
1625 |
> |
tempParaItem.havingZPos = zconStamp[i]->haveZpos(); |
1626 |
> |
tempParaItem.zPos = zconStamp[i]->getZpos(); |
1627 |
> |
tempParaItem.zconsIndex = zconStamp[i]->getMolIndex(); |
1628 |
> |
tempParaItem.kRatio = zconStamp[i]->getKratio(); |
1629 |
|
|
1630 |
< |
bond_pair* theBonds; |
1631 |
< |
bend_set* theBends; |
975 |
< |
torsion_set* theTorsions; |
1630 |
> |
zconsParaData->addItem(tempParaItem); |
1631 |
> |
} |
1632 |
|
|
1633 |
< |
|
1634 |
< |
//init the forceField paramters |
1633 |
> |
//sort the parameters by index of molecules |
1634 |
> |
zconsParaData->sortByIndex(); |
1635 |
> |
|
1636 |
> |
//push data into siminfo, therefore, we can retrieve later |
1637 |
> |
theInfo.addProperty(zconsParaData); |
1638 |
|
|
1639 |
< |
the_ff->readParams(); |
1639 |
> |
//push zconsTol into siminfo, if user does not specify |
1640 |
> |
//value for zconsTol, a default value will be used |
1641 |
> |
DoubleData* zconsTol = new DoubleData(); |
1642 |
> |
zconsTol->setID(ZCONSTOL_ID); |
1643 |
> |
if(globals->haveZconsTol()){ |
1644 |
> |
zconsTol->setData(globals->getZconsTol()); |
1645 |
> |
} |
1646 |
> |
else{ |
1647 |
> |
double defaultZConsTol = 1E-6; |
1648 |
> |
sprintf( painCave.errMsg, |
1649 |
> |
"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n" |
1650 |
> |
" , default value %f is used.\n", defaultZConsTol); |
1651 |
> |
painCave.isFatal = 0; |
1652 |
> |
simError(); |
1653 |
|
|
1654 |
< |
|
1655 |
< |
// init the atoms |
1656 |
< |
|
1657 |
< |
double ux, uy, uz, u, uSqr; |
1658 |
< |
|
1659 |
< |
atomOffset = 0; |
1660 |
< |
excludeOffset = 0; |
989 |
< |
for(i=0; i<simnfo->n_mol; i++){ |
1654 |
> |
zconsTol->setData(defaultZConsTol); |
1655 |
> |
} |
1656 |
> |
theInfo.addProperty(zconsTol); |
1657 |
> |
|
1658 |
> |
//Determine the name of ouput file and add it into SimInfo's property list |
1659 |
> |
//Be careful, do not use inFileName, since it is a pointer which |
1660 |
> |
//point to a string at master node, and slave nodes do not contain that string |
1661 |
|
|
1662 |
< |
stampID = the_molecules[i].getStampID(); |
992 |
< |
|
993 |
< |
info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
994 |
< |
info.nBonds = comp_stamps[stampID]->getNBonds(); |
995 |
< |
info.nBends = comp_stamps[stampID]->getNBends(); |
996 |
< |
info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
997 |
< |
info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
998 |
< |
|
999 |
< |
info.myAtoms = &the_atoms[atomOffset]; |
1000 |
< |
info.myExcludes = &the_excludes[excludeOffset]; |
1001 |
< |
info.myBonds = new Bond*[info.nBonds]; |
1002 |
< |
info.myBends = new Bend*[info.nBends]; |
1003 |
< |
info.myTorsions = new Torsion*[info.nTorsions]; |
1004 |
< |
|
1005 |
< |
theBonds = new bond_pair[info.nBonds]; |
1006 |
< |
theBends = new bend_set[info.nBends]; |
1007 |
< |
theTorsions = new torsion_set[info.nTorsions]; |
1662 |
> |
string zconsOutput(theInfo.finalName); |
1663 |
|
|
1664 |
< |
// make the Atoms |
1664 |
> |
zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1665 |
|
|
1666 |
< |
for(j=0; j<info.nAtoms; j++){ |
1667 |
< |
|
1668 |
< |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
1014 |
< |
if( currentAtom->haveOrientation() ){ |
1015 |
< |
|
1016 |
< |
dAtom = new DirectionalAtom(j + atomOffset); |
1017 |
< |
simnfo->n_oriented++; |
1018 |
< |
info.myAtoms[j] = dAtom; |
1019 |
< |
|
1020 |
< |
ux = currentAtom->getOrntX(); |
1021 |
< |
uy = currentAtom->getOrntY(); |
1022 |
< |
uz = currentAtom->getOrntZ(); |
1023 |
< |
|
1024 |
< |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
1025 |
< |
|
1026 |
< |
u = sqrt( uSqr ); |
1027 |
< |
ux = ux / u; |
1028 |
< |
uy = uy / u; |
1029 |
< |
uz = uz / u; |
1030 |
< |
|
1031 |
< |
dAtom->setSUx( ux ); |
1032 |
< |
dAtom->setSUy( uy ); |
1033 |
< |
dAtom->setSUz( uz ); |
1034 |
< |
} |
1035 |
< |
else{ |
1036 |
< |
info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
1037 |
< |
} |
1038 |
< |
info.myAtoms[j]->setType( currentAtom->getType() ); |
1666 |
> |
StringData* zconsFilename = new StringData(); |
1667 |
> |
zconsFilename->setID(ZCONSFILENAME_ID); |
1668 |
> |
zconsFilename->setData(zconsOutput); |
1669 |
|
|
1670 |
< |
#ifdef IS_MPI |
1041 |
< |
|
1042 |
< |
info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
1043 |
< |
|
1044 |
< |
#endif // is_mpi |
1045 |
< |
} |
1046 |
< |
|
1047 |
< |
// make the bonds |
1048 |
< |
for(j=0; j<info.nBonds; j++){ |
1049 |
< |
|
1050 |
< |
currentBond = comp_stamps[stampID]->getBond( j ); |
1051 |
< |
theBonds[j].a = currentBond->getA() + atomOffset; |
1052 |
< |
theBonds[j].b = currentBond->getB() + atomOffset; |
1053 |
< |
|
1054 |
< |
exI = theBonds[j].a; |
1055 |
< |
exJ = theBonds[j].b; |
1056 |
< |
|
1057 |
< |
// exclude_I must always be the smaller of the pair |
1058 |
< |
if( exI > exJ ){ |
1059 |
< |
tempEx = exI; |
1060 |
< |
exI = exJ; |
1061 |
< |
exJ = tempEx; |
1062 |
< |
} |
1063 |
< |
#ifdef IS_MPI |
1064 |
< |
tempEx = exI; |
1065 |
< |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
1066 |
< |
tempEx = exJ; |
1067 |
< |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1068 |
< |
|
1069 |
< |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1070 |
< |
#else // isn't MPI |
1071 |
< |
|
1072 |
< |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1073 |
< |
#endif //is_mpi |
1074 |
< |
} |
1075 |
< |
excludeOffset += info.nBonds; |
1076 |
< |
|
1077 |
< |
//make the bends |
1078 |
< |
for(j=0; j<info.nBends; j++){ |
1079 |
< |
|
1080 |
< |
currentBend = comp_stamps[stampID]->getBend( j ); |
1081 |
< |
theBends[j].a = currentBend->getA() + atomOffset; |
1082 |
< |
theBends[j].b = currentBend->getB() + atomOffset; |
1083 |
< |
theBends[j].c = currentBend->getC() + atomOffset; |
1084 |
< |
|
1085 |
< |
if( currentBend->haveExtras() ){ |
1086 |
< |
|
1087 |
< |
extras = currentBend->getExtras(); |
1088 |
< |
current_extra = extras; |
1089 |
< |
|
1090 |
< |
while( current_extra != NULL ){ |
1091 |
< |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
1092 |
< |
|
1093 |
< |
switch( current_extra->getType() ){ |
1094 |
< |
|
1095 |
< |
case 0: |
1096 |
< |
theBends[j].ghost = |
1097 |
< |
current_extra->getInt() + atomOffset; |
1098 |
< |
theBends[j].isGhost = 1; |
1099 |
< |
break; |
1100 |
< |
|
1101 |
< |
case 1: |
1102 |
< |
theBends[j].ghost = |
1103 |
< |
(int)current_extra->getDouble() + atomOffset; |
1104 |
< |
theBends[j].isGhost = 1; |
1105 |
< |
break; |
1106 |
< |
|
1107 |
< |
default: |
1108 |
< |
sprintf( painCave.errMsg, |
1109 |
< |
"SimSetup Error: ghostVectorSource was neither a " |
1110 |
< |
"double nor an int.\n" |
1111 |
< |
"-->Bend[%d] in %s\n", |
1112 |
< |
j, comp_stamps[stampID]->getID() ); |
1113 |
< |
painCave.isFatal = 1; |
1114 |
< |
simError(); |
1115 |
< |
} |
1116 |
< |
} |
1117 |
< |
|
1118 |
< |
else{ |
1119 |
< |
|
1120 |
< |
sprintf( painCave.errMsg, |
1121 |
< |
"SimSetup Error: unhandled bend assignment:\n" |
1122 |
< |
" -->%s in Bend[%d] in %s\n", |
1123 |
< |
current_extra->getlhs(), |
1124 |
< |
j, comp_stamps[stampID]->getID() ); |
1125 |
< |
painCave.isFatal = 1; |
1126 |
< |
simError(); |
1127 |
< |
} |
1128 |
< |
|
1129 |
< |
current_extra = current_extra->getNext(); |
1130 |
< |
} |
1131 |
< |
} |
1132 |
< |
|
1133 |
< |
if( !theBends[j].isGhost ){ |
1134 |
< |
|
1135 |
< |
exI = theBends[j].a; |
1136 |
< |
exJ = theBends[j].c; |
1137 |
< |
} |
1138 |
< |
else{ |
1139 |
< |
|
1140 |
< |
exI = theBends[j].a; |
1141 |
< |
exJ = theBends[j].b; |
1142 |
< |
} |
1143 |
< |
|
1144 |
< |
// exclude_I must always be the smaller of the pair |
1145 |
< |
if( exI > exJ ){ |
1146 |
< |
tempEx = exI; |
1147 |
< |
exI = exJ; |
1148 |
< |
exJ = tempEx; |
1149 |
< |
} |
1150 |
< |
#ifdef IS_MPI |
1151 |
< |
tempEx = exI; |
1152 |
< |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
1153 |
< |
tempEx = exJ; |
1154 |
< |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1155 |
< |
|
1156 |
< |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1157 |
< |
#else // isn't MPI |
1158 |
< |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1159 |
< |
#endif //is_mpi |
1160 |
< |
} |
1161 |
< |
excludeOffset += info.nBends; |
1162 |
< |
|
1163 |
< |
for(j=0; j<info.nTorsions; j++){ |
1164 |
< |
|
1165 |
< |
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
1166 |
< |
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
1167 |
< |
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
1168 |
< |
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
1169 |
< |
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
1170 |
< |
|
1171 |
< |
exI = theTorsions[j].a; |
1172 |
< |
exJ = theTorsions[j].d; |
1173 |
< |
|
1174 |
< |
// exclude_I must always be the smaller of the pair |
1175 |
< |
if( exI > exJ ){ |
1176 |
< |
tempEx = exI; |
1177 |
< |
exI = exJ; |
1178 |
< |
exJ = tempEx; |
1179 |
< |
} |
1180 |
< |
#ifdef IS_MPI |
1181 |
< |
tempEx = exI; |
1182 |
< |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
1183 |
< |
tempEx = exJ; |
1184 |
< |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1185 |
< |
|
1186 |
< |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1187 |
< |
#else // isn't MPI |
1188 |
< |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1189 |
< |
#endif //is_mpi |
1190 |
< |
} |
1191 |
< |
excludeOffset += info.nTorsions; |
1192 |
< |
|
1193 |
< |
|
1194 |
< |
// send the arrays off to the forceField for init. |
1195 |
< |
|
1196 |
< |
the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
1197 |
< |
the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
1198 |
< |
the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
1199 |
< |
the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
1200 |
< |
|
1201 |
< |
|
1202 |
< |
the_molecules[i].initialize( info ); |
1203 |
< |
|
1204 |
< |
|
1205 |
< |
atomOffset += info.nAtoms; |
1206 |
< |
delete[] theBonds; |
1207 |
< |
delete[] theBends; |
1208 |
< |
delete[] theTorsions; |
1209 |
< |
} |
1210 |
< |
|
1211 |
< |
#ifdef IS_MPI |
1212 |
< |
sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
1213 |
< |
MPIcheckPoint(); |
1214 |
< |
#endif // is_mpi |
1215 |
< |
|
1216 |
< |
// clean up the forcefield |
1217 |
< |
the_ff->calcRcut(); |
1218 |
< |
the_ff->cleanMe(); |
1219 |
< |
|
1670 |
> |
theInfo.addProperty(zconsFilename); |
1671 |
|
} |
1221 |
– |
|
1222 |
– |
void SimSetup::initFromBass( void ){ |
1223 |
– |
|
1224 |
– |
int i, j, k; |
1225 |
– |
int n_cells; |
1226 |
– |
double cellx, celly, cellz; |
1227 |
– |
double temp1, temp2, temp3; |
1228 |
– |
int n_per_extra; |
1229 |
– |
int n_extra; |
1230 |
– |
int have_extra, done; |
1231 |
– |
|
1232 |
– |
temp1 = (double)tot_nmol / 4.0; |
1233 |
– |
temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
1234 |
– |
temp3 = ceil( temp2 ); |
1235 |
– |
|
1236 |
– |
have_extra =0; |
1237 |
– |
if( temp2 < temp3 ){ // we have a non-complete lattice |
1238 |
– |
have_extra =1; |
1239 |
– |
|
1240 |
– |
n_cells = (int)temp3 - 1; |
1241 |
– |
cellx = simnfo->boxLx / temp3; |
1242 |
– |
celly = simnfo->boxLy / temp3; |
1243 |
– |
cellz = simnfo->boxLz / temp3; |
1244 |
– |
n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
1245 |
– |
temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
1246 |
– |
n_per_extra = (int)ceil( temp1 ); |
1247 |
– |
|
1248 |
– |
if( n_per_extra > 4){ |
1249 |
– |
sprintf( painCave.errMsg, |
1250 |
– |
"SimSetup error. There has been an error in constructing" |
1251 |
– |
" the non-complete lattice.\n" ); |
1252 |
– |
painCave.isFatal = 1; |
1253 |
– |
simError(); |
1254 |
– |
} |
1255 |
– |
} |
1256 |
– |
else{ |
1257 |
– |
n_cells = (int)temp3; |
1258 |
– |
cellx = simnfo->boxLx / temp3; |
1259 |
– |
celly = simnfo->boxLy / temp3; |
1260 |
– |
cellz = simnfo->boxLz / temp3; |
1261 |
– |
} |
1262 |
– |
|
1263 |
– |
current_mol = 0; |
1264 |
– |
current_comp_mol = 0; |
1265 |
– |
current_comp = 0; |
1266 |
– |
current_atom_ndx = 0; |
1267 |
– |
|
1268 |
– |
for( i=0; i < n_cells ; i++ ){ |
1269 |
– |
for( j=0; j < n_cells; j++ ){ |
1270 |
– |
for( k=0; k < n_cells; k++ ){ |
1271 |
– |
|
1272 |
– |
makeElement( i * cellx, |
1273 |
– |
j * celly, |
1274 |
– |
k * cellz ); |
1275 |
– |
|
1276 |
– |
makeElement( i * cellx + 0.5 * cellx, |
1277 |
– |
j * celly + 0.5 * celly, |
1278 |
– |
k * cellz ); |
1279 |
– |
|
1280 |
– |
makeElement( i * cellx, |
1281 |
– |
j * celly + 0.5 * celly, |
1282 |
– |
k * cellz + 0.5 * cellz ); |
1283 |
– |
|
1284 |
– |
makeElement( i * cellx + 0.5 * cellx, |
1285 |
– |
j * celly, |
1286 |
– |
k * cellz + 0.5 * cellz ); |
1287 |
– |
} |
1288 |
– |
} |
1289 |
– |
} |
1290 |
– |
|
1291 |
– |
if( have_extra ){ |
1292 |
– |
done = 0; |
1293 |
– |
|
1294 |
– |
int start_ndx; |
1295 |
– |
for( i=0; i < (n_cells+1) && !done; i++ ){ |
1296 |
– |
for( j=0; j < (n_cells+1) && !done; j++ ){ |
1297 |
– |
|
1298 |
– |
if( i < n_cells ){ |
1299 |
– |
|
1300 |
– |
if( j < n_cells ){ |
1301 |
– |
start_ndx = n_cells; |
1302 |
– |
} |
1303 |
– |
else start_ndx = 0; |
1304 |
– |
} |
1305 |
– |
else start_ndx = 0; |
1306 |
– |
|
1307 |
– |
for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
1308 |
– |
|
1309 |
– |
makeElement( i * cellx, |
1310 |
– |
j * celly, |
1311 |
– |
k * cellz ); |
1312 |
– |
done = ( current_mol >= tot_nmol ); |
1313 |
– |
|
1314 |
– |
if( !done && n_per_extra > 1 ){ |
1315 |
– |
makeElement( i * cellx + 0.5 * cellx, |
1316 |
– |
j * celly + 0.5 * celly, |
1317 |
– |
k * cellz ); |
1318 |
– |
done = ( current_mol >= tot_nmol ); |
1319 |
– |
} |
1320 |
– |
|
1321 |
– |
if( !done && n_per_extra > 2){ |
1322 |
– |
makeElement( i * cellx, |
1323 |
– |
j * celly + 0.5 * celly, |
1324 |
– |
k * cellz + 0.5 * cellz ); |
1325 |
– |
done = ( current_mol >= tot_nmol ); |
1326 |
– |
} |
1327 |
– |
|
1328 |
– |
if( !done && n_per_extra > 3){ |
1329 |
– |
makeElement( i * cellx + 0.5 * cellx, |
1330 |
– |
j * celly, |
1331 |
– |
k * cellz + 0.5 * cellz ); |
1332 |
– |
done = ( current_mol >= tot_nmol ); |
1333 |
– |
} |
1334 |
– |
} |
1335 |
– |
} |
1336 |
– |
} |
1337 |
– |
} |
1338 |
– |
|
1339 |
– |
|
1340 |
– |
for( i=0; i<simnfo->n_atoms; i++ ){ |
1341 |
– |
simnfo->atoms[i]->set_vx( 0.0 ); |
1342 |
– |
simnfo->atoms[i]->set_vy( 0.0 ); |
1343 |
– |
simnfo->atoms[i]->set_vz( 0.0 ); |
1344 |
– |
} |
1345 |
– |
} |
1346 |
– |
|
1347 |
– |
void SimSetup::makeElement( double x, double y, double z ){ |
1348 |
– |
|
1349 |
– |
int k; |
1350 |
– |
AtomStamp* current_atom; |
1351 |
– |
DirectionalAtom* dAtom; |
1352 |
– |
double rotMat[3][3]; |
1353 |
– |
|
1354 |
– |
for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
1355 |
– |
|
1356 |
– |
current_atom = comp_stamps[current_comp]->getAtom( k ); |
1357 |
– |
if( !current_atom->havePosition() ){ |
1358 |
– |
sprintf( painCave.errMsg, |
1359 |
– |
"SimSetup:initFromBass error.\n" |
1360 |
– |
"\tComponent %s, atom %s does not have a position specified.\n" |
1361 |
– |
"\tThe initialization routine is unable to give a start" |
1362 |
– |
" position.\n", |
1363 |
– |
comp_stamps[current_comp]->getID(), |
1364 |
– |
current_atom->getType() ); |
1365 |
– |
painCave.isFatal = 1; |
1366 |
– |
simError(); |
1367 |
– |
} |
1368 |
– |
|
1369 |
– |
the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() ); |
1370 |
– |
the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() ); |
1371 |
– |
the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() ); |
1372 |
– |
|
1373 |
– |
if( the_atoms[current_atom_ndx]->isDirectional() ){ |
1374 |
– |
|
1375 |
– |
dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx]; |
1376 |
– |
|
1377 |
– |
rotMat[0][0] = 1.0; |
1378 |
– |
rotMat[0][1] = 0.0; |
1379 |
– |
rotMat[0][2] = 0.0; |
1380 |
– |
|
1381 |
– |
rotMat[1][0] = 0.0; |
1382 |
– |
rotMat[1][1] = 1.0; |
1383 |
– |
rotMat[1][2] = 0.0; |
1384 |
– |
|
1385 |
– |
rotMat[2][0] = 0.0; |
1386 |
– |
rotMat[2][1] = 0.0; |
1387 |
– |
rotMat[2][2] = 1.0; |
1388 |
– |
|
1389 |
– |
dAtom->setA( rotMat ); |
1390 |
– |
} |
1391 |
– |
|
1392 |
– |
current_atom_ndx++; |
1393 |
– |
} |
1394 |
– |
|
1395 |
– |
current_mol++; |
1396 |
– |
current_comp_mol++; |
1397 |
– |
|
1398 |
– |
if( current_comp_mol >= components_nmol[current_comp] ){ |
1399 |
– |
|
1400 |
– |
current_comp_mol = 0; |
1401 |
– |
current_comp++; |
1402 |
– |
} |
1403 |
– |
} |