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mmeineke |
377 |
#include <cstdlib> |
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#include <iostream> |
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#include <cmath> |
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#include "SimSetup.hpp" |
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#include "parse_me.h" |
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#include "Integrator.hpp" |
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#include "simError.h" |
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#ifdef IS_MPI |
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#include "mpiBASS.h" |
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#include "mpiSimulation.hpp" |
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#endif |
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mmeineke |
557 |
// some defines for ensemble and Forcefield cases |
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gezelter |
604 |
#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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mmeineke |
557 |
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mmeineke |
582 |
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mmeineke |
557 |
#define FF_DUFF 0 |
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#define FF_LJ 1 |
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chuckv |
653 |
#define FF_EAM 2 |
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mmeineke |
557 |
|
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mmeineke |
377 |
SimSetup::SimSetup(){ |
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stamps = new MakeStamps(); |
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globals = new Globals(); |
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#ifdef IS_MPI |
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strcpy( checkPointMsg, "SimSetup creation successful" ); |
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MPIcheckPoint(); |
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#endif // IS_MPI |
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} |
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SimSetup::~SimSetup(){ |
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delete stamps; |
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delete globals; |
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} |
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void SimSetup::parseFile( char* fileName ){ |
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#ifdef IS_MPI |
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if( worldRank == 0 ){ |
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#endif // is_mpi |
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inFileName = fileName; |
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set_interface_stamps( stamps, globals ); |
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#ifdef IS_MPI |
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mpiEventInit(); |
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#endif |
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yacc_BASS( fileName ); |
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#ifdef IS_MPI |
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throwMPIEvent(NULL); |
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} |
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else receiveParse(); |
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#endif |
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} |
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#ifdef IS_MPI |
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void SimSetup::receiveParse(void){ |
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set_interface_stamps( stamps, globals ); |
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mpiEventInit(); |
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MPIcheckPoint(); |
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mpiEventLoop(); |
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} |
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#endif // is_mpi |
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void SimSetup::createSim( void ){ |
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gezelter |
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int i, j, k, globalAtomIndex; |
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mmeineke |
557 |
|
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mmeineke |
614 |
// gather all of the information from the Bass file |
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mmeineke |
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|
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mmeineke |
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gatherInfo(); |
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mmeineke |
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|
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mmeineke |
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// creation of complex system objects |
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mmeineke |
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|
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mmeineke |
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sysObjectsCreation(); |
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mmeineke |
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|
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mmeineke |
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// check on the post processing info |
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gezelter |
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|
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mmeineke |
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finalInfoCheck(); |
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mmeineke |
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|
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mmeineke |
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// initialize the system coordinates |
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mmeineke |
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|
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mmeineke |
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initSystemCoords(); |
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mmeineke |
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|
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mmeineke |
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// make the output filenames |
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mmeineke |
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|
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mmeineke |
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makeOutNames(); |
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mmeineke |
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|
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mmeineke |
555 |
// make the integrator |
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mmeineke |
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|
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mmeineke |
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makeIntegrator(); |
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mmeineke |
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|
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chuckv |
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#ifdef IS_MPI |
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mpiSim->mpiRefresh(); |
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#endif |
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mmeineke |
377 |
|
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chuckv |
432 |
// initialize the Fortran |
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mmeineke |
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|
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mmeineke |
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initFortran(); |
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chuckv |
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mmeineke |
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} |
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mmeineke |
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void SimSetup::makeMolecules( void ){ |
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mmeineke |
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int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
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mmeineke |
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molInit molInfo; |
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mmeineke |
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DirectionalAtom* dAtom; |
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mmeineke |
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LinkedAssign* extras; |
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LinkedAssign* current_extra; |
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mmeineke |
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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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mmeineke |
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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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mmeineke |
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//init the forceField paramters |
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the_ff->readParams(); |
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mmeineke |
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// init the atoms |
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mmeineke |
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|
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mmeineke |
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double ux, uy, uz, u, uSqr; |
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mmeineke |
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atomOffset = 0; |
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mmeineke |
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excludeOffset = 0; |
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mmeineke |
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for(i=0; i<info->n_mol; i++){ |
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mmeineke |
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stampID = the_molecules[i].getStampID(); |
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mmeineke |
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molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
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molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
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molInfo.nBends = comp_stamps[stampID]->getNBends(); |
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molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
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molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
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mmeineke |
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|
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mmeineke |
616 |
molInfo.myAtoms = &the_atoms[atomOffset]; |
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molInfo.myExcludes = &the_excludes[excludeOffset]; |
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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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mmeineke |
407 |
|
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mmeineke |
616 |
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]; |
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mmeineke |
407 |
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// make the Atoms |
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mmeineke |
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for(j=0; j<molInfo.nAtoms; j++){ |
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mmeineke |
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|
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mmeineke |
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currentAtom = comp_stamps[stampID]->getAtom( j ); |
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mmeineke |
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if( currentAtom->haveOrientation() ){ |
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dAtom = new DirectionalAtom(j + atomOffset); |
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mmeineke |
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info->n_oriented++; |
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mmeineke |
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molInfo.myAtoms[j] = dAtom; |
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mmeineke |
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ux = currentAtom->getOrntX(); |
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uy = currentAtom->getOrntY(); |
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uz = currentAtom->getOrntZ(); |
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uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
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u = sqrt( uSqr ); |
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ux = ux / u; |
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uy = uy / u; |
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uz = uz / u; |
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dAtom->setSUx( ux ); |
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dAtom->setSUy( uy ); |
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dAtom->setSUz( uz ); |
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} |
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else{ |
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mmeineke |
616 |
molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset); |
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mmeineke |
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} |
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mmeineke |
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molInfo.myAtoms[j]->setType( currentAtom->getType() ); |
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mmeineke |
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#ifdef IS_MPI |
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mmeineke |
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molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
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mmeineke |
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#endif // is_mpi |
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} |
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// make the bonds |
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mmeineke |
616 |
for(j=0; j<molInfo.nBonds; j++){ |
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mmeineke |
407 |
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currentBond = comp_stamps[stampID]->getBond( j ); |
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theBonds[j].a = currentBond->getA() + atomOffset; |
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theBonds[j].b = currentBond->getB() + atomOffset; |
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mmeineke |
435 |
exI = theBonds[j].a; |
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exJ = theBonds[j].b; |
216 |
mmeineke |
407 |
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// exclude_I must always be the smaller of the pair |
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if( exI > exJ ){ |
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tempEx = exI; |
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exI = exJ; |
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exJ = tempEx; |
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} |
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#ifdef IS_MPI |
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mmeineke |
412 |
tempEx = exI; |
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exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
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tempEx = exJ; |
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exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
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mmeineke |
407 |
|
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mmeineke |
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the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
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#else // isn't MPI |
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mmeineke |
435 |
|
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mmeineke |
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the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
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#endif //is_mpi |
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} |
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mmeineke |
616 |
excludeOffset += molInfo.nBonds; |
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mmeineke |
412 |
|
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//make the bends |
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mmeineke |
616 |
for(j=0; j<molInfo.nBends; j++){ |
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mmeineke |
407 |
|
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mmeineke |
412 |
currentBend = comp_stamps[stampID]->getBend( j ); |
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theBends[j].a = currentBend->getA() + atomOffset; |
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theBends[j].b = currentBend->getB() + atomOffset; |
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theBends[j].c = currentBend->getC() + atomOffset; |
244 |
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if( currentBend->haveExtras() ){ |
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mmeineke |
427 |
extras = currentBend->getExtras(); |
248 |
mmeineke |
412 |
current_extra = extras; |
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while( current_extra != NULL ){ |
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if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
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switch( current_extra->getType() ){ |
254 |
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case 0: |
256 |
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theBends[j].ghost = |
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current_extra->getInt() + atomOffset; |
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theBends[j].isGhost = 1; |
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break; |
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case 1: |
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theBends[j].ghost = |
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(int)current_extra->getDouble() + atomOffset; |
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theBends[j].isGhost = 1; |
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break; |
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default: |
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sprintf( painCave.errMsg, |
269 |
chuckv |
434 |
"SimSetup Error: ghostVectorSource was neither a " |
270 |
mmeineke |
412 |
"double nor an int.\n" |
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"-->Bend[%d] in %s\n", |
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j, comp_stamps[stampID]->getID() ); |
273 |
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painCave.isFatal = 1; |
274 |
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simError(); |
275 |
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} |
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} |
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else{ |
279 |
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sprintf( painCave.errMsg, |
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"SimSetup Error: unhandled bend assignment:\n" |
282 |
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" -->%s in Bend[%d] in %s\n", |
283 |
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current_extra->getlhs(), |
284 |
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j, comp_stamps[stampID]->getID() ); |
285 |
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painCave.isFatal = 1; |
286 |
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simError(); |
287 |
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} |
288 |
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289 |
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current_extra = current_extra->getNext(); |
290 |
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} |
291 |
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} |
292 |
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293 |
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if( !theBends[j].isGhost ){ |
294 |
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295 |
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exI = theBends[j].a; |
296 |
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exJ = theBends[j].c; |
297 |
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} |
298 |
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else{ |
299 |
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300 |
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exI = theBends[j].a; |
301 |
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exJ = theBends[j].b; |
302 |
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} |
303 |
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304 |
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// exclude_I must always be the smaller of the pair |
305 |
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if( exI > exJ ){ |
306 |
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tempEx = exI; |
307 |
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exI = exJ; |
308 |
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exJ = tempEx; |
309 |
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} |
310 |
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#ifdef IS_MPI |
311 |
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tempEx = exI; |
312 |
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exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
313 |
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tempEx = exJ; |
314 |
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exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
315 |
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316 |
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the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
317 |
mmeineke |
407 |
#else // isn't MPI |
318 |
mmeineke |
412 |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
319 |
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#endif //is_mpi |
320 |
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} |
321 |
mmeineke |
616 |
excludeOffset += molInfo.nBends; |
322 |
mmeineke |
412 |
|
323 |
mmeineke |
616 |
for(j=0; j<molInfo.nTorsions; j++){ |
324 |
mmeineke |
407 |
|
325 |
mmeineke |
412 |
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
326 |
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theTorsions[j].a = currentTorsion->getA() + atomOffset; |
327 |
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theTorsions[j].b = currentTorsion->getB() + atomOffset; |
328 |
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theTorsions[j].c = currentTorsion->getC() + atomOffset; |
329 |
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theTorsions[j].d = currentTorsion->getD() + atomOffset; |
330 |
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331 |
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exI = theTorsions[j].a; |
332 |
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exJ = theTorsions[j].d; |
333 |
mmeineke |
407 |
|
334 |
mmeineke |
412 |
// exclude_I must always be the smaller of the pair |
335 |
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if( exI > exJ ){ |
336 |
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tempEx = exI; |
337 |
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exI = exJ; |
338 |
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exJ = tempEx; |
339 |
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} |
340 |
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#ifdef IS_MPI |
341 |
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tempEx = exI; |
342 |
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exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
343 |
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tempEx = exJ; |
344 |
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exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
345 |
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346 |
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the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
347 |
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#else // isn't MPI |
348 |
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the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
349 |
mmeineke |
407 |
#endif //is_mpi |
350 |
mmeineke |
412 |
} |
351 |
mmeineke |
616 |
excludeOffset += molInfo.nTorsions; |
352 |
mmeineke |
412 |
|
353 |
mmeineke |
407 |
|
354 |
mmeineke |
414 |
// send the arrays off to the forceField for init. |
355 |
mmeineke |
407 |
|
356 |
mmeineke |
616 |
the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms ); |
357 |
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the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds ); |
358 |
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the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends ); |
359 |
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the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions ); |
360 |
mmeineke |
407 |
|
361 |
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362 |
mmeineke |
616 |
the_molecules[i].initialize( molInfo ); |
363 |
chuckv |
438 |
|
364 |
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365 |
mmeineke |
616 |
atomOffset += molInfo.nAtoms; |
366 |
mmeineke |
427 |
delete[] theBonds; |
367 |
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delete[] theBends; |
368 |
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delete[] theTorsions; |
369 |
mmeineke |
414 |
} |
370 |
mmeineke |
407 |
|
371 |
chuckv |
434 |
#ifdef IS_MPI |
372 |
|
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sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
373 |
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MPIcheckPoint(); |
374 |
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#endif // is_mpi |
375 |
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|
376 |
mmeineke |
414 |
// clean up the forcefield |
377 |
mmeineke |
420 |
the_ff->calcRcut(); |
378 |
mmeineke |
414 |
the_ff->cleanMe(); |
379 |
chuckv |
434 |
|
380 |
mmeineke |
414 |
} |
381 |
mmeineke |
407 |
|
382 |
mmeineke |
377 |
void SimSetup::initFromBass( void ){ |
383 |
|
|
|
384 |
|
|
int i, j, k; |
385 |
|
|
int n_cells; |
386 |
|
|
double cellx, celly, cellz; |
387 |
|
|
double temp1, temp2, temp3; |
388 |
|
|
int n_per_extra; |
389 |
|
|
int n_extra; |
390 |
|
|
int have_extra, done; |
391 |
|
|
|
392 |
|
|
temp1 = (double)tot_nmol / 4.0; |
393 |
|
|
temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
394 |
|
|
temp3 = ceil( temp2 ); |
395 |
|
|
|
396 |
|
|
have_extra =0; |
397 |
|
|
if( temp2 < temp3 ){ // we have a non-complete lattice |
398 |
|
|
have_extra =1; |
399 |
|
|
|
400 |
|
|
n_cells = (int)temp3 - 1; |
401 |
gezelter |
621 |
cellx = info->boxL[0] / temp3; |
402 |
|
|
celly = info->boxL[1] / temp3; |
403 |
|
|
cellz = info->boxL[2] / temp3; |
404 |
mmeineke |
377 |
n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
405 |
|
|
temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
406 |
|
|
n_per_extra = (int)ceil( temp1 ); |
407 |
|
|
|
408 |
|
|
if( n_per_extra > 4){ |
409 |
|
|
sprintf( painCave.errMsg, |
410 |
|
|
"SimSetup error. There has been an error in constructing" |
411 |
|
|
" the non-complete lattice.\n" ); |
412 |
|
|
painCave.isFatal = 1; |
413 |
|
|
simError(); |
414 |
|
|
} |
415 |
|
|
} |
416 |
|
|
else{ |
417 |
|
|
n_cells = (int)temp3; |
418 |
gezelter |
621 |
cellx = info->boxL[0] / temp3; |
419 |
|
|
celly = info->boxL[1] / temp3; |
420 |
|
|
cellz = info->boxL[2] / temp3; |
421 |
mmeineke |
377 |
} |
422 |
|
|
|
423 |
|
|
current_mol = 0; |
424 |
|
|
current_comp_mol = 0; |
425 |
|
|
current_comp = 0; |
426 |
|
|
current_atom_ndx = 0; |
427 |
|
|
|
428 |
|
|
for( i=0; i < n_cells ; i++ ){ |
429 |
|
|
for( j=0; j < n_cells; j++ ){ |
430 |
|
|
for( k=0; k < n_cells; k++ ){ |
431 |
|
|
|
432 |
|
|
makeElement( i * cellx, |
433 |
|
|
j * celly, |
434 |
|
|
k * cellz ); |
435 |
|
|
|
436 |
|
|
makeElement( i * cellx + 0.5 * cellx, |
437 |
|
|
j * celly + 0.5 * celly, |
438 |
|
|
k * cellz ); |
439 |
|
|
|
440 |
|
|
makeElement( i * cellx, |
441 |
|
|
j * celly + 0.5 * celly, |
442 |
|
|
k * cellz + 0.5 * cellz ); |
443 |
|
|
|
444 |
|
|
makeElement( i * cellx + 0.5 * cellx, |
445 |
|
|
j * celly, |
446 |
|
|
k * cellz + 0.5 * cellz ); |
447 |
|
|
} |
448 |
|
|
} |
449 |
|
|
} |
450 |
|
|
|
451 |
|
|
if( have_extra ){ |
452 |
|
|
done = 0; |
453 |
|
|
|
454 |
|
|
int start_ndx; |
455 |
|
|
for( i=0; i < (n_cells+1) && !done; i++ ){ |
456 |
|
|
for( j=0; j < (n_cells+1) && !done; j++ ){ |
457 |
|
|
|
458 |
|
|
if( i < n_cells ){ |
459 |
|
|
|
460 |
|
|
if( j < n_cells ){ |
461 |
|
|
start_ndx = n_cells; |
462 |
|
|
} |
463 |
|
|
else start_ndx = 0; |
464 |
|
|
} |
465 |
|
|
else start_ndx = 0; |
466 |
|
|
|
467 |
|
|
for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
468 |
|
|
|
469 |
|
|
makeElement( i * cellx, |
470 |
|
|
j * celly, |
471 |
|
|
k * cellz ); |
472 |
|
|
done = ( current_mol >= tot_nmol ); |
473 |
|
|
|
474 |
|
|
if( !done && n_per_extra > 1 ){ |
475 |
|
|
makeElement( i * cellx + 0.5 * cellx, |
476 |
|
|
j * celly + 0.5 * celly, |
477 |
|
|
k * cellz ); |
478 |
|
|
done = ( current_mol >= tot_nmol ); |
479 |
|
|
} |
480 |
|
|
|
481 |
|
|
if( !done && n_per_extra > 2){ |
482 |
|
|
makeElement( i * cellx, |
483 |
|
|
j * celly + 0.5 * celly, |
484 |
|
|
k * cellz + 0.5 * cellz ); |
485 |
|
|
done = ( current_mol >= tot_nmol ); |
486 |
|
|
} |
487 |
|
|
|
488 |
|
|
if( !done && n_per_extra > 3){ |
489 |
|
|
makeElement( i * cellx + 0.5 * cellx, |
490 |
|
|
j * celly, |
491 |
|
|
k * cellz + 0.5 * cellz ); |
492 |
|
|
done = ( current_mol >= tot_nmol ); |
493 |
|
|
} |
494 |
|
|
} |
495 |
|
|
} |
496 |
|
|
} |
497 |
|
|
} |
498 |
|
|
|
499 |
|
|
|
500 |
mmeineke |
614 |
for( i=0; i<info->n_atoms; i++ ){ |
501 |
|
|
info->atoms[i]->set_vx( 0.0 ); |
502 |
|
|
info->atoms[i]->set_vy( 0.0 ); |
503 |
|
|
info->atoms[i]->set_vz( 0.0 ); |
504 |
mmeineke |
377 |
} |
505 |
|
|
} |
506 |
|
|
|
507 |
|
|
void SimSetup::makeElement( double x, double y, double z ){ |
508 |
|
|
|
509 |
|
|
int k; |
510 |
|
|
AtomStamp* current_atom; |
511 |
|
|
DirectionalAtom* dAtom; |
512 |
|
|
double rotMat[3][3]; |
513 |
|
|
|
514 |
|
|
for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
515 |
|
|
|
516 |
|
|
current_atom = comp_stamps[current_comp]->getAtom( k ); |
517 |
|
|
if( !current_atom->havePosition() ){ |
518 |
|
|
sprintf( painCave.errMsg, |
519 |
|
|
"SimSetup:initFromBass error.\n" |
520 |
|
|
"\tComponent %s, atom %s does not have a position specified.\n" |
521 |
|
|
"\tThe initialization routine is unable to give a start" |
522 |
|
|
" position.\n", |
523 |
|
|
comp_stamps[current_comp]->getID(), |
524 |
|
|
current_atom->getType() ); |
525 |
|
|
painCave.isFatal = 1; |
526 |
|
|
simError(); |
527 |
|
|
} |
528 |
|
|
|
529 |
|
|
the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() ); |
530 |
|
|
the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() ); |
531 |
|
|
the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() ); |
532 |
|
|
|
533 |
|
|
if( the_atoms[current_atom_ndx]->isDirectional() ){ |
534 |
|
|
|
535 |
|
|
dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx]; |
536 |
|
|
|
537 |
|
|
rotMat[0][0] = 1.0; |
538 |
|
|
rotMat[0][1] = 0.0; |
539 |
|
|
rotMat[0][2] = 0.0; |
540 |
|
|
|
541 |
|
|
rotMat[1][0] = 0.0; |
542 |
|
|
rotMat[1][1] = 1.0; |
543 |
|
|
rotMat[1][2] = 0.0; |
544 |
|
|
|
545 |
|
|
rotMat[2][0] = 0.0; |
546 |
|
|
rotMat[2][1] = 0.0; |
547 |
|
|
rotMat[2][2] = 1.0; |
548 |
|
|
|
549 |
|
|
dAtom->setA( rotMat ); |
550 |
|
|
} |
551 |
|
|
|
552 |
|
|
current_atom_ndx++; |
553 |
|
|
} |
554 |
|
|
|
555 |
|
|
current_mol++; |
556 |
|
|
current_comp_mol++; |
557 |
|
|
|
558 |
|
|
if( current_comp_mol >= components_nmol[current_comp] ){ |
559 |
|
|
|
560 |
|
|
current_comp_mol = 0; |
561 |
|
|
current_comp++; |
562 |
|
|
} |
563 |
|
|
} |
564 |
mmeineke |
614 |
|
565 |
|
|
|
566 |
|
|
void SimSetup::gatherInfo( void ){ |
567 |
mmeineke |
616 |
int i,j,k; |
568 |
mmeineke |
614 |
|
569 |
|
|
ensembleCase = -1; |
570 |
|
|
ffCase = -1; |
571 |
|
|
|
572 |
|
|
// get the stamps and globals; |
573 |
mmeineke |
616 |
stamps = stamps; |
574 |
|
|
globals = globals; |
575 |
mmeineke |
614 |
|
576 |
|
|
// set the easy ones first |
577 |
mmeineke |
616 |
info->target_temp = globals->getTargetTemp(); |
578 |
|
|
info->dt = globals->getDt(); |
579 |
|
|
info->run_time = globals->getRunTime(); |
580 |
|
|
n_components = globals->getNComponents(); |
581 |
mmeineke |
614 |
|
582 |
|
|
|
583 |
|
|
// get the forceField |
584 |
|
|
|
585 |
mmeineke |
616 |
strcpy( force_field, globals->getForceField() ); |
586 |
mmeineke |
614 |
|
587 |
|
|
if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
588 |
|
|
else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
589 |
chuckv |
653 |
else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM; |
590 |
mmeineke |
614 |
else{ |
591 |
|
|
sprintf( painCave.errMsg, |
592 |
|
|
"SimSetup Error. Unrecognized force field -> %s\n", |
593 |
|
|
force_field ); |
594 |
|
|
painCave.isFatal = 1; |
595 |
|
|
simError(); |
596 |
|
|
} |
597 |
|
|
|
598 |
|
|
// get the ensemble |
599 |
|
|
|
600 |
mmeineke |
616 |
strcpy( ensemble, globals->getEnsemble() ); |
601 |
mmeineke |
614 |
|
602 |
|
|
if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
603 |
|
|
else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
604 |
|
|
else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") ) |
605 |
|
|
ensembleCase = NPTi_ENS; |
606 |
|
|
else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; |
607 |
|
|
else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS; |
608 |
|
|
else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; |
609 |
|
|
else{ |
610 |
|
|
sprintf( painCave.errMsg, |
611 |
|
|
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
612 |
|
|
"reverting to NVE for this simulation.\n", |
613 |
|
|
ensemble ); |
614 |
|
|
painCave.isFatal = 0; |
615 |
|
|
simError(); |
616 |
|
|
strcpy( ensemble, "NVE" ); |
617 |
|
|
ensembleCase = NVE_ENS; |
618 |
|
|
} |
619 |
|
|
strcpy( info->ensemble, ensemble ); |
620 |
|
|
|
621 |
|
|
// get the mixing rule |
622 |
|
|
|
623 |
mmeineke |
616 |
strcpy( info->mixingRule, globals->getMixingRule() ); |
624 |
|
|
info->usePBC = globals->getPBC(); |
625 |
mmeineke |
614 |
|
626 |
|
|
|
627 |
|
|
// get the components and calculate the tot_nMol and indvidual n_mol |
628 |
|
|
|
629 |
mmeineke |
616 |
the_components = globals->getComponents(); |
630 |
mmeineke |
614 |
components_nmol = new int[n_components]; |
631 |
|
|
|
632 |
|
|
|
633 |
mmeineke |
616 |
if( !globals->haveNMol() ){ |
634 |
mmeineke |
614 |
// we don't have the total number of molecules, so we assume it is |
635 |
|
|
// given in each component |
636 |
|
|
|
637 |
|
|
tot_nmol = 0; |
638 |
|
|
for( i=0; i<n_components; i++ ){ |
639 |
|
|
|
640 |
|
|
if( !the_components[i]->haveNMol() ){ |
641 |
|
|
// we have a problem |
642 |
|
|
sprintf( painCave.errMsg, |
643 |
|
|
"SimSetup Error. No global NMol or component NMol" |
644 |
|
|
" given. Cannot calculate the number of atoms.\n" ); |
645 |
|
|
painCave.isFatal = 1; |
646 |
|
|
simError(); |
647 |
|
|
} |
648 |
|
|
|
649 |
|
|
tot_nmol += the_components[i]->getNMol(); |
650 |
|
|
components_nmol[i] = the_components[i]->getNMol(); |
651 |
|
|
} |
652 |
|
|
} |
653 |
|
|
else{ |
654 |
|
|
sprintf( painCave.errMsg, |
655 |
|
|
"SimSetup error.\n" |
656 |
|
|
"\tSorry, the ability to specify total" |
657 |
|
|
" nMols and then give molfractions in the components\n" |
658 |
|
|
"\tis not currently supported." |
659 |
|
|
" Please give nMol in the components.\n" ); |
660 |
|
|
painCave.isFatal = 1; |
661 |
|
|
simError(); |
662 |
|
|
} |
663 |
|
|
|
664 |
|
|
// set the status, sample, and thermal kick times |
665 |
|
|
|
666 |
mmeineke |
616 |
if( globals->haveSampleTime() ){ |
667 |
|
|
info->sampleTime = globals->getSampleTime(); |
668 |
mmeineke |
614 |
info->statusTime = info->sampleTime; |
669 |
|
|
info->thermalTime = info->sampleTime; |
670 |
|
|
} |
671 |
|
|
else{ |
672 |
mmeineke |
616 |
info->sampleTime = globals->getRunTime(); |
673 |
mmeineke |
614 |
info->statusTime = info->sampleTime; |
674 |
|
|
info->thermalTime = info->sampleTime; |
675 |
|
|
} |
676 |
|
|
|
677 |
mmeineke |
616 |
if( globals->haveStatusTime() ){ |
678 |
|
|
info->statusTime = globals->getStatusTime(); |
679 |
mmeineke |
614 |
} |
680 |
|
|
|
681 |
mmeineke |
616 |
if( globals->haveThermalTime() ){ |
682 |
|
|
info->thermalTime = globals->getThermalTime(); |
683 |
mmeineke |
614 |
} |
684 |
|
|
|
685 |
|
|
// check for the temperature set flag |
686 |
|
|
|
687 |
mmeineke |
616 |
if( globals->haveTempSet() ) info->setTemp = globals->getTempSet(); |
688 |
mmeineke |
614 |
|
689 |
|
|
// get some of the tricky things that may still be in the globals |
690 |
|
|
|
691 |
|
|
double boxVector[3]; |
692 |
mmeineke |
616 |
if( globals->haveBox() ){ |
693 |
|
|
boxVector[0] = globals->getBox(); |
694 |
|
|
boxVector[1] = globals->getBox(); |
695 |
|
|
boxVector[2] = globals->getBox(); |
696 |
mmeineke |
614 |
|
697 |
|
|
info->setBox( boxVector ); |
698 |
|
|
} |
699 |
mmeineke |
616 |
else if( globals->haveDensity() ){ |
700 |
mmeineke |
614 |
|
701 |
|
|
double vol; |
702 |
mmeineke |
616 |
vol = (double)tot_nmol / globals->getDensity(); |
703 |
mmeineke |
614 |
boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
704 |
|
|
boxVector[1] = boxVector[0]; |
705 |
|
|
boxVector[2] = boxVector[0]; |
706 |
|
|
|
707 |
|
|
info->setBox( boxVector ); |
708 |
|
|
} |
709 |
|
|
else{ |
710 |
mmeineke |
616 |
if( !globals->haveBoxX() ){ |
711 |
mmeineke |
614 |
sprintf( painCave.errMsg, |
712 |
|
|
"SimSetup error, no periodic BoxX size given.\n" ); |
713 |
|
|
painCave.isFatal = 1; |
714 |
|
|
simError(); |
715 |
|
|
} |
716 |
mmeineke |
616 |
boxVector[0] = globals->getBoxX(); |
717 |
mmeineke |
614 |
|
718 |
mmeineke |
616 |
if( !globals->haveBoxY() ){ |
719 |
mmeineke |
614 |
sprintf( painCave.errMsg, |
720 |
|
|
"SimSetup error, no periodic BoxY size given.\n" ); |
721 |
|
|
painCave.isFatal = 1; |
722 |
|
|
simError(); |
723 |
|
|
} |
724 |
mmeineke |
616 |
boxVector[1] = globals->getBoxY(); |
725 |
mmeineke |
614 |
|
726 |
mmeineke |
616 |
if( !globals->haveBoxZ() ){ |
727 |
mmeineke |
614 |
sprintf( painCave.errMsg, |
728 |
|
|
"SimSetup error, no periodic BoxZ size given.\n" ); |
729 |
|
|
painCave.isFatal = 1; |
730 |
|
|
simError(); |
731 |
|
|
} |
732 |
mmeineke |
616 |
boxVector[2] = globals->getBoxZ(); |
733 |
mmeineke |
614 |
|
734 |
|
|
info->setBox( boxVector ); |
735 |
|
|
} |
736 |
|
|
|
737 |
|
|
|
738 |
|
|
|
739 |
|
|
#ifdef IS_MPI |
740 |
|
|
strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" ); |
741 |
|
|
MPIcheckPoint(); |
742 |
|
|
#endif // is_mpi |
743 |
|
|
|
744 |
|
|
} |
745 |
|
|
|
746 |
|
|
|
747 |
|
|
void SimSetup::finalInfoCheck( void ){ |
748 |
|
|
int index; |
749 |
|
|
int usesDipoles; |
750 |
|
|
|
751 |
|
|
|
752 |
|
|
// check electrostatic parameters |
753 |
|
|
|
754 |
|
|
index = 0; |
755 |
|
|
usesDipoles = 0; |
756 |
|
|
while( (index < info->n_atoms) && !usesDipoles ){ |
757 |
|
|
usesDipoles = ((info->atoms)[index])->hasDipole(); |
758 |
|
|
index++; |
759 |
|
|
} |
760 |
|
|
|
761 |
|
|
#ifdef IS_MPI |
762 |
mmeineke |
616 |
int myUse = usesDipoles; |
763 |
|
|
MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
764 |
mmeineke |
614 |
#endif //is_mpi |
765 |
|
|
|
766 |
mmeineke |
626 |
double theEcr, theEst; |
767 |
mmeineke |
614 |
|
768 |
mmeineke |
616 |
if (globals->getUseRF() ) { |
769 |
mmeineke |
614 |
info->useReactionField = 1; |
770 |
|
|
|
771 |
mmeineke |
616 |
if( !globals->haveECR() ){ |
772 |
mmeineke |
614 |
sprintf( painCave.errMsg, |
773 |
|
|
"SimSetup Warning: using default value of 1/2 the smallest " |
774 |
|
|
"box length for the electrostaticCutoffRadius.\n" |
775 |
|
|
"I hope you have a very fast processor!\n"); |
776 |
|
|
painCave.isFatal = 0; |
777 |
|
|
simError(); |
778 |
|
|
double smallest; |
779 |
gezelter |
621 |
smallest = info->boxL[0]; |
780 |
|
|
if (info->boxL[1] <= smallest) smallest = info->boxL[1]; |
781 |
|
|
if (info->boxL[2] <= smallest) smallest = info->boxL[2]; |
782 |
mmeineke |
626 |
theEcr = 0.5 * smallest; |
783 |
mmeineke |
614 |
} else { |
784 |
mmeineke |
626 |
theEcr = globals->getECR(); |
785 |
mmeineke |
614 |
} |
786 |
|
|
|
787 |
mmeineke |
616 |
if( !globals->haveEST() ){ |
788 |
mmeineke |
614 |
sprintf( painCave.errMsg, |
789 |
|
|
"SimSetup Warning: using default value of 0.05 * the " |
790 |
|
|
"electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
791 |
|
|
); |
792 |
|
|
painCave.isFatal = 0; |
793 |
|
|
simError(); |
794 |
mmeineke |
626 |
theEst = 0.05 * theEcr; |
795 |
mmeineke |
614 |
} else { |
796 |
mmeineke |
626 |
theEst= globals->getEST(); |
797 |
mmeineke |
614 |
} |
798 |
mmeineke |
626 |
|
799 |
|
|
info->setEcr( theEcr, theEst ); |
800 |
mmeineke |
614 |
|
801 |
mmeineke |
616 |
if(!globals->haveDielectric() ){ |
802 |
mmeineke |
614 |
sprintf( painCave.errMsg, |
803 |
|
|
"SimSetup Error: You are trying to use Reaction Field without" |
804 |
|
|
"setting a dielectric constant!\n" |
805 |
|
|
); |
806 |
|
|
painCave.isFatal = 1; |
807 |
|
|
simError(); |
808 |
|
|
} |
809 |
mmeineke |
616 |
info->dielectric = globals->getDielectric(); |
810 |
mmeineke |
614 |
} |
811 |
|
|
else { |
812 |
|
|
if (usesDipoles) { |
813 |
|
|
|
814 |
mmeineke |
616 |
if( !globals->haveECR() ){ |
815 |
mmeineke |
626 |
sprintf( painCave.errMsg, |
816 |
|
|
"SimSetup Warning: using default value of 1/2 the smallest " |
817 |
|
|
"box length for the electrostaticCutoffRadius.\n" |
818 |
|
|
"I hope you have a very fast processor!\n"); |
819 |
|
|
painCave.isFatal = 0; |
820 |
|
|
simError(); |
821 |
|
|
double smallest; |
822 |
|
|
smallest = info->boxL[0]; |
823 |
|
|
if (info->boxL[1] <= smallest) smallest = info->boxL[1]; |
824 |
|
|
if (info->boxL[2] <= smallest) smallest = info->boxL[2]; |
825 |
|
|
theEcr = 0.5 * smallest; |
826 |
mmeineke |
614 |
} else { |
827 |
mmeineke |
626 |
theEcr = globals->getECR(); |
828 |
mmeineke |
614 |
} |
829 |
|
|
|
830 |
mmeineke |
616 |
if( !globals->haveEST() ){ |
831 |
mmeineke |
626 |
sprintf( painCave.errMsg, |
832 |
|
|
"SimSetup Warning: using default value of 0.05 * the " |
833 |
|
|
"electrostaticCutoffRadius for the " |
834 |
|
|
"electrostaticSkinThickness\n" |
835 |
|
|
); |
836 |
|
|
painCave.isFatal = 0; |
837 |
|
|
simError(); |
838 |
|
|
theEst = 0.05 * theEcr; |
839 |
mmeineke |
614 |
} else { |
840 |
mmeineke |
626 |
theEst= globals->getEST(); |
841 |
mmeineke |
614 |
} |
842 |
mmeineke |
626 |
|
843 |
|
|
info->setEcr( theEcr, theEst ); |
844 |
mmeineke |
614 |
} |
845 |
|
|
} |
846 |
|
|
|
847 |
|
|
#ifdef IS_MPI |
848 |
|
|
strcpy( checkPointMsg, "post processing checks out" ); |
849 |
|
|
MPIcheckPoint(); |
850 |
|
|
#endif // is_mpi |
851 |
|
|
|
852 |
|
|
} |
853 |
|
|
|
854 |
|
|
void SimSetup::initSystemCoords( void ){ |
855 |
|
|
|
856 |
mmeineke |
616 |
if( globals->haveInitialConfig() ){ |
857 |
mmeineke |
614 |
|
858 |
|
|
InitializeFromFile* fileInit; |
859 |
|
|
#ifdef IS_MPI // is_mpi |
860 |
|
|
if( worldRank == 0 ){ |
861 |
|
|
#endif //is_mpi |
862 |
mmeineke |
616 |
fileInit = new InitializeFromFile( globals->getInitialConfig() ); |
863 |
mmeineke |
614 |
#ifdef IS_MPI |
864 |
|
|
}else fileInit = new InitializeFromFile( NULL ); |
865 |
|
|
#endif |
866 |
mmeineke |
644 |
fileInit->readInit( info ); // default velocities on |
867 |
mmeineke |
614 |
|
868 |
|
|
delete fileInit; |
869 |
|
|
} |
870 |
|
|
else{ |
871 |
|
|
|
872 |
|
|
#ifdef IS_MPI |
873 |
|
|
|
874 |
|
|
// no init from bass |
875 |
|
|
|
876 |
|
|
sprintf( painCave.errMsg, |
877 |
|
|
"Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
878 |
|
|
painCave.isFatal; |
879 |
|
|
simError(); |
880 |
|
|
|
881 |
|
|
#else |
882 |
|
|
|
883 |
|
|
initFromBass(); |
884 |
|
|
|
885 |
|
|
|
886 |
|
|
#endif |
887 |
|
|
} |
888 |
|
|
|
889 |
|
|
#ifdef IS_MPI |
890 |
|
|
strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
891 |
|
|
MPIcheckPoint(); |
892 |
|
|
#endif // is_mpi |
893 |
|
|
|
894 |
|
|
} |
895 |
|
|
|
896 |
|
|
|
897 |
|
|
void SimSetup::makeOutNames( void ){ |
898 |
|
|
|
899 |
|
|
#ifdef IS_MPI |
900 |
|
|
if( worldRank == 0 ){ |
901 |
|
|
#endif // is_mpi |
902 |
|
|
|
903 |
mmeineke |
616 |
if( globals->haveFinalConfig() ){ |
904 |
|
|
strcpy( info->finalName, globals->getFinalConfig() ); |
905 |
mmeineke |
614 |
} |
906 |
|
|
else{ |
907 |
|
|
strcpy( info->finalName, inFileName ); |
908 |
|
|
char* endTest; |
909 |
|
|
int nameLength = strlen( info->finalName ); |
910 |
|
|
endTest = &(info->finalName[nameLength - 5]); |
911 |
|
|
if( !strcmp( endTest, ".bass" ) ){ |
912 |
|
|
strcpy( endTest, ".eor" ); |
913 |
|
|
} |
914 |
|
|
else if( !strcmp( endTest, ".BASS" ) ){ |
915 |
|
|
strcpy( endTest, ".eor" ); |
916 |
|
|
} |
917 |
|
|
else{ |
918 |
|
|
endTest = &(info->finalName[nameLength - 4]); |
919 |
|
|
if( !strcmp( endTest, ".bss" ) ){ |
920 |
|
|
strcpy( endTest, ".eor" ); |
921 |
|
|
} |
922 |
|
|
else if( !strcmp( endTest, ".mdl" ) ){ |
923 |
|
|
strcpy( endTest, ".eor" ); |
924 |
|
|
} |
925 |
|
|
else{ |
926 |
|
|
strcat( info->finalName, ".eor" ); |
927 |
|
|
} |
928 |
|
|
} |
929 |
|
|
} |
930 |
|
|
|
931 |
|
|
// make the sample and status out names |
932 |
|
|
|
933 |
|
|
strcpy( info->sampleName, inFileName ); |
934 |
|
|
char* endTest; |
935 |
|
|
int nameLength = strlen( info->sampleName ); |
936 |
|
|
endTest = &(info->sampleName[nameLength - 5]); |
937 |
|
|
if( !strcmp( endTest, ".bass" ) ){ |
938 |
|
|
strcpy( endTest, ".dump" ); |
939 |
|
|
} |
940 |
|
|
else if( !strcmp( endTest, ".BASS" ) ){ |
941 |
|
|
strcpy( endTest, ".dump" ); |
942 |
|
|
} |
943 |
|
|
else{ |
944 |
|
|
endTest = &(info->sampleName[nameLength - 4]); |
945 |
|
|
if( !strcmp( endTest, ".bss" ) ){ |
946 |
|
|
strcpy( endTest, ".dump" ); |
947 |
|
|
} |
948 |
|
|
else if( !strcmp( endTest, ".mdl" ) ){ |
949 |
|
|
strcpy( endTest, ".dump" ); |
950 |
|
|
} |
951 |
|
|
else{ |
952 |
|
|
strcat( info->sampleName, ".dump" ); |
953 |
|
|
} |
954 |
|
|
} |
955 |
|
|
|
956 |
|
|
strcpy( info->statusName, inFileName ); |
957 |
|
|
nameLength = strlen( info->statusName ); |
958 |
|
|
endTest = &(info->statusName[nameLength - 5]); |
959 |
|
|
if( !strcmp( endTest, ".bass" ) ){ |
960 |
|
|
strcpy( endTest, ".stat" ); |
961 |
|
|
} |
962 |
|
|
else if( !strcmp( endTest, ".BASS" ) ){ |
963 |
|
|
strcpy( endTest, ".stat" ); |
964 |
|
|
} |
965 |
|
|
else{ |
966 |
|
|
endTest = &(info->statusName[nameLength - 4]); |
967 |
|
|
if( !strcmp( endTest, ".bss" ) ){ |
968 |
|
|
strcpy( endTest, ".stat" ); |
969 |
|
|
} |
970 |
|
|
else if( !strcmp( endTest, ".mdl" ) ){ |
971 |
|
|
strcpy( endTest, ".stat" ); |
972 |
|
|
} |
973 |
|
|
else{ |
974 |
|
|
strcat( info->statusName, ".stat" ); |
975 |
|
|
} |
976 |
|
|
} |
977 |
|
|
|
978 |
|
|
#ifdef IS_MPI |
979 |
|
|
} |
980 |
|
|
#endif // is_mpi |
981 |
|
|
|
982 |
|
|
} |
983 |
|
|
|
984 |
|
|
|
985 |
|
|
void SimSetup::sysObjectsCreation( void ){ |
986 |
|
|
|
987 |
mmeineke |
616 |
int i; |
988 |
|
|
|
989 |
mmeineke |
614 |
// create the forceField |
990 |
|
|
|
991 |
|
|
createFF(); |
992 |
|
|
|
993 |
|
|
// extract componentList |
994 |
|
|
|
995 |
|
|
compList(); |
996 |
|
|
|
997 |
|
|
// calc the number of atoms, bond, bends, and torsions |
998 |
|
|
|
999 |
|
|
calcSysValues(); |
1000 |
|
|
|
1001 |
|
|
#ifdef IS_MPI |
1002 |
|
|
// divide the molecules among the processors |
1003 |
|
|
|
1004 |
|
|
mpiMolDivide(); |
1005 |
|
|
#endif //is_mpi |
1006 |
|
|
|
1007 |
|
|
// create the atom and SRI arrays. Also initialize Molecule Stamp ID's |
1008 |
|
|
|
1009 |
|
|
makeSysArrays(); |
1010 |
|
|
|
1011 |
mmeineke |
616 |
// make and initialize the molecules (all but atomic coordinates) |
1012 |
mmeineke |
614 |
|
1013 |
mmeineke |
616 |
makeMolecules(); |
1014 |
|
|
info->identArray = new int[info->n_atoms]; |
1015 |
|
|
for(i=0; i<info->n_atoms; i++){ |
1016 |
|
|
info->identArray[i] = the_atoms[i]->getIdent(); |
1017 |
|
|
} |
1018 |
|
|
|
1019 |
mmeineke |
614 |
|
1020 |
|
|
|
1021 |
|
|
} |
1022 |
|
|
|
1023 |
|
|
|
1024 |
|
|
void SimSetup::createFF( void ){ |
1025 |
|
|
|
1026 |
|
|
switch( ffCase ){ |
1027 |
|
|
|
1028 |
|
|
case FF_DUFF: |
1029 |
|
|
the_ff = new DUFF(); |
1030 |
|
|
break; |
1031 |
|
|
|
1032 |
|
|
case FF_LJ: |
1033 |
|
|
the_ff = new LJFF(); |
1034 |
|
|
break; |
1035 |
|
|
|
1036 |
chuckv |
653 |
case FF_EAM: |
1037 |
|
|
the_ff = new EAM_FF(); |
1038 |
|
|
break; |
1039 |
|
|
|
1040 |
mmeineke |
614 |
default: |
1041 |
|
|
sprintf( painCave.errMsg, |
1042 |
|
|
"SimSetup Error. Unrecognized force field in case statement.\n"); |
1043 |
|
|
painCave.isFatal = 1; |
1044 |
|
|
simError(); |
1045 |
|
|
} |
1046 |
|
|
|
1047 |
|
|
#ifdef IS_MPI |
1048 |
|
|
strcpy( checkPointMsg, "ForceField creation successful" ); |
1049 |
|
|
MPIcheckPoint(); |
1050 |
|
|
#endif // is_mpi |
1051 |
|
|
|
1052 |
|
|
} |
1053 |
|
|
|
1054 |
|
|
|
1055 |
|
|
void SimSetup::compList( void ){ |
1056 |
|
|
|
1057 |
mmeineke |
616 |
int i; |
1058 |
|
|
|
1059 |
mmeineke |
614 |
comp_stamps = new MoleculeStamp*[n_components]; |
1060 |
|
|
|
1061 |
|
|
// make an array of molecule stamps that match the components used. |
1062 |
|
|
// also extract the used stamps out into a separate linked list |
1063 |
|
|
|
1064 |
|
|
info->nComponents = n_components; |
1065 |
|
|
info->componentsNmol = components_nmol; |
1066 |
|
|
info->compStamps = comp_stamps; |
1067 |
|
|
info->headStamp = new LinkedMolStamp(); |
1068 |
|
|
|
1069 |
|
|
char* id; |
1070 |
|
|
LinkedMolStamp* headStamp = info->headStamp; |
1071 |
|
|
LinkedMolStamp* currentStamp = NULL; |
1072 |
|
|
for( i=0; i<n_components; i++ ){ |
1073 |
|
|
|
1074 |
|
|
id = the_components[i]->getType(); |
1075 |
|
|
comp_stamps[i] = NULL; |
1076 |
|
|
|
1077 |
|
|
// check to make sure the component isn't already in the list |
1078 |
|
|
|
1079 |
|
|
comp_stamps[i] = headStamp->match( id ); |
1080 |
|
|
if( comp_stamps[i] == NULL ){ |
1081 |
|
|
|
1082 |
|
|
// extract the component from the list; |
1083 |
|
|
|
1084 |
mmeineke |
616 |
currentStamp = stamps->extractMolStamp( id ); |
1085 |
mmeineke |
614 |
if( currentStamp == NULL ){ |
1086 |
|
|
sprintf( painCave.errMsg, |
1087 |
|
|
"SimSetup error: Component \"%s\" was not found in the " |
1088 |
|
|
"list of declared molecules\n", |
1089 |
|
|
id ); |
1090 |
|
|
painCave.isFatal = 1; |
1091 |
|
|
simError(); |
1092 |
|
|
} |
1093 |
|
|
|
1094 |
|
|
headStamp->add( currentStamp ); |
1095 |
|
|
comp_stamps[i] = headStamp->match( id ); |
1096 |
|
|
} |
1097 |
|
|
} |
1098 |
|
|
|
1099 |
|
|
#ifdef IS_MPI |
1100 |
|
|
strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
1101 |
|
|
MPIcheckPoint(); |
1102 |
|
|
#endif // is_mpi |
1103 |
|
|
|
1104 |
|
|
|
1105 |
|
|
} |
1106 |
|
|
|
1107 |
|
|
void SimSetup::calcSysValues( void ){ |
1108 |
mmeineke |
616 |
int i, j, k; |
1109 |
mmeineke |
614 |
|
1110 |
mmeineke |
616 |
|
1111 |
mmeineke |
614 |
tot_atoms = 0; |
1112 |
|
|
tot_bonds = 0; |
1113 |
|
|
tot_bends = 0; |
1114 |
|
|
tot_torsions = 0; |
1115 |
|
|
for( i=0; i<n_components; i++ ){ |
1116 |
|
|
|
1117 |
|
|
tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1118 |
|
|
tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1119 |
|
|
tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1120 |
|
|
tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
1121 |
|
|
} |
1122 |
|
|
|
1123 |
|
|
tot_SRI = tot_bonds + tot_bends + tot_torsions; |
1124 |
|
|
|
1125 |
|
|
info->n_atoms = tot_atoms; |
1126 |
|
|
info->n_bonds = tot_bonds; |
1127 |
|
|
info->n_bends = tot_bends; |
1128 |
|
|
info->n_torsions = tot_torsions; |
1129 |
|
|
info->n_SRI = tot_SRI; |
1130 |
|
|
info->n_mol = tot_nmol; |
1131 |
|
|
|
1132 |
|
|
info->molMembershipArray = new int[tot_atoms]; |
1133 |
|
|
} |
1134 |
|
|
|
1135 |
|
|
|
1136 |
|
|
#ifdef IS_MPI |
1137 |
|
|
|
1138 |
|
|
void SimSetup::mpiMolDivide( void ){ |
1139 |
|
|
|
1140 |
mmeineke |
616 |
int i, j, k; |
1141 |
mmeineke |
614 |
int localMol, allMol; |
1142 |
|
|
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
1143 |
|
|
|
1144 |
|
|
mpiSim = new mpiSimulation( info ); |
1145 |
|
|
|
1146 |
|
|
globalIndex = mpiSim->divideLabor(); |
1147 |
|
|
|
1148 |
|
|
// set up the local variables |
1149 |
|
|
|
1150 |
|
|
mol2proc = mpiSim->getMolToProcMap(); |
1151 |
|
|
molCompType = mpiSim->getMolComponentType(); |
1152 |
|
|
|
1153 |
|
|
allMol = 0; |
1154 |
|
|
localMol = 0; |
1155 |
|
|
local_atoms = 0; |
1156 |
|
|
local_bonds = 0; |
1157 |
|
|
local_bends = 0; |
1158 |
|
|
local_torsions = 0; |
1159 |
|
|
globalAtomIndex = 0; |
1160 |
|
|
|
1161 |
|
|
|
1162 |
|
|
for( i=0; i<n_components; i++ ){ |
1163 |
|
|
|
1164 |
|
|
for( j=0; j<components_nmol[i]; j++ ){ |
1165 |
|
|
|
1166 |
|
|
if( mol2proc[allMol] == worldRank ){ |
1167 |
|
|
|
1168 |
|
|
local_atoms += comp_stamps[i]->getNAtoms(); |
1169 |
|
|
local_bonds += comp_stamps[i]->getNBonds(); |
1170 |
|
|
local_bends += comp_stamps[i]->getNBends(); |
1171 |
|
|
local_torsions += comp_stamps[i]->getNTorsions(); |
1172 |
|
|
localMol++; |
1173 |
|
|
} |
1174 |
|
|
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1175 |
|
|
info->molMembershipArray[globalAtomIndex] = allMol; |
1176 |
|
|
globalAtomIndex++; |
1177 |
|
|
} |
1178 |
|
|
|
1179 |
|
|
allMol++; |
1180 |
|
|
} |
1181 |
|
|
} |
1182 |
|
|
local_SRI = local_bonds + local_bends + local_torsions; |
1183 |
|
|
|
1184 |
|
|
info->n_atoms = mpiSim->getMyNlocal(); |
1185 |
|
|
|
1186 |
|
|
if( local_atoms != info->n_atoms ){ |
1187 |
|
|
sprintf( painCave.errMsg, |
1188 |
|
|
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1189 |
|
|
" localAtom (%d) are not equal.\n", |
1190 |
|
|
info->n_atoms, |
1191 |
|
|
local_atoms ); |
1192 |
|
|
painCave.isFatal = 1; |
1193 |
|
|
simError(); |
1194 |
|
|
} |
1195 |
|
|
|
1196 |
|
|
info->n_bonds = local_bonds; |
1197 |
|
|
info->n_bends = local_bends; |
1198 |
|
|
info->n_torsions = local_torsions; |
1199 |
|
|
info->n_SRI = local_SRI; |
1200 |
|
|
info->n_mol = localMol; |
1201 |
|
|
|
1202 |
|
|
strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
1203 |
|
|
MPIcheckPoint(); |
1204 |
|
|
} |
1205 |
|
|
|
1206 |
|
|
#endif // is_mpi |
1207 |
|
|
|
1208 |
|
|
|
1209 |
|
|
void SimSetup::makeSysArrays( void ){ |
1210 |
mmeineke |
616 |
int i, j, k; |
1211 |
mmeineke |
614 |
|
1212 |
mmeineke |
616 |
|
1213 |
mmeineke |
614 |
// create the atom and short range interaction arrays |
1214 |
|
|
|
1215 |
|
|
Atom::createArrays(info->n_atoms); |
1216 |
|
|
the_atoms = new Atom*[info->n_atoms]; |
1217 |
|
|
the_molecules = new Molecule[info->n_mol]; |
1218 |
|
|
int molIndex; |
1219 |
|
|
|
1220 |
|
|
// initialize the molecule's stampID's |
1221 |
|
|
|
1222 |
|
|
#ifdef IS_MPI |
1223 |
|
|
|
1224 |
|
|
|
1225 |
|
|
molIndex = 0; |
1226 |
|
|
for(i=0; i<mpiSim->getTotNmol(); i++){ |
1227 |
|
|
|
1228 |
|
|
if(mol2proc[i] == worldRank ){ |
1229 |
|
|
the_molecules[molIndex].setStampID( molCompType[i] ); |
1230 |
|
|
the_molecules[molIndex].setMyIndex( molIndex ); |
1231 |
|
|
the_molecules[molIndex].setGlobalIndex( i ); |
1232 |
|
|
molIndex++; |
1233 |
|
|
} |
1234 |
|
|
} |
1235 |
|
|
|
1236 |
|
|
#else // is_mpi |
1237 |
|
|
|
1238 |
|
|
molIndex = 0; |
1239 |
|
|
globalAtomIndex = 0; |
1240 |
|
|
for(i=0; i<n_components; i++){ |
1241 |
|
|
for(j=0; j<components_nmol[i]; j++ ){ |
1242 |
|
|
the_molecules[molIndex].setStampID( i ); |
1243 |
|
|
the_molecules[molIndex].setMyIndex( molIndex ); |
1244 |
|
|
the_molecules[molIndex].setGlobalIndex( molIndex ); |
1245 |
|
|
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1246 |
|
|
info->molMembershipArray[globalAtomIndex] = molIndex; |
1247 |
|
|
globalAtomIndex++; |
1248 |
|
|
} |
1249 |
|
|
molIndex++; |
1250 |
|
|
} |
1251 |
|
|
} |
1252 |
|
|
|
1253 |
|
|
|
1254 |
|
|
#endif // is_mpi |
1255 |
|
|
|
1256 |
|
|
|
1257 |
|
|
if( info->n_SRI ){ |
1258 |
|
|
|
1259 |
|
|
Exclude::createArray(info->n_SRI); |
1260 |
|
|
the_excludes = new Exclude*[info->n_SRI]; |
1261 |
|
|
for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
1262 |
|
|
info->globalExcludes = new int; |
1263 |
|
|
info->n_exclude = info->n_SRI; |
1264 |
|
|
} |
1265 |
|
|
else{ |
1266 |
|
|
|
1267 |
|
|
Exclude::createArray( 1 ); |
1268 |
|
|
the_excludes = new Exclude*; |
1269 |
|
|
the_excludes[0] = new Exclude(0); |
1270 |
|
|
the_excludes[0]->setPair( 0,0 ); |
1271 |
|
|
info->globalExcludes = new int; |
1272 |
|
|
info->globalExcludes[0] = 0; |
1273 |
|
|
info->n_exclude = 0; |
1274 |
|
|
} |
1275 |
|
|
|
1276 |
|
|
// set the arrays into the SimInfo object |
1277 |
|
|
|
1278 |
|
|
info->atoms = the_atoms; |
1279 |
|
|
info->molecules = the_molecules; |
1280 |
|
|
info->nGlobalExcludes = 0; |
1281 |
|
|
info->excludes = the_excludes; |
1282 |
|
|
|
1283 |
|
|
the_ff->setSimInfo( info ); |
1284 |
|
|
|
1285 |
|
|
} |
1286 |
mmeineke |
616 |
|
1287 |
|
|
void SimSetup::makeIntegrator( void ){ |
1288 |
|
|
|
1289 |
tim |
645 |
NVT<RealIntegrator>* myNVT = NULL; |
1290 |
|
|
NPTi<RealIntegrator>* myNPTi = NULL; |
1291 |
|
|
NPTf<RealIntegrator>* myNPTf = NULL; |
1292 |
|
|
NPTim<RealIntegrator>* myNPTim = NULL; |
1293 |
|
|
NPTfm<RealIntegrator>* myNPTfm = NULL; |
1294 |
mmeineke |
616 |
|
1295 |
|
|
switch( ensembleCase ){ |
1296 |
|
|
|
1297 |
|
|
case NVE_ENS: |
1298 |
tim |
645 |
new NVE<RealIntegrator>( info, the_ff ); |
1299 |
mmeineke |
616 |
break; |
1300 |
|
|
|
1301 |
|
|
case NVT_ENS: |
1302 |
tim |
645 |
myNVT = new NVT<RealIntegrator>( info, the_ff ); |
1303 |
mmeineke |
616 |
myNVT->setTargetTemp(globals->getTargetTemp()); |
1304 |
|
|
|
1305 |
|
|
if (globals->haveTauThermostat()) |
1306 |
|
|
myNVT->setTauThermostat(globals->getTauThermostat()); |
1307 |
|
|
|
1308 |
|
|
else { |
1309 |
|
|
sprintf( painCave.errMsg, |
1310 |
|
|
"SimSetup error: If you use the NVT\n" |
1311 |
|
|
" ensemble, you must set tauThermostat.\n"); |
1312 |
|
|
painCave.isFatal = 1; |
1313 |
|
|
simError(); |
1314 |
|
|
} |
1315 |
|
|
break; |
1316 |
|
|
|
1317 |
|
|
case NPTi_ENS: |
1318 |
tim |
645 |
myNPTi = new NPTi<RealIntegrator>( info, the_ff ); |
1319 |
mmeineke |
616 |
myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1320 |
|
|
|
1321 |
|
|
if (globals->haveTargetPressure()) |
1322 |
|
|
myNPTi->setTargetPressure(globals->getTargetPressure()); |
1323 |
|
|
else { |
1324 |
|
|
sprintf( painCave.errMsg, |
1325 |
|
|
"SimSetup error: If you use a constant pressure\n" |
1326 |
|
|
" ensemble, you must set targetPressure in the BASS file.\n"); |
1327 |
|
|
painCave.isFatal = 1; |
1328 |
|
|
simError(); |
1329 |
|
|
} |
1330 |
|
|
|
1331 |
|
|
if( globals->haveTauThermostat() ) |
1332 |
|
|
myNPTi->setTauThermostat( globals->getTauThermostat() ); |
1333 |
|
|
else{ |
1334 |
|
|
sprintf( painCave.errMsg, |
1335 |
|
|
"SimSetup error: If you use an NPT\n" |
1336 |
|
|
" ensemble, you must set tauThermostat.\n"); |
1337 |
|
|
painCave.isFatal = 1; |
1338 |
|
|
simError(); |
1339 |
|
|
} |
1340 |
|
|
|
1341 |
|
|
if( globals->haveTauBarostat() ) |
1342 |
|
|
myNPTi->setTauBarostat( globals->getTauBarostat() ); |
1343 |
|
|
else{ |
1344 |
|
|
sprintf( painCave.errMsg, |
1345 |
|
|
"SimSetup error: If you use an NPT\n" |
1346 |
|
|
" ensemble, you must set tauBarostat.\n"); |
1347 |
|
|
painCave.isFatal = 1; |
1348 |
|
|
simError(); |
1349 |
|
|
} |
1350 |
|
|
break; |
1351 |
|
|
|
1352 |
|
|
case NPTf_ENS: |
1353 |
tim |
645 |
myNPTf = new NPTf<RealIntegrator>( info, the_ff ); |
1354 |
mmeineke |
616 |
myNPTf->setTargetTemp( globals->getTargetTemp()); |
1355 |
|
|
|
1356 |
|
|
if (globals->haveTargetPressure()) |
1357 |
|
|
myNPTf->setTargetPressure(globals->getTargetPressure()); |
1358 |
|
|
else { |
1359 |
|
|
sprintf( painCave.errMsg, |
1360 |
|
|
"SimSetup error: If you use a constant pressure\n" |
1361 |
|
|
" ensemble, you must set targetPressure in the BASS file.\n"); |
1362 |
|
|
painCave.isFatal = 1; |
1363 |
|
|
simError(); |
1364 |
|
|
} |
1365 |
|
|
|
1366 |
|
|
if( globals->haveTauThermostat() ) |
1367 |
|
|
myNPTf->setTauThermostat( globals->getTauThermostat() ); |
1368 |
|
|
else{ |
1369 |
|
|
sprintf( painCave.errMsg, |
1370 |
|
|
"SimSetup error: If you use an NPT\n" |
1371 |
|
|
" ensemble, you must set tauThermostat.\n"); |
1372 |
|
|
painCave.isFatal = 1; |
1373 |
|
|
simError(); |
1374 |
|
|
} |
1375 |
|
|
|
1376 |
|
|
if( globals->haveTauBarostat() ) |
1377 |
|
|
myNPTf->setTauBarostat( globals->getTauBarostat() ); |
1378 |
|
|
else{ |
1379 |
|
|
sprintf( painCave.errMsg, |
1380 |
|
|
"SimSetup error: If you use an NPT\n" |
1381 |
|
|
" ensemble, you must set tauBarostat.\n"); |
1382 |
|
|
painCave.isFatal = 1; |
1383 |
|
|
simError(); |
1384 |
|
|
} |
1385 |
|
|
break; |
1386 |
|
|
|
1387 |
|
|
case NPTim_ENS: |
1388 |
tim |
645 |
myNPTim = new NPTim<RealIntegrator>( info, the_ff ); |
1389 |
mmeineke |
616 |
myNPTim->setTargetTemp( globals->getTargetTemp()); |
1390 |
|
|
|
1391 |
|
|
if (globals->haveTargetPressure()) |
1392 |
|
|
myNPTim->setTargetPressure(globals->getTargetPressure()); |
1393 |
|
|
else { |
1394 |
|
|
sprintf( painCave.errMsg, |
1395 |
|
|
"SimSetup error: If you use a constant pressure\n" |
1396 |
|
|
" ensemble, you must set targetPressure in the BASS file.\n"); |
1397 |
|
|
painCave.isFatal = 1; |
1398 |
|
|
simError(); |
1399 |
|
|
} |
1400 |
|
|
|
1401 |
|
|
if( globals->haveTauThermostat() ) |
1402 |
|
|
myNPTim->setTauThermostat( globals->getTauThermostat() ); |
1403 |
|
|
else{ |
1404 |
|
|
sprintf( painCave.errMsg, |
1405 |
|
|
"SimSetup error: If you use an NPT\n" |
1406 |
|
|
" ensemble, you must set tauThermostat.\n"); |
1407 |
|
|
painCave.isFatal = 1; |
1408 |
|
|
simError(); |
1409 |
|
|
} |
1410 |
|
|
|
1411 |
|
|
if( globals->haveTauBarostat() ) |
1412 |
|
|
myNPTim->setTauBarostat( globals->getTauBarostat() ); |
1413 |
|
|
else{ |
1414 |
|
|
sprintf( painCave.errMsg, |
1415 |
|
|
"SimSetup error: If you use an NPT\n" |
1416 |
|
|
" ensemble, you must set tauBarostat.\n"); |
1417 |
|
|
painCave.isFatal = 1; |
1418 |
|
|
simError(); |
1419 |
|
|
} |
1420 |
|
|
break; |
1421 |
|
|
|
1422 |
|
|
case NPTfm_ENS: |
1423 |
tim |
645 |
myNPTfm = new NPTfm<RealIntegrator>( info, the_ff ); |
1424 |
mmeineke |
616 |
myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1425 |
|
|
|
1426 |
|
|
if (globals->haveTargetPressure()) |
1427 |
|
|
myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1428 |
|
|
else { |
1429 |
|
|
sprintf( painCave.errMsg, |
1430 |
|
|
"SimSetup error: If you use a constant pressure\n" |
1431 |
|
|
" ensemble, you must set targetPressure in the BASS file.\n"); |
1432 |
|
|
painCave.isFatal = 1; |
1433 |
|
|
simError(); |
1434 |
|
|
} |
1435 |
|
|
|
1436 |
|
|
if( globals->haveTauThermostat() ) |
1437 |
|
|
myNPTfm->setTauThermostat( globals->getTauThermostat() ); |
1438 |
|
|
else{ |
1439 |
|
|
sprintf( painCave.errMsg, |
1440 |
|
|
"SimSetup error: If you use an NPT\n" |
1441 |
|
|
" ensemble, you must set tauThermostat.\n"); |
1442 |
|
|
painCave.isFatal = 1; |
1443 |
|
|
simError(); |
1444 |
|
|
} |
1445 |
|
|
|
1446 |
|
|
if( globals->haveTauBarostat() ) |
1447 |
|
|
myNPTfm->setTauBarostat( globals->getTauBarostat() ); |
1448 |
|
|
else{ |
1449 |
|
|
sprintf( painCave.errMsg, |
1450 |
|
|
"SimSetup error: If you use an NPT\n" |
1451 |
|
|
" ensemble, you must set tauBarostat.\n"); |
1452 |
|
|
painCave.isFatal = 1; |
1453 |
|
|
simError(); |
1454 |
|
|
} |
1455 |
|
|
break; |
1456 |
|
|
|
1457 |
|
|
default: |
1458 |
|
|
sprintf( painCave.errMsg, |
1459 |
|
|
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1460 |
|
|
painCave.isFatal = 1; |
1461 |
|
|
simError(); |
1462 |
|
|
} |
1463 |
|
|
|
1464 |
|
|
} |
1465 |
|
|
|
1466 |
|
|
void SimSetup::initFortran( void ){ |
1467 |
|
|
|
1468 |
|
|
info->refreshSim(); |
1469 |
|
|
|
1470 |
|
|
if( !strcmp( info->mixingRule, "standard") ){ |
1471 |
|
|
the_ff->initForceField( LB_MIXING_RULE ); |
1472 |
|
|
} |
1473 |
|
|
else if( !strcmp( info->mixingRule, "explicit") ){ |
1474 |
|
|
the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
1475 |
|
|
} |
1476 |
|
|
else{ |
1477 |
|
|
sprintf( painCave.errMsg, |
1478 |
|
|
"SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1479 |
|
|
info->mixingRule ); |
1480 |
|
|
painCave.isFatal = 1; |
1481 |
|
|
simError(); |
1482 |
|
|
} |
1483 |
|
|
|
1484 |
|
|
|
1485 |
|
|
#ifdef IS_MPI |
1486 |
|
|
strcpy( checkPointMsg, |
1487 |
|
|
"Successfully intialized the mixingRule for Fortran." ); |
1488 |
|
|
MPIcheckPoint(); |
1489 |
|
|
#endif // is_mpi |
1490 |
|
|
|
1491 |
|
|
} |