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tim |
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#include <algorithm> |
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gezelter |
829 |
#include <stdlib.h> |
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mmeineke |
377 |
#include <iostream> |
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gezelter |
829 |
#include <math.h> |
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tim |
658 |
#include <string> |
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tim |
722 |
#include <sprng.h> |
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mmeineke |
377 |
#include "SimSetup.hpp" |
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tim |
689 |
#include "ReadWrite.hpp" |
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mmeineke |
377 |
#include "parse_me.h" |
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#include "Integrator.hpp" |
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#include "simError.h" |
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tim |
1031 |
#include "ConjugateMinimizer.hpp" |
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mmeineke |
377 |
|
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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 |
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// some defines for ensemble and Forcefield cases |
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tim |
660 |
#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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mmeineke |
812 |
#define NPTxyz_ENS 4 |
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mmeineke |
557 |
|
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mmeineke |
812 |
|
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chrisfen |
999 |
#define FF_DUFF 0 |
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#define FF_LJ 1 |
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#define FF_EAM 2 |
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#define FF_H2O 3 |
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mmeineke |
557 |
|
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tim |
658 |
using namespace std; |
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tim |
962 |
/** |
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* Check whether dividend is divisble by divisor or not |
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*/ |
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bool isDivisible(double dividend, double divisor){ |
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double tolerance = 0.000001; |
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double quotient; |
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double diff; |
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int intQuotient; |
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quotient = dividend / divisor; |
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if (quotient < 0) |
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quotient = -quotient; |
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intQuotient = int (quotient + tolerance); |
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diff = fabs(fabs(dividend) - intQuotient * fabs(divisor)); |
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if (diff <= tolerance) |
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return true; |
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else |
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return false; |
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} |
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mmeineke |
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SimSetup::SimSetup(){ |
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mmeineke |
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|
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initSuspend = false; |
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mmeineke |
656 |
isInfoArray = 0; |
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nInfo = 1; |
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tim |
722 |
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mmeineke |
377 |
stamps = new MakeStamps(); |
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globals = new Globals(); |
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tim |
722 |
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mmeineke |
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#ifdef IS_MPI |
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tim |
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strcpy(checkPointMsg, "SimSetup creation successful"); |
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mmeineke |
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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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tim |
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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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mmeineke |
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initSuspend = true; |
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mmeineke |
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} |
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mmeineke |
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tim |
722 |
void SimSetup::parseFile(char* fileName){ |
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mmeineke |
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#ifdef IS_MPI |
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tim |
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if (worldRank == 0){ |
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mmeineke |
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#endif // is_mpi |
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tim |
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|
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mmeineke |
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inFileName = fileName; |
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tim |
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set_interface_stamps(stamps, globals); |
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mmeineke |
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#ifdef IS_MPI |
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mpiEventInit(); |
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#endif |
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tim |
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yacc_BASS(fileName); |
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mmeineke |
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#ifdef IS_MPI |
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throwMPIEvent(NULL); |
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} |
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tim |
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else{ |
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receiveParse(); |
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} |
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mmeineke |
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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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tim |
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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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mmeineke |
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} |
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#endif // is_mpi |
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mmeineke |
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void SimSetup::createSim(void){ |
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mmeineke |
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|
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mmeineke |
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// gather all of the information from the Bass file |
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tim |
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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 |
859 |
// check on the post processing info |
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finalInfoCheck(); |
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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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if ( !initSuspend ){ |
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tim |
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initSystemCoords(); |
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mmeineke |
811 |
|
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if( !(globals->getUseInitTime()) ) |
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info[0].currentTime = 0.0; |
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tim |
722 |
} |
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mmeineke |
377 |
|
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mmeineke |
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// make the output filenames |
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mmeineke |
377 |
|
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mmeineke |
614 |
makeOutNames(); |
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tim |
722 |
|
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tim |
1031 |
if (globals->haveMinimizer()) |
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// make minimizer |
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makeMinimizer(); |
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else |
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// make the integrator |
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makeIntegrator(); |
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156 |
chuckv |
432 |
#ifdef IS_MPI |
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mpiSim->mpiRefresh(); |
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#endif |
159 |
mmeineke |
377 |
|
160 |
chuckv |
432 |
// initialize the Fortran |
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mmeineke |
377 |
|
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mmeineke |
616 |
initFortran(); |
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mmeineke |
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} |
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mmeineke |
407 |
|
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tim |
722 |
void SimSetup::makeMolecules(void){ |
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mmeineke |
787 |
int k; |
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mmeineke |
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int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
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mmeineke |
616 |
molInit molInfo; |
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mmeineke |
407 |
DirectionalAtom* dAtom; |
171 |
mmeineke |
412 |
LinkedAssign* extras; |
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LinkedAssign* current_extra; |
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mmeineke |
407 |
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 |
427 |
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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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182 |
mmeineke |
407 |
//init the forceField paramters |
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the_ff->readParams(); |
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186 |
tim |
722 |
|
187 |
mmeineke |
427 |
// init the atoms |
188 |
mmeineke |
407 |
|
189 |
gezelter |
983 |
double phi, theta, psi; |
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double sux, suy, suz; |
191 |
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double Axx, Axy, Axz, Ayx, Ayy, Ayz, Azx, Azy, Azz; |
192 |
mmeineke |
427 |
double ux, uy, uz, u, uSqr; |
193 |
mmeineke |
407 |
|
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tim |
722 |
for (k = 0; k < nInfo; k++){ |
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the_ff->setSimInfo(&(info[k])); |
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mmeineke |
670 |
atomOffset = 0; |
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excludeOffset = 0; |
199 |
tim |
722 |
for (i = 0; i < info[k].n_mol; i++){ |
200 |
mmeineke |
670 |
stampID = info[k].molecules[i].getStampID(); |
201 |
mmeineke |
412 |
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tim |
722 |
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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mmeineke |
670 |
molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
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molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
207 |
tim |
722 |
|
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mmeineke |
670 |
molInfo.myAtoms = &(info[k].atoms[atomOffset]); |
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molInfo.myExcludes = &(info[k].excludes[excludeOffset]); |
210 |
tim |
722 |
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]; |
213 |
mmeineke |
407 |
|
214 |
mmeineke |
670 |
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]; |
217 |
tim |
722 |
|
218 |
mmeineke |
670 |
// make the Atoms |
219 |
tim |
722 |
|
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for (j = 0; j < molInfo.nAtoms; j++){ |
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currentAtom = comp_stamps[stampID]->getAtom(j); |
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if (currentAtom->haveOrientation()){ |
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dAtom = new DirectionalAtom((j + atomOffset), |
224 |
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info[k].getConfiguration()); |
225 |
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info[k].n_oriented++; |
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molInfo.myAtoms[j] = dAtom; |
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228 |
gezelter |
983 |
// Directional Atoms have standard unit vectors which are oriented |
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// in space using the three Euler angles. We assume the standard |
230 |
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// unit vector was originally along the z axis below. |
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tim |
722 |
|
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gezelter |
984 |
phi = currentAtom->getEulerPhi() * M_PI / 180.0; |
233 |
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theta = currentAtom->getEulerTheta() * M_PI / 180.0; |
234 |
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psi = currentAtom->getEulerPsi()* M_PI / 180.0; |
235 |
gezelter |
983 |
|
236 |
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Axx = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi)); |
237 |
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Axy = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi)); |
238 |
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Axz = sin(theta) * sin(psi); |
239 |
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240 |
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Ayx = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi)); |
241 |
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Ayy = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi)); |
242 |
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Ayz = sin(theta) * cos(psi); |
243 |
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244 |
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Azx = sin(phi) * sin(theta); |
245 |
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Azy = -cos(phi) * sin(theta); |
246 |
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Azz = cos(theta); |
247 |
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248 |
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sux = 0.0; |
249 |
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suy = 0.0; |
250 |
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suz = 1.0; |
251 |
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252 |
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ux = (Axx * sux) + (Ayx * suy) + (Azx * suz); |
253 |
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uy = (Axy * sux) + (Ayy * suy) + (Azy * suz); |
254 |
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uz = (Axz * sux) + (Ayz * suy) + (Azz * suz); |
255 |
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256 |
tim |
722 |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
257 |
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258 |
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u = sqrt(uSqr); |
259 |
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ux = ux / u; |
260 |
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uy = uy / u; |
261 |
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uz = uz / u; |
262 |
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263 |
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dAtom->setSUx(ux); |
264 |
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dAtom->setSUy(uy); |
265 |
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dAtom->setSUz(uz); |
266 |
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} |
267 |
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else{ |
268 |
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molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset), |
269 |
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info[k].getConfiguration()); |
270 |
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} |
271 |
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molInfo.myAtoms[j]->setType(currentAtom->getType()); |
272 |
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273 |
mmeineke |
407 |
#ifdef IS_MPI |
274 |
tim |
722 |
|
275 |
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molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]); |
276 |
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277 |
mmeineke |
407 |
#endif // is_mpi |
278 |
mmeineke |
670 |
} |
279 |
tim |
722 |
|
280 |
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// make the bonds |
281 |
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for (j = 0; j < molInfo.nBonds; j++){ |
282 |
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currentBond = comp_stamps[stampID]->getBond(j); |
283 |
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theBonds[j].a = currentBond->getA() + atomOffset; |
284 |
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theBonds[j].b = currentBond->getB() + atomOffset; |
285 |
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286 |
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exI = theBonds[j].a; |
287 |
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exJ = theBonds[j].b; |
288 |
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289 |
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// exclude_I must always be the smaller of the pair |
290 |
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if (exI > exJ){ |
291 |
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tempEx = exI; |
292 |
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exI = exJ; |
293 |
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exJ = tempEx; |
294 |
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} |
295 |
mmeineke |
670 |
#ifdef IS_MPI |
296 |
tim |
722 |
tempEx = exI; |
297 |
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exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
298 |
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tempEx = exJ; |
299 |
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exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
300 |
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301 |
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info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
302 |
mmeineke |
412 |
#else // isn't MPI |
303 |
tim |
722 |
|
304 |
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info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
305 |
mmeineke |
412 |
#endif //is_mpi |
306 |
mmeineke |
670 |
} |
307 |
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excludeOffset += molInfo.nBonds; |
308 |
tim |
722 |
|
309 |
mmeineke |
670 |
//make the bends |
310 |
tim |
722 |
for (j = 0; j < molInfo.nBends; j++){ |
311 |
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currentBend = comp_stamps[stampID]->getBend(j); |
312 |
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theBends[j].a = currentBend->getA() + atomOffset; |
313 |
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theBends[j].b = currentBend->getB() + atomOffset; |
314 |
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theBends[j].c = currentBend->getC() + atomOffset; |
315 |
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316 |
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if (currentBend->haveExtras()){ |
317 |
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extras = currentBend->getExtras(); |
318 |
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current_extra = extras; |
319 |
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320 |
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while (current_extra != NULL){ |
321 |
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if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){ |
322 |
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switch (current_extra->getType()){ |
323 |
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case 0: |
324 |
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theBends[j].ghost = current_extra->getInt() + atomOffset; |
325 |
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theBends[j].isGhost = 1; |
326 |
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break; |
327 |
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328 |
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case 1: |
329 |
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theBends[j].ghost = (int) current_extra->getDouble() + |
330 |
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atomOffset; |
331 |
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theBends[j].isGhost = 1; |
332 |
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break; |
333 |
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334 |
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default: |
335 |
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sprintf(painCave.errMsg, |
336 |
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"SimSetup Error: ghostVectorSource was neither a " |
337 |
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"double nor an int.\n" |
338 |
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"-->Bend[%d] in %s\n", |
339 |
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j, comp_stamps[stampID]->getID()); |
340 |
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painCave.isFatal = 1; |
341 |
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simError(); |
342 |
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} |
343 |
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} |
344 |
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else{ |
345 |
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sprintf(painCave.errMsg, |
346 |
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"SimSetup Error: unhandled bend assignment:\n" |
347 |
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" -->%s in Bend[%d] in %s\n", |
348 |
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current_extra->getlhs(), j, comp_stamps[stampID]->getID()); |
349 |
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painCave.isFatal = 1; |
350 |
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simError(); |
351 |
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} |
352 |
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353 |
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current_extra = current_extra->getNext(); |
354 |
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} |
355 |
tim |
701 |
} |
356 |
tim |
722 |
|
357 |
|
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if (!theBends[j].isGhost){ |
358 |
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exI = theBends[j].a; |
359 |
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exJ = theBends[j].c; |
360 |
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} |
361 |
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else{ |
362 |
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exI = theBends[j].a; |
363 |
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exJ = theBends[j].b; |
364 |
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} |
365 |
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366 |
|
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// exclude_I must always be the smaller of the pair |
367 |
|
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if (exI > exJ){ |
368 |
|
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tempEx = exI; |
369 |
|
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exI = exJ; |
370 |
|
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exJ = tempEx; |
371 |
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} |
372 |
mmeineke |
670 |
#ifdef IS_MPI |
373 |
tim |
722 |
tempEx = exI; |
374 |
|
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exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
375 |
|
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tempEx = exJ; |
376 |
|
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exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
377 |
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|
378 |
|
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info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
379 |
mmeineke |
670 |
#else // isn't MPI |
380 |
tim |
722 |
info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
381 |
mmeineke |
670 |
#endif //is_mpi |
382 |
mmeineke |
412 |
} |
383 |
mmeineke |
670 |
excludeOffset += molInfo.nBends; |
384 |
tim |
722 |
|
385 |
|
|
for (j = 0; j < molInfo.nTorsions; j++){ |
386 |
|
|
currentTorsion = comp_stamps[stampID]->getTorsion(j); |
387 |
|
|
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
388 |
|
|
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
389 |
|
|
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
390 |
|
|
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
391 |
|
|
|
392 |
|
|
exI = theTorsions[j].a; |
393 |
|
|
exJ = theTorsions[j].d; |
394 |
|
|
|
395 |
|
|
// exclude_I must always be the smaller of the pair |
396 |
|
|
if (exI > exJ){ |
397 |
|
|
tempEx = exI; |
398 |
|
|
exI = exJ; |
399 |
|
|
exJ = tempEx; |
400 |
|
|
} |
401 |
mmeineke |
670 |
#ifdef IS_MPI |
402 |
tim |
722 |
tempEx = exI; |
403 |
|
|
exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
404 |
|
|
tempEx = exJ; |
405 |
|
|
exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
406 |
|
|
|
407 |
|
|
info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
408 |
mmeineke |
407 |
#else // isn't MPI |
409 |
tim |
722 |
info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
410 |
mmeineke |
412 |
#endif //is_mpi |
411 |
mmeineke |
670 |
} |
412 |
|
|
excludeOffset += molInfo.nTorsions; |
413 |
tim |
722 |
|
414 |
|
|
|
415 |
mmeineke |
670 |
// send the arrays off to the forceField for init. |
416 |
mmeineke |
407 |
|
417 |
tim |
722 |
the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms); |
418 |
|
|
the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds); |
419 |
|
|
the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends); |
420 |
|
|
the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions, |
421 |
|
|
theTorsions); |
422 |
|
|
|
423 |
|
|
|
424 |
|
|
info[k].molecules[i].initialize(molInfo); |
425 |
|
|
|
426 |
|
|
|
427 |
mmeineke |
670 |
atomOffset += molInfo.nAtoms; |
428 |
|
|
delete[] theBonds; |
429 |
|
|
delete[] theBends; |
430 |
|
|
delete[] theTorsions; |
431 |
mmeineke |
412 |
} |
432 |
mmeineke |
414 |
} |
433 |
tim |
722 |
|
434 |
chuckv |
434 |
#ifdef IS_MPI |
435 |
tim |
722 |
sprintf(checkPointMsg, "all molecules initialized succesfully"); |
436 |
chuckv |
434 |
MPIcheckPoint(); |
437 |
|
|
#endif // is_mpi |
438 |
tim |
722 |
|
439 |
mmeineke |
670 |
// clean up the forcefield |
440 |
chuckv |
434 |
|
441 |
mmeineke |
420 |
the_ff->calcRcut(); |
442 |
mmeineke |
414 |
the_ff->cleanMe(); |
443 |
|
|
} |
444 |
mmeineke |
407 |
|
445 |
tim |
722 |
void SimSetup::initFromBass(void){ |
446 |
mmeineke |
377 |
int i, j, k; |
447 |
|
|
int n_cells; |
448 |
|
|
double cellx, celly, cellz; |
449 |
|
|
double temp1, temp2, temp3; |
450 |
|
|
int n_per_extra; |
451 |
|
|
int n_extra; |
452 |
|
|
int have_extra, done; |
453 |
|
|
|
454 |
mmeineke |
670 |
double vel[3]; |
455 |
|
|
vel[0] = 0.0; |
456 |
|
|
vel[1] = 0.0; |
457 |
|
|
vel[2] = 0.0; |
458 |
|
|
|
459 |
tim |
722 |
temp1 = (double) tot_nmol / 4.0; |
460 |
|
|
temp2 = pow(temp1, (1.0 / 3.0)); |
461 |
|
|
temp3 = ceil(temp2); |
462 |
mmeineke |
377 |
|
463 |
tim |
722 |
have_extra = 0; |
464 |
|
|
if (temp2 < temp3){ |
465 |
|
|
// we have a non-complete lattice |
466 |
|
|
have_extra = 1; |
467 |
mmeineke |
377 |
|
468 |
tim |
722 |
n_cells = (int) temp3 - 1; |
469 |
mmeineke |
670 |
cellx = info[0].boxL[0] / temp3; |
470 |
|
|
celly = info[0].boxL[1] / temp3; |
471 |
|
|
cellz = info[0].boxL[2] / temp3; |
472 |
tim |
722 |
n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells); |
473 |
|
|
temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0)); |
474 |
|
|
n_per_extra = (int) ceil(temp1); |
475 |
mmeineke |
377 |
|
476 |
tim |
722 |
if (n_per_extra > 4){ |
477 |
|
|
sprintf(painCave.errMsg, |
478 |
|
|
"SimSetup error. There has been an error in constructing" |
479 |
|
|
" the non-complete lattice.\n"); |
480 |
mmeineke |
377 |
painCave.isFatal = 1; |
481 |
|
|
simError(); |
482 |
|
|
} |
483 |
|
|
} |
484 |
|
|
else{ |
485 |
tim |
722 |
n_cells = (int) temp3; |
486 |
mmeineke |
670 |
cellx = info[0].boxL[0] / temp3; |
487 |
|
|
celly = info[0].boxL[1] / temp3; |
488 |
|
|
cellz = info[0].boxL[2] / temp3; |
489 |
mmeineke |
377 |
} |
490 |
|
|
|
491 |
|
|
current_mol = 0; |
492 |
|
|
current_comp_mol = 0; |
493 |
|
|
current_comp = 0; |
494 |
|
|
current_atom_ndx = 0; |
495 |
|
|
|
496 |
tim |
722 |
for (i = 0; i < n_cells ; i++){ |
497 |
|
|
for (j = 0; j < n_cells; j++){ |
498 |
|
|
for (k = 0; k < n_cells; k++){ |
499 |
|
|
makeElement(i * cellx, j * celly, k * cellz); |
500 |
mmeineke |
377 |
|
501 |
tim |
722 |
makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz); |
502 |
mmeineke |
377 |
|
503 |
tim |
722 |
makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz); |
504 |
mmeineke |
377 |
|
505 |
tim |
722 |
makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz); |
506 |
mmeineke |
377 |
} |
507 |
|
|
} |
508 |
|
|
} |
509 |
|
|
|
510 |
tim |
722 |
if (have_extra){ |
511 |
mmeineke |
377 |
done = 0; |
512 |
|
|
|
513 |
|
|
int start_ndx; |
514 |
tim |
722 |
for (i = 0; i < (n_cells + 1) && !done; i++){ |
515 |
|
|
for (j = 0; j < (n_cells + 1) && !done; j++){ |
516 |
|
|
if (i < n_cells){ |
517 |
|
|
if (j < n_cells){ |
518 |
|
|
start_ndx = n_cells; |
519 |
|
|
} |
520 |
|
|
else |
521 |
|
|
start_ndx = 0; |
522 |
|
|
} |
523 |
|
|
else |
524 |
|
|
start_ndx = 0; |
525 |
mmeineke |
377 |
|
526 |
tim |
722 |
for (k = start_ndx; k < (n_cells + 1) && !done; k++){ |
527 |
|
|
makeElement(i * cellx, j * celly, k * cellz); |
528 |
|
|
done = (current_mol >= tot_nmol); |
529 |
mmeineke |
377 |
|
530 |
tim |
722 |
if (!done && n_per_extra > 1){ |
531 |
|
|
makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, |
532 |
|
|
k * cellz); |
533 |
|
|
done = (current_mol >= tot_nmol); |
534 |
|
|
} |
535 |
mmeineke |
377 |
|
536 |
tim |
722 |
if (!done && n_per_extra > 2){ |
537 |
|
|
makeElement(i * cellx, j * celly + 0.5 * celly, |
538 |
|
|
k * cellz + 0.5 * cellz); |
539 |
|
|
done = (current_mol >= tot_nmol); |
540 |
|
|
} |
541 |
mmeineke |
377 |
|
542 |
tim |
722 |
if (!done && n_per_extra > 3){ |
543 |
|
|
makeElement(i * cellx + 0.5 * cellx, j * celly, |
544 |
|
|
k * cellz + 0.5 * cellz); |
545 |
|
|
done = (current_mol >= tot_nmol); |
546 |
|
|
} |
547 |
|
|
} |
548 |
mmeineke |
377 |
} |
549 |
|
|
} |
550 |
|
|
} |
551 |
|
|
|
552 |
tim |
722 |
for (i = 0; i < info[0].n_atoms; i++){ |
553 |
|
|
info[0].atoms[i]->setVel(vel); |
554 |
mmeineke |
377 |
} |
555 |
|
|
} |
556 |
|
|
|
557 |
tim |
722 |
void SimSetup::makeElement(double x, double y, double z){ |
558 |
mmeineke |
377 |
int k; |
559 |
|
|
AtomStamp* current_atom; |
560 |
|
|
DirectionalAtom* dAtom; |
561 |
|
|
double rotMat[3][3]; |
562 |
mmeineke |
670 |
double pos[3]; |
563 |
mmeineke |
377 |
|
564 |
tim |
722 |
for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){ |
565 |
|
|
current_atom = comp_stamps[current_comp]->getAtom(k); |
566 |
|
|
if (!current_atom->havePosition()){ |
567 |
|
|
sprintf(painCave.errMsg, |
568 |
|
|
"SimSetup:initFromBass error.\n" |
569 |
|
|
"\tComponent %s, atom %s does not have a position specified.\n" |
570 |
|
|
"\tThe initialization routine is unable to give a start" |
571 |
|
|
" position.\n", |
572 |
|
|
comp_stamps[current_comp]->getID(), current_atom->getType()); |
573 |
mmeineke |
377 |
painCave.isFatal = 1; |
574 |
|
|
simError(); |
575 |
|
|
} |
576 |
tim |
722 |
|
577 |
mmeineke |
670 |
pos[0] = x + current_atom->getPosX(); |
578 |
|
|
pos[1] = y + current_atom->getPosY(); |
579 |
|
|
pos[2] = z + current_atom->getPosZ(); |
580 |
mmeineke |
377 |
|
581 |
tim |
722 |
info[0].atoms[current_atom_ndx]->setPos(pos); |
582 |
mmeineke |
377 |
|
583 |
tim |
722 |
if (info[0].atoms[current_atom_ndx]->isDirectional()){ |
584 |
|
|
dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx]; |
585 |
mmeineke |
377 |
|
586 |
|
|
rotMat[0][0] = 1.0; |
587 |
|
|
rotMat[0][1] = 0.0; |
588 |
|
|
rotMat[0][2] = 0.0; |
589 |
|
|
|
590 |
|
|
rotMat[1][0] = 0.0; |
591 |
|
|
rotMat[1][1] = 1.0; |
592 |
|
|
rotMat[1][2] = 0.0; |
593 |
|
|
|
594 |
|
|
rotMat[2][0] = 0.0; |
595 |
|
|
rotMat[2][1] = 0.0; |
596 |
|
|
rotMat[2][2] = 1.0; |
597 |
|
|
|
598 |
tim |
722 |
dAtom->setA(rotMat); |
599 |
mmeineke |
377 |
} |
600 |
|
|
|
601 |
|
|
current_atom_ndx++; |
602 |
|
|
} |
603 |
|
|
|
604 |
|
|
current_mol++; |
605 |
|
|
current_comp_mol++; |
606 |
|
|
|
607 |
tim |
722 |
if (current_comp_mol >= components_nmol[current_comp]){ |
608 |
mmeineke |
377 |
current_comp_mol = 0; |
609 |
|
|
current_comp++; |
610 |
|
|
} |
611 |
|
|
} |
612 |
mmeineke |
614 |
|
613 |
|
|
|
614 |
tim |
722 |
void SimSetup::gatherInfo(void){ |
615 |
mmeineke |
787 |
int i; |
616 |
mmeineke |
614 |
|
617 |
|
|
ensembleCase = -1; |
618 |
|
|
ffCase = -1; |
619 |
|
|
|
620 |
mmeineke |
670 |
// set the easy ones first |
621 |
mmeineke |
614 |
|
622 |
tim |
722 |
for (i = 0; i < nInfo; i++){ |
623 |
mmeineke |
670 |
info[i].target_temp = globals->getTargetTemp(); |
624 |
|
|
info[i].dt = globals->getDt(); |
625 |
|
|
info[i].run_time = globals->getRunTime(); |
626 |
|
|
} |
627 |
mmeineke |
616 |
n_components = globals->getNComponents(); |
628 |
mmeineke |
614 |
|
629 |
|
|
|
630 |
|
|
// get the forceField |
631 |
|
|
|
632 |
tim |
722 |
strcpy(force_field, globals->getForceField()); |
633 |
mmeineke |
614 |
|
634 |
tim |
722 |
if (!strcasecmp(force_field, "DUFF")){ |
635 |
|
|
ffCase = FF_DUFF; |
636 |
|
|
} |
637 |
|
|
else if (!strcasecmp(force_field, "LJ")){ |
638 |
|
|
ffCase = FF_LJ; |
639 |
|
|
} |
640 |
|
|
else if (!strcasecmp(force_field, "EAM")){ |
641 |
|
|
ffCase = FF_EAM; |
642 |
|
|
} |
643 |
chrisfen |
999 |
else if (!strcasecmp(force_field, "WATER")){ |
644 |
|
|
ffCase = FF_H2O; |
645 |
|
|
} |
646 |
mmeineke |
614 |
else{ |
647 |
tim |
722 |
sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n", |
648 |
|
|
force_field); |
649 |
|
|
painCave.isFatal = 1; |
650 |
|
|
simError(); |
651 |
mmeineke |
614 |
} |
652 |
|
|
|
653 |
tim |
722 |
// get the ensemble |
654 |
mmeineke |
614 |
|
655 |
tim |
722 |
strcpy(ensemble, globals->getEnsemble()); |
656 |
mmeineke |
614 |
|
657 |
tim |
722 |
if (!strcasecmp(ensemble, "NVE")){ |
658 |
|
|
ensembleCase = NVE_ENS; |
659 |
|
|
} |
660 |
|
|
else if (!strcasecmp(ensemble, "NVT")){ |
661 |
|
|
ensembleCase = NVT_ENS; |
662 |
|
|
} |
663 |
|
|
else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){ |
664 |
mmeineke |
614 |
ensembleCase = NPTi_ENS; |
665 |
tim |
722 |
} |
666 |
|
|
else if (!strcasecmp(ensemble, "NPTf")){ |
667 |
|
|
ensembleCase = NPTf_ENS; |
668 |
|
|
} |
669 |
mmeineke |
812 |
else if (!strcasecmp(ensemble, "NPTxyz")){ |
670 |
|
|
ensembleCase = NPTxyz_ENS; |
671 |
|
|
} |
672 |
mmeineke |
614 |
else{ |
673 |
tim |
722 |
sprintf(painCave.errMsg, |
674 |
gezelter |
965 |
"SimSetup Warning. Unrecognized Ensemble -> %s \n" |
675 |
|
|
"\treverting to NVE for this simulation.\n", |
676 |
tim |
722 |
ensemble); |
677 |
|
|
painCave.isFatal = 0; |
678 |
|
|
simError(); |
679 |
|
|
strcpy(ensemble, "NVE"); |
680 |
|
|
ensembleCase = NVE_ENS; |
681 |
mmeineke |
614 |
} |
682 |
|
|
|
683 |
tim |
722 |
for (i = 0; i < nInfo; i++){ |
684 |
|
|
strcpy(info[i].ensemble, ensemble); |
685 |
|
|
|
686 |
mmeineke |
670 |
// get the mixing rule |
687 |
mmeineke |
614 |
|
688 |
tim |
722 |
strcpy(info[i].mixingRule, globals->getMixingRule()); |
689 |
mmeineke |
670 |
info[i].usePBC = globals->getPBC(); |
690 |
|
|
} |
691 |
tim |
722 |
|
692 |
mmeineke |
614 |
// get the components and calculate the tot_nMol and indvidual n_mol |
693 |
tim |
722 |
|
694 |
mmeineke |
616 |
the_components = globals->getComponents(); |
695 |
mmeineke |
614 |
components_nmol = new int[n_components]; |
696 |
|
|
|
697 |
|
|
|
698 |
tim |
722 |
if (!globals->haveNMol()){ |
699 |
mmeineke |
614 |
// we don't have the total number of molecules, so we assume it is |
700 |
|
|
// given in each component |
701 |
|
|
|
702 |
|
|
tot_nmol = 0; |
703 |
tim |
722 |
for (i = 0; i < n_components; i++){ |
704 |
|
|
if (!the_components[i]->haveNMol()){ |
705 |
|
|
// we have a problem |
706 |
|
|
sprintf(painCave.errMsg, |
707 |
gezelter |
965 |
"SimSetup Error. No global NMol or component NMol given.\n" |
708 |
|
|
"\tCannot calculate the number of atoms.\n"); |
709 |
tim |
722 |
painCave.isFatal = 1; |
710 |
|
|
simError(); |
711 |
mmeineke |
614 |
} |
712 |
|
|
|
713 |
|
|
tot_nmol += the_components[i]->getNMol(); |
714 |
|
|
components_nmol[i] = the_components[i]->getNMol(); |
715 |
|
|
} |
716 |
|
|
} |
717 |
|
|
else{ |
718 |
tim |
722 |
sprintf(painCave.errMsg, |
719 |
|
|
"SimSetup error.\n" |
720 |
|
|
"\tSorry, the ability to specify total" |
721 |
|
|
" nMols and then give molfractions in the components\n" |
722 |
|
|
"\tis not currently supported." |
723 |
|
|
" Please give nMol in the components.\n"); |
724 |
mmeineke |
614 |
painCave.isFatal = 1; |
725 |
|
|
simError(); |
726 |
|
|
} |
727 |
|
|
|
728 |
tim |
962 |
//check whether sample time, status time, thermal time and reset time are divisble by dt |
729 |
|
|
if (!isDivisible(globals->getSampleTime(), globals->getDt())){ |
730 |
|
|
sprintf(painCave.errMsg, |
731 |
gezelter |
965 |
"Sample time is not divisible by dt.\n" |
732 |
|
|
"\tThis will result in samples that are not uniformly\n" |
733 |
|
|
"\tdistributed in time. If this is a problem, change\n" |
734 |
|
|
"\tyour sampleTime variable.\n"); |
735 |
tim |
962 |
painCave.isFatal = 0; |
736 |
|
|
simError(); |
737 |
|
|
} |
738 |
|
|
|
739 |
|
|
if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){ |
740 |
|
|
sprintf(painCave.errMsg, |
741 |
gezelter |
965 |
"Status time is not divisible by dt.\n" |
742 |
|
|
"\tThis will result in status reports that are not uniformly\n" |
743 |
|
|
"\tdistributed in time. If this is a problem, change \n" |
744 |
|
|
"\tyour statusTime variable.\n"); |
745 |
tim |
962 |
painCave.isFatal = 0; |
746 |
|
|
simError(); |
747 |
|
|
} |
748 |
|
|
|
749 |
|
|
if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){ |
750 |
|
|
sprintf(painCave.errMsg, |
751 |
gezelter |
965 |
"Thermal time is not divisible by dt.\n" |
752 |
|
|
"\tThis will result in thermalizations that are not uniformly\n" |
753 |
|
|
"\tdistributed in time. If this is a problem, change \n" |
754 |
|
|
"\tyour thermalTime variable.\n"); |
755 |
tim |
962 |
painCave.isFatal = 0; |
756 |
|
|
simError(); |
757 |
|
|
} |
758 |
|
|
|
759 |
|
|
if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){ |
760 |
|
|
sprintf(painCave.errMsg, |
761 |
gezelter |
965 |
"Reset time is not divisible by dt.\n" |
762 |
|
|
"\tThis will result in integrator resets that are not uniformly\n" |
763 |
|
|
"\tdistributed in time. If this is a problem, change\n" |
764 |
|
|
"\tyour resetTime variable.\n"); |
765 |
tim |
962 |
painCave.isFatal = 0; |
766 |
|
|
simError(); |
767 |
|
|
} |
768 |
|
|
|
769 |
mmeineke |
614 |
// set the status, sample, and thermal kick times |
770 |
|
|
|
771 |
tim |
722 |
for (i = 0; i < nInfo; i++){ |
772 |
|
|
if (globals->haveSampleTime()){ |
773 |
mmeineke |
670 |
info[i].sampleTime = globals->getSampleTime(); |
774 |
|
|
info[i].statusTime = info[i].sampleTime; |
775 |
|
|
info[i].thermalTime = info[i].sampleTime; |
776 |
|
|
} |
777 |
|
|
else{ |
778 |
|
|
info[i].sampleTime = globals->getRunTime(); |
779 |
|
|
info[i].statusTime = info[i].sampleTime; |
780 |
|
|
info[i].thermalTime = info[i].sampleTime; |
781 |
|
|
} |
782 |
tim |
722 |
|
783 |
|
|
if (globals->haveStatusTime()){ |
784 |
mmeineke |
670 |
info[i].statusTime = globals->getStatusTime(); |
785 |
|
|
} |
786 |
tim |
722 |
|
787 |
|
|
if (globals->haveThermalTime()){ |
788 |
mmeineke |
670 |
info[i].thermalTime = globals->getThermalTime(); |
789 |
|
|
} |
790 |
mmeineke |
614 |
|
791 |
mmeineke |
746 |
info[i].resetIntegrator = 0; |
792 |
|
|
if( globals->haveResetTime() ){ |
793 |
|
|
info[i].resetTime = globals->getResetTime(); |
794 |
|
|
info[i].resetIntegrator = 1; |
795 |
|
|
} |
796 |
|
|
|
797 |
mmeineke |
670 |
// check for the temperature set flag |
798 |
mmeineke |
841 |
|
799 |
tim |
722 |
if (globals->haveTempSet()) |
800 |
|
|
info[i].setTemp = globals->getTempSet(); |
801 |
mmeineke |
855 |
|
802 |
|
|
// check for the extended State init |
803 |
|
|
|
804 |
|
|
info[i].useInitXSstate = globals->getUseInitXSstate(); |
805 |
|
|
info[i].orthoTolerance = globals->getOrthoBoxTolerance(); |
806 |
mmeineke |
841 |
|
807 |
tim |
708 |
} |
808 |
mmeineke |
841 |
|
809 |
tim |
722 |
//setup seed for random number generator |
810 |
tim |
708 |
int seedValue; |
811 |
|
|
|
812 |
tim |
722 |
if (globals->haveSeed()){ |
813 |
tim |
708 |
seedValue = globals->getSeed(); |
814 |
tim |
722 |
|
815 |
|
|
if(seedValue / 1E9 == 0){ |
816 |
|
|
sprintf(painCave.errMsg, |
817 |
|
|
"Seed for sprng library should contain at least 9 digits\n" |
818 |
|
|
"OOPSE will generate a seed for user\n"); |
819 |
|
|
painCave.isFatal = 0; |
820 |
|
|
simError(); |
821 |
|
|
|
822 |
|
|
//using seed generated by system instead of invalid seed set by user |
823 |
|
|
#ifndef IS_MPI |
824 |
|
|
seedValue = make_sprng_seed(); |
825 |
|
|
#else |
826 |
|
|
if (worldRank == 0){ |
827 |
|
|
seedValue = make_sprng_seed(); |
828 |
|
|
} |
829 |
|
|
MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
830 |
|
|
#endif |
831 |
|
|
} |
832 |
|
|
}//end of if branch of globals->haveSeed() |
833 |
tim |
708 |
else{ |
834 |
tim |
722 |
|
835 |
tim |
708 |
#ifndef IS_MPI |
836 |
tim |
722 |
seedValue = make_sprng_seed(); |
837 |
tim |
708 |
#else |
838 |
tim |
722 |
if (worldRank == 0){ |
839 |
|
|
seedValue = make_sprng_seed(); |
840 |
tim |
708 |
} |
841 |
tim |
722 |
MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
842 |
tim |
708 |
#endif |
843 |
tim |
722 |
}//end of globals->haveSeed() |
844 |
tim |
708 |
|
845 |
tim |
722 |
for (int i = 0; i < nInfo; i++){ |
846 |
tim |
708 |
info[i].setSeed(seedValue); |
847 |
|
|
} |
848 |
tim |
1031 |
|
849 |
mmeineke |
614 |
#ifdef IS_MPI |
850 |
chrisfen |
999 |
strcpy(checkPointMsg, "Successfully gathered all information from Bass\n"); |
851 |
mmeineke |
614 |
MPIcheckPoint(); |
852 |
|
|
#endif // is_mpi |
853 |
|
|
} |
854 |
|
|
|
855 |
|
|
|
856 |
tim |
722 |
void SimSetup::finalInfoCheck(void){ |
857 |
mmeineke |
614 |
int index; |
858 |
|
|
int usesDipoles; |
859 |
mmeineke |
670 |
int i; |
860 |
mmeineke |
614 |
|
861 |
tim |
722 |
for (i = 0; i < nInfo; i++){ |
862 |
mmeineke |
670 |
// check electrostatic parameters |
863 |
tim |
722 |
|
864 |
mmeineke |
670 |
index = 0; |
865 |
|
|
usesDipoles = 0; |
866 |
tim |
722 |
while ((index < info[i].n_atoms) && !usesDipoles){ |
867 |
mmeineke |
670 |
usesDipoles = (info[i].atoms[index])->hasDipole(); |
868 |
|
|
index++; |
869 |
|
|
} |
870 |
tim |
722 |
|
871 |
mmeineke |
614 |
#ifdef IS_MPI |
872 |
mmeineke |
670 |
int myUse = usesDipoles; |
873 |
tim |
722 |
MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
874 |
mmeineke |
614 |
#endif //is_mpi |
875 |
tim |
722 |
|
876 |
mmeineke |
670 |
double theEcr, theEst; |
877 |
tim |
722 |
|
878 |
|
|
if (globals->getUseRF()){ |
879 |
mmeineke |
670 |
info[i].useReactionField = 1; |
880 |
tim |
722 |
|
881 |
|
|
if (!globals->haveECR()){ |
882 |
|
|
sprintf(painCave.errMsg, |
883 |
gezelter |
965 |
"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n" |
884 |
|
|
"\tOOPSE will use a default value of 15.0 angstroms" |
885 |
|
|
"\tfor the electrostaticCutoffRadius.\n"); |
886 |
tim |
722 |
painCave.isFatal = 0; |
887 |
|
|
simError(); |
888 |
mmeineke |
859 |
theEcr = 15.0; |
889 |
mmeineke |
614 |
} |
890 |
tim |
722 |
else{ |
891 |
|
|
theEcr = globals->getECR(); |
892 |
mmeineke |
614 |
} |
893 |
tim |
722 |
|
894 |
|
|
if (!globals->haveEST()){ |
895 |
|
|
sprintf(painCave.errMsg, |
896 |
gezelter |
965 |
"SimSetup Warning: No value was set for electrostaticSkinThickness.\n" |
897 |
|
|
"\tOOPSE will use a default value of\n" |
898 |
|
|
"\t0.05 * electrostaticCutoffRadius\n" |
899 |
|
|
"\tfor the electrostaticSkinThickness\n"); |
900 |
tim |
722 |
painCave.isFatal = 0; |
901 |
|
|
simError(); |
902 |
|
|
theEst = 0.05 * theEcr; |
903 |
mmeineke |
670 |
} |
904 |
tim |
722 |
else{ |
905 |
|
|
theEst = globals->getEST(); |
906 |
mmeineke |
670 |
} |
907 |
tim |
722 |
|
908 |
mmeineke |
841 |
info[i].setDefaultEcr(theEcr, theEst); |
909 |
tim |
722 |
|
910 |
|
|
if (!globals->haveDielectric()){ |
911 |
|
|
sprintf(painCave.errMsg, |
912 |
gezelter |
965 |
"SimSetup Error: No Dielectric constant was set.\n" |
913 |
|
|
"\tYou are trying to use Reaction Field without" |
914 |
|
|
"\tsetting a dielectric constant!\n"); |
915 |
tim |
722 |
painCave.isFatal = 1; |
916 |
|
|
simError(); |
917 |
|
|
} |
918 |
|
|
info[i].dielectric = globals->getDielectric(); |
919 |
|
|
} |
920 |
|
|
else{ |
921 |
|
|
if (usesDipoles){ |
922 |
|
|
if (!globals->haveECR()){ |
923 |
|
|
sprintf(painCave.errMsg, |
924 |
gezelter |
965 |
"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n" |
925 |
|
|
"\tOOPSE will use a default value of 15.0 angstroms" |
926 |
|
|
"\tfor the electrostaticCutoffRadius.\n"); |
927 |
mmeineke |
859 |
painCave.isFatal = 0; |
928 |
|
|
simError(); |
929 |
|
|
theEcr = 15.0; |
930 |
tim |
722 |
} |
931 |
|
|
else{ |
932 |
|
|
theEcr = globals->getECR(); |
933 |
|
|
} |
934 |
mmeineke |
859 |
|
935 |
tim |
722 |
if (!globals->haveEST()){ |
936 |
|
|
sprintf(painCave.errMsg, |
937 |
gezelter |
965 |
"SimSetup Warning: No value was set for electrostaticSkinThickness.\n" |
938 |
|
|
"\tOOPSE will use a default value of\n" |
939 |
|
|
"\t0.05 * electrostaticCutoffRadius\n" |
940 |
|
|
"\tfor the electrostaticSkinThickness\n"); |
941 |
tim |
722 |
painCave.isFatal = 0; |
942 |
|
|
simError(); |
943 |
|
|
theEst = 0.05 * theEcr; |
944 |
|
|
} |
945 |
|
|
else{ |
946 |
|
|
theEst = globals->getEST(); |
947 |
|
|
} |
948 |
mmeineke |
859 |
|
949 |
mmeineke |
841 |
info[i].setDefaultEcr(theEcr, theEst); |
950 |
tim |
722 |
} |
951 |
|
|
} |
952 |
mmeineke |
670 |
} |
953 |
mmeineke |
614 |
#ifdef IS_MPI |
954 |
tim |
722 |
strcpy(checkPointMsg, "post processing checks out"); |
955 |
mmeineke |
614 |
MPIcheckPoint(); |
956 |
|
|
#endif // is_mpi |
957 |
|
|
} |
958 |
mmeineke |
859 |
|
959 |
tim |
722 |
void SimSetup::initSystemCoords(void){ |
960 |
mmeineke |
670 |
int i; |
961 |
tim |
722 |
|
962 |
tim |
689 |
char* inName; |
963 |
|
|
|
964 |
tim |
722 |
(info[0].getConfiguration())->createArrays(info[0].n_atoms); |
965 |
mmeineke |
614 |
|
966 |
tim |
722 |
for (i = 0; i < info[0].n_atoms; i++) |
967 |
|
|
info[0].atoms[i]->setCoords(); |
968 |
|
|
|
969 |
|
|
if (globals->haveInitialConfig()){ |
970 |
mmeineke |
670 |
InitializeFromFile* fileInit; |
971 |
mmeineke |
614 |
#ifdef IS_MPI // is_mpi |
972 |
tim |
722 |
if (worldRank == 0){ |
973 |
mmeineke |
614 |
#endif //is_mpi |
974 |
tim |
689 |
inName = globals->getInitialConfig(); |
975 |
tim |
722 |
fileInit = new InitializeFromFile(inName); |
976 |
mmeineke |
614 |
#ifdef IS_MPI |
977 |
tim |
722 |
} |
978 |
|
|
else |
979 |
|
|
fileInit = new InitializeFromFile(NULL); |
980 |
mmeineke |
614 |
#endif |
981 |
tim |
722 |
fileInit->readInit(info); // default velocities on |
982 |
|
|
|
983 |
mmeineke |
670 |
delete fileInit; |
984 |
|
|
} |
985 |
|
|
else{ |
986 |
mmeineke |
859 |
|
987 |
mmeineke |
670 |
// no init from bass |
988 |
mmeineke |
859 |
|
989 |
tim |
722 |
sprintf(painCave.errMsg, |
990 |
mmeineke |
859 |
"Cannot intialize a simulation without an initial configuration file.\n"); |
991 |
mmeineke |
787 |
painCave.isFatal = 1;; |
992 |
mmeineke |
670 |
simError(); |
993 |
mmeineke |
859 |
|
994 |
mmeineke |
670 |
} |
995 |
tim |
722 |
|
996 |
mmeineke |
614 |
#ifdef IS_MPI |
997 |
tim |
722 |
strcpy(checkPointMsg, "Successfully read in the initial configuration"); |
998 |
mmeineke |
614 |
MPIcheckPoint(); |
999 |
|
|
#endif // is_mpi |
1000 |
|
|
} |
1001 |
|
|
|
1002 |
|
|
|
1003 |
tim |
722 |
void SimSetup::makeOutNames(void){ |
1004 |
mmeineke |
670 |
int k; |
1005 |
mmeineke |
614 |
|
1006 |
mmeineke |
670 |
|
1007 |
tim |
722 |
for (k = 0; k < nInfo; k++){ |
1008 |
mmeineke |
614 |
#ifdef IS_MPI |
1009 |
tim |
722 |
if (worldRank == 0){ |
1010 |
mmeineke |
614 |
#endif // is_mpi |
1011 |
tim |
722 |
|
1012 |
|
|
if (globals->haveFinalConfig()){ |
1013 |
|
|
strcpy(info[k].finalName, globals->getFinalConfig()); |
1014 |
mmeineke |
614 |
} |
1015 |
|
|
else{ |
1016 |
tim |
722 |
strcpy(info[k].finalName, inFileName); |
1017 |
|
|
char* endTest; |
1018 |
|
|
int nameLength = strlen(info[k].finalName); |
1019 |
|
|
endTest = &(info[k].finalName[nameLength - 5]); |
1020 |
|
|
if (!strcmp(endTest, ".bass")){ |
1021 |
|
|
strcpy(endTest, ".eor"); |
1022 |
|
|
} |
1023 |
|
|
else if (!strcmp(endTest, ".BASS")){ |
1024 |
|
|
strcpy(endTest, ".eor"); |
1025 |
|
|
} |
1026 |
|
|
else{ |
1027 |
|
|
endTest = &(info[k].finalName[nameLength - 4]); |
1028 |
|
|
if (!strcmp(endTest, ".bss")){ |
1029 |
|
|
strcpy(endTest, ".eor"); |
1030 |
|
|
} |
1031 |
|
|
else if (!strcmp(endTest, ".mdl")){ |
1032 |
|
|
strcpy(endTest, ".eor"); |
1033 |
|
|
} |
1034 |
|
|
else{ |
1035 |
|
|
strcat(info[k].finalName, ".eor"); |
1036 |
|
|
} |
1037 |
|
|
} |
1038 |
mmeineke |
614 |
} |
1039 |
tim |
722 |
|
1040 |
mmeineke |
670 |
// make the sample and status out names |
1041 |
tim |
722 |
|
1042 |
|
|
strcpy(info[k].sampleName, inFileName); |
1043 |
mmeineke |
670 |
char* endTest; |
1044 |
tim |
722 |
int nameLength = strlen(info[k].sampleName); |
1045 |
mmeineke |
670 |
endTest = &(info[k].sampleName[nameLength - 5]); |
1046 |
tim |
722 |
if (!strcmp(endTest, ".bass")){ |
1047 |
|
|
strcpy(endTest, ".dump"); |
1048 |
mmeineke |
614 |
} |
1049 |
tim |
722 |
else if (!strcmp(endTest, ".BASS")){ |
1050 |
|
|
strcpy(endTest, ".dump"); |
1051 |
mmeineke |
614 |
} |
1052 |
|
|
else{ |
1053 |
tim |
722 |
endTest = &(info[k].sampleName[nameLength - 4]); |
1054 |
|
|
if (!strcmp(endTest, ".bss")){ |
1055 |
|
|
strcpy(endTest, ".dump"); |
1056 |
|
|
} |
1057 |
|
|
else if (!strcmp(endTest, ".mdl")){ |
1058 |
|
|
strcpy(endTest, ".dump"); |
1059 |
|
|
} |
1060 |
|
|
else{ |
1061 |
|
|
strcat(info[k].sampleName, ".dump"); |
1062 |
|
|
} |
1063 |
mmeineke |
614 |
} |
1064 |
tim |
722 |
|
1065 |
|
|
strcpy(info[k].statusName, inFileName); |
1066 |
|
|
nameLength = strlen(info[k].statusName); |
1067 |
mmeineke |
670 |
endTest = &(info[k].statusName[nameLength - 5]); |
1068 |
tim |
722 |
if (!strcmp(endTest, ".bass")){ |
1069 |
|
|
strcpy(endTest, ".stat"); |
1070 |
mmeineke |
614 |
} |
1071 |
tim |
722 |
else if (!strcmp(endTest, ".BASS")){ |
1072 |
|
|
strcpy(endTest, ".stat"); |
1073 |
mmeineke |
614 |
} |
1074 |
|
|
else{ |
1075 |
tim |
722 |
endTest = &(info[k].statusName[nameLength - 4]); |
1076 |
|
|
if (!strcmp(endTest, ".bss")){ |
1077 |
|
|
strcpy(endTest, ".stat"); |
1078 |
|
|
} |
1079 |
|
|
else if (!strcmp(endTest, ".mdl")){ |
1080 |
|
|
strcpy(endTest, ".stat"); |
1081 |
|
|
} |
1082 |
|
|
else{ |
1083 |
|
|
strcat(info[k].statusName, ".stat"); |
1084 |
|
|
} |
1085 |
mmeineke |
614 |
} |
1086 |
tim |
722 |
|
1087 |
mmeineke |
670 |
#ifdef IS_MPI |
1088 |
tim |
722 |
|
1089 |
mmeineke |
614 |
} |
1090 |
mmeineke |
670 |
#endif // is_mpi |
1091 |
mmeineke |
614 |
} |
1092 |
|
|
} |
1093 |
|
|
|
1094 |
|
|
|
1095 |
tim |
722 |
void SimSetup::sysObjectsCreation(void){ |
1096 |
|
|
int i, k; |
1097 |
|
|
|
1098 |
mmeineke |
614 |
// create the forceField |
1099 |
tim |
689 |
|
1100 |
mmeineke |
614 |
createFF(); |
1101 |
|
|
|
1102 |
|
|
// extract componentList |
1103 |
|
|
|
1104 |
|
|
compList(); |
1105 |
|
|
|
1106 |
|
|
// calc the number of atoms, bond, bends, and torsions |
1107 |
|
|
|
1108 |
|
|
calcSysValues(); |
1109 |
|
|
|
1110 |
|
|
#ifdef IS_MPI |
1111 |
|
|
// divide the molecules among the processors |
1112 |
tim |
722 |
|
1113 |
mmeineke |
614 |
mpiMolDivide(); |
1114 |
|
|
#endif //is_mpi |
1115 |
tim |
722 |
|
1116 |
mmeineke |
614 |
// create the atom and SRI arrays. Also initialize Molecule Stamp ID's |
1117 |
tim |
722 |
|
1118 |
mmeineke |
614 |
makeSysArrays(); |
1119 |
|
|
|
1120 |
mmeineke |
616 |
// make and initialize the molecules (all but atomic coordinates) |
1121 |
tim |
722 |
|
1122 |
mmeineke |
616 |
makeMolecules(); |
1123 |
tim |
722 |
|
1124 |
|
|
for (k = 0; k < nInfo; k++){ |
1125 |
mmeineke |
670 |
info[k].identArray = new int[info[k].n_atoms]; |
1126 |
tim |
722 |
for (i = 0; i < info[k].n_atoms; i++){ |
1127 |
mmeineke |
670 |
info[k].identArray[i] = info[k].atoms[i]->getIdent(); |
1128 |
|
|
} |
1129 |
mmeineke |
616 |
} |
1130 |
mmeineke |
614 |
} |
1131 |
|
|
|
1132 |
|
|
|
1133 |
tim |
722 |
void SimSetup::createFF(void){ |
1134 |
|
|
switch (ffCase){ |
1135 |
|
|
case FF_DUFF: |
1136 |
|
|
the_ff = new DUFF(); |
1137 |
|
|
break; |
1138 |
mmeineke |
614 |
|
1139 |
tim |
722 |
case FF_LJ: |
1140 |
|
|
the_ff = new LJFF(); |
1141 |
|
|
break; |
1142 |
mmeineke |
614 |
|
1143 |
tim |
722 |
case FF_EAM: |
1144 |
|
|
the_ff = new EAM_FF(); |
1145 |
|
|
break; |
1146 |
mmeineke |
614 |
|
1147 |
chrisfen |
999 |
case FF_H2O: |
1148 |
|
|
the_ff = new WATER(); |
1149 |
|
|
break; |
1150 |
|
|
|
1151 |
tim |
722 |
default: |
1152 |
|
|
sprintf(painCave.errMsg, |
1153 |
|
|
"SimSetup Error. Unrecognized force field in case statement.\n"); |
1154 |
|
|
painCave.isFatal = 1; |
1155 |
|
|
simError(); |
1156 |
mmeineke |
614 |
} |
1157 |
|
|
|
1158 |
|
|
#ifdef IS_MPI |
1159 |
tim |
722 |
strcpy(checkPointMsg, "ForceField creation successful"); |
1160 |
mmeineke |
614 |
MPIcheckPoint(); |
1161 |
|
|
#endif // is_mpi |
1162 |
|
|
} |
1163 |
|
|
|
1164 |
|
|
|
1165 |
tim |
722 |
void SimSetup::compList(void){ |
1166 |
mmeineke |
616 |
int i; |
1167 |
mmeineke |
670 |
char* id; |
1168 |
|
|
LinkedMolStamp* headStamp = new LinkedMolStamp(); |
1169 |
|
|
LinkedMolStamp* currentStamp = NULL; |
1170 |
tim |
722 |
comp_stamps = new MoleculeStamp * [n_components]; |
1171 |
|
|
|
1172 |
mmeineke |
614 |
// make an array of molecule stamps that match the components used. |
1173 |
|
|
// also extract the used stamps out into a separate linked list |
1174 |
tim |
722 |
|
1175 |
|
|
for (i = 0; i < nInfo; i++){ |
1176 |
mmeineke |
670 |
info[i].nComponents = n_components; |
1177 |
|
|
info[i].componentsNmol = components_nmol; |
1178 |
|
|
info[i].compStamps = comp_stamps; |
1179 |
|
|
info[i].headStamp = headStamp; |
1180 |
|
|
} |
1181 |
mmeineke |
614 |
|
1182 |
|
|
|
1183 |
tim |
722 |
for (i = 0; i < n_components; i++){ |
1184 |
mmeineke |
614 |
id = the_components[i]->getType(); |
1185 |
|
|
comp_stamps[i] = NULL; |
1186 |
tim |
722 |
|
1187 |
mmeineke |
614 |
// check to make sure the component isn't already in the list |
1188 |
|
|
|
1189 |
tim |
722 |
comp_stamps[i] = headStamp->match(id); |
1190 |
|
|
if (comp_stamps[i] == NULL){ |
1191 |
mmeineke |
614 |
// extract the component from the list; |
1192 |
tim |
722 |
|
1193 |
|
|
currentStamp = stamps->extractMolStamp(id); |
1194 |
|
|
if (currentStamp == NULL){ |
1195 |
|
|
sprintf(painCave.errMsg, |
1196 |
|
|
"SimSetup error: Component \"%s\" was not found in the " |
1197 |
|
|
"list of declared molecules\n", |
1198 |
|
|
id); |
1199 |
|
|
painCave.isFatal = 1; |
1200 |
|
|
simError(); |
1201 |
mmeineke |
614 |
} |
1202 |
tim |
722 |
|
1203 |
|
|
headStamp->add(currentStamp); |
1204 |
|
|
comp_stamps[i] = headStamp->match(id); |
1205 |
mmeineke |
614 |
} |
1206 |
|
|
} |
1207 |
|
|
|
1208 |
|
|
#ifdef IS_MPI |
1209 |
tim |
722 |
strcpy(checkPointMsg, "Component stamps successfully extracted\n"); |
1210 |
mmeineke |
614 |
MPIcheckPoint(); |
1211 |
|
|
#endif // is_mpi |
1212 |
tim |
722 |
} |
1213 |
mmeineke |
614 |
|
1214 |
tim |
722 |
void SimSetup::calcSysValues(void){ |
1215 |
mmeineke |
787 |
int i; |
1216 |
mmeineke |
614 |
|
1217 |
tim |
722 |
int* molMembershipArray; |
1218 |
mmeineke |
614 |
|
1219 |
|
|
tot_atoms = 0; |
1220 |
|
|
tot_bonds = 0; |
1221 |
|
|
tot_bends = 0; |
1222 |
|
|
tot_torsions = 0; |
1223 |
tim |
722 |
for (i = 0; i < n_components; i++){ |
1224 |
|
|
tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1225 |
|
|
tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1226 |
|
|
tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1227 |
mmeineke |
614 |
tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
1228 |
|
|
} |
1229 |
tim |
722 |
|
1230 |
mmeineke |
614 |
tot_SRI = tot_bonds + tot_bends + tot_torsions; |
1231 |
mmeineke |
670 |
molMembershipArray = new int[tot_atoms]; |
1232 |
tim |
722 |
|
1233 |
|
|
for (i = 0; i < nInfo; i++){ |
1234 |
mmeineke |
670 |
info[i].n_atoms = tot_atoms; |
1235 |
|
|
info[i].n_bonds = tot_bonds; |
1236 |
|
|
info[i].n_bends = tot_bends; |
1237 |
|
|
info[i].n_torsions = tot_torsions; |
1238 |
|
|
info[i].n_SRI = tot_SRI; |
1239 |
|
|
info[i].n_mol = tot_nmol; |
1240 |
tim |
722 |
|
1241 |
mmeineke |
670 |
info[i].molMembershipArray = molMembershipArray; |
1242 |
tim |
722 |
} |
1243 |
mmeineke |
614 |
} |
1244 |
|
|
|
1245 |
|
|
#ifdef IS_MPI |
1246 |
|
|
|
1247 |
tim |
722 |
void SimSetup::mpiMolDivide(void){ |
1248 |
mmeineke |
616 |
int i, j, k; |
1249 |
mmeineke |
614 |
int localMol, allMol; |
1250 |
|
|
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
1251 |
|
|
|
1252 |
tim |
722 |
mpiSim = new mpiSimulation(info); |
1253 |
|
|
|
1254 |
mmeineke |
614 |
globalIndex = mpiSim->divideLabor(); |
1255 |
|
|
|
1256 |
|
|
// set up the local variables |
1257 |
tim |
722 |
|
1258 |
mmeineke |
614 |
mol2proc = mpiSim->getMolToProcMap(); |
1259 |
|
|
molCompType = mpiSim->getMolComponentType(); |
1260 |
tim |
722 |
|
1261 |
mmeineke |
614 |
allMol = 0; |
1262 |
|
|
localMol = 0; |
1263 |
|
|
local_atoms = 0; |
1264 |
|
|
local_bonds = 0; |
1265 |
|
|
local_bends = 0; |
1266 |
|
|
local_torsions = 0; |
1267 |
|
|
globalAtomIndex = 0; |
1268 |
|
|
|
1269 |
|
|
|
1270 |
tim |
722 |
for (i = 0; i < n_components; i++){ |
1271 |
|
|
for (j = 0; j < components_nmol[i]; j++){ |
1272 |
|
|
if (mol2proc[allMol] == worldRank){ |
1273 |
|
|
local_atoms += comp_stamps[i]->getNAtoms(); |
1274 |
|
|
local_bonds += comp_stamps[i]->getNBonds(); |
1275 |
|
|
local_bends += comp_stamps[i]->getNBends(); |
1276 |
|
|
local_torsions += comp_stamps[i]->getNTorsions(); |
1277 |
|
|
localMol++; |
1278 |
mmeineke |
614 |
} |
1279 |
tim |
722 |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ |
1280 |
mmeineke |
670 |
info[0].molMembershipArray[globalAtomIndex] = allMol; |
1281 |
mmeineke |
614 |
globalAtomIndex++; |
1282 |
|
|
} |
1283 |
|
|
|
1284 |
tim |
722 |
allMol++; |
1285 |
mmeineke |
614 |
} |
1286 |
|
|
} |
1287 |
|
|
local_SRI = local_bonds + local_bends + local_torsions; |
1288 |
tim |
722 |
|
1289 |
mmeineke |
670 |
info[0].n_atoms = mpiSim->getMyNlocal(); |
1290 |
tim |
722 |
|
1291 |
|
|
if (local_atoms != info[0].n_atoms){ |
1292 |
|
|
sprintf(painCave.errMsg, |
1293 |
gezelter |
965 |
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n" |
1294 |
|
|
"\tlocalAtom (%d) are not equal.\n", |
1295 |
tim |
722 |
info[0].n_atoms, local_atoms); |
1296 |
mmeineke |
614 |
painCave.isFatal = 1; |
1297 |
|
|
simError(); |
1298 |
|
|
} |
1299 |
|
|
|
1300 |
mmeineke |
670 |
info[0].n_bonds = local_bonds; |
1301 |
|
|
info[0].n_bends = local_bends; |
1302 |
|
|
info[0].n_torsions = local_torsions; |
1303 |
|
|
info[0].n_SRI = local_SRI; |
1304 |
|
|
info[0].n_mol = localMol; |
1305 |
mmeineke |
614 |
|
1306 |
tim |
722 |
strcpy(checkPointMsg, "Passed nlocal consistency check."); |
1307 |
mmeineke |
614 |
MPIcheckPoint(); |
1308 |
|
|
} |
1309 |
tim |
722 |
|
1310 |
mmeineke |
614 |
#endif // is_mpi |
1311 |
|
|
|
1312 |
|
|
|
1313 |
tim |
722 |
void SimSetup::makeSysArrays(void){ |
1314 |
mmeineke |
787 |
|
1315 |
|
|
#ifndef IS_MPI |
1316 |
|
|
int k, j; |
1317 |
|
|
#endif // is_mpi |
1318 |
|
|
int i, l; |
1319 |
mmeineke |
614 |
|
1320 |
mmeineke |
670 |
Atom** the_atoms; |
1321 |
|
|
Molecule* the_molecules; |
1322 |
|
|
Exclude** the_excludes; |
1323 |
mmeineke |
616 |
|
1324 |
tim |
722 |
|
1325 |
|
|
for (l = 0; l < nInfo; l++){ |
1326 |
mmeineke |
670 |
// create the atom and short range interaction arrays |
1327 |
tim |
722 |
|
1328 |
|
|
the_atoms = new Atom * [info[l].n_atoms]; |
1329 |
mmeineke |
670 |
the_molecules = new Molecule[info[l].n_mol]; |
1330 |
|
|
int molIndex; |
1331 |
mmeineke |
614 |
|
1332 |
mmeineke |
670 |
// initialize the molecule's stampID's |
1333 |
tim |
722 |
|
1334 |
mmeineke |
670 |
#ifdef IS_MPI |
1335 |
tim |
722 |
|
1336 |
|
|
|
1337 |
mmeineke |
670 |
molIndex = 0; |
1338 |
tim |
722 |
for (i = 0; i < mpiSim->getTotNmol(); i++){ |
1339 |
|
|
if (mol2proc[i] == worldRank){ |
1340 |
|
|
the_molecules[molIndex].setStampID(molCompType[i]); |
1341 |
|
|
the_molecules[molIndex].setMyIndex(molIndex); |
1342 |
|
|
the_molecules[molIndex].setGlobalIndex(i); |
1343 |
|
|
molIndex++; |
1344 |
mmeineke |
670 |
} |
1345 |
mmeineke |
614 |
} |
1346 |
tim |
722 |
|
1347 |
mmeineke |
614 |
#else // is_mpi |
1348 |
tim |
722 |
|
1349 |
mmeineke |
670 |
molIndex = 0; |
1350 |
|
|
globalAtomIndex = 0; |
1351 |
tim |
722 |
for (i = 0; i < n_components; i++){ |
1352 |
|
|
for (j = 0; j < components_nmol[i]; j++){ |
1353 |
|
|
the_molecules[molIndex].setStampID(i); |
1354 |
|
|
the_molecules[molIndex].setMyIndex(molIndex); |
1355 |
|
|
the_molecules[molIndex].setGlobalIndex(molIndex); |
1356 |
|
|
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ |
1357 |
|
|
info[l].molMembershipArray[globalAtomIndex] = molIndex; |
1358 |
|
|
globalAtomIndex++; |
1359 |
|
|
} |
1360 |
|
|
molIndex++; |
1361 |
mmeineke |
614 |
} |
1362 |
|
|
} |
1363 |
tim |
722 |
|
1364 |
|
|
|
1365 |
mmeineke |
614 |
#endif // is_mpi |
1366 |
|
|
|
1367 |
|
|
|
1368 |
tim |
722 |
if (info[l].n_SRI){ |
1369 |
mmeineke |
670 |
Exclude::createArray(info[l].n_SRI); |
1370 |
tim |
722 |
the_excludes = new Exclude * [info[l].n_SRI]; |
1371 |
|
|
for (int ex = 0; ex < info[l].n_SRI; ex++){ |
1372 |
|
|
the_excludes[ex] = new Exclude(ex); |
1373 |
mmeineke |
670 |
} |
1374 |
|
|
info[l].globalExcludes = new int; |
1375 |
|
|
info[l].n_exclude = info[l].n_SRI; |
1376 |
|
|
} |
1377 |
|
|
else{ |
1378 |
tim |
722 |
Exclude::createArray(1); |
1379 |
|
|
the_excludes = new Exclude * ; |
1380 |
mmeineke |
670 |
the_excludes[0] = new Exclude(0); |
1381 |
tim |
722 |
the_excludes[0]->setPair(0, 0); |
1382 |
mmeineke |
670 |
info[l].globalExcludes = new int; |
1383 |
|
|
info[l].globalExcludes[0] = 0; |
1384 |
|
|
info[l].n_exclude = 0; |
1385 |
|
|
} |
1386 |
mmeineke |
614 |
|
1387 |
mmeineke |
670 |
// set the arrays into the SimInfo object |
1388 |
mmeineke |
614 |
|
1389 |
mmeineke |
670 |
info[l].atoms = the_atoms; |
1390 |
|
|
info[l].molecules = the_molecules; |
1391 |
|
|
info[l].nGlobalExcludes = 0; |
1392 |
|
|
info[l].excludes = the_excludes; |
1393 |
mmeineke |
614 |
|
1394 |
tim |
722 |
the_ff->setSimInfo(info); |
1395 |
mmeineke |
670 |
} |
1396 |
mmeineke |
614 |
} |
1397 |
mmeineke |
616 |
|
1398 |
tim |
722 |
void SimSetup::makeIntegrator(void){ |
1399 |
mmeineke |
670 |
int k; |
1400 |
|
|
|
1401 |
mmeineke |
782 |
NVE<RealIntegrator>* myNVE = NULL; |
1402 |
tim |
722 |
NVT<RealIntegrator>* myNVT = NULL; |
1403 |
mmeineke |
778 |
NPTi<NPT<RealIntegrator> >* myNPTi = NULL; |
1404 |
mmeineke |
780 |
NPTf<NPT<RealIntegrator> >* myNPTf = NULL; |
1405 |
mmeineke |
812 |
NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL; |
1406 |
tim |
733 |
|
1407 |
tim |
722 |
for (k = 0; k < nInfo; k++){ |
1408 |
|
|
switch (ensembleCase){ |
1409 |
|
|
case NVE_ENS: |
1410 |
|
|
if (globals->haveZconstraints()){ |
1411 |
|
|
setupZConstraint(info[k]); |
1412 |
mmeineke |
782 |
myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff); |
1413 |
tim |
722 |
} |
1414 |
mmeineke |
782 |
else{ |
1415 |
|
|
myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff); |
1416 |
|
|
} |
1417 |
|
|
|
1418 |
|
|
info->the_integrator = myNVE; |
1419 |
tim |
722 |
break; |
1420 |
tim |
676 |
|
1421 |
tim |
722 |
case NVT_ENS: |
1422 |
|
|
if (globals->haveZconstraints()){ |
1423 |
|
|
setupZConstraint(info[k]); |
1424 |
|
|
myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff); |
1425 |
|
|
} |
1426 |
|
|
else |
1427 |
|
|
myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff); |
1428 |
|
|
|
1429 |
tim |
701 |
myNVT->setTargetTemp(globals->getTargetTemp()); |
1430 |
tim |
722 |
|
1431 |
|
|
if (globals->haveTauThermostat()) |
1432 |
tim |
701 |
myNVT->setTauThermostat(globals->getTauThermostat()); |
1433 |
tim |
722 |
else{ |
1434 |
|
|
sprintf(painCave.errMsg, |
1435 |
|
|
"SimSetup error: If you use the NVT\n" |
1436 |
gezelter |
965 |
"\tensemble, you must set tauThermostat.\n"); |
1437 |
tim |
701 |
painCave.isFatal = 1; |
1438 |
|
|
simError(); |
1439 |
|
|
} |
1440 |
mmeineke |
782 |
|
1441 |
|
|
info->the_integrator = myNVT; |
1442 |
tim |
701 |
break; |
1443 |
tim |
676 |
|
1444 |
tim |
722 |
case NPTi_ENS: |
1445 |
|
|
if (globals->haveZconstraints()){ |
1446 |
|
|
setupZConstraint(info[k]); |
1447 |
mmeineke |
778 |
myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1448 |
tim |
722 |
} |
1449 |
|
|
else |
1450 |
mmeineke |
778 |
myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff); |
1451 |
tim |
722 |
|
1452 |
|
|
myNPTi->setTargetTemp(globals->getTargetTemp()); |
1453 |
|
|
|
1454 |
|
|
if (globals->haveTargetPressure()) |
1455 |
|
|
myNPTi->setTargetPressure(globals->getTargetPressure()); |
1456 |
|
|
else{ |
1457 |
|
|
sprintf(painCave.errMsg, |
1458 |
|
|
"SimSetup error: If you use a constant pressure\n" |
1459 |
gezelter |
965 |
"\tensemble, you must set targetPressure in the BASS file.\n"); |
1460 |
tim |
722 |
painCave.isFatal = 1; |
1461 |
|
|
simError(); |
1462 |
|
|
} |
1463 |
|
|
|
1464 |
|
|
if (globals->haveTauThermostat()) |
1465 |
|
|
myNPTi->setTauThermostat(globals->getTauThermostat()); |
1466 |
|
|
else{ |
1467 |
|
|
sprintf(painCave.errMsg, |
1468 |
|
|
"SimSetup error: If you use an NPT\n" |
1469 |
gezelter |
965 |
"\tensemble, you must set tauThermostat.\n"); |
1470 |
tim |
722 |
painCave.isFatal = 1; |
1471 |
|
|
simError(); |
1472 |
|
|
} |
1473 |
|
|
|
1474 |
|
|
if (globals->haveTauBarostat()) |
1475 |
|
|
myNPTi->setTauBarostat(globals->getTauBarostat()); |
1476 |
|
|
else{ |
1477 |
|
|
sprintf(painCave.errMsg, |
1478 |
tim |
701 |
"SimSetup error: If you use an NPT\n" |
1479 |
gezelter |
965 |
"\tensemble, you must set tauBarostat.\n"); |
1480 |
tim |
722 |
painCave.isFatal = 1; |
1481 |
|
|
simError(); |
1482 |
|
|
} |
1483 |
mmeineke |
782 |
|
1484 |
|
|
info->the_integrator = myNPTi; |
1485 |
tim |
722 |
break; |
1486 |
tim |
676 |
|
1487 |
tim |
722 |
case NPTf_ENS: |
1488 |
|
|
if (globals->haveZconstraints()){ |
1489 |
|
|
setupZConstraint(info[k]); |
1490 |
mmeineke |
780 |
myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1491 |
tim |
722 |
} |
1492 |
|
|
else |
1493 |
mmeineke |
780 |
myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1494 |
tim |
722 |
|
1495 |
|
|
myNPTf->setTargetTemp(globals->getTargetTemp()); |
1496 |
|
|
|
1497 |
|
|
if (globals->haveTargetPressure()) |
1498 |
|
|
myNPTf->setTargetPressure(globals->getTargetPressure()); |
1499 |
|
|
else{ |
1500 |
|
|
sprintf(painCave.errMsg, |
1501 |
tim |
701 |
"SimSetup error: If you use a constant pressure\n" |
1502 |
gezelter |
965 |
"\tensemble, you must set targetPressure in the BASS file.\n"); |
1503 |
tim |
722 |
painCave.isFatal = 1; |
1504 |
|
|
simError(); |
1505 |
|
|
} |
1506 |
|
|
|
1507 |
|
|
if (globals->haveTauThermostat()) |
1508 |
|
|
myNPTf->setTauThermostat(globals->getTauThermostat()); |
1509 |
mmeineke |
843 |
|
1510 |
tim |
722 |
else{ |
1511 |
|
|
sprintf(painCave.errMsg, |
1512 |
tim |
701 |
"SimSetup error: If you use an NPT\n" |
1513 |
gezelter |
965 |
"\tensemble, you must set tauThermostat.\n"); |
1514 |
tim |
722 |
painCave.isFatal = 1; |
1515 |
|
|
simError(); |
1516 |
|
|
} |
1517 |
|
|
|
1518 |
|
|
if (globals->haveTauBarostat()) |
1519 |
|
|
myNPTf->setTauBarostat(globals->getTauBarostat()); |
1520 |
mmeineke |
843 |
|
1521 |
tim |
722 |
else{ |
1522 |
|
|
sprintf(painCave.errMsg, |
1523 |
|
|
"SimSetup error: If you use an NPT\n" |
1524 |
gezelter |
965 |
"\tensemble, you must set tauBarostat.\n"); |
1525 |
tim |
722 |
painCave.isFatal = 1; |
1526 |
|
|
simError(); |
1527 |
|
|
} |
1528 |
mmeineke |
782 |
|
1529 |
|
|
info->the_integrator = myNPTf; |
1530 |
tim |
722 |
break; |
1531 |
tim |
676 |
|
1532 |
mmeineke |
812 |
case NPTxyz_ENS: |
1533 |
|
|
if (globals->haveZconstraints()){ |
1534 |
|
|
setupZConstraint(info[k]); |
1535 |
|
|
myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1536 |
|
|
} |
1537 |
|
|
else |
1538 |
|
|
myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1539 |
|
|
|
1540 |
|
|
myNPTxyz->setTargetTemp(globals->getTargetTemp()); |
1541 |
|
|
|
1542 |
|
|
if (globals->haveTargetPressure()) |
1543 |
|
|
myNPTxyz->setTargetPressure(globals->getTargetPressure()); |
1544 |
|
|
else{ |
1545 |
|
|
sprintf(painCave.errMsg, |
1546 |
|
|
"SimSetup error: If you use a constant pressure\n" |
1547 |
gezelter |
965 |
"\tensemble, you must set targetPressure in the BASS file.\n"); |
1548 |
mmeineke |
812 |
painCave.isFatal = 1; |
1549 |
|
|
simError(); |
1550 |
|
|
} |
1551 |
|
|
|
1552 |
|
|
if (globals->haveTauThermostat()) |
1553 |
|
|
myNPTxyz->setTauThermostat(globals->getTauThermostat()); |
1554 |
|
|
else{ |
1555 |
|
|
sprintf(painCave.errMsg, |
1556 |
|
|
"SimSetup error: If you use an NPT\n" |
1557 |
gezelter |
965 |
"\tensemble, you must set tauThermostat.\n"); |
1558 |
mmeineke |
812 |
painCave.isFatal = 1; |
1559 |
|
|
simError(); |
1560 |
|
|
} |
1561 |
|
|
|
1562 |
|
|
if (globals->haveTauBarostat()) |
1563 |
|
|
myNPTxyz->setTauBarostat(globals->getTauBarostat()); |
1564 |
|
|
else{ |
1565 |
|
|
sprintf(painCave.errMsg, |
1566 |
|
|
"SimSetup error: If you use an NPT\n" |
1567 |
gezelter |
965 |
"\tensemble, you must set tauBarostat.\n"); |
1568 |
mmeineke |
812 |
painCave.isFatal = 1; |
1569 |
|
|
simError(); |
1570 |
|
|
} |
1571 |
|
|
|
1572 |
|
|
info->the_integrator = myNPTxyz; |
1573 |
|
|
break; |
1574 |
|
|
|
1575 |
tim |
722 |
default: |
1576 |
|
|
sprintf(painCave.errMsg, |
1577 |
|
|
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1578 |
tim |
701 |
painCave.isFatal = 1; |
1579 |
|
|
simError(); |
1580 |
tim |
660 |
} |
1581 |
mmeineke |
616 |
} |
1582 |
|
|
} |
1583 |
|
|
|
1584 |
tim |
722 |
void SimSetup::initFortran(void){ |
1585 |
|
|
info[0].refreshSim(); |
1586 |
mmeineke |
616 |
|
1587 |
tim |
722 |
if (!strcmp(info[0].mixingRule, "standard")){ |
1588 |
|
|
the_ff->initForceField(LB_MIXING_RULE); |
1589 |
mmeineke |
616 |
} |
1590 |
tim |
722 |
else if (!strcmp(info[0].mixingRule, "explicit")){ |
1591 |
|
|
the_ff->initForceField(EXPLICIT_MIXING_RULE); |
1592 |
mmeineke |
616 |
} |
1593 |
|
|
else{ |
1594 |
tim |
722 |
sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1595 |
|
|
info[0].mixingRule); |
1596 |
mmeineke |
616 |
painCave.isFatal = 1; |
1597 |
|
|
simError(); |
1598 |
|
|
} |
1599 |
|
|
|
1600 |
|
|
|
1601 |
|
|
#ifdef IS_MPI |
1602 |
tim |
722 |
strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran."); |
1603 |
mmeineke |
616 |
MPIcheckPoint(); |
1604 |
|
|
#endif // is_mpi |
1605 |
|
|
} |
1606 |
tim |
660 |
|
1607 |
tim |
722 |
void SimSetup::setupZConstraint(SimInfo& theInfo){ |
1608 |
tim |
701 |
int nZConstraints; |
1609 |
|
|
ZconStamp** zconStamp; |
1610 |
tim |
682 |
|
1611 |
tim |
722 |
if (globals->haveZconstraintTime()){ |
1612 |
tim |
701 |
//add sample time of z-constraint into SimInfo's property list |
1613 |
|
|
DoubleData* zconsTimeProp = new DoubleData(); |
1614 |
|
|
zconsTimeProp->setID(ZCONSTIME_ID); |
1615 |
|
|
zconsTimeProp->setData(globals->getZconsTime()); |
1616 |
|
|
theInfo.addProperty(zconsTimeProp); |
1617 |
|
|
} |
1618 |
|
|
else{ |
1619 |
tim |
722 |
sprintf(painCave.errMsg, |
1620 |
gezelter |
965 |
"ZConstraint error: If you use a ZConstraint,\n" |
1621 |
|
|
"\tyou must set zconsTime.\n"); |
1622 |
tim |
701 |
painCave.isFatal = 1; |
1623 |
tim |
722 |
simError(); |
1624 |
tim |
701 |
} |
1625 |
tim |
682 |
|
1626 |
tim |
701 |
//push zconsTol into siminfo, if user does not specify |
1627 |
|
|
//value for zconsTol, a default value will be used |
1628 |
|
|
DoubleData* zconsTol = new DoubleData(); |
1629 |
|
|
zconsTol->setID(ZCONSTOL_ID); |
1630 |
tim |
722 |
if (globals->haveZconsTol()){ |
1631 |
tim |
701 |
zconsTol->setData(globals->getZconsTol()); |
1632 |
|
|
} |
1633 |
|
|
else{ |
1634 |
tim |
722 |
double defaultZConsTol = 0.01; |
1635 |
|
|
sprintf(painCave.errMsg, |
1636 |
gezelter |
965 |
"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n" |
1637 |
|
|
"\tOOPSE will use a default value of %f.\n" |
1638 |
|
|
"\tTo set the tolerance, use the zconsTol variable.\n", |
1639 |
tim |
722 |
defaultZConsTol); |
1640 |
tim |
701 |
painCave.isFatal = 0; |
1641 |
|
|
simError(); |
1642 |
tim |
699 |
|
1643 |
tim |
701 |
zconsTol->setData(defaultZConsTol); |
1644 |
|
|
} |
1645 |
|
|
theInfo.addProperty(zconsTol); |
1646 |
tim |
699 |
|
1647 |
tim |
738 |
//set Force Subtraction Policy |
1648 |
tim |
722 |
StringData* zconsForcePolicy = new StringData(); |
1649 |
tim |
701 |
zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID); |
1650 |
tim |
722 |
|
1651 |
|
|
if (globals->haveZconsForcePolicy()){ |
1652 |
tim |
701 |
zconsForcePolicy->setData(globals->getZconsForcePolicy()); |
1653 |
tim |
722 |
} |
1654 |
tim |
701 |
else{ |
1655 |
tim |
722 |
sprintf(painCave.errMsg, |
1656 |
gezelter |
965 |
"ZConstraint Warning: No force subtraction policy was set.\n" |
1657 |
|
|
"\tOOPSE will use PolicyByMass.\n" |
1658 |
|
|
"\tTo set the policy, use the zconsForcePolicy variable.\n"); |
1659 |
tim |
722 |
painCave.isFatal = 0; |
1660 |
|
|
simError(); |
1661 |
tim |
736 |
zconsForcePolicy->setData("BYMASS"); |
1662 |
tim |
701 |
} |
1663 |
tim |
722 |
|
1664 |
|
|
theInfo.addProperty(zconsForcePolicy); |
1665 |
|
|
|
1666 |
tim |
701 |
//Determine the name of ouput file and add it into SimInfo's property list |
1667 |
|
|
//Be careful, do not use inFileName, since it is a pointer which |
1668 |
|
|
//point to a string at master node, and slave nodes do not contain that string |
1669 |
tim |
722 |
|
1670 |
tim |
701 |
string zconsOutput(theInfo.finalName); |
1671 |
tim |
722 |
|
1672 |
tim |
701 |
zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1673 |
tim |
722 |
|
1674 |
tim |
701 |
StringData* zconsFilename = new StringData(); |
1675 |
|
|
zconsFilename->setID(ZCONSFILENAME_ID); |
1676 |
|
|
zconsFilename->setData(zconsOutput); |
1677 |
tim |
722 |
|
1678 |
tim |
701 |
theInfo.addProperty(zconsFilename); |
1679 |
tim |
722 |
|
1680 |
tim |
701 |
//setup index, pos and other parameters of z-constraint molecules |
1681 |
|
|
nZConstraints = globals->getNzConstraints(); |
1682 |
|
|
theInfo.nZconstraints = nZConstraints; |
1683 |
|
|
|
1684 |
|
|
zconStamp = globals->getZconStamp(); |
1685 |
|
|
ZConsParaItem tempParaItem; |
1686 |
|
|
|
1687 |
|
|
ZConsParaData* zconsParaData = new ZConsParaData(); |
1688 |
|
|
zconsParaData->setID(ZCONSPARADATA_ID); |
1689 |
tim |
722 |
|
1690 |
|
|
for (int i = 0; i < nZConstraints; i++){ |
1691 |
tim |
699 |
tempParaItem.havingZPos = zconStamp[i]->haveZpos(); |
1692 |
|
|
tempParaItem.zPos = zconStamp[i]->getZpos(); |
1693 |
|
|
tempParaItem.zconsIndex = zconStamp[i]->getMolIndex(); |
1694 |
|
|
tempParaItem.kRatio = zconStamp[i]->getKratio(); |
1695 |
|
|
|
1696 |
|
|
zconsParaData->addItem(tempParaItem); |
1697 |
tim |
701 |
} |
1698 |
tim |
699 |
|
1699 |
tim |
736 |
//check the uniqueness of index |
1700 |
|
|
if(!zconsParaData->isIndexUnique()){ |
1701 |
|
|
sprintf(painCave.errMsg, |
1702 |
gezelter |
965 |
"ZConstraint Error: molIndex is not unique!\n"); |
1703 |
tim |
736 |
painCave.isFatal = 1; |
1704 |
|
|
simError(); |
1705 |
|
|
} |
1706 |
|
|
|
1707 |
tim |
701 |
//sort the parameters by index of molecules |
1708 |
|
|
zconsParaData->sortByIndex(); |
1709 |
tim |
736 |
|
1710 |
tim |
701 |
//push data into siminfo, therefore, we can retrieve later |
1711 |
|
|
theInfo.addProperty(zconsParaData); |
1712 |
tim |
660 |
} |
1713 |
tim |
1031 |
|
1714 |
|
|
void SimSetup::makeMinimizer(){ |
1715 |
tim |
1032 |
|
1716 |
tim |
1031 |
OOPSEMinimizerBase* myOOPSEMinimizerBase; |
1717 |
|
|
ObjFunctor1 * objFunc; |
1718 |
|
|
OutputFunctor* outputFunc; |
1719 |
|
|
ConcreteNLModel1* nlp; |
1720 |
|
|
MinimizerParameterSet* param; |
1721 |
|
|
ConjugateMinimizerBase* minimizer; |
1722 |
|
|
int dim; |
1723 |
|
|
|
1724 |
|
|
for (int i = 0; i < nInfo; i++){ |
1725 |
|
|
//creat |
1726 |
|
|
myOOPSEMinimizerBase = new OOPSEMinimizerBase(&(info[i]), the_ff); |
1727 |
|
|
|
1728 |
tim |
1035 |
info[i].the_integrator = myOOPSEMinimizerBase; |
1729 |
tim |
1031 |
//creat the object functor; |
1730 |
|
|
objFunc = (ObjFunctor1*) new ClassMemObjFunctor1<OOPSEMinimizerBase> |
1731 |
|
|
(myOOPSEMinimizerBase, &OOPSEMinimizerBase::calcGradient); |
1732 |
|
|
|
1733 |
|
|
//creat output functor; |
1734 |
|
|
outputFunc = new ClassMemOutputFunctor<OOPSEMinimizerBase> |
1735 |
|
|
(myOOPSEMinimizerBase, &OOPSEMinimizerBase::output); |
1736 |
|
|
|
1737 |
|
|
//creat nonlinear model |
1738 |
|
|
dim = myOOPSEMinimizerBase->getDim(); |
1739 |
|
|
nlp = new ConcreteNLModel1(dim, objFunc); |
1740 |
|
|
|
1741 |
tim |
1035 |
nlp->setX(myOOPSEMinimizerBase->getCoor()); |
1742 |
|
|
|
1743 |
tim |
1031 |
//prepare parameter set for minimizer |
1744 |
|
|
param = new MinimizerParameterSet(); |
1745 |
|
|
param->setDefaultParameter(); |
1746 |
|
|
|
1747 |
|
|
if (globals->haveMinimizer()){ |
1748 |
|
|
param->setFTol(globals->getMinFTol()); |
1749 |
|
|
} |
1750 |
|
|
|
1751 |
|
|
if (globals->haveMinGTol()){ |
1752 |
|
|
param->setGTol(globals->getMinGTol()); |
1753 |
|
|
} |
1754 |
|
|
|
1755 |
|
|
if (globals->haveMinMaxIter()){ |
1756 |
|
|
param->setMaxIteration(globals->getMinMaxIter()); |
1757 |
|
|
} |
1758 |
|
|
|
1759 |
|
|
if (globals->haveMinWriteFrq()){ |
1760 |
|
|
param->setMaxIteration(globals->getMinMaxIter()); |
1761 |
|
|
} |
1762 |
|
|
|
1763 |
|
|
if (globals->haveMinWriteFrq()){ |
1764 |
|
|
param->setWriteFrq(globals->getMinWriteFrq()); |
1765 |
|
|
} |
1766 |
|
|
|
1767 |
|
|
if (globals->haveMinResetFrq()){ |
1768 |
|
|
param->setResetFrq(globals->getMinResetFrq()); |
1769 |
|
|
} |
1770 |
|
|
|
1771 |
|
|
if (globals->haveMinLSMaxIter()){ |
1772 |
|
|
param->setLineSearchMaxIteration(globals->getMinLSMaxIter()); |
1773 |
|
|
} |
1774 |
|
|
|
1775 |
|
|
if (globals->haveMinLSTol()){ |
1776 |
|
|
param->setLineSearchTol(globals->getMinLSTol()); |
1777 |
|
|
} |
1778 |
|
|
|
1779 |
|
|
//creat the minimizer |
1780 |
|
|
minimizer = new PRCGMinimizer(nlp, param); |
1781 |
|
|
minimizer->setLineSearchStrategy(nlp, GoldenSection); |
1782 |
|
|
minimizer->setOutputFunctor(outputFunc); |
1783 |
|
|
|
1784 |
|
|
//store the minimizer into simInfo |
1785 |
|
|
info[i].the_minimizer = minimizer; |
1786 |
|
|
info[i].has_minimizer = true; |
1787 |
|
|
} |
1788 |
tim |
1032 |
|
1789 |
tim |
1031 |
} |