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tim |
658 |
#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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#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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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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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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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 |
377 |
SimSetup::SimSetup(){ |
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mmeineke |
823 |
|
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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 |
377 |
#ifdef IS_MPI |
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tim |
722 |
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 |
823 |
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 |
722 |
if (worldRank == 0){ |
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mmeineke |
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#endif // is_mpi |
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tim |
722 |
|
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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 |
377 |
#ifdef IS_MPI |
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mpiEventInit(); |
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#endif |
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tim |
722 |
yacc_BASS(fileName); |
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mmeineke |
377 |
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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 |
689 |
|
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mmeineke |
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gatherInfo(); |
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mmeineke |
377 |
|
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mmeineke |
614 |
// 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 |
614 |
// initialize the system coordinates |
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mmeineke |
377 |
|
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mmeineke |
823 |
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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mmeineke |
555 |
// make the integrator |
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tim |
722 |
|
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mmeineke |
616 |
makeIntegrator(); |
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tim |
722 |
|
151 |
chuckv |
432 |
#ifdef IS_MPI |
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mpiSim->mpiRefresh(); |
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#endif |
154 |
mmeineke |
377 |
|
155 |
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 |
|
161 |
tim |
722 |
void SimSetup::makeMolecules(void){ |
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mmeineke |
787 |
int k; |
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mmeineke |
412 |
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; |
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mmeineke |
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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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177 |
mmeineke |
407 |
//init the forceField paramters |
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the_ff->readParams(); |
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tim |
722 |
|
182 |
mmeineke |
427 |
// init the atoms |
183 |
mmeineke |
407 |
|
184 |
gezelter |
983 |
double phi, theta, psi; |
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double sux, suy, suz; |
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double Axx, Axy, Axz, Ayx, Ayy, Ayz, Azx, Azy, Azz; |
187 |
mmeineke |
427 |
double ux, uy, uz, u, uSqr; |
188 |
mmeineke |
407 |
|
189 |
tim |
722 |
for (k = 0; k < nInfo; k++){ |
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the_ff->setSimInfo(&(info[k])); |
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192 |
mmeineke |
670 |
atomOffset = 0; |
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excludeOffset = 0; |
194 |
tim |
722 |
for (i = 0; i < info[k].n_mol; i++){ |
195 |
mmeineke |
670 |
stampID = info[k].molecules[i].getStampID(); |
196 |
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(); |
200 |
mmeineke |
670 |
molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
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molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
202 |
tim |
722 |
|
203 |
mmeineke |
670 |
molInfo.myAtoms = &(info[k].atoms[atomOffset]); |
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molInfo.myExcludes = &(info[k].excludes[excludeOffset]); |
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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]; |
208 |
mmeineke |
407 |
|
209 |
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]; |
212 |
tim |
722 |
|
213 |
mmeineke |
670 |
// make the Atoms |
214 |
tim |
722 |
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for (j = 0; j < molInfo.nAtoms; j++){ |
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currentAtom = comp_stamps[stampID]->getAtom(j); |
217 |
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if (currentAtom->haveOrientation()){ |
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dAtom = new DirectionalAtom((j + atomOffset), |
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info[k].getConfiguration()); |
220 |
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info[k].n_oriented++; |
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molInfo.myAtoms[j] = dAtom; |
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223 |
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 |
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// unit vector was originally along the z axis below. |
226 |
tim |
722 |
|
227 |
gezelter |
983 |
phi = currentAtom->getEulerPhi(); |
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theta = currentAtom->getEulerTheta(); |
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psi = currentAtom->getEulerPsi(); |
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231 |
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Axx = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi)); |
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Axy = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi)); |
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Axz = sin(theta) * sin(psi); |
234 |
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235 |
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Ayx = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi)); |
236 |
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Ayy = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi)); |
237 |
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Ayz = sin(theta) * cos(psi); |
238 |
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239 |
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Azx = sin(phi) * sin(theta); |
240 |
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Azy = -cos(phi) * sin(theta); |
241 |
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Azz = cos(theta); |
242 |
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243 |
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sux = 0.0; |
244 |
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suy = 0.0; |
245 |
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suz = 1.0; |
246 |
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247 |
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ux = (Axx * sux) + (Ayx * suy) + (Azx * suz); |
248 |
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uy = (Axy * sux) + (Ayy * suy) + (Azy * suz); |
249 |
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uz = (Axz * sux) + (Ayz * suy) + (Azz * suz); |
250 |
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251 |
tim |
722 |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
252 |
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253 |
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u = sqrt(uSqr); |
254 |
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ux = ux / u; |
255 |
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uy = uy / u; |
256 |
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uz = uz / u; |
257 |
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258 |
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dAtom->setSUx(ux); |
259 |
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dAtom->setSUy(uy); |
260 |
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dAtom->setSUz(uz); |
261 |
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} |
262 |
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else{ |
263 |
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molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset), |
264 |
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info[k].getConfiguration()); |
265 |
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} |
266 |
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molInfo.myAtoms[j]->setType(currentAtom->getType()); |
267 |
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268 |
mmeineke |
407 |
#ifdef IS_MPI |
269 |
tim |
722 |
|
270 |
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molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]); |
271 |
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272 |
mmeineke |
407 |
#endif // is_mpi |
273 |
mmeineke |
670 |
} |
274 |
tim |
722 |
|
275 |
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// make the bonds |
276 |
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for (j = 0; j < molInfo.nBonds; j++){ |
277 |
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currentBond = comp_stamps[stampID]->getBond(j); |
278 |
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theBonds[j].a = currentBond->getA() + atomOffset; |
279 |
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theBonds[j].b = currentBond->getB() + atomOffset; |
280 |
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281 |
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exI = theBonds[j].a; |
282 |
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exJ = theBonds[j].b; |
283 |
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284 |
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// exclude_I must always be the smaller of the pair |
285 |
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if (exI > exJ){ |
286 |
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tempEx = exI; |
287 |
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exI = exJ; |
288 |
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exJ = tempEx; |
289 |
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} |
290 |
mmeineke |
670 |
#ifdef IS_MPI |
291 |
tim |
722 |
tempEx = exI; |
292 |
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exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
293 |
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tempEx = exJ; |
294 |
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exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
295 |
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296 |
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info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
297 |
mmeineke |
412 |
#else // isn't MPI |
298 |
tim |
722 |
|
299 |
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info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
300 |
mmeineke |
412 |
#endif //is_mpi |
301 |
mmeineke |
670 |
} |
302 |
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excludeOffset += molInfo.nBonds; |
303 |
tim |
722 |
|
304 |
mmeineke |
670 |
//make the bends |
305 |
tim |
722 |
for (j = 0; j < molInfo.nBends; j++){ |
306 |
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currentBend = comp_stamps[stampID]->getBend(j); |
307 |
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theBends[j].a = currentBend->getA() + atomOffset; |
308 |
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theBends[j].b = currentBend->getB() + atomOffset; |
309 |
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theBends[j].c = currentBend->getC() + atomOffset; |
310 |
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311 |
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if (currentBend->haveExtras()){ |
312 |
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extras = currentBend->getExtras(); |
313 |
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current_extra = extras; |
314 |
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315 |
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while (current_extra != NULL){ |
316 |
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if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){ |
317 |
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switch (current_extra->getType()){ |
318 |
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case 0: |
319 |
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theBends[j].ghost = current_extra->getInt() + atomOffset; |
320 |
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theBends[j].isGhost = 1; |
321 |
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break; |
322 |
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323 |
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case 1: |
324 |
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theBends[j].ghost = (int) current_extra->getDouble() + |
325 |
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atomOffset; |
326 |
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theBends[j].isGhost = 1; |
327 |
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break; |
328 |
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329 |
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default: |
330 |
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sprintf(painCave.errMsg, |
331 |
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"SimSetup Error: ghostVectorSource was neither a " |
332 |
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"double nor an int.\n" |
333 |
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"-->Bend[%d] in %s\n", |
334 |
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j, comp_stamps[stampID]->getID()); |
335 |
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painCave.isFatal = 1; |
336 |
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simError(); |
337 |
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} |
338 |
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} |
339 |
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else{ |
340 |
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sprintf(painCave.errMsg, |
341 |
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"SimSetup Error: unhandled bend assignment:\n" |
342 |
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" -->%s in Bend[%d] in %s\n", |
343 |
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current_extra->getlhs(), j, comp_stamps[stampID]->getID()); |
344 |
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painCave.isFatal = 1; |
345 |
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simError(); |
346 |
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} |
347 |
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348 |
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current_extra = current_extra->getNext(); |
349 |
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} |
350 |
tim |
701 |
} |
351 |
tim |
722 |
|
352 |
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if (!theBends[j].isGhost){ |
353 |
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exI = theBends[j].a; |
354 |
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exJ = theBends[j].c; |
355 |
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} |
356 |
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else{ |
357 |
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exI = theBends[j].a; |
358 |
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exJ = theBends[j].b; |
359 |
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} |
360 |
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361 |
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// exclude_I must always be the smaller of the pair |
362 |
|
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if (exI > exJ){ |
363 |
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tempEx = exI; |
364 |
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exI = exJ; |
365 |
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exJ = tempEx; |
366 |
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} |
367 |
mmeineke |
670 |
#ifdef IS_MPI |
368 |
tim |
722 |
tempEx = exI; |
369 |
|
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exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
370 |
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tempEx = exJ; |
371 |
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exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
372 |
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373 |
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info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
374 |
mmeineke |
670 |
#else // isn't MPI |
375 |
tim |
722 |
info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
376 |
mmeineke |
670 |
#endif //is_mpi |
377 |
mmeineke |
412 |
} |
378 |
mmeineke |
670 |
excludeOffset += molInfo.nBends; |
379 |
tim |
722 |
|
380 |
|
|
for (j = 0; j < molInfo.nTorsions; j++){ |
381 |
|
|
currentTorsion = comp_stamps[stampID]->getTorsion(j); |
382 |
|
|
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
383 |
|
|
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
384 |
|
|
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
385 |
|
|
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
386 |
|
|
|
387 |
|
|
exI = theTorsions[j].a; |
388 |
|
|
exJ = theTorsions[j].d; |
389 |
|
|
|
390 |
|
|
// exclude_I must always be the smaller of the pair |
391 |
|
|
if (exI > exJ){ |
392 |
|
|
tempEx = exI; |
393 |
|
|
exI = exJ; |
394 |
|
|
exJ = tempEx; |
395 |
|
|
} |
396 |
mmeineke |
670 |
#ifdef IS_MPI |
397 |
tim |
722 |
tempEx = exI; |
398 |
|
|
exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
399 |
|
|
tempEx = exJ; |
400 |
|
|
exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
401 |
|
|
|
402 |
|
|
info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
403 |
mmeineke |
407 |
#else // isn't MPI |
404 |
tim |
722 |
info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
405 |
mmeineke |
412 |
#endif //is_mpi |
406 |
mmeineke |
670 |
} |
407 |
|
|
excludeOffset += molInfo.nTorsions; |
408 |
tim |
722 |
|
409 |
|
|
|
410 |
mmeineke |
670 |
// send the arrays off to the forceField for init. |
411 |
mmeineke |
407 |
|
412 |
tim |
722 |
the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms); |
413 |
|
|
the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds); |
414 |
|
|
the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends); |
415 |
|
|
the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions, |
416 |
|
|
theTorsions); |
417 |
|
|
|
418 |
|
|
|
419 |
|
|
info[k].molecules[i].initialize(molInfo); |
420 |
|
|
|
421 |
|
|
|
422 |
mmeineke |
670 |
atomOffset += molInfo.nAtoms; |
423 |
|
|
delete[] theBonds; |
424 |
|
|
delete[] theBends; |
425 |
|
|
delete[] theTorsions; |
426 |
mmeineke |
412 |
} |
427 |
mmeineke |
414 |
} |
428 |
tim |
722 |
|
429 |
chuckv |
434 |
#ifdef IS_MPI |
430 |
tim |
722 |
sprintf(checkPointMsg, "all molecules initialized succesfully"); |
431 |
chuckv |
434 |
MPIcheckPoint(); |
432 |
|
|
#endif // is_mpi |
433 |
tim |
722 |
|
434 |
mmeineke |
670 |
// clean up the forcefield |
435 |
chuckv |
434 |
|
436 |
mmeineke |
420 |
the_ff->calcRcut(); |
437 |
mmeineke |
414 |
the_ff->cleanMe(); |
438 |
|
|
} |
439 |
mmeineke |
407 |
|
440 |
tim |
722 |
void SimSetup::initFromBass(void){ |
441 |
mmeineke |
377 |
int i, j, k; |
442 |
|
|
int n_cells; |
443 |
|
|
double cellx, celly, cellz; |
444 |
|
|
double temp1, temp2, temp3; |
445 |
|
|
int n_per_extra; |
446 |
|
|
int n_extra; |
447 |
|
|
int have_extra, done; |
448 |
|
|
|
449 |
mmeineke |
670 |
double vel[3]; |
450 |
|
|
vel[0] = 0.0; |
451 |
|
|
vel[1] = 0.0; |
452 |
|
|
vel[2] = 0.0; |
453 |
|
|
|
454 |
tim |
722 |
temp1 = (double) tot_nmol / 4.0; |
455 |
|
|
temp2 = pow(temp1, (1.0 / 3.0)); |
456 |
|
|
temp3 = ceil(temp2); |
457 |
mmeineke |
377 |
|
458 |
tim |
722 |
have_extra = 0; |
459 |
|
|
if (temp2 < temp3){ |
460 |
|
|
// we have a non-complete lattice |
461 |
|
|
have_extra = 1; |
462 |
mmeineke |
377 |
|
463 |
tim |
722 |
n_cells = (int) temp3 - 1; |
464 |
mmeineke |
670 |
cellx = info[0].boxL[0] / temp3; |
465 |
|
|
celly = info[0].boxL[1] / temp3; |
466 |
|
|
cellz = info[0].boxL[2] / temp3; |
467 |
tim |
722 |
n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells); |
468 |
|
|
temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0)); |
469 |
|
|
n_per_extra = (int) ceil(temp1); |
470 |
mmeineke |
377 |
|
471 |
tim |
722 |
if (n_per_extra > 4){ |
472 |
|
|
sprintf(painCave.errMsg, |
473 |
|
|
"SimSetup error. There has been an error in constructing" |
474 |
|
|
" the non-complete lattice.\n"); |
475 |
mmeineke |
377 |
painCave.isFatal = 1; |
476 |
|
|
simError(); |
477 |
|
|
} |
478 |
|
|
} |
479 |
|
|
else{ |
480 |
tim |
722 |
n_cells = (int) temp3; |
481 |
mmeineke |
670 |
cellx = info[0].boxL[0] / temp3; |
482 |
|
|
celly = info[0].boxL[1] / temp3; |
483 |
|
|
cellz = info[0].boxL[2] / temp3; |
484 |
mmeineke |
377 |
} |
485 |
|
|
|
486 |
|
|
current_mol = 0; |
487 |
|
|
current_comp_mol = 0; |
488 |
|
|
current_comp = 0; |
489 |
|
|
current_atom_ndx = 0; |
490 |
|
|
|
491 |
tim |
722 |
for (i = 0; i < n_cells ; i++){ |
492 |
|
|
for (j = 0; j < n_cells; j++){ |
493 |
|
|
for (k = 0; k < n_cells; k++){ |
494 |
|
|
makeElement(i * cellx, j * celly, k * cellz); |
495 |
mmeineke |
377 |
|
496 |
tim |
722 |
makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz); |
497 |
mmeineke |
377 |
|
498 |
tim |
722 |
makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz); |
499 |
mmeineke |
377 |
|
500 |
tim |
722 |
makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz); |
501 |
mmeineke |
377 |
} |
502 |
|
|
} |
503 |
|
|
} |
504 |
|
|
|
505 |
tim |
722 |
if (have_extra){ |
506 |
mmeineke |
377 |
done = 0; |
507 |
|
|
|
508 |
|
|
int start_ndx; |
509 |
tim |
722 |
for (i = 0; i < (n_cells + 1) && !done; i++){ |
510 |
|
|
for (j = 0; j < (n_cells + 1) && !done; j++){ |
511 |
|
|
if (i < n_cells){ |
512 |
|
|
if (j < n_cells){ |
513 |
|
|
start_ndx = n_cells; |
514 |
|
|
} |
515 |
|
|
else |
516 |
|
|
start_ndx = 0; |
517 |
|
|
} |
518 |
|
|
else |
519 |
|
|
start_ndx = 0; |
520 |
mmeineke |
377 |
|
521 |
tim |
722 |
for (k = start_ndx; k < (n_cells + 1) && !done; k++){ |
522 |
|
|
makeElement(i * cellx, j * celly, k * cellz); |
523 |
|
|
done = (current_mol >= tot_nmol); |
524 |
mmeineke |
377 |
|
525 |
tim |
722 |
if (!done && n_per_extra > 1){ |
526 |
|
|
makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, |
527 |
|
|
k * cellz); |
528 |
|
|
done = (current_mol >= tot_nmol); |
529 |
|
|
} |
530 |
mmeineke |
377 |
|
531 |
tim |
722 |
if (!done && n_per_extra > 2){ |
532 |
|
|
makeElement(i * cellx, j * celly + 0.5 * celly, |
533 |
|
|
k * cellz + 0.5 * cellz); |
534 |
|
|
done = (current_mol >= tot_nmol); |
535 |
|
|
} |
536 |
mmeineke |
377 |
|
537 |
tim |
722 |
if (!done && n_per_extra > 3){ |
538 |
|
|
makeElement(i * cellx + 0.5 * cellx, j * celly, |
539 |
|
|
k * cellz + 0.5 * cellz); |
540 |
|
|
done = (current_mol >= tot_nmol); |
541 |
|
|
} |
542 |
|
|
} |
543 |
mmeineke |
377 |
} |
544 |
|
|
} |
545 |
|
|
} |
546 |
|
|
|
547 |
tim |
722 |
for (i = 0; i < info[0].n_atoms; i++){ |
548 |
|
|
info[0].atoms[i]->setVel(vel); |
549 |
mmeineke |
377 |
} |
550 |
|
|
} |
551 |
|
|
|
552 |
tim |
722 |
void SimSetup::makeElement(double x, double y, double z){ |
553 |
mmeineke |
377 |
int k; |
554 |
|
|
AtomStamp* current_atom; |
555 |
|
|
DirectionalAtom* dAtom; |
556 |
|
|
double rotMat[3][3]; |
557 |
mmeineke |
670 |
double pos[3]; |
558 |
mmeineke |
377 |
|
559 |
tim |
722 |
for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){ |
560 |
|
|
current_atom = comp_stamps[current_comp]->getAtom(k); |
561 |
|
|
if (!current_atom->havePosition()){ |
562 |
|
|
sprintf(painCave.errMsg, |
563 |
|
|
"SimSetup:initFromBass error.\n" |
564 |
|
|
"\tComponent %s, atom %s does not have a position specified.\n" |
565 |
|
|
"\tThe initialization routine is unable to give a start" |
566 |
|
|
" position.\n", |
567 |
|
|
comp_stamps[current_comp]->getID(), current_atom->getType()); |
568 |
mmeineke |
377 |
painCave.isFatal = 1; |
569 |
|
|
simError(); |
570 |
|
|
} |
571 |
tim |
722 |
|
572 |
mmeineke |
670 |
pos[0] = x + current_atom->getPosX(); |
573 |
|
|
pos[1] = y + current_atom->getPosY(); |
574 |
|
|
pos[2] = z + current_atom->getPosZ(); |
575 |
mmeineke |
377 |
|
576 |
tim |
722 |
info[0].atoms[current_atom_ndx]->setPos(pos); |
577 |
mmeineke |
377 |
|
578 |
tim |
722 |
if (info[0].atoms[current_atom_ndx]->isDirectional()){ |
579 |
|
|
dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx]; |
580 |
mmeineke |
377 |
|
581 |
|
|
rotMat[0][0] = 1.0; |
582 |
|
|
rotMat[0][1] = 0.0; |
583 |
|
|
rotMat[0][2] = 0.0; |
584 |
|
|
|
585 |
|
|
rotMat[1][0] = 0.0; |
586 |
|
|
rotMat[1][1] = 1.0; |
587 |
|
|
rotMat[1][2] = 0.0; |
588 |
|
|
|
589 |
|
|
rotMat[2][0] = 0.0; |
590 |
|
|
rotMat[2][1] = 0.0; |
591 |
|
|
rotMat[2][2] = 1.0; |
592 |
|
|
|
593 |
tim |
722 |
dAtom->setA(rotMat); |
594 |
mmeineke |
377 |
} |
595 |
|
|
|
596 |
|
|
current_atom_ndx++; |
597 |
|
|
} |
598 |
|
|
|
599 |
|
|
current_mol++; |
600 |
|
|
current_comp_mol++; |
601 |
|
|
|
602 |
tim |
722 |
if (current_comp_mol >= components_nmol[current_comp]){ |
603 |
mmeineke |
377 |
current_comp_mol = 0; |
604 |
|
|
current_comp++; |
605 |
|
|
} |
606 |
|
|
} |
607 |
mmeineke |
614 |
|
608 |
|
|
|
609 |
tim |
722 |
void SimSetup::gatherInfo(void){ |
610 |
mmeineke |
787 |
int i; |
611 |
mmeineke |
614 |
|
612 |
|
|
ensembleCase = -1; |
613 |
|
|
ffCase = -1; |
614 |
|
|
|
615 |
mmeineke |
670 |
// set the easy ones first |
616 |
mmeineke |
614 |
|
617 |
tim |
722 |
for (i = 0; i < nInfo; i++){ |
618 |
mmeineke |
670 |
info[i].target_temp = globals->getTargetTemp(); |
619 |
|
|
info[i].dt = globals->getDt(); |
620 |
|
|
info[i].run_time = globals->getRunTime(); |
621 |
|
|
} |
622 |
mmeineke |
616 |
n_components = globals->getNComponents(); |
623 |
mmeineke |
614 |
|
624 |
|
|
|
625 |
|
|
// get the forceField |
626 |
|
|
|
627 |
tim |
722 |
strcpy(force_field, globals->getForceField()); |
628 |
mmeineke |
614 |
|
629 |
tim |
722 |
if (!strcasecmp(force_field, "DUFF")){ |
630 |
|
|
ffCase = FF_DUFF; |
631 |
|
|
} |
632 |
|
|
else if (!strcasecmp(force_field, "LJ")){ |
633 |
|
|
ffCase = FF_LJ; |
634 |
|
|
} |
635 |
|
|
else if (!strcasecmp(force_field, "EAM")){ |
636 |
|
|
ffCase = FF_EAM; |
637 |
|
|
} |
638 |
mmeineke |
614 |
else{ |
639 |
tim |
722 |
sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n", |
640 |
|
|
force_field); |
641 |
|
|
painCave.isFatal = 1; |
642 |
|
|
simError(); |
643 |
mmeineke |
614 |
} |
644 |
|
|
|
645 |
tim |
722 |
// get the ensemble |
646 |
mmeineke |
614 |
|
647 |
tim |
722 |
strcpy(ensemble, globals->getEnsemble()); |
648 |
mmeineke |
614 |
|
649 |
tim |
722 |
if (!strcasecmp(ensemble, "NVE")){ |
650 |
|
|
ensembleCase = NVE_ENS; |
651 |
|
|
} |
652 |
|
|
else if (!strcasecmp(ensemble, "NVT")){ |
653 |
|
|
ensembleCase = NVT_ENS; |
654 |
|
|
} |
655 |
|
|
else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){ |
656 |
mmeineke |
614 |
ensembleCase = NPTi_ENS; |
657 |
tim |
722 |
} |
658 |
|
|
else if (!strcasecmp(ensemble, "NPTf")){ |
659 |
|
|
ensembleCase = NPTf_ENS; |
660 |
|
|
} |
661 |
mmeineke |
812 |
else if (!strcasecmp(ensemble, "NPTxyz")){ |
662 |
|
|
ensembleCase = NPTxyz_ENS; |
663 |
|
|
} |
664 |
mmeineke |
614 |
else{ |
665 |
tim |
722 |
sprintf(painCave.errMsg, |
666 |
gezelter |
965 |
"SimSetup Warning. Unrecognized Ensemble -> %s \n" |
667 |
|
|
"\treverting to NVE for this simulation.\n", |
668 |
tim |
722 |
ensemble); |
669 |
|
|
painCave.isFatal = 0; |
670 |
|
|
simError(); |
671 |
|
|
strcpy(ensemble, "NVE"); |
672 |
|
|
ensembleCase = NVE_ENS; |
673 |
mmeineke |
614 |
} |
674 |
|
|
|
675 |
tim |
722 |
for (i = 0; i < nInfo; i++){ |
676 |
|
|
strcpy(info[i].ensemble, ensemble); |
677 |
|
|
|
678 |
mmeineke |
670 |
// get the mixing rule |
679 |
mmeineke |
614 |
|
680 |
tim |
722 |
strcpy(info[i].mixingRule, globals->getMixingRule()); |
681 |
mmeineke |
670 |
info[i].usePBC = globals->getPBC(); |
682 |
|
|
} |
683 |
tim |
722 |
|
684 |
mmeineke |
614 |
// get the components and calculate the tot_nMol and indvidual n_mol |
685 |
tim |
722 |
|
686 |
mmeineke |
616 |
the_components = globals->getComponents(); |
687 |
mmeineke |
614 |
components_nmol = new int[n_components]; |
688 |
|
|
|
689 |
|
|
|
690 |
tim |
722 |
if (!globals->haveNMol()){ |
691 |
mmeineke |
614 |
// we don't have the total number of molecules, so we assume it is |
692 |
|
|
// given in each component |
693 |
|
|
|
694 |
|
|
tot_nmol = 0; |
695 |
tim |
722 |
for (i = 0; i < n_components; i++){ |
696 |
|
|
if (!the_components[i]->haveNMol()){ |
697 |
|
|
// we have a problem |
698 |
|
|
sprintf(painCave.errMsg, |
699 |
gezelter |
965 |
"SimSetup Error. No global NMol or component NMol given.\n" |
700 |
|
|
"\tCannot calculate the number of atoms.\n"); |
701 |
tim |
722 |
painCave.isFatal = 1; |
702 |
|
|
simError(); |
703 |
mmeineke |
614 |
} |
704 |
|
|
|
705 |
|
|
tot_nmol += the_components[i]->getNMol(); |
706 |
|
|
components_nmol[i] = the_components[i]->getNMol(); |
707 |
|
|
} |
708 |
|
|
} |
709 |
|
|
else{ |
710 |
tim |
722 |
sprintf(painCave.errMsg, |
711 |
|
|
"SimSetup error.\n" |
712 |
|
|
"\tSorry, the ability to specify total" |
713 |
|
|
" nMols and then give molfractions in the components\n" |
714 |
|
|
"\tis not currently supported." |
715 |
|
|
" Please give nMol in the components.\n"); |
716 |
mmeineke |
614 |
painCave.isFatal = 1; |
717 |
|
|
simError(); |
718 |
|
|
} |
719 |
|
|
|
720 |
tim |
962 |
//check whether sample time, status time, thermal time and reset time are divisble by dt |
721 |
|
|
if (!isDivisible(globals->getSampleTime(), globals->getDt())){ |
722 |
|
|
sprintf(painCave.errMsg, |
723 |
gezelter |
965 |
"Sample time is not divisible by dt.\n" |
724 |
|
|
"\tThis will result in samples that are not uniformly\n" |
725 |
|
|
"\tdistributed in time. If this is a problem, change\n" |
726 |
|
|
"\tyour sampleTime variable.\n"); |
727 |
tim |
962 |
painCave.isFatal = 0; |
728 |
|
|
simError(); |
729 |
|
|
} |
730 |
|
|
|
731 |
|
|
if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){ |
732 |
|
|
sprintf(painCave.errMsg, |
733 |
gezelter |
965 |
"Status time is not divisible by dt.\n" |
734 |
|
|
"\tThis will result in status reports that are not uniformly\n" |
735 |
|
|
"\tdistributed in time. If this is a problem, change \n" |
736 |
|
|
"\tyour statusTime variable.\n"); |
737 |
tim |
962 |
painCave.isFatal = 0; |
738 |
|
|
simError(); |
739 |
|
|
} |
740 |
|
|
|
741 |
|
|
if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){ |
742 |
|
|
sprintf(painCave.errMsg, |
743 |
gezelter |
965 |
"Thermal time is not divisible by dt.\n" |
744 |
|
|
"\tThis will result in thermalizations that are not uniformly\n" |
745 |
|
|
"\tdistributed in time. If this is a problem, change \n" |
746 |
|
|
"\tyour thermalTime variable.\n"); |
747 |
tim |
962 |
painCave.isFatal = 0; |
748 |
|
|
simError(); |
749 |
|
|
} |
750 |
|
|
|
751 |
|
|
if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){ |
752 |
|
|
sprintf(painCave.errMsg, |
753 |
gezelter |
965 |
"Reset time is not divisible by dt.\n" |
754 |
|
|
"\tThis will result in integrator resets that are not uniformly\n" |
755 |
|
|
"\tdistributed in time. If this is a problem, change\n" |
756 |
|
|
"\tyour resetTime variable.\n"); |
757 |
tim |
962 |
painCave.isFatal = 0; |
758 |
|
|
simError(); |
759 |
|
|
} |
760 |
|
|
|
761 |
mmeineke |
614 |
// set the status, sample, and thermal kick times |
762 |
|
|
|
763 |
tim |
722 |
for (i = 0; i < nInfo; i++){ |
764 |
|
|
if (globals->haveSampleTime()){ |
765 |
mmeineke |
670 |
info[i].sampleTime = globals->getSampleTime(); |
766 |
|
|
info[i].statusTime = info[i].sampleTime; |
767 |
|
|
info[i].thermalTime = info[i].sampleTime; |
768 |
|
|
} |
769 |
|
|
else{ |
770 |
|
|
info[i].sampleTime = globals->getRunTime(); |
771 |
|
|
info[i].statusTime = info[i].sampleTime; |
772 |
|
|
info[i].thermalTime = info[i].sampleTime; |
773 |
|
|
} |
774 |
tim |
722 |
|
775 |
|
|
if (globals->haveStatusTime()){ |
776 |
mmeineke |
670 |
info[i].statusTime = globals->getStatusTime(); |
777 |
|
|
} |
778 |
tim |
722 |
|
779 |
|
|
if (globals->haveThermalTime()){ |
780 |
mmeineke |
670 |
info[i].thermalTime = globals->getThermalTime(); |
781 |
|
|
} |
782 |
mmeineke |
614 |
|
783 |
mmeineke |
746 |
info[i].resetIntegrator = 0; |
784 |
|
|
if( globals->haveResetTime() ){ |
785 |
|
|
info[i].resetTime = globals->getResetTime(); |
786 |
|
|
info[i].resetIntegrator = 1; |
787 |
|
|
} |
788 |
|
|
|
789 |
mmeineke |
670 |
// check for the temperature set flag |
790 |
mmeineke |
841 |
|
791 |
tim |
722 |
if (globals->haveTempSet()) |
792 |
|
|
info[i].setTemp = globals->getTempSet(); |
793 |
mmeineke |
855 |
|
794 |
|
|
// check for the extended State init |
795 |
|
|
|
796 |
|
|
info[i].useInitXSstate = globals->getUseInitXSstate(); |
797 |
|
|
info[i].orthoTolerance = globals->getOrthoBoxTolerance(); |
798 |
mmeineke |
841 |
|
799 |
tim |
708 |
} |
800 |
mmeineke |
841 |
|
801 |
tim |
722 |
//setup seed for random number generator |
802 |
tim |
708 |
int seedValue; |
803 |
|
|
|
804 |
tim |
722 |
if (globals->haveSeed()){ |
805 |
tim |
708 |
seedValue = globals->getSeed(); |
806 |
tim |
722 |
|
807 |
|
|
if(seedValue / 1E9 == 0){ |
808 |
|
|
sprintf(painCave.errMsg, |
809 |
|
|
"Seed for sprng library should contain at least 9 digits\n" |
810 |
|
|
"OOPSE will generate a seed for user\n"); |
811 |
|
|
painCave.isFatal = 0; |
812 |
|
|
simError(); |
813 |
|
|
|
814 |
|
|
//using seed generated by system instead of invalid seed set by user |
815 |
|
|
#ifndef IS_MPI |
816 |
|
|
seedValue = make_sprng_seed(); |
817 |
|
|
#else |
818 |
|
|
if (worldRank == 0){ |
819 |
|
|
seedValue = make_sprng_seed(); |
820 |
|
|
} |
821 |
|
|
MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
822 |
|
|
#endif |
823 |
|
|
} |
824 |
|
|
}//end of if branch of globals->haveSeed() |
825 |
tim |
708 |
else{ |
826 |
tim |
722 |
|
827 |
tim |
708 |
#ifndef IS_MPI |
828 |
tim |
722 |
seedValue = make_sprng_seed(); |
829 |
tim |
708 |
#else |
830 |
tim |
722 |
if (worldRank == 0){ |
831 |
|
|
seedValue = make_sprng_seed(); |
832 |
tim |
708 |
} |
833 |
tim |
722 |
MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
834 |
tim |
708 |
#endif |
835 |
tim |
722 |
}//end of globals->haveSeed() |
836 |
tim |
708 |
|
837 |
tim |
722 |
for (int i = 0; i < nInfo; i++){ |
838 |
tim |
708 |
info[i].setSeed(seedValue); |
839 |
|
|
} |
840 |
|
|
|
841 |
mmeineke |
614 |
#ifdef IS_MPI |
842 |
tim |
722 |
strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n"); |
843 |
mmeineke |
614 |
MPIcheckPoint(); |
844 |
|
|
#endif // is_mpi |
845 |
|
|
} |
846 |
|
|
|
847 |
|
|
|
848 |
tim |
722 |
void SimSetup::finalInfoCheck(void){ |
849 |
mmeineke |
614 |
int index; |
850 |
|
|
int usesDipoles; |
851 |
mmeineke |
670 |
int i; |
852 |
mmeineke |
614 |
|
853 |
tim |
722 |
for (i = 0; i < nInfo; i++){ |
854 |
mmeineke |
670 |
// check electrostatic parameters |
855 |
tim |
722 |
|
856 |
mmeineke |
670 |
index = 0; |
857 |
|
|
usesDipoles = 0; |
858 |
tim |
722 |
while ((index < info[i].n_atoms) && !usesDipoles){ |
859 |
mmeineke |
670 |
usesDipoles = (info[i].atoms[index])->hasDipole(); |
860 |
|
|
index++; |
861 |
|
|
} |
862 |
tim |
722 |
|
863 |
mmeineke |
614 |
#ifdef IS_MPI |
864 |
mmeineke |
670 |
int myUse = usesDipoles; |
865 |
tim |
722 |
MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
866 |
mmeineke |
614 |
#endif //is_mpi |
867 |
tim |
722 |
|
868 |
mmeineke |
670 |
double theEcr, theEst; |
869 |
tim |
722 |
|
870 |
|
|
if (globals->getUseRF()){ |
871 |
mmeineke |
670 |
info[i].useReactionField = 1; |
872 |
tim |
722 |
|
873 |
|
|
if (!globals->haveECR()){ |
874 |
|
|
sprintf(painCave.errMsg, |
875 |
gezelter |
965 |
"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n" |
876 |
|
|
"\tOOPSE will use a default value of 15.0 angstroms" |
877 |
|
|
"\tfor the electrostaticCutoffRadius.\n"); |
878 |
tim |
722 |
painCave.isFatal = 0; |
879 |
|
|
simError(); |
880 |
mmeineke |
859 |
theEcr = 15.0; |
881 |
mmeineke |
614 |
} |
882 |
tim |
722 |
else{ |
883 |
|
|
theEcr = globals->getECR(); |
884 |
mmeineke |
614 |
} |
885 |
tim |
722 |
|
886 |
|
|
if (!globals->haveEST()){ |
887 |
|
|
sprintf(painCave.errMsg, |
888 |
gezelter |
965 |
"SimSetup Warning: No value was set for electrostaticSkinThickness.\n" |
889 |
|
|
"\tOOPSE will use a default value of\n" |
890 |
|
|
"\t0.05 * electrostaticCutoffRadius\n" |
891 |
|
|
"\tfor the electrostaticSkinThickness\n"); |
892 |
tim |
722 |
painCave.isFatal = 0; |
893 |
|
|
simError(); |
894 |
|
|
theEst = 0.05 * theEcr; |
895 |
mmeineke |
670 |
} |
896 |
tim |
722 |
else{ |
897 |
|
|
theEst = globals->getEST(); |
898 |
mmeineke |
670 |
} |
899 |
tim |
722 |
|
900 |
mmeineke |
841 |
info[i].setDefaultEcr(theEcr, theEst); |
901 |
tim |
722 |
|
902 |
|
|
if (!globals->haveDielectric()){ |
903 |
|
|
sprintf(painCave.errMsg, |
904 |
gezelter |
965 |
"SimSetup Error: No Dielectric constant was set.\n" |
905 |
|
|
"\tYou are trying to use Reaction Field without" |
906 |
|
|
"\tsetting a dielectric constant!\n"); |
907 |
tim |
722 |
painCave.isFatal = 1; |
908 |
|
|
simError(); |
909 |
|
|
} |
910 |
|
|
info[i].dielectric = globals->getDielectric(); |
911 |
|
|
} |
912 |
|
|
else{ |
913 |
|
|
if (usesDipoles){ |
914 |
|
|
if (!globals->haveECR()){ |
915 |
|
|
sprintf(painCave.errMsg, |
916 |
gezelter |
965 |
"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n" |
917 |
|
|
"\tOOPSE will use a default value of 15.0 angstroms" |
918 |
|
|
"\tfor the electrostaticCutoffRadius.\n"); |
919 |
mmeineke |
859 |
painCave.isFatal = 0; |
920 |
|
|
simError(); |
921 |
|
|
theEcr = 15.0; |
922 |
tim |
722 |
} |
923 |
|
|
else{ |
924 |
|
|
theEcr = globals->getECR(); |
925 |
|
|
} |
926 |
mmeineke |
859 |
|
927 |
tim |
722 |
if (!globals->haveEST()){ |
928 |
|
|
sprintf(painCave.errMsg, |
929 |
gezelter |
965 |
"SimSetup Warning: No value was set for electrostaticSkinThickness.\n" |
930 |
|
|
"\tOOPSE will use a default value of\n" |
931 |
|
|
"\t0.05 * electrostaticCutoffRadius\n" |
932 |
|
|
"\tfor the electrostaticSkinThickness\n"); |
933 |
tim |
722 |
painCave.isFatal = 0; |
934 |
|
|
simError(); |
935 |
|
|
theEst = 0.05 * theEcr; |
936 |
|
|
} |
937 |
|
|
else{ |
938 |
|
|
theEst = globals->getEST(); |
939 |
|
|
} |
940 |
mmeineke |
859 |
|
941 |
mmeineke |
841 |
info[i].setDefaultEcr(theEcr, theEst); |
942 |
tim |
722 |
} |
943 |
|
|
} |
944 |
mmeineke |
670 |
} |
945 |
mmeineke |
614 |
#ifdef IS_MPI |
946 |
tim |
722 |
strcpy(checkPointMsg, "post processing checks out"); |
947 |
mmeineke |
614 |
MPIcheckPoint(); |
948 |
|
|
#endif // is_mpi |
949 |
|
|
} |
950 |
mmeineke |
859 |
|
951 |
tim |
722 |
void SimSetup::initSystemCoords(void){ |
952 |
mmeineke |
670 |
int i; |
953 |
tim |
722 |
|
954 |
tim |
689 |
char* inName; |
955 |
|
|
|
956 |
tim |
722 |
(info[0].getConfiguration())->createArrays(info[0].n_atoms); |
957 |
mmeineke |
614 |
|
958 |
tim |
722 |
for (i = 0; i < info[0].n_atoms; i++) |
959 |
|
|
info[0].atoms[i]->setCoords(); |
960 |
|
|
|
961 |
|
|
if (globals->haveInitialConfig()){ |
962 |
mmeineke |
670 |
InitializeFromFile* fileInit; |
963 |
mmeineke |
614 |
#ifdef IS_MPI // is_mpi |
964 |
tim |
722 |
if (worldRank == 0){ |
965 |
mmeineke |
614 |
#endif //is_mpi |
966 |
tim |
689 |
inName = globals->getInitialConfig(); |
967 |
tim |
722 |
fileInit = new InitializeFromFile(inName); |
968 |
mmeineke |
614 |
#ifdef IS_MPI |
969 |
tim |
722 |
} |
970 |
|
|
else |
971 |
|
|
fileInit = new InitializeFromFile(NULL); |
972 |
mmeineke |
614 |
#endif |
973 |
tim |
722 |
fileInit->readInit(info); // default velocities on |
974 |
|
|
|
975 |
mmeineke |
670 |
delete fileInit; |
976 |
|
|
} |
977 |
|
|
else{ |
978 |
mmeineke |
859 |
|
979 |
mmeineke |
670 |
// no init from bass |
980 |
mmeineke |
859 |
|
981 |
tim |
722 |
sprintf(painCave.errMsg, |
982 |
mmeineke |
859 |
"Cannot intialize a simulation without an initial configuration file.\n"); |
983 |
mmeineke |
787 |
painCave.isFatal = 1;; |
984 |
mmeineke |
670 |
simError(); |
985 |
mmeineke |
859 |
|
986 |
mmeineke |
670 |
} |
987 |
tim |
722 |
|
988 |
mmeineke |
614 |
#ifdef IS_MPI |
989 |
tim |
722 |
strcpy(checkPointMsg, "Successfully read in the initial configuration"); |
990 |
mmeineke |
614 |
MPIcheckPoint(); |
991 |
|
|
#endif // is_mpi |
992 |
|
|
} |
993 |
|
|
|
994 |
|
|
|
995 |
tim |
722 |
void SimSetup::makeOutNames(void){ |
996 |
mmeineke |
670 |
int k; |
997 |
mmeineke |
614 |
|
998 |
mmeineke |
670 |
|
999 |
tim |
722 |
for (k = 0; k < nInfo; k++){ |
1000 |
mmeineke |
614 |
#ifdef IS_MPI |
1001 |
tim |
722 |
if (worldRank == 0){ |
1002 |
mmeineke |
614 |
#endif // is_mpi |
1003 |
tim |
722 |
|
1004 |
|
|
if (globals->haveFinalConfig()){ |
1005 |
|
|
strcpy(info[k].finalName, globals->getFinalConfig()); |
1006 |
mmeineke |
614 |
} |
1007 |
|
|
else{ |
1008 |
tim |
722 |
strcpy(info[k].finalName, inFileName); |
1009 |
|
|
char* endTest; |
1010 |
|
|
int nameLength = strlen(info[k].finalName); |
1011 |
|
|
endTest = &(info[k].finalName[nameLength - 5]); |
1012 |
|
|
if (!strcmp(endTest, ".bass")){ |
1013 |
|
|
strcpy(endTest, ".eor"); |
1014 |
|
|
} |
1015 |
|
|
else if (!strcmp(endTest, ".BASS")){ |
1016 |
|
|
strcpy(endTest, ".eor"); |
1017 |
|
|
} |
1018 |
|
|
else{ |
1019 |
|
|
endTest = &(info[k].finalName[nameLength - 4]); |
1020 |
|
|
if (!strcmp(endTest, ".bss")){ |
1021 |
|
|
strcpy(endTest, ".eor"); |
1022 |
|
|
} |
1023 |
|
|
else if (!strcmp(endTest, ".mdl")){ |
1024 |
|
|
strcpy(endTest, ".eor"); |
1025 |
|
|
} |
1026 |
|
|
else{ |
1027 |
|
|
strcat(info[k].finalName, ".eor"); |
1028 |
|
|
} |
1029 |
|
|
} |
1030 |
mmeineke |
614 |
} |
1031 |
tim |
722 |
|
1032 |
mmeineke |
670 |
// make the sample and status out names |
1033 |
tim |
722 |
|
1034 |
|
|
strcpy(info[k].sampleName, inFileName); |
1035 |
mmeineke |
670 |
char* endTest; |
1036 |
tim |
722 |
int nameLength = strlen(info[k].sampleName); |
1037 |
mmeineke |
670 |
endTest = &(info[k].sampleName[nameLength - 5]); |
1038 |
tim |
722 |
if (!strcmp(endTest, ".bass")){ |
1039 |
|
|
strcpy(endTest, ".dump"); |
1040 |
mmeineke |
614 |
} |
1041 |
tim |
722 |
else if (!strcmp(endTest, ".BASS")){ |
1042 |
|
|
strcpy(endTest, ".dump"); |
1043 |
mmeineke |
614 |
} |
1044 |
|
|
else{ |
1045 |
tim |
722 |
endTest = &(info[k].sampleName[nameLength - 4]); |
1046 |
|
|
if (!strcmp(endTest, ".bss")){ |
1047 |
|
|
strcpy(endTest, ".dump"); |
1048 |
|
|
} |
1049 |
|
|
else if (!strcmp(endTest, ".mdl")){ |
1050 |
|
|
strcpy(endTest, ".dump"); |
1051 |
|
|
} |
1052 |
|
|
else{ |
1053 |
|
|
strcat(info[k].sampleName, ".dump"); |
1054 |
|
|
} |
1055 |
mmeineke |
614 |
} |
1056 |
tim |
722 |
|
1057 |
|
|
strcpy(info[k].statusName, inFileName); |
1058 |
|
|
nameLength = strlen(info[k].statusName); |
1059 |
mmeineke |
670 |
endTest = &(info[k].statusName[nameLength - 5]); |
1060 |
tim |
722 |
if (!strcmp(endTest, ".bass")){ |
1061 |
|
|
strcpy(endTest, ".stat"); |
1062 |
mmeineke |
614 |
} |
1063 |
tim |
722 |
else if (!strcmp(endTest, ".BASS")){ |
1064 |
|
|
strcpy(endTest, ".stat"); |
1065 |
mmeineke |
614 |
} |
1066 |
|
|
else{ |
1067 |
tim |
722 |
endTest = &(info[k].statusName[nameLength - 4]); |
1068 |
|
|
if (!strcmp(endTest, ".bss")){ |
1069 |
|
|
strcpy(endTest, ".stat"); |
1070 |
|
|
} |
1071 |
|
|
else if (!strcmp(endTest, ".mdl")){ |
1072 |
|
|
strcpy(endTest, ".stat"); |
1073 |
|
|
} |
1074 |
|
|
else{ |
1075 |
|
|
strcat(info[k].statusName, ".stat"); |
1076 |
|
|
} |
1077 |
mmeineke |
614 |
} |
1078 |
tim |
722 |
|
1079 |
mmeineke |
670 |
#ifdef IS_MPI |
1080 |
tim |
722 |
|
1081 |
mmeineke |
614 |
} |
1082 |
mmeineke |
670 |
#endif // is_mpi |
1083 |
mmeineke |
614 |
} |
1084 |
|
|
} |
1085 |
|
|
|
1086 |
|
|
|
1087 |
tim |
722 |
void SimSetup::sysObjectsCreation(void){ |
1088 |
|
|
int i, k; |
1089 |
|
|
|
1090 |
mmeineke |
614 |
// create the forceField |
1091 |
tim |
689 |
|
1092 |
mmeineke |
614 |
createFF(); |
1093 |
|
|
|
1094 |
|
|
// extract componentList |
1095 |
|
|
|
1096 |
|
|
compList(); |
1097 |
|
|
|
1098 |
|
|
// calc the number of atoms, bond, bends, and torsions |
1099 |
|
|
|
1100 |
|
|
calcSysValues(); |
1101 |
|
|
|
1102 |
|
|
#ifdef IS_MPI |
1103 |
|
|
// divide the molecules among the processors |
1104 |
tim |
722 |
|
1105 |
mmeineke |
614 |
mpiMolDivide(); |
1106 |
|
|
#endif //is_mpi |
1107 |
tim |
722 |
|
1108 |
mmeineke |
614 |
// create the atom and SRI arrays. Also initialize Molecule Stamp ID's |
1109 |
tim |
722 |
|
1110 |
mmeineke |
614 |
makeSysArrays(); |
1111 |
|
|
|
1112 |
mmeineke |
616 |
// make and initialize the molecules (all but atomic coordinates) |
1113 |
tim |
722 |
|
1114 |
mmeineke |
616 |
makeMolecules(); |
1115 |
tim |
722 |
|
1116 |
|
|
for (k = 0; k < nInfo; k++){ |
1117 |
mmeineke |
670 |
info[k].identArray = new int[info[k].n_atoms]; |
1118 |
tim |
722 |
for (i = 0; i < info[k].n_atoms; i++){ |
1119 |
mmeineke |
670 |
info[k].identArray[i] = info[k].atoms[i]->getIdent(); |
1120 |
|
|
} |
1121 |
mmeineke |
616 |
} |
1122 |
mmeineke |
614 |
} |
1123 |
|
|
|
1124 |
|
|
|
1125 |
tim |
722 |
void SimSetup::createFF(void){ |
1126 |
|
|
switch (ffCase){ |
1127 |
|
|
case FF_DUFF: |
1128 |
|
|
the_ff = new DUFF(); |
1129 |
|
|
break; |
1130 |
mmeineke |
614 |
|
1131 |
tim |
722 |
case FF_LJ: |
1132 |
|
|
the_ff = new LJFF(); |
1133 |
|
|
break; |
1134 |
mmeineke |
614 |
|
1135 |
tim |
722 |
case FF_EAM: |
1136 |
|
|
the_ff = new EAM_FF(); |
1137 |
|
|
break; |
1138 |
mmeineke |
614 |
|
1139 |
tim |
722 |
default: |
1140 |
|
|
sprintf(painCave.errMsg, |
1141 |
|
|
"SimSetup Error. Unrecognized force field in case statement.\n"); |
1142 |
|
|
painCave.isFatal = 1; |
1143 |
|
|
simError(); |
1144 |
mmeineke |
614 |
} |
1145 |
|
|
|
1146 |
|
|
#ifdef IS_MPI |
1147 |
tim |
722 |
strcpy(checkPointMsg, "ForceField creation successful"); |
1148 |
mmeineke |
614 |
MPIcheckPoint(); |
1149 |
|
|
#endif // is_mpi |
1150 |
|
|
} |
1151 |
|
|
|
1152 |
|
|
|
1153 |
tim |
722 |
void SimSetup::compList(void){ |
1154 |
mmeineke |
616 |
int i; |
1155 |
mmeineke |
670 |
char* id; |
1156 |
|
|
LinkedMolStamp* headStamp = new LinkedMolStamp(); |
1157 |
|
|
LinkedMolStamp* currentStamp = NULL; |
1158 |
tim |
722 |
comp_stamps = new MoleculeStamp * [n_components]; |
1159 |
|
|
|
1160 |
mmeineke |
614 |
// make an array of molecule stamps that match the components used. |
1161 |
|
|
// also extract the used stamps out into a separate linked list |
1162 |
tim |
722 |
|
1163 |
|
|
for (i = 0; i < nInfo; i++){ |
1164 |
mmeineke |
670 |
info[i].nComponents = n_components; |
1165 |
|
|
info[i].componentsNmol = components_nmol; |
1166 |
|
|
info[i].compStamps = comp_stamps; |
1167 |
|
|
info[i].headStamp = headStamp; |
1168 |
|
|
} |
1169 |
mmeineke |
614 |
|
1170 |
|
|
|
1171 |
tim |
722 |
for (i = 0; i < n_components; i++){ |
1172 |
mmeineke |
614 |
id = the_components[i]->getType(); |
1173 |
|
|
comp_stamps[i] = NULL; |
1174 |
tim |
722 |
|
1175 |
mmeineke |
614 |
// check to make sure the component isn't already in the list |
1176 |
|
|
|
1177 |
tim |
722 |
comp_stamps[i] = headStamp->match(id); |
1178 |
|
|
if (comp_stamps[i] == NULL){ |
1179 |
mmeineke |
614 |
// extract the component from the list; |
1180 |
tim |
722 |
|
1181 |
|
|
currentStamp = stamps->extractMolStamp(id); |
1182 |
|
|
if (currentStamp == NULL){ |
1183 |
|
|
sprintf(painCave.errMsg, |
1184 |
|
|
"SimSetup error: Component \"%s\" was not found in the " |
1185 |
|
|
"list of declared molecules\n", |
1186 |
|
|
id); |
1187 |
|
|
painCave.isFatal = 1; |
1188 |
|
|
simError(); |
1189 |
mmeineke |
614 |
} |
1190 |
tim |
722 |
|
1191 |
|
|
headStamp->add(currentStamp); |
1192 |
|
|
comp_stamps[i] = headStamp->match(id); |
1193 |
mmeineke |
614 |
} |
1194 |
|
|
} |
1195 |
|
|
|
1196 |
|
|
#ifdef IS_MPI |
1197 |
tim |
722 |
strcpy(checkPointMsg, "Component stamps successfully extracted\n"); |
1198 |
mmeineke |
614 |
MPIcheckPoint(); |
1199 |
|
|
#endif // is_mpi |
1200 |
tim |
722 |
} |
1201 |
mmeineke |
614 |
|
1202 |
tim |
722 |
void SimSetup::calcSysValues(void){ |
1203 |
mmeineke |
787 |
int i; |
1204 |
mmeineke |
614 |
|
1205 |
tim |
722 |
int* molMembershipArray; |
1206 |
mmeineke |
614 |
|
1207 |
|
|
tot_atoms = 0; |
1208 |
|
|
tot_bonds = 0; |
1209 |
|
|
tot_bends = 0; |
1210 |
|
|
tot_torsions = 0; |
1211 |
tim |
722 |
for (i = 0; i < n_components; i++){ |
1212 |
|
|
tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1213 |
|
|
tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1214 |
|
|
tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1215 |
mmeineke |
614 |
tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
1216 |
|
|
} |
1217 |
tim |
722 |
|
1218 |
mmeineke |
614 |
tot_SRI = tot_bonds + tot_bends + tot_torsions; |
1219 |
mmeineke |
670 |
molMembershipArray = new int[tot_atoms]; |
1220 |
tim |
722 |
|
1221 |
|
|
for (i = 0; i < nInfo; i++){ |
1222 |
mmeineke |
670 |
info[i].n_atoms = tot_atoms; |
1223 |
|
|
info[i].n_bonds = tot_bonds; |
1224 |
|
|
info[i].n_bends = tot_bends; |
1225 |
|
|
info[i].n_torsions = tot_torsions; |
1226 |
|
|
info[i].n_SRI = tot_SRI; |
1227 |
|
|
info[i].n_mol = tot_nmol; |
1228 |
tim |
722 |
|
1229 |
mmeineke |
670 |
info[i].molMembershipArray = molMembershipArray; |
1230 |
tim |
722 |
} |
1231 |
mmeineke |
614 |
} |
1232 |
|
|
|
1233 |
|
|
#ifdef IS_MPI |
1234 |
|
|
|
1235 |
tim |
722 |
void SimSetup::mpiMolDivide(void){ |
1236 |
mmeineke |
616 |
int i, j, k; |
1237 |
mmeineke |
614 |
int localMol, allMol; |
1238 |
|
|
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
1239 |
|
|
|
1240 |
tim |
722 |
mpiSim = new mpiSimulation(info); |
1241 |
|
|
|
1242 |
mmeineke |
614 |
globalIndex = mpiSim->divideLabor(); |
1243 |
|
|
|
1244 |
|
|
// set up the local variables |
1245 |
tim |
722 |
|
1246 |
mmeineke |
614 |
mol2proc = mpiSim->getMolToProcMap(); |
1247 |
|
|
molCompType = mpiSim->getMolComponentType(); |
1248 |
tim |
722 |
|
1249 |
mmeineke |
614 |
allMol = 0; |
1250 |
|
|
localMol = 0; |
1251 |
|
|
local_atoms = 0; |
1252 |
|
|
local_bonds = 0; |
1253 |
|
|
local_bends = 0; |
1254 |
|
|
local_torsions = 0; |
1255 |
|
|
globalAtomIndex = 0; |
1256 |
|
|
|
1257 |
|
|
|
1258 |
tim |
722 |
for (i = 0; i < n_components; i++){ |
1259 |
|
|
for (j = 0; j < components_nmol[i]; j++){ |
1260 |
|
|
if (mol2proc[allMol] == worldRank){ |
1261 |
|
|
local_atoms += comp_stamps[i]->getNAtoms(); |
1262 |
|
|
local_bonds += comp_stamps[i]->getNBonds(); |
1263 |
|
|
local_bends += comp_stamps[i]->getNBends(); |
1264 |
|
|
local_torsions += comp_stamps[i]->getNTorsions(); |
1265 |
|
|
localMol++; |
1266 |
mmeineke |
614 |
} |
1267 |
tim |
722 |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ |
1268 |
mmeineke |
670 |
info[0].molMembershipArray[globalAtomIndex] = allMol; |
1269 |
mmeineke |
614 |
globalAtomIndex++; |
1270 |
|
|
} |
1271 |
|
|
|
1272 |
tim |
722 |
allMol++; |
1273 |
mmeineke |
614 |
} |
1274 |
|
|
} |
1275 |
|
|
local_SRI = local_bonds + local_bends + local_torsions; |
1276 |
tim |
722 |
|
1277 |
mmeineke |
670 |
info[0].n_atoms = mpiSim->getMyNlocal(); |
1278 |
tim |
722 |
|
1279 |
|
|
if (local_atoms != info[0].n_atoms){ |
1280 |
|
|
sprintf(painCave.errMsg, |
1281 |
gezelter |
965 |
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n" |
1282 |
|
|
"\tlocalAtom (%d) are not equal.\n", |
1283 |
tim |
722 |
info[0].n_atoms, local_atoms); |
1284 |
mmeineke |
614 |
painCave.isFatal = 1; |
1285 |
|
|
simError(); |
1286 |
|
|
} |
1287 |
|
|
|
1288 |
mmeineke |
670 |
info[0].n_bonds = local_bonds; |
1289 |
|
|
info[0].n_bends = local_bends; |
1290 |
|
|
info[0].n_torsions = local_torsions; |
1291 |
|
|
info[0].n_SRI = local_SRI; |
1292 |
|
|
info[0].n_mol = localMol; |
1293 |
mmeineke |
614 |
|
1294 |
tim |
722 |
strcpy(checkPointMsg, "Passed nlocal consistency check."); |
1295 |
mmeineke |
614 |
MPIcheckPoint(); |
1296 |
|
|
} |
1297 |
tim |
722 |
|
1298 |
mmeineke |
614 |
#endif // is_mpi |
1299 |
|
|
|
1300 |
|
|
|
1301 |
tim |
722 |
void SimSetup::makeSysArrays(void){ |
1302 |
mmeineke |
787 |
|
1303 |
|
|
#ifndef IS_MPI |
1304 |
|
|
int k, j; |
1305 |
|
|
#endif // is_mpi |
1306 |
|
|
int i, l; |
1307 |
mmeineke |
614 |
|
1308 |
mmeineke |
670 |
Atom** the_atoms; |
1309 |
|
|
Molecule* the_molecules; |
1310 |
|
|
Exclude** the_excludes; |
1311 |
mmeineke |
616 |
|
1312 |
tim |
722 |
|
1313 |
|
|
for (l = 0; l < nInfo; l++){ |
1314 |
mmeineke |
670 |
// create the atom and short range interaction arrays |
1315 |
tim |
722 |
|
1316 |
|
|
the_atoms = new Atom * [info[l].n_atoms]; |
1317 |
mmeineke |
670 |
the_molecules = new Molecule[info[l].n_mol]; |
1318 |
|
|
int molIndex; |
1319 |
mmeineke |
614 |
|
1320 |
mmeineke |
670 |
// initialize the molecule's stampID's |
1321 |
tim |
722 |
|
1322 |
mmeineke |
670 |
#ifdef IS_MPI |
1323 |
tim |
722 |
|
1324 |
|
|
|
1325 |
mmeineke |
670 |
molIndex = 0; |
1326 |
tim |
722 |
for (i = 0; i < mpiSim->getTotNmol(); i++){ |
1327 |
|
|
if (mol2proc[i] == worldRank){ |
1328 |
|
|
the_molecules[molIndex].setStampID(molCompType[i]); |
1329 |
|
|
the_molecules[molIndex].setMyIndex(molIndex); |
1330 |
|
|
the_molecules[molIndex].setGlobalIndex(i); |
1331 |
|
|
molIndex++; |
1332 |
mmeineke |
670 |
} |
1333 |
mmeineke |
614 |
} |
1334 |
tim |
722 |
|
1335 |
mmeineke |
614 |
#else // is_mpi |
1336 |
tim |
722 |
|
1337 |
mmeineke |
670 |
molIndex = 0; |
1338 |
|
|
globalAtomIndex = 0; |
1339 |
tim |
722 |
for (i = 0; i < n_components; i++){ |
1340 |
|
|
for (j = 0; j < components_nmol[i]; j++){ |
1341 |
|
|
the_molecules[molIndex].setStampID(i); |
1342 |
|
|
the_molecules[molIndex].setMyIndex(molIndex); |
1343 |
|
|
the_molecules[molIndex].setGlobalIndex(molIndex); |
1344 |
|
|
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ |
1345 |
|
|
info[l].molMembershipArray[globalAtomIndex] = molIndex; |
1346 |
|
|
globalAtomIndex++; |
1347 |
|
|
} |
1348 |
|
|
molIndex++; |
1349 |
mmeineke |
614 |
} |
1350 |
|
|
} |
1351 |
tim |
722 |
|
1352 |
|
|
|
1353 |
mmeineke |
614 |
#endif // is_mpi |
1354 |
|
|
|
1355 |
|
|
|
1356 |
tim |
722 |
if (info[l].n_SRI){ |
1357 |
mmeineke |
670 |
Exclude::createArray(info[l].n_SRI); |
1358 |
tim |
722 |
the_excludes = new Exclude * [info[l].n_SRI]; |
1359 |
|
|
for (int ex = 0; ex < info[l].n_SRI; ex++){ |
1360 |
|
|
the_excludes[ex] = new Exclude(ex); |
1361 |
mmeineke |
670 |
} |
1362 |
|
|
info[l].globalExcludes = new int; |
1363 |
|
|
info[l].n_exclude = info[l].n_SRI; |
1364 |
|
|
} |
1365 |
|
|
else{ |
1366 |
tim |
722 |
Exclude::createArray(1); |
1367 |
|
|
the_excludes = new Exclude * ; |
1368 |
mmeineke |
670 |
the_excludes[0] = new Exclude(0); |
1369 |
tim |
722 |
the_excludes[0]->setPair(0, 0); |
1370 |
mmeineke |
670 |
info[l].globalExcludes = new int; |
1371 |
|
|
info[l].globalExcludes[0] = 0; |
1372 |
|
|
info[l].n_exclude = 0; |
1373 |
|
|
} |
1374 |
mmeineke |
614 |
|
1375 |
mmeineke |
670 |
// set the arrays into the SimInfo object |
1376 |
mmeineke |
614 |
|
1377 |
mmeineke |
670 |
info[l].atoms = the_atoms; |
1378 |
|
|
info[l].molecules = the_molecules; |
1379 |
|
|
info[l].nGlobalExcludes = 0; |
1380 |
|
|
info[l].excludes = the_excludes; |
1381 |
mmeineke |
614 |
|
1382 |
tim |
722 |
the_ff->setSimInfo(info); |
1383 |
mmeineke |
670 |
} |
1384 |
mmeineke |
614 |
} |
1385 |
mmeineke |
616 |
|
1386 |
tim |
722 |
void SimSetup::makeIntegrator(void){ |
1387 |
mmeineke |
670 |
int k; |
1388 |
|
|
|
1389 |
mmeineke |
782 |
NVE<RealIntegrator>* myNVE = NULL; |
1390 |
tim |
722 |
NVT<RealIntegrator>* myNVT = NULL; |
1391 |
mmeineke |
778 |
NPTi<NPT<RealIntegrator> >* myNPTi = NULL; |
1392 |
mmeineke |
780 |
NPTf<NPT<RealIntegrator> >* myNPTf = NULL; |
1393 |
mmeineke |
812 |
NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL; |
1394 |
tim |
733 |
|
1395 |
tim |
722 |
for (k = 0; k < nInfo; k++){ |
1396 |
|
|
switch (ensembleCase){ |
1397 |
|
|
case NVE_ENS: |
1398 |
|
|
if (globals->haveZconstraints()){ |
1399 |
|
|
setupZConstraint(info[k]); |
1400 |
mmeineke |
782 |
myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff); |
1401 |
tim |
722 |
} |
1402 |
mmeineke |
782 |
else{ |
1403 |
|
|
myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff); |
1404 |
|
|
} |
1405 |
|
|
|
1406 |
|
|
info->the_integrator = myNVE; |
1407 |
tim |
722 |
break; |
1408 |
tim |
676 |
|
1409 |
tim |
722 |
case NVT_ENS: |
1410 |
|
|
if (globals->haveZconstraints()){ |
1411 |
|
|
setupZConstraint(info[k]); |
1412 |
|
|
myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff); |
1413 |
|
|
} |
1414 |
|
|
else |
1415 |
|
|
myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff); |
1416 |
|
|
|
1417 |
tim |
701 |
myNVT->setTargetTemp(globals->getTargetTemp()); |
1418 |
tim |
722 |
|
1419 |
|
|
if (globals->haveTauThermostat()) |
1420 |
tim |
701 |
myNVT->setTauThermostat(globals->getTauThermostat()); |
1421 |
tim |
722 |
else{ |
1422 |
|
|
sprintf(painCave.errMsg, |
1423 |
|
|
"SimSetup error: If you use the NVT\n" |
1424 |
gezelter |
965 |
"\tensemble, you must set tauThermostat.\n"); |
1425 |
tim |
701 |
painCave.isFatal = 1; |
1426 |
|
|
simError(); |
1427 |
|
|
} |
1428 |
mmeineke |
782 |
|
1429 |
|
|
info->the_integrator = myNVT; |
1430 |
tim |
701 |
break; |
1431 |
tim |
676 |
|
1432 |
tim |
722 |
case NPTi_ENS: |
1433 |
|
|
if (globals->haveZconstraints()){ |
1434 |
|
|
setupZConstraint(info[k]); |
1435 |
mmeineke |
778 |
myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1436 |
tim |
722 |
} |
1437 |
|
|
else |
1438 |
mmeineke |
778 |
myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff); |
1439 |
tim |
722 |
|
1440 |
|
|
myNPTi->setTargetTemp(globals->getTargetTemp()); |
1441 |
|
|
|
1442 |
|
|
if (globals->haveTargetPressure()) |
1443 |
|
|
myNPTi->setTargetPressure(globals->getTargetPressure()); |
1444 |
|
|
else{ |
1445 |
|
|
sprintf(painCave.errMsg, |
1446 |
|
|
"SimSetup error: If you use a constant pressure\n" |
1447 |
gezelter |
965 |
"\tensemble, you must set targetPressure in the BASS file.\n"); |
1448 |
tim |
722 |
painCave.isFatal = 1; |
1449 |
|
|
simError(); |
1450 |
|
|
} |
1451 |
|
|
|
1452 |
|
|
if (globals->haveTauThermostat()) |
1453 |
|
|
myNPTi->setTauThermostat(globals->getTauThermostat()); |
1454 |
|
|
else{ |
1455 |
|
|
sprintf(painCave.errMsg, |
1456 |
|
|
"SimSetup error: If you use an NPT\n" |
1457 |
gezelter |
965 |
"\tensemble, you must set tauThermostat.\n"); |
1458 |
tim |
722 |
painCave.isFatal = 1; |
1459 |
|
|
simError(); |
1460 |
|
|
} |
1461 |
|
|
|
1462 |
|
|
if (globals->haveTauBarostat()) |
1463 |
|
|
myNPTi->setTauBarostat(globals->getTauBarostat()); |
1464 |
|
|
else{ |
1465 |
|
|
sprintf(painCave.errMsg, |
1466 |
tim |
701 |
"SimSetup error: If you use an NPT\n" |
1467 |
gezelter |
965 |
"\tensemble, you must set tauBarostat.\n"); |
1468 |
tim |
722 |
painCave.isFatal = 1; |
1469 |
|
|
simError(); |
1470 |
|
|
} |
1471 |
mmeineke |
782 |
|
1472 |
|
|
info->the_integrator = myNPTi; |
1473 |
tim |
722 |
break; |
1474 |
tim |
676 |
|
1475 |
tim |
722 |
case NPTf_ENS: |
1476 |
|
|
if (globals->haveZconstraints()){ |
1477 |
|
|
setupZConstraint(info[k]); |
1478 |
mmeineke |
780 |
myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1479 |
tim |
722 |
} |
1480 |
|
|
else |
1481 |
mmeineke |
780 |
myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1482 |
tim |
722 |
|
1483 |
|
|
myNPTf->setTargetTemp(globals->getTargetTemp()); |
1484 |
|
|
|
1485 |
|
|
if (globals->haveTargetPressure()) |
1486 |
|
|
myNPTf->setTargetPressure(globals->getTargetPressure()); |
1487 |
|
|
else{ |
1488 |
|
|
sprintf(painCave.errMsg, |
1489 |
tim |
701 |
"SimSetup error: If you use a constant pressure\n" |
1490 |
gezelter |
965 |
"\tensemble, you must set targetPressure in the BASS file.\n"); |
1491 |
tim |
722 |
painCave.isFatal = 1; |
1492 |
|
|
simError(); |
1493 |
|
|
} |
1494 |
|
|
|
1495 |
|
|
if (globals->haveTauThermostat()) |
1496 |
|
|
myNPTf->setTauThermostat(globals->getTauThermostat()); |
1497 |
mmeineke |
843 |
|
1498 |
tim |
722 |
else{ |
1499 |
|
|
sprintf(painCave.errMsg, |
1500 |
tim |
701 |
"SimSetup error: If you use an NPT\n" |
1501 |
gezelter |
965 |
"\tensemble, you must set tauThermostat.\n"); |
1502 |
tim |
722 |
painCave.isFatal = 1; |
1503 |
|
|
simError(); |
1504 |
|
|
} |
1505 |
|
|
|
1506 |
|
|
if (globals->haveTauBarostat()) |
1507 |
|
|
myNPTf->setTauBarostat(globals->getTauBarostat()); |
1508 |
mmeineke |
843 |
|
1509 |
tim |
722 |
else{ |
1510 |
|
|
sprintf(painCave.errMsg, |
1511 |
|
|
"SimSetup error: If you use an NPT\n" |
1512 |
gezelter |
965 |
"\tensemble, you must set tauBarostat.\n"); |
1513 |
tim |
722 |
painCave.isFatal = 1; |
1514 |
|
|
simError(); |
1515 |
|
|
} |
1516 |
mmeineke |
782 |
|
1517 |
|
|
info->the_integrator = myNPTf; |
1518 |
tim |
722 |
break; |
1519 |
tim |
676 |
|
1520 |
mmeineke |
812 |
case NPTxyz_ENS: |
1521 |
|
|
if (globals->haveZconstraints()){ |
1522 |
|
|
setupZConstraint(info[k]); |
1523 |
|
|
myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1524 |
|
|
} |
1525 |
|
|
else |
1526 |
|
|
myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1527 |
|
|
|
1528 |
|
|
myNPTxyz->setTargetTemp(globals->getTargetTemp()); |
1529 |
|
|
|
1530 |
|
|
if (globals->haveTargetPressure()) |
1531 |
|
|
myNPTxyz->setTargetPressure(globals->getTargetPressure()); |
1532 |
|
|
else{ |
1533 |
|
|
sprintf(painCave.errMsg, |
1534 |
|
|
"SimSetup error: If you use a constant pressure\n" |
1535 |
gezelter |
965 |
"\tensemble, you must set targetPressure in the BASS file.\n"); |
1536 |
mmeineke |
812 |
painCave.isFatal = 1; |
1537 |
|
|
simError(); |
1538 |
|
|
} |
1539 |
|
|
|
1540 |
|
|
if (globals->haveTauThermostat()) |
1541 |
|
|
myNPTxyz->setTauThermostat(globals->getTauThermostat()); |
1542 |
|
|
else{ |
1543 |
|
|
sprintf(painCave.errMsg, |
1544 |
|
|
"SimSetup error: If you use an NPT\n" |
1545 |
gezelter |
965 |
"\tensemble, you must set tauThermostat.\n"); |
1546 |
mmeineke |
812 |
painCave.isFatal = 1; |
1547 |
|
|
simError(); |
1548 |
|
|
} |
1549 |
|
|
|
1550 |
|
|
if (globals->haveTauBarostat()) |
1551 |
|
|
myNPTxyz->setTauBarostat(globals->getTauBarostat()); |
1552 |
|
|
else{ |
1553 |
|
|
sprintf(painCave.errMsg, |
1554 |
|
|
"SimSetup error: If you use an NPT\n" |
1555 |
gezelter |
965 |
"\tensemble, you must set tauBarostat.\n"); |
1556 |
mmeineke |
812 |
painCave.isFatal = 1; |
1557 |
|
|
simError(); |
1558 |
|
|
} |
1559 |
|
|
|
1560 |
|
|
info->the_integrator = myNPTxyz; |
1561 |
|
|
break; |
1562 |
|
|
|
1563 |
tim |
722 |
default: |
1564 |
|
|
sprintf(painCave.errMsg, |
1565 |
|
|
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1566 |
tim |
701 |
painCave.isFatal = 1; |
1567 |
|
|
simError(); |
1568 |
tim |
660 |
} |
1569 |
mmeineke |
616 |
} |
1570 |
|
|
} |
1571 |
|
|
|
1572 |
tim |
722 |
void SimSetup::initFortran(void){ |
1573 |
|
|
info[0].refreshSim(); |
1574 |
mmeineke |
616 |
|
1575 |
tim |
722 |
if (!strcmp(info[0].mixingRule, "standard")){ |
1576 |
|
|
the_ff->initForceField(LB_MIXING_RULE); |
1577 |
mmeineke |
616 |
} |
1578 |
tim |
722 |
else if (!strcmp(info[0].mixingRule, "explicit")){ |
1579 |
|
|
the_ff->initForceField(EXPLICIT_MIXING_RULE); |
1580 |
mmeineke |
616 |
} |
1581 |
|
|
else{ |
1582 |
tim |
722 |
sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1583 |
|
|
info[0].mixingRule); |
1584 |
mmeineke |
616 |
painCave.isFatal = 1; |
1585 |
|
|
simError(); |
1586 |
|
|
} |
1587 |
|
|
|
1588 |
|
|
|
1589 |
|
|
#ifdef IS_MPI |
1590 |
tim |
722 |
strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran."); |
1591 |
mmeineke |
616 |
MPIcheckPoint(); |
1592 |
|
|
#endif // is_mpi |
1593 |
|
|
} |
1594 |
tim |
660 |
|
1595 |
tim |
722 |
void SimSetup::setupZConstraint(SimInfo& theInfo){ |
1596 |
tim |
701 |
int nZConstraints; |
1597 |
|
|
ZconStamp** zconStamp; |
1598 |
tim |
682 |
|
1599 |
tim |
722 |
if (globals->haveZconstraintTime()){ |
1600 |
tim |
701 |
//add sample time of z-constraint into SimInfo's property list |
1601 |
|
|
DoubleData* zconsTimeProp = new DoubleData(); |
1602 |
|
|
zconsTimeProp->setID(ZCONSTIME_ID); |
1603 |
|
|
zconsTimeProp->setData(globals->getZconsTime()); |
1604 |
|
|
theInfo.addProperty(zconsTimeProp); |
1605 |
|
|
} |
1606 |
|
|
else{ |
1607 |
tim |
722 |
sprintf(painCave.errMsg, |
1608 |
gezelter |
965 |
"ZConstraint error: If you use a ZConstraint,\n" |
1609 |
|
|
"\tyou must set zconsTime.\n"); |
1610 |
tim |
701 |
painCave.isFatal = 1; |
1611 |
tim |
722 |
simError(); |
1612 |
tim |
701 |
} |
1613 |
tim |
682 |
|
1614 |
tim |
701 |
//push zconsTol into siminfo, if user does not specify |
1615 |
|
|
//value for zconsTol, a default value will be used |
1616 |
|
|
DoubleData* zconsTol = new DoubleData(); |
1617 |
|
|
zconsTol->setID(ZCONSTOL_ID); |
1618 |
tim |
722 |
if (globals->haveZconsTol()){ |
1619 |
tim |
701 |
zconsTol->setData(globals->getZconsTol()); |
1620 |
|
|
} |
1621 |
|
|
else{ |
1622 |
tim |
722 |
double defaultZConsTol = 0.01; |
1623 |
|
|
sprintf(painCave.errMsg, |
1624 |
gezelter |
965 |
"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n" |
1625 |
|
|
"\tOOPSE will use a default value of %f.\n" |
1626 |
|
|
"\tTo set the tolerance, use the zconsTol variable.\n", |
1627 |
tim |
722 |
defaultZConsTol); |
1628 |
tim |
701 |
painCave.isFatal = 0; |
1629 |
|
|
simError(); |
1630 |
tim |
699 |
|
1631 |
tim |
701 |
zconsTol->setData(defaultZConsTol); |
1632 |
|
|
} |
1633 |
|
|
theInfo.addProperty(zconsTol); |
1634 |
tim |
699 |
|
1635 |
tim |
738 |
//set Force Subtraction Policy |
1636 |
tim |
722 |
StringData* zconsForcePolicy = new StringData(); |
1637 |
tim |
701 |
zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID); |
1638 |
tim |
722 |
|
1639 |
|
|
if (globals->haveZconsForcePolicy()){ |
1640 |
tim |
701 |
zconsForcePolicy->setData(globals->getZconsForcePolicy()); |
1641 |
tim |
722 |
} |
1642 |
tim |
701 |
else{ |
1643 |
tim |
722 |
sprintf(painCave.errMsg, |
1644 |
gezelter |
965 |
"ZConstraint Warning: No force subtraction policy was set.\n" |
1645 |
|
|
"\tOOPSE will use PolicyByMass.\n" |
1646 |
|
|
"\tTo set the policy, use the zconsForcePolicy variable.\n"); |
1647 |
tim |
722 |
painCave.isFatal = 0; |
1648 |
|
|
simError(); |
1649 |
tim |
736 |
zconsForcePolicy->setData("BYMASS"); |
1650 |
tim |
701 |
} |
1651 |
tim |
722 |
|
1652 |
|
|
theInfo.addProperty(zconsForcePolicy); |
1653 |
|
|
|
1654 |
tim |
701 |
//Determine the name of ouput file and add it into SimInfo's property list |
1655 |
|
|
//Be careful, do not use inFileName, since it is a pointer which |
1656 |
|
|
//point to a string at master node, and slave nodes do not contain that string |
1657 |
tim |
722 |
|
1658 |
tim |
701 |
string zconsOutput(theInfo.finalName); |
1659 |
tim |
722 |
|
1660 |
tim |
701 |
zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1661 |
tim |
722 |
|
1662 |
tim |
701 |
StringData* zconsFilename = new StringData(); |
1663 |
|
|
zconsFilename->setID(ZCONSFILENAME_ID); |
1664 |
|
|
zconsFilename->setData(zconsOutput); |
1665 |
tim |
722 |
|
1666 |
tim |
701 |
theInfo.addProperty(zconsFilename); |
1667 |
tim |
722 |
|
1668 |
tim |
701 |
//setup index, pos and other parameters of z-constraint molecules |
1669 |
|
|
nZConstraints = globals->getNzConstraints(); |
1670 |
|
|
theInfo.nZconstraints = nZConstraints; |
1671 |
|
|
|
1672 |
|
|
zconStamp = globals->getZconStamp(); |
1673 |
|
|
ZConsParaItem tempParaItem; |
1674 |
|
|
|
1675 |
|
|
ZConsParaData* zconsParaData = new ZConsParaData(); |
1676 |
|
|
zconsParaData->setID(ZCONSPARADATA_ID); |
1677 |
tim |
722 |
|
1678 |
|
|
for (int i = 0; i < nZConstraints; i++){ |
1679 |
tim |
699 |
tempParaItem.havingZPos = zconStamp[i]->haveZpos(); |
1680 |
|
|
tempParaItem.zPos = zconStamp[i]->getZpos(); |
1681 |
|
|
tempParaItem.zconsIndex = zconStamp[i]->getMolIndex(); |
1682 |
|
|
tempParaItem.kRatio = zconStamp[i]->getKratio(); |
1683 |
|
|
|
1684 |
|
|
zconsParaData->addItem(tempParaItem); |
1685 |
tim |
701 |
} |
1686 |
tim |
699 |
|
1687 |
tim |
736 |
//check the uniqueness of index |
1688 |
|
|
if(!zconsParaData->isIndexUnique()){ |
1689 |
|
|
sprintf(painCave.errMsg, |
1690 |
gezelter |
965 |
"ZConstraint Error: molIndex is not unique!\n"); |
1691 |
tim |
736 |
painCave.isFatal = 1; |
1692 |
|
|
simError(); |
1693 |
|
|
} |
1694 |
|
|
|
1695 |
tim |
701 |
//sort the parameters by index of molecules |
1696 |
|
|
zconsParaData->sortByIndex(); |
1697 |
tim |
736 |
|
1698 |
tim |
701 |
//push data into siminfo, therefore, we can retrieve later |
1699 |
|
|
theInfo.addProperty(zconsParaData); |
1700 |
tim |
660 |
} |