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#include <algorithm> |
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#include <cstdlib> |
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#include <iostream> |
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#include <cmath> |
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#include <string> |
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#include <sprng.h> |
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#include "SimSetup.hpp" |
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#include "ReadWrite.hpp" |
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#include "parse_me.h" |
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#include "Integrator.hpp" |
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#include "simError.h" |
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// some defines for ensemble and Forcefield cases |
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|
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#define NVE_ENS 0 |
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#define NVT_ENS 1 |
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#define NPTi_ENS 2 |
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#define NPTf_ENS 3 |
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#define NPTim_ENS 4 |
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#define NPTfm_ENS 5 |
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#define NVE_ENS 0 |
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#define NVT_ENS 1 |
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#define NPTi_ENS 2 |
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#define NPTf_ENS 3 |
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#define NPTxyz_ENS 4 |
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|
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|
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#define FF_DUFF 0 |
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#define FF_LJ 1 |
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#define FF_EAM 2 |
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|
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using namespace std; |
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|
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SimSetup::SimSetup(){ |
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isInfoArray = 0; |
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nInfo = 1; |
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|
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stamps = new MakeStamps(); |
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globals = new Globals(); |
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|
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|
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|
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#ifdef IS_MPI |
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strcpy( checkPointMsg, "SimSetup creation successful" ); |
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strcpy(checkPointMsg, "SimSetup creation successful"); |
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MPIcheckPoint(); |
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#endif // IS_MPI |
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} |
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delete globals; |
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} |
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|
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void SimSetup::parseFile( char* fileName ){ |
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void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){ |
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info = the_info; |
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nInfo = theNinfo; |
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isInfoArray = 1; |
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} |
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|
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|
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void SimSetup::parseFile(char* fileName){ |
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#ifdef IS_MPI |
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if( worldRank == 0 ){ |
61 |
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if (worldRank == 0){ |
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#endif // is_mpi |
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|
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|
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inFileName = fileName; |
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set_interface_stamps( stamps, globals ); |
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|
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set_interface_stamps(stamps, globals); |
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|
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#ifdef IS_MPI |
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mpiEventInit(); |
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#endif |
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|
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yacc_BASS( fileName ); |
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yacc_BASS(fileName); |
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|
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#ifdef IS_MPI |
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throwMPIEvent(NULL); |
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} |
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else receiveParse(); |
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else{ |
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receiveParse(); |
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} |
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#endif |
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|
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} |
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|
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#ifdef IS_MPI |
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void SimSetup::receiveParse(void){ |
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|
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set_interface_stamps( stamps, globals ); |
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mpiEventInit(); |
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MPIcheckPoint(); |
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mpiEventLoop(); |
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|
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set_interface_stamps(stamps, globals); |
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mpiEventInit(); |
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MPIcheckPoint(); |
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mpiEventLoop(); |
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} |
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#endif // is_mpi |
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void SimSetup::createSim( void ){ |
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void SimSetup::createSim(void){ |
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|
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int i, j, k, globalAtomIndex; |
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|
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// gather all of the information from the Bass file |
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|
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|
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gatherInfo(); |
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|
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// creation of complex system objects |
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sysObjectsCreation(); |
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// check on the post processing info |
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|
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finalInfoCheck(); |
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// initialize the system coordinates |
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initSystemCoords(); |
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|
109 |
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if (!isInfoArray){ |
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initSystemCoords(); |
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|
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if( !(globals->getUseInitTime()) ) |
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info[0].currentTime = 0.0; |
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} |
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|
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// make the output filenames |
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makeOutNames(); |
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|
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// make the integrator |
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|
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makeIntegrator(); |
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|
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|
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#ifdef IS_MPI |
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mpiSim->mpiRefresh(); |
126 |
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#endif |
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// initialize the Fortran |
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|
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initFortran(); |
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|
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|
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} |
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void SimSetup::makeMolecules( void ){ |
135 |
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|
134 |
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void SimSetup::makeMolecules(void){ |
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int k; |
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int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
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molInit molInfo; |
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DirectionalAtom* dAtom; |
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bend_set* theBends; |
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torsion_set* theTorsions; |
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|
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|
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|
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//init the forceField paramters |
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the_ff->readParams(); |
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|
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// init the atoms |
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|
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double ux, uy, uz, u, uSqr; |
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|
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atomOffset = 0; |
148 |
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excludeOffset = 0; |
149 |
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for(i=0; i<info->n_mol; i++){ |
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|
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stampID = the_molecules[i].getStampID(); |
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|
160 |
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molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
161 |
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molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
155 |
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molInfo.nBends = comp_stamps[stampID]->getNBends(); |
156 |
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molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
157 |
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molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
160 |
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for (k = 0; k < nInfo; k++){ |
161 |
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the_ff->setSimInfo(&(info[k])); |
162 |
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|
163 |
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molInfo.myAtoms = &the_atoms[atomOffset]; |
164 |
< |
molInfo.myExcludes = &the_excludes[excludeOffset]; |
165 |
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molInfo.myBonds = new Bond*[molInfo.nBonds]; |
166 |
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molInfo.myBends = new Bend*[molInfo.nBends]; |
163 |
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molInfo.myTorsions = new Torsion*[molInfo.nTorsions]; |
163 |
> |
atomOffset = 0; |
164 |
> |
excludeOffset = 0; |
165 |
> |
for (i = 0; i < info[k].n_mol; i++){ |
166 |
> |
stampID = info[k].molecules[i].getStampID(); |
167 |
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|
168 |
< |
theBonds = new bond_pair[molInfo.nBonds]; |
169 |
< |
theBends = new bend_set[molInfo.nBends]; |
170 |
< |
theTorsions = new torsion_set[molInfo.nTorsions]; |
171 |
< |
|
172 |
< |
// make the Atoms |
173 |
< |
|
174 |
< |
for(j=0; j<molInfo.nAtoms; j++){ |
175 |
< |
|
176 |
< |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
177 |
< |
if( currentAtom->haveOrientation() ){ |
178 |
< |
|
179 |
< |
dAtom = new DirectionalAtom(j + atomOffset); |
180 |
< |
info->n_oriented++; |
181 |
< |
molInfo.myAtoms[j] = dAtom; |
182 |
< |
|
183 |
< |
ux = currentAtom->getOrntX(); |
184 |
< |
uy = currentAtom->getOrntY(); |
185 |
< |
uz = currentAtom->getOrntZ(); |
186 |
< |
|
187 |
< |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
188 |
< |
|
189 |
< |
u = sqrt( uSqr ); |
190 |
< |
ux = ux / u; |
191 |
< |
uy = uy / u; |
192 |
< |
uz = uz / u; |
193 |
< |
|
194 |
< |
dAtom->setSUx( ux ); |
195 |
< |
dAtom->setSUy( uy ); |
196 |
< |
dAtom->setSUz( uz ); |
197 |
< |
} |
198 |
< |
else{ |
199 |
< |
molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset); |
200 |
< |
} |
201 |
< |
molInfo.myAtoms[j]->setType( currentAtom->getType() ); |
202 |
< |
|
168 |
> |
molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
169 |
> |
molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
170 |
> |
molInfo.nBends = comp_stamps[stampID]->getNBends(); |
171 |
> |
molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
172 |
> |
molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
173 |
> |
|
174 |
> |
molInfo.myAtoms = &(info[k].atoms[atomOffset]); |
175 |
> |
molInfo.myExcludes = &(info[k].excludes[excludeOffset]); |
176 |
> |
molInfo.myBonds = new Bond * [molInfo.nBonds]; |
177 |
> |
molInfo.myBends = new Bend * [molInfo.nBends]; |
178 |
> |
molInfo.myTorsions = new Torsion * [molInfo.nTorsions]; |
179 |
> |
|
180 |
> |
theBonds = new bond_pair[molInfo.nBonds]; |
181 |
> |
theBends = new bend_set[molInfo.nBends]; |
182 |
> |
theTorsions = new torsion_set[molInfo.nTorsions]; |
183 |
> |
|
184 |
> |
// make the Atoms |
185 |
> |
|
186 |
> |
for (j = 0; j < molInfo.nAtoms; j++){ |
187 |
> |
currentAtom = comp_stamps[stampID]->getAtom(j); |
188 |
> |
if (currentAtom->haveOrientation()){ |
189 |
> |
dAtom = new DirectionalAtom((j + atomOffset), |
190 |
> |
info[k].getConfiguration()); |
191 |
> |
info[k].n_oriented++; |
192 |
> |
molInfo.myAtoms[j] = dAtom; |
193 |
> |
|
194 |
> |
ux = currentAtom->getOrntX(); |
195 |
> |
uy = currentAtom->getOrntY(); |
196 |
> |
uz = currentAtom->getOrntZ(); |
197 |
> |
|
198 |
> |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
199 |
> |
|
200 |
> |
u = sqrt(uSqr); |
201 |
> |
ux = ux / u; |
202 |
> |
uy = uy / u; |
203 |
> |
uz = uz / u; |
204 |
> |
|
205 |
> |
dAtom->setSUx(ux); |
206 |
> |
dAtom->setSUy(uy); |
207 |
> |
dAtom->setSUz(uz); |
208 |
> |
} |
209 |
> |
else{ |
210 |
> |
molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset), |
211 |
> |
info[k].getConfiguration()); |
212 |
> |
} |
213 |
> |
molInfo.myAtoms[j]->setType(currentAtom->getType()); |
214 |
> |
|
215 |
|
#ifdef IS_MPI |
216 |
< |
|
217 |
< |
molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
218 |
< |
|
216 |
> |
|
217 |
> |
molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]); |
218 |
> |
|
219 |
|
#endif // is_mpi |
220 |
< |
} |
206 |
< |
|
207 |
< |
// make the bonds |
208 |
< |
for(j=0; j<molInfo.nBonds; j++){ |
209 |
< |
|
210 |
< |
currentBond = comp_stamps[stampID]->getBond( j ); |
211 |
< |
theBonds[j].a = currentBond->getA() + atomOffset; |
212 |
< |
theBonds[j].b = currentBond->getB() + atomOffset; |
220 |
> |
} |
221 |
|
|
222 |
< |
exI = theBonds[j].a; |
223 |
< |
exJ = theBonds[j].b; |
222 |
> |
// make the bonds |
223 |
> |
for (j = 0; j < molInfo.nBonds; j++){ |
224 |
> |
currentBond = comp_stamps[stampID]->getBond(j); |
225 |
> |
theBonds[j].a = currentBond->getA() + atomOffset; |
226 |
> |
theBonds[j].b = currentBond->getB() + atomOffset; |
227 |
|
|
228 |
< |
// exclude_I must always be the smaller of the pair |
229 |
< |
if( exI > exJ ){ |
230 |
< |
tempEx = exI; |
231 |
< |
exI = exJ; |
232 |
< |
exJ = tempEx; |
233 |
< |
} |
228 |
> |
exI = theBonds[j].a; |
229 |
> |
exJ = theBonds[j].b; |
230 |
> |
|
231 |
> |
// exclude_I must always be the smaller of the pair |
232 |
> |
if (exI > exJ){ |
233 |
> |
tempEx = exI; |
234 |
> |
exI = exJ; |
235 |
> |
exJ = tempEx; |
236 |
> |
} |
237 |
|
#ifdef IS_MPI |
238 |
< |
tempEx = exI; |
239 |
< |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
240 |
< |
tempEx = exJ; |
241 |
< |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
242 |
< |
|
243 |
< |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
238 |
> |
tempEx = exI; |
239 |
> |
exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
240 |
> |
tempEx = exJ; |
241 |
> |
exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
242 |
> |
|
243 |
> |
info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
244 |
|
#else // isn't MPI |
245 |
|
|
246 |
< |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
246 |
> |
info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
247 |
|
#endif //is_mpi |
248 |
< |
} |
249 |
< |
excludeOffset += molInfo.nBonds; |
248 |
> |
} |
249 |
> |
excludeOffset += molInfo.nBonds; |
250 |
|
|
251 |
< |
//make the bends |
252 |
< |
for(j=0; j<molInfo.nBends; j++){ |
253 |
< |
|
254 |
< |
currentBend = comp_stamps[stampID]->getBend( j ); |
255 |
< |
theBends[j].a = currentBend->getA() + atomOffset; |
256 |
< |
theBends[j].b = currentBend->getB() + atomOffset; |
257 |
< |
theBends[j].c = currentBend->getC() + atomOffset; |
258 |
< |
|
259 |
< |
if( currentBend->haveExtras() ){ |
260 |
< |
|
261 |
< |
extras = currentBend->getExtras(); |
262 |
< |
current_extra = extras; |
263 |
< |
|
264 |
< |
while( current_extra != NULL ){ |
265 |
< |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
266 |
< |
|
267 |
< |
switch( current_extra->getType() ){ |
268 |
< |
|
269 |
< |
case 0: |
270 |
< |
theBends[j].ghost = |
271 |
< |
current_extra->getInt() + atomOffset; |
272 |
< |
theBends[j].isGhost = 1; |
273 |
< |
break; |
274 |
< |
|
275 |
< |
case 1: |
276 |
< |
theBends[j].ghost = |
277 |
< |
(int)current_extra->getDouble() + atomOffset; |
278 |
< |
theBends[j].isGhost = 1; |
279 |
< |
break; |
280 |
< |
|
281 |
< |
default: |
282 |
< |
sprintf( painCave.errMsg, |
283 |
< |
"SimSetup Error: ghostVectorSource was neither a " |
284 |
< |
"double nor an int.\n" |
285 |
< |
"-->Bend[%d] in %s\n", |
286 |
< |
j, comp_stamps[stampID]->getID() ); |
287 |
< |
painCave.isFatal = 1; |
288 |
< |
simError(); |
289 |
< |
} |
290 |
< |
} |
291 |
< |
|
292 |
< |
else{ |
293 |
< |
|
294 |
< |
sprintf( painCave.errMsg, |
295 |
< |
"SimSetup Error: unhandled bend assignment:\n" |
296 |
< |
" -->%s in Bend[%d] in %s\n", |
297 |
< |
current_extra->getlhs(), |
298 |
< |
j, comp_stamps[stampID]->getID() ); |
299 |
< |
painCave.isFatal = 1; |
300 |
< |
simError(); |
301 |
< |
} |
302 |
< |
|
303 |
< |
current_extra = current_extra->getNext(); |
304 |
< |
} |
305 |
< |
} |
306 |
< |
|
307 |
< |
if( !theBends[j].isGhost ){ |
308 |
< |
|
309 |
< |
exI = theBends[j].a; |
310 |
< |
exJ = theBends[j].c; |
311 |
< |
} |
312 |
< |
else{ |
313 |
< |
|
300 |
< |
exI = theBends[j].a; |
301 |
< |
exJ = theBends[j].b; |
302 |
< |
} |
303 |
< |
|
304 |
< |
// exclude_I must always be the smaller of the pair |
305 |
< |
if( exI > exJ ){ |
306 |
< |
tempEx = exI; |
307 |
< |
exI = exJ; |
308 |
< |
exJ = tempEx; |
309 |
< |
} |
251 |
> |
//make the bends |
252 |
> |
for (j = 0; j < molInfo.nBends; j++){ |
253 |
> |
currentBend = comp_stamps[stampID]->getBend(j); |
254 |
> |
theBends[j].a = currentBend->getA() + atomOffset; |
255 |
> |
theBends[j].b = currentBend->getB() + atomOffset; |
256 |
> |
theBends[j].c = currentBend->getC() + atomOffset; |
257 |
> |
|
258 |
> |
if (currentBend->haveExtras()){ |
259 |
> |
extras = currentBend->getExtras(); |
260 |
> |
current_extra = extras; |
261 |
> |
|
262 |
> |
while (current_extra != NULL){ |
263 |
> |
if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){ |
264 |
> |
switch (current_extra->getType()){ |
265 |
> |
case 0: |
266 |
> |
theBends[j].ghost = current_extra->getInt() + atomOffset; |
267 |
> |
theBends[j].isGhost = 1; |
268 |
> |
break; |
269 |
> |
|
270 |
> |
case 1: |
271 |
> |
theBends[j].ghost = (int) current_extra->getDouble() + |
272 |
> |
atomOffset; |
273 |
> |
theBends[j].isGhost = 1; |
274 |
> |
break; |
275 |
> |
|
276 |
> |
default: |
277 |
> |
sprintf(painCave.errMsg, |
278 |
> |
"SimSetup Error: ghostVectorSource was neither a " |
279 |
> |
"double nor an int.\n" |
280 |
> |
"-->Bend[%d] in %s\n", |
281 |
> |
j, comp_stamps[stampID]->getID()); |
282 |
> |
painCave.isFatal = 1; |
283 |
> |
simError(); |
284 |
> |
} |
285 |
> |
} |
286 |
> |
else{ |
287 |
> |
sprintf(painCave.errMsg, |
288 |
> |
"SimSetup Error: unhandled bend assignment:\n" |
289 |
> |
" -->%s in Bend[%d] in %s\n", |
290 |
> |
current_extra->getlhs(), j, comp_stamps[stampID]->getID()); |
291 |
> |
painCave.isFatal = 1; |
292 |
> |
simError(); |
293 |
> |
} |
294 |
> |
|
295 |
> |
current_extra = current_extra->getNext(); |
296 |
> |
} |
297 |
> |
} |
298 |
> |
|
299 |
> |
if (!theBends[j].isGhost){ |
300 |
> |
exI = theBends[j].a; |
301 |
> |
exJ = theBends[j].c; |
302 |
> |
} |
303 |
> |
else{ |
304 |
> |
exI = theBends[j].a; |
305 |
> |
exJ = theBends[j].b; |
306 |
> |
} |
307 |
> |
|
308 |
> |
// exclude_I must always be the smaller of the pair |
309 |
> |
if (exI > exJ){ |
310 |
> |
tempEx = exI; |
311 |
> |
exI = exJ; |
312 |
> |
exJ = tempEx; |
313 |
> |
} |
314 |
|
#ifdef IS_MPI |
315 |
< |
tempEx = exI; |
316 |
< |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
317 |
< |
tempEx = exJ; |
318 |
< |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
319 |
< |
|
320 |
< |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
315 |
> |
tempEx = exI; |
316 |
> |
exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
317 |
> |
tempEx = exJ; |
318 |
> |
exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
319 |
> |
|
320 |
> |
info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
321 |
|
#else // isn't MPI |
322 |
< |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
322 |
> |
info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
323 |
|
#endif //is_mpi |
324 |
< |
} |
325 |
< |
excludeOffset += molInfo.nBends; |
324 |
> |
} |
325 |
> |
excludeOffset += molInfo.nBends; |
326 |
|
|
327 |
< |
for(j=0; j<molInfo.nTorsions; j++){ |
328 |
< |
|
329 |
< |
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
330 |
< |
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
331 |
< |
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
332 |
< |
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
329 |
< |
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
330 |
< |
|
331 |
< |
exI = theTorsions[j].a; |
332 |
< |
exJ = theTorsions[j].d; |
327 |
> |
for (j = 0; j < molInfo.nTorsions; j++){ |
328 |
> |
currentTorsion = comp_stamps[stampID]->getTorsion(j); |
329 |
> |
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
330 |
> |
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
331 |
> |
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
332 |
> |
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
333 |
|
|
334 |
< |
// exclude_I must always be the smaller of the pair |
335 |
< |
if( exI > exJ ){ |
336 |
< |
tempEx = exI; |
337 |
< |
exI = exJ; |
338 |
< |
exJ = tempEx; |
339 |
< |
} |
334 |
> |
exI = theTorsions[j].a; |
335 |
> |
exJ = theTorsions[j].d; |
336 |
> |
|
337 |
> |
// exclude_I must always be the smaller of the pair |
338 |
> |
if (exI > exJ){ |
339 |
> |
tempEx = exI; |
340 |
> |
exI = exJ; |
341 |
> |
exJ = tempEx; |
342 |
> |
} |
343 |
|
#ifdef IS_MPI |
344 |
< |
tempEx = exI; |
345 |
< |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
346 |
< |
tempEx = exJ; |
347 |
< |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
348 |
< |
|
349 |
< |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
344 |
> |
tempEx = exI; |
345 |
> |
exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
346 |
> |
tempEx = exJ; |
347 |
> |
exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
348 |
> |
|
349 |
> |
info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
350 |
|
#else // isn't MPI |
351 |
< |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
351 |
> |
info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
352 |
|
#endif //is_mpi |
353 |
< |
} |
354 |
< |
excludeOffset += molInfo.nTorsions; |
353 |
> |
} |
354 |
> |
excludeOffset += molInfo.nTorsions; |
355 |
|
|
353 |
– |
|
354 |
– |
// send the arrays off to the forceField for init. |
356 |
|
|
357 |
< |
the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms ); |
357 |
< |
the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds ); |
358 |
< |
the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends ); |
359 |
< |
the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions ); |
357 |
> |
// send the arrays off to the forceField for init. |
358 |
|
|
359 |
+ |
the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms); |
360 |
+ |
the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds); |
361 |
+ |
the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends); |
362 |
+ |
the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions, |
363 |
+ |
theTorsions); |
364 |
|
|
362 |
– |
the_molecules[i].initialize( molInfo ); |
365 |
|
|
366 |
+ |
info[k].molecules[i].initialize(molInfo); |
367 |
|
|
368 |
< |
atomOffset += molInfo.nAtoms; |
369 |
< |
delete[] theBonds; |
370 |
< |
delete[] theBends; |
371 |
< |
delete[] theTorsions; |
368 |
> |
|
369 |
> |
atomOffset += molInfo.nAtoms; |
370 |
> |
delete[] theBonds; |
371 |
> |
delete[] theBends; |
372 |
> |
delete[] theTorsions; |
373 |
> |
} |
374 |
|
} |
375 |
|
|
376 |
|
#ifdef IS_MPI |
377 |
< |
sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
377 |
> |
sprintf(checkPointMsg, "all molecules initialized succesfully"); |
378 |
|
MPIcheckPoint(); |
379 |
|
#endif // is_mpi |
380 |
|
|
381 |
|
// clean up the forcefield |
382 |
+ |
|
383 |
|
the_ff->calcRcut(); |
384 |
|
the_ff->cleanMe(); |
379 |
– |
|
385 |
|
} |
386 |
|
|
387 |
< |
void SimSetup::initFromBass( void ){ |
383 |
< |
|
387 |
> |
void SimSetup::initFromBass(void){ |
388 |
|
int i, j, k; |
389 |
|
int n_cells; |
390 |
|
double cellx, celly, cellz; |
393 |
|
int n_extra; |
394 |
|
int have_extra, done; |
395 |
|
|
396 |
< |
temp1 = (double)tot_nmol / 4.0; |
397 |
< |
temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
398 |
< |
temp3 = ceil( temp2 ); |
396 |
> |
double vel[3]; |
397 |
> |
vel[0] = 0.0; |
398 |
> |
vel[1] = 0.0; |
399 |
> |
vel[2] = 0.0; |
400 |
|
|
401 |
< |
have_extra =0; |
402 |
< |
if( temp2 < temp3 ){ // we have a non-complete lattice |
403 |
< |
have_extra =1; |
401 |
> |
temp1 = (double) tot_nmol / 4.0; |
402 |
> |
temp2 = pow(temp1, (1.0 / 3.0)); |
403 |
> |
temp3 = ceil(temp2); |
404 |
|
|
405 |
< |
n_cells = (int)temp3 - 1; |
406 |
< |
cellx = info->boxL[0] / temp3; |
407 |
< |
celly = info->boxL[1] / temp3; |
408 |
< |
cellz = info->boxL[2] / temp3; |
404 |
< |
n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
405 |
< |
temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
406 |
< |
n_per_extra = (int)ceil( temp1 ); |
405 |
> |
have_extra = 0; |
406 |
> |
if (temp2 < temp3){ |
407 |
> |
// we have a non-complete lattice |
408 |
> |
have_extra = 1; |
409 |
|
|
410 |
< |
if( n_per_extra > 4){ |
411 |
< |
sprintf( painCave.errMsg, |
412 |
< |
"SimSetup error. There has been an error in constructing" |
413 |
< |
" the non-complete lattice.\n" ); |
410 |
> |
n_cells = (int) temp3 - 1; |
411 |
> |
cellx = info[0].boxL[0] / temp3; |
412 |
> |
celly = info[0].boxL[1] / temp3; |
413 |
> |
cellz = info[0].boxL[2] / temp3; |
414 |
> |
n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells); |
415 |
> |
temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0)); |
416 |
> |
n_per_extra = (int) ceil(temp1); |
417 |
> |
|
418 |
> |
if (n_per_extra > 4){ |
419 |
> |
sprintf(painCave.errMsg, |
420 |
> |
"SimSetup error. There has been an error in constructing" |
421 |
> |
" the non-complete lattice.\n"); |
422 |
|
painCave.isFatal = 1; |
423 |
|
simError(); |
424 |
|
} |
425 |
|
} |
426 |
|
else{ |
427 |
< |
n_cells = (int)temp3; |
428 |
< |
cellx = info->boxL[0] / temp3; |
429 |
< |
celly = info->boxL[1] / temp3; |
430 |
< |
cellz = info->boxL[2] / temp3; |
427 |
> |
n_cells = (int) temp3; |
428 |
> |
cellx = info[0].boxL[0] / temp3; |
429 |
> |
celly = info[0].boxL[1] / temp3; |
430 |
> |
cellz = info[0].boxL[2] / temp3; |
431 |
|
} |
432 |
|
|
433 |
|
current_mol = 0; |
435 |
|
current_comp = 0; |
436 |
|
current_atom_ndx = 0; |
437 |
|
|
438 |
< |
for( i=0; i < n_cells ; i++ ){ |
439 |
< |
for( j=0; j < n_cells; j++ ){ |
440 |
< |
for( k=0; k < n_cells; k++ ){ |
438 |
> |
for (i = 0; i < n_cells ; i++){ |
439 |
> |
for (j = 0; j < n_cells; j++){ |
440 |
> |
for (k = 0; k < n_cells; k++){ |
441 |
> |
makeElement(i * cellx, j * celly, k * cellz); |
442 |
|
|
443 |
< |
makeElement( i * cellx, |
433 |
< |
j * celly, |
434 |
< |
k * cellz ); |
443 |
> |
makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz); |
444 |
|
|
445 |
< |
makeElement( i * cellx + 0.5 * cellx, |
437 |
< |
j * celly + 0.5 * celly, |
438 |
< |
k * cellz ); |
445 |
> |
makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz); |
446 |
|
|
447 |
< |
makeElement( i * cellx, |
441 |
< |
j * celly + 0.5 * celly, |
442 |
< |
k * cellz + 0.5 * cellz ); |
443 |
< |
|
444 |
< |
makeElement( i * cellx + 0.5 * cellx, |
445 |
< |
j * celly, |
446 |
< |
k * cellz + 0.5 * cellz ); |
447 |
> |
makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz); |
448 |
|
} |
449 |
|
} |
450 |
|
} |
451 |
|
|
452 |
< |
if( have_extra ){ |
452 |
> |
if (have_extra){ |
453 |
|
done = 0; |
454 |
|
|
455 |
|
int start_ndx; |
456 |
< |
for( i=0; i < (n_cells+1) && !done; i++ ){ |
457 |
< |
for( j=0; j < (n_cells+1) && !done; j++ ){ |
456 |
> |
for (i = 0; i < (n_cells + 1) && !done; i++){ |
457 |
> |
for (j = 0; j < (n_cells + 1) && !done; j++){ |
458 |
> |
if (i < n_cells){ |
459 |
> |
if (j < n_cells){ |
460 |
> |
start_ndx = n_cells; |
461 |
> |
} |
462 |
> |
else |
463 |
> |
start_ndx = 0; |
464 |
> |
} |
465 |
> |
else |
466 |
> |
start_ndx = 0; |
467 |
|
|
468 |
< |
if( i < n_cells ){ |
468 |
> |
for (k = start_ndx; k < (n_cells + 1) && !done; k++){ |
469 |
> |
makeElement(i * cellx, j * celly, k * cellz); |
470 |
> |
done = (current_mol >= tot_nmol); |
471 |
|
|
472 |
< |
if( j < n_cells ){ |
473 |
< |
start_ndx = n_cells; |
474 |
< |
} |
475 |
< |
else start_ndx = 0; |
476 |
< |
} |
465 |
< |
else start_ndx = 0; |
472 |
> |
if (!done && n_per_extra > 1){ |
473 |
> |
makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, |
474 |
> |
k * cellz); |
475 |
> |
done = (current_mol >= tot_nmol); |
476 |
> |
} |
477 |
|
|
478 |
< |
for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
478 |
> |
if (!done && n_per_extra > 2){ |
479 |
> |
makeElement(i * cellx, j * celly + 0.5 * celly, |
480 |
> |
k * cellz + 0.5 * cellz); |
481 |
> |
done = (current_mol >= tot_nmol); |
482 |
> |
} |
483 |
|
|
484 |
< |
makeElement( i * cellx, |
485 |
< |
j * celly, |
486 |
< |
k * cellz ); |
487 |
< |
done = ( current_mol >= tot_nmol ); |
488 |
< |
|
489 |
< |
if( !done && n_per_extra > 1 ){ |
475 |
< |
makeElement( i * cellx + 0.5 * cellx, |
476 |
< |
j * celly + 0.5 * celly, |
477 |
< |
k * cellz ); |
478 |
< |
done = ( current_mol >= tot_nmol ); |
479 |
< |
} |
480 |
< |
|
481 |
< |
if( !done && n_per_extra > 2){ |
482 |
< |
makeElement( i * cellx, |
483 |
< |
j * celly + 0.5 * celly, |
484 |
< |
k * cellz + 0.5 * cellz ); |
485 |
< |
done = ( current_mol >= tot_nmol ); |
486 |
< |
} |
487 |
< |
|
488 |
< |
if( !done && n_per_extra > 3){ |
489 |
< |
makeElement( i * cellx + 0.5 * cellx, |
490 |
< |
j * celly, |
491 |
< |
k * cellz + 0.5 * cellz ); |
492 |
< |
done = ( current_mol >= tot_nmol ); |
493 |
< |
} |
494 |
< |
} |
484 |
> |
if (!done && n_per_extra > 3){ |
485 |
> |
makeElement(i * cellx + 0.5 * cellx, j * celly, |
486 |
> |
k * cellz + 0.5 * cellz); |
487 |
> |
done = (current_mol >= tot_nmol); |
488 |
> |
} |
489 |
> |
} |
490 |
|
} |
491 |
|
} |
492 |
|
} |
493 |
|
|
494 |
< |
|
495 |
< |
for( i=0; i<info->n_atoms; i++ ){ |
501 |
< |
info->atoms[i]->set_vx( 0.0 ); |
502 |
< |
info->atoms[i]->set_vy( 0.0 ); |
503 |
< |
info->atoms[i]->set_vz( 0.0 ); |
494 |
> |
for (i = 0; i < info[0].n_atoms; i++){ |
495 |
> |
info[0].atoms[i]->setVel(vel); |
496 |
|
} |
497 |
|
} |
498 |
|
|
499 |
< |
void SimSetup::makeElement( double x, double y, double z ){ |
508 |
< |
|
499 |
> |
void SimSetup::makeElement(double x, double y, double z){ |
500 |
|
int k; |
501 |
|
AtomStamp* current_atom; |
502 |
|
DirectionalAtom* dAtom; |
503 |
|
double rotMat[3][3]; |
504 |
+ |
double pos[3]; |
505 |
|
|
506 |
< |
for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
507 |
< |
|
508 |
< |
current_atom = comp_stamps[current_comp]->getAtom( k ); |
509 |
< |
if( !current_atom->havePosition() ){ |
510 |
< |
sprintf( painCave.errMsg, |
511 |
< |
"SimSetup:initFromBass error.\n" |
512 |
< |
"\tComponent %s, atom %s does not have a position specified.\n" |
513 |
< |
"\tThe initialization routine is unable to give a start" |
514 |
< |
" position.\n", |
523 |
< |
comp_stamps[current_comp]->getID(), |
524 |
< |
current_atom->getType() ); |
506 |
> |
for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){ |
507 |
> |
current_atom = comp_stamps[current_comp]->getAtom(k); |
508 |
> |
if (!current_atom->havePosition()){ |
509 |
> |
sprintf(painCave.errMsg, |
510 |
> |
"SimSetup:initFromBass error.\n" |
511 |
> |
"\tComponent %s, atom %s does not have a position specified.\n" |
512 |
> |
"\tThe initialization routine is unable to give a start" |
513 |
> |
" position.\n", |
514 |
> |
comp_stamps[current_comp]->getID(), current_atom->getType()); |
515 |
|
painCave.isFatal = 1; |
516 |
|
simError(); |
517 |
|
} |
518 |
|
|
519 |
< |
the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() ); |
520 |
< |
the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() ); |
521 |
< |
the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() ); |
519 |
> |
pos[0] = x + current_atom->getPosX(); |
520 |
> |
pos[1] = y + current_atom->getPosY(); |
521 |
> |
pos[2] = z + current_atom->getPosZ(); |
522 |
|
|
523 |
< |
if( the_atoms[current_atom_ndx]->isDirectional() ){ |
523 |
> |
info[0].atoms[current_atom_ndx]->setPos(pos); |
524 |
|
|
525 |
< |
dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx]; |
525 |
> |
if (info[0].atoms[current_atom_ndx]->isDirectional()){ |
526 |
> |
dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx]; |
527 |
|
|
528 |
|
rotMat[0][0] = 1.0; |
529 |
|
rotMat[0][1] = 0.0; |
537 |
|
rotMat[2][1] = 0.0; |
538 |
|
rotMat[2][2] = 1.0; |
539 |
|
|
540 |
< |
dAtom->setA( rotMat ); |
540 |
> |
dAtom->setA(rotMat); |
541 |
|
} |
542 |
|
|
543 |
|
current_atom_ndx++; |
546 |
|
current_mol++; |
547 |
|
current_comp_mol++; |
548 |
|
|
549 |
< |
if( current_comp_mol >= components_nmol[current_comp] ){ |
559 |
< |
|
549 |
> |
if (current_comp_mol >= components_nmol[current_comp]){ |
550 |
|
current_comp_mol = 0; |
551 |
|
current_comp++; |
552 |
|
} |
553 |
|
} |
554 |
|
|
555 |
|
|
556 |
< |
void SimSetup::gatherInfo( void ){ |
557 |
< |
int i,j,k; |
556 |
> |
void SimSetup::gatherInfo(void){ |
557 |
> |
int i; |
558 |
|
|
559 |
|
ensembleCase = -1; |
560 |
|
ffCase = -1; |
561 |
|
|
572 |
– |
// get the stamps and globals; |
573 |
– |
stamps = stamps; |
574 |
– |
globals = globals; |
575 |
– |
|
562 |
|
// set the easy ones first |
563 |
< |
info->target_temp = globals->getTargetTemp(); |
564 |
< |
info->dt = globals->getDt(); |
565 |
< |
info->run_time = globals->getRunTime(); |
563 |
> |
|
564 |
> |
for (i = 0; i < nInfo; i++){ |
565 |
> |
info[i].target_temp = globals->getTargetTemp(); |
566 |
> |
info[i].dt = globals->getDt(); |
567 |
> |
info[i].run_time = globals->getRunTime(); |
568 |
> |
} |
569 |
|
n_components = globals->getNComponents(); |
570 |
|
|
571 |
|
|
572 |
|
// get the forceField |
573 |
|
|
574 |
< |
strcpy( force_field, globals->getForceField() ); |
574 |
> |
strcpy(force_field, globals->getForceField()); |
575 |
|
|
576 |
< |
if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
577 |
< |
else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
576 |
> |
if (!strcasecmp(force_field, "DUFF")){ |
577 |
> |
ffCase = FF_DUFF; |
578 |
> |
} |
579 |
> |
else if (!strcasecmp(force_field, "LJ")){ |
580 |
> |
ffCase = FF_LJ; |
581 |
> |
} |
582 |
> |
else if (!strcasecmp(force_field, "EAM")){ |
583 |
> |
ffCase = FF_EAM; |
584 |
> |
} |
585 |
|
else{ |
586 |
< |
sprintf( painCave.errMsg, |
587 |
< |
"SimSetup Error. Unrecognized force field -> %s\n", |
588 |
< |
force_field ); |
589 |
< |
painCave.isFatal = 1; |
594 |
< |
simError(); |
586 |
> |
sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n", |
587 |
> |
force_field); |
588 |
> |
painCave.isFatal = 1; |
589 |
> |
simError(); |
590 |
|
} |
591 |
|
|
592 |
< |
// get the ensemble |
592 |
> |
// get the ensemble |
593 |
|
|
594 |
< |
strcpy( ensemble, globals->getEnsemble() ); |
594 |
> |
strcpy(ensemble, globals->getEnsemble()); |
595 |
|
|
596 |
< |
if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
597 |
< |
else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
598 |
< |
else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") ) |
596 |
> |
if (!strcasecmp(ensemble, "NVE")){ |
597 |
> |
ensembleCase = NVE_ENS; |
598 |
> |
} |
599 |
> |
else if (!strcasecmp(ensemble, "NVT")){ |
600 |
> |
ensembleCase = NVT_ENS; |
601 |
> |
} |
602 |
> |
else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){ |
603 |
|
ensembleCase = NPTi_ENS; |
604 |
< |
else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; |
605 |
< |
else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS; |
606 |
< |
else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; |
604 |
> |
} |
605 |
> |
else if (!strcasecmp(ensemble, "NPTf")){ |
606 |
> |
ensembleCase = NPTf_ENS; |
607 |
> |
} |
608 |
> |
else if (!strcasecmp(ensemble, "NPTxyz")){ |
609 |
> |
ensembleCase = NPTxyz_ENS; |
610 |
> |
} |
611 |
|
else{ |
612 |
< |
sprintf( painCave.errMsg, |
613 |
< |
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
614 |
< |
"reverting to NVE for this simulation.\n", |
615 |
< |
ensemble ); |
616 |
< |
painCave.isFatal = 0; |
617 |
< |
simError(); |
618 |
< |
strcpy( ensemble, "NVE" ); |
619 |
< |
ensembleCase = NVE_ENS; |
612 |
> |
sprintf(painCave.errMsg, |
613 |
> |
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
614 |
> |
"reverting to NVE for this simulation.\n", |
615 |
> |
ensemble); |
616 |
> |
painCave.isFatal = 0; |
617 |
> |
simError(); |
618 |
> |
strcpy(ensemble, "NVE"); |
619 |
> |
ensembleCase = NVE_ENS; |
620 |
|
} |
618 |
– |
strcpy( info->ensemble, ensemble ); |
621 |
|
|
622 |
< |
// get the mixing rule |
622 |
> |
for (i = 0; i < nInfo; i++){ |
623 |
> |
strcpy(info[i].ensemble, ensemble); |
624 |
|
|
625 |
< |
strcpy( info->mixingRule, globals->getMixingRule() ); |
626 |
< |
info->usePBC = globals->getPBC(); |
627 |
< |
|
628 |
< |
|
625 |
> |
// get the mixing rule |
626 |
> |
|
627 |
> |
strcpy(info[i].mixingRule, globals->getMixingRule()); |
628 |
> |
info[i].usePBC = globals->getPBC(); |
629 |
> |
} |
630 |
> |
|
631 |
|
// get the components and calculate the tot_nMol and indvidual n_mol |
632 |
< |
|
632 |
> |
|
633 |
|
the_components = globals->getComponents(); |
634 |
|
components_nmol = new int[n_components]; |
635 |
|
|
636 |
|
|
637 |
< |
if( !globals->haveNMol() ){ |
637 |
> |
if (!globals->haveNMol()){ |
638 |
|
// we don't have the total number of molecules, so we assume it is |
639 |
|
// given in each component |
640 |
|
|
641 |
|
tot_nmol = 0; |
642 |
< |
for( i=0; i<n_components; i++ ){ |
643 |
< |
|
644 |
< |
if( !the_components[i]->haveNMol() ){ |
645 |
< |
// we have a problem |
646 |
< |
sprintf( painCave.errMsg, |
647 |
< |
"SimSetup Error. No global NMol or component NMol" |
648 |
< |
" given. Cannot calculate the number of atoms.\n" ); |
649 |
< |
painCave.isFatal = 1; |
645 |
< |
simError(); |
642 |
> |
for (i = 0; i < n_components; i++){ |
643 |
> |
if (!the_components[i]->haveNMol()){ |
644 |
> |
// we have a problem |
645 |
> |
sprintf(painCave.errMsg, |
646 |
> |
"SimSetup Error. No global NMol or component NMol" |
647 |
> |
" given. Cannot calculate the number of atoms.\n"); |
648 |
> |
painCave.isFatal = 1; |
649 |
> |
simError(); |
650 |
|
} |
651 |
|
|
652 |
|
tot_nmol += the_components[i]->getNMol(); |
654 |
|
} |
655 |
|
} |
656 |
|
else{ |
657 |
< |
sprintf( painCave.errMsg, |
658 |
< |
"SimSetup error.\n" |
659 |
< |
"\tSorry, the ability to specify total" |
660 |
< |
" nMols and then give molfractions in the components\n" |
661 |
< |
"\tis not currently supported." |
662 |
< |
" Please give nMol in the components.\n" ); |
657 |
> |
sprintf(painCave.errMsg, |
658 |
> |
"SimSetup error.\n" |
659 |
> |
"\tSorry, the ability to specify total" |
660 |
> |
" nMols and then give molfractions in the components\n" |
661 |
> |
"\tis not currently supported." |
662 |
> |
" Please give nMol in the components.\n"); |
663 |
|
painCave.isFatal = 1; |
664 |
|
simError(); |
665 |
|
} |
666 |
|
|
667 |
|
// set the status, sample, and thermal kick times |
668 |
< |
|
669 |
< |
if( globals->haveSampleTime() ){ |
670 |
< |
info->sampleTime = globals->getSampleTime(); |
671 |
< |
info->statusTime = info->sampleTime; |
672 |
< |
info->thermalTime = info->sampleTime; |
673 |
< |
} |
674 |
< |
else{ |
675 |
< |
info->sampleTime = globals->getRunTime(); |
676 |
< |
info->statusTime = info->sampleTime; |
677 |
< |
info->thermalTime = info->sampleTime; |
678 |
< |
} |
668 |
> |
|
669 |
> |
for (i = 0; i < nInfo; i++){ |
670 |
> |
if (globals->haveSampleTime()){ |
671 |
> |
info[i].sampleTime = globals->getSampleTime(); |
672 |
> |
info[i].statusTime = info[i].sampleTime; |
673 |
> |
info[i].thermalTime = info[i].sampleTime; |
674 |
> |
} |
675 |
> |
else{ |
676 |
> |
info[i].sampleTime = globals->getRunTime(); |
677 |
> |
info[i].statusTime = info[i].sampleTime; |
678 |
> |
info[i].thermalTime = info[i].sampleTime; |
679 |
> |
} |
680 |
|
|
681 |
< |
if( globals->haveStatusTime() ){ |
682 |
< |
info->statusTime = globals->getStatusTime(); |
683 |
< |
} |
681 |
> |
if (globals->haveStatusTime()){ |
682 |
> |
info[i].statusTime = globals->getStatusTime(); |
683 |
> |
} |
684 |
|
|
685 |
< |
if( globals->haveThermalTime() ){ |
686 |
< |
info->thermalTime = globals->getThermalTime(); |
687 |
< |
} |
685 |
> |
if (globals->haveThermalTime()){ |
686 |
> |
info[i].thermalTime = globals->getThermalTime(); |
687 |
> |
} |
688 |
|
|
689 |
< |
// check for the temperature set flag |
689 |
> |
info[i].resetIntegrator = 0; |
690 |
> |
if( globals->haveResetTime() ){ |
691 |
> |
info[i].resetTime = globals->getResetTime(); |
692 |
> |
info[i].resetIntegrator = 1; |
693 |
> |
} |
694 |
|
|
695 |
< |
if( globals->haveTempSet() ) info->setTemp = globals->getTempSet(); |
695 |
> |
// check for the temperature set flag |
696 |
|
|
697 |
< |
// get some of the tricky things that may still be in the globals |
697 |
> |
if (globals->haveTempSet()) |
698 |
> |
info[i].setTemp = globals->getTempSet(); |
699 |
|
|
700 |
< |
double boxVector[3]; |
691 |
< |
if( globals->haveBox() ){ |
692 |
< |
boxVector[0] = globals->getBox(); |
693 |
< |
boxVector[1] = globals->getBox(); |
694 |
< |
boxVector[2] = globals->getBox(); |
695 |
< |
|
696 |
< |
info->setBox( boxVector ); |
697 |
< |
} |
698 |
< |
else if( globals->haveDensity() ){ |
700 |
> |
// get some of the tricky things that may still be in the globals |
701 |
|
|
702 |
< |
double vol; |
703 |
< |
vol = (double)tot_nmol / globals->getDensity(); |
704 |
< |
boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
705 |
< |
boxVector[1] = boxVector[0]; |
706 |
< |
boxVector[2] = boxVector[0]; |
702 |
> |
double boxVector[3]; |
703 |
> |
if (globals->haveBox()){ |
704 |
> |
boxVector[0] = globals->getBox(); |
705 |
> |
boxVector[1] = globals->getBox(); |
706 |
> |
boxVector[2] = globals->getBox(); |
707 |
|
|
708 |
< |
info->setBox( boxVector ); |
707 |
< |
} |
708 |
< |
else{ |
709 |
< |
if( !globals->haveBoxX() ){ |
710 |
< |
sprintf( painCave.errMsg, |
711 |
< |
"SimSetup error, no periodic BoxX size given.\n" ); |
712 |
< |
painCave.isFatal = 1; |
713 |
< |
simError(); |
708 |
> |
info[i].setBox(boxVector); |
709 |
|
} |
710 |
< |
boxVector[0] = globals->getBoxX(); |
710 |
> |
else if (globals->haveDensity()){ |
711 |
> |
double vol; |
712 |
> |
vol = (double) tot_nmol / globals->getDensity(); |
713 |
> |
boxVector[0] = pow(vol, (1.0 / 3.0)); |
714 |
> |
boxVector[1] = boxVector[0]; |
715 |
> |
boxVector[2] = boxVector[0]; |
716 |
|
|
717 |
< |
if( !globals->haveBoxY() ){ |
718 |
< |
sprintf( painCave.errMsg, |
719 |
< |
"SimSetup error, no periodic BoxY size given.\n" ); |
720 |
< |
painCave.isFatal = 1; |
721 |
< |
simError(); |
717 |
> |
info[i].setBox(boxVector); |
718 |
|
} |
719 |
< |
boxVector[1] = globals->getBoxY(); |
719 |
> |
else{ |
720 |
> |
if (!globals->haveBoxX()){ |
721 |
> |
sprintf(painCave.errMsg, |
722 |
> |
"SimSetup error, no periodic BoxX size given.\n"); |
723 |
> |
painCave.isFatal = 1; |
724 |
> |
simError(); |
725 |
> |
} |
726 |
> |
boxVector[0] = globals->getBoxX(); |
727 |
|
|
728 |
< |
if( !globals->haveBoxZ() ){ |
729 |
< |
sprintf( painCave.errMsg, |
730 |
< |
"SimSetup error, no periodic BoxZ size given.\n" ); |
731 |
< |
painCave.isFatal = 1; |
732 |
< |
simError(); |
733 |
< |
} |
734 |
< |
boxVector[2] = globals->getBoxZ(); |
728 |
> |
if (!globals->haveBoxY()){ |
729 |
> |
sprintf(painCave.errMsg, |
730 |
> |
"SimSetup error, no periodic BoxY size given.\n"); |
731 |
> |
painCave.isFatal = 1; |
732 |
> |
simError(); |
733 |
> |
} |
734 |
> |
boxVector[1] = globals->getBoxY(); |
735 |
|
|
736 |
< |
info->setBox( boxVector ); |
736 |
> |
if (!globals->haveBoxZ()){ |
737 |
> |
sprintf(painCave.errMsg, |
738 |
> |
"SimSetup error, no periodic BoxZ size given.\n"); |
739 |
> |
painCave.isFatal = 1; |
740 |
> |
simError(); |
741 |
> |
} |
742 |
> |
boxVector[2] = globals->getBoxZ(); |
743 |
> |
|
744 |
> |
info[i].setBox(boxVector); |
745 |
> |
} |
746 |
|
} |
747 |
|
|
748 |
+ |
//setup seed for random number generator |
749 |
+ |
int seedValue; |
750 |
|
|
751 |
+ |
if (globals->haveSeed()){ |
752 |
+ |
seedValue = globals->getSeed(); |
753 |
+ |
|
754 |
+ |
if(seedValue / 1E9 == 0){ |
755 |
+ |
sprintf(painCave.errMsg, |
756 |
+ |
"Seed for sprng library should contain at least 9 digits\n" |
757 |
+ |
"OOPSE will generate a seed for user\n"); |
758 |
+ |
painCave.isFatal = 0; |
759 |
+ |
simError(); |
760 |
+ |
|
761 |
+ |
//using seed generated by system instead of invalid seed set by user |
762 |
+ |
#ifndef IS_MPI |
763 |
+ |
seedValue = make_sprng_seed(); |
764 |
+ |
#else |
765 |
+ |
if (worldRank == 0){ |
766 |
+ |
seedValue = make_sprng_seed(); |
767 |
+ |
} |
768 |
+ |
MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
769 |
+ |
#endif |
770 |
+ |
} |
771 |
+ |
}//end of if branch of globals->haveSeed() |
772 |
+ |
else{ |
773 |
|
|
774 |
+ |
#ifndef IS_MPI |
775 |
+ |
seedValue = make_sprng_seed(); |
776 |
+ |
#else |
777 |
+ |
if (worldRank == 0){ |
778 |
+ |
seedValue = make_sprng_seed(); |
779 |
+ |
} |
780 |
+ |
MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
781 |
+ |
#endif |
782 |
+ |
}//end of globals->haveSeed() |
783 |
+ |
|
784 |
+ |
for (int i = 0; i < nInfo; i++){ |
785 |
+ |
info[i].setSeed(seedValue); |
786 |
+ |
} |
787 |
+ |
|
788 |
|
#ifdef IS_MPI |
789 |
< |
strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" ); |
789 |
> |
strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n"); |
790 |
|
MPIcheckPoint(); |
791 |
|
#endif // is_mpi |
742 |
– |
|
792 |
|
} |
793 |
|
|
794 |
|
|
795 |
< |
void SimSetup::finalInfoCheck( void ){ |
795 |
> |
void SimSetup::finalInfoCheck(void){ |
796 |
|
int index; |
797 |
|
int usesDipoles; |
798 |
< |
|
798 |
> |
int i; |
799 |
|
|
800 |
< |
// check electrostatic parameters |
801 |
< |
|
802 |
< |
index = 0; |
803 |
< |
usesDipoles = 0; |
804 |
< |
while( (index < info->n_atoms) && !usesDipoles ){ |
805 |
< |
usesDipoles = ((info->atoms)[index])->hasDipole(); |
806 |
< |
index++; |
807 |
< |
} |
808 |
< |
|
800 |
> |
for (i = 0; i < nInfo; i++){ |
801 |
> |
// check electrostatic parameters |
802 |
> |
|
803 |
> |
index = 0; |
804 |
> |
usesDipoles = 0; |
805 |
> |
while ((index < info[i].n_atoms) && !usesDipoles){ |
806 |
> |
usesDipoles = (info[i].atoms[index])->hasDipole(); |
807 |
> |
index++; |
808 |
> |
} |
809 |
> |
|
810 |
|
#ifdef IS_MPI |
811 |
< |
int myUse = usesDipoles; |
812 |
< |
MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
811 |
> |
int myUse = usesDipoles; |
812 |
> |
MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
813 |
|
#endif //is_mpi |
814 |
|
|
815 |
< |
double theEcr, theEst; |
815 |
> |
double theEcr, theEst; |
816 |
|
|
817 |
< |
if (globals->getUseRF() ) { |
818 |
< |
info->useReactionField = 1; |
769 |
< |
|
770 |
< |
if( !globals->haveECR() ){ |
771 |
< |
sprintf( painCave.errMsg, |
772 |
< |
"SimSetup Warning: using default value of 1/2 the smallest " |
773 |
< |
"box length for the electrostaticCutoffRadius.\n" |
774 |
< |
"I hope you have a very fast processor!\n"); |
775 |
< |
painCave.isFatal = 0; |
776 |
< |
simError(); |
777 |
< |
double smallest; |
778 |
< |
smallest = info->boxL[0]; |
779 |
< |
if (info->boxL[1] <= smallest) smallest = info->boxL[1]; |
780 |
< |
if (info->boxL[2] <= smallest) smallest = info->boxL[2]; |
781 |
< |
theEcr = 0.5 * smallest; |
782 |
< |
} else { |
783 |
< |
theEcr = globals->getECR(); |
784 |
< |
} |
817 |
> |
if (globals->getUseRF()){ |
818 |
> |
info[i].useReactionField = 1; |
819 |
|
|
820 |
< |
if( !globals->haveEST() ){ |
821 |
< |
sprintf( painCave.errMsg, |
822 |
< |
"SimSetup Warning: using default value of 0.05 * the " |
823 |
< |
"electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
824 |
< |
); |
825 |
< |
painCave.isFatal = 0; |
826 |
< |
simError(); |
827 |
< |
theEst = 0.05 * theEcr; |
828 |
< |
} else { |
829 |
< |
theEst= globals->getEST(); |
830 |
< |
} |
831 |
< |
|
832 |
< |
info->setEcr( theEcr, theEst ); |
833 |
< |
|
800 |
< |
if(!globals->haveDielectric() ){ |
801 |
< |
sprintf( painCave.errMsg, |
802 |
< |
"SimSetup Error: You are trying to use Reaction Field without" |
803 |
< |
"setting a dielectric constant!\n" |
804 |
< |
); |
805 |
< |
painCave.isFatal = 1; |
806 |
< |
simError(); |
807 |
< |
} |
808 |
< |
info->dielectric = globals->getDielectric(); |
809 |
< |
} |
810 |
< |
else { |
811 |
< |
if (usesDipoles) { |
812 |
< |
|
813 |
< |
if( !globals->haveECR() ){ |
814 |
< |
sprintf( painCave.errMsg, |
815 |
< |
"SimSetup Warning: using default value of 1/2 the smallest " |
816 |
< |
"box length for the electrostaticCutoffRadius.\n" |
817 |
< |
"I hope you have a very fast processor!\n"); |
818 |
< |
painCave.isFatal = 0; |
819 |
< |
simError(); |
820 |
< |
double smallest; |
821 |
< |
smallest = info->boxL[0]; |
822 |
< |
if (info->boxL[1] <= smallest) smallest = info->boxL[1]; |
823 |
< |
if (info->boxL[2] <= smallest) smallest = info->boxL[2]; |
824 |
< |
theEcr = 0.5 * smallest; |
825 |
< |
} else { |
826 |
< |
theEcr = globals->getECR(); |
820 |
> |
if (!globals->haveECR()){ |
821 |
> |
sprintf(painCave.errMsg, |
822 |
> |
"SimSetup Warning: using default value of 1/2 the smallest " |
823 |
> |
"box length for the electrostaticCutoffRadius.\n" |
824 |
> |
"I hope you have a very fast processor!\n"); |
825 |
> |
painCave.isFatal = 0; |
826 |
> |
simError(); |
827 |
> |
double smallest; |
828 |
> |
smallest = info[i].boxL[0]; |
829 |
> |
if (info[i].boxL[1] <= smallest) |
830 |
> |
smallest = info[i].boxL[1]; |
831 |
> |
if (info[i].boxL[2] <= smallest) |
832 |
> |
smallest = info[i].boxL[2]; |
833 |
> |
theEcr = 0.5 * smallest; |
834 |
|
} |
835 |
< |
|
836 |
< |
if( !globals->haveEST() ){ |
830 |
< |
sprintf( painCave.errMsg, |
831 |
< |
"SimSetup Warning: using default value of 0.05 * the " |
832 |
< |
"electrostaticCutoffRadius for the " |
833 |
< |
"electrostaticSkinThickness\n" |
834 |
< |
); |
835 |
< |
painCave.isFatal = 0; |
836 |
< |
simError(); |
837 |
< |
theEst = 0.05 * theEcr; |
838 |
< |
} else { |
839 |
< |
theEst= globals->getEST(); |
835 |
> |
else{ |
836 |
> |
theEcr = globals->getECR(); |
837 |
|
} |
838 |
|
|
839 |
< |
info->setEcr( theEcr, theEst ); |
839 |
> |
if (!globals->haveEST()){ |
840 |
> |
sprintf(painCave.errMsg, |
841 |
> |
"SimSetup Warning: using default value of 0.05 * the " |
842 |
> |
"electrostaticCutoffRadius for the electrostaticSkinThickness\n"); |
843 |
> |
painCave.isFatal = 0; |
844 |
> |
simError(); |
845 |
> |
theEst = 0.05 * theEcr; |
846 |
> |
} |
847 |
> |
else{ |
848 |
> |
theEst = globals->getEST(); |
849 |
> |
} |
850 |
> |
|
851 |
> |
info[i].setEcr(theEcr, theEst); |
852 |
> |
|
853 |
> |
if (!globals->haveDielectric()){ |
854 |
> |
sprintf(painCave.errMsg, |
855 |
> |
"SimSetup Error: You are trying to use Reaction Field without" |
856 |
> |
"setting a dielectric constant!\n"); |
857 |
> |
painCave.isFatal = 1; |
858 |
> |
simError(); |
859 |
> |
} |
860 |
> |
info[i].dielectric = globals->getDielectric(); |
861 |
|
} |
862 |
< |
} |
862 |
> |
else{ |
863 |
> |
if (usesDipoles){ |
864 |
> |
if (!globals->haveECR()){ |
865 |
> |
sprintf(painCave.errMsg, |
866 |
> |
"SimSetup Warning: using default value of 1/2 the smallest " |
867 |
> |
"box length for the electrostaticCutoffRadius.\n" |
868 |
> |
"I hope you have a very fast processor!\n"); |
869 |
> |
painCave.isFatal = 0; |
870 |
> |
simError(); |
871 |
> |
double smallest; |
872 |
> |
smallest = info[i].boxL[0]; |
873 |
> |
if (info[i].boxL[1] <= smallest) |
874 |
> |
smallest = info[i].boxL[1]; |
875 |
> |
if (info[i].boxL[2] <= smallest) |
876 |
> |
smallest = info[i].boxL[2]; |
877 |
> |
theEcr = 0.5 * smallest; |
878 |
> |
} |
879 |
> |
else{ |
880 |
> |
theEcr = globals->getECR(); |
881 |
> |
} |
882 |
|
|
883 |
+ |
if (!globals->haveEST()){ |
884 |
+ |
sprintf(painCave.errMsg, |
885 |
+ |
"SimSetup Warning: using default value of 0.05 * the " |
886 |
+ |
"electrostaticCutoffRadius for the " |
887 |
+ |
"electrostaticSkinThickness\n"); |
888 |
+ |
painCave.isFatal = 0; |
889 |
+ |
simError(); |
890 |
+ |
theEst = 0.05 * theEcr; |
891 |
+ |
} |
892 |
+ |
else{ |
893 |
+ |
theEst = globals->getEST(); |
894 |
+ |
} |
895 |
+ |
|
896 |
+ |
info[i].setEcr(theEcr, theEst); |
897 |
+ |
} |
898 |
+ |
} |
899 |
+ |
} |
900 |
+ |
|
901 |
|
#ifdef IS_MPI |
902 |
< |
strcpy( checkPointMsg, "post processing checks out" ); |
902 |
> |
strcpy(checkPointMsg, "post processing checks out"); |
903 |
|
MPIcheckPoint(); |
904 |
|
#endif // is_mpi |
850 |
– |
|
905 |
|
} |
906 |
|
|
907 |
< |
void SimSetup::initSystemCoords( void ){ |
907 |
> |
void SimSetup::initSystemCoords(void){ |
908 |
> |
int i; |
909 |
|
|
910 |
< |
if( globals->haveInitialConfig() ){ |
911 |
< |
|
912 |
< |
InitializeFromFile* fileInit; |
910 |
> |
char* inName; |
911 |
> |
|
912 |
> |
(info[0].getConfiguration())->createArrays(info[0].n_atoms); |
913 |
> |
|
914 |
> |
for (i = 0; i < info[0].n_atoms; i++) |
915 |
> |
info[0].atoms[i]->setCoords(); |
916 |
> |
|
917 |
> |
if (globals->haveInitialConfig()){ |
918 |
> |
InitializeFromFile* fileInit; |
919 |
|
#ifdef IS_MPI // is_mpi |
920 |
< |
if( worldRank == 0 ){ |
920 |
> |
if (worldRank == 0){ |
921 |
|
#endif //is_mpi |
922 |
< |
fileInit = new InitializeFromFile( globals->getInitialConfig() ); |
922 |
> |
inName = globals->getInitialConfig(); |
923 |
> |
fileInit = new InitializeFromFile(inName); |
924 |
|
#ifdef IS_MPI |
925 |
< |
}else fileInit = new InitializeFromFile( NULL ); |
925 |
> |
} |
926 |
> |
else |
927 |
> |
fileInit = new InitializeFromFile(NULL); |
928 |
|
#endif |
929 |
< |
fileInit->readInit( info ); // default velocities on |
929 |
> |
fileInit->readInit(info); // default velocities on |
930 |
|
|
931 |
< |
delete fileInit; |
932 |
< |
} |
933 |
< |
else{ |
870 |
< |
|
931 |
> |
delete fileInit; |
932 |
> |
} |
933 |
> |
else{ |
934 |
|
#ifdef IS_MPI |
935 |
|
|
936 |
< |
// no init from bass |
937 |
< |
|
938 |
< |
sprintf( painCave.errMsg, |
939 |
< |
"Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
940 |
< |
painCave.isFatal; |
941 |
< |
simError(); |
942 |
< |
|
936 |
> |
// no init from bass |
937 |
> |
|
938 |
> |
sprintf(painCave.errMsg, |
939 |
> |
"Cannot intialize a parallel simulation without an initial configuration file.\n"); |
940 |
> |
painCave.isFatal = 1;; |
941 |
> |
simError(); |
942 |
> |
|
943 |
|
#else |
944 |
|
|
945 |
< |
initFromBass(); |
945 |
> |
initFromBass(); |
946 |
|
|
947 |
|
|
948 |
|
#endif |
949 |
< |
} |
949 |
> |
} |
950 |
|
|
951 |
|
#ifdef IS_MPI |
952 |
< |
strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
952 |
> |
strcpy(checkPointMsg, "Successfully read in the initial configuration"); |
953 |
|
MPIcheckPoint(); |
954 |
|
#endif // is_mpi |
892 |
– |
|
955 |
|
} |
956 |
|
|
957 |
|
|
958 |
< |
void SimSetup::makeOutNames( void ){ |
958 |
> |
void SimSetup::makeOutNames(void){ |
959 |
> |
int k; |
960 |
|
|
961 |
+ |
|
962 |
+ |
for (k = 0; k < nInfo; k++){ |
963 |
|
#ifdef IS_MPI |
964 |
< |
if( worldRank == 0 ){ |
964 |
> |
if (worldRank == 0){ |
965 |
|
#endif // is_mpi |
966 |
< |
|
967 |
< |
if( globals->haveFinalConfig() ){ |
968 |
< |
strcpy( info->finalName, globals->getFinalConfig() ); |
904 |
< |
} |
905 |
< |
else{ |
906 |
< |
strcpy( info->finalName, inFileName ); |
907 |
< |
char* endTest; |
908 |
< |
int nameLength = strlen( info->finalName ); |
909 |
< |
endTest = &(info->finalName[nameLength - 5]); |
910 |
< |
if( !strcmp( endTest, ".bass" ) ){ |
911 |
< |
strcpy( endTest, ".eor" ); |
966 |
> |
|
967 |
> |
if (globals->haveFinalConfig()){ |
968 |
> |
strcpy(info[k].finalName, globals->getFinalConfig()); |
969 |
|
} |
913 |
– |
else if( !strcmp( endTest, ".BASS" ) ){ |
914 |
– |
strcpy( endTest, ".eor" ); |
915 |
– |
} |
970 |
|
else{ |
971 |
< |
endTest = &(info->finalName[nameLength - 4]); |
972 |
< |
if( !strcmp( endTest, ".bss" ) ){ |
973 |
< |
strcpy( endTest, ".eor" ); |
974 |
< |
} |
975 |
< |
else if( !strcmp( endTest, ".mdl" ) ){ |
976 |
< |
strcpy( endTest, ".eor" ); |
977 |
< |
} |
978 |
< |
else{ |
979 |
< |
strcat( info->finalName, ".eor" ); |
980 |
< |
} |
971 |
> |
strcpy(info[k].finalName, inFileName); |
972 |
> |
char* endTest; |
973 |
> |
int nameLength = strlen(info[k].finalName); |
974 |
> |
endTest = &(info[k].finalName[nameLength - 5]); |
975 |
> |
if (!strcmp(endTest, ".bass")){ |
976 |
> |
strcpy(endTest, ".eor"); |
977 |
> |
} |
978 |
> |
else if (!strcmp(endTest, ".BASS")){ |
979 |
> |
strcpy(endTest, ".eor"); |
980 |
> |
} |
981 |
> |
else{ |
982 |
> |
endTest = &(info[k].finalName[nameLength - 4]); |
983 |
> |
if (!strcmp(endTest, ".bss")){ |
984 |
> |
strcpy(endTest, ".eor"); |
985 |
> |
} |
986 |
> |
else if (!strcmp(endTest, ".mdl")){ |
987 |
> |
strcpy(endTest, ".eor"); |
988 |
> |
} |
989 |
> |
else{ |
990 |
> |
strcat(info[k].finalName, ".eor"); |
991 |
> |
} |
992 |
> |
} |
993 |
|
} |
994 |
< |
} |
995 |
< |
|
996 |
< |
// make the sample and status out names |
997 |
< |
|
998 |
< |
strcpy( info->sampleName, inFileName ); |
999 |
< |
char* endTest; |
1000 |
< |
int nameLength = strlen( info->sampleName ); |
1001 |
< |
endTest = &(info->sampleName[nameLength - 5]); |
1002 |
< |
if( !strcmp( endTest, ".bass" ) ){ |
937 |
< |
strcpy( endTest, ".dump" ); |
938 |
< |
} |
939 |
< |
else if( !strcmp( endTest, ".BASS" ) ){ |
940 |
< |
strcpy( endTest, ".dump" ); |
941 |
< |
} |
942 |
< |
else{ |
943 |
< |
endTest = &(info->sampleName[nameLength - 4]); |
944 |
< |
if( !strcmp( endTest, ".bss" ) ){ |
945 |
< |
strcpy( endTest, ".dump" ); |
994 |
> |
|
995 |
> |
// make the sample and status out names |
996 |
> |
|
997 |
> |
strcpy(info[k].sampleName, inFileName); |
998 |
> |
char* endTest; |
999 |
> |
int nameLength = strlen(info[k].sampleName); |
1000 |
> |
endTest = &(info[k].sampleName[nameLength - 5]); |
1001 |
> |
if (!strcmp(endTest, ".bass")){ |
1002 |
> |
strcpy(endTest, ".dump"); |
1003 |
|
} |
1004 |
< |
else if( !strcmp( endTest, ".mdl" ) ){ |
1005 |
< |
strcpy( endTest, ".dump" ); |
1004 |
> |
else if (!strcmp(endTest, ".BASS")){ |
1005 |
> |
strcpy(endTest, ".dump"); |
1006 |
|
} |
1007 |
|
else{ |
1008 |
< |
strcat( info->sampleName, ".dump" ); |
1008 |
> |
endTest = &(info[k].sampleName[nameLength - 4]); |
1009 |
> |
if (!strcmp(endTest, ".bss")){ |
1010 |
> |
strcpy(endTest, ".dump"); |
1011 |
> |
} |
1012 |
> |
else if (!strcmp(endTest, ".mdl")){ |
1013 |
> |
strcpy(endTest, ".dump"); |
1014 |
> |
} |
1015 |
> |
else{ |
1016 |
> |
strcat(info[k].sampleName, ".dump"); |
1017 |
> |
} |
1018 |
|
} |
1019 |
< |
} |
1020 |
< |
|
1021 |
< |
strcpy( info->statusName, inFileName ); |
1022 |
< |
nameLength = strlen( info->statusName ); |
1023 |
< |
endTest = &(info->statusName[nameLength - 5]); |
1024 |
< |
if( !strcmp( endTest, ".bass" ) ){ |
959 |
< |
strcpy( endTest, ".stat" ); |
960 |
< |
} |
961 |
< |
else if( !strcmp( endTest, ".BASS" ) ){ |
962 |
< |
strcpy( endTest, ".stat" ); |
963 |
< |
} |
964 |
< |
else{ |
965 |
< |
endTest = &(info->statusName[nameLength - 4]); |
966 |
< |
if( !strcmp( endTest, ".bss" ) ){ |
967 |
< |
strcpy( endTest, ".stat" ); |
1019 |
> |
|
1020 |
> |
strcpy(info[k].statusName, inFileName); |
1021 |
> |
nameLength = strlen(info[k].statusName); |
1022 |
> |
endTest = &(info[k].statusName[nameLength - 5]); |
1023 |
> |
if (!strcmp(endTest, ".bass")){ |
1024 |
> |
strcpy(endTest, ".stat"); |
1025 |
|
} |
1026 |
< |
else if( !strcmp( endTest, ".mdl" ) ){ |
1027 |
< |
strcpy( endTest, ".stat" ); |
1026 |
> |
else if (!strcmp(endTest, ".BASS")){ |
1027 |
> |
strcpy(endTest, ".stat"); |
1028 |
|
} |
1029 |
|
else{ |
1030 |
< |
strcat( info->statusName, ".stat" ); |
1030 |
> |
endTest = &(info[k].statusName[nameLength - 4]); |
1031 |
> |
if (!strcmp(endTest, ".bss")){ |
1032 |
> |
strcpy(endTest, ".stat"); |
1033 |
> |
} |
1034 |
> |
else if (!strcmp(endTest, ".mdl")){ |
1035 |
> |
strcpy(endTest, ".stat"); |
1036 |
> |
} |
1037 |
> |
else{ |
1038 |
> |
strcat(info[k].statusName, ".stat"); |
1039 |
> |
} |
1040 |
|
} |
1041 |
< |
} |
976 |
< |
|
1041 |
> |
|
1042 |
|
#ifdef IS_MPI |
978 |
– |
} |
979 |
– |
#endif // is_mpi |
1043 |
|
|
1044 |
+ |
} |
1045 |
+ |
#endif // is_mpi |
1046 |
+ |
} |
1047 |
|
} |
1048 |
|
|
1049 |
|
|
1050 |
< |
void SimSetup::sysObjectsCreation( void ){ |
1051 |
< |
|
986 |
< |
int i; |
1050 |
> |
void SimSetup::sysObjectsCreation(void){ |
1051 |
> |
int i, k; |
1052 |
|
|
1053 |
|
// create the forceField |
1054 |
|
|
1064 |
|
|
1065 |
|
#ifdef IS_MPI |
1066 |
|
// divide the molecules among the processors |
1067 |
< |
|
1067 |
> |
|
1068 |
|
mpiMolDivide(); |
1069 |
|
#endif //is_mpi |
1070 |
< |
|
1070 |
> |
|
1071 |
|
// create the atom and SRI arrays. Also initialize Molecule Stamp ID's |
1072 |
< |
|
1072 |
> |
|
1073 |
|
makeSysArrays(); |
1074 |
|
|
1075 |
|
// make and initialize the molecules (all but atomic coordinates) |
1076 |
< |
|
1076 |
> |
|
1077 |
|
makeMolecules(); |
1013 |
– |
info->identArray = new int[info->n_atoms]; |
1014 |
– |
for(i=0; i<info->n_atoms; i++){ |
1015 |
– |
info->identArray[i] = the_atoms[i]->getIdent(); |
1016 |
– |
} |
1017 |
– |
|
1078 |
|
|
1079 |
< |
|
1079 |
> |
for (k = 0; k < nInfo; k++){ |
1080 |
> |
info[k].identArray = new int[info[k].n_atoms]; |
1081 |
> |
for (i = 0; i < info[k].n_atoms; i++){ |
1082 |
> |
info[k].identArray[i] = info[k].atoms[i]->getIdent(); |
1083 |
> |
} |
1084 |
> |
} |
1085 |
|
} |
1086 |
|
|
1087 |
|
|
1088 |
< |
void SimSetup::createFF( void ){ |
1088 |
> |
void SimSetup::createFF(void){ |
1089 |
> |
switch (ffCase){ |
1090 |
> |
case FF_DUFF: |
1091 |
> |
the_ff = new DUFF(); |
1092 |
> |
break; |
1093 |
|
|
1094 |
< |
switch( ffCase ){ |
1094 |
> |
case FF_LJ: |
1095 |
> |
the_ff = new LJFF(); |
1096 |
> |
break; |
1097 |
|
|
1098 |
< |
case FF_DUFF: |
1099 |
< |
the_ff = new DUFF(); |
1100 |
< |
break; |
1098 |
> |
case FF_EAM: |
1099 |
> |
the_ff = new EAM_FF(); |
1100 |
> |
break; |
1101 |
|
|
1102 |
< |
case FF_LJ: |
1103 |
< |
the_ff = new LJFF(); |
1104 |
< |
break; |
1105 |
< |
|
1106 |
< |
default: |
1036 |
< |
sprintf( painCave.errMsg, |
1037 |
< |
"SimSetup Error. Unrecognized force field in case statement.\n"); |
1038 |
< |
painCave.isFatal = 1; |
1039 |
< |
simError(); |
1102 |
> |
default: |
1103 |
> |
sprintf(painCave.errMsg, |
1104 |
> |
"SimSetup Error. Unrecognized force field in case statement.\n"); |
1105 |
> |
painCave.isFatal = 1; |
1106 |
> |
simError(); |
1107 |
|
} |
1108 |
|
|
1109 |
|
#ifdef IS_MPI |
1110 |
< |
strcpy( checkPointMsg, "ForceField creation successful" ); |
1110 |
> |
strcpy(checkPointMsg, "ForceField creation successful"); |
1111 |
|
MPIcheckPoint(); |
1112 |
|
#endif // is_mpi |
1046 |
– |
|
1113 |
|
} |
1114 |
|
|
1115 |
|
|
1116 |
< |
void SimSetup::compList( void ){ |
1051 |
< |
|
1116 |
> |
void SimSetup::compList(void){ |
1117 |
|
int i; |
1118 |
+ |
char* id; |
1119 |
+ |
LinkedMolStamp* headStamp = new LinkedMolStamp(); |
1120 |
+ |
LinkedMolStamp* currentStamp = NULL; |
1121 |
+ |
comp_stamps = new MoleculeStamp * [n_components]; |
1122 |
|
|
1054 |
– |
comp_stamps = new MoleculeStamp*[n_components]; |
1055 |
– |
|
1123 |
|
// make an array of molecule stamps that match the components used. |
1124 |
|
// also extract the used stamps out into a separate linked list |
1125 |
|
|
1126 |
< |
info->nComponents = n_components; |
1127 |
< |
info->componentsNmol = components_nmol; |
1128 |
< |
info->compStamps = comp_stamps; |
1129 |
< |
info->headStamp = new LinkedMolStamp(); |
1130 |
< |
|
1131 |
< |
char* id; |
1065 |
< |
LinkedMolStamp* headStamp = info->headStamp; |
1066 |
< |
LinkedMolStamp* currentStamp = NULL; |
1067 |
< |
for( i=0; i<n_components; i++ ){ |
1126 |
> |
for (i = 0; i < nInfo; i++){ |
1127 |
> |
info[i].nComponents = n_components; |
1128 |
> |
info[i].componentsNmol = components_nmol; |
1129 |
> |
info[i].compStamps = comp_stamps; |
1130 |
> |
info[i].headStamp = headStamp; |
1131 |
> |
} |
1132 |
|
|
1133 |
+ |
|
1134 |
+ |
for (i = 0; i < n_components; i++){ |
1135 |
|
id = the_components[i]->getType(); |
1136 |
|
comp_stamps[i] = NULL; |
1137 |
< |
|
1137 |
> |
|
1138 |
|
// check to make sure the component isn't already in the list |
1139 |
|
|
1140 |
< |
comp_stamps[i] = headStamp->match( id ); |
1141 |
< |
if( comp_stamps[i] == NULL ){ |
1076 |
< |
|
1140 |
> |
comp_stamps[i] = headStamp->match(id); |
1141 |
> |
if (comp_stamps[i] == NULL){ |
1142 |
|
// extract the component from the list; |
1143 |
< |
|
1144 |
< |
currentStamp = stamps->extractMolStamp( id ); |
1145 |
< |
if( currentStamp == NULL ){ |
1146 |
< |
sprintf( painCave.errMsg, |
1147 |
< |
"SimSetup error: Component \"%s\" was not found in the " |
1148 |
< |
"list of declared molecules\n", |
1149 |
< |
id ); |
1150 |
< |
painCave.isFatal = 1; |
1151 |
< |
simError(); |
1143 |
> |
|
1144 |
> |
currentStamp = stamps->extractMolStamp(id); |
1145 |
> |
if (currentStamp == NULL){ |
1146 |
> |
sprintf(painCave.errMsg, |
1147 |
> |
"SimSetup error: Component \"%s\" was not found in the " |
1148 |
> |
"list of declared molecules\n", |
1149 |
> |
id); |
1150 |
> |
painCave.isFatal = 1; |
1151 |
> |
simError(); |
1152 |
|
} |
1153 |
< |
|
1154 |
< |
headStamp->add( currentStamp ); |
1155 |
< |
comp_stamps[i] = headStamp->match( id ); |
1153 |
> |
|
1154 |
> |
headStamp->add(currentStamp); |
1155 |
> |
comp_stamps[i] = headStamp->match(id); |
1156 |
|
} |
1157 |
|
} |
1158 |
|
|
1159 |
|
#ifdef IS_MPI |
1160 |
< |
strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
1160 |
> |
strcpy(checkPointMsg, "Component stamps successfully extracted\n"); |
1161 |
|
MPIcheckPoint(); |
1162 |
|
#endif // is_mpi |
1098 |
– |
|
1099 |
– |
|
1163 |
|
} |
1164 |
|
|
1165 |
< |
void SimSetup::calcSysValues( void ){ |
1166 |
< |
int i, j, k; |
1165 |
> |
void SimSetup::calcSysValues(void){ |
1166 |
> |
int i; |
1167 |
|
|
1168 |
+ |
int* molMembershipArray; |
1169 |
|
|
1170 |
|
tot_atoms = 0; |
1171 |
|
tot_bonds = 0; |
1172 |
|
tot_bends = 0; |
1173 |
|
tot_torsions = 0; |
1174 |
< |
for( i=0; i<n_components; i++ ){ |
1175 |
< |
|
1176 |
< |
tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1177 |
< |
tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1114 |
< |
tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1174 |
> |
for (i = 0; i < n_components; i++){ |
1175 |
> |
tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1176 |
> |
tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1177 |
> |
tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1178 |
|
tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
1179 |
|
} |
1180 |
|
|
1181 |
|
tot_SRI = tot_bonds + tot_bends + tot_torsions; |
1182 |
+ |
molMembershipArray = new int[tot_atoms]; |
1183 |
|
|
1184 |
< |
info->n_atoms = tot_atoms; |
1185 |
< |
info->n_bonds = tot_bonds; |
1186 |
< |
info->n_bends = tot_bends; |
1187 |
< |
info->n_torsions = tot_torsions; |
1188 |
< |
info->n_SRI = tot_SRI; |
1189 |
< |
info->n_mol = tot_nmol; |
1190 |
< |
|
1191 |
< |
info->molMembershipArray = new int[tot_atoms]; |
1184 |
> |
for (i = 0; i < nInfo; i++){ |
1185 |
> |
info[i].n_atoms = tot_atoms; |
1186 |
> |
info[i].n_bonds = tot_bonds; |
1187 |
> |
info[i].n_bends = tot_bends; |
1188 |
> |
info[i].n_torsions = tot_torsions; |
1189 |
> |
info[i].n_SRI = tot_SRI; |
1190 |
> |
info[i].n_mol = tot_nmol; |
1191 |
> |
|
1192 |
> |
info[i].molMembershipArray = molMembershipArray; |
1193 |
> |
} |
1194 |
|
} |
1195 |
|
|
1130 |
– |
|
1196 |
|
#ifdef IS_MPI |
1197 |
|
|
1198 |
< |
void SimSetup::mpiMolDivide( void ){ |
1134 |
< |
|
1198 |
> |
void SimSetup::mpiMolDivide(void){ |
1199 |
|
int i, j, k; |
1200 |
|
int localMol, allMol; |
1201 |
|
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
1202 |
|
|
1203 |
< |
mpiSim = new mpiSimulation( info ); |
1204 |
< |
|
1203 |
> |
mpiSim = new mpiSimulation(info); |
1204 |
> |
|
1205 |
|
globalIndex = mpiSim->divideLabor(); |
1206 |
|
|
1207 |
|
// set up the local variables |
1208 |
< |
|
1208 |
> |
|
1209 |
|
mol2proc = mpiSim->getMolToProcMap(); |
1210 |
|
molCompType = mpiSim->getMolComponentType(); |
1211 |
< |
|
1211 |
> |
|
1212 |
|
allMol = 0; |
1213 |
|
localMol = 0; |
1214 |
|
local_atoms = 0; |
1218 |
|
globalAtomIndex = 0; |
1219 |
|
|
1220 |
|
|
1221 |
< |
for( i=0; i<n_components; i++ ){ |
1222 |
< |
|
1223 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
1224 |
< |
|
1225 |
< |
if( mol2proc[allMol] == worldRank ){ |
1226 |
< |
|
1227 |
< |
local_atoms += comp_stamps[i]->getNAtoms(); |
1228 |
< |
local_bonds += comp_stamps[i]->getNBonds(); |
1165 |
< |
local_bends += comp_stamps[i]->getNBends(); |
1166 |
< |
local_torsions += comp_stamps[i]->getNTorsions(); |
1167 |
< |
localMol++; |
1221 |
> |
for (i = 0; i < n_components; i++){ |
1222 |
> |
for (j = 0; j < components_nmol[i]; j++){ |
1223 |
> |
if (mol2proc[allMol] == worldRank){ |
1224 |
> |
local_atoms += comp_stamps[i]->getNAtoms(); |
1225 |
> |
local_bonds += comp_stamps[i]->getNBonds(); |
1226 |
> |
local_bends += comp_stamps[i]->getNBends(); |
1227 |
> |
local_torsions += comp_stamps[i]->getNTorsions(); |
1228 |
> |
localMol++; |
1229 |
|
} |
1230 |
< |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1231 |
< |
info->molMembershipArray[globalAtomIndex] = allMol; |
1230 |
> |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ |
1231 |
> |
info[0].molMembershipArray[globalAtomIndex] = allMol; |
1232 |
|
globalAtomIndex++; |
1233 |
|
} |
1234 |
|
|
1235 |
< |
allMol++; |
1235 |
> |
allMol++; |
1236 |
|
} |
1237 |
|
} |
1238 |
|
local_SRI = local_bonds + local_bends + local_torsions; |
1239 |
< |
|
1240 |
< |
info->n_atoms = mpiSim->getMyNlocal(); |
1241 |
< |
|
1242 |
< |
if( local_atoms != info->n_atoms ){ |
1243 |
< |
sprintf( painCave.errMsg, |
1244 |
< |
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1245 |
< |
" localAtom (%d) are not equal.\n", |
1246 |
< |
info->n_atoms, |
1186 |
< |
local_atoms ); |
1239 |
> |
|
1240 |
> |
info[0].n_atoms = mpiSim->getMyNlocal(); |
1241 |
> |
|
1242 |
> |
if (local_atoms != info[0].n_atoms){ |
1243 |
> |
sprintf(painCave.errMsg, |
1244 |
> |
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1245 |
> |
" localAtom (%d) are not equal.\n", |
1246 |
> |
info[0].n_atoms, local_atoms); |
1247 |
|
painCave.isFatal = 1; |
1248 |
|
simError(); |
1249 |
|
} |
1250 |
|
|
1251 |
< |
info->n_bonds = local_bonds; |
1252 |
< |
info->n_bends = local_bends; |
1253 |
< |
info->n_torsions = local_torsions; |
1254 |
< |
info->n_SRI = local_SRI; |
1255 |
< |
info->n_mol = localMol; |
1251 |
> |
info[0].n_bonds = local_bonds; |
1252 |
> |
info[0].n_bends = local_bends; |
1253 |
> |
info[0].n_torsions = local_torsions; |
1254 |
> |
info[0].n_SRI = local_SRI; |
1255 |
> |
info[0].n_mol = localMol; |
1256 |
|
|
1257 |
< |
strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
1257 |
> |
strcpy(checkPointMsg, "Passed nlocal consistency check."); |
1258 |
|
MPIcheckPoint(); |
1259 |
|
} |
1260 |
< |
|
1260 |
> |
|
1261 |
|
#endif // is_mpi |
1262 |
|
|
1263 |
|
|
1264 |
< |
void SimSetup::makeSysArrays( void ){ |
1265 |
< |
int i, j, k; |
1264 |
> |
void SimSetup::makeSysArrays(void){ |
1265 |
> |
|
1266 |
> |
#ifndef IS_MPI |
1267 |
> |
int k, j; |
1268 |
> |
#endif // is_mpi |
1269 |
> |
int i, l; |
1270 |
|
|
1271 |
+ |
Atom** the_atoms; |
1272 |
+ |
Molecule* the_molecules; |
1273 |
+ |
Exclude** the_excludes; |
1274 |
|
|
1208 |
– |
// create the atom and short range interaction arrays |
1275 |
|
|
1276 |
< |
Atom::createArrays(info->n_atoms); |
1277 |
< |
the_atoms = new Atom*[info->n_atoms]; |
1212 |
< |
the_molecules = new Molecule[info->n_mol]; |
1213 |
< |
int molIndex; |
1276 |
> |
for (l = 0; l < nInfo; l++){ |
1277 |
> |
// create the atom and short range interaction arrays |
1278 |
|
|
1279 |
< |
// initialize the molecule's stampID's |
1279 |
> |
the_atoms = new Atom * [info[l].n_atoms]; |
1280 |
> |
the_molecules = new Molecule[info[l].n_mol]; |
1281 |
> |
int molIndex; |
1282 |
|
|
1283 |
+ |
// initialize the molecule's stampID's |
1284 |
+ |
|
1285 |
|
#ifdef IS_MPI |
1218 |
– |
|
1286 |
|
|
1287 |
< |
molIndex = 0; |
1288 |
< |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
1289 |
< |
|
1290 |
< |
if(mol2proc[i] == worldRank ){ |
1291 |
< |
the_molecules[molIndex].setStampID( molCompType[i] ); |
1292 |
< |
the_molecules[molIndex].setMyIndex( molIndex ); |
1293 |
< |
the_molecules[molIndex].setGlobalIndex( i ); |
1294 |
< |
molIndex++; |
1287 |
> |
|
1288 |
> |
molIndex = 0; |
1289 |
> |
for (i = 0; i < mpiSim->getTotNmol(); i++){ |
1290 |
> |
if (mol2proc[i] == worldRank){ |
1291 |
> |
the_molecules[molIndex].setStampID(molCompType[i]); |
1292 |
> |
the_molecules[molIndex].setMyIndex(molIndex); |
1293 |
> |
the_molecules[molIndex].setGlobalIndex(i); |
1294 |
> |
molIndex++; |
1295 |
> |
} |
1296 |
|
} |
1229 |
– |
} |
1297 |
|
|
1298 |
|
#else // is_mpi |
1299 |
< |
|
1300 |
< |
molIndex = 0; |
1301 |
< |
globalAtomIndex = 0; |
1302 |
< |
for(i=0; i<n_components; i++){ |
1303 |
< |
for(j=0; j<components_nmol[i]; j++ ){ |
1304 |
< |
the_molecules[molIndex].setStampID( i ); |
1305 |
< |
the_molecules[molIndex].setMyIndex( molIndex ); |
1306 |
< |
the_molecules[molIndex].setGlobalIndex( molIndex ); |
1307 |
< |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1308 |
< |
info->molMembershipArray[globalAtomIndex] = molIndex; |
1309 |
< |
globalAtomIndex++; |
1299 |
> |
|
1300 |
> |
molIndex = 0; |
1301 |
> |
globalAtomIndex = 0; |
1302 |
> |
for (i = 0; i < n_components; i++){ |
1303 |
> |
for (j = 0; j < components_nmol[i]; j++){ |
1304 |
> |
the_molecules[molIndex].setStampID(i); |
1305 |
> |
the_molecules[molIndex].setMyIndex(molIndex); |
1306 |
> |
the_molecules[molIndex].setGlobalIndex(molIndex); |
1307 |
> |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ |
1308 |
> |
info[l].molMembershipArray[globalAtomIndex] = molIndex; |
1309 |
> |
globalAtomIndex++; |
1310 |
> |
} |
1311 |
> |
molIndex++; |
1312 |
|
} |
1244 |
– |
molIndex++; |
1313 |
|
} |
1246 |
– |
} |
1247 |
– |
|
1314 |
|
|
1315 |
+ |
|
1316 |
|
#endif // is_mpi |
1317 |
|
|
1318 |
|
|
1319 |
< |
if( info->n_SRI ){ |
1320 |
< |
|
1321 |
< |
Exclude::createArray(info->n_SRI); |
1322 |
< |
the_excludes = new Exclude*[info->n_SRI]; |
1323 |
< |
for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
1324 |
< |
info->globalExcludes = new int; |
1325 |
< |
info->n_exclude = info->n_SRI; |
1326 |
< |
} |
1327 |
< |
else{ |
1328 |
< |
|
1329 |
< |
Exclude::createArray( 1 ); |
1330 |
< |
the_excludes = new Exclude*; |
1331 |
< |
the_excludes[0] = new Exclude(0); |
1332 |
< |
the_excludes[0]->setPair( 0,0 ); |
1333 |
< |
info->globalExcludes = new int; |
1334 |
< |
info->globalExcludes[0] = 0; |
1335 |
< |
info->n_exclude = 0; |
1336 |
< |
} |
1319 |
> |
if (info[l].n_SRI){ |
1320 |
> |
Exclude::createArray(info[l].n_SRI); |
1321 |
> |
the_excludes = new Exclude * [info[l].n_SRI]; |
1322 |
> |
for (int ex = 0; ex < info[l].n_SRI; ex++){ |
1323 |
> |
the_excludes[ex] = new Exclude(ex); |
1324 |
> |
} |
1325 |
> |
info[l].globalExcludes = new int; |
1326 |
> |
info[l].n_exclude = info[l].n_SRI; |
1327 |
> |
} |
1328 |
> |
else{ |
1329 |
> |
Exclude::createArray(1); |
1330 |
> |
the_excludes = new Exclude * ; |
1331 |
> |
the_excludes[0] = new Exclude(0); |
1332 |
> |
the_excludes[0]->setPair(0, 0); |
1333 |
> |
info[l].globalExcludes = new int; |
1334 |
> |
info[l].globalExcludes[0] = 0; |
1335 |
> |
info[l].n_exclude = 0; |
1336 |
> |
} |
1337 |
|
|
1338 |
< |
// set the arrays into the SimInfo object |
1338 |
> |
// set the arrays into the SimInfo object |
1339 |
|
|
1340 |
< |
info->atoms = the_atoms; |
1341 |
< |
info->molecules = the_molecules; |
1342 |
< |
info->nGlobalExcludes = 0; |
1343 |
< |
info->excludes = the_excludes; |
1340 |
> |
info[l].atoms = the_atoms; |
1341 |
> |
info[l].molecules = the_molecules; |
1342 |
> |
info[l].nGlobalExcludes = 0; |
1343 |
> |
info[l].excludes = the_excludes; |
1344 |
|
|
1345 |
< |
the_ff->setSimInfo( info ); |
1346 |
< |
|
1345 |
> |
the_ff->setSimInfo(info); |
1346 |
> |
} |
1347 |
|
} |
1348 |
|
|
1349 |
< |
void SimSetup::makeIntegrator( void ){ |
1349 |
> |
void SimSetup::makeIntegrator(void){ |
1350 |
> |
int k; |
1351 |
|
|
1352 |
< |
NVT* myNVT = NULL; |
1353 |
< |
NPTi* myNPTi = NULL; |
1354 |
< |
NPTf* myNPTf = NULL; |
1355 |
< |
NPTim* myNPTim = NULL; |
1356 |
< |
NPTfm* myNPTfm = NULL; |
1352 |
> |
NVE<RealIntegrator>* myNVE = NULL; |
1353 |
> |
NVT<RealIntegrator>* myNVT = NULL; |
1354 |
> |
NPTi<NPT<RealIntegrator> >* myNPTi = NULL; |
1355 |
> |
NPTf<NPT<RealIntegrator> >* myNPTf = NULL; |
1356 |
> |
NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL; |
1357 |
> |
|
1358 |
> |
for (k = 0; k < nInfo; k++){ |
1359 |
> |
switch (ensembleCase){ |
1360 |
> |
case NVE_ENS: |
1361 |
> |
if (globals->haveZconstraints()){ |
1362 |
> |
setupZConstraint(info[k]); |
1363 |
> |
myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff); |
1364 |
> |
} |
1365 |
> |
else{ |
1366 |
> |
myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff); |
1367 |
> |
} |
1368 |
> |
|
1369 |
> |
info->the_integrator = myNVE; |
1370 |
> |
break; |
1371 |
|
|
1372 |
< |
switch( ensembleCase ){ |
1372 |
> |
case NVT_ENS: |
1373 |
> |
if (globals->haveZconstraints()){ |
1374 |
> |
setupZConstraint(info[k]); |
1375 |
> |
myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff); |
1376 |
> |
} |
1377 |
> |
else |
1378 |
> |
myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff); |
1379 |
|
|
1380 |
< |
case NVE_ENS: |
1293 |
< |
new NVE( info, the_ff ); |
1294 |
< |
break; |
1380 |
> |
myNVT->setTargetTemp(globals->getTargetTemp()); |
1381 |
|
|
1382 |
< |
case NVT_ENS: |
1383 |
< |
myNVT = new NVT( info, the_ff ); |
1384 |
< |
myNVT->setTargetTemp(globals->getTargetTemp()); |
1382 |
> |
if (globals->haveTauThermostat()) |
1383 |
> |
myNVT->setTauThermostat(globals->getTauThermostat()); |
1384 |
> |
else{ |
1385 |
> |
sprintf(painCave.errMsg, |
1386 |
> |
"SimSetup error: If you use the NVT\n" |
1387 |
> |
" ensemble, you must set tauThermostat.\n"); |
1388 |
> |
painCave.isFatal = 1; |
1389 |
> |
simError(); |
1390 |
> |
} |
1391 |
|
|
1392 |
< |
if (globals->haveTauThermostat()) |
1393 |
< |
myNVT->setTauThermostat(globals->getTauThermostat()); |
1392 |
> |
info->the_integrator = myNVT; |
1393 |
> |
break; |
1394 |
|
|
1395 |
< |
else { |
1396 |
< |
sprintf( painCave.errMsg, |
1397 |
< |
"SimSetup error: If you use the NVT\n" |
1398 |
< |
" ensemble, you must set tauThermostat.\n"); |
1399 |
< |
painCave.isFatal = 1; |
1400 |
< |
simError(); |
1401 |
< |
} |
1310 |
< |
break; |
1395 |
> |
case NPTi_ENS: |
1396 |
> |
if (globals->haveZconstraints()){ |
1397 |
> |
setupZConstraint(info[k]); |
1398 |
> |
myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1399 |
> |
} |
1400 |
> |
else |
1401 |
> |
myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff); |
1402 |
|
|
1403 |
< |
case NPTi_ENS: |
1313 |
< |
myNPTi = new NPTi( info, the_ff ); |
1314 |
< |
myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1403 |
> |
myNPTi->setTargetTemp(globals->getTargetTemp()); |
1404 |
|
|
1405 |
< |
if (globals->haveTargetPressure()) |
1406 |
< |
myNPTi->setTargetPressure(globals->getTargetPressure()); |
1407 |
< |
else { |
1408 |
< |
sprintf( painCave.errMsg, |
1409 |
< |
"SimSetup error: If you use a constant pressure\n" |
1410 |
< |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1411 |
< |
painCave.isFatal = 1; |
1412 |
< |
simError(); |
1413 |
< |
} |
1325 |
< |
|
1326 |
< |
if( globals->haveTauThermostat() ) |
1327 |
< |
myNPTi->setTauThermostat( globals->getTauThermostat() ); |
1328 |
< |
else{ |
1329 |
< |
sprintf( painCave.errMsg, |
1330 |
< |
"SimSetup error: If you use an NPT\n" |
1331 |
< |
" ensemble, you must set tauThermostat.\n"); |
1332 |
< |
painCave.isFatal = 1; |
1333 |
< |
simError(); |
1334 |
< |
} |
1405 |
> |
if (globals->haveTargetPressure()) |
1406 |
> |
myNPTi->setTargetPressure(globals->getTargetPressure()); |
1407 |
> |
else{ |
1408 |
> |
sprintf(painCave.errMsg, |
1409 |
> |
"SimSetup error: If you use a constant pressure\n" |
1410 |
> |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1411 |
> |
painCave.isFatal = 1; |
1412 |
> |
simError(); |
1413 |
> |
} |
1414 |
|
|
1415 |
< |
if( globals->haveTauBarostat() ) |
1416 |
< |
myNPTi->setTauBarostat( globals->getTauBarostat() ); |
1417 |
< |
else{ |
1418 |
< |
sprintf( painCave.errMsg, |
1419 |
< |
"SimSetup error: If you use an NPT\n" |
1420 |
< |
" ensemble, you must set tauBarostat.\n"); |
1421 |
< |
painCave.isFatal = 1; |
1422 |
< |
simError(); |
1423 |
< |
} |
1345 |
< |
break; |
1415 |
> |
if (globals->haveTauThermostat()) |
1416 |
> |
myNPTi->setTauThermostat(globals->getTauThermostat()); |
1417 |
> |
else{ |
1418 |
> |
sprintf(painCave.errMsg, |
1419 |
> |
"SimSetup error: If you use an NPT\n" |
1420 |
> |
" ensemble, you must set tauThermostat.\n"); |
1421 |
> |
painCave.isFatal = 1; |
1422 |
> |
simError(); |
1423 |
> |
} |
1424 |
|
|
1425 |
< |
case NPTf_ENS: |
1426 |
< |
myNPTf = new NPTf( info, the_ff ); |
1427 |
< |
myNPTf->setTargetTemp( globals->getTargetTemp()); |
1425 |
> |
if (globals->haveTauBarostat()) |
1426 |
> |
myNPTi->setTauBarostat(globals->getTauBarostat()); |
1427 |
> |
else{ |
1428 |
> |
sprintf(painCave.errMsg, |
1429 |
> |
"SimSetup error: If you use an NPT\n" |
1430 |
> |
" ensemble, you must set tauBarostat.\n"); |
1431 |
> |
painCave.isFatal = 1; |
1432 |
> |
simError(); |
1433 |
> |
} |
1434 |
|
|
1435 |
< |
if (globals->haveTargetPressure()) |
1436 |
< |
myNPTf->setTargetPressure(globals->getTargetPressure()); |
1353 |
< |
else { |
1354 |
< |
sprintf( painCave.errMsg, |
1355 |
< |
"SimSetup error: If you use a constant pressure\n" |
1356 |
< |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1357 |
< |
painCave.isFatal = 1; |
1358 |
< |
simError(); |
1359 |
< |
} |
1435 |
> |
info->the_integrator = myNPTi; |
1436 |
> |
break; |
1437 |
|
|
1438 |
< |
if( globals->haveTauThermostat() ) |
1439 |
< |
myNPTf->setTauThermostat( globals->getTauThermostat() ); |
1440 |
< |
else{ |
1441 |
< |
sprintf( painCave.errMsg, |
1442 |
< |
"SimSetup error: If you use an NPT\n" |
1443 |
< |
" ensemble, you must set tauThermostat.\n"); |
1444 |
< |
painCave.isFatal = 1; |
1368 |
< |
simError(); |
1369 |
< |
} |
1438 |
> |
case NPTf_ENS: |
1439 |
> |
if (globals->haveZconstraints()){ |
1440 |
> |
setupZConstraint(info[k]); |
1441 |
> |
myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1442 |
> |
} |
1443 |
> |
else |
1444 |
> |
myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1445 |
|
|
1446 |
< |
if( globals->haveTauBarostat() ) |
1372 |
< |
myNPTf->setTauBarostat( globals->getTauBarostat() ); |
1373 |
< |
else{ |
1374 |
< |
sprintf( painCave.errMsg, |
1375 |
< |
"SimSetup error: If you use an NPT\n" |
1376 |
< |
" ensemble, you must set tauBarostat.\n"); |
1377 |
< |
painCave.isFatal = 1; |
1378 |
< |
simError(); |
1379 |
< |
} |
1380 |
< |
break; |
1381 |
< |
|
1382 |
< |
case NPTim_ENS: |
1383 |
< |
myNPTim = new NPTim( info, the_ff ); |
1384 |
< |
myNPTim->setTargetTemp( globals->getTargetTemp()); |
1446 |
> |
myNPTf->setTargetTemp(globals->getTargetTemp()); |
1447 |
|
|
1448 |
< |
if (globals->haveTargetPressure()) |
1449 |
< |
myNPTim->setTargetPressure(globals->getTargetPressure()); |
1450 |
< |
else { |
1451 |
< |
sprintf( painCave.errMsg, |
1452 |
< |
"SimSetup error: If you use a constant pressure\n" |
1453 |
< |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1454 |
< |
painCave.isFatal = 1; |
1455 |
< |
simError(); |
1456 |
< |
} |
1395 |
< |
|
1396 |
< |
if( globals->haveTauThermostat() ) |
1397 |
< |
myNPTim->setTauThermostat( globals->getTauThermostat() ); |
1398 |
< |
else{ |
1399 |
< |
sprintf( painCave.errMsg, |
1400 |
< |
"SimSetup error: If you use an NPT\n" |
1401 |
< |
" ensemble, you must set tauThermostat.\n"); |
1402 |
< |
painCave.isFatal = 1; |
1403 |
< |
simError(); |
1404 |
< |
} |
1448 |
> |
if (globals->haveTargetPressure()) |
1449 |
> |
myNPTf->setTargetPressure(globals->getTargetPressure()); |
1450 |
> |
else{ |
1451 |
> |
sprintf(painCave.errMsg, |
1452 |
> |
"SimSetup error: If you use a constant pressure\n" |
1453 |
> |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1454 |
> |
painCave.isFatal = 1; |
1455 |
> |
simError(); |
1456 |
> |
} |
1457 |
|
|
1458 |
< |
if( globals->haveTauBarostat() ) |
1459 |
< |
myNPTim->setTauBarostat( globals->getTauBarostat() ); |
1460 |
< |
else{ |
1461 |
< |
sprintf( painCave.errMsg, |
1462 |
< |
"SimSetup error: If you use an NPT\n" |
1463 |
< |
" ensemble, you must set tauBarostat.\n"); |
1464 |
< |
painCave.isFatal = 1; |
1465 |
< |
simError(); |
1466 |
< |
} |
1415 |
< |
break; |
1458 |
> |
if (globals->haveTauThermostat()) |
1459 |
> |
myNPTf->setTauThermostat(globals->getTauThermostat()); |
1460 |
> |
else{ |
1461 |
> |
sprintf(painCave.errMsg, |
1462 |
> |
"SimSetup error: If you use an NPT\n" |
1463 |
> |
" ensemble, you must set tauThermostat.\n"); |
1464 |
> |
painCave.isFatal = 1; |
1465 |
> |
simError(); |
1466 |
> |
} |
1467 |
|
|
1468 |
< |
case NPTfm_ENS: |
1469 |
< |
myNPTfm = new NPTfm( info, the_ff ); |
1470 |
< |
myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1468 |
> |
if (globals->haveTauBarostat()) |
1469 |
> |
myNPTf->setTauBarostat(globals->getTauBarostat()); |
1470 |
> |
else{ |
1471 |
> |
sprintf(painCave.errMsg, |
1472 |
> |
"SimSetup error: If you use an NPT\n" |
1473 |
> |
" ensemble, you must set tauBarostat.\n"); |
1474 |
> |
painCave.isFatal = 1; |
1475 |
> |
simError(); |
1476 |
> |
} |
1477 |
|
|
1478 |
< |
if (globals->haveTargetPressure()) |
1479 |
< |
myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1423 |
< |
else { |
1424 |
< |
sprintf( painCave.errMsg, |
1425 |
< |
"SimSetup error: If you use a constant pressure\n" |
1426 |
< |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1427 |
< |
painCave.isFatal = 1; |
1428 |
< |
simError(); |
1429 |
< |
} |
1430 |
< |
|
1431 |
< |
if( globals->haveTauThermostat() ) |
1432 |
< |
myNPTfm->setTauThermostat( globals->getTauThermostat() ); |
1433 |
< |
else{ |
1434 |
< |
sprintf( painCave.errMsg, |
1435 |
< |
"SimSetup error: If you use an NPT\n" |
1436 |
< |
" ensemble, you must set tauThermostat.\n"); |
1437 |
< |
painCave.isFatal = 1; |
1438 |
< |
simError(); |
1439 |
< |
} |
1478 |
> |
info->the_integrator = myNPTf; |
1479 |
> |
break; |
1480 |
|
|
1481 |
< |
if( globals->haveTauBarostat() ) |
1482 |
< |
myNPTfm->setTauBarostat( globals->getTauBarostat() ); |
1483 |
< |
else{ |
1484 |
< |
sprintf( painCave.errMsg, |
1485 |
< |
"SimSetup error: If you use an NPT\n" |
1486 |
< |
" ensemble, you must set tauBarostat.\n"); |
1487 |
< |
painCave.isFatal = 1; |
1448 |
< |
simError(); |
1449 |
< |
} |
1450 |
< |
break; |
1481 |
> |
case NPTxyz_ENS: |
1482 |
> |
if (globals->haveZconstraints()){ |
1483 |
> |
setupZConstraint(info[k]); |
1484 |
> |
myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1485 |
> |
} |
1486 |
> |
else |
1487 |
> |
myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1488 |
|
|
1489 |
< |
default: |
1453 |
< |
sprintf( painCave.errMsg, |
1454 |
< |
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1455 |
< |
painCave.isFatal = 1; |
1456 |
< |
simError(); |
1457 |
< |
} |
1489 |
> |
myNPTxyz->setTargetTemp(globals->getTargetTemp()); |
1490 |
|
|
1491 |
+ |
if (globals->haveTargetPressure()) |
1492 |
+ |
myNPTxyz->setTargetPressure(globals->getTargetPressure()); |
1493 |
+ |
else{ |
1494 |
+ |
sprintf(painCave.errMsg, |
1495 |
+ |
"SimSetup error: If you use a constant pressure\n" |
1496 |
+ |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1497 |
+ |
painCave.isFatal = 1; |
1498 |
+ |
simError(); |
1499 |
+ |
} |
1500 |
+ |
|
1501 |
+ |
if (globals->haveTauThermostat()) |
1502 |
+ |
myNPTxyz->setTauThermostat(globals->getTauThermostat()); |
1503 |
+ |
else{ |
1504 |
+ |
sprintf(painCave.errMsg, |
1505 |
+ |
"SimSetup error: If you use an NPT\n" |
1506 |
+ |
" ensemble, you must set tauThermostat.\n"); |
1507 |
+ |
painCave.isFatal = 1; |
1508 |
+ |
simError(); |
1509 |
+ |
} |
1510 |
+ |
|
1511 |
+ |
if (globals->haveTauBarostat()) |
1512 |
+ |
myNPTxyz->setTauBarostat(globals->getTauBarostat()); |
1513 |
+ |
else{ |
1514 |
+ |
sprintf(painCave.errMsg, |
1515 |
+ |
"SimSetup error: If you use an NPT\n" |
1516 |
+ |
" ensemble, you must set tauBarostat.\n"); |
1517 |
+ |
painCave.isFatal = 1; |
1518 |
+ |
simError(); |
1519 |
+ |
} |
1520 |
+ |
|
1521 |
+ |
info->the_integrator = myNPTxyz; |
1522 |
+ |
break; |
1523 |
+ |
|
1524 |
+ |
default: |
1525 |
+ |
sprintf(painCave.errMsg, |
1526 |
+ |
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1527 |
+ |
painCave.isFatal = 1; |
1528 |
+ |
simError(); |
1529 |
+ |
} |
1530 |
+ |
} |
1531 |
|
} |
1532 |
|
|
1533 |
< |
void SimSetup::initFortran( void ){ |
1533 |
> |
void SimSetup::initFortran(void){ |
1534 |
> |
info[0].refreshSim(); |
1535 |
|
|
1536 |
< |
info->refreshSim(); |
1537 |
< |
|
1465 |
< |
if( !strcmp( info->mixingRule, "standard") ){ |
1466 |
< |
the_ff->initForceField( LB_MIXING_RULE ); |
1536 |
> |
if (!strcmp(info[0].mixingRule, "standard")){ |
1537 |
> |
the_ff->initForceField(LB_MIXING_RULE); |
1538 |
|
} |
1539 |
< |
else if( !strcmp( info->mixingRule, "explicit") ){ |
1540 |
< |
the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
1539 |
> |
else if (!strcmp(info[0].mixingRule, "explicit")){ |
1540 |
> |
the_ff->initForceField(EXPLICIT_MIXING_RULE); |
1541 |
|
} |
1542 |
|
else{ |
1543 |
< |
sprintf( painCave.errMsg, |
1544 |
< |
"SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1474 |
< |
info->mixingRule ); |
1543 |
> |
sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1544 |
> |
info[0].mixingRule); |
1545 |
|
painCave.isFatal = 1; |
1546 |
|
simError(); |
1547 |
|
} |
1548 |
|
|
1549 |
|
|
1550 |
|
#ifdef IS_MPI |
1551 |
< |
strcpy( checkPointMsg, |
1482 |
< |
"Successfully intialized the mixingRule for Fortran." ); |
1551 |
> |
strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran."); |
1552 |
|
MPIcheckPoint(); |
1553 |
|
#endif // is_mpi |
1554 |
+ |
} |
1555 |
|
|
1556 |
+ |
void SimSetup::setupZConstraint(SimInfo& theInfo){ |
1557 |
+ |
int nZConstraints; |
1558 |
+ |
ZconStamp** zconStamp; |
1559 |
+ |
|
1560 |
+ |
if (globals->haveZconstraintTime()){ |
1561 |
+ |
//add sample time of z-constraint into SimInfo's property list |
1562 |
+ |
DoubleData* zconsTimeProp = new DoubleData(); |
1563 |
+ |
zconsTimeProp->setID(ZCONSTIME_ID); |
1564 |
+ |
zconsTimeProp->setData(globals->getZconsTime()); |
1565 |
+ |
theInfo.addProperty(zconsTimeProp); |
1566 |
+ |
} |
1567 |
+ |
else{ |
1568 |
+ |
sprintf(painCave.errMsg, |
1569 |
+ |
"ZConstraint error: If you use an ZConstraint\n" |
1570 |
+ |
" , you must set sample time.\n"); |
1571 |
+ |
painCave.isFatal = 1; |
1572 |
+ |
simError(); |
1573 |
+ |
} |
1574 |
+ |
|
1575 |
+ |
//push zconsTol into siminfo, if user does not specify |
1576 |
+ |
//value for zconsTol, a default value will be used |
1577 |
+ |
DoubleData* zconsTol = new DoubleData(); |
1578 |
+ |
zconsTol->setID(ZCONSTOL_ID); |
1579 |
+ |
if (globals->haveZconsTol()){ |
1580 |
+ |
zconsTol->setData(globals->getZconsTol()); |
1581 |
+ |
} |
1582 |
+ |
else{ |
1583 |
+ |
double defaultZConsTol = 0.01; |
1584 |
+ |
sprintf(painCave.errMsg, |
1585 |
+ |
"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n" |
1586 |
+ |
" , default value %f is used.\n", |
1587 |
+ |
defaultZConsTol); |
1588 |
+ |
painCave.isFatal = 0; |
1589 |
+ |
simError(); |
1590 |
+ |
|
1591 |
+ |
zconsTol->setData(defaultZConsTol); |
1592 |
+ |
} |
1593 |
+ |
theInfo.addProperty(zconsTol); |
1594 |
+ |
|
1595 |
+ |
//set Force Subtraction Policy |
1596 |
+ |
StringData* zconsForcePolicy = new StringData(); |
1597 |
+ |
zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID); |
1598 |
+ |
|
1599 |
+ |
if (globals->haveZconsForcePolicy()){ |
1600 |
+ |
zconsForcePolicy->setData(globals->getZconsForcePolicy()); |
1601 |
+ |
} |
1602 |
+ |
else{ |
1603 |
+ |
sprintf(painCave.errMsg, |
1604 |
+ |
"ZConstraint Warning: User does not set force Subtraction policy, " |
1605 |
+ |
"PolicyByMass is used\n"); |
1606 |
+ |
painCave.isFatal = 0; |
1607 |
+ |
simError(); |
1608 |
+ |
zconsForcePolicy->setData("BYMASS"); |
1609 |
+ |
} |
1610 |
+ |
|
1611 |
+ |
theInfo.addProperty(zconsForcePolicy); |
1612 |
+ |
|
1613 |
+ |
//Determine the name of ouput file and add it into SimInfo's property list |
1614 |
+ |
//Be careful, do not use inFileName, since it is a pointer which |
1615 |
+ |
//point to a string at master node, and slave nodes do not contain that string |
1616 |
+ |
|
1617 |
+ |
string zconsOutput(theInfo.finalName); |
1618 |
+ |
|
1619 |
+ |
zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1620 |
+ |
|
1621 |
+ |
StringData* zconsFilename = new StringData(); |
1622 |
+ |
zconsFilename->setID(ZCONSFILENAME_ID); |
1623 |
+ |
zconsFilename->setData(zconsOutput); |
1624 |
+ |
|
1625 |
+ |
theInfo.addProperty(zconsFilename); |
1626 |
+ |
|
1627 |
+ |
//setup index, pos and other parameters of z-constraint molecules |
1628 |
+ |
nZConstraints = globals->getNzConstraints(); |
1629 |
+ |
theInfo.nZconstraints = nZConstraints; |
1630 |
+ |
|
1631 |
+ |
zconStamp = globals->getZconStamp(); |
1632 |
+ |
ZConsParaItem tempParaItem; |
1633 |
+ |
|
1634 |
+ |
ZConsParaData* zconsParaData = new ZConsParaData(); |
1635 |
+ |
zconsParaData->setID(ZCONSPARADATA_ID); |
1636 |
+ |
|
1637 |
+ |
for (int i = 0; i < nZConstraints; i++){ |
1638 |
+ |
tempParaItem.havingZPos = zconStamp[i]->haveZpos(); |
1639 |
+ |
tempParaItem.zPos = zconStamp[i]->getZpos(); |
1640 |
+ |
tempParaItem.zconsIndex = zconStamp[i]->getMolIndex(); |
1641 |
+ |
tempParaItem.kRatio = zconStamp[i]->getKratio(); |
1642 |
+ |
|
1643 |
+ |
zconsParaData->addItem(tempParaItem); |
1644 |
+ |
} |
1645 |
+ |
|
1646 |
+ |
//check the uniqueness of index |
1647 |
+ |
if(!zconsParaData->isIndexUnique()){ |
1648 |
+ |
sprintf(painCave.errMsg, |
1649 |
+ |
"ZConstraint Error: molIndex is not unique\n"); |
1650 |
+ |
painCave.isFatal = 1; |
1651 |
+ |
simError(); |
1652 |
+ |
} |
1653 |
+ |
|
1654 |
+ |
//sort the parameters by index of molecules |
1655 |
+ |
zconsParaData->sortByIndex(); |
1656 |
+ |
|
1657 |
+ |
//push data into siminfo, therefore, we can retrieve later |
1658 |
+ |
theInfo.addProperty(zconsParaData); |
1659 |
|
} |