41 |
|
ForceField* ff, Globals* globals) : |
42 |
|
forceField_(ff), globals_(globals), nAtoms_(0), nBonds_(0), |
43 |
|
nBends_(0), nTorsions_(0), nRigidBodies_(0), nIntegrableObjects_(0), |
44 |
< |
nCutoffGroups_(0), nConstraints_(0), nZConstraint_(0), sman_(NULL) { |
44 |
> |
nCutoffGroups_(0), nConstraints_(0), nZConstraint_(0), sman_(NULL), |
45 |
> |
fortranInitialized_(false) { |
46 |
|
|
47 |
|
std::vector<std::pair<MoleculeStamp*, int> >::iterator i; |
47 |
– |
int nCutoffAtoms; // number of atoms belong to cutoff groups |
48 |
– |
int ngroups; //total cutoff groups defined in meta-data file |
48 |
|
MoleculeStamp* molStamp; |
49 |
|
int nMolWithSameStamp; |
50 |
+ |
int nCutoffAtoms; // number of atoms belong to cutoff groups |
51 |
+ |
int nGroups; //total cutoff groups defined in meta-data file |
52 |
|
CutoffGroupStamp* cgStamp; |
53 |
< |
int nAtomsIngroups; |
54 |
< |
int nCutoffGroupsInStamp; |
55 |
< |
|
53 |
> |
int nAtomsInGroups; |
54 |
> |
int nCutoffGroupsInStamp; |
55 |
> |
|
56 |
> |
RigidBodyStamp* rbStamp; |
57 |
> |
int nAtomsInRigidBodies; |
58 |
> |
int nRigidBodiesInStamp; |
59 |
> |
int nRigidAtoms; |
60 |
> |
int nRigidBodies; |
61 |
> |
|
62 |
|
nGlobalAtoms_ = 0; |
56 |
– |
ngroups = 0; |
63 |
|
|
64 |
+ |
nGroups = 0; |
65 |
+ |
nCutoffAtoms = 0; |
66 |
+ |
|
67 |
+ |
nRigidBodies |
68 |
+ |
nRigidBodies = 0; |
69 |
+ |
|
70 |
|
for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) { |
71 |
|
molStamp = i->first; |
72 |
|
nMolWithSameStamp = i->second; |
73 |
|
|
74 |
|
addMoleculeStamp(molStamp, nMolWithSameStamp); |
75 |
< |
|
75 |
> |
|
76 |
> |
//calculate atoms in molecules |
77 |
|
nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp; |
78 |
< |
|
79 |
< |
nAtomsIngroups = 0; |
78 |
> |
|
79 |
> |
|
80 |
> |
//calculate atoms in cutoff groups |
81 |
> |
nAtomsInGroups = 0; |
82 |
|
nCutoffGroupsInStamp = molStamp->getNCutoffGroups(); |
83 |
|
|
84 |
|
for (int j=0; j < nCutoffGroupsInStamp; j++) { |
85 |
|
cgStamp = molStamp->getCutoffGroup(j); |
86 |
< |
nAtomsIngroups += cgStamp->getNMembers(); |
86 |
> |
nAtomsInGroups += cgStamp->getNMembers(); |
87 |
|
} |
88 |
|
|
89 |
< |
ngroups += *nMolWithSameStamp; |
90 |
< |
nCutoffAtoms += nAtomsIngroups * nMolWithSameStamp; |
89 |
> |
nGroups += nCutoffGroupsInStamp * nMolWithSameStamp; |
90 |
> |
nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp; |
91 |
> |
|
92 |
> |
//calculate atoms in rigid bodies |
93 |
> |
nAtomsInRigidBodies = 0; |
94 |
> |
nRigidBodiesInStamp = molStamp->getNCutoffGroups(); |
95 |
> |
|
96 |
> |
for (int j=0; j < nRigidBodiesInStamp; j++) { |
97 |
> |
rbStamp = molStamp->getRigidBody(j); |
98 |
> |
nRigidBodiesInStamp += rbStamp->getNMembers(); |
99 |
> |
} |
100 |
> |
|
101 |
> |
nRigidBodies += nRigidBodiesInStamp * nMolWithSameStamp; |
102 |
> |
nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp; |
103 |
> |
|
104 |
|
} |
105 |
|
|
106 |
|
//every free atom (atom does not belong to cutoff groups) is a cutoff group |
107 |
|
//therefore the total number of cutoff groups in the system is equal to |
108 |
|
//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data |
109 |
|
//file plus the number of cutoff groups defined in meta-data file |
110 |
< |
nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + ngroups; |
110 |
> |
nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups; |
111 |
|
|
112 |
+ |
//every free atom (atom does not belong to rigid bodies) is a rigid body |
113 |
+ |
//therefore the total number of cutoff groups in the system is equal to |
114 |
+ |
//the total number of atoms minus number of atoms belong to rigid body defined in meta-data |
115 |
+ |
//file plus the number of rigid bodies defined in meta-data file |
116 |
+ |
nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nRigidBodies; |
117 |
+ |
|
118 |
|
//initialize globalGroupMembership_, every element of this array will be 0 |
119 |
|
globalGroupMembership_.insert(globalGroupMembership_.end(), nGlobalAtoms_, 0); |
120 |
|
|
193 |
|
|
194 |
|
Molecule* SimInfo::beginMolecule(MoleculeIterator& i) { |
195 |
|
i = molecules_.begin(); |
196 |
< |
return i == molecules_.end() ? NULL : *i; |
196 |
> |
return i == molecules_.end() ? NULL : i->second; |
197 |
|
} |
198 |
|
|
199 |
|
Molecule* SimInfo::nextMolecule(MoleculeIterator& i) { |
200 |
|
++i; |
201 |
< |
return i == molecules_.end() ? NULL : *i; |
201 |
> |
return i == molecules_.end() ? NULL : i->second; |
202 |
|
} |
203 |
|
|
204 |
|
|
396 |
|
|
397 |
|
void SimInfo::update() { |
398 |
|
|
399 |
+ |
setupSimType(); |
400 |
+ |
|
401 |
|
#ifdef IS_MPI |
402 |
|
setupFortranParallel(); |
403 |
|
#endif |
404 |
|
|
405 |
|
setupFortranSim(); |
406 |
+ |
|
407 |
+ |
setupCutoff(); |
408 |
+ |
|
409 |
+ |
//notify fortran whether reaction field is used or not. It is deprecated now |
410 |
+ |
//int isError = 0; |
411 |
+ |
//initFortranFF( &useReactionField, &isError ); |
412 |
|
|
413 |
+ |
//if(isError){ |
414 |
+ |
// sprintf( painCave.errMsg, |
415 |
+ |
// "SimCreator::initFortran() error: There was an error initializing the forceField in fortran.\n" ); |
416 |
+ |
// painCave.isFatal = 1; |
417 |
+ |
// simError(); |
418 |
+ |
//} |
419 |
+ |
|
420 |
|
calcNdf(); |
421 |
|
calcNdfRaw(); |
422 |
|
calcNdfTrans(); |
423 |
+ |
|
424 |
+ |
fortranInitialized_ = true; |
425 |
|
} |
426 |
|
|
427 |
|
std::set<AtomType*> SimInfo::getUniqueAtomTypes() { |
595 |
|
} |
596 |
|
} |
597 |
|
|
598 |
+ |
//fill molMembershipArray |
599 |
+ |
//molMembershipArray is filled by SimCreator |
600 |
+ |
std::vector<int> molMembershipArray(nGlobalAtoms_); |
601 |
+ |
for (int i = 0; i < nGlobalAtoms_; i++) { |
602 |
+ |
molMembershipArray.push_back(globalMolMembership_[i] + 1); |
603 |
+ |
} |
604 |
+ |
|
605 |
|
//setup fortran simulation |
606 |
|
//gloalExcludes and molMembershipArray should go away (They are never used) |
607 |
|
//why the hell fortran need to know molecule? |
687 |
|
|
688 |
|
#endif |
689 |
|
|
690 |
+ |
double SimInfo::calcMaxCutoffRadius() { |
691 |
+ |
|
692 |
+ |
|
693 |
+ |
std::vector<AtomType*> atomTypes; |
694 |
+ |
std::vector<AtomType*>::iterator i; |
695 |
+ |
std::vector<double> cutoffRadius; |
696 |
+ |
|
697 |
+ |
//get the unique atom types |
698 |
+ |
atomTypes = getUniqueAtomTypes(); |
699 |
+ |
|
700 |
+ |
//query the max cutoff radius among these atom types |
701 |
+ |
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
702 |
+ |
cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i)); |
703 |
+ |
} |
704 |
+ |
|
705 |
+ |
double maxCutoffRadius = std::max_element(cutoffRadius.begin(), cutoffRadius.end()); |
706 |
+ |
#ifdef IS_MPI |
707 |
+ |
//pick the max cutoff radius among the processors |
708 |
+ |
#endif |
709 |
+ |
|
710 |
+ |
return maxCutoffRadius; |
711 |
+ |
} |
712 |
+ |
|
713 |
+ |
void SimInfo::setupCutoff() { |
714 |
+ |
double rcut_; //cutoff radius |
715 |
+ |
double rsw_; //switching radius |
716 |
+ |
|
717 |
+ |
if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { |
718 |
+ |
|
719 |
+ |
if (!globals_->haveRcut()){ |
720 |
+ |
sprintf(painCave.errMsg, |
721 |
+ |
"SimCreator Warning: No value was set for the cutoffRadius.\n" |
722 |
+ |
"\tOOPSE will use a default value of 15.0 angstroms" |
723 |
+ |
"\tfor the cutoffRadius.\n"); |
724 |
+ |
painCave.isFatal = 0; |
725 |
+ |
simError(); |
726 |
+ |
rcut_ = 15.0; |
727 |
+ |
} else{ |
728 |
+ |
rcut_ = globals_->getRcut(); |
729 |
+ |
} |
730 |
+ |
|
731 |
+ |
if (!globals_->haveRsw()){ |
732 |
+ |
sprintf(painCave.errMsg, |
733 |
+ |
"SimCreator Warning: No value was set for switchingRadius.\n" |
734 |
+ |
"\tOOPSE will use a default value of\n" |
735 |
+ |
"\t0.95 * cutoffRadius for the switchingRadius\n"); |
736 |
+ |
painCave.isFatal = 0; |
737 |
+ |
simError(); |
738 |
+ |
rsw_ = 0.95 * rcut_; |
739 |
+ |
} else{ |
740 |
+ |
rsw_ = globals_->getRsw(); |
741 |
+ |
} |
742 |
+ |
|
743 |
+ |
} else { |
744 |
+ |
// if charge, dipole or reaction field is not used and the cutofff radius is not specified in |
745 |
+ |
//meta-data file, the maximum cutoff radius calculated from forcefiled will be used |
746 |
+ |
|
747 |
+ |
if (globals_->haveRcut()) { |
748 |
+ |
rcut_ = globals_->getRcut(); |
749 |
+ |
} else { |
750 |
+ |
//set cutoff radius to the maximum cutoff radius based on atom types in the whole system |
751 |
+ |
rcut_ = calcMaxCutoffRadius(); |
752 |
+ |
} |
753 |
+ |
|
754 |
+ |
if (globals_->haveRsw()) { |
755 |
+ |
rsw_ = globals_->getRsw() |
756 |
+ |
} else { |
757 |
+ |
rsw_ = rcut_; |
758 |
+ |
} |
759 |
+ |
|
760 |
+ |
} |
761 |
+ |
|
762 |
+ |
double rnblist = rcut_ + 1; // skin of neighbor list |
763 |
+ |
|
764 |
+ |
//Pass these cutoff radius etc. to fortran. This function should be called once and only once |
765 |
+ |
notifyFortranCutoffs(&rcut_, &rsw_, &rnblist); |
766 |
+ |
} |
767 |
+ |
|
768 |
|
void SimInfo::addProperty(GenericData* genData) { |
769 |
|
properties_.addProperty(genData); |
770 |
|
} |