48 |
|
|
49 |
|
#include <algorithm> |
50 |
|
#include <set> |
51 |
+ |
#include <map> |
52 |
|
|
53 |
|
#include "brains/SimInfo.hpp" |
54 |
|
#include "math/Vector3.hpp" |
59 |
|
#include "UseTheForce/DarkSide/fSwitchingFunctionType.h" |
60 |
|
#include "UseTheForce/doForces_interface.h" |
61 |
|
#include "UseTheForce/DarkSide/electrostatic_interface.h" |
61 |
– |
#include "UseTheForce/notifyCutoffs_interface.h" |
62 |
|
#include "UseTheForce/DarkSide/switcheroo_interface.h" |
63 |
|
#include "utils/MemoryUtils.hpp" |
64 |
|
#include "utils/simError.h" |
70 |
|
#endif |
71 |
|
|
72 |
|
namespace oopse { |
73 |
+ |
std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) { |
74 |
+ |
std::map<int, std::set<int> >::iterator i = container.find(index); |
75 |
+ |
std::set<int> result; |
76 |
+ |
if (i != container.end()) { |
77 |
+ |
result = i->second; |
78 |
+ |
} |
79 |
|
|
80 |
< |
SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, |
81 |
< |
ForceField* ff, Globals* simParams) : |
82 |
< |
stamps_(stamps), forceField_(ff), simParams_(simParams), |
80 |
> |
return result; |
81 |
> |
} |
82 |
> |
|
83 |
> |
SimInfo::SimInfo(ForceField* ff, Globals* simParams) : |
84 |
> |
forceField_(ff), simParams_(simParams), |
85 |
|
ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0), |
86 |
|
nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0), |
87 |
|
nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), |
89 |
|
nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0), |
90 |
|
sman_(NULL), fortranInitialized_(false) { |
91 |
|
|
84 |
– |
|
85 |
– |
std::vector<std::pair<MoleculeStamp*, int> >::iterator i; |
92 |
|
MoleculeStamp* molStamp; |
93 |
|
int nMolWithSameStamp; |
94 |
|
int nCutoffAtoms = 0; // number of atoms belong to cutoff groups |
96 |
|
CutoffGroupStamp* cgStamp; |
97 |
|
RigidBodyStamp* rbStamp; |
98 |
|
int nRigidAtoms = 0; |
99 |
< |
|
100 |
< |
for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) { |
101 |
< |
molStamp = i->first; |
102 |
< |
nMolWithSameStamp = i->second; |
99 |
> |
std::vector<Component*> components = simParams->getComponents(); |
100 |
> |
|
101 |
> |
for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) { |
102 |
> |
molStamp = (*i)->getMoleculeStamp(); |
103 |
> |
nMolWithSameStamp = (*i)->getNMol(); |
104 |
|
|
105 |
|
addMoleculeStamp(molStamp, nMolWithSameStamp); |
106 |
|
|
107 |
|
//calculate atoms in molecules |
108 |
|
nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp; |
109 |
|
|
103 |
– |
|
110 |
|
//calculate atoms in cutoff groups |
111 |
|
int nAtomsInGroups = 0; |
112 |
|
int nCutoffGroupsInStamp = molStamp->getNCutoffGroups(); |
113 |
|
|
114 |
|
for (int j=0; j < nCutoffGroupsInStamp; j++) { |
115 |
< |
cgStamp = molStamp->getCutoffGroup(j); |
115 |
> |
cgStamp = molStamp->getCutoffGroupStamp(j); |
116 |
|
nAtomsInGroups += cgStamp->getNMembers(); |
117 |
|
} |
118 |
|
|
125 |
|
int nRigidBodiesInStamp = molStamp->getNRigidBodies(); |
126 |
|
|
127 |
|
for (int j=0; j < nRigidBodiesInStamp; j++) { |
128 |
< |
rbStamp = molStamp->getRigidBody(j); |
128 |
> |
rbStamp = molStamp->getRigidBodyStamp(j); |
129 |
|
nAtomsInRigidBodies += rbStamp->getNMembers(); |
130 |
|
} |
131 |
|
|
164 |
|
} |
165 |
|
molecules_.clear(); |
166 |
|
|
161 |
– |
delete stamps_; |
167 |
|
delete sman_; |
168 |
|
delete simParams_; |
169 |
|
delete forceField_; |
270 |
|
} |
271 |
|
} |
272 |
|
|
273 |
< |
}//end for (integrableObject) |
274 |
< |
}// end for (mol) |
273 |
> |
} |
274 |
> |
} |
275 |
|
|
276 |
|
// n_constraints is local, so subtract them on each processor |
277 |
|
ndf_local -= nConstraints_; |
350 |
|
int b; |
351 |
|
int c; |
352 |
|
int d; |
353 |
+ |
|
354 |
+ |
std::map<int, std::set<int> > atomGroups; |
355 |
+ |
|
356 |
+ |
Molecule::RigidBodyIterator rbIter; |
357 |
+ |
RigidBody* rb; |
358 |
+ |
Molecule::IntegrableObjectIterator ii; |
359 |
+ |
StuntDouble* integrableObject; |
360 |
|
|
361 |
+ |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
362 |
+ |
integrableObject = mol->nextIntegrableObject(ii)) { |
363 |
+ |
|
364 |
+ |
if (integrableObject->isRigidBody()) { |
365 |
+ |
rb = static_cast<RigidBody*>(integrableObject); |
366 |
+ |
std::vector<Atom*> atoms = rb->getAtoms(); |
367 |
+ |
std::set<int> rigidAtoms; |
368 |
+ |
for (int i = 0; i < atoms.size(); ++i) { |
369 |
+ |
rigidAtoms.insert(atoms[i]->getGlobalIndex()); |
370 |
+ |
} |
371 |
+ |
for (int i = 0; i < atoms.size(); ++i) { |
372 |
+ |
atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms)); |
373 |
+ |
} |
374 |
+ |
} else { |
375 |
+ |
std::set<int> oneAtomSet; |
376 |
+ |
oneAtomSet.insert(integrableObject->getGlobalIndex()); |
377 |
+ |
atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet)); |
378 |
+ |
} |
379 |
+ |
} |
380 |
+ |
|
381 |
+ |
|
382 |
+ |
|
383 |
|
for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) { |
384 |
|
a = bond->getAtomA()->getGlobalIndex(); |
385 |
|
b = bond->getAtomB()->getGlobalIndex(); |
390 |
|
a = bend->getAtomA()->getGlobalIndex(); |
391 |
|
b = bend->getAtomB()->getGlobalIndex(); |
392 |
|
c = bend->getAtomC()->getGlobalIndex(); |
393 |
+ |
std::set<int> rigidSetA = getRigidSet(a, atomGroups); |
394 |
+ |
std::set<int> rigidSetB = getRigidSet(b, atomGroups); |
395 |
+ |
std::set<int> rigidSetC = getRigidSet(c, atomGroups); |
396 |
|
|
397 |
< |
exclude_.addPair(a, b); |
398 |
< |
exclude_.addPair(a, c); |
399 |
< |
exclude_.addPair(b, c); |
397 |
> |
exclude_.addPairs(rigidSetA, rigidSetB); |
398 |
> |
exclude_.addPairs(rigidSetA, rigidSetC); |
399 |
> |
exclude_.addPairs(rigidSetB, rigidSetC); |
400 |
> |
|
401 |
> |
//exclude_.addPair(a, b); |
402 |
> |
//exclude_.addPair(a, c); |
403 |
> |
//exclude_.addPair(b, c); |
404 |
|
} |
405 |
|
|
406 |
|
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) { |
408 |
|
b = torsion->getAtomB()->getGlobalIndex(); |
409 |
|
c = torsion->getAtomC()->getGlobalIndex(); |
410 |
|
d = torsion->getAtomD()->getGlobalIndex(); |
411 |
+ |
std::set<int> rigidSetA = getRigidSet(a, atomGroups); |
412 |
+ |
std::set<int> rigidSetB = getRigidSet(b, atomGroups); |
413 |
+ |
std::set<int> rigidSetC = getRigidSet(c, atomGroups); |
414 |
+ |
std::set<int> rigidSetD = getRigidSet(d, atomGroups); |
415 |
|
|
416 |
+ |
exclude_.addPairs(rigidSetA, rigidSetB); |
417 |
+ |
exclude_.addPairs(rigidSetA, rigidSetC); |
418 |
+ |
exclude_.addPairs(rigidSetA, rigidSetD); |
419 |
+ |
exclude_.addPairs(rigidSetB, rigidSetC); |
420 |
+ |
exclude_.addPairs(rigidSetB, rigidSetD); |
421 |
+ |
exclude_.addPairs(rigidSetC, rigidSetD); |
422 |
+ |
|
423 |
+ |
/* |
424 |
+ |
exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end()); |
425 |
+ |
exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end()); |
426 |
+ |
exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end()); |
427 |
+ |
exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end()); |
428 |
+ |
exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end()); |
429 |
+ |
exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end()); |
430 |
+ |
|
431 |
+ |
|
432 |
|
exclude_.addPair(a, b); |
433 |
|
exclude_.addPair(a, c); |
434 |
|
exclude_.addPair(a, d); |
435 |
|
exclude_.addPair(b, c); |
436 |
|
exclude_.addPair(b, d); |
437 |
|
exclude_.addPair(c, d); |
438 |
+ |
*/ |
439 |
|
} |
440 |
|
|
379 |
– |
Molecule::RigidBodyIterator rbIter; |
380 |
– |
RigidBody* rb; |
441 |
|
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
442 |
|
std::vector<Atom*> atoms = rb->getAtoms(); |
443 |
|
for (int i = 0; i < atoms.size() -1 ; ++i) { |
462 |
|
int b; |
463 |
|
int c; |
464 |
|
int d; |
465 |
+ |
|
466 |
+ |
std::map<int, std::set<int> > atomGroups; |
467 |
+ |
|
468 |
+ |
Molecule::RigidBodyIterator rbIter; |
469 |
+ |
RigidBody* rb; |
470 |
+ |
Molecule::IntegrableObjectIterator ii; |
471 |
+ |
StuntDouble* integrableObject; |
472 |
|
|
473 |
+ |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
474 |
+ |
integrableObject = mol->nextIntegrableObject(ii)) { |
475 |
+ |
|
476 |
+ |
if (integrableObject->isRigidBody()) { |
477 |
+ |
rb = static_cast<RigidBody*>(integrableObject); |
478 |
+ |
std::vector<Atom*> atoms = rb->getAtoms(); |
479 |
+ |
std::set<int> rigidAtoms; |
480 |
+ |
for (int i = 0; i < atoms.size(); ++i) { |
481 |
+ |
rigidAtoms.insert(atoms[i]->getGlobalIndex()); |
482 |
+ |
} |
483 |
+ |
for (int i = 0; i < atoms.size(); ++i) { |
484 |
+ |
atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms)); |
485 |
+ |
} |
486 |
+ |
} else { |
487 |
+ |
std::set<int> oneAtomSet; |
488 |
+ |
oneAtomSet.insert(integrableObject->getGlobalIndex()); |
489 |
+ |
atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet)); |
490 |
+ |
} |
491 |
+ |
} |
492 |
+ |
|
493 |
+ |
|
494 |
|
for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) { |
495 |
|
a = bond->getAtomA()->getGlobalIndex(); |
496 |
|
b = bond->getAtomB()->getGlobalIndex(); |
502 |
|
b = bend->getAtomB()->getGlobalIndex(); |
503 |
|
c = bend->getAtomC()->getGlobalIndex(); |
504 |
|
|
505 |
< |
exclude_.removePair(a, b); |
506 |
< |
exclude_.removePair(a, c); |
507 |
< |
exclude_.removePair(b, c); |
505 |
> |
std::set<int> rigidSetA = getRigidSet(a, atomGroups); |
506 |
> |
std::set<int> rigidSetB = getRigidSet(b, atomGroups); |
507 |
> |
std::set<int> rigidSetC = getRigidSet(c, atomGroups); |
508 |
> |
|
509 |
> |
exclude_.removePairs(rigidSetA, rigidSetB); |
510 |
> |
exclude_.removePairs(rigidSetA, rigidSetC); |
511 |
> |
exclude_.removePairs(rigidSetB, rigidSetC); |
512 |
> |
|
513 |
> |
//exclude_.removePair(a, b); |
514 |
> |
//exclude_.removePair(a, c); |
515 |
> |
//exclude_.removePair(b, c); |
516 |
|
} |
517 |
|
|
518 |
|
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) { |
520 |
|
b = torsion->getAtomB()->getGlobalIndex(); |
521 |
|
c = torsion->getAtomC()->getGlobalIndex(); |
522 |
|
d = torsion->getAtomD()->getGlobalIndex(); |
523 |
+ |
|
524 |
+ |
std::set<int> rigidSetA = getRigidSet(a, atomGroups); |
525 |
+ |
std::set<int> rigidSetB = getRigidSet(b, atomGroups); |
526 |
+ |
std::set<int> rigidSetC = getRigidSet(c, atomGroups); |
527 |
+ |
std::set<int> rigidSetD = getRigidSet(d, atomGroups); |
528 |
+ |
|
529 |
+ |
exclude_.removePairs(rigidSetA, rigidSetB); |
530 |
+ |
exclude_.removePairs(rigidSetA, rigidSetC); |
531 |
+ |
exclude_.removePairs(rigidSetA, rigidSetD); |
532 |
+ |
exclude_.removePairs(rigidSetB, rigidSetC); |
533 |
+ |
exclude_.removePairs(rigidSetB, rigidSetD); |
534 |
+ |
exclude_.removePairs(rigidSetC, rigidSetD); |
535 |
+ |
|
536 |
+ |
/* |
537 |
+ |
exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end()); |
538 |
+ |
exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end()); |
539 |
+ |
exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end()); |
540 |
+ |
exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end()); |
541 |
+ |
exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end()); |
542 |
+ |
exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end()); |
543 |
|
|
544 |
+ |
|
545 |
|
exclude_.removePair(a, b); |
546 |
|
exclude_.removePair(a, c); |
547 |
|
exclude_.removePair(a, d); |
548 |
|
exclude_.removePair(b, c); |
549 |
|
exclude_.removePair(b, d); |
550 |
|
exclude_.removePair(c, d); |
551 |
+ |
*/ |
552 |
|
} |
553 |
|
|
436 |
– |
Molecule::RigidBodyIterator rbIter; |
437 |
– |
RigidBody* rb; |
554 |
|
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
555 |
|
std::vector<Atom*> atoms = rb->getAtoms(); |
556 |
|
for (int i = 0; i < atoms.size() -1 ; ++i) { |
915 |
|
|
916 |
|
|
917 |
|
} |
802 |
– |
|
803 |
– |
#endif |
804 |
– |
|
805 |
– |
double SimInfo::calcMaxCutoffRadius() { |
918 |
|
|
807 |
– |
|
808 |
– |
std::set<AtomType*> atomTypes; |
809 |
– |
std::set<AtomType*>::iterator i; |
810 |
– |
std::vector<double> cutoffRadius; |
811 |
– |
|
812 |
– |
//get the unique atom types |
813 |
– |
atomTypes = getUniqueAtomTypes(); |
814 |
– |
|
815 |
– |
//query the max cutoff radius among these atom types |
816 |
– |
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
817 |
– |
cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i)); |
818 |
– |
} |
819 |
– |
|
820 |
– |
double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end())); |
821 |
– |
#ifdef IS_MPI |
822 |
– |
//pick the max cutoff radius among the processors |
919 |
|
#endif |
920 |
|
|
921 |
< |
return maxCutoffRadius; |
826 |
< |
} |
827 |
< |
|
828 |
< |
void SimInfo::getCutoff(double& rcut, double& rsw) { |
921 |
> |
void SimInfo::setupCutoff() { |
922 |
|
|
923 |
< |
if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { |
831 |
< |
|
832 |
< |
if (!simParams_->haveCutoffRadius()){ |
833 |
< |
sprintf(painCave.errMsg, |
834 |
< |
"SimCreator Warning: No value was set for the cutoffRadius.\n" |
835 |
< |
"\tOOPSE will use a default value of 15.0 angstroms" |
836 |
< |
"\tfor the cutoffRadius.\n"); |
837 |
< |
painCave.isFatal = 0; |
838 |
< |
simError(); |
839 |
< |
rcut = 15.0; |
840 |
< |
} else{ |
841 |
< |
rcut = simParams_->getCutoffRadius(); |
842 |
< |
} |
843 |
< |
|
844 |
< |
if (!simParams_->haveSwitchingRadius()){ |
845 |
< |
sprintf(painCave.errMsg, |
846 |
< |
"SimCreator Warning: No value was set for switchingRadius.\n" |
847 |
< |
"\tOOPSE will use a default value of\n" |
848 |
< |
"\t0.85 * cutoffRadius for the switchingRadius\n"); |
849 |
< |
painCave.isFatal = 0; |
850 |
< |
simError(); |
851 |
< |
rsw = 0.85 * rcut; |
852 |
< |
} else{ |
853 |
< |
rsw = simParams_->getSwitchingRadius(); |
854 |
< |
} |
855 |
< |
|
856 |
< |
} else { |
857 |
< |
// if charge, dipole or reaction field is not used and the cutofff radius is not specified in |
858 |
< |
//meta-data file, the maximum cutoff radius calculated from forcefiled will be used |
859 |
< |
|
860 |
< |
if (simParams_->haveCutoffRadius()) { |
861 |
< |
rcut = simParams_->getCutoffRadius(); |
862 |
< |
} else { |
863 |
< |
//set cutoff radius to the maximum cutoff radius based on atom types in the whole system |
864 |
< |
rcut = calcMaxCutoffRadius(); |
865 |
< |
} |
866 |
< |
|
867 |
< |
if (simParams_->haveSwitchingRadius()) { |
868 |
< |
rsw = simParams_->getSwitchingRadius(); |
869 |
< |
} else { |
870 |
< |
rsw = rcut; |
871 |
< |
} |
872 |
< |
|
873 |
< |
} |
874 |
< |
} |
875 |
< |
|
876 |
< |
void SimInfo::setupCutoff() { |
877 |
< |
getCutoff(rcut_, rsw_); |
878 |
< |
double rnblist = rcut_ + 1; // skin of neighbor list |
879 |
< |
|
880 |
< |
//Pass these cutoff radius etc. to fortran. This function should be called once and only once |
881 |
< |
|
923 |
> |
// Check the cutoff policy |
924 |
|
int cp = TRADITIONAL_CUTOFF_POLICY; |
925 |
|
if (simParams_->haveCutoffPolicy()) { |
926 |
|
std::string myPolicy = simParams_->getCutoffPolicy(); |
942 |
|
} |
943 |
|
} |
944 |
|
} |
945 |
< |
} |
945 |
> |
} |
946 |
> |
notifyFortranCutoffPolicy(&cp); |
947 |
|
|
948 |
< |
|
948 |
> |
// Check the Skin Thickness for neighborlists |
949 |
> |
double skin; |
950 |
|
if (simParams_->haveSkinThickness()) { |
951 |
< |
double skinThickness = simParams_->getSkinThickness(); |
952 |
< |
} |
951 |
> |
skin = simParams_->getSkinThickness(); |
952 |
> |
notifyFortranSkinThickness(&skin); |
953 |
> |
} |
954 |
> |
|
955 |
> |
// Check if the cutoff was set explicitly: |
956 |
> |
if (simParams_->haveCutoffRadius()) { |
957 |
> |
rcut_ = simParams_->getCutoffRadius(); |
958 |
> |
if (simParams_->haveSwitchingRadius()) { |
959 |
> |
rsw_ = simParams_->getSwitchingRadius(); |
960 |
> |
} else { |
961 |
> |
rsw_ = rcut_; |
962 |
> |
} |
963 |
> |
notifyFortranCutoffs(&rcut_, &rsw_); |
964 |
> |
|
965 |
> |
} else { |
966 |
> |
|
967 |
> |
// For electrostatic atoms, we'll assume a large safe value: |
968 |
> |
if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { |
969 |
> |
sprintf(painCave.errMsg, |
970 |
> |
"SimCreator Warning: No value was set for the cutoffRadius.\n" |
971 |
> |
"\tOOPSE will use a default value of 15.0 angstroms" |
972 |
> |
"\tfor the cutoffRadius.\n"); |
973 |
> |
painCave.isFatal = 0; |
974 |
> |
simError(); |
975 |
> |
rcut_ = 15.0; |
976 |
> |
|
977 |
> |
if (simParams_->haveElectrostaticSummationMethod()) { |
978 |
> |
std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
979 |
> |
toUpper(myMethod); |
980 |
> |
if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") { |
981 |
> |
if (simParams_->haveSwitchingRadius()){ |
982 |
> |
sprintf(painCave.errMsg, |
983 |
> |
"SimInfo Warning: A value was set for the switchingRadius\n" |
984 |
> |
"\teven though the electrostaticSummationMethod was\n" |
985 |
> |
"\tset to %s\n", myMethod.c_str()); |
986 |
> |
painCave.isFatal = 1; |
987 |
> |
simError(); |
988 |
> |
} |
989 |
> |
} |
990 |
> |
} |
991 |
> |
|
992 |
> |
if (simParams_->haveSwitchingRadius()){ |
993 |
> |
rsw_ = simParams_->getSwitchingRadius(); |
994 |
> |
} else { |
995 |
> |
sprintf(painCave.errMsg, |
996 |
> |
"SimCreator Warning: No value was set for switchingRadius.\n" |
997 |
> |
"\tOOPSE will use a default value of\n" |
998 |
> |
"\t0.85 * cutoffRadius for the switchingRadius\n"); |
999 |
> |
painCave.isFatal = 0; |
1000 |
> |
simError(); |
1001 |
> |
rsw_ = 0.85 * rcut_; |
1002 |
> |
} |
1003 |
> |
notifyFortranCutoffs(&rcut_, &rsw_); |
1004 |
> |
} else { |
1005 |
> |
// We didn't set rcut explicitly, and we don't have electrostatic atoms, so |
1006 |
> |
// We'll punt and let fortran figure out the cutoffs later. |
1007 |
> |
|
1008 |
> |
notifyFortranYouAreOnYourOwn(); |
1009 |
|
|
1010 |
< |
notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp); |
1011 |
< |
// also send cutoff notification to electrostatics |
912 |
< |
setElectrostaticCutoffRadius(&rcut_, &rsw_); |
1010 |
> |
} |
1011 |
> |
} |
1012 |
|
} |
1013 |
|
|
1014 |
|
void SimInfo::setupElectrostaticSummationMethod( int isError ) { |
1043 |
|
} else { |
1044 |
|
// throw error |
1045 |
|
sprintf( painCave.errMsg, |
1046 |
< |
"SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"none\", \"shifted_potential\", \"shifted_force\", or \"reaction_field\".", myMethod.c_str() ); |
1046 |
> |
"SimInfo error: Unknown electrostaticSummationMethod.\n" |
1047 |
> |
"\t(Input file specified %s .)\n" |
1048 |
> |
"\telectrostaticSummationMethod must be one of: \"none\",\n" |
1049 |
> |
"\t\"shifted_potential\", \"shifted_force\", or \n" |
1050 |
> |
"\t\"reaction_field\".\n", myMethod.c_str() ); |
1051 |
|
painCave.isFatal = 1; |
1052 |
|
simError(); |
1053 |
|
} |
1068 |
|
if (!simParams_->haveDampingAlpha()) { |
1069 |
|
//throw error |
1070 |
|
sprintf( painCave.errMsg, |
1071 |
< |
"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used.", alphaVal); |
1071 |
> |
"SimInfo warning: dampingAlpha was not specified in the input file.\n" |
1072 |
> |
"\tA default value of %f (1/ang) will be used.\n", alphaVal); |
1073 |
|
painCave.isFatal = 0; |
1074 |
|
simError(); |
1075 |
|
} |
1076 |
|
} else { |
1077 |
|
// throw error |
1078 |
|
sprintf( painCave.errMsg, |
1079 |
< |
"SimInfo error: Unknown electrostaticScreeningMethod. (Input file specified %s .)\n\telectrostaticScreeningMethod must be one of: \"undamped\" or \"damped\".", myScreen.c_str() ); |
1079 |
> |
"SimInfo error: Unknown electrostaticScreeningMethod.\n" |
1080 |
> |
"\t(Input file specified %s .)\n" |
1081 |
> |
"\telectrostaticScreeningMethod must be one of: \"undamped\"\n" |
1082 |
> |
"or \"damped\".\n", myScreen.c_str() ); |
1083 |
|
painCave.isFatal = 1; |
1084 |
|
simError(); |
1085 |
|
} |
1087 |
|
} |
1088 |
|
|
1089 |
|
// let's pass some summation method variables to fortran |
1090 |
< |
setElectrostaticSummationMethod( &esm ); |
1090 |
> |
setElectrostaticSumMethod( &esm ); |
1091 |
> |
setFortranElectrostaticMethod( &esm ); |
1092 |
|
setScreeningMethod( &sm ); |
1093 |
|
setDampingAlpha( &alphaVal ); |
1094 |
|
setReactionFieldDielectric( &dielectric ); |
1095 |
< |
initFortranFF( &esm, &errorOut ); |
1095 |
> |
initFortranFF( &errorOut ); |
1096 |
|
} |
1097 |
|
|
1098 |
|
void SimInfo::setupSwitchingFunction() { |