Vec3D Reorient::fromNormal() {
Crystal* c;
if (!fromIndex.isNull() && (c = Clip::getInstance()->getMostRecentCrystal(true))) {
if (ui->RezicheckBox->isChecked()) {
return c->hkl2Reziprocal(fromIndex).normalized();
} else {
return c->uvw2Real(fromIndex).normalized();
}
}
return Vec3D();
}
/**
* \brief This function is called when a crystal detects a collision with this entity.
* \param crystal the crystal
* \param collision_mode the collision mode that detected the event
*/
void Arrow::notify_collision_with_crystal(Crystal& crystal, CollisionMode collision_mode) {
if (collision_mode == COLLISION_OVERLAPPING && is_flying()) {
crystal.activate(*this);
attach_to(crystal);
}
}
/**
* \copydoc MapEntity::is_crystal_obstacle
*/
bool CustomEntity::is_crystal_obstacle(Crystal& crystal) {
const TraversableInfo& info = get_can_traverse_entity_info(crystal.get_type());
if (!info.is_empty()) {
return !info.is_traversable(*this, crystal);
}
return Detector::is_crystal_obstacle(crystal);
}
Vec3D Reorient::toNormal() {
int index=ui->toCombo->currentIndex();
if (index>2) {
Crystal* c;
if (!toIndex.isNull() && (c = Clip::getInstance()->getMostRecentCrystal(true))) {
if (index==3) {
return c->hkl2Reziprocal(fromIndex).normalized();
} else {
return c->uvw2Real(fromIndex).normalized();
}
}
} else {
Vec3D normal;
normal(index)=1;
return normal;
}
return Vec3D();
}
/**
* \brief This function is called when a crystal detects a collision with this entity.
* \param crystal the crystal
* \param collision_mode the collision mode that detected the event
*/
void Boomerang::notify_collision_with_crystal(Crystal &crystal, CollisionMode collision_mode) {
if (collision_mode == COLLISION_RECTANGLE) {
crystal.activate(*this);
if (!is_going_back()) {
go_back();
}
}
}
/**
* \brief This function is called when a crystal detects a collision with this entity.
* \param crystal the crystal
* \param collision_mode the collision mode that detected the event
*/
void CarriedItem::notify_collision_with_crystal(Crystal& crystal, CollisionMode collision_mode) {
if (collision_mode == COLLISION_OVERLAPPING
&& is_being_thrown()
&& !can_explode()) {
crystal.activate(*this);
break_item();
}
}
/**
* @brief This function is called when a crystal detects a collision with this entity.
* @param crystal the crystal
* @param collision_mode the collision mode that detected the event
*/
void Hookshot::notify_collision_with_crystal(Crystal& crystal, CollisionMode collision_mode) {
if (is_flying()) {
crystal.activate(*this);
if (!is_going_back()) {
go_back();
}
}
}
/**
* \brief This function is called when a the sprite of a crystal
* detects a pixel-precise collision with a sprite of this entity.
* \param crystal the crystal
* \param sprite_overlapping the sprite of the current entity that collides with the crystal
*/
void Explosion::notify_collision_with_crystal(Crystal& crystal, Sprite& /* sprite_overlapping */) {
crystal.activate(*this);
}
/**
* \copydoc MapEntity::notify_collision_with_crystal(Crystal&,Sprite&)
*/
void CustomEntity::notify_collision_with_crystal(
Crystal& crystal, Sprite& sprite_overlapping) {
notify_collision_from(crystal, crystal.get_sprite(), sprite_overlapping);
}
Crystal RandSpg::randSpgCrystal(const randSpgInput& input)
{
START_FT;
// Convenience: so we don't have to say 'input.<option>' for every call
uint spg = input.spg;
const vector<uint>& atoms = input.atoms;
const latticeStruct& latticeMins = input.latticeMins;
const latticeStruct& latticeMaxes = input.latticeMaxes;
double IADScalingFactor = input.IADScalingFactor;
double minRadius = input.minRadius;
const std::vector<std::pair<uint, double>>& manualAtomicRadii = input.manualAtomicRadii;
double minVolume = input.minVolume;
double maxVolume = input.maxVolume;
vector<pair<uint, char>> forcedWyckAssignments = input.forcedWyckAssignments;
char verbosity = input.verbosity;
int numAttempts = input.maxAttempts;
bool forceMostGeneralWyckPos = input.forceMostGeneralWyckPos;
// Change the atomic radii as necessary
ElemInfo::applyScalingFactor(IADScalingFactor);
// Set the min radius
ElemInfo::setMinRadius(minRadius);
// Set some explicit radii
for (size_t i = 0; i < manualAtomicRadii.size(); i++) {
uint atomicNum = manualAtomicRadii[i].first;
double rad = manualAtomicRadii[i].second;
ElemInfo::setRadius(atomicNum, rad);
}
systemPossibilities possibilities = RandSpgCombinatorics::getSystemPossibilities(spg, atoms);
if (possibilities.size() == 0) {
cout << "Error in RandSpg::" << __FUNCTION__ << "(): this spg '" << spg
<< "' cannot be generated with this composition\n";
return Crystal();
}
// force the most general Wyckoff position to be used at least once?
if (forceMostGeneralWyckPos)
possibilities = RandSpgCombinatorics::removePossibilitiesWithoutGeneralWyckPos(possibilities, spg);
if (possibilities.size() == 0) {
cout << "Error in RandSpg::" << __FUNCTION__ << "(): this spg '" << spg
<< "' cannot be generated with this composition.\n";
cout << "It can be generated if option 'forceMostGeneralWyckPos' is "
<< "turned off, but the correct spacegroup will not be guaranteed.\n";
return Crystal();
}
// The tuple is as follows: <atomicNum, wyckLet, numTimesUsed>
vector<tuple<uint, char, uint>> forcedWyckAssignmentsAndNumber = getForcedWyckAssignmentsAndNumber(forcedWyckAssignments);
for (size_t i = 0; i < forcedWyckAssignmentsAndNumber.size(); i++) {
possibilities =
RandSpgCombinatorics::removePossibilitiesWithoutWyckPos(possibilities,
get<1>(forcedWyckAssignmentsAndNumber[i]),
get<2>(forcedWyckAssignmentsAndNumber[i]),
get<0>(forcedWyckAssignmentsAndNumber[i]));
}
if (possibilities.size() == 0) {
cout << "Error in RandSpg::" << __FUNCTION__ << "(): this spg '" << spg
<< "' cannot be generated with this composition due to the forced "
<< "Wyckoff position constraints.\nPlease change them or remove them "
<< "if you wish to generate the space group.\n";
return Crystal();
}
//RandSpgCombinatorics::printSystemPossibilities(possibilities);
// If we desire verbose output, print the system possibility to the log file
if (verbosity == 'v')
appendToLogFile(RandSpgCombinatorics::getVerbosePossibilitiesString(possibilities));
// Create a modified forced wyck vector for later...
vector<pair<uint, wyckPos>> modifiedForcedWyckVector = getModifiedForcedWyckVector(forcedWyckAssignments, spg);
// Begin the attempt loop!
for (size_t i = 0; i < numAttempts; i++) {
Crystal crystal = createValidCrystal(spg, latticeMins, latticeMaxes,
minVolume, maxVolume);
// Now, let's assign some atoms!
atomAssignments assignments = RandSpgCombinatorics::getRandomAtomAssignments(possibilities, modifiedForcedWyckVector);
//printAtomAssignments(assignments);
// If we desire any output, print the atom assignments to the log file
if (verbosity == 'r' || verbosity == 'v')
appendToLogFile(getAtomAssignmentsString(assignments));
if (assignments.size() == 0) {
cout << "Error in RandSpg::randSpgXtal(): atoms were not successfully"
<< " assigned positions in assignAtomsToWyckPos()\n";
continue;
}
#ifdef RANDSPG_DEBUG
cout << "\natomAssignments are the following (atomicNum, wyckLet, wyckPos):"
<< "\n";
for (size_t j = 0; j < assignments.size(); j++)
cout << " " << assignments[j].second << ", "
<< getWyckLet(assignments[j].first)
<< ", " << getWyckCoords(assignments[j].first) << "\n";
cout << "\n";
#endif
bool assignmentsSuccessful = true;
for (size_t j = 0; j < assignments.size(); j++) {
const wyckPos& pos = assignments[j].first;
uint atomicNum = assignments[j].second;
if (!addWyckoffAtomRandomly(crystal, pos, atomicNum, spg)) {
assignmentsSuccessful = false;
break;
}
}
// If we succeeded, and the number of atoms match, return the crystal!
// There are rare cases where an atom may be placed on top of another
// one and the essentially get merged into one. We check to make sure the
// sizes of the atomic numbers match for this reason. We shouldn't have to
// worry about types.
if (assignmentsSuccessful &&
atoms.size() == crystal.getVectorOfAtomicNums().size()) {
if (verbosity != 'n') appendToLogFile("*** Success! ***\n");
return crystal;
}
else {
if (verbosity == 'r' || verbosity == 'v') {
stringstream ss;
ss << "Failed to add atoms to satisfy MinIAD.\nObtaining new atom "
<< "assignments and trying again. Failure count: " << i + 1 << "\n\n";
appendToLogFile(ss.str());
}
continue;
}
}
// If we made it here, we failed to generate the crystal
stringstream errMsg;
errMsg << "After " << numAttempts << " attempts: failed to generate "
<< "a crystal of spg " << spg << ".\n";
if (verbosity != 'n') appendToLogFile(errMsg.str());
cerr << errMsg.str();
return Crystal();
}
bool RandSpg::addWyckoffAtomRandomly(Crystal& crystal, const wyckPos& position,
uint atomicNum, uint spg, int maxAttempts)
{
START_FT;
#ifdef RANDSPG_WYCK_DEBUG
cout << "At beginning of addWyckoffAtomRandomly(), atom info is:\n";
crystal.printAtomInfo();
cout << "Attempting to add an atom of atomicNum " << atomicNum
<< " at position " << getWyckCoords(position) << "\n";
#endif
// If this contains a unique position, we only need to try once
// Otherwise, we'd be repeatedly trying the same thing...
if (containsUniquePosition(position)) {
maxAttempts = 1;
}
int i = 0;
bool success = false;
do {
// Generate random coordinates in the wyckoff position
// Numbers are between 0 and 1
double x = getRandDouble(0,1);
double y = getRandDouble(0,1);
double z = getRandDouble(0,1);
vector<string> components = split(getWyckCoords(position), ',');
// Interpret the three components of the Wyckoff position coordinates...
double newX = interpretComponent(components[0], x, y, z);
double newY = interpretComponent(components[1], x, y, z);
double newZ = interpretComponent(components[2], x, y, z);
// interpretComponenet() returns -1 if it failed to read the component
if (newX == -1 || newY == -1 || newZ == -1) {
cout << "addWyckoffAtomRandomly() failed due to a component not being "
<< "read successfully!\n";
return false;
}
atomStruct newAtom(atomicNum, newX, newY, newZ);
crystal.addAtom(newAtom);
// Check the interatomic distances
if (crystal.areIADsOkay(newAtom)) {
// Now try to fill the cell using this new atom
if (crystal.fillCellWithAtom(spg, newAtom)) success = true;
}
if (!success) {
// Remove this atom and try again
crystal.removeAtom(newAtom);
}
i++;
} while (i < maxAttempts && !success);
if (!success) return false;
#ifdef RANDSPG_WYCK_DEBUG
cout << "After an atom with atomic num " << atomicNum << " was added and "
<< "the cell filled, the following is the atom info:\n";
crystal.printAtomInfo();
#endif
return true;
}
