-
-
-
-
-
-
+
+
-
+
-
-
-
-
-
+
+
+
+
+
+
-
-
-
-
-
-
-
-
-
+
+
+
+
-
-
-
-
-
+
+
-
-
-
-
152 for (
const auto& symbol : symbols) {
-
-
-
-
-
-
-
-
158 for (
const auto& symbol : symbols) {
-
-
+
+
-
-
164 if (symbols.size() != fractions.size()) {
-
165 LOG_CRITICAL(m_logger,
"The number of symbols and fractions must be equal (got {} symbols and {} fractions).", symbols.size(), fractions.size());
-
166 throw exceptions::InvalidCompositionError(
"The number of symbols and fractions must be equal. Got " + std::to_string(symbols.size()) +
" symbols and " + std::to_string(fractions.size()) +
" fractions.");
-
-
-
-
-
171 for (
const auto &symbol : symbols) {
-
-
-
-
175 for (
size_t i = 0; i < symbols.size(); ++i) {
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
177 for (
const auto& symbol : symbols) {
+
+
+
+
+
+
+
+
183 for (
const auto& symbol : symbols) {
+
+
+
+
+
+
+
+
189 if (symbols.size() != fractions.size()) {
+
190 LOG_CRITICAL(m_logger,
"The number of symbols and fractions must be equal (got {} symbols and {} fractions).", symbols.size(), fractions.size());
+
191 throw exceptions::InvalidCompositionError(
"The number of symbols and fractions must be equal. Got " + std::to_string(symbols.size()) +
" symbols and " + std::to_string(fractions.size()) +
" fractions.");
+
-
-
-
195 if (
this != &other) {
-
-
-
-
-
-
-
-
-
-
-
+
+
+
196 for (
const auto &symbol : symbols) {
+
+
+
+
200 for (
size_t i = 0; i < symbols.size(); ++i) {
+
+
+
+
+
+
+
+
-
-
-
-
-
210 LOG_ERROR(
m_logger,
"Invalid symbol: {}", symbol);
-
-
-
-
-
-
-
-
-
219 LOG_ERROR(
m_logger,
"Composition is in mass fraction mode. Cannot register symbol ({}) in number fraction mode.", symbol);
-
-
-
-
-
-
225 LOG_WARNING(
m_logger,
"Symbol {} is already registered.", symbol);
-
-
-
-
-
-
-
232 LOG_TRACE_L3(
m_logger,
"Registered symbol: {}", symbol);
-
+
+
-
-
-
-
236 for (
const auto& symbol : symbols) {
-
-
-
+
+
+
+
220 if (
this != &other) {
+
+
+
+
+
+
+
+
+
+
+
-
-
-
-
-
+
+
+
+
+
235 LOG_ERROR(
m_logger,
"Invalid symbol: {}", symbol);
+
+
+
+
+
+
+
+
+
244 LOG_ERROR(
m_logger,
"Composition is in mass fraction mode. Cannot register symbol ({}) in number fraction mode.", symbol);
+
+
+
+
+
+
250 LOG_WARNING(
m_logger,
"Symbol {} is already registered.", symbol);
+
+
+
+
+
+
+
257 LOG_TRACE_L3(
m_logger,
"Registered symbol: {}", symbol);
+
-
-
-
-
246 for (
const auto& s : species) {
-
-
-
+
+
+
+
261 for (
const auto& symbol : symbols) {
+
+
+
-
-
-
-
-
-
256 std::set<fourdst::atomic::Species> result;
-
-
258 result.insert(entry.isotope());
-
-
-
-
-
-
-
-
-
265 LOG_ERROR(
m_logger,
"Invalid composition.");
-
-
+
+
-
-
-
272 for (
const auto& fraction : fractions) {
-
-
-
275 if (sum < 0.999999 || sum > 1.000001) {
-
276 LOG_ERROR(
m_logger,
"The sum of fractions must be equal to 1 (expected 1, got {}).", sum);
-
-
+
+
271 for (
const auto& s : species) {
+
+
+
+
+
+
-
-
+
+
+
281 std::set<fourdst::atomic::Species> result;
+
+
283 result.insert(entry.isotope());
+
+
+
-
-
-
-
-
+
+
+
+
+
290 LOG_ERROR(
m_logger,
"Invalid composition.");
+
+
+
-
-
-
-
-
289 LOG_ERROR(
m_logger,
"Symbol {} is not registered.", symbol);
-
-
-
-
-
294 LOG_ERROR(
m_logger,
"Composition is in number fraction mode.");
-
-
-
-
298 if (mass_fraction < 0.0 || mass_fraction > 1.0) {
-
299 LOG_ERROR(
m_logger,
"Mass fraction must be between 0 and 1 for symbol {}. Currently it is {}.", symbol, mass_fraction);
-
-
-
-
-
304 const double old_mass_fraction =
m_compositions.at(symbol).mass_fraction();
-
-
-
307 return old_mass_fraction;
-
+
+
+
+
+
297 for (
const auto& fraction : fractions) {
+
+
+
300 if (sum < 0.999999 || sum > 1.000001) {
+
301 LOG_ERROR(
m_logger,
"The sum of fractions must be equal to 1 (expected 1, got {}).", sum);
+
+
+
+
+
-
-
-
-
311 if (symbols.size() != mass_fractions.size()) {
-
312 LOG_ERROR(
m_logger,
"The number of symbols and mass fractions must be equal (currently {} symbols and {} mass fractions).", symbols.size(), mass_fractions.size());
-
313 throw exceptions::InvalidCompositionError(
"The number of symbols and mass fractions must be equal (currently " + std::to_string(symbols.size()) +
" symbols and " + std::to_string(mass_fractions.size()) +
" mass fractions).");
-
-
-
316 std::vector<double> old_mass_fractions;
-
317 old_mass_fractions.reserve(symbols.size());
-
318 for (
size_t i = 0; i < symbols.size(); ++i) {
-
319 old_mass_fractions.push_back(
setMassFraction(symbols[i], mass_fractions[i]));
-
-
321 return old_mass_fractions;
-
-
-
-
-
-
-
+
+
+
+
+
+
+
314 LOG_ERROR(
m_logger,
"Symbol {} is not registered.", symbol);
+
+
+
+
+
319 LOG_ERROR(
m_logger,
"Composition is in number fraction mode.");
+
+
+
+
323 if (mass_fraction < 0.0 || mass_fraction > 1.0) {
+
324 LOG_ERROR(
m_logger,
"Mass fraction must be between 0 and 1 for symbol {}. Currently it is {}.", symbol, mass_fraction);
+
+
-
-
-
329 const std::vector<double> &mass_fractions) {
-
330 std::vector<double> old_mass_fractions;
-
331 old_mass_fractions.reserve(species.size());
-
332 for (
const auto& spec : species) {
-
333 old_mass_fractions.push_back(
setMassFraction(spec, mass_fractions[&spec - &species[0]]));
-
-
335 return old_mass_fractions;
-
+
+
329 const double old_mass_fraction =
m_compositions.at(symbol).mass_fraction();
+
+
+
332 return old_mass_fraction;
+
+
+
+
+
+
336 if (symbols.size() != mass_fractions.size()) {
+
337 LOG_ERROR(
m_logger,
"The number of symbols and mass fractions must be equal (currently {} symbols and {} mass fractions).", symbols.size(), mass_fractions.size());
+
338 throw exceptions::InvalidCompositionError(
"The number of symbols and mass fractions must be equal (currently " + std::to_string(symbols.size()) +
" symbols and " + std::to_string(mass_fractions.size()) +
" mass fractions).");
+
+
+
341 std::vector<double> old_mass_fractions;
+
342 old_mass_fractions.reserve(symbols.size());
+
343 for (
size_t i = 0; i < symbols.size(); ++i) {
+
344 old_mass_fractions.push_back(
setMassFraction(symbols[i], mass_fractions[i]));
+
+
346 return old_mass_fractions;
+
-
-
-
-
-
340 LOG_ERROR(
m_logger,
"Symbol {} is not registered.", symbol);
-
-
-
-
-
345 LOG_ERROR(
m_logger,
"Composition is in mass fraction mode, should be in number fraction mode to call setNumberFraction. Hint: The mode can be switched by first finalizing and then calling setCompositionMode(false).");
-
346 throw exceptions::CompositionModeError(
"Composition is in mass fraction mode, should be in number fraction mode to call setNumberFraction. Hint: The mode can be switched by first finalizing and then calling setCompositionMode(false).");
-
-
349 if (number_fraction < 0.0 || number_fraction > 1.0) {
-
350 LOG_ERROR(
m_logger,
"Number fraction must be between 0 and 1 for symbol {}. Currently it is {}.", symbol, number_fraction);
-
-
-
-
-
355 const double old_number_fraction =
m_compositions.at(symbol).number_fraction();
-
-
-
358 return old_number_fraction;
-
+
-
-
-
-
362 if (symbols.size() != number_fractions.size()) {
-
363 LOG_ERROR(
m_logger,
"The number of symbols and number fractions must be equal. (Currently {} symbols and {} number fractions).", symbols.size(), number_fractions.size());
-
364 throw exceptions::InvalidCompositionError(
"The number of symbols and number fractions must be equal. (Currently " + std::to_string(symbols.size()) +
" symbols and " + std::to_string(number_fractions.size()) +
" number fractions).");
-
-
-
367 std::vector<double> old_number_fractions;
-
368 old_number_fractions.reserve(symbols.size());
-
369 for (
size_t i = 0; i < symbols.size(); ++i) {
-
370 old_number_fractions.push_back(
setNumberFraction(symbols[i], number_fractions[i]));
-
-
372 return old_number_fractions;
-
-
-
-
-
-
-
+
+
+
+
354 const std::vector<double> &mass_fractions) {
+
355 std::vector<double> old_mass_fractions;
+
356 old_mass_fractions.reserve(species.size());
+
357 for (
const auto& spec : species) {
+
358 old_mass_fractions.push_back(
setMassFraction(spec, mass_fractions[&spec - &species[0]]));
+
+
360 return old_mass_fractions;
+
+
+
+
+
+
365 LOG_ERROR(
m_logger,
"Symbol {} is not registered.", symbol);
+
+
+
+
+
370 LOG_ERROR(
m_logger,
"Composition is in mass fraction mode, should be in number fraction mode to call setNumberFraction. Hint: The mode can be switched by first finalizing and then calling setCompositionMode(false).");
+
371 throw exceptions::CompositionModeError(
"Composition is in mass fraction mode, should be in number fraction mode to call setNumberFraction. Hint: The mode can be switched by first finalizing and then calling setCompositionMode(false).");
+
+
+
374 if (number_fraction < 0.0 || number_fraction > 1.0) {
+
375 LOG_ERROR(
m_logger,
"Number fraction must be between 0 and 1 for symbol {}. Currently it is {}.", symbol, number_fraction);
+
+
-
-
-
380 const std::vector<double> &number_fractions) {
-
381 std::vector<double> old_number_fractions;
-
382 old_number_fractions.reserve(species.size());
-
383 for (
const auto& spec : species) {
-
384 old_number_fractions.push_back(
setNumberFraction(spec, number_fractions[&spec - &species[0]]));
-
-
386 return old_number_fractions;
-
+
+
380 const double old_number_fraction =
m_compositions.at(symbol).number_fraction();
+
+
+
383 return old_number_fraction;
+
-
-
-
-
390 bool finalized =
false;
-
-
-
-
-
-
-
-
-
-
+
+
+
+
387 if (symbols.size() != number_fractions.size()) {
+
388 LOG_ERROR(
m_logger,
"The number of symbols and number fractions must be equal. (Currently {} symbols and {} number fractions).", symbols.size(), number_fractions.size());
+
389 throw exceptions::InvalidCompositionError(
"The number of symbols and number fractions must be equal. (Currently " + std::to_string(symbols.size()) +
" symbols and " + std::to_string(number_fractions.size()) +
" number fractions).");
+
+
+
392 std::vector<double> old_number_fractions;
+
393 old_number_fractions.reserve(symbols.size());
+
394 for (
size_t i = 0; i < symbols.size(); ++i) {
+
395 old_number_fractions.push_back(
setNumberFraction(symbols[i], number_fractions[i]));
+
+
397 return old_number_fractions;
+
-
-
-
-
403 std::vector<double> mass_fractions;
-
-
-
406 mass_fractions.push_back(entry.mass_fraction());
-
-
-
-
410 for (
const auto& mass_fraction : mass_fractions) {
-
411 sum += mass_fraction;
-
-
413 for (
double & mass_fraction : mass_fractions) {
-
414 mass_fraction /= sum;
-
-
-
-
-
-
-
-
-
423 double massSum = 0.0;
-
-
425 massSum += entry.mass_fraction();
-
-
427 LOG_ERROR(
m_logger,
"Composition is invalid (Total mass {}).", massSum);
-
-
-
-
-
-
-
-
-
-
+
+
-
-
-
-
440 std::vector<double> number_fractions;
-
-
-
443 number_fractions.push_back(entry.number_fraction());
+
+
+
+
405 const std::vector<double> &number_fractions) {
+
406 std::vector<double> old_number_fractions;
+
407 old_number_fractions.reserve(species.size());
+
408 for (
const auto& spec : species) {
+
409 old_number_fractions.push_back(
setNumberFraction(spec, number_fractions[&spec - &species[0]]));
+
+
411 return old_number_fractions;
+
+
+
+
+
+
415 bool finalized =
false;
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
428 std::vector<double> mass_fractions;
+
+
+
431 mass_fractions.push_back(entry.mass_fraction());
+
+
+
+
435 for (
const auto& mass_fraction : mass_fractions) {
+
436 sum += mass_fraction;
+
+
438 for (
double & mass_fraction : mass_fractions) {
+
439 mass_fraction /= sum;
+
+
+
+
-
-
-
447 for (
const auto& number_fraction : number_fractions) {
-
448 sum += number_fraction;
-
-
-
-
-
-
-
-
456 }
catch ([[maybe_unused]]
const std::runtime_error& e) {
-
457 double numberSum = 0.0;
-
-
459 numberSum += entry.number_fraction();
-
-
461 LOG_ERROR(
m_logger,
"Composition is invalid (Total number {}).", numberSum);
-
-
-
-
-
-
-
-
-
-
+
+
+
+
448 double massSum = 0.0;
+
+
450 massSum += entry.mass_fraction();
+
+
452 LOG_ERROR(
m_logger,
"Composition is invalid (Total mass {}).", massSum);
+
+
+
+
+
+
+
+
+
+
-
-
-
-
-
475 LOG_ERROR(
m_logger,
"Compositions have not both been finalized. Hint: Consider running .finalize() on both compositions before mixing.");
-
-
-
-
479 if (fraction < 0.0 || fraction > 1.0) {
-
480 LOG_ERROR(
m_logger,
"Mixing fraction must be between 0 and 1. Currently it is {}.", fraction);
-
-
-
-
-
-
-
-
-
489 for (
const auto& symbol : mixedSymbols) {
-
490 double otherMassFrac = 0.0;
-
-
-
-
-
-
496 double massFraction = fraction * thisMassFrac + otherMassFrac * (1-fraction);
-
-
-
-
500 return mixedComposition;
-
+
+
+
+
465 std::vector<double> number_fractions;
+
+
+
468 number_fractions.push_back(entry.number_fraction());
+
+
+
+
472 for (
const auto& number_fraction : number_fractions) {
+
473 sum += number_fraction;
+
+
+
+
+
+
+
+
481 }
catch ([[maybe_unused]]
const std::runtime_error& e) {
+
482 double numberSum = 0.0;
+
+
484 numberSum += entry.number_fraction();
+
+
486 LOG_ERROR(
m_logger,
"Composition is invalid (Total number {}).", numberSum);
+
+
+
+
+
+
+
+
+
+
-
-
-
-
-
505 LOG_ERROR(
m_logger,
"Composition has not been finalized. Hint: Consider running .finalize().");
-
+
+
+
+
+
500 LOG_ERROR(
m_logger,
"Compositions have not both been finalized. Hint: Consider running .finalize() on both compositions before mixing.");
+
+
+
+
504 if (fraction < 0.0 || fraction > 1.0) {
+
505 LOG_ERROR(
m_logger,
"Mixing fraction must be between 0 and 1. Currently it is {}.", fraction);
+
-
-
509 LOG_ERROR(
m_logger,
"Symbol {} is not in the composition.", symbol);
-
510 std::string currentSymbols;
-
-
-
513 currentSymbols += sym;
-
-
515 currentSymbols +=
", ";
-
-
517 currentSymbols +=
", and ";
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
514 for (
const auto& symbol : mixedSymbols) {
+
515 double otherMassFrac = 0.0;
+
+
+
+
+
+
521 double massFraction = fraction * thisMassFrac + otherMassFrac * (1-fraction);
+
+
+
+
525 return mixedComposition;
+
-
-
-
-
-
-
535 std::unordered_map<std::string, double> mass_fractions;
-
-
-
-
539 return mass_fractions;
-
-
-
-
-
-
-
-
545 LOG_ERROR(
m_logger,
"Composition has not been finalized. Hint: Consider running .finalize().");
-
+
+
+
+
+
530 LOG_ERROR(
m_logger,
"Composition has not been finalized. Hint: Consider running .finalize().");
+
+
+
+
534 LOG_ERROR(
m_logger,
"Symbol {} is not in the composition.", symbol);
+
535 std::string currentSymbols;
+
+
+
538 currentSymbols += sym;
+
+
540 currentSymbols +=
", ";
+
+
542 currentSymbols +=
", and ";
+
+
+
+
-
-
549 LOG_ERROR(
m_logger,
"Symbol {} is not in the composition.", symbol);
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
-
-
-
+
+
560 std::unordered_map<std::string, double> mass_fractions;
+
+
+
+
564 return mass_fractions;
+
-
-
-
-
564 std::unordered_map<std::string, double> number_fractions;
-
-
-
-
568 return number_fractions;
-
-
-
-
-
-
-
573 LOG_ERROR(
m_logger,
"Composition has not been finalized. Hint: Consider running .finalize().");
-
-
-
-
577 LOG_ERROR(
m_logger,
"Symbol {} is not in the composition.", symbol);
-
-
-
-
+
+
+
+
+
+
570 LOG_ERROR(
m_logger,
"Composition has not been finalized. Hint: Consider running .finalize().");
+
+
+
+
574 LOG_ERROR(
m_logger,
"Symbol {} is not in the composition.", symbol);
+
+
+
+
+
+
+
-
-
-
590 LOG_ERROR(
m_logger,
"Composition has not been finalized. Hint: Consider running .finalize().");
-
+
+
589 std::unordered_map<std::string, double> number_fractions;
+
+
-
-
594 LOG_ERROR(
m_logger,
"Symbol {} is not in the composition.", symbol);
-
-
-
-
+
593 return number_fractions;
+
-
-
-
-
-
-
+
+
+
+
+
598 LOG_ERROR(
m_logger,
"Composition has not been finalized. Hint: Consider running .finalize().");
+
+
+
+
602 LOG_ERROR(
m_logger,
"Symbol {} is not in the composition.", symbol);
+
+
+
+
+
-
-
-
-
-
607 LOG_ERROR(
m_logger,
"Composition has not been finalized. Hint: Consider running .finalize().");
-
-
-
+
+
-
+
615 LOG_ERROR(
m_logger,
"Composition has not been finalized. Hint: Consider running .finalize().");
-
-
+
+
619 LOG_ERROR(
m_logger,
"Symbol {} is not in the composition.", symbol);
+
+
+
+
-
-
-
-
-
623 LOG_ERROR(
m_logger,
"Composition must be finalized before getting the mean atomic mass number. Hint: Consider running .finalize().");
-
-
-
-
-
-
-
-
-
632 zSum += (val.mass_fraction() * val.m_isotope.z())/val.m_isotope.a();
-
-
-
-
-
-
+
+
-
-
-
-
641 const std::array<std::string, 2> methods = {
"norm",
"none"};
-
-
643 if (std::ranges::find(methods, method) == methods.end()) {
-
644 const std::string errorMessage =
"Invalid method: " + method +
". Valid methods are 'norm' and 'none'.";
-
645 LOG_ERROR(
m_logger,
"Invalid method: {}. Valid methods are norm and none.", method);
-
-
-
-
-
650 for (
const auto& symbol : symbols) {
-
-
652 LOG_ERROR(
m_logger,
"Symbol {} is not in the composition.", symbol);
-
-
-
-
-
+
+
+
+
+
632 LOG_ERROR(
m_logger,
"Composition has not been finalized. Hint: Consider running .finalize().");
+
+
+
+
+
+
+
+
+
+
640 LOG_ERROR(
m_logger,
"Composition has not been finalized. Hint: Consider running .finalize().");
+
+
+
+
+
+
+
+
+
+
648 LOG_ERROR(
m_logger,
"Composition must be finalized before getting the mean atomic mass number. Hint: Consider running .finalize().");
+
+
+
+
+
+
+
+
+
657 zSum += (val.mass_fraction() * val.m_isotope.z())/val.m_isotope.a();
-
659 if (method ==
"norm") {
-
660 const bool isNorm = subsetComposition.
finalize(
true);
-
-
662 LOG_ERROR(
m_logger,
"Subset composition is invalid. (Unable to finalize with normalization).");
-
-
-
-
666 return subsetComposition;
-
+
+
+
+
+
-
-
-
-
-
671 LOG_ERROR(
m_logger,
"Composition has not been finalized. Mode cannot be set unless composition is finalized. Hint: Consider running .finalize().");
-
-
-
-
-
-
-
+
+
+
+
666 const std::array<std::string, 2> methods = {
"norm",
"none"};
+
+
668 if (std::ranges::find(methods, method) == methods.end()) {
+
669 const std::string errorMessage =
"Invalid method: " + method +
". Valid methods are 'norm' and 'none'.";
+
670 LOG_ERROR(
m_logger,
"Invalid method: {}. Valid methods are norm and none.", method);
+
+
+
+
+
675 for (
const auto& symbol : symbols) {
+
+
677 LOG_ERROR(
m_logger,
"Symbol {} is not in the composition.", symbol);
+
-
+
-
-
683 LOG_ERROR(
m_logger,
"Composition mode could not be set due to some unknown error.");
-
684 throw std::runtime_error(
"Composition mode could not be set due to an unknown error.");
-
-
-
-
+
+
+
684 if (method ==
"norm") {
+
685 const bool isNorm = subsetComposition.
finalize(
true);
+
+
687 LOG_ERROR(
m_logger,
"Subset composition is invalid. (Unable to finalize with normalization).");
+
+
+
+
691 return subsetComposition;
+
-
-
-
-
-
692 LOG_ERROR(
m_logger,
"Composition has not been finalized. Hint: Consider running .finalize().");
-
-
-
-
696 const std::array<std::string, 7> canonicalH = {
-
697 "H-1",
"H-2",
"H-3",
"H-4",
"H-5",
"H-6",
"H-7"
-
-
699 const std::array<std::string, 8> canonicalHe = {
-
700 "He-3",
"He-4",
"He-5",
"He-6",
"He-7",
"He-8",
"He-9",
"He-10"
-
-
702 for (
const auto& symbol : canonicalH) {
-
-
-
-
-
707 for (
const auto& symbol : canonicalHe) {
-
-
+
+
+
+
+
696 LOG_ERROR(
m_logger,
"Composition has not been finalized. Mode cannot be set unless composition is finalized. Hint: Consider running .finalize().");
+
+
+
+
+
+
+
+
+
+
+
+
708 LOG_ERROR(
m_logger,
"Composition mode could not be set due to some unknown error.");
+
709 throw std::runtime_error(
"Composition mode could not be set due to an unknown error.");
-
-
-
714 const bool isHSymbol = std::ranges::find(canonicalH, symbol) != std::end(canonicalH);
-
715 const bool isHeSymbol = std::ranges::find(canonicalHe, symbol) != std::end(canonicalHe);
-
-
717 if (isHSymbol || isHeSymbol) {
-
-
-
-
-
-
-
724 const double Z = 1.0 - (canonicalComposition.
X + canonicalComposition.
Y);
-
725 if (std::abs(Z - canonicalComposition.
Z) > 1e-6) {
-
-
727 LOG_WARNING(
m_logger,
"Validation composition Z (X-Y = {}) is different than canonical composition Z ({}) (∑a_i where a_i != H/He).", Z, canonicalComposition.
Z);
-
-
-
730 LOG_ERROR(
m_logger,
"Validation composition Z (X-Y = {}) is different than canonical composition Z ({}) (∑a_i where a_i != H/He).", Z, canonicalComposition.
Z);
-
731 throw std::runtime_error(
"Validation composition Z (X-Y = " + std::to_string(Z) +
") is different than canonical composition Z (" + std::to_string(canonicalComposition.
Z) +
") (∑a_i where a_i != H/He).");
-
-
-
734 return canonicalComposition;
-
+
+
-
-
-
-
-
+
+
+
+
+
717 LOG_ERROR(
m_logger,
"Composition has not been finalized. Hint: Consider running .finalize().");
+
+
+
+
721 const std::array<std::string, 7> canonicalH = {
+
722 "H-1",
"H-2",
"H-3",
"H-4",
"H-5",
"H-6",
"H-7"
+
+
724 const std::array<std::string, 8> canonicalHe = {
+
725 "He-3",
"He-4",
"He-5",
"He-6",
"He-7",
"He-8",
"He-9",
"He-10"
+
+
727 for (
const auto& symbol : canonicalH) {
+
+
+
+
+
732 for (
const auto& symbol : canonicalHe) {
+
+
+
+
+
+
+
739 const bool isHSymbol = std::ranges::find(canonicalH, symbol) != std::end(canonicalH);
+
740 const bool isHeSymbol = std::ranges::find(canonicalHe, symbol) != std::end(canonicalHe);
+
+
742 if (isHSymbol || isHeSymbol) {
+
+
+
+
+
+
+
749 const double Z = 1.0 - (canonicalComposition.
X + canonicalComposition.
Y);
+
750 if (std::abs(Z - canonicalComposition.
Z) > 1e-6) {
+
+
752 LOG_WARNING(
m_logger,
"Validation composition Z (X-Y = {}) is different than canonical composition Z ({}) (∑a_i where a_i != H/He).", Z, canonicalComposition.
Z);
+
+
+
755 LOG_ERROR(
m_logger,
"Validation composition Z (X-Y = {}) is different than canonical composition Z ({}) (∑a_i where a_i != H/He).", Z, canonicalComposition.
Z);
+
756 throw std::runtime_error(
"Validation composition Z (X-Y = " + std::to_string(Z) +
") is different than canonical composition Z (" + std::to_string(canonicalComposition.
Z) +
") (∑a_i where a_i != H/He).");
+
+
+
759 return canonicalComposition;
+
-
-
-
-
-
-
744 LOG_ERROR(
m_logger,
"Composition has not been finalized. Hint: Consider running .finalize().");
-
-
-
747 const auto symbol =
static_cast<std::string
>(isotope.
name());
-
-
-
-
-
+
+
+
+
+
764 LOG_ERROR(
m_logger,
"Composition has not been finalized. Hint: Consider running .finalize().");
+
+
+
+
768 std::vector<double> massFractionVector;
+
769 std::vector<double> speciesMass;
+
+
+
+
+
+
775 massFractionVector.push_back(entry.mass_fraction());
+
776 speciesMass.push_back(entry.isotope().mass());
+
+
+
779 return sortVectorBy(massFractionVector, speciesMass);
+
+
-
-
-
-
-
757 return mix(other, 0.5);
-
+
+
+
+
+
785 LOG_ERROR(
m_logger,
"Composition has not been finalized. Hint: Consider running .finalize().");
+
+
+
+
789 std::vector<double> numberFractionVector;
+
790 std::vector<double> speciesMass;
+
+
+
+
+
+
796 numberFractionVector.push_back(entry.number_fraction());
+
797 speciesMass.push_back(entry.isotope().mass());
+
+
+
800 return sortVectorBy(numberFractionVector, speciesMass);
+
-
-
-
-
761 os <<
"Global Composition: \n";
-
-
-
-
+
+
+
+
+
805 LOG_ERROR(
m_logger,
"Composition has not been finalized. Hint: Consider running .finalize().");
+
+
+
+
809 std::vector<double> molarAbundanceVector;
+
810 std::vector<double> speciesMass;
+
+
+
+
+
+
+
817 speciesMass.push_back(entry.isotope().mass());
+
+
+
820 return sortVectorBy(molarAbundanceVector, speciesMass);
+
-
-
-
-
-
-
+
+
+
+
+
825 LOG_ERROR(
m_logger,
"Composition has not been finalized. Hint: Consider running .finalize().");
+
+
+
+
829 LOG_ERROR(
m_logger,
"Symbol {} is not in the composition.", symbol);
+
+
+
+
833 std::vector<std::string> symbols;
+
834 std::vector<double> speciesMass;
+
+
+
+
+
+
840 symbols.emplace_back(entry.isotope().name());
+
841 speciesMass.push_back(entry.isotope().mass());
+
+
+
844 std::vector<std::string> sortedSymbols = sortVectorBy(symbols, speciesMass);
+
845 return std::distance(sortedSymbols.begin(), std::ranges::find(sortedSymbols, symbol));
+
-
-
-
-
773 os <<
"Composition(finalized: " << (
composition.m_finalized ?
"true" :
"false") <<
", " ;
-
-
775 for (
const auto &entry:
composition.m_compositions | std::views::values) {
-
-
777 if (count <
composition.m_compositions.size() - 1) {
-
-
-
-
-
-
+
+
+
+
+
850 LOG_ERROR(
m_logger,
"Composition has not been finalized. Hint: Consider running .finalize().");
+
+
+
+
854 LOG_ERROR(
m_logger,
"Species {} is not in the composition.", species.
name());
+
+
+
+
858 std::vector<atomic::Species> speciesVector;
+
859 std::vector<double> speciesMass;
+
+
+
+
+
+
865 speciesVector.emplace_back(entry.isotope());
+
866 speciesMass.push_back(entry.isotope().mass());
+
+
+
869 std::vector<atomic::Species> sortedSpecies = sortVectorBy(speciesVector, speciesMass);
+
870 return std::distance(sortedSpecies.begin(), std::ranges::find(sortedSpecies, species));
+
-
-
+
+
+
+
+
875 LOG_ERROR(
m_logger,
"Composition has not been finalized. Hint: Consider running .finalize().");
+
+
+
+
879 LOG_ERROR(
m_logger,
"Index {} is out of bounds for composition of size {}.", index,
m_compositions.size());
+
880 throw std::out_of_range(
"Index " + std::to_string(index) +
" is out of bounds for composition of size " + std::to_string(
m_compositions.size()) +
".");
+
+
+
883 LOG_ERROR(
m_logger,
"Index {} is negative. Cannot get species at negative index.", index);
+
884 throw std::out_of_range(
"Index " + std::to_string(index) +
" is negative. Cannot get species at negative index.");
+
+
+
887 std::vector<atomic::Species> speciesVector;
+
888 std::vector<double> speciesMass;
+
+
+
+
+
+
894 speciesVector.emplace_back(entry.isotope());
+
895 speciesMass.push_back(entry.isotope().mass());
+
+
+
898 std::vector<atomic::Species> sortedSymbols = sortVectorBy(speciesVector, speciesMass);
+
899 return sortedSymbols.at(index);
+
+
+
+
+
+
+
+
+
+
909 LOG_ERROR(
m_logger,
"Composition has not been finalized. Hint: Consider running .finalize().");
+
+
+
912 const auto symbol =
static_cast<std::string
>(isotope.
name());
+
+
+
+
+
+
+
+
+
+
+
922 return mix(other, 0.5);
+
+
+
+
+
+
926 os <<
"Global Composition: \n";
+
+
+
+
+
+
+
+
+
+
+
938 os <<
"Composition(finalized: " << (
composition.m_finalized ?
"true" :
"false") <<
", " ;
+
+
940 for (
const auto &entry:
composition.m_compositions | std::views::values) {
+
+
942 if (count <
composition.m_compositions.size() - 1) {
+
+
+
+
+
+
+
+
+
-
void setCompositionMode(bool massFracMode)
Sets the composition mode (mass fraction vs. number fraction).
-
std::pair< std::unordered_map< std::string, CompositionEntry >, GlobalComposition > getComposition() const
Gets all composition entries and the global composition data.
-
Composition subset(const std::vector< std::string > &symbols, const std::string &method="norm") const
Creates a new Composition object containing a subset of species from this one.
-
void registerSymbol(const std::string &symbol, bool massFracMode=true)
Registers a new symbol for inclusion in the composition.
+
void setCompositionMode(bool massFracMode)
Sets the composition mode (mass fraction vs. number fraction).
+
std::pair< std::unordered_map< std::string, CompositionEntry >, GlobalComposition > getComposition() const
Gets all composition entries and the global composition data.
+
size_t getSpeciesIndex(const std::string &symbol) const
get the index in the sorted vector representation for a given symbol
+
Composition subset(const std::vector< std::string > &symbols, const std::string &method="norm") const
Creates a new Composition object containing a subset of species from this one.
+
void registerSymbol(const std::string &symbol, bool massFracMode=true)
Registers a new symbol for inclusion in the composition.
Composition()=default
Default constructor.
-
Composition operator+(const Composition &other) const
Overloads the + operator to mix two compositions with a 50/50 fraction.
+
Composition operator+(const Composition &other) const
Overloads the + operator to mix two compositions with a 50/50 fraction.
+
std::vector< double > getNumberFractionVector() const
Get a uniform vector representation of the number fractions stored in the composition object sorted s...
std::set< std::string > m_registeredSymbols
The registered symbols.
-
Composition mix(const Composition &other, double fraction) const
Mixes this composition with another to produce a new composition.
-
std::set< fourdst::atomic::Species > getRegisteredSpecies() const
Get a set of all species that are registered in the composition.
-
bool finalizeNumberFracMode(bool norm)
Finalizes the composition in number fraction mode.
-
double setMassFraction(const std::string &symbol, const double &mass_fraction)
Sets the mass fraction for a given symbol.
+
Composition mix(const Composition &other, double fraction) const
Mixes this composition with another to produce a new composition.
+
std::set< fourdst::atomic::Species > getRegisteredSpecies() const
Get a set of all species that are registered in the composition.
+
bool finalizeNumberFracMode(bool norm)
Finalizes the composition in number fraction mode.
+
double setMassFraction(const std::string &symbol, const double &mass_fraction)
Sets the mass fraction for a given symbol.
double m_meanParticleMass
The mean particle mass of the composition (\sum_{i} \frac{n_i}{m_i}. where n_i is the number fraction...
-
void registerSpecies(const fourdst::atomic::Species &species, bool massFracMode=true)
Registers a new species by extracting its symbol.
-
Composition & operator=(Composition const &other)
Assignment operator.
-
double getMeanParticleMass() const
Compute the mean particle mass of the composition.
+
void registerSpecies(const fourdst::atomic::Species &species, bool massFracMode=true)
Registers a new species by extracting its symbol.
+
Composition & operator=(Composition const &other)
Assignment operator.
+
double getMeanParticleMass() const
Compute the mean particle mass of the composition.
bool m_massFracMode
True if mass fraction mode, false if number fraction mode.
-
double getMolarAbundance(const std::string &symbol) const
Gets the molar abundance (X_i / A_i) for a given symbol.
-
bool hasSymbol(const std::string &symbol) const
Checks if a symbol is registered in the composition.
-
bool finalize(bool norm=false)
Finalizes the composition, making it ready for querying.
-
std::unordered_map< std::string, double > getNumberFraction() const
Gets the number fractions of all species in the composition.
-
double setNumberFraction(const std::string &symbol, const double &number_fraction)
Sets the number fraction for a given symbol.
-
std::set< std::string > getRegisteredSymbols() const
Gets the registered symbols.
-
void validateComposition(const std::vector< double > &fractions) const
Validates the given fractions, throwing an exception on failure.
-
bool finalizeMassFracMode(bool norm)
Finalizes the composition in mass fraction mode.
-
static bool isValidSymbol(const std::string &symbol)
Checks if the given symbol is valid by checking against the global species database.
-
double getMeanAtomicNumber() const
Compute the mean atomic number of the composition.
+
double getMolarAbundance(const std::string &symbol) const
Gets the molar abundance (X_i / A_i) for a given symbol.
+
bool hasSymbol(const std::string &symbol) const
Checks if a symbol is registered in the composition.
+
bool finalize(bool norm=false)
Finalizes the composition, making it ready for querying.
+
std::unordered_map< std::string, double > getNumberFraction() const
Gets the number fractions of all species in the composition.
+
double setNumberFraction(const std::string &symbol, const double &number_fraction)
Sets the number fraction for a given symbol.
+
std::set< std::string > getRegisteredSymbols() const
Gets the registered symbols.
+
std::vector< double > getMolarAbundanceVector() const
Get a uniform vector representation of the molar abundances stored in the composition object sorted s...
+
void validateComposition(const std::vector< double > &fractions) const
Validates the given fractions, throwing an exception on failure.
+
bool finalizeMassFracMode(bool norm)
Finalizes the composition in mass fraction mode.
+
static bool isValidSymbol(const std::string &symbol)
Checks if the given symbol is valid by checking against the global species database.
+
double getMeanAtomicNumber() const
Compute the mean atomic number of the composition.
bool m_finalized
True if the composition is finalized.
+
atomic::Species getSpeciesAtIndex(size_t index) const
Get the species at a given index in the sorted vector representation.
std::unordered_map< std::string, CompositionEntry > m_compositions
The compositions.
-
CanonicalComposition getCanonicalComposition(bool harsh=false) const
Gets the current canonical composition (X, Y, Z).
-
bool contains(const fourdst::atomic::Species &isotope) const
Checks if a given isotope is present in the composition.
-
std::unordered_map< std::string, double > getMassFraction() const
Gets the mass fractions of all species in the composition.
+
CanonicalComposition getCanonicalComposition(bool harsh=false) const
Gets the current canonical composition (X, Y, Z).
+
bool contains(const fourdst::atomic::Species &isotope) const
Checks if a given isotope is present in the composition.
+
std::vector< double > getMassFractionVector() const
Get a uniform vector representation of the mass fraction stored in the composition object sorted such...
+
std::unordered_map< std::string, double > getMassFraction() const
Gets the mass fractions of all species in the composition.
double m_specificNumberDensity
The specific number density of the composition (\sum_{i} X_i m_i. Where X_i is the number fraction of...
-
bool isValidComposition(const std::vector< double > &fractions) const
Checks if the given fractions are valid (sum to ~1.0).
+
bool isValidComposition(const std::vector< double > &fractions) const
Checks if the given fractions are valid (sum to ~1.0).
Exception thrown due to a conflict in composition modes at the entry level.
Exception thrown when an operation is attempted on a composition that has not been finalized.
Exception thrown when attempting to initialize a composition entry that has already been initialized.
@@ -1061,37 +1243,37 @@ $(function(){initNavTree('composition_8cpp_source.html',''); initResizable(true)
Contains classes and functions related to atomic data, such as properties of atomic species.
-
static const std::unordered_map< std::string, const Species & > species
+
static const std::unordered_map< std::string, const Species & > species
-
std::ostream & operator<<(std::ostream &os, const GlobalComposition &comp)
+
std::ostream & operator<<(std::ostream &os, const GlobalComposition &comp)
-
Represents an atomic species (isotope) with its fundamental physical properties.
-
std::string_view name() const
Gets the name of the species.
+
Represents an atomic species (isotope) with its fundamental physical properties.
+
std::string_view name() const
Gets the name of the species.
Represents the canonical (X, Y, Z) composition of stellar material.
double Y
Mass fraction of Helium.
double X
Mass fraction of Hydrogen.
double Z
Mass fraction of Metals.
Represents a single entry (an isotope) within a composition.
double m_relAbundance
The relative abundance, used internally for conversions. For mass fraction mode, this is X_i / A_i; f...
-
bool getMassFracMode() const
Gets the mode of the composition entry.
-
CompositionEntry()
Default constructor. Initializes a default entry (H-1), but in an uninitialized state.
+
bool getMassFracMode() const
Gets the mode of the composition entry.
+
CompositionEntry()
Default constructor. Initializes a default entry (H-1), but in an uninitialized state.
bool m_massFracMode
The mode of the composition entry. True if mass fraction, false if number fraction.
double m_numberFraction
The number fraction (mole fraction) of the species. Valid only if m_massFracMode is false.
-
double number_fraction() const
Gets the number fraction of the species.
+
double number_fraction() const
Gets the number fraction of the species.
bool m_initialized
True if the composition entry has been initialized with a valid species.
-
bool setMassFracMode(double meanMolarMass)
Switches the mode to mass fraction mode.
-
void setMassFraction(double mass_fraction)
Sets the mass fraction of the species.
-
std::string symbol() const
Gets the chemical symbol of the species.
-
void setSpecies(const std::string &symbol)
Sets the species for the composition entry. This can only be done once.
-
double mass_fraction() const
Gets the mass fraction of the species.
-
bool setNumberFracMode(double totalMoles)
Switches the mode to number fraction mode.
+
bool setMassFracMode(double meanMolarMass)
Switches the mode to mass fraction mode.
+
void setMassFraction(double mass_fraction)
Sets the mass fraction of the species.
+
std::string symbol() const
Gets the chemical symbol of the species.
+
void setSpecies(const std::string &symbol)
Sets the species for the composition entry. This can only be done once.
+
double mass_fraction() const
Gets the mass fraction of the species.
+
bool setNumberFracMode(double totalMoles)
Switches the mode to number fraction mode.
atomic::Species m_isotope
The atomic::Species object containing detailed isotope data.
-
void setNumberFraction(double number_fraction)
Sets the number fraction of the species.
-
double rel_abundance() const
Gets the relative abundance of the species.
+
void setNumberFraction(double number_fraction)
Sets the number fraction of the species.
+
double rel_abundance() const
Gets the relative abundance of the species.
std::string m_symbol
The chemical symbol of the species (e.g., "H-1", "Fe-56").
double m_massFraction
The mass fraction of the species. Valid only if m_massFracMode is true.
-
atomic::Species isotope() const
Gets the isotope data for the species.
+
atomic::Species isotope() const
Gets the isotope data for the species.
Represents global properties of a finalized composition.
double specificNumberDensity
The specific number density (moles per unit mass, sum of X_i/M_i), where X_i is mass fraction and M_i...
double meanParticleMass
The mean mass per particle (inverse of specific number density). Units: g/mol.
diff --git a/docs/html/composition_8h_source.html b/docs/html/composition_8h_source.html
index eb78474..5b0fcb1 100644
--- a/docs/html/composition_8h_source.html
+++ b/docs/html/composition_8h_source.html
@@ -322,111 +322,128 @@ $(function(){initNavTree('composition_8h_source.html',''); initResizable(true);
-
-
-
+
+
+
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
-
-
-
-
-
+
+
-
-
-
-
-
+
+
-
-
-
-
-
+
+
+
845 [[nodiscard]]
auto end()
const {
+
+
-
-
+
+
-
+
-
void setCompositionMode(bool massFracMode)
Sets the composition mode (mass fraction vs. number fraction).
-
std::pair< std::unordered_map< std::string, CompositionEntry >, GlobalComposition > getComposition() const
Gets all composition entries and the global composition data.
-
Composition subset(const std::vector< std::string > &symbols, const std::string &method="norm") const
Creates a new Composition object containing a subset of species from this one.
-
void registerSymbol(const std::string &symbol, bool massFracMode=true)
Registers a new symbol for inclusion in the composition.
+
void setCompositionMode(bool massFracMode)
Sets the composition mode (mass fraction vs. number fraction).
+
std::pair< std::unordered_map< std::string, CompositionEntry >, GlobalComposition > getComposition() const
Gets all composition entries and the global composition data.
+
size_t getSpeciesIndex(const std::string &symbol) const
get the index in the sorted vector representation for a given symbol
+
Composition subset(const std::vector< std::string > &symbols, const std::string &method="norm") const
Creates a new Composition object containing a subset of species from this one.
+
void registerSymbol(const std::string &symbol, bool massFracMode=true)
Registers a new symbol for inclusion in the composition.
Composition()=default
Default constructor.
-
Composition operator+(const Composition &other) const
Overloads the + operator to mix two compositions with a 50/50 fraction.
-
friend std::ostream & operator<<(std::ostream &os, const Composition &composition)
Overloaded output stream operator for Composition.
+
Composition operator+(const Composition &other) const
Overloads the + operator to mix two compositions with a 50/50 fraction.
+
std::vector< double > getNumberFractionVector() const
Get a uniform vector representation of the number fractions stored in the composition object sorted s...
+
friend std::ostream & operator<<(std::ostream &os, const Composition &composition)
Overloaded output stream operator for Composition.
std::set< std::string > m_registeredSymbols
The registered symbols.
-
Composition mix(const Composition &other, double fraction) const
Mixes this composition with another to produce a new composition.
-
std::set< fourdst::atomic::Species > getRegisteredSpecies() const
Get a set of all species that are registered in the composition.
-
bool finalizeNumberFracMode(bool norm)
Finalizes the composition in number fraction mode.
-
double setMassFraction(const std::string &symbol, const double &mass_fraction)
Sets the mass fraction for a given symbol.
+
Composition mix(const Composition &other, double fraction) const
Mixes this composition with another to produce a new composition.
+
std::set< fourdst::atomic::Species > getRegisteredSpecies() const
Get a set of all species that are registered in the composition.
+
bool finalizeNumberFracMode(bool norm)
Finalizes the composition in number fraction mode.
+
double setMassFraction(const std::string &symbol, const double &mass_fraction)
Sets the mass fraction for a given symbol.
double m_meanParticleMass
The mean particle mass of the composition (\sum_{i} \frac{n_i}{m_i}. where n_i is the number fraction...
-
void registerSpecies(const fourdst::atomic::Species &species, bool massFracMode=true)
Registers a new species by extracting its symbol.
-
Composition & operator=(Composition const &other)
Assignment operator.
-
double getMeanParticleMass() const
Compute the mean particle mass of the composition.
+
void registerSpecies(const fourdst::atomic::Species &species, bool massFracMode=true)
Registers a new species by extracting its symbol.
+
Composition & operator=(Composition const &other)
Assignment operator.
+
double getMeanParticleMass() const
Compute the mean particle mass of the composition.
bool m_massFracMode
True if mass fraction mode, false if number fraction mode.
-
double getMolarAbundance(const std::string &symbol) const
Gets the molar abundance (X_i / A_i) for a given symbol.
+
double getMolarAbundance(const std::string &symbol) const
Gets the molar abundance (X_i / A_i) for a given symbol.
fourdst::logging::LogManager & m_logManager
-
bool hasSymbol(const std::string &symbol) const
Checks if a symbol is registered in the composition.
-
bool finalize(bool norm=false)
Finalizes the composition, making it ready for querying.
-
std::unordered_map< std::string, double > getNumberFraction() const
Gets the number fractions of all species in the composition.
-
double setNumberFraction(const std::string &symbol, const double &number_fraction)
Sets the number fraction for a given symbol.
-
std::set< std::string > getRegisteredSymbols() const
Gets the registered symbols.
-
void validateComposition(const std::vector< double > &fractions) const
Validates the given fractions, throwing an exception on failure.
-
bool finalizeMassFracMode(bool norm)
Finalizes the composition in mass fraction mode.
+
bool hasSymbol(const std::string &symbol) const
Checks if a symbol is registered in the composition.
+
bool finalize(bool norm=false)
Finalizes the composition, making it ready for querying.
+
std::unordered_map< std::string, double > getNumberFraction() const
Gets the number fractions of all species in the composition.
+
double setNumberFraction(const std::string &symbol, const double &number_fraction)
Sets the number fraction for a given symbol.
+
std::set< std::string > getRegisteredSymbols() const
Gets the registered symbols.
+
std::vector< double > getMolarAbundanceVector() const
Get a uniform vector representation of the molar abundances stored in the composition object sorted s...
+
void validateComposition(const std::vector< double > &fractions) const
Validates the given fractions, throwing an exception on failure.
+
bool finalizeMassFracMode(bool norm)
Finalizes the composition in mass fraction mode.
fourdst::config::Config & m_config
-
static bool isValidSymbol(const std::string &symbol)
Checks if the given symbol is valid by checking against the global species database.
-
double getMeanAtomicNumber() const
Compute the mean atomic number of the composition.
+
static bool isValidSymbol(const std::string &symbol)
Checks if the given symbol is valid by checking against the global species database.
+
double getMeanAtomicNumber() const
Compute the mean atomic number of the composition.
bool m_finalized
True if the composition is finalized.
~Composition()=default
Default destructor.
+
atomic::Species getSpeciesAtIndex(size_t index) const
Get the species at a given index in the sorted vector representation.
std::unordered_map< std::string, CompositionEntry > m_compositions
The compositions.
-
auto begin()
Returns an iterator to the beginning of the composition map.
+
auto begin()
Returns an iterator to the beginning of the composition map.
-
CanonicalComposition getCanonicalComposition(bool harsh=false) const
Gets the current canonical composition (X, Y, Z).
-
bool contains(const fourdst::atomic::Species &isotope) const
Checks if a given isotope is present in the composition.
-
std::unordered_map< std::string, double > getMassFraction() const
Gets the mass fractions of all species in the composition.
+
CanonicalComposition getCanonicalComposition(bool harsh=false) const
Gets the current canonical composition (X, Y, Z).
+
bool contains(const fourdst::atomic::Species &isotope) const
Checks if a given isotope is present in the composition.
+
std::vector< double > getMassFractionVector() const
Get a uniform vector representation of the mass fraction stored in the composition object sorted such...
+
std::unordered_map< std::string, double > getMassFraction() const
Gets the mass fractions of all species in the composition.
double m_specificNumberDensity
The specific number density of the composition (\sum_{i} X_i m_i. Where X_i is the number fraction of...
-
bool isValidComposition(const std::vector< double > &fractions) const
Checks if the given fractions are valid (sum to ~1.0).
-
auto end()
Returns an iterator to the end of the composition map.
-
auto begin() const
Returns a const iterator to the beginning of the composition map.
-
auto end() const
Returns a const iterator to the end of the composition map.
+
bool isValidComposition(const std::vector< double > &fractions) const
Checks if the given fractions are valid (sum to ~1.0).
+
auto end()
Returns an iterator to the end of the composition map.
+
auto begin() const
Returns a const iterator to the beginning of the composition map.
+
auto end() const
Returns a const iterator to the end of the composition map.
-
Represents an atomic species (isotope) with its fundamental physical properties.
+
Represents an atomic species (isotope) with its fundamental physical properties.
Represents the canonical (X, Y, Z) composition of stellar material.
friend std::ostream & operator<<(std::ostream &os, const CanonicalComposition &composition)
Overloads the stream insertion operator for easy printing.
double Y
Mass fraction of Helium.
double X
Mass fraction of Hydrogen.
double Z
Mass fraction of Metals.
double m_relAbundance
The relative abundance, used internally for conversions. For mass fraction mode, this is X_i / A_i; f...
-
bool getMassFracMode() const
Gets the mode of the composition entry.
-
CompositionEntry()
Default constructor. Initializes a default entry (H-1), but in an uninitialized state.
+
bool getMassFracMode() const
Gets the mode of the composition entry.
+
CompositionEntry()
Default constructor. Initializes a default entry (H-1), but in an uninitialized state.
bool m_massFracMode
The mode of the composition entry. True if mass fraction, false if number fraction.
double m_numberFraction
The number fraction (mole fraction) of the species. Valid only if m_massFracMode is false.
-
double number_fraction() const
Gets the number fraction of the species.
+
double number_fraction() const
Gets the number fraction of the species.
bool m_initialized
True if the composition entry has been initialized with a valid species.
-
bool setMassFracMode(double meanMolarMass)
Switches the mode to mass fraction mode.
-
void setMassFraction(double mass_fraction)
Sets the mass fraction of the species.
-
std::string symbol() const
Gets the chemical symbol of the species.
-
void setSpecies(const std::string &symbol)
Sets the species for the composition entry. This can only be done once.
-
double mass_fraction() const
Gets the mass fraction of the species.
-
bool setNumberFracMode(double totalMoles)
Switches the mode to number fraction mode.
+
bool setMassFracMode(double meanMolarMass)
Switches the mode to mass fraction mode.
+
void setMassFraction(double mass_fraction)
Sets the mass fraction of the species.
+
std::string symbol() const
Gets the chemical symbol of the species.
+
void setSpecies(const std::string &symbol)
Sets the species for the composition entry. This can only be done once.
+
double mass_fraction() const
Gets the mass fraction of the species.
+
bool setNumberFracMode(double totalMoles)
Switches the mode to number fraction mode.
atomic::Species m_isotope
The atomic::Species object containing detailed isotope data.
-
void setNumberFraction(double number_fraction)
Sets the number fraction of the species.
-
double rel_abundance() const
Gets the relative abundance of the species.
+
void setNumberFraction(double number_fraction)
Sets the number fraction of the species.
+
double rel_abundance() const
Gets the relative abundance of the species.
std::string m_symbol
The chemical symbol of the species (e.g., "H-1", "Fe-56").
double m_massFraction
The mass fraction of the species. Valid only if m_massFracMode is true.
-
friend std::ostream & operator<<(std::ostream &os, const CompositionEntry &entry)
Overloaded output stream operator for CompositionEntry.
-
atomic::Species isotope() const
Gets the isotope data for the species.
+
friend std::ostream & operator<<(std::ostream &os, const CompositionEntry &entry)
Overloaded output stream operator for CompositionEntry.
+
atomic::Species isotope() const
Gets the isotope data for the species.
Represents global properties of a finalized composition.
double specificNumberDensity
The specific number density (moles per unit mass, sum of X_i/M_i), where X_i is mass fraction and M_i...
-
friend std::ostream & operator<<(std::ostream &os, const GlobalComposition &comp)
+
friend std::ostream & operator<<(std::ostream &os, const GlobalComposition &comp)
double meanParticleMass
The mean mass per particle (inverse of specific number density). Units: g/mol.
diff --git a/docs/html/dir_f0fdd83dd0cb4aa6fd6a832374ae4f05.html b/docs/html/dir_f0fdd83dd0cb4aa6fd6a832374ae4f05.html
index 6a2d0db..95377aa 100644
--- a/docs/html/dir_f0fdd83dd0cb4aa6fd6a832374ae4f05.html
+++ b/docs/html/dir_f0fdd83dd0cb4aa6fd6a832374ae4f05.html
@@ -114,6 +114,8 @@ Files
| |
| | composition.h |
| |
+
| | elements.h |
+
| |
| | species.h |
| |
diff --git a/docs/html/dir_f0fdd83dd0cb4aa6fd6a832374ae4f05.js b/docs/html/dir_f0fdd83dd0cb4aa6fd6a832374ae4f05.js
index d722c38..65b250c 100644
--- a/docs/html/dir_f0fdd83dd0cb4aa6fd6a832374ae4f05.js
+++ b/docs/html/dir_f0fdd83dd0cb4aa6fd6a832374ae4f05.js
@@ -3,5 +3,6 @@ var dir_f0fdd83dd0cb4aa6fd6a832374ae4f05 =
[ "exceptions", "dir_88aa30610c51652b536406602eb05405.html", "dir_88aa30610c51652b536406602eb05405" ],
[ "atomicSpecies.h", "atomic_species_8h.html", "atomic_species_8h" ],
[ "composition.h", "composition_8h.html", "composition_8h" ],
+ [ "elements.h", "elements_8h.html", "elements_8h" ],
[ "species.h", "species_8h.html", "species_8h" ]
];
\ No newline at end of file
diff --git a/docs/html/doxygen_crawl.html b/docs/html/doxygen_crawl.html
index acbc4a3..d5d14a8 100644
--- a/docs/html/doxygen_crawl.html
+++ b/docs/html/doxygen_crawl.html
@@ -18,11 +18,13 @@
+
+
@@ -45,6 +47,7 @@
+
@@ -57,6 +60,7 @@
+
@@ -65,7 +69,9 @@
+
+
@@ -126,6 +132,8 @@
+
+
@@ -757,6 +765,7 @@
+
@@ -2001,6 +2010,7 @@
+
@@ -2847,6 +2857,7 @@
+
diff --git a/docs/html/files.html b/docs/html/files.html
index 933db7e..ff11627 100644
--- a/docs/html/files.html
+++ b/docs/html/files.html
@@ -115,9 +115,10 @@ $(function(){initNavTree('files.html',''); initResizable(true); });
| exceptions_composition.h | |
| atomicSpecies.h | |
| composition.h | |
-
| species.h | |
-
| ▼ lib | |
-
| composition.cpp | |
+
| elements.h | |
+
| species.h | |
+
| ▼ lib | |
+
| composition.cpp | |
diff --git a/docs/html/functions.html b/docs/html/functions.html
index 6943bd6..6f40f97 100644
--- a/docs/html/functions.html
+++ b/docs/html/functions.html
@@ -146,12 +146,17 @@ $(function(){initNavTree('functions.html',''); initResizable(true); });
getComposition() : fourdst::composition::Composition
getMassFracMode() : fourdst::composition::CompositionEntry
getMassFraction() : fourdst::composition::Composition
+
getMassFractionVector() : fourdst::composition::Composition
getMeanAtomicNumber() : fourdst::composition::Composition
getMeanParticleMass() : fourdst::composition::Composition
getMolarAbundance() : fourdst::composition::Composition
+
getMolarAbundanceVector() : fourdst::composition::Composition
getNumberFraction() : fourdst::composition::Composition
+
getNumberFractionVector() : fourdst::composition::Composition
getRegisteredSpecies() : fourdst::composition::Composition
getRegisteredSymbols() : fourdst::composition::Composition
+
getSpeciesAtIndex() : fourdst::composition::Composition
+
getSpeciesIndex() : fourdst::composition::Composition
diff --git a/docs/html/functions_func.html b/docs/html/functions_func.html
index 0834963..70dd236 100644
--- a/docs/html/functions_func.html
+++ b/docs/html/functions_func.html
@@ -146,12 +146,17 @@ $(function(){initNavTree('functions_func.html',''); initResizable(true); });
getComposition() : fourdst::composition::Composition
getMassFracMode() : fourdst::composition::CompositionEntry
getMassFraction() : fourdst::composition::Composition
+
getMassFractionVector() : fourdst::composition::Composition
getMeanAtomicNumber() : fourdst::composition::Composition
getMeanParticleMass() : fourdst::composition::Composition
getMolarAbundance() : fourdst::composition::Composition
+
getMolarAbundanceVector() : fourdst::composition::Composition
getNumberFraction() : fourdst::composition::Composition
+
getNumberFractionVector() : fourdst::composition::Composition
getRegisteredSpecies() : fourdst::composition::Composition
getRegisteredSymbols() : fourdst::composition::Composition
+
getSpeciesAtIndex() : fourdst::composition::Composition
+
getSpeciesIndex() : fourdst::composition::Composition
diff --git a/docs/html/index.html b/docs/html/index.html
index 6b21a08..7540f61 100644
--- a/docs/html/index.html
+++ b/docs/html/index.html
@@ -178,11 +178,11 @@ C++ Usage Examples
return 0;
}
Manages a collection of chemical species and their abundances.
-
void registerSymbol(const std::string &symbol, bool massFracMode=true)
Registers a new symbol for inclusion in the composition.
-
double setMassFraction(const std::string &symbol, const double &mass_fraction)
Sets the mass fraction for a given symbol.
-
double getMeanParticleMass() const
Compute the mean particle mass of the composition.
-
bool finalize(bool norm=false)
Finalizes the composition, making it ready for querying.
-
std::unordered_map< std::string, double > getMassFraction() const
Gets the mass fractions of all species in the composition.
+
void registerSymbol(const std::string &symbol, bool massFracMode=true)
Registers a new symbol for inclusion in the composition.
+
double setMassFraction(const std::string &symbol, const double &mass_fraction)
Sets the mass fraction for a given symbol.
+
double getMeanParticleMass() const
Compute the mean particle mass of the composition.
+
bool finalize(bool norm=false)
Finalizes the composition, making it ready for querying.
+
std::unordered_map< std::string, double > getMassFraction() const
Gets the mass fractions of all species in the composition.
2. Number Fraction Composition and Mode Switching
@@ -214,9 +214,9 @@ C++ Usage Examples
std::cout <<
"He-4 Mass Fraction (after mode switch): " << comp.
getMassFraction(
"He-4") << std::endl;
}
}
-
void setCompositionMode(bool massFracMode)
Sets the composition mode (mass fraction vs. number fraction).
-
double setNumberFraction(const std::string &symbol, const double &number_fraction)
Sets the number fraction for a given symbol.
-
double getNumberFraction(const std::string &symbol) const
Gets the number fraction for a given symbol.
+
void setCompositionMode(bool massFracMode)
Sets the composition mode (mass fraction vs. number fraction).
+
double setNumberFraction(const std::string &symbol, const double &number_fraction)
Sets the number fraction for a given symbol.
+
double getNumberFraction(const std::string &symbol) const
Gets the number fraction for a given symbol.
3. Mixing Two Compositions
@@ -240,7 +240,7 @@ C++ Usage Examples
std::cout <<
"50/50 Mix H-1: " << mixed.
getMassFraction(
"H-1") << std::endl;
std::cout <<
"75/25 Mix H-1: " << mixed2.
getMassFraction(
"H-1") << std::endl;
}
-
Composition mix(const Composition &other, double fraction) const
Mixes this composition with another to produce a new composition.
+
Composition mix(const Composition &other, double fraction) const
Mixes this composition with another to produce a new composition.
4. Error Handling
The library uses exceptions to report errors. Always wrap calls in a try-catch block for robust code.
@@ -286,7 +286,7 @@ C++ Usage Examples
}
static const Species F_18("F-18", "F", 0, 9, 9, 18, 7631.6383, "B-", -4444.5049, 6584.04, "+", "+=100", 18.000937324, 0.497)
-
static const std::unordered_map< std::string, const Species & > species
+
static const std::unordered_map< std::string, const Species & > species
static const Species H_1("H-1", "H", -1, 0, 1, 1, 0.0, "B-", std::numeric_limits< double >::quiet_NaN(), std::numeric_limits< double >::infinity(), "/2+*", "S=99.9855 78", 1.007825031898, 1.4e-05)
diff --git a/docs/html/namespacefourdst_1_1atomic.html b/docs/html/namespacefourdst_1_1atomic.html
index 54169ae..ea8946a 100644
--- a/docs/html/namespacefourdst_1_1atomic.html
+++ b/docs/html/namespacefourdst_1_1atomic.html
@@ -7249,9 +7249,15 @@ Functions
| |
| static const Species | Og_295 ("Og-295", "Og", 59, 177, 118, 295, 7076.0, "B-", std::numeric_limits< double >::quiet_NaN(), 680.0, "", "~100", 295.216178, 703.0) |
| |
+
| Species | az_to_species (const int a, const int z) |
+
| |
@@ -27940,6 +27946,37 @@ Variables
+
+
+
+
◆ az_to_species()
+
+
+
+
+
+
+
+
+ | Species fourdst::atomic::az_to_species |
+ ( |
+ const int | a, |
+
+
+ |
+ |
+ const int | z ) |
+
+
+ |
+
+inline |
+
+
+
@@ -60721,7 +60758,7 @@ Variables
- Postcondition
- The function returns a
double representing the spin, or NaN if parsing fails. The input string is not modified.
- Returns
- The spin value as a
double. Returns NaN for invalid or unparsable strings.
-
Definition at line 345 of file atomicSpecies.h.
+
Definition at line 348 of file atomicSpecies.h.
@@ -164124,7 +164161,7 @@ Variables
- Returns
true if the names are different, false otherwise.
-
Definition at line 293 of file atomicSpecies.h.
+
Definition at line 296 of file atomicSpecies.h.
@@ -164165,7 +164202,7 @@ Variables
- Returns
true if lhs atomic mass is less than rhs atomic mass, false otherwise.
-
Definition at line 302 of file atomicSpecies.h.
+
Definition at line 305 of file atomicSpecies.h.
@@ -164206,7 +164243,7 @@ Variables
- Returns
true if the names are identical, false otherwise.
-
Definition at line 284 of file atomicSpecies.h.
+
Definition at line 287 of file atomicSpecies.h.
@@ -164247,7 +164284,7 @@ Variables
- Returns
true if lhs atomic mass is greater than rhs atomic mass, false otherwise.
-
Definition at line 311 of file atomicSpecies.h.
+
Definition at line 314 of file atomicSpecies.h.
@@ -280154,6 +280191,30 @@ Variables
+
+
◆ element_symbol_map
+
+
+
+
+
+
+
+
+ | const std::unordered_map<uint8_t, std::string> fourdst::atomic::element_symbol_map |
+
+
+ |
+
+static |
+
+
+
+
◆ species
@@ -280174,7 +280235,31 @@ Variables
+
+
+
◆ symbol_element_map
+
+
+
+
+
+
+
+
+ | const std::unordered_map<std::string, uint8_t> fourdst::atomic::symbol_element_map |
+
+
+ |
+
+static |
+
+
+
diff --git a/docs/html/namespacefourdst_1_1atomic.js b/docs/html/namespacefourdst_1_1atomic.js
index 7c918a3..eedc21b 100644
--- a/docs/html/namespacefourdst_1_1atomic.js
+++ b/docs/html/namespacefourdst_1_1atomic.js
@@ -267,6 +267,7 @@ var namespacefourdst_1_1atomic =
[ "Au_208", "namespacefourdst_1_1atomic.html#a0bd121d3b47fc0e2675adca750751a4b", null ],
[ "Au_209", "namespacefourdst_1_1atomic.html#a44faf7f0ec7dfec4cac5ee0eb9e9f254", null ],
[ "Au_210", "namespacefourdst_1_1atomic.html#afff955be16cbe4538218312291b8afe4", null ],
+ [ "az_to_species", "namespacefourdst_1_1atomic.html#a29fe92b293db689c5da78599b8958c70", null ],
[ "B_10", "namespacefourdst_1_1atomic.html#ac5cd3b25b3beb7010ce868e475e3ab74", null ],
[ "B_11", "namespacefourdst_1_1atomic.html#afab1780e9187ea28b0f847f816e35f15", null ],
[ "B_12", "namespacefourdst_1_1atomic.html#a8a04db3a85c4949266d0b81cbee5b797", null ],
@@ -3564,5 +3565,7 @@ var namespacefourdst_1_1atomic =
[ "Zr_97", "namespacefourdst_1_1atomic.html#a3ab0772e3ab0eb92a22a708a5f30f56c", null ],
[ "Zr_98", "namespacefourdst_1_1atomic.html#a794c1722fbda32caddf625291864a1a5", null ],
[ "Zr_99", "namespacefourdst_1_1atomic.html#a62b790c25aa06247822b0273e8da0cd1", null ],
- [ "species", "namespacefourdst_1_1atomic.html#a3f619cc8f8b2cd718a4082c6adb0de90", null ]
+ [ "element_symbol_map", "namespacefourdst_1_1atomic.html#a82a2234f3c538636cc10293abd30e4a8", null ],
+ [ "species", "namespacefourdst_1_1atomic.html#a3f619cc8f8b2cd718a4082c6adb0de90", null ],
+ [ "symbol_element_map", "namespacefourdst_1_1atomic.html#ac39cc5fb90b416556e93bdc93f627203", null ]
];
\ No newline at end of file
diff --git a/docs/html/namespacefourdst_1_1composition.html b/docs/html/namespacefourdst_1_1composition.html
index 523dba7..962b180 100644
--- a/docs/html/namespacefourdst_1_1composition.html
+++ b/docs/html/namespacefourdst_1_1composition.html
@@ -164,7 +164,7 @@ Functions
- Returns
- The output stream.
-
Definition at line 772 of file composition.cpp.
+
Definition at line 937 of file composition.cpp.
@@ -195,7 +195,7 @@ Functions
- Returns
- The output stream.
-
Definition at line 767 of file composition.cpp.
+
Definition at line 932 of file composition.cpp.
@@ -218,7 +218,7 @@ Functions
diff --git a/docs/html/namespacemembers.html b/docs/html/namespacemembers.html
index f6ab56e..c61904a 100644
--- a/docs/html/namespacemembers.html
+++ b/docs/html/namespacemembers.html
@@ -368,6 +368,7 @@ $(function(){initNavTree('namespacemembers.html',''); initResizable(true); });
Au_208() : fourdst::atomic
Au_209() : fourdst::atomic
Au_210() : fourdst::atomic
+
az_to_species() : fourdst::atomic
diff --git a/docs/html/namespacemembers_e.html b/docs/html/namespacemembers_e.html
index 5f9b551..eff6364 100644
--- a/docs/html/namespacemembers_e.html
+++ b/docs/html/namespacemembers_e.html
@@ -102,6 +102,7 @@ $(function(){initNavTree('namespacemembers_e.html',''); initResizable(true); });
Here is a list of all namespace members with links to the namespace documentation for each member:
- e -
diff --git a/docs/html/namespacemembers_s.html b/docs/html/namespacemembers_s.html
index f38be0e..d40c66e 100644
--- a/docs/html/namespacemembers_s.html
+++ b/docs/html/namespacemembers_s.html
@@ -388,6 +388,7 @@ $(function(){initNavTree('namespacemembers_s.html',''); initResizable(true); });
Sr_97() : fourdst::atomic
Sr_98() : fourdst::atomic
Sr_99() : fourdst::atomic
+
symbol_element_map : fourdst::atomic
diff --git a/docs/html/namespacemembers_vars.html b/docs/html/namespacemembers_vars.html
index 8e5f823..407b6cd 100644
--- a/docs/html/namespacemembers_vars.html
+++ b/docs/html/namespacemembers_vars.html
@@ -100,7 +100,9 @@ $(function(){initNavTree('namespacemembers_vars.html',''); initResizable(true);
Here is a list of all namespace variables with links to the namespace documentation for each variable:
diff --git a/docs/html/navtreedata.js b/docs/html/navtreedata.js
index 1f981cf..37e5298 100644
--- a/docs/html/navtreedata.js
+++ b/docs/html/navtreedata.js
@@ -58,36 +58,36 @@ var NAVTREE =
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#include <string>
#include <limits>
#include "fourdst/composition/atomicSpecies.h"
+
#include "fourdst/composition/elements.h"