Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Fixes regarding component ID #319

Open
wants to merge 6 commits into
base: master
Choose a base branch
from
Open

Fixes regarding component ID #319

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
6 commits
Select commit Hold shift + click to select a range
8b1f10a
Fix component ID in Basis to match ID in components.xml
HomesGH Jun 4, 2024
3219b7a
Add check for component input
HomesGH Jun 4, 2024
dea55d8
Undo wrong change
HomesGH Jun 4, 2024
a3e3c14
Add debug print
HomesGH Jun 4, 2024
cd0c330
Add further debug
HomesGH Jun 4, 2024
c243c52
Undo debug prints
HomesGH Jun 4, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion examples/Adsorption/Generator/adsorption.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,7 @@
<lattice system="cubic" centering="face"/>
<basis>
<site>
<componentid>0</componentid>
<componentid>1</componentid>
<coordinate>
<x>0</x>
<y>0</y>
Expand Down
2 changes: 1 addition & 1 deletion examples/Adsorption/Generator/adsorption_autopas_default.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,7 @@
<lattice system="cubic" centering="face"/>
<basis>
<site>
<componentid>0</componentid>
<componentid>1</componentid>
<coordinate>
<x>0</x>
<y>0</y>
Expand Down
2 changes: 1 addition & 1 deletion examples/Adsorption/Generator/adsorption_autopas_tuning.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,7 @@
<lattice system="cubic" centering="face"/>
<basis>
<site>
<componentid>0</componentid>
<componentid>1</componentid>
<coordinate>
<x>0</x>
<y>0</y>
Expand Down
2 changes: 1 addition & 1 deletion examples/DropletCoalescence/liq/config_1_generateLiq.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,7 @@
</lattice>
<basis>
<site>
<componentid>0</componentid>
<componentid>1</componentid>
<coordinate> <x>0.5</x> <y>0.5</y> <z>0.5</z> </coordinate>
</site>
</basis>
Expand Down
2 changes: 1 addition & 1 deletion examples/DropletCoalescence/vap/config_3_generateVap.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,7 @@
</lattice>
<basis>
<site>
<componentid>0</componentid>
<componentid>1</componentid>
<coordinate> <x>0.5</x> <y>0.5</y> <z>0.5</z> </coordinate>
</site>
</basis>
Expand Down
2 changes: 1 addition & 1 deletion examples/Evaporation/stationary/sim01/run01/config.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,7 @@
</lattice>
<basis>
<site>
<componentid>1</componentid>
<componentid>2</componentid>
<coordinate> <x>0.5</x> <y>0.5</y> <z>0.5</z> </coordinate>
</site>
</basis>
Expand Down
2 changes: 1 addition & 1 deletion examples/Generators/MultiObjectGenerator/mixing_isotopic_1CLJ/liq1/run01/config.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -52,7 +52,7 @@
</lattice>
<basis>
<site>
<componentid>0</componentid>
<componentid>1</componentid>
<coordinate> <x>0.5</x> <y>0.5</y> <z>0.5</z> </coordinate>
</site>
</basis>
Expand Down
2 changes: 1 addition & 1 deletion examples/Generators/MultiObjectGenerator/mixing_isotopic_1CLJ/liq2/run01/config.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -52,7 +52,7 @@
</lattice>
<basis>
<site>
<componentid>1</componentid>
<componentid>2</componentid>
<coordinate> <x>0.5</x> <y>0.5</y> <z>0.5</z> </coordinate>
</site>
</basis>
Expand Down
2 changes: 1 addition & 1 deletion examples/Injection/liq/sim02/run01/config.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@
</lattice>
<basis>
<site>
<componentid>0</componentid>
<componentid>1</componentid>
<coordinate> <x>0.5</x> <y>0.5</y> <z>0.5</z> </coordinate>
</site>
</basis>
Expand Down
2 changes: 1 addition & 1 deletion examples/Injection/nemd/sim01/run01/config.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -60,7 +60,7 @@
</lattice>
<basis>
<site>
<componentid>2</componentid>
<componentid>3</componentid>
<coordinate> <x>0.5</x> <y>0.5</y> <z>0.5</z> </coordinate>
</site>
</basis>
Expand Down
2 changes: 1 addition & 1 deletion examples/Injection/nemd/sim02/run01/config.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -60,7 +60,7 @@
</lattice>
<basis>
<site>
<componentid>2</componentid>
<componentid>3</componentid>
<coordinate> <x>0.5</x> <y>0.5</y> <z>0.5</z> </coordinate>
</site>
</basis>
Expand Down
4 changes: 2 additions & 2 deletions examples/KDD-vectorization-tuner/one-component/config.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@
</lattice>
<basis>
<site>
<componentid>0</componentid>
<componentid>1</componentid>
<coordinate> <x>0.5</x> <y>0.5</y> <z>0.5</z> </coordinate>
</site>
</basis>
Expand All @@ -58,7 +58,7 @@
</lattice>
<basis>
<site>
<componentid>0</componentid>
<componentid>1</componentid>
<coordinate> <x>0.5</x> <y>0.5</y> <z>0.5</z> </coordinate>
</site>
</basis>
Expand Down
4 changes: 2 additions & 2 deletions examples/KDD-vectorization-tuner/two-components/config.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@
</lattice>
<basis>
<site>
<componentid>1</componentid>
<componentid>2</componentid>
<coordinate> <x>0.5</x> <y>0.5</y> <z>0.5</z> </coordinate>
</site>
</basis>
Expand All @@ -58,7 +58,7 @@
</lattice>
<basis>
<site>
<componentid>0</componentid>
<componentid>1</componentid>
<coordinate> <x>0.5</x> <y>0.5</y> <z>0.5</z> </coordinate>
</site>
</basis>
Expand Down
2 changes: 1 addition & 1 deletion examples/Mamico-couette/ls1configNoCP.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,7 @@
</lattice>
<basis>
<site>
<componentid>0</componentid>
<componentid>1</componentid>
<coordinate> <x>0.5</x> <y>0.5</y> <z>0.5</z> </coordinate>
</site>
</basis>
Expand Down
2 changes: 1 addition & 1 deletion examples/SpinodalDecomposition/config_1_genGrid.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,7 @@
</lattice>
<basis>
<site>
<componentid>0</componentid>
<componentid>1</componentid>
<coordinate> <x>0.5</x> <y>0.5</y> <z>0.5</z> </coordinate>
</site>
</basis>
Expand Down
4 changes: 2 additions & 2 deletions examples/adios/write/config_mix.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -78,7 +78,7 @@
</lattice>
<basis>
<site>
<componentid>0</componentid>
<componentid>1</componentid>
<coordinate> <x>0.5</x> <y>0.5</y> <z>0.5</z> </coordinate>
</site>
</basis>
Expand All @@ -102,7 +102,7 @@
</lattice>
<basis>
<site>
<componentid>1</componentid>
<componentid>2</componentid>
<coordinate> <x>0.5</x> <y>0.5</y> <z>0.5</z> </coordinate>
</site>
</basis>
Expand Down
4 changes: 2 additions & 2 deletions examples/general-plugins/CavityWriter/CavityWriterTest.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -68,7 +68,7 @@ It detects the less dense space around the dense drop as a cavity.
</lattice>
<basis>
<site>
<componentid>0</componentid>
<componentid>1</componentid>
<coordinate> <x>0.5</x> <y>0.5</y> <z>0.5</z> </coordinate>
</site>
</basis>
Expand All @@ -92,7 +92,7 @@ It detects the less dense space around the dense drop as a cavity.
</lattice>
<basis>
<site>
<componentid>0</componentid>
<componentid>1</componentid>
<coordinate> <x>0.5</x> <y>0.5</y> <z>0.5</z> </coordinate>
</site>
</basis>
Expand Down
2 changes: 1 addition & 1 deletion examples/general-plugins/RegionSampling/case01/run01/config.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -52,7 +52,7 @@
</lattice>
<basis>
<site>
<componentid>0</componentid>
<componentid>1</componentid>
<coordinate> <x>0.5</x> <y>0.5</y> <z>0.5</z> </coordinate>
</site>
</basis>
Expand Down
4 changes: 2 additions & 2 deletions examples/general-plugins/SpatialProfiles/CylinderProfileDrop/CylinderOutputDrop.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,7 @@
</lattice>
<basis>
<site>
<componentid>0</componentid>
<componentid>1</componentid>
<coordinate> <x>0.5</x> <y>0.5</y> <z>0.5</z> </coordinate>
</site>
</basis>
Expand All @@ -82,7 +82,7 @@
</lattice>
<basis>
<site>
<componentid>0</componentid>
<componentid>1</componentid>
<coordinate> <x>0.5</x> <y>0.5</y> <z>0.5</z> </coordinate>
</site>
</basis>
Expand Down
2 changes: 1 addition & 1 deletion examples/surface-tension_LRC/2CLJ/liq/T1-508/run01/config.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,7 @@
</lattice>
<basis>
<site>
<componentid>0</componentid>
<componentid>1</componentid>
<coordinate> <x>0.5</x> <y>0.5</y> <z>0.5</z> </coordinate>
</site>
</basis>
Expand Down
2 changes: 1 addition & 1 deletion examples/surface-tension_LRC/2CLJ/liq/T1-691/run01/config.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,7 @@
</lattice>
<basis>
<site>
<componentid>0</componentid>
<componentid>1</componentid>
<coordinate> <x>0.5</x> <y>0.5</y> <z>0.5</z> </coordinate>
</site>
</basis>
Expand Down
2 changes: 1 addition & 1 deletion examples/surface-tension_LRC/C6H12/liq/330K/run01/config.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,7 @@
</lattice>
<basis>
<site>
<componentid>0</componentid>
<componentid>1</componentid>
<coordinate> <x>0.5</x> <y>0.5</y> <z>0.5</z> </coordinate>
</site>
</basis>
Expand Down
2 changes: 1 addition & 1 deletion examples/surface-tension_LRC/C6H12/liq/415K/run01/config.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,7 @@
</lattice>
<basis>
<site>
<componentid>0</componentid>
<componentid>1</componentid>
<coordinate> <x>0.5</x> <y>0.5</y> <z>0.5</z> </coordinate>
</site>
</basis>
Expand Down
2 changes: 1 addition & 1 deletion examples/surface-tension_LRC/C6H12/liq/500K/run01/config.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,7 @@
</lattice>
<basis>
<site>
<componentid>0</componentid>
<componentid>1</componentid>
<coordinate> <x>0.5</x> <y>0.5</y> <z>0.5</z> </coordinate>
</site>
</basis>
Expand Down
2 changes: 1 addition & 1 deletion examples/surface-tension_LRC/CO2_Merker/liq/220K/run01/config.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,7 @@
</lattice>
<basis>
<site>
<componentid>0</componentid>
<componentid>1</componentid>
<coordinate> <x>0.5</x> <y>0.5</y> <z>0.5</z> </coordinate>
</site>
</basis>
Expand Down
2 changes: 1 addition & 1 deletion examples/surface-tension_LRC/CO2_Merker/liq/250K/run01/config.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,7 @@
</lattice>
<basis>
<site>
<componentid>0</componentid>
<componentid>1</componentid>
<coordinate> <x>0.5</x> <y>0.5</y> <z>0.5</z> </coordinate>
</site>
</basis>
Expand Down
2 changes: 1 addition & 1 deletion examples/surface-tension_LRC/CO2_Merker/liq/280K/run01/config.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,7 @@
</lattice>
<basis>
<site>
<componentid>0</componentid>
<componentid>1</componentid>
<coordinate> <x>0.5</x> <y>0.5</y> <z>0.5</z> </coordinate>
</site>
</basis>
Expand Down
21 changes: 17 additions & 4 deletions src/ensemble/EnsembleBase.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -26,16 +26,29 @@ void Ensemble::readXML(XMLfileUnits& xmlconfig) {
Log::global_log->fatal() << "No components found. Please verify that you have input them correctly." << std::endl;
Simulation::exit(96123);
}
_components.resize(numComponents);
// Initialize _components vector using components with ID=0
_components.resize(numComponents, Component(0));
XMLfile::Query::const_iterator componentIter;
std::string oldpath = xmlconfig.getcurrentnodepath();
for(componentIter = query.begin(); componentIter; componentIter++) {
xmlconfig.changecurrentnode(componentIter);
unsigned int cid = 0;
xmlconfig.getNodeValue("@id", cid);
_components[cid - 1].readXML(xmlconfig);
_componentnamesToIds[_components[cid - 1].getName()] = cid - 1;
Log::global_log->debug() << _components[cid - 1].getName() << " --> " << cid - 1 << std::endl;
// Check if cid in valid range
if ((cid < 1) || (cid > numComponents)) {
Log::global_log->error() << "Specified componentid is invalid. Valid range: 1 <= componentid <= " << numComponents << std::endl;
Simulation::exit(1);
}
// Check if cid was not set before
if (_components[cid - 1].ID() == 0) {
// Add component
_components[cid - 1].readXML(xmlconfig);
_componentnamesToIds[_components[cid - 1].getName()] = cid - 1;
Log::global_log->debug() << _components[cid - 1].getName() << " --> " << cid - 1 << std::endl;
} else {
Log::global_log->error() << "Component " << cid << " was already added! ID might be set twice in <components>" << std::endl;
Simulation::exit(1);
}
}
xmlconfig.changecurrentnode(oldpath);

Expand Down
13 changes: 11 additions & 2 deletions src/utils/generator/Basis.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -20,12 +20,21 @@ void Basis::readXML(XMLfileUnits& xmlconfig) {
XMLfile::Query query = xmlconfig.query("site");
Ensemble* ensemble = _simulation.getEnsemble();
std::string oldpath = xmlconfig.getcurrentnodepath();
const size_t numComps = ensemble->getComponents()->size();
for(auto siteIter = query.begin(); siteIter; siteIter++) {
Molecule molecule;
xmlconfig.changecurrentnode(siteIter);
int componentid;
xmlconfig.getNodeValue("componentid", componentid);
molecule.setComponent(ensemble->getComponent(componentid));
if (xmlconfig.getNodeValue("componentid", componentid)) {
if ((componentid < 1) || (componentid > numComps)) {
Log::global_log->error() << "[Basis] Specified componentid is invalid. Valid range: 1 <= componentid <= " << numComps << std::endl;
Simulation::exit(1);
}
} else {
Log::global_log->error() << "[Basis] No componentid specified. Set <componentid>!" << std::endl;
Simulation::exit(1);
}
molecule.setComponent(ensemble->getComponent(componentid - 1)); // Internally stored in vector starting at index 0
Comment on lines +23 to +37
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This kind of code should go in the ensemble->getComponent method and not here.

Copy link
Contributor Author

@HomesGH HomesGH Jun 5, 2024 •
edited
Loading

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I am not sure if I fully understand your intention.
The actual bug fix is changing
ensemble->getComponent(componentid) to ensemble->getComponent(componentid - 1)
since getComponent uses the "internal" ID (starting with 0).

I added the checks to validate the user input via the xml file. This must be done here to print meaningful error messages.

A basic check in the getComponent method is already kind of (only with Debug build) implemented:

ls1-mardyn/src/ensemble/EnsembleBase.h

Lines 81 to 84 in f785526

Component* getComponent(int cid) {
mardyn_assert(cid < static_cast<int>(_components.size()));
return &_components.at(cid);
}

But this will print a more generic, not user-friendly error message.

double r[3];
Coordinate3D sitePosition(xmlconfig, "coordinate");
sitePosition.get(r);
Expand Down
Loading