Merge retQSS into the new solver version.

[joaquinffernandez]

No description provided.

[joaquinffernandez]

As a first step we should merge the current code in https://gitlab.com/lukius/retqss/-/tree/master and check that everything works.

[joaquinffernandez]

Current output for model/scripts/run.py covid19:

Exit code: 0
gcc -I/home/joaquin/work/qss-prs/qss-solver/src/engine/ -I/home/joaquin/work/qss-prs/qss-solver/src/lib/retqss -I/home/joaquin/work/qss-prs/qss-solver/packages -I/home/joaquin/work/qss-prs/qss-solver/src/usr/include -c /home/joaquin/work/qss-prs/qss-solver/packages/pkg_retQSS_covid19.c -o /home/joaquin/work/qss-prs/qss-solver/packages/pkg_retQSS_covid19.o -Wall -g -msse2 -mfpmath=sse -rdynamic -L /home/joaquin/work/qss-prs/qss-solver/lib -Wl,-rpath=/home/joaquin/work/qss-prs/qss-solver/lib -L /home/joaquin/work/qss-prs/qss-solver/lib -Wl,-rpath=/home/joaquin/work/qss-prs/qss-solver/lib -L /home/joaquin/work/qss-prs/qss-solver/usr/lib -lqssd -ltimestepd -lretqssd
/home/joaquin/work/qss-prs/qss-solver/packages/pkg_retQSS_covid19.c: In function ‘__retQSS_covid19__getContactsCount’:
/home/joaquin/work/qss-prs/qss-solver/packages/pkg_retQSS_covid19.c:13:9: warning: implicit declaration of function ‘covid19_getContactsCount’ [-Wimplicit-function-declaration]
 count = covid19_getContactsCount(particleID);
         ^~~~~~~~~~~~~~~~~~~~~~~~
/home/joaquin/work/qss-prs/qss-solver/packages/pkg_retQSS_covid19.c: In function ‘__retQSS_covid19__interactWithParticlesInVolume’:
/home/joaquin/work/qss-prs/qss-solver/packages/pkg_retQSS_covid19.c:21:5: warning: implicit declaration of function ‘covid19_interactWithParticlesInVolume’ [-Wimplicit-function-declaration]
 _ = covid19_interactWithParticlesInVolume(time,particleID,volumeID,closeContactProbability,&incubationStartTime[0]);
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

/home/joaquin/work/qss-prs/qss-solver/packages/pkg_retQSS_covid19.c: In function ‘__retQSS_covid19__processContacts’:
/home/joaquin/work/qss-prs/qss-solver/packages/pkg_retQSS_covid19.c:230:18: warning: implicit declaration of function ‘covid19_traceContacts’ [-Wimplicit-function-declaration]
 tracedContacts = covid19_traceContacts(level,time,particleID,&contactTimeArray[0]);
                  ^~~~~~~~~~~~~~~~~~~~~
/home/joaquin/work/qss-prs/qss-solver/packages/pkg_retQSS_covid19.c: In function ‘__retQSS_covid19__setContactsTracingConstants’:
/home/joaquin/work/qss-prs/qss-solver/packages/pkg_retQSS_covid19.c:238:10: warning: implicit declaration of function ‘covid19_setContactsTracingConstants’ [-Wimplicit-function-declaration]
 status = covid19_setContactsTracingConstants(level,desiredContactsCount,contactRememberedProbBase,contactRememberedProbDecay,delayTimeMin,delayTimeMax,successProbability);
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/joaquin/work/qss-prs/qss-solver/packages/pkg_retQSS_covid19.c: In function ‘__retQSS_covid19__setContagionConstants’:
/home/joaquin/work/qss-prs/qss-solver/packages/pkg_retQSS_covid19.c:246:5: warning: implicit declaration of function ‘covid19_setContagionConstants’ [-Wimplicit-function-declaration]
 _ = covid19_setContagionConstants(susceptibleStatus,unknownTrackingStatus,presymptomaticStatus,presymptomaticContagionProbability,symptomaticStatus,symptomaticContagionProbability,asymptomaticStatus,asymptomaticContagionProbability,particleToParticleInfectionProbability);
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/joaquin/work/qss-prs/qss-solver/packages/pkg_retQSS_covid19.c: In function ‘__retQSS_covid19__setRandomDiseaseOutcomesProperties’:
/home/joaquin/work/qss-prs/qss-solver/packages/pkg_retQSS_covid19.c:254:8: warning: unused variable ‘_efficiencyFactor’ [-Wunused-variable]
 double _efficiencyFactor;
        ^~~~~~~~~~~~~~~~~
/home/joaquin/work/qss-prs/qss-solver/packages/pkg_retQSS_covid19.c: In function ‘__retQSS_covid19__setUpParticles’:
/home/joaquin/work/qss-prs/qss-solver/packages/pkg_retQSS_covid19.c:307:5: warning: implicit declaration of function ‘covid19_setUpParticles’ [-Wimplicit-function-declaration]
 _ = covid19_setUpParticles(N,cellEdgeLength,gridDivisions,&x[0]);
     ^~~~~~~~~~~~~~~~~~~~~~
make: *** [/home/joaquin/work/qss-prs/qss-solver/build/covid19/covid19.makefile:21: /home/joaquin/work/qss-prs/qss-solver/packages/pkg_retQSS_covid19.o] Error 1

[joaquinffernandez]

Current status:

[Fri Apr 19 15:16:39 2024] (t=0.00) 
[Fri Apr 19 15:16:39 2024] (t=0.00) 
retQSS exception: Invalid volume ID: 1

Aborting retQSS simulation.
Aborted (core dumped)

The model compiles correctly, I need to check if the configuration error comes from a library error from the merge or if I'm missing something regarding configuration files.