microphysics and chemistry with krome - uni-hamburg.de · microphysics and chemistry with krome ......

Microphysics and chemistry with KROME

Tommaso GrassiT. Haugbølle (NBI/Starplan), S. Bovino (UniHam), T. Frostholm (NBI/Starplan)

D. Schleicher (Uni Conceptión), J. Ramsey (NBI/Starplan), P. Padoan (ICCUB)

Centre for Star and Planet FormationNiels Bohr Institute

Jul 2017

CENTRE FOR STAR AND PLANET FORMATION

T. Grassi (NBI/STARPLAN) Astrochem Workshop, Jul 2017 1

Microphysics at glance

• Extremely CPU demanding (solving stiff ODEs)

• Many complex and interconnected physical processes

• Needs atomic/molecular and thermochemical data, reaction rate coefficients, . . .


Microphysics at glance/2


KROME

What is KROME?• Python pre-processor creates ad hoc optimized F90 modules

• Chemistry, dust-related physics, cooling, heating, photoionization, . . .

• Open source→ bitbucket.org/tgrassi/krome, (Grassi+2014)

• Highly optimized code, based on “fast” solver (DLSODES)

• Hydrocodes-ready, RAMSES, ENZO, FLASH, GASOLINE, GIZMO, . . .

• 30 papers (CEMP-stars, molecular clouds, galaxies, BHs, AGBs, pp-disks, . . . )


bitbucket.org/tgrassi/krome

KROME bootcamp

kromepackage.org/bootcamp


kromepackage.org/bootcamp

Call KROME


KROME as anetwork explorer

(aka DOCMAKE)


Documentation/1

your network→ DOCMAKE→ HTML documentation→ your server


Documentation/2


Documentation/3


Documentation/4


Documentation/5


Documentation/6

KROME-DOCMAKE as a flexible Python class

try demo @ tools/docmake/test.py


Consistent post-processingwith KROME

(3D-MHD with tracer partcles)


RAMSES+KROME

Molecular cloud• RAMSES-CPH + KROME (see

T. Haugbølle talk tomorrow)• Non-equilibrium H-C-O chemistry

(+CRs, +photo)• Fully coupled cooling/heating

(on-the-fly fine-structure +tables)• > 18 Mcells (now ∼ 100 Mcells)• 4.7 Myr ' 3.5 τd ' 4.5 τff

• ∼ 300 rates, ∼ 40 species• more on Grassi+2017

Species available (non-equilibrium)

C, C+, C−, C2, CH, CH+, CH2, CH+2 , CH+

3 , CO, CO+, e−, H, H+, H−, H2, H+2 , H2O,

H2O+, H+3 , H3O+, HCO, HCO+, HOC+, He, He+, He++, O, O+, O−, O2, O+

2 , OH,OH+, CO (ice), and H2O (ice)


Tracer particles and consistent post-processing/1



MOVIE HERE Preliminary test:kida.uva.2014∼ 3000 particles1.8× 107 (total)e.g. C6H−/C6H vs Av


Tracer particles and consistent post-processing/6C− , C1

−0 , C10H− , C−

3 , C3N− , C−4 , C4H− , C−

5 , C5H− , C−6 , C6H− , C−

7 , C7H− , C−8 , C8H− , C−

9 , C9H− , H− , S− , e− , CN− , O− ,

OH− , C, C10 , C10H, C10H2 , CH2 , H2 , H, C2 , C10N, C9 , C2H2 , C2H3 , C2H4 , CH, C2H5 , C2H6 , CH3 , C3 , C3N, C3O, CO, O, C3P, P, C3S, S, C4H,C4H2 , CCH, C4H3 , C4N, C4P, C4S, C4 , C5H, C5H2 , C5 , C6H, C6H2 , C6N, C6 , C7H, C7H2 , C7 , C8H, C8H2 , C8N, C8 , C9H, C9H2 , CCN, CN, CCO,CCP, CCS, CCl, CH2CCH, CH2CHCN, CH2NH, CH2PH, CH3C3N, CH3C4H, CH3C5N, CH3C6H, CH3C7N, CH3CCH, CH3CH2OH, CH3CHO, CH3CN,CH3COCH3 , CH3NH2 , CH3OCH3 , CH3OH, HCO, CH4 , CO2 , CP, CS, ClO, FE, H2CCN, H2CCO, H2CO, H2CS, H2O, H2S, H2SiO, HC3N, HC5N,HC7N, HC9N, HCCNC, HCCP, HCCSi, HCNCC, HCN, HCOOCH3 , HCP, HCSi, HCl, HF, HNCCC, HNC, HNSi, HPO, HS, MgH, Mg, N2O, NH2CHO, OH,N, NH2 , NH3 , NH, NO, NS, NaH, NaOH, Na, O2 , OCN, OCS, PH, PO, SO2 , SO, SiC3H, SiCH2 , SiCH3 , SiC, SiH2 , SiH3 , SiH4 , SiH, SiN, SiO2 , SiO, SiS,Si, c-C3H2 , c-C3H, c-HCCHSi, c-SiC2 , l-C3H2 , l-C3H, l-SiC3 , CH2CHC2H, C6H6 , F, Cl, HNO, HSSH, HCS, He, N2 , O2H, C7N, C5N, C9N, C11 ,H2CSiCH, H2CN, NC4N, SiC4H, C5O, SiC6H, C7O, SiC8H, C9O, PH2 , SiC2CH3 , HSS, CH3CHCH2 , SiC3H5 , HCOOH, CH2CHCHCH2 , HC4N, HC6N,

HC8N, NC6N, NC8N, NO2 , S2 , NH2CN, PN, SiC4 , SiNC, HOOH, C+ , C1+0 , C11

+ , C9H+ , C10H+ , C2N+ , CNC+ , C10N+ , C3H+ , C2H+3 ,

c-C3H+2 , l-C3H+

2 , C2H+4 , c-C3H+

3 , C2H+5 , l-C3H+

3 , C+3 , C+

4 , C3O+ , C3S+ , C+5 , C5H+ , C4H+

2 , C5H+2 , C4H+

3 , C4N+ , C4S+ , C+2 , C+

6 ,

C6H+ , C+7 , C7H+ , C6N+ , C+

8 , C8H+ , C+9 , C8N+ , H+ , C2O+ , CP+ , CCP+ , C2S+ , CCl+ , C4H+ , C3H3N+ , CH2CN+ , PC2H+ , C2H+ ,

CH+2 , C5H+

3 , C6H+2 , C6H+

3 , C7H+3 , C8H+

2 , C8H+3 , C2H+

2 , C3H+4 , H2COH+ , CH3CHOH+ , C2H5OH+ , CH3CO+ , C2H4O+ , HC2NCH+ ,

C2H6CO+ , CH2NH+2 , CH3NH+

2 , CH3OCH+3 , CH+

3 , CH3OH+ , CH+ , CO+ , CS+ , ClO+ , FE+ , H2CCO+ , HCO+ , H2CO+ , HOC+ , H2S+ ,

HCS+ , H2SiO+ , HC3N+ , SiC2H+ , l-SiC+3 , C3N+ , HCN+ , COOCH+

4 , HCP+ , SiC+2 , CF+ , HNC+ , SiNC+ , HPO+ , Mg+ , NO+ , CH3CN+ ,

NH+3 , HCNH+ , CN+ , N+ , NS+ , Na+ , O+ , OCS+ , PH+ , PO+ , P+ , SO+ , S+ , SiC+

4 , CH2Si+ , SiCH+3 , SiC2H+

2 , Si+ , SiC+ , CHSi+ ,

SiH+2 , SiH+

3 , SiN+ , SiO+ , SiS+ , SiC3H+ , C10H+2 , C3H+

5 , C4H+5 , C5H+

5 , C6H+7 , C7H+

2 , C7H2N+ , C7H+5 , C8H+

4 , C9H+2 , C9H2N+ ,

C9H+3 , C9H+

4 , Cl+ , F+ , H2C5N+ , H2NO+ , H2S+2 , H+3 , H3CS+ , H3O+ , H3S+ , H3S+2 , HC2S+ , HC3NH+ , HC3S+ , HC4S+ , HOCS+ ,

HS+ , HSO+ , HSiO+ , He+ , N2H+ , NH+4 , PCH+

2 , C10H+3 , HC10N+ , C2HO+ , NH+

2 , HC2N+ , C5H+4 , H2C3O+ , C5H3N+ , H3C7N+ ,

C9H3N+ , C6H+4 , C6H+

5 , C4H+4 , CH+

4 , CH+5 , H+

2 , C5H4N+ , C3H3NH+ , HOCO+ , PC2H+2 , PC4H+

2 , PH+2 , PH+

3 , PC2H+3 , SiC4H+ , C7H+

4 ,

H3C3O+ , SiC2H+3 , C4H+

7 , C2H5OH+2 , PC2H+

4 , C2H+6 , C2H+

7 , C2N+2 , H2O+ , HNO+ , HO+

2 , N+2 , NH+ , O+

2 , OH+ , HC3O+ , HC4O+ ,

H2NC+ , C3H6OH+ , PC3H+ , HC4N+ , PC4H+ , C8H+5 , C9H+

5 , H2C4N+ , H3C4NH+ , C4P+ , C5N+ , HC5N+ , HC5O+ , H3C6NH+ , HC6N+ ,

C7N+ , HC7N+ , HC7O+ , C8H4N+ , HC8N+ , C9N+ , C9HN+ , HC9O+ , CH3OH+2 , H2CS+ , SiC3H+

2 , PCH+3 , PCH+

4 , CH3OCH+4 , CH3CNH+ ,

H2CCl+ , CH3NH+3 , S+2 , CH3O+

2 , H5C2O+2 , CO+

2 , SiCH+4 , HN2O+ , NCO+ , HNCO+ , H2Cl+ , HNSi+ , SO+

2 , SiH+4 , HSiNH+ , SiNCH+ ,

SiH+ , SiH+5 , HCl+ , HF+ , H2F+ , HCOOH+ , HS+2 , PN+ , H2C10N+ , H2C6N+ , H2C8N+ , HSO+

2 , NaH2O+ , NaH+2 , H2PO+ , H3SiO+ ,

H3C4N+ , HeH+ , NO+2 , HSiS+ , NH2CH2O+ , NH2CNH+ , HNS+ , HPN+ , HSiO+

2 , SiF+ , PNH+2 , PNH+

3


Summary

KROME

• KROME is a state-of-the-art code for microphysics, open-source and flexible

• self-consistent non-equilibrium microphysics/chemistry

• successfully coupled with 3D simulations (but not only)

• DOCMAKE: HTML documentation (+reproducibility and benchmarking)

Recently add to my wishlist• import astrochemistry

• (Most of) databases access (e.g. KIDA, Hitran, Jena, SWRI, NIST, . . . )• Often-used algorithms (e.g. (n, k)→ Qabs, CO self-shielding, charged dust k, . . . )• Toy models (e.g. constant Tgas, ntot evolution, pp-disk, collapse, . . . )

“All models are wrong but some are useful”


microphysics and chemistry with krome - uni-hamburg.de · microphysics and chemistry with krome ......

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