Code: modify the Biodegradation module in TMVOC
Hi everyone! I am trying to modify the code of the biodegradation module in TMVOC, and add the microbial growth equation into the code. How can I modify the code related to microbial degradation? At present, our team is trying to build the knowledge system of the microbial field, welcome all the interested scholars to communicate actively! Thank you!
ALAM(Microbial degradation factor)
! REASSIGN OCKM AND ALAMM DO I=1,NHC OCKM(1+NCG+I)=OCKM(I) ALAMM(1+NCG+I)=ALAMM(I) ENDDO DO 1100 I=1, NCG OCKM(1+I)=OCKMN(I) ALAMM(1+I)=ALAMMN(I) DO 1101 J=1,NCGEOS IF(NCGINP(I).EQ.NCGNAME(J)) THEN AMWTM(NHC+I)=GAMW(J) PCRITM(NHC+I)=GPCRIT(J) TCRITM(NHC+I)=GTCRIT(J) OMEGAM(NHC+I)=GOMEGA(J) CPAM(NHC+I) = GCPA(J) CPBM(NHC+I) = GCPB(J) CPCM(NHC+I) = GCPC(J) CPDDM(NHC+I)= GCPDD(J) HCNCGOIL(I)= HCGASOIL(J) NCGCODE(I)=J GOTO 1100 ENDIF 1101 CONTINUE !.....IF THE REQUESTED NCG IS NOT INCLUDED IN THE 'DATA BANK', ! THEN PRINT A MESSAGE AND STOP THE RUN !! IF(PARALLEL_IOPROCESSOR()) WRITE(36,910) NCGINP(I) 910 FORMAT(/' ***** NCG NAME = ',A10, & & ' ***** IS NOT AVAILABLE IN THE INTERNAL NCG DATA BANK:', & & ' CHECK THE INPUT FILE OR INCLUDE THE NEW NCG !!!!'//) STOP 1100 END DO ! NKMN=NK-NTR IF(NTR.GT.0) THEN !.....INITIALIZE DISSOLVED SOLIDS CONCENTRATIONS IN GAS AND NAPL DO I=1,NTR CMOLEFG(NKMN+I)=0.D0 CMOLEFO(NKMN+I)=0.D0 END DO ! ASSIGN DISSOLVED SOLID PROPERTIES TO LOCAL EOS ARRAYS DO I=1,NTR AMWTM(NKMN+I)=AMWTMS(I) OCKM(NKMN+I)=OCKMS(I) ALAMM(NKMN+I)=ALAMMS(I) END DO ENDIF ! !.....ASSIGN WATER PROPERTIES AMWTM(NKMN)=AMS PCRITM(NKMN)=221.2D0 TCRITM(NKMN)=647.3D0 OMEGAM(NKMN)=0.344D0 CMOLEFW(NKMN)=0.D0 CMOLEFG(NKMN)=0.D0 CMOLEFO(NKMN)=0.D0 OCKM(1)=0.D0 ALAMM(1)=0.D0 ! !.....ASSIGN BIODEGRADATION REACTION RELATED VARIABLES BMW(1)=AMWTM(NKMN) L=1 DO 95 L=2,NK IF(L.LE.1+NCG) THEN !.....dealing with NCGs BMW(L)=AMWTM(NHC+L-1) ELSEIF(L.GT.1+NCG.AND.L.LE.1+NCG+NHC) THEN !.....dealing with VOCs BMW(L)=AMWTM(L-1-NCG) ELSE !.....dealing with NTRs BMW(L)=AMWTM(L) ENDIF 95 CONTINUE
!.... initialize substrate concentrations in the aqueous phase for ! biodegradation reaction !.... Initialize microbial mass per unit volume porous medium if(kcyc.eq.0 .and. IAEROB.gt.0) then phisrho=phi(n)*par(nloc2l+1)*par(nloc2l+4)*AMWTM(nk-ntr)*1.d-3 do 100 L=1,NK Xaq(Nloc+L)=PAR(NLOC2L+NB+L) 100 continue ! DO 110 I=1,NPOP BMM(N,I)=BA(N,I)*phisrho 110 CONTINUE endif END IF
biodegradation capabilities were added to TMVOC V.1.0 (Pruess and Battistelli, 2002) in a version called TMVOCBio, which was not distributed at the time. References for that version are:
- Battistelli A. (2003). Modeling the biodegradation of organic contaminants with TMVOCBio. Proceedings TOUGH2 Symposium, May 12-14, 2003, Berkeley (CA).
- Battistelli A. (2004). Modeling biodegradation of organic contaminants under multiphase conditions with TMVOCBio. Vadose Zone Journal, Vol. 3, n.3, 875-883.
More recently, the same biodegradation capabilities have been included in TMVOC under the iTOUGH2 simulator and finally in TOUGH3:
Jung Y., Battistelli A. (2017). User’s Guide for Biodegradation Reactions in TMVOCBio. Lawrence Berkeley National Laboratory, Report LBNL-1005179.
The above references give a quite complete description of the biodegadation model implemented, the assumptions and approximations involved, and about the numerical approach followed to solve the biodegradation equations in the presence of multiple degradation processes, with multiple substrates, electron acceptors, microbial populations, etc.
I guess it would be easier to use the already available TMVOC+Biodegradation capabilities, rather than rewriting the code. It can, of course, be improved
As an example, the capability to model the biodegradation in coastal aquifers and in the presence of cometabolic processes has not been included in the latest distributed TMVOC version. It was coded in a non distributed version provisionally called TMVOC V.2.0:
- Battistelli A. (2006). Modeling organic spills in coastal sites with TMVOC V.2.0. Proceedings TOUGH2 Symposium, May 15-17, 2006, Berkeley (CA).
- Battistelli A. (2008). Modeling multiphase organic spills in coastal sites with TMVOC V.2.0. Vadose Zone Journal, Vol.7, pp. 316-324.