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

 

Biodegradation

!.... 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  
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  • Dear Guiyao,

    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.

    Regards,

    Alfredo

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    • Alfredo Battistelli Very appreciated. This guidance is very helpful! I will seriously study the relevant literature. Thanks again.

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