Compile ADM1F

0. Download or clone the ADM1F model to your local computer:

   $ git clone https://github.com/wwtmodels/Anaerobic-Digestion-Models.git
   

   $ cd ADM1F
   

1. ADM1F uses external numerical library package PETSc. First download PETSc:

   $ cd build; git clone -b release https://gitlab.com/petsc/petsc.git petsc
   

   $ cd petsc; git checkout v3.14
   

2. Set PETSC_DIR and PETSC_ARCH in your environmental variables. We suggest to put these lines in your ~/.bashrc or similar files (~/.bash_profile on Mac OS X). Once you add it into the bash file, run source ~/.bash_profile:

   $ export PETSC_DIR=/path-to-my-ADM1F-folder/build/petsc
   

   and:

   $ export PETSC_ARCH=macx-debug
   

   Make sure that ‘adolc-utils’ folder is in the ‘build’ folder.

3. Configure PETSC:

   $ ./configure --download-mpich --with-cc=clang --with-fc=gfortran --with-debugging=0 --download-adolc PETSC_ARCH=macx-debug --with-cxx-dialect=C++11 --download-colpack
   

NOTE: that these are for Mac OSX. If you are installing on a linux machine, then replace clang with gcc. Also, sometimes turning off –with-fc=0 could help with compilation. This step will take awhile.

4. If configuration goes well, you can then compile. This step will take awhile too.:

   $ make PETSC_DIR=/path-to-my-ADM1F-folder/build/petsc PETSC_ARCH=macx-debug all
   

5. After compilation, PETSc will show you how to test your installation (testing is optional).

6. Navigate back to the build folder (cd ../) and compile adm1f:

   $ make adm1f
   

   or:

   $ make
   

7. Set ADM1F_EXE in your environmental variable. Add this line in your ~/.bashrc or similar files (~/.bash_profile on Mac OS X). Once you add it into the bash file, do not forget to source ~/.bash_profile:

   $ export ADM1F_EXE=path-to-my-ADM1F-folder/build/adm1f
   

8. NOTE: There are two versions of the ADMF1: the original version (adm1f.cxx), and the modified version of the model (adm1f_srt.cxx, see ADM1F SRT).

Running ADM1F

1. Make sure that ADM1F_EXE: is not empty (see step 7 from the previous section).:

   $ echo $ADM1F_EXE
   

2. Navigate to the simulations folder and run the model:

   $ $ADM1F_EXE
   
   or using command-line options (see 4 and 5):
   
   $ $ADM1F_EXE -ts_monitor -steady
   

3. Note that adm1f will look for three files ic.dat, params.dat, and influent.dat, which contain the initial conditions (45 values), parameters (100 values), and influent values (28 values), see Inputs/Outputs.

4. The command-line options are:

   • -Cat [val] - mass of Cat+ added [kmol/m3]

   • -Vliq [val] - volume of liquid [m3]

   • -Vgas [val] - volume of liquid [m3]

   • -t_resx [val] -SRT adjustment: t_resx = SRT-HRT, [d] (works only for adm1f_srt.cxx)

   • -params_file [filename] - specify params filename (default is params.dat)

   • -ic_file [filename] - specify initial conditions filename (default is ic.dat)

   • -influent_file [filename] - specify influent filename (default is influent.dat)

   • -ts_monitor - shows the timestep and time information on screen

   • -steady - run as steady state else runs as transient

   • -debug - gives out more details on the screen

5. More command-line options can be found here.

ADM1F SRT

The adm1f_srt.cxx version includes solid retention time (SRT) and other modifications described below. To switch to the SRT version of the model change ‘EXAMPLESC = adm1f_srt.cxx’ , ‘OBJECTS_PF = adm1f_srt.o’, and ‘adm1f: adm1f_srt.o’ in the build/makefile. Then recompile the model (Compile ADM1F, step 6).

• Includes a term (T_resx) in the mass balance to separate the solids retention time from hydraulic retention time.

• Uses the empirical Hill function that describes the inhibition of acetogenesis and hydrogenotrophic methanogenesis by acetic acid with the noncompetitive inhibition model 1 2.

• Describes the inhibition of acetic acid on acetoclastic methanogenesis with the Haldane equation 3 4.

• Includes a adsorption-inhibition term describing the long-chain fatty acid 6 (LCFA) inhibition of LCFA degradation and methanogenesis.

• Includes Arrhenius equations describing the effect of temperature on bioreaction kinetics 5.

• Includes a cation term to simulate the addition of NaOH for pH adjustment.

References

1

Love, N. G., R. J. Smith, K. R. Gilmore, and C. W. Randall. 1999. Oxime inhibition of nitrification during treatment of an ammonia-containing industrial waste. Water Environment Research 71:418–26.

2

Oslislo, A., and Z. Lewandowski. 1985. Inhibition of nitrification in the packed bed reactors by selected organic compounds. Water Research 19:423–26.

3

Haldane, J. B. S. 1930. Enzymes. London: Longmans.

4

Andrews, J. F. 1968. A mathematical model for the continuous culture of microorganisms utilizing inhibitory substrates. Biotechnology and Bioengineering 10:707–23.

5

Novak, J. T. 1974. Temperature-substrate interactions in biological treatment. Journal, Water Pollution Control Federation 46:1984–94.

6

Palatsi, J., Illa, J., Prenafeta-Boldú, F.X., Laureni, M., Fernandez, B., Angelidaki, I., Flotats. X. 2010. Long-chain fatty acids inhibition and adaptation process in anaerobic thermophilic digestion: Batch tests, microbial community structure and mathematical modelling. Bioresource Technology. 101, 7, 2243-2251.