**Quoted from**: Zheng, Chunmiao. "MT3DMS v5. 3 supplemental user’s guide." *Department of Geological Sciences, University of Alabama, Tuscaloosa, Alabama* (2010). https://hydro.geo.ua.edu/mt3d/mt3dms_v5_supplemental.pdf

There are a couple of significant organizational changes to Version 5 compared to the previous Version 4. First, the Name-File procedure becomes the only method to start a MT3DMS simulation run since v5.0. A Name-File specifies the names of most input and output files used in a model simulation. In addition, it controls the parts of the model program that are active, i.e., the “packages” that are used in the current simulation.

Second, the implicit matrix solver, the General Conjugate-Gradient (GCG) solver, must be used in every simulation since v5.0. In other words, the dispersion, sink/source and reaction terms are now always solved by the implicit finite-difference method, regardless of whether the advection term is solved by the implicit finite-difference method, the mixed Eulerian-Lagrangian methods, or the third-order TVD method.

A major new feature for MT3DMS since v5.0 is the Transport Observation (TOB) Package to save the calculated concentration at any observation location within the model domain and the calculated mass flux at any sink/source location. The calculated values are saved to output files, and optionally, along with the statistics of residuals between the calculated and observed values at the observation locations. The calculated concentrations can be interpolated from the nodal values if the observation point does not coincide with a model node. The calculated mass flux can be defined over any arbitrary group of sink/source cells referred to as a mass flux object.

Another important addition to MT3DMS since v5.0 is the support for the MultiNode Well (MNW) Package (Halford and Hanson, 2002) used by MODFLOW-2000 (Harbaugh et al., 2000) and MODFLOW-2005 (Harbaugh, 2005) to simulate the flow to a well screened over multiple nodes (layers). The MNW Package automatically partitions the total flow prescribed for a MNW into individual nodes (layers) and determines a single head value in the wellbore. Accordingly, MT3DMS computes a single composite concentration for the same wellbore based on the flux-weighted concentrations of the injected fluid (if any) and the flow rates from different layers.

Since Version 5.0, MT3DMS has also added support for more new MODFLOW sink/source packages, including Drain with Return Flow (DRT) and Evapotranspiration with a Segmented Function (ETS), both documented in Banta (2000). The DRT Package in MODFLOW-2000 simulates the re-injection of a portion of the outflow from a drain cell back into the aquifer. MT3DMS assigns the concentration at the outflow cell as that of the re-injected source at the return drain-flow location. The ETS package is supported in a manner similar to the original EVT package.

New since Version 5.1 is the capability to simulate zeroth-order reactions in both single- and dual-domain systems. The standard MT3DMS code prior to v5.1 includes only the first-order kinetic reactions in the Chemical Reaction (RCT) Package. However, zeroth-order reactions may be useful for describing certain types of biogeochemical decay or production. In addition, zeroth-order reactions are needed in direct simulation of groundwater ages (e.g., Goode, 1996) and calculation of parameter sensitivities (e.g., Tsai et al., 2003). Thus starting with Version 5.1, zeroth-order reactions are available as a standard option through the RCT Package in either single- or dual-domain formulation.

Version 5.2 introduces a new option to include component-dependent and/or three-dimensional diffusion coefficients in the transport simulation. Prior to v5.2, the molecular diffusion coefficient can only be specified on a layer-by-layer basis (i.e., one uniform diffusion coefficient per model layer). Moreover, all solute components are assumed to have the same diffusion coefficient. Starting with Version 5.2, users are permitted to specify different diffusion coefficients for different solute components on a cell-by-cell basis (i.e., one diffusion coefficient per model cell, if necessary).

Another new feature since Version 5.2 is the capability to simulate a “recirculation well.” A recirculation well refers to an injection well whose input concentration is not user-specified, but set internally equal to that of extracted water from a pumping well. This option is convenient for modeling some commonly encountered field situations, such as a “dipole” tracer test.

With MT3DMS Version 5.3, it is possible to specify an arbitrarily defined timevarying mass loading source or boundary condition. This new capability allows the complete mass loading distribution to be specified at a source or boundary without being restricted by the definition of stress periods. The new capability is accomplished through a new package called the Hydrocarbon Spill Source (HSS) Package that has been developed for MT3DMS v5.3 (Zheng et al., 2010).

Another significant change to Version 5.3 is the addition of a steady-state transport simulation option. This steady-state transport option may be useful for longterm transport simulation runs in which the concentration field reaches an equilibrium state with the net change in total mass equal to zero. Also, direct groundwater age simulation usually requires a steady-state concentration solution.

Finally, a new section is added to this documentation to describe the use of MT3DMS for heat transport modeling. Heat is increasingly being recognized as an excellent groundwater tracer because of its usefulness in identifying multiple hydrologic processes and recent availability of improved temperature sensors and measurement technologies. The mathematical equivalency between the heat and solute transport equations makes it possible to use MT3DMS directly and efficiently to simulate heat transport with simple variable conversion.