USG-Transport Version 1.1.0 - Updates to USG-Transport Code and documentation:
----------------------------  ------------------------------------------------

Updated CLN input structure: (changed hardwired input to read as an OPTION to be bacaward compatible with MF-USG files). Also included output formatting for transport in CLNs; and included rectangular type CLNs.
------------------------------------------------------------------------------------------------
 
Added capabilities and/or input instructions for the following packages: 

	Transient IBOUND (TIB) Package updated for transport in GLO2BASU1
	Updated TVM package of Damian Merrick to include transport parameters
	Recharge (RCH) Package with Transport - include non-zero inflow concentrations 
	Segmented Evapotranspiration (ETS) Package with Transport
	Drain with Return Flow (DRT) Package
	Sink with Return Flow (QRT) Package 
	Added "SOLVEACTIVE" option in Sparse Matrix Solver (SMS) Package to only send active nodes to linear solvers. 
	Added "DAMPBOT" option in Sparse Matrix Solver (SMS) Package (similar option in MODFLOW-NWT helps convergence). This was added to Version 1.4 of MODFLOW-USG also (but as the default).  
	Included the "SHARED" option in opening files from the NAME-file to allow Parallel runs to access common files. 
	Include "MERGE_BED_K1" option in RIV package to incorporate leakance of river-bed and of GW cell (from river bottom to cell center) in calculations

-------------------------------------------------------------------------------------------------

Fixed bugs/documentation errors for the following packages: 

	Documentation for ICBUND input fixed (when ICBNDFLG is zero it is read)
	BTN Package: Check for input errors of porosity (being less than Sy of transient flow run); 
	BTN Package: Fixed bug if transient flow situation for setting SC2 for confined cases
	GNCN Package: Fixed allocate issue when ISYMGNCn=1 and also for when I2Kn=0 
	WEL Package: fixed bug where NNPWCLN (# of non-parameter CLN wells) was getting reinitialized incorrectly
	SMS Package: bottom dampening feature of NWT was added to Version 1.4 of MODFLOW-USG and is updated here (was added incorrectly)
	CLN Package: Included the "TRANSIENT" option to be backward compatible with MODFLOW-USG v.1.4. The TIB (Transient Ibound) Package can do this also. 
	CLN Package: Included option for "PRINTIAJA" available in MODFLOW-USG v.1.4. 



-------------------------------------------------------------------------------------------------
USG-Transport Version 1.2.0 - Updates to USG-Transport Code and documentation:
----------------------------  -------------------------------------------------------------------

	Added to documentation: Input instructions for transport within CLN. 

	DDF Package: Added option to use vertical thickness weighted averaging for computing z, h, and density at interface instead of just arithmetic averaging. Included documentation for flag ITHICKAV to indicate if arithmetic averating (=0) or vertical thickness weighted averaging would be used in a simulation.

	DDF Package: Included option for implicit update of the head in the density update term. Included documentation for flag IMPDD to indicate explicit or implicit treatment of head in the density term.

Fix saturation initialization for CLN cells in glo2bas1u; 
Fix bug in anisotropic horizontal conductivity formulation (use flux not K in direction of flow)
Fix underrelaxation bug in glo2sms-u1; 
Initialize SC2 in gwf2bcf-lpf-u1; 
Fix budget output in gwf2sfr7u1; 
Fix budget outputs for transport in gwt2bndsu1; 
Fixed bugs in dual porosity transport when dual porosity flow is not run in gwt2dptu1; 
Updated Version number in mfusg
 
Fixed error in dispersion term with updates to code (Glo2btn1u.f) and document. 
Fixed error in WEL, STR, SFR and GHB computation of flux balance for IFMB=1 option in transport. 

--------------------V 1.2.1-4 bug fixes:	
Sorted out CLN and GWF mass flux output for transport - CLN mass flux saved to unit number specified with option SAVECLNMAS (in CLN input file), GWF output on unit IBCTCB (in BCT input file); 
Added FULLYDRY option to Richards equation (Sr is only applied to Kr and not to retention curve); 
Fixed bug in dual porosity flow (was using retention parameters from mobile instead of immobile domain if solving Richards Equation); 
For dual porosity transport with single porosity transient flow needed scaling only for IFRAHK option; 
Fixed CBC boundary flow output for DRT and QRT packages for DRTs and QRTs in GWF and CLN domain; 
Fixed situation where porosity is less than Sy for dual porosity transport with single porosity flow where flow properties are for entire volume (fracture plus matrix)
Fixed initialization error in PCGU
Fixed error in AUX indexing for concentrations

--------------------V 1.3.0 enhancements and bug fixes: 

Fixed FASTFORWARD Option to be flexible (did not work previously if all steps were not saved). 
Added formulation and input instructions for Dual Porosity Flow (DPF) package. 
Added formulation and input instructions for Specified Gradient Boundary (SGB) Package. 
Updated capability in CLN for well efficiency computations is included as an input document update.
Change output TEXT in binary file to identify species for multispecies run (BCT and DPT); 
Fixed LAK package output of budget terms; 
For BCT boundaries, default to zero conc for BCs where AUX is not provided for a species;
Added capability of transport with the LAKE Package (by Dr. Vivek Bedekar at SSPA)

--------------------V 1.4.0 enhancements and bug fixes: 

BCT Package: Included transport of heat as the HEAT option. Updated documentation of BCT to include heat as one of the transport components. 
Included immobile components after the mobile ones in preparation for geochemical reactions. 
Added options for output of binary concentration files to different files instead of just one CON file. 
All these options are documented with the HEAT option package. 
Included ability to add concentration (temperature for thermal component) or mass (heat for thermal component) to the return-flow portion of QRT and DRT packages when solving transport; updated document for QRT and DRT

DRT: Included option for "GHB with return of fixed Q" to help with borehole heat exchanger (BHE) simulations. 

EVT: fixed indexing bugs with zones

TVM v2 Package documentation has been added. THe TVM package was developed by Damian Merrick with solute transport additions by Vivek Bedekar. 

--------------------V 1.5.0 enhancements and bug fixes: 

BCF-LPF: Included tabular input for retention curves for Richards Equation (integrated RE solution needs to be removed). 
Update the "Unsaturated Flow Solution" section of document to include tabular input for Richards equation. 

LAK: Compact budget output of LAKE SEEPAGE did not include all cells due to lake conductivity if-check which was moved to before the II==2 if-check. Flux is zeroed for each lake cell so no residual or undetermined values are written. LAK fixed indexing bug for horizontal connection

CLN Turbulent FLow: Updated document to include details of turbulent flow formulations. 

BCT: Added ITRNSP = 3 option (SS flow w SPs only for transient BCs; BTN fixed dual porosity PCN mass balance component, added time weighting option; added chain decay option; fixed dispersion bug that got formed in V1.3.0; included a MULTIFILE concentration output so each species is written to a separate file instead of all in one file. 

fixed bug in ETS, EVT, RCH transport (to include MCOMPT with temperature input and processing); QRT, DRT fixed initialization bug;  

DPT: Dual porosity transport updated to include heat equation and chain decay. Document updated also. 

WEL: Included WELLBOTTOM  option to read bottom-hole elevation of sink instead of using cell bottom only. 

--------------------V 1.6.0 enhancements and bug fixes: 

BCT: Include ITRNSP=2 option to run transport from previous flow run results. Fixed bug in MULTIFILE option. 
BAS: Added FASTFORWARDC option in BAS to restart transport
CLN: Include documentation of CLN coordinates to assist with placement of CLN cells in GUIs; Include BHE details in CLN cells for heat transport due to conduction through BHE wall, different BHE fluid thermal properties from pore water; and boundary layer within the CLN (convective heat transfer). 
SMS: Added option to SHIFT the RHS and solution vectors before/after linear solve. 

Bug fixes: Fixed MULTIFILE bug for CLN domain , fixed indexing bug in LAKE transport BD; undefined variable IOUTS in MFUSG, Check MXITER of SMS versus restes in OC and stop if OC is larger. Avoid dispersion singularities; add write statement for sequential transport iteration; 

--------------v 1.6.1 fixes bug on MXITER reset in OC package

--------------------V 1.7.0 enhancements and bug fixes: 

QRT: Added transient FHB type hydrogoraph table input for QRT;
FHB: Deallocate variables; include document for FHB for stepped representation of hydrograph
BCT: Solubility limit computations have been added through the option SOLUBILITY. 
BCT: Options for running transport after completion of a flow run (ITRNSP = 2 OR 4) have been revamped from V 1.6.0 where it was implemented. Instead of reading the CBC files, the options now skip the flow solution, read the HDS file, compute all fluid fluxes and mass balances, and enters the BCT packages for transport solution at each time step as needed. 
BCF/LPF: Included alternate compressible storage calculation option (kicks in from zero to full over a small epsilon interval from top instead of changing with grid saturation from zero to full)
DDF: Dual domain flow output of heads bug was fixed (used HNNEW instead of HNEWIM). 
BCT Document: Document for convective heat transfer (BCT Package) shows table calculated using 1 m for characteristic length. The diameter of the BHE tube should be used and the table was updated accordingly. 

--------------------V 1.8.0 enhancements and bug fixes: 

WEL: added WELLBOT option to have different WELLBOT from cell bottom (but not below cell bottom). 
MDT: added matrix diffusion routines (and document) using analytical solutions for matrix diffusion.
BCT: added ITRNSP = 5 option to bypass flow and only run transport using initial concentrations in mobile domain as prescribed concentration boundaries (good for dual porosity or matrix diffusion initialization to load up the matrix with solutes)
SMS: added truncated Newton option (by Damian Merrick).  
Initialization updates in LAK (CNDFC1=0), BAS (TMAXAT default set incorrectly), BTN (MASLOPR = 0; REPLACE status for MULTIFILE option), BCF (IKVFLAG=1 for INLPF NE.0). 
Expanded capability of FASTFORWARD and FASTFORWARDC to start / continue a simulation from an intermediate stress period or time step by reading heads and concentrations from a binary file of a previous run (did not previously work with adaptive time stepping or if binary output was not written at every time step, but does now). 

--------------------V 1.9.0 enhancements and bug fixes: 

Made small changes to source code to make it compatible with other compilers; Fixed CLN-GW CBC flux term bug; Commented out Newton on turbulent gradient function term in CLN-CLN flow (works better with Picard on that term for very flat gradients); Allow CHD to run with head below bottom of cell; fix OPTIONS in LAKE package; pass undefined NCOUNDUITYP into SMS; Fix DDREF for CLN domain; Include DOUBLE PRECISION outputs for heads, drawdowns and concentrations (and associated time variables) in binary files; INCLUDE DOUBLE PRECISION inputs for heads (and associated time variables) from binary files; BAS package input instructions included in documentation (where double precision I/O OPTIONS are provided)' Expand ITRNSP = 5 capability (see Matrix diffusion chapter for details) to include multiple stress periods for initialization of matrix domain in simulating matrix diffusion transport. 

--------------------V 1.9.1 enhancements and bug fixes: 

Made minor WRITE and FORMAT statement changes for compatiblity with GFortran; Fixed bug in reading binary files with Readbin4 or Readbin8; Open binary/unformatted files using FORM specifier from openspec.inc; provide output for Autoflowreduce in QRT package; For ETS and EVT, ETFACTOR allowing solute to leave with water did not work for NETSOP (or NEVTOP) = 2 (highest active layer option) and that is fixed to work with all options. In TIB, skip activating cell if already active (do not use AVHEAD or HEAD to reset heads); 

GLO2BTNU1: Add code to build TEXT with species number for output files for multiple species simulations; changed formula for computing V for dispersion term (does not affect rectangular grid results); changed cross-dispersion term to connection-by-connection calculation (does not affect rectangular grid results); Fixed bug of heat conductivity term not getting initalized; Use a 1e-3 saturation in transport storage term if fully dry for stability.
 
GLO2BASU1: Add check for both binary and unformatted file in SGWF2BAS8OPEN - though may need only unformatted now with openspec.inc changes (?). Also comment out duplicated DEALLOCATE statements for NOCVCO and ICONCV in GWF2BAS7U1DA. 

--------------------V 1.10.0 enhancements and bug fixes: 
BOOTSTRAPPING option included; fix bug on initialization of heat conductivity term; Override IDFLOW for ITRANSP=2 if flow is SS and KPER and KSTP are both equal to one. Reorganize the document to first discuss theory for USG-Transport BTN modules, then theory for other add-on modules to MODFLOW-USG, followed by example problems for additions to MODFLOW-USG, followed by input instructions for capabilities of USG-Transport that need additional documentation for the input instructions than for MODFLOW-USG. 

--------------------V 2.1.0 enhancements and bug fixes: 
BCT and DPT: Include Langmuir isotherm for retardation on soil; Include option to use only saturated zone adsorption ONLY_SATADSORB using saturations from 1st time step of 1st stress period. Include air-water interface adsorption (for PFAS compounds) BUT not yet the decay or generation terms on a-w interface; Separates out mass balance components for storage on water versus storage on soil (was lumped previously but now with air-water interface adsorption, the CBB files and mass balance summary in LST file have separate mass outputs for solutes in water and on soil). 

BCT: Fixed bug in CNST H Mass Flux output for IBD=2 (was outputing all cells instead of only the const. head cells)

BCF-LPF: van Genuchten relative permeability can be used on any cell by setting the Brooks-Corey exponent to a negative value. 

DIS: Include TRTOSS option in addition to TR/SS, to indicate a "transient to steady-state" stress period.  TRTOSS is followed by a real number indicating the fraction of storage change compared to total mass balance. 

MDT: skip computations for inactive portions of domain. 

RCH / EVT: update documentation to include seepage face and time series inputs

SMS: Include TRUNCATEDNEWTONCUTOFF option for user input to the cutoff value (superscedes default value of 0.9) 

Other bug fixes: Bugs fixed with writing transport CBB outputs for RIV (with IBD=1), SFR (header had NEQS not NODES), SGB (uninitialized). Bug fixed in FASTFORWARDing concentrations. MULTIFILE conc. outputs now includes structured grids; deallocated some arrays not done before

--------------------V 2.2.0 enhancements and bug fixes: 
Included IHM (Integrated Hydrologic Model) integration capabilities. Separate out Theory Document from Input Instructions; Include all input instructions from MF-USG into one comprehensive input document

BAS: Initialize ICLNHD and IDPFHD for FASTFORWARD capability; Use compiler directive for "Buffered" instead of in open statement;  

BCF: Fix alternate storage bug;

BCT: Fixed bug in A-W interface adsorption area calculation when AMAX is used in BCT and DPT; Fix initial mass calculation for mass on A-W interface; Include "remaining mass" calculation at every time step (output to LST file); Redo prescribed head boundary in transport (USe CHD only and no more IBOUND=-1 backdoor support). 

DDF: Fixed undefined OMEGA in density

QRT: bug in QRT CBC output for IBD=1 fixed. 

SFR: Fix uninitialized indices IL, IR, IC for structured grid output in SFR; some precision cleanups;

DPF: Fix undefined variables for ALTSTO in FM and IDPOUT in drawdown output

--------------------V 2.2.2 enhancements and bug fixes: 
Using BINARY instead of UNFORMATTED and SEQUENTIAL instead of STREAM for Intel Fortran in Openspec.inc. Can comment out this line and use UNFORMATTED and STREAM for GNU compilers in OPENSPEC.INC. There were file opening compatibility issues with Intel Fortran UNFORMATTED open statement otherwise. 

BCF: computing compressible storage reduction with old saturation when cell dries up (instead of new saturation) for a mass balanced formulation.  

BCT: Fixed initialization for PFAS Iarea-fn=2 option for air-water interface adsorption; included cell by cell output of mass of a species added up in water, soil and air-water interface adsorbed phase (if exists), to a binary file in similar formats to concentration output (all to a single file). 

Fixed inconsistencies in input instructions in the air-water interface input instructions.  

--------------------V 2.3.0 enhancements and bug fixes: 
Minor updates to the documentation. 

Using OPENSPEC.INC to provide file opening formats. All binary output files opened using OPENSPEC to keep consistency with formats (UNFORMATTED, BINARY, STREAM, SEQUENTIAL, etc). 

BCT: option included to write mass of each component species to a binary file (same format as for concentration output). If MULTIFILE option is used for output of binary concentrations then it will also be used for output of binary file with component mass in each cell. MULTIFILE also extended to AI1 and AI2 matrices of MDT module. Fix bug for solving solute and heat simultaneously (refill ADMAT to accommodate heat conduction separately from diffusion for solution and mass balance).

DDF: Added density storage term of flow into storage term for output in binary file to be compatible with FloPy and other MODFLOW tools 

CLN: Fixed undefined variable in CLN-GWF interface (affects solving Richards Equation with CLN)

--------------------V 2.4.0 enhancements and bug fixes: 
BCF: added option RICHARDS_HP to have initial head input be pressure head instead of hydraulic head (since many codes use pressure head to solve Richards' Equation.

BCT: Fixed bug in compressible storage term - shows up with high SF1 value - should be like a decay term where it is lost to compressible storage; Fixed writing transport budget terms (some terms were being written to flow budget file); 

AWI: Added modules for decay and generation (zeroth order and first order) on air-water interface; Fixed bug in area_AWI table calculation for tabular area input; removed option IAREA_FN = 3 which was incorrect. 

QRT / DRT with transport: added options for fixing the value of concentration or mass of return flow, and option for reducing concentration or mass to a prescribed amount (if over that prescribed amount) before returning the water. 

HFB: Added option to have transient HFBs. 

Updates to documentation as needed for the changes above. 

--------------------V 2.5.0 enhancements and bug fixes: 

SFR: Fixed stream budget on segments bug in SFR. 

AWI: DPT IAW_adsorbim was not being called in some subroutines from the module (used IAW-adsorb instead)

DPT: Fixed unit number and bug in multifile output for concentrations of immobile domain. 

SMS: Added option to write a separate solver output file. 

TVM: Fixed mass balance error when only one of SS or SY was changed by TVM. 

--------------------V 2.6.0 enhancements and bug fixes: 
Document updated to include EVT discussion for Richards' Equation simulations. Document updated on PFAS discussion. 

HFB: Fixed uninitalized thickness when staggered connection (IVCVON = 2)

BCT: Transport output for mass, RCH, EVT and ETS mass balances were written every time step. Gave control on these outputs (will be written when CON is written). Also, Changed binary output for mass to CON and HDS format (was in budget format). Change is only for unstructured grids. Need to change for structured. BINARY MASS OUTPUT IS NOT DONE YET For CLN or dual porosity.  

BCT: Fix bug in starting transport from, a prerun flow run, where code was using PERTIM and TOTIM from saved file instead of from input (saved file could have odd PERTIM and TOTIM for steady-state run which could mess up steppig through transport). 

BCT: Added Variable_Solubility option for if it varies in space - NOT DONE YET for dual porosity matrix part. 

DRT: Removed check in DRT for return flow proportion to be between 0 and 1 when GHB-Q condition is simulated. 

DRT: Extended capability to include multiple return flow cells per drain cell to allow uniform distribution of drained water onto spreading grounds or ag field (like QRT capability). 

BCF: returned to using SNEW instead of SOLD for compressible term scaling. Also, allocating error fixed. 

SFR: Fixed index on mass balance looping to fill BUFF. 

BAS: for steady-state flow, delt for transport does not depend on iteration count; 

SMS: do not write if isolverfile = 0;

TVM2: passed KPER into HFB7MC

--------------------V 2.6.1 enhancements and bug fixes: 

Deallocated some variables that were not done before 

--------------------V 2.6.2 enhancements and bug fixes: 

Deallocated some more variables that were not done before 

Fixed indexing in LAK package

---------------------


 