epanet-plus 0.0.1__cp310-cp310-macosx_10_9_x86_64.whl

epanet-msx-src/msxqual.c

@@ -0,0 +1,2011 @@
+/******************************************************************************
+**  MODULE:        MSXQUAL.C
+**  PROJECT:       EPANET-MSX
+**  DESCRIPTION:   Water quality routing routines.
+**  COPYRIGHT:     Copyright (C) 2007 Feng Shang, Lewis Rossman, and James Uber.
+**                 All Rights Reserved. See license information in LICENSE.TXT.
+**  AUTHORS:       See AUTHORS
+**  VERSION:       2.0.00
+**  LAST UPDATE:   08/30/2022
+******************************************************************************/
+
+#include <stdio.h>
+#include <string.h>
+#include <math.h>
+#include <stdlib.h>
+
+#include "msxtypes.h"
+//#include "mempool.h"
+#include "msxutils.h"
+#include "dispersion.h"
+
+// Macros to identify upstream & downstream nodes of a link
+// under the current flow and to compute link volume
+//
+#define   UP_NODE(x)   ( (MSX.FlowDir[(x)]==POSITIVE) ? MSX.Link[(x)].n1 : MSX.Link[(x)].n2 )
+#define   DOWN_NODE(x) ( (MSX.FlowDir[(x)]==POSITIVE) ? MSX.Link[(x)].n2 : MSX.Link[(x)].n1 )
+#define   LINKVOL(k)   ( 0.785398*MSX.Link[(k)].len*SQR(MSX.Link[(k)].diam) )
+
+//  External variables
+//--------------------
+extern MSXproject  MSX;                // MSX project data
+
+//  Local variables
+//-----------------
+//static Pseg           FreeSeg;         // pointer to unused pipe segment
+//static Pseg           *NewSeg;         // new segment added to each pipe
+//static char           *FlowDir;        // flow direction for each pipe
+//static double         *VolIn;          // inflow flow volume to each node
+//static double         **MassIn;        // mass inflow of each species to each node
+//static double         **X;             // work matrix
+//static char           HasWallSpecies;  // wall species indicator
+//static char           OutOfMemory;     // out of memory indicator
+//static alloc_handle_t *QualPool;       // memory pool
+
+// Stagnant flow tolerance
+//const double Q_STAGNANT = 0.005 / GPMperCFS;     // 0.005 gpm = 1.114e-5 cfs
+extern double Q_STAGNANT;   // Already defined in quality.c (EPANET)
+
+//  Imported functions
+//--------------------
+int    MSXchem_open(void);
+void   MSXchem_close(void);
+extern int    MSXchem_react(double dt);
+extern int    MSXchem_equil(int zone, int k, double *c);
+
+extern void   MSXtank_mix1(int i, double vin, double *massin, double vnet);
+extern void   MSXtank_mix2(int i, double vin, double *massin, double vnet);
+extern void   MSXtank_mix3(int i, double vin, double *massin, double vnet);
+extern void   MSXtank_mix4(int i, double vIn, double *massin, double vnet);
+
+
+
+int    MSXout_open(void);
+int    MSXout_saveResults(void);
+int    MSXout_saveFinalResults(void);
+
+void   MSXerr_clearMathError(void);                                            
+int    MSXerr_mathError(void);                                                 
+char*  MSXerr_writeMathErrorMsg(void);                                         
+
+//  Exported functions
+//--------------------
+int    MSXqual_open(void);
+int    MSXqual_init(void);
+int    MSXqual_step(double *t, double *tleft);
+int    MSXqual_close(void);
+double MSXqual_getNodeQual(int j, int m);
+double MSXqual_getLinkQual(int k, int m);
+int    MSXqual_isSame(double c1[], double c2[]);
+void   MSXqual_removeSeg(Pseg seg);
+Pseg   MSXqual_getFreeSeg(double v, double c[]);
+void   MSXqual_addSeg(int k, Pseg seg);
+void   MSXqual_reversesegs(int k);
+
+//  Local functions
+//-----------------
+static int    getHydVars(void);
+static int    transport(int64_t tstep);
+static void   initSegs(void);
+static int    flowdirchanged(void);
+static void   advectSegs(double dt);
+static void   getNewSegWallQual(int k, double dt, Pseg seg);
+static void   shiftSegWallQual(int k, double dt);
+static void   sourceInput(int n, double vout, double dt);
+static void   addSource(int n, Psource source, double v, double dt);
+static double getSourceQual(Psource source);
+static void   removeAllSegs(int k);
+
+static void topological_transport(double dt);
+static void findnodequal(int n, double volin, double* massin, double volout, double tstep);
+static void noflowqual(int n);
+static void evalnodeinflow(int, double, double*, double*);
+static void evalnodeoutflow(int k, double* upnodequal, double tstep);
+static int sortNodes();
+static int selectnonstacknode(int numsorted, int* indegree);
+static void findstoredmass(double* mass);
+
+static void   evalHydVariables(int k);
+//=============================================================================
+
+int  MSXqual_open()
+/*
+**   Purpose:
+**     opens the WQ routing system.
+**
+**   Returns:
+**     an error code (0 if no errors).
+*/
+{
+    int errcode = 0;
+    int n;
+
+    // --- set flags
+
+    MSX.QualityOpened = FALSE;
+    MSX.Saveflag = 0;
+    MSX.OutOfMemory = FALSE;
+    MSX.HasWallSpecies = FALSE;
+
+    // --- initialize array pointers to null
+
+    MSX.C1 = NULL;
+    MSX.FirstSeg = NULL;
+    MSX.LastSeg = NULL;
+    MSX.NewSeg = NULL;
+    MSX.FlowDir = NULL;
+    MSX.MassIn = NULL;
+
+
+    // --- open the chemistry system
+
+    errcode = MSXchem_open();
+    if (errcode > 0) return errcode;
+
+    // --- allocate a memory pool for pipe segments
+
+    MSX.QualPool = AllocInit();
+    if (MSX.QualPool == NULL) return ERR_MEMORY;
+
+// --- allocate memory used for species concentrations
+
+    MSX.C1 = (double *) calloc(MSX.Nobjects[SPECIES]+1, sizeof(double));
+   
+    MSX.MassBalance.initial = (double*)calloc(MSX.Nobjects[SPECIES] + 1, sizeof(double));
+    MSX.MassBalance.inflow =  (double*)calloc(MSX.Nobjects[SPECIES] + 1, sizeof(double));
+    MSX.MassBalance.indisperse = (double*)calloc(MSX.Nobjects[SPECIES] + 1, sizeof(double));
+    MSX.MassBalance.outflow = (double*)calloc(MSX.Nobjects[SPECIES] + 1, sizeof(double));
+    MSX.MassBalance.reacted = (double*)calloc(MSX.Nobjects[SPECIES] + 1, sizeof(double));
+    MSX.MassBalance.final   = (double*)calloc(MSX.Nobjects[SPECIES] + 1, sizeof(double));
+    MSX.MassBalance.ratio   = (double*)calloc(MSX.Nobjects[SPECIES] + 1, sizeof(double));
+
+// --- allocate memory used for pointers to the first, last,
+//     and new WQ segments in each link and tank
+
+    n = MSX.Nobjects[LINK] + MSX.Nobjects[TANK] + 1;
+    MSX.FirstSeg = (Pseg *) calloc(n, sizeof(Pseg));
+    MSX.LastSeg  = (Pseg *) calloc(n, sizeof(Pseg));
+    MSX.NewSeg = (Pseg *) calloc(n, sizeof(Pseg));
+
+// --- allocate memory used for flow direction in each link
+
+    MSX.FlowDir  = (FlowDirection *) calloc(n, sizeof(FlowDirection));
+
+// --- allocate memory used to accumulate mass and volume
+//     inflows to each node
+
+    n = MSX.Nobjects[NODE] + 1;
+    MSX.MassIn   = (double *) calloc(MSX.Nobjects[SPECIES]+1, sizeof(double));
+    MSX.SourceIn = (double*)calloc(MSX.Nobjects[SPECIES] + 1, sizeof(double));
+
+// --- allocate memory for topologically sorted nodes
+
+    MSX.SortedNodes = (int*)calloc(n, sizeof(int));
+
+// --- check for successful memory allocation
+
+    CALL(errcode, MEMCHECK(MSX.C1));
+    CALL(errcode, MEMCHECK(MSX.FirstSeg));
+    CALL(errcode, MEMCHECK(MSX.LastSeg));
+    CALL(errcode, MEMCHECK(MSX.NewSeg));
+    CALL(errcode, MEMCHECK(MSX.FlowDir));
+    CALL(errcode, MEMCHECK(MSX.MassIn));
+    CALL(errcode, MEMCHECK(MSX.SourceIn));
+    CALL(errcode, MEMCHECK(MSX.SortedNodes));
+    CALL(errcode, MEMCHECK(MSX.MassBalance.initial));
+    CALL(errcode, MEMCHECK(MSX.MassBalance.inflow));
+    CALL(errcode, MEMCHECK(MSX.MassBalance.indisperse));
+    CALL(errcode, MEMCHECK(MSX.MassBalance.outflow));
+    CALL(errcode, MEMCHECK(MSX.MassBalance.reacted));
+    CALL(errcode, MEMCHECK(MSX.MassBalance.final));
+    CALL(errcode, MEMCHECK(MSX.MassBalance.ratio));
+
+// --- check if wall species are present
+
+    for (n=1; n<=MSX.Nobjects[SPECIES]; n++)
+    {
+        if ( MSX.Species[n].type == WALL ) MSX.HasWallSpecies = TRUE;
+    }
+    if ( !errcode ) MSX.QualityOpened = TRUE;
+    return(errcode);
+}
+
+//=============================================================================
+
+int  MSXqual_init()
+/*
+**  Purpose:
+**     re-initializes the WQ routing system.
+**
+**  Input:
+**    none.
+**
+**  Returns:
+**    an error code (or 0 if no errors).
+*/
+{
+    int i, n, m;
+    int errcode = 0;
+
+// --- initialize node concentrations, tank volumes, & source mass flows
+
+    for (i=1; i<=MSX.Nobjects[NODE]; i++)
+    {
+        for (m=1; m<=MSX.Nobjects[SPECIES]; m++)
+            MSX.Node[i].c[m] = MSX.Node[i].c0[m];
+    }
+    for (i = 1; i <= MSX.Nobjects[LINK]; i++)
+    {
+        for (m = 1; m <= MSX.Nobjects[SPECIES]; m++)
+            MSX.Link[i].reacted[m] = 0.0;
+    }
+
+    for (i=1; i<=MSX.Nobjects[TANK]; i++)
+    {
+        MSX.Tank[i].hstep = 0.0;
+        MSX.Tank[i].v = MSX.Tank[i].v0;
+        n = MSX.Tank[i].node;
+        for (m = 1; m <= MSX.Nobjects[SPECIES]; m++)
+        {
+            MSX.Tank[i].c[m] = MSX.Node[n].c0[m];
+            MSX.Tank[i].reacted[m] = 0.0;
+        }
+    }
+
+    for (i=1; i<=MSX.Nobjects[PATTERN]; i++)
+    {
+        MSX.Pattern[i].interval = 0;
+        MSX.Pattern[i].current = MSX.Pattern[i].first;
+    }
+
+// --- copy expression constants to vector MSX.K[]                             
+
+    for (i=1; i<=MSX.Nobjects[CONSTANT]; i++)
+    {
+        MSX.K[i] = MSX.Const[i].value;
+    }
+
+// --- check if a separate WQ report is required
+
+    MSX.Rptflag = 0;
+    n = 0;
+    for (i=1; i<=MSX.Nobjects[NODE]; i++) n += MSX.Node[i].rpt;
+    for (i=1; i<=MSX.Nobjects[LINK]; i++) n += MSX.Link[i].rpt;
+    if ( n > 0 )
+    {
+        n = 0;
+        for (m=1; m<=MSX.Nobjects[SPECIES]; m++) n += MSX.Species[m].rpt;
+    }
+    if ( n > 0 ) MSX.Rptflag = 1;
+    if ( MSX.Rptflag ) MSX.Saveflag = 1;
+
+// --- reset memory pool
+
+    AllocSetPool(MSX.QualPool);
+    MSX.FreeSeg = NULL;
+    AllocReset();
+
+// --- re-position hydraulics file
+
+    fseek(MSX.HydFile.file, MSX.HydOffset, SEEK_SET);
+
+// --- set elapsed times to zero
+
+    MSX.Htime = 0;                         //Hydraulic solution time
+    MSX.Qtime = 0;                         //Quality routing time
+    MSX.Rtime = MSX.Rstart * 1000;         //Reporting time
+    MSX.Nperiods = 0;                      //Number fo reporting periods
+
+    for (m = 1; m <= MSX.Nobjects[SPECIES]; m++)
+    {
+        MSX.MassBalance.initial[m] = 0.0;
+        MSX.MassBalance.final[m] = 0.0;
+        MSX.MassBalance.inflow[m] = 0.0;
+        MSX.MassBalance.indisperse[m] = 0.0;
+        MSX.MassBalance.outflow[m] = 0.0;
+        MSX.MassBalance.reacted[m] = 0.0;
+        MSX.MassBalance.ratio[m] = 0.0;
+    }
+
+// --- open binary output file if results are to be saved
+
+    if ( MSX.Saveflag ) errcode = MSXout_open();
+    return errcode;
+}
+
+//=============================================================================
+
+int MSXqual_step(double *t, double *tleft)
+/*
+**  Purpose:
+**    updates WQ conditions over a single WQ time step.
+**
+**  Input:
+**    none.
+**
+**  Output:
+**    *t = current simulation time (sec)
+**    *tleft = time left in simulation (sec)
+**
+**  Returns:
+**    an error code:
+**      0 = no error
+**      501 = memory error
+**      307 = can't read hydraulics file
+**      513 = can't integrate reaction rates
+*/
+{
+    int  k, errcode = 0, flowchanged;
+    int m;
+    double smassin, smassout, sreacted;
+    int64_t  hstep, tstep, dt;
+    
+// --- set the shared memory pool to the water quality pool
+//     and the overall time step to nominal WQ time step
+
+    AllocSetPool(MSX.QualPool);
+    tstep = MSX.Qstep;
+    if (MSX.Qtime + tstep > MSX.Dur) tstep = MSX.Dur - MSX.Qtime;
+
+// --- repeat until the end of the time step
+
+    do
+    {
+    // --- find the time until the next hydraulic event occurs
+        dt = tstep;
+        hstep = MSX.Htime - MSX.Qtime;
+
+    // --- check if next hydraulic event occurs within the current time step
+
+        if (hstep <= dt)
+        {
+
+        // --- reduce current time step to end at next hydraulic event
+            dt = hstep;
+
+        // --- route WQ over this time step
+            if ( dt > 0 ) CALL(errcode, transport(dt));
+            MSX.Qtime += dt;
+
+        // --- retrieve new hydraulic solution
+            if (MSX.Qtime == MSX.Htime)
+            {
+                CALL(errcode, getHydVars());
+
+                for (int kl = 1; kl <= MSX.Nobjects[LINK]; kl++)
+                {
+                    // --- skip non-pipe links
+
+                    if (MSX.Link[kl].len == 0.0) continue;
+
+                    // --- evaluate hydraulic variables
+
+                    evalHydVariables(kl);
+                }
+
+                if (MSX.Qtime < MSX.Dur)
+                {
+                    // --- initialize pipe segments (at time 0) or else re-orient segments
+                    //     to accommodate any flow reversals
+                    if (MSX.Qtime == 0)
+                    {
+                        flowchanged = 1;
+                        initSegs();
+                    }
+                    else 
+                        flowchanged = flowdirchanged();
+
+                    if (flowchanged)
+                    {
+                        CALL(errcode, sortNodes());
+                    }
+                }
+            }
+
+        // --- report results if its time to do so
+            if (MSX.Saveflag && MSX.Qtime == MSX.Rtime)
+            {
+                CALL(errcode, MSXout_saveResults());
+                MSX.Rtime += MSX.Rstep * 1000;
+                MSX.Nperiods++;
+            }
+        }
+
+    // --- otherwise just route WQ over the current time step
+
+        else
+        {
+            CALL(errcode, transport(dt));
+            MSX.Qtime += dt;
+        }
+
+    // --- reduce overall time step by the size of the current time step
+
+        tstep -= dt;
+        if (MSX.OutOfMemory) errcode = ERR_MEMORY;
+    } while (!errcode && tstep > 0);
+
+// --- update the current time into the simulation and the amount remaining
+
+    *t = MSX.Qtime / 1000.;
+    *tleft = (MSX.Dur - MSX.Qtime) / 1000.;
+
+// --- if there's no time remaining, then save the final records to output file
+
+    if ( *tleft <= 0 && MSX.Saveflag )
+    {
+        findstoredmass(MSX.MassBalance.final);
+        for (m = 1; m <= MSX.Nobjects[SPECIES]; m++)
+        {
+            sreacted = 0.0;
+            for (k = 1; k <= MSX.Nobjects[LINK]; k++)
+                sreacted += MSX.Link[k].reacted[m];
+            for (k = 1; k <= MSX.Nobjects[TANK]; k++)
+                sreacted += MSX.Tank[k].reacted[m];
+
+            MSX.MassBalance.reacted[m] = sreacted;
+            smassin = MSX.MassBalance.initial[m] + MSX.MassBalance.inflow[m] + MSX.MassBalance.indisperse[m];
+            smassout = MSX.MassBalance.outflow[m]+MSX.MassBalance.final[m];
+            if (sreacted < 0)  //loss
+                smassout -= sreacted;
+            else
+                smassin += sreacted;
+
+            if (smassin == 0)
+                MSX.MassBalance.ratio[m] = 1.0;
+            else
+                MSX.MassBalance.ratio[m] = smassout / smassin;
+        }
+        CALL(errcode, MSXout_saveFinalResults());
+    }
+    return errcode;
+}
+
+//=============================================================================
+
+double  MSXqual_getNodeQual(int j, int m)
+/*
+**   Purpose:
+**     retrieves WQ for species m at node n.
+**
+**   Input:
+**     j = node index
+**     m = species index.
+**
+**   Returns:
+**     WQ value of node.
+*/
+{
+    int k;
+
+// --- return 0 for WALL species
+
+    if ( MSX.Species[m].type == WALL ) return 0.0;
+
+// --- if node is a tank, return its internal concentration
+
+    k = MSX.Node[j].tank;
+    if (k > 0 && MSX.Tank[k].a > 0.0)
+    {
+        return MSX.Tank[k].c[m];
+    }
+
+// --- otherwise return node's concentration (which includes
+//     any contribution from external sources)
+
+    return MSX.Node[j].c[m];
+}
+
+//=============================================================================
+
+double  MSXqual_getLinkQual(int k, int m)
+/*
+**   Purpose:
+**     computes average quality in link k.
+**
+**   Input:
+**     k = link index
+**     m = species index.
+**
+**   Returns:
+**     WQ value of link.
+*/
+{
+    double  vsum = 0.0,
+            msum = 0.0;
+    Pseg    seg;
+
+    seg = MSX.FirstSeg[k];
+    while (seg != NULL)
+    {
+        vsum += seg->v;
+        msum += (seg->c[m])*(seg->v);
+        seg = seg->prev;
+    }
+    if (vsum > 0.0) return(msum/vsum);
+    else
+    {
+        return (MSXqual_getNodeQual(MSX.Link[k].n1, m) +
+                MSXqual_getNodeQual(MSX.Link[k].n2, m)) / 2.0;
+    }
+}
+
+//=============================================================================
+
+int MSXqual_close()
+/*
+**   Purpose:
+**     closes the WQ routing system.
+**
+**   Input:
+**     none.
+**
+**   Returns:
+**     error code (0 if no error).
+*/
+{
+    int errcode = 0;
+    if (!MSX.ProjectOpened) return 0;
+    MSXchem_close();
+
+    FREE(MSX.C1);
+    FREE(MSX.FirstSeg);
+    FREE(MSX.LastSeg);
+    FREE(MSX.NewSeg);
+    FREE(MSX.FlowDir);
+    FREE(MSX.SortedNodes);
+    FREE(MSX.MassIn);
+    FREE(MSX.SourceIn);
+    if ( MSX.QualPool)
+    {
+        AllocSetPool(MSX.QualPool);
+        AllocFreePool();
+    }
+    FREE(MSX.MassBalance.initial);
+    FREE(MSX.MassBalance.inflow);
+    FREE(MSX.MassBalance.indisperse);
+    FREE(MSX.MassBalance.outflow);
+    FREE(MSX.MassBalance.reacted);
+    FREE(MSX.MassBalance.final);
+    FREE(MSX.MassBalance.ratio);
+
+    MSX.QualityOpened = FALSE;
+    return errcode;
+}
+
+//=============================================================================
+
+int  MSXqual_isSame(double c1[], double c2[])
+/*
+**   Purpose:
+**     checks if two sets of concentrations are the same
+**
+**   Input:
+**     c1[] = first set of species concentrations
+**     c2[] = second set of species concentrations
+**
+**   Returns:
+**     1 if the concentrations are all within a specific tolerance of each
+**     other or 0 if they are not.
+*/
+{
+    int m;
+    for (m=1; m<=MSX.Nobjects[SPECIES]; m++)
+    {
+        if (fabs(c1[m] - c2[m]) >= MSX.Species[m].aTol ) return 0;
+    }
+    return 1;
+}
+
+
+//=============================================================================
+
+int  getHydVars()
+/*
+**   Purpose:
+**     retrieves hydraulic solution and time step for next hydraulic event
+**     from a hydraulics file.
+**
+**   Input:
+**     none.
+**
+**   Returns:
+**     error code
+**
+**   NOTE:
+**     A hydraulic solution consists of the current time
+**     (hydtime), nodal demands (D) and heads (H), link
+**     flows (Q), and link status values and settings (which are not used).
+*/
+{
+    int  errcode = 0;
+    long hydtime, hydstep;
+    INT4 n;
+
+// --- read hydraulic time, demands, heads, and flows from the file
+
+    if (fread(&n, sizeof(INT4), 1, MSX.HydFile.file) < 1)
+        return ERR_READ_HYD_FILE;
+    hydtime = (long)n;
+    n = MSX.Nobjects[NODE];
+    if (fread(MSX.D+1, sizeof(REAL4), n, MSX.HydFile.file) < (unsigned)n)
+        return ERR_READ_HYD_FILE;
+    if (fread(MSX.H+1, sizeof(REAL4), n, MSX.HydFile.file) < (unsigned)n)
+        return ERR_READ_HYD_FILE;
+    n = MSX.Nobjects[LINK];
+    if (fread(MSX.Q+1, sizeof(REAL4), n, MSX.HydFile.file) < (unsigned)n)
+        return ERR_READ_HYD_FILE;
+    if (fread(MSX.S + 1, sizeof(REAL4), n, MSX.HydFile.file) < (unsigned)n) //03/17/2022
+        return ERR_READ_HYD_FILE;
+    
+    for (int pi = 1; pi <= n; pi++)    //06/10/2021 Shang
+        if (fabs(MSX.Q[pi]) < Q_STAGNANT)
+            MSX.Q[pi] = 0.0;
+
+// --- skip over link settings
+
+    fseek(MSX.HydFile.file, 1*n*sizeof(REAL4), SEEK_CUR);
+
+// --- read time step until next hydraulic event
+
+    if (fread(&n, sizeof(INT4), 1, MSX.HydFile.file) < 1)
+        return ERR_READ_HYD_FILE;
+    hydstep = (long)n;
+
+// --- update elapsed time until next hydraulic event
+
+    MSX.Htime = hydtime + hydstep;
+    MSX.Htime *= 1000;
+
+/*
+    if (MSX.Qtime < MSX.Dur)
+    {
+        if (MSX.Qtime == 0)
+        {
+            flowchanged = 1;
+            initSegs();
+        }
+        else flowchanged = flowdirchanged();
+    }
+    return flowchanged;*/
+
+    return errcode;
+}
+
+//=============================================================================
+
+int  transport(int64_t tstep)
+/*
+**  Purpose:
+**    transports constituent mass through pipe network
+**    under a period of constant hydraulic conditions.
+**
+**  Input:
+**    tstep = length of current time step (sec).
+**
+**  Returns:
+**    an error code or 0 if no error.
+*/
+{
+    int64_t qtime, dt64;
+    double dt;
+    int  errcode = 0;
+
+// --- repeat until time step is exhausted
+
+    MSXerr_clearMathError();                // clear math error flag           
+    qtime = 0;
+    while (!MSX.OutOfMemory &&
+           !errcode &&
+           qtime < tstep)
+    {                                       // Qstep is nominal quality time step
+        dt64 = MIN(MSX.Qstep, tstep-qtime); // get actual time step
+        qtime += dt64;                      // update amount of input tstep taken
+        dt = dt64 / 1000.;                  // time step as fractional seconds
+        
+        errcode = MSXchem_react(dt);        // react species in each pipe & tank
+        if ( errcode ) return errcode;
+        advectSegs(dt);                     // advect segments in each pipe
+        
+        topological_transport(dt);          //replace accumulate, updateNodes, sourceInput and release
+
+		if (MSXerr_mathError())             // check for any math error        
+		{
+			MSXerr_writeMathErrorMsg();
+			errcode = ERR_ILLEGAL_MATH;
+		}
+   }
+   return errcode;
+}
+
+//=============================================================================
+
+void  initSegs()
+/*
+**   Purpose:
+**     initializes water quality in pipe segments.
+**
+**   Input:
+**     none.
+*/
+{
+    int     j, k, m;
+    double  v;
+
+// --- examine each link
+
+    for (k=1; k<=MSX.Nobjects[LINK]; k++)
+    {
+    // --- establish flow direction
+
+        if (fabs(MSX.Q[k]) < Q_STAGNANT)
+            MSX.FlowDir[k] = ZERO_FLOW;
+        else if (MSX.Q[k] > 0.0)
+            MSX.FlowDir[k] = POSITIVE;
+        else 
+            MSX.FlowDir[k] = NEGATIVE;
+
+    // --- start with no segments
+
+        MSX.LastSeg[k] = NULL;
+        MSX.FirstSeg[k] = NULL;
+        MSX.NewSeg[k] = NULL;
+
+    // --- use quality of downstream node for BULK species
+    //     if no initial link quality supplied
+
+//        j = DOWN_NODE(k);
+        j = MSX.Link[k].n2;
+        for (m=1; m<=MSX.Nobjects[SPECIES]; m++)
+        {
+            if ( MSX.Link[k].c0[m] != MISSING )
+                MSX.C1[m] = MSX.Link[k].c0[m];
+            else if ( MSX.Species[m].type == BULK )
+                MSX.C1[m] = MSX.Node[j].c0[m];
+            else MSX.C1[m] = 0.0;
+        }
+
+    // --- fill link with a single segment of this quality
+
+        MSXchem_equil(LINK, k, MSX.C1);
+        v = LINKVOL(k);
+        if (v > 0.0)
+        {
+            int ninitsegs = MIN(100, MSX.MaxSegments);
+  
+            for (int ns = 0; ns < ninitsegs; ns++)
+                MSXqual_addSeg(k, MSXqual_getFreeSeg(v / (1.0*ninitsegs), MSX.C1));
+        }
+    }
+
+// --- initialize segments in tanks
+
+    for (j=1; j<=MSX.Nobjects[TANK]; j++)
+    {
+    // --- skip reservoirs
+
+        if ( MSX.Tank[j].a == 0.0 ) continue;
+
+    // --- tank segment pointers are stored after those for links
+
+        k = MSX.Tank[j].node;
+        for (m=1; m<=MSX.Nobjects[SPECIES]; m++)
+            MSX.C1[m] = MSX.Node[k].c0[m];
+        k = MSX.Nobjects[LINK] + j;
+        MSX.LastSeg[k] = NULL;
+        MSX.FirstSeg[k] = NULL;
+
+        MSXchem_equil(NODE, j, MSX.C1);
+
+    // --- add 2 segments for 2-compartment model
+
+        if (MSX.Tank[j].mixModel == MIX2)
+        {
+            v = MAX(0, MSX.Tank[j].v - MSX.Tank[j].vMix);
+            MSXqual_addSeg(k, MSXqual_getFreeSeg(v, MSX.C1));
+            v = MSX.Tank[j].v - v;
+            MSXqual_addSeg(k, MSXqual_getFreeSeg(v, MSX.C1));
+        }
+
+    // --- add one segment for all other models
+
+        else
+        {
+            v = MSX.Tank[j].v;
+            MSXqual_addSeg(k, MSXqual_getFreeSeg(v, MSX.C1));
+        }
+    }
+
+    findstoredmass(MSX.MassBalance.initial);    // initial mass
+}
+
+//=============================================================================
+
+int  flowdirchanged()
+/*
+**   Purpose:
+**     re-orients pipe segments (if flow reverses).
+**
+**   Input:
+**     none.
+*/
+{
+    int    k, flowchanged=0;
+    FlowDirection  newdir;
+ 
+
+// --- examine each link
+
+    for (k=1; k<=MSX.Nobjects[LINK]; k++)
+    {
+    // --- find new flow direction
+
+        newdir = POSITIVE;
+        if (fabs(MSX.Q[k]) < Q_STAGNANT) 
+            newdir = ZERO_FLOW;
+        else if (MSX.Q[k] < 0.0) newdir = NEGATIVE;
+
+    // --- if direction changes, then reverse the order of segments
+    //     (first to last) and save new direction
+              
+        if (newdir*MSX.FlowDir[k] < 0)
+        {
+            MSXqual_reversesegs(k);
+        }
+        if (newdir != MSX.FlowDir[k])
+        {
+            flowchanged = 1;            
+        }
+        MSX.FlowDir[k] = newdir;
+    }
+    return flowchanged;
+}
+
+
+//=============================================================================
+
+void advectSegs(double dt)
+/*
+**   Purpose:
+**     advects WQ segments within each pipe.
+**
+**   Input:
+**     dt = current WQ time step (sec).
+*/
+{
+    int k, m;
+
+// --- examine each link
+
+    for (k=1; k<=MSX.Nobjects[LINK]; k++)
+    {
+    // --- zero out WQ in new segment to be added at entrance of link
+
+        for (m=1; m<=MSX.Nobjects[SPECIES]; m++) MSX.C1[m] = 0.0;
+
+    // --- get a free segment to add to entrance of link
+
+        MSX.NewSeg[k] = MSXqual_getFreeSeg(0.0, MSX.C1);
+
+    // --- skip zero-length links (pumps & valves) & no-flow links
+
+        if ( MSX.NewSeg[k] == NULL ||
+             MSX.Link[(k)].len == 0.0 || MSX.Q[k] == 0.0 ) continue;
+
+    // --- find conc. of wall species in new segment to be added
+    //     and adjust conc. of wall species to reflect shifted
+    //     positions of existing segments
+
+        if ( MSX.HasWallSpecies )
+        {
+            getNewSegWallQual(k, dt, MSX.NewSeg[k]);
+            shiftSegWallQual(k, dt);
+        }
+    }
+}
+
+//=============================================================================
+
+void getNewSegWallQual(int k, double dt, Pseg newseg)
+/*
+**  Purpose:
+**     computes wall species concentrations for a new WQ segment that
+**     enters a pipe from its upstream node.
+**
+**  Input:
+**    k = link index
+**    dt = current WQ time step (sec)
+**    newseg = pointer to a new, unused WQ segment
+**
+**  Output:
+**    newseg->c[] = wall species concentrations in the new WQ segment
+*/
+{
+    Pseg  seg;
+    int   m;
+    double v, vin, vsum, vadded, vleft;
+
+// --- get volume of inflow to link
+
+    if ( newseg == NULL ) return;
+    v = LINKVOL(k);
+	vin = ABS(MSX.Q[k])*dt;
+    if (vin > v) vin = v;
+
+// --- start at last (most upstream) existing WQ segment
+
+	seg = MSX.LastSeg[k];
+	vsum = 0.0;
+    vleft = vin;
+    for (m = 1; m <= MSX.Nobjects[SPECIES]; m++)
+    {
+        if ( MSX.Species[m].type == WALL ) newseg->c[m] = 0.0;
+    }
+
+// --- repeat while some inflow volume still remains
+
+    while ( vleft > 0.0 && seg != NULL )
+    {
+
+    // --- find volume added by this segment
+
+        vadded = seg->v;
+        if ( vadded > vleft ) vadded = vleft;
+
+    // --- update total volume added and inflow volume remaining
+
+        vsum += vadded;
+        vleft -= vadded;
+
+    // --- add wall species mass contributed by this segment to new segment
+
+        for (m = 1; m <= MSX.Nobjects[SPECIES]; m++)
+        {
+            if ( MSX.Species[m].type == WALL ) newseg->c[m] += vadded*seg->c[m];
+        }
+
+    // --- move to next downstream WQ segment
+
+        seg = seg->next;
+    }
+
+// --- convert mass of wall species in new segment to concentration
+
+    if ( vsum > 0.0 )
+    {
+        for (m = 1; m <= MSX.Nobjects[SPECIES]; m++)
+        {
+            if ( MSX.Species[m].type == WALL ) newseg->c[m] /= vsum;
+        }
+    }
+}
+
+//=============================================================================
+
+void shiftSegWallQual(int k, double dt)
+/*
+**  Purpose:
+**    recomputes wall species concentrations in segments that remain
+**    within a pipe after flow is advected over current time step.
+**
+**  Input:
+**    k = link index
+**    dt = current WQ time step (sec)
+*/
+{
+    Pseg  seg1, seg2;
+    int   m;
+    double v, vin, vstart, vend, vcur, vsum;
+
+// --- find volume of water displaced in pipe
+
+    v = LINKVOL(k);
+	vin = ABS((double)MSX.Q[k])*dt;
+    if (vin > v) vin = v;
+
+// --- set future start position (measured by pipe volume) of original last segment
+
+    vstart = vin;
+
+// --- examine each segment, from upstream to downstream
+
+    for( seg1 = MSX.LastSeg[k]; seg1 != NULL; seg1 = seg1->next )
+    {
+
+        // --- initialize a "mixture" WQ
+        //     if vstart >= v the segment seg1 will be out of the pipe,
+        //     so no need to track wall concentration of this segment
+        if (vstart >= v) break;   //2020 moved up
+        
+        for (m = 1; m <= MSX.Nobjects[SPECIES]; m++) MSX.C1[m] = 0.0;
+
+    // --- find the future end position of this segment
+
+        vend = vstart + seg1->v;   //
+        if (vend > v) vend = v;
+        vcur = vstart;
+        vsum = 0;
+
+    // --- find volume taken up by the segment after it moves down the pipe
+
+        for (seg2 = MSX.LastSeg[k]; seg2 != NULL; seg2 = seg2->next)
+        {
+            if ( seg2->v == 0.0 ) continue;
+            vsum += seg2->v;
+            if ( vsum >= vstart && vsum <= vend )  //DS end of seg2 is between vstart and vend 
+            {
+                for (m = 1; m <= MSX.Nobjects[SPECIES]; m++)
+                {
+                    if ( MSX.Species[m].type == WALL )
+                        MSX.C1[m] += (vsum - vcur) * seg2->c[m];
+                }
+                vcur = vsum;
+            }
+            if ( vsum >= vend ) break;  //DS of seg2 is at DS of vend 
+        }
+
+    // --- update the wall species concentrations in the segment
+
+        for (m = 1; m <= MSX.Nobjects[SPECIES]; m++)
+        {
+            if ( MSX.Species[m].type != WALL ) continue;
+            if (seg2 != NULL) MSX.C1[m] += (vend - vcur) * seg2->c[m]; //only part of seg2
+            seg1->c[m] = MSX.C1[m] / (vend - vstart);
+            if ( seg1->c[m] < 0.0 ) seg1->c[m] = 0.0;
+        }
+
+    // --- re-start at the current end location
+
+        vstart = vend;
+    //    if ( vstart >= v ) break;   //2020 moved up
+    }
+}
+
+
+//=============================================================================
+
+void sourceInput(int n, double volout, double dt)
+/*
+**  Purpose:
+**    computes contribution (if any) of mass additions from WQ
+**    sources at each node.
+**
+**  Input:
+**    n = nodeindex
+**    dt = current WQ time step (sec)
+*/
+{
+    int m;
+    double  qout, qcutoff;
+    Psource source;
+
+// --- establish a flow cutoff which indicates no outflow from a node
+
+    qcutoff = 10.0*TINY;
+
+// --- consider each node
+
+    // --- skip node if no WQ source
+
+    source = MSX.Node[n].sources;
+    if (source == NULL) return;
+
+
+    qout = volout / dt;
+
+    // --- evaluate source input only if node outflow > cutoff flow
+    if (qout <= qcutoff) return;
+
+    // --- add contribution of each source species
+    for (m = 1; m <= MSX.Nobjects[SPECIES]; m++)
+        MSX.SourceIn[m] = 0.0;   
+    while (source)
+    {
+        addSource(n, source, volout, dt);
+        source = source->next;
+    }
+
+    // --- compute a new chemical equilibrium at the source node
+    MSXchem_equil(NODE, 0, MSX.Node[n].c);
+ 
+    for (m = 1; m <= MSX.Nobjects[SPECIES]; m++)   
+    {
+        MSX.MassBalance.inflow[m] += MSX.SourceIn[m] * LperFT3;
+    }
+}
+
+//=============================================================================
+
+void addSource(int n, Psource source, double volout, double dt)
+/*
+**  Purpose:
+**    updates concentration of particular species leaving a node
+**    that receives external source input.
+**
+**  Input:
+**    n = index of source node
+**    source = pointer to WQ source data
+**    volout = volume of water leaving node during current time step
+**    dt     = current WQ time step (sec)
+*/
+{
+    int     m;
+    double  massadded, s;
+
+// --- only analyze bulk species
+
+    m = source->species;
+    massadded = 0.0;
+    if (source->c0 > 0.0 && MSX.Species[m].type == BULK)
+    {
+
+    // --- mass added depends on type of source
+
+        s = getSourceQual(source);
+        switch(source->type)
+        {
+        // Concen. Source:
+        // Mass added = source concen. * -(demand)
+
+          case CONCEN:
+
+          // Only add source mass if demand is negative
+              if (MSX.Node[n].tank <=0 && MSX.D[n] < 0.0) massadded = -s*MSX.D[n]*dt;
+
+          // If node is a tank then set concen. to 0.
+          // (It will be re-set to true value later on)
+
+          //  if (MSX.Node[n].tank > 0) MSX.Node[n].c[m] = 0.0;
+              break;
+
+        // Mass Inflow Booster Source:
+
+          case MASS:
+              massadded = s*dt/LperFT3;
+              break;
+
+        // Setpoint Booster Source:
+        // Mass added is difference between source
+        // & node concen. times outflow volume
+
+          case SETPOINT:
+              if (s > MSX.Node[n].c[m])
+                  massadded = (s - MSX.Node[n].c[m])*volout;
+              break;
+
+        // Flow-Paced Booster Source:
+        // Mass added = source concen. times outflow volume
+
+          case FLOWPACED:
+              massadded = s*volout;
+              break;
+        }
+
+    // --- adjust nodal concentration to reflect source addition
+        MSX.Node[n].c[m] += massadded / volout;
+        MSX.SourceIn[m] += massadded;
+    }
+}
+
+
+//=============================================================================
+
+double  getSourceQual(Psource source)
+/*
+**   Input:   j = source index
+**   Output:  returns source WQ value
+**   Purpose: determines source concentration in current time period
+*/
+{
+    int    i;
+    long   k;
+    double c, f = 1.0;
+
+// --- get source concentration (or mass flow) in original units
+    c = source->c0;
+
+// --- convert mass flow rate from min. to sec.
+    if (source->type == MASS) c /= 60.0;
+
+// --- apply time pattern if assigned
+    i = source->pat;
+    if (i == 0) return(c);
+    k = (int)((MSX.Qtime + MSX.Pstart*1000) / (MSX.Pstep*1000)) % MSX.Pattern[i].length;
+    if (k != MSX.Pattern[i].interval)
+    {
+        if ( k < MSX.Pattern[i].interval )
+        {
+            MSX.Pattern[i].current = MSX.Pattern[i].first;
+            MSX.Pattern[i].interval = 0;
+        }
+        while (MSX.Pattern[i].current && MSX.Pattern[i].interval < k)
+        {
+             MSX.Pattern[i].current = MSX.Pattern[i].current->next;
+             MSX.Pattern[i].interval++;
+        }
+    }
+    if (MSX.Pattern[i].current) f = MSX.Pattern[i].current->value;
+    return c*f;
+}
+
+//=============================================================================
+
+void  removeAllSegs(int k)
+/*
+**   Purpose:
+**     removes all segments in a pipe link.
+**
+**   Input:
+**     k = link index.
+*/
+{
+    Pseg seg;
+    seg = MSX.FirstSeg[k];
+    while (seg != NULL)
+    {
+        MSX.FirstSeg[k] = seg->prev;
+        MSXqual_removeSeg(seg);
+        seg = MSX.FirstSeg[k];
+    }
+    MSX.LastSeg[k] = NULL;
+    if (k <= MSX.Nobjects[LINK])
+        MSX.Link[k].nsegs =  0;
+}
+
+void topological_transport(double dt)
+{
+    int j, n, k, m;
+    double volin, volout;
+    Padjlist  alink;
+
+
+    // Analyze each node in topological order
+    for (j = 1; j <= MSX.Nobjects[NODE]; j++)
+    {
+        // ... index of node to be processed
+        n = MSX.SortedNodes[j];
+
+        // ... zero out mass & flow volumes for this node
+        volin = 0.0;
+        volout = 0.0;
+        memset(MSX.MassIn, 0, (MSX.Nobjects[SPECIES] + 1) * sizeof(double));
+        memset(MSX.SourceIn, 0, (MSX.Nobjects[SPECIES] + 1) * sizeof(double));
+
+        // ... examine each link with flow into the node
+        for (alink = MSX.Adjlist[n]; alink != NULL; alink = alink->next)
+        {
+            // ... k is index of next link incident on node n
+            k = alink->link;
+
+            // ... link has flow into node - add it to node's inflow
+            //     (m is index of link's downstream node)
+            m = MSX.Link[k].n2;
+            if (MSX.FlowDir[k] < 0) m = MSX.Link[k].n1;
+            if (m == n)
+            {
+                evalnodeinflow(k, dt, &volin, MSX.MassIn);
+            }
+
+            // ... link has flow out of node - add it to node's outflow
+            else volout += fabs(MSX.Q[k]);
+        }
+
+        // ... if node is a junction, add on any external outflow (e.g., demands)
+        if (MSX.Node[n].tank == 0)
+        {
+            volout += fmax(0.0, MSX.D[n]);
+        }
+
+        // ... convert from outflow rate to volume
+        volout *= dt;
+
+        // ... find the concentration of flow leaving the node
+        findnodequal(n, volin, MSX.MassIn, volout, dt);
+
+        // ... examine each link with flow out of the node
+        for (alink = MSX.Adjlist[n]; alink != NULL; alink = alink->next)
+        {
+            // ... link k incident on node n has upstream node m equal to n
+            k = alink->link;
+            m = MSX.Link[k].n1;
+            if (MSX.FlowDir[k] < 0) m = MSX.Link[k].n2;
+            if (m == n)
+            {
+                // ... send flow at new node concen. into link
+                evalnodeoutflow(k, MSX.Node[n].c, dt);
+            }
+        }
+
+    }
+    /*Advection-Reaction Done, Dispersion Starts*/
+    //1. Linear relationship for each pipe
+    //2. Compose the nodal equations
+    //3. Solve the matrix to update nodal concentration
+    //4. Update segment concentration
+    for (int m = 1; m <= MSX.Nobjects[SPECIES]; m++)
+    {
+        if (MSX.Dispersion.md[m] > 0 || MSX.Dispersion.ld[m] > 0)
+        {
+            dispersion_pipe(m, dt);
+            solve_nodequal(m, dt);
+            segqual_update(m, dt);
+        }
+    }
+}
+
+
+void evalnodeoutflow(int k, double * upnodequal, double tstep)
+/*
+**--------------------------------------------------------------
+**   Input:   k = link index
+**            c = quality from upstream node
+**            tstep = time step
+**   Output:  none
+**   Purpose: releases flow volume and mass from the upstream
+**            node of a link over a time step.
+**--------------------------------------------------------------
+*/
+{
+
+    double v;
+    Pseg seg;
+    int m;
+    int useNewSeg = 0;
+
+    // Find flow volume (v) released over time step
+    v = fabs(MSX.Q[k]) * tstep;
+    if (v == 0.0) return;
+
+    // Release flow and mass into upstream end of the link
+
+    for (m = 1; m <= MSX.Nobjects[SPECIES]; m++)
+    {
+        if (MSX.Species[m].type == BULK)
+            MSX.NewSeg[k]->c[m] = upnodequal[m];
+    }
+
+    // ... case where link has a last (most upstream) segment
+    seg = MSX.LastSeg[k];
+
+    if (seg)
+    {
+        if (!MSXqual_isSame(seg->c, upnodequal) && MSX.Link[k].nsegs < MSX.MaxSegments)
+        {
+            useNewSeg = 1;
+        }
+        else
+            useNewSeg = 0;
+
+//        if (MSX.DispersionFlag == 1 && MSX.Link[k].nsegs >= MSX.MaxSegments)
+//            useNewSeg = 0;
+ 
+        if (useNewSeg == 0)
+        {
+            for (m = 1; m <= MSX.Nobjects[SPECIES]; m++)
+            {
+                if (MSX.Species[m].type == BULK)
+                   seg->c[m] = (seg->c[m]*seg->v+upnodequal[m]*v)/(seg->v+v);
+            }
+            seg->v += v;
+            MSXqual_removeSeg(MSX.NewSeg[k]);
+        }
+
+        // --- otherwise add the new seg to the end of the link
+
+        else
+        {
+            MSX.NewSeg[k]->v = v;
+            MSXqual_addSeg(k, MSX.NewSeg[k]);
+        }
+    }
+
+    // ... link has no segments so add one
+    else
+    {
+        MSX.NewSeg[k]->v = v;
+        MSXqual_addSeg(k, MSX.NewSeg[k]);
+    }
+
+}
+
+
+void  evalnodeinflow(int k, double tstep, double* volin, double* massin)
+    /*
+    **--------------------------------------------------------------
+    **   Input:   k = link index
+    **            tstep = quality routing time step
+    **   Output:  volin = flow volume entering a node
+    **            massin = constituent mass entering a node
+    **   Purpose: adds the contribution of a link's outflow volume
+    **            and constituent mass to the total inflow into its
+    **            downstream node over a time step.
+    **--------------------------------------------------------------
+    */
+{
+
+    double q, v, vseg;
+    int sindex;
+    Pseg seg;
+
+    // Get flow rate (q) and flow volume (v) through link
+    q = MSX.Q[k];
+    v = fabs(q) * tstep;
+
+    // Transport flow volume v from link's leading segments into downstream
+    // node, removing segments once their full volume is consumed
+    while (v > 0.0)
+    {
+        seg = MSX.FirstSeg[k];
+        if (!seg) break;
+
+        // ... volume transported from first segment is smaller of
+        //     remaining flow volume & segment volume
+        vseg = seg->v;
+        vseg = MIN(vseg, v);
+
+        // ... update total volume & mass entering downstream node
+        *volin += vseg;
+        for (sindex = 1; sindex <= MSX.Nobjects[SPECIES]; sindex++)
+            massin[sindex] += vseg * seg->c[sindex] * LperFT3;
+
+        // ... reduce remaining flow volume by amount transported
+        v -= vseg;
+
+        // ... if all of segment's volume was transferred
+        if (v >= 0.0 && vseg >= seg->v)
+        {
+            // ... replace this leading segment with the one behind it
+            MSX.FirstSeg[k] = seg->prev;
+            MSX.Link[k].nsegs--;
+            if (MSX.FirstSeg[k] == NULL) MSX.LastSeg[k] = NULL;
+            else MSX.FirstSeg[k]->next = NULL; //03/19/2024 added to break the linked segments 
+		    
+            // ... recycle the used up segment
+            seg->prev = MSX.FreeSeg;
+            MSX.FreeSeg = seg;
+        }
+
+        // ... otherwise just reduce this segment's volume
+        else seg->v -= vseg;
+    }
+}
+
+
+void findnodequal(int n, double volin, double* massin, double volout, double tstep)
+    /*
+    **--------------------------------------------------------------
+    **   Input:   n = node index
+    **            volin = flow volume entering node
+    **            massin = mass entering node
+    **            volout = flow volume leaving node
+    **            tstep = length of current time step
+    **   Output:  returns water quality in a node's outflow
+    **   Purpose: computes a node's new quality from its inflow
+    **            volume and mass, including any source contribution.
+    **--------------------------------------------------------------
+    */
+{
+    int m, j;
+    // Node is a junction - update its water quality
+    j = MSX.Node[n].tank;
+    if (j <= 0)
+    {
+        // ... dilute inflow with any external negative demand
+        volin -= fmin(0.0, MSX.D[n]) * tstep;
+
+        // ... new concen. is mass inflow / volume inflow
+        if (volin > 0.0)
+        {
+            for(m = 1; m <= MSX.Nobjects[SPECIES]; m++)
+                MSX.Node[n].c[m] = massin[m] / volin / LperFT3;
+        }
+
+        // ... if no inflow adjust quality for reaction in connecting pipes
+        else 
+            noflowqual(n);
+
+        MSXchem_equil(NODE, 0, MSX.Node[n].c);
+
+    }
+    else
+    {
+        // --- use initial quality for reservoirs
+
+        if (MSX.Tank[j].a == 0.0)
+        {
+            for (m = 1; m <= MSX.Nobjects[SPECIES]; m++)
+            {
+                MSX.Node[n].c[m] = MSX.Node[n].c0[m];
+            }
+            MSXchem_equil(NODE, 0, MSX.Node[n].c);
+            for (m = 1; m <= MSX.Nobjects[SPECIES]; m++)
+            {
+               
+                MSX.MassBalance.inflow[m] += MSX.Node[n].c[m] * volout * LperFT3;
+                MSX.MassBalance.outflow[m] += massin[m];
+            }
+        }
+
+        // --- otherwise update tank WQ based on mixing model
+
+        else
+        {
+            if (volin > 0.0)
+            {
+                for (m = 1; m <= MSX.Nobjects[SPECIES]; m++)
+                {
+                    MSX.C1[m] = massin[m] / volin / LperFT3;
+                }
+            }
+            else for (m = 1; m <= MSX.Nobjects[SPECIES]; m++)
+                MSX.C1[m] = 0.0;
+            switch (MSX.Tank[j].mixModel)
+            {
+            case MIX1: MSXtank_mix1(j, volin, massin, volin-volout);
+                break;
+            case MIX2: MSXtank_mix2(j, volin, massin, volin-volout);
+                break;
+            case FIFO: MSXtank_mix3(j, volin, massin, volin-volout);
+                break;
+            case LIFO: MSXtank_mix4(j, volin, massin, volin-volout);
+                break;
+            }
+            for (m = 1; m <= MSX.Nobjects[SPECIES]; m++)
+            {
+                MSX.Node[n].c[m] = MSX.Tank[j].c[m];
+            }
+            MSX.Tank[j].v += (double)MSX.D[n] * tstep;
+        }
+    }
+
+    // Find quality contribued by any external chemical source
+    sourceInput(n, volout, tstep);
+    if (MSX.Node[n].tank == 0)
+    {
+        for (m = 1; m <= MSX.Nobjects[SPECIES]; m++)
+            if(MSX.Species[m].type == BULK)
+                MSX.MassBalance.outflow[m] += MAX(0.0, MSX.D[n]) * tstep * MSX.Node[n].c[m]*LperFT3;
+    }
+}
+
+
+int sortNodes()
+/*
+**--------------------------------------------------------------
+**   Input:   none
+**   Output:  returns an error code
+**   Purpose: topologically sorts nodes from upstream to downstream.
+**   Note:    links with negligible flow are ignored since they can
+**            create spurious cycles that cause the sort to fail.
+**--------------------------------------------------------------
+*/
+{
+
+    int i, j, k, n;
+    int* indegree = NULL;
+    int* stack = NULL;
+    int stacksize = 0;
+    int numsorted = 0;
+    int errcode = 0;
+    FlowDirection dir;
+    Padjlist  alink;
+
+    // Allocate an array to count # links with inflow to each node
+    // and for a stack to hold nodes waiting to be processed
+    indegree = (int*)calloc(MSX.Nobjects[NODE] + 1, sizeof(int));
+    stack = (int*)calloc(MSX.Nobjects[NODE] + 1, sizeof(int));
+    if (indegree && stack)
+    {
+        // Count links with "non-negligible" inflow to each node
+        for (k = 1; k <= MSX.Nobjects[LINK]; k++)
+        {
+            dir = MSX.FlowDir[k];
+            if (dir == POSITIVE) n = MSX.Link[k].n2;
+            else if (dir == NEGATIVE) n = MSX.Link[k].n1;
+            else continue;
+            indegree[n]++;
+        }
+
+        // Place nodes with no inflow onto a stack
+        for (i = 1; i <= MSX.Nobjects[NODE]; i++)
+        {
+            if (indegree[i] == 0)
+            {
+                stacksize++;
+                stack[stacksize] = i;
+            }
+        }
+
+        // Examine each node on the stack until none are left
+        while (numsorted < MSX.Nobjects[NODE])
+        {
+            // ... if stack is empty then a cycle exists
+            if (stacksize == 0)
+            {
+                //  ... add a non-sorted node connected to a sorted one to stack
+                j = selectnonstacknode(numsorted, indegree);
+                if (j == 0) break;  // This shouldn't happen.
+                indegree[j] = 0;
+                stacksize++;
+                stack[stacksize] = j;
+            }
+
+            // ... make the last node added to the stack the next
+            //     in sorted order & remove it from the stack
+            i = stack[stacksize];
+            stacksize--;
+            numsorted++;
+            MSX.SortedNodes[numsorted] = i;
+
+            // ... for each outflow link from this node reduce the in-degree
+            //     of its downstream node
+            for (alink = MSX.Adjlist[i]; alink != NULL; alink = alink->next)
+            {
+                // ... k is the index of the next link incident on node i
+                k = alink->link;
+
+                // ... skip link if flow is negligible
+                if (MSX.FlowDir[k] == 0) continue;
+
+                // ... link has flow out of node (downstream node n not equal to i)
+                n = MSX.Link[k].n2;
+                if (MSX.FlowDir[k] < 0) n = MSX.Link[k].n1;
+
+                // ... reduce degree of node n
+                if (n != i && indegree[n] > 0)
+                {
+                    indegree[n]--;
+
+                    // ... no more degree left so add node n to stack
+                    if (indegree[n] == 0)
+                    {
+                        stacksize++;
+                        stack[stacksize] = n;
+                    }
+                }
+            }
+        }
+    }
+    else errcode = 101;
+    if (numsorted < MSX.Nobjects[NODE]) errcode = 120;
+    FREE(indegree);
+    FREE(stack);
+    return errcode;
+}
+
+int selectnonstacknode(int numsorted, int* indegree)
+/*
+**--------------------------------------------------------------
+**   Input:   numsorted = number of nodes that have been sorted
+**            indegree = number of inflow links to each node
+**   Output:  returns a node index
+**   Purpose: selects a next node for sorting when a cycle exists.
+**--------------------------------------------------------------
+*/
+{
+
+    int i, m, n;
+    Padjlist  alink;
+
+    // Examine each sorted node in last in - first out order
+    for (i = numsorted; i > 0; i--)
+    {
+        // For each link connected to the sorted node
+        m = MSX.SortedNodes[i];
+        for (alink = MSX.Adjlist[m]; alink != NULL; alink = alink->next)
+        {
+            // ... n is the node of link k opposite to node m
+            n = alink->node;
+
+            // ... select node n if it still has inflow links
+            if (indegree[n] > 0) return n;
+        }
+    }
+
+    // If no node was selected by the above process then return the
+    // first node that still has inflow links remaining
+    for (i = 1; i <= MSX.Nobjects[NODE]; i++)
+    {
+        if (indegree[i] > 0) return i;
+    }
+
+    // If all else fails return 0 indicating that no node was selected
+    return 0;
+}
+
+void  noflowqual(int n)
+/*
+**--------------------------------------------------------------
+**   Input:   n = node index
+**   Output:  quality for node n
+**   Purpose: sets the quality for a junction node that has no
+**            inflow to the average of the quality in its
+**            adjoining link segments.
+**   Note:    this function is only used for reactive substances.
+**--------------------------------------------------------------
+*/
+{
+
+    int k, m, inflow, kount = 0;
+    double c = 0.0;
+    FlowDirection dir;
+    Padjlist  alink;
+
+    for (m = 1; m <= MSX.Nobjects[SPECIES]; m++)
+        MSX.Node[n].c[m] = 0.0;
+    // Examine each link incident on the node
+    for (alink = MSX.Adjlist[n]; alink != NULL; alink = alink->next)
+    {
+        // ... index of an incident link
+        k = alink->link;
+        dir = MSX.FlowDir[k];
+
+        // Node n is link's downstream node - add quality
+        // of link's first segment to average
+        if (MSX.Link[k].n2 == n && dir >= 0) inflow = TRUE;
+        else if (MSX.Link[k].n1 == n && dir < 0)  inflow = TRUE;
+        else inflow = FALSE;
+        if (inflow == TRUE && MSX.FirstSeg[k] != NULL)
+        {
+            for (m = 1; m <= MSX.Nobjects[SPECIES]; m++)
+                MSX.Node[n].c[m] += MSX.FirstSeg[k]->c[m];
+            kount++;
+        }
+
+        // Node n is link's upstream node - add quality
+        // of link's last segment to average
+        else if (inflow == FALSE && MSX.LastSeg[k] != NULL)
+        {
+            for (m = 1; m <= MSX.Nobjects[SPECIES]; m++)
+                MSX.Node[n].c[m] += MSX.LastSeg[k]->c[m];
+            kount++;
+        }
+    }
+    if (kount > 0) 
+        for (m = 1; m <= MSX.Nobjects[SPECIES]; m++)
+            MSX.Node[n].c[m] = MSX.Node[n].c[m] / (double)kount;
+}
+
+void findstoredmass(double * mass)
+/*
+**--------------------------------------------------------------
+**   Input:   none
+**   Output:  returns total constituent mass stored in the network
+**   Purpose: finds the current mass stored in
+**            all pipes and tanks.
+**--------------------------------------------------------------
+*/
+{
+
+    int    i, k, m;
+    Pseg   seg;
+
+    for (m = 1; m <= MSX.Nobjects[SPECIES]; m++)
+    {
+        mass[m] = 0;
+    }
+
+    // Mass residing in each pipe
+    for (k = 1; k <= MSX.Nobjects[LINK]; k++)
+    {
+        // Sum up the quality and volume in each segment of the link
+        seg = MSX.FirstSeg[k];
+        while (seg != NULL)
+        {
+            for (m = 1; m <= MSX.Nobjects[SPECIES]; m++)
+            {
+                if (MSX.Species[m].type == BULK)
+                    mass[m] += seg->c[m] * seg->v * LperFT3;  //M/L * ft3 * L/Ft3 = M
+                else
+                    mass[m] += seg->c[m] * seg->v * 4.0 / MSX.Link[k].diam * MSX.Ucf[AREA_UNITS]; //Mass per area unit * ft3 / ft * area unit per ft2;
+            }
+            seg = seg->prev;
+        }
+    }
+
+    // Mass residing in each tank
+    for (i = 1; i <= MSX.Nobjects[TANK]; i++)
+    {
+        // ... skip reservoirs
+        if (MSX.Tank[i].a == 0.0) continue;
+
+        // ... add up mass in each volume segment
+        else
+        {
+            k = MSX.Nobjects[LINK] + i;
+            seg = MSX.FirstSeg[k];
+            while (seg != NULL)
+            {
+                for (m = 1; m <= MSX.Nobjects[SPECIES]; m++)
+                {
+                    if (MSX.Species[m].type == BULK)
+                        mass[m] += seg->c[m] * seg->v * LperFT3;
+                }
+                seg = seg->prev;
+            }
+        }
+    }
+}
+
+void MSXqual_reversesegs(int k)
+/*
+**--------------------------------------------------------------
+**   Input:   k = link index
+**   Output:  none
+**   Purpose: re-orients a link's segments when flow reverses.
+**--------------------------------------------------------------
+*/
+{
+    Pseg  seg, cseg, pseg;
+
+    seg = MSX.FirstSeg[k];
+    MSX.FirstSeg[k] = MSX.LastSeg[k];
+    MSX.LastSeg[k] = seg;
+    pseg = NULL;
+    while (seg != NULL)
+    {
+        cseg = seg->prev;
+        seg->prev = pseg;
+        seg->next = cseg;
+        pseg = seg;
+        seg = cseg;
+    }
+}
+
+
+
+//=============================================================================
+
+void MSXqual_removeSeg(Pseg seg)
+/*
+**   Purpose:
+**     places a WQ segment back into the memory pool of segments.
+**
+**   Input:
+**     seg = pointer to a WQ segment.
+*/
+{
+    if ( seg == NULL ) return;
+    seg->prev = MSX.FreeSeg;
+    seg->next = NULL;
+    MSX.FreeSeg = seg;
+}
+
+//=============================================================================
+
+Pseg MSXqual_getFreeSeg(double v, double c[])
+/*
+**   Purpose:
+**     retrieves an unused water quality volume segment from the memory pool.
+**
+**   Input:
+**     v = segment volume (ft3)
+**     c[] = segment quality
+**
+**   Returns:
+**     a pointer to an unused water quality segment.
+*/
+{
+    Pseg seg;
+    int  m;
+
+// --- try using the last discarded segment if one is available
+
+    if (MSX.FreeSeg != NULL)
+    {
+        seg = MSX.FreeSeg;
+        MSX.FreeSeg = seg->prev;
+    }
+
+// --- otherwise create a new segment from the memory pool
+
+    else
+    {
+        seg = (struct Sseg *) Alloc(sizeof(struct Sseg));
+        if (seg == NULL)
+        {
+            MSX.OutOfMemory = TRUE;
+            return NULL;
+        }
+        seg->c = (double *) Alloc((MSX.Nobjects[SPECIES]+1)*sizeof(double));
+        seg->lastc = (double *)Alloc((MSX.Nobjects[SPECIES] + 1) * sizeof(double));
+        if ( seg->c == NULL||seg->lastc == NULL)
+        {
+            MSX.OutOfMemory = TRUE;
+            return NULL;
+        }
+    }
+
+// --- assign volume, WQ, & integration time step to the new segment
+
+    seg->v = v;
+    for (m=1; m<=MSX.Nobjects[SPECIES]; m++) seg->c[m] = c[m];
+    seg->hstep = 0.0;
+    return seg;
+}
+
+//=============================================================================
+
+void  MSXqual_addSeg(int k, Pseg seg)
+/*
+**   Purpose:
+**     adds a new segment to the upstream end of a link.
+**
+**   Input:
+**     k = link index
+**     seg = pointer to a free WQ segment.
+*/
+
+{
+    seg->prev = NULL;
+    seg->next = NULL;
+    if (MSX.FirstSeg[k] == NULL) MSX.FirstSeg[k] = seg;
+    if (MSX.LastSeg[k] != NULL)
+    {
+        MSX.LastSeg[k]->prev = seg;
+        seg->next = MSX.LastSeg[k];
+    }
+    MSX.LastSeg[k] = seg;
+    if (k <= MSX.Nobjects[LINK])
+        MSX.Link[k].nsegs++;
+}
+
+void evalHydVariables(int k)
+/*
+**  Purpose:
+**    retrieves current values of hydraulic variables for the
+**    current link being analyzed.
+**
+**  Input:
+**    k = link index
+**
+**  Output:
+**    updates values stored in vector HydVar[]
+*/
+{
+    double dh;                         // headloss in ft
+    double diam = MSX.Link[k].diam;    // diameter in ft
+    double length = MSX.Link[k].len;   // length in ft
+    double av;                         // area per unit volume
+
+// --- pipe diameter and length in user's units (ft or m)
+    MSX.Link[k].HydVar[DIAMETER] = diam * MSX.Ucf[LENGTH_UNITS];
+    MSX.Link[k].HydVar[LENGTH] = length * MSX.Ucf[LENGTH_UNITS];
+
+    // --- flow rate in user's units
+    MSX.Link[k].HydVar[FLOW] = fabs(MSX.Q[k]) * MSX.Ucf[FLOW_UNITS];
+
+    // --- flow velocity in ft/sec
+    if (diam == 0.0) MSX.Link[k].HydVar[VELOCITY] = 0.0;
+    else MSX.Link[k].HydVar[VELOCITY] = fabs(MSX.Q[k]) * 4.0 / PI / SQR(diam);
+
+    // --- Reynolds number
+    MSX.Link[k].HydVar[REYNOLDS] = MSX.Link[k].HydVar[VELOCITY] * diam / VISCOS;
+
+    // --- flow velocity in user's units (ft/sec or m/sec)
+    MSX.Link[k].HydVar[VELOCITY] *= MSX.Ucf[LENGTH_UNITS];
+
+    // --- Darcy Weisbach friction factor
+    if (MSX.Link[k].len == 0.0) MSX.Link[k].HydVar[FRICTION] = 0.0;
+    else
+    {
+        dh = ABS(MSX.H[MSX.Link[k].n1] - MSX.H[MSX.Link[k].n2]);
+        MSX.Link[k].HydVar[FRICTION] = 39.725 * dh * pow(diam, 5.0) /
+            MSX.Link[k].len / SQR((double)MSX.Q[k]);
+    }
+
+    // --- shear velocity in user's units (ft/sec or m/sec)
+    MSX.Link[k].HydVar[SHEAR] = MSX.Link[k].HydVar[VELOCITY] * sqrt(MSX.Link[k].HydVar[FRICTION] / 8.0);
+
+    // --- pipe surface area / volume in area_units/L
+    MSX.Link[k].HydVar[AREAVOL] = 1.0;
+    if (diam > 0.0)
+    {
+        av = 4.0 / diam;                // ft2/ft3
+        av *= MSX.Ucf[AREA_UNITS];     // area_units/ft3
+        av /= LperFT3;                 // area_units/L
+        MSX.Link[k].HydVar[AREAVOL] = av;
+    }
+
+    MSX.Link[k].HydVar[ROUGHNESS] = MSX.Link[k].roughness;
+}