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User manual - Wageningen UR

1. 5 6 FITECO bat ECOCALC iteration 6 Outman dat Y calc OUTMAN 7 Output Fit results ECO bat Figure 9 Parameter optimization with FIT and ECOSAT processes see text for explanation of the indicated numbers programs and files 26 2 2 Database files The database files contain data for the variable groups components species gases minerals organic liquids particle surfaces surface components surface species and chemicals These data files are user expandable select DBASE DBASE GROUP The database files always have a default extension db For every variable group a different third extension character is used Except for components you can create for all variable groups your own database files Maximum capacity for the database files 200 items rows ECOSAT standard default database files Components ECOCOMP dbA Species ECOSPEC1 dbB Gases ECOGAS dbC Minerals ECOMIN1 dbD Organic liquids ECO ORG dbE Particle surfaces ECOPART dbP Surface sorption data ECOPART dbS Chemicals ECO CHEM dbG Available standard ECOSAT database files for species and minerals ECOSPEC1 dbB all species not present in the other species database files ECOSPEC2 dbB all Ag Hg Ni SiO4 SeO4 Se AsO Br I F and B OH species ECOCHELA dbB all EGTA DTPA HEDTA CDTA EDTA NTA species ECOCYAN dbB all CN and Fe CN s species ECOACIDS dbB all Acetate
2. 0 699 In the third and fourth row the kinetic terms of equation 12 are formulated Transport mobility table All transport and soil column data are inserted in the transport edit tables parameters soil column and feed Finally we have to inform ECOSAT that the dissolved species Cim is immobile We can do this by choosing menu option Transport mobility ECOSAT then shows a list of all dissolved species In this table we can indicate whether a species is mobile or not Ecosat File pS Beti Run tase Teels Setup Quit a Gas TWO REG2 En ee en oe ae ae _Transp Mobility We remark that for gas flow we need not to use this option because only gas species are mobile then and not dissolved species If you want to express Cim in mol l immobile water you have to change the data for the total amount of component Cim r Transport Components and the constants in the rate equations Kinetics Rate Equations See example file TWO_REG1 eco In the following 2 ECOSAT screen dumps you see the calculated result of both approaches in the form of diagrams for the concentration profiles see also VIEW chapter 2 1 13 Note the difference for the concentration and adsorbed amount of Cim 56 Concentration profile for file TWO REG1 ECOSAT transport Day 7 8800e 01 U Vo 3 940000 Concentration Concentration C_m C_im o E 0 m 1 0 0 0 2 0 0 0 2 E 2 E 2 Ads_Concentr Ads_Concentr Q _Cnm Qx _Cinm o E 0 m 1 0 0 0
3. Due to the numerical solution method finite differences one should take care of proper choices for the numerical grid These choices depend on the values for the flux vo and the diffusion dispersion coefficient D Which of these two variables is the most important can be estimated with the column Peclet number Pe y VE oD Pe column Peclet number L column length For Pe gt 100 convection dominates and for Pe lt 100 diffusion becomes important For large Pe stable solutions are found at least for mono component transport if Bmix lt 1 v At R Ax poQ R retardation factor R 1 LOC lt 1 mix with Q the adsorbed amount mg kg C the concentration in the water phase mg l p the dry bulk density kg l and 6 the volumetric water content For small Pe values stable solutions are found for amix lt Ye at least for mono component transport D At y W RA For multicomponent transport more strict stability criteria are often necessary e g a lt 1 3 partly because R varies then often with time Too small time steps increase numerical dispersion caused by to many calculations each with numerical truncation errors Sharp concentration fronts will always become diffuse due to numerical dispersion Take At as large as possible for a certain choice of Ax To increase accuracy smaller Ax values and thus also smaller At values stability criterion can be taken Combination of for example s
4. plane gel 12 Charge models Diffuse Double Layer Constant Capacitance Basic Stern Three planes Donnan only for gel geometry Examples of possible choices for the sorption model nvc Freundlich nvc Langmuir normal nvc lon exchange Gaines Thomas nvc lon exchange Donnan nvc Heterogeneous NICA vc Langmuir normal plane Basic Stern vc Langmuir advanced plane Diffuse double layer vc Heterogeneous NICA gel Donnan See the help text F1 for more detailed information about the sorption models When all particle surfaces are added to the edit table you have to save this edit table Quit and Save press Esc or F2 or F3 After specifying particle surface data you have to define the surface components not for Freundlich surface species and model parameters select EDIT ADSORPTION SURFACE SORPTION All variables surface components and surface species and all model parameters can be added automatically after saving this particle surface edit table if the database auto fill parameter is set to Yes default value see chapter 2 2 Selection is based on particle surface name sorption model and already defined normal components See chapter 2 1 9 for multiple run calculations with particle surface total amount EDIT MULTIPLE RUN See chapter 2 1 13 for optimization calculations for particle surface total amount with FIT ECOSAT EDIT FIT To edit the surface components
5. Build Webs Run Dbase Tools Setup Quit Rate equations Group Part Surf kAAAAAAAAKAKAK A 1 0000 C species 1 0000 Q 52 species 1 0000 species 1 0000 Q 52 species In the first row of this table we have formulated the term p 8 k2 1 F Ka Cm of equation 21 with log p 0 kz 1 F Ka 0 5814 The second row represents the second kinetic term of equation 21 k2S with log k2 0 1761 In the third and fourth row the kinetic terms of equation 22 are formulated Transport mobility edit table Finally we have to inform ECOSAT that the species Q_S is immobile Ecosat File Build Weil Run Dbase Tools Setup Quit 62 Concentration profile for file TWO SITE ECOSAT transport Day 3 7500e 01 U Vo 0 750000 Concentration Ads_Concentr Total_Solut ion c Q_si Q_s2 References Gaber H M W P Inskeep S D Comfort and J M Wraith Nonequilibrium transport of atrazine through large intact soil cores Soil Sci Soc Am J 59 60 67 1995 Parker J C M Th van Genuchten Determining transport parameters from laboratory and field tracer experiments Virginia Agric Exp Stn Bull no 84 3 63 Appendix 5 Semi 2D and Semi 3D transport in ECOSAT Semi 2D and semi 3D transport in ECOSAT General introduction The formulation of the continuity equation which is the basis for description of mass transport in soils is given in general terms by oC E V vC V DVC concentration diffusion disp
6. PARAMETERS Choose as transport calculation type 1D water flow 1 dimensional flow in the water phase 1D gas flow f 1 dimensional flow in the gas phase s2D water flow semi 2 dimensional water flow s2D gas flow semi 2 dimensional gas flow s3D water flow semi 3 dimensional water flow s3D gas flow semi 3 dimensional gas flow For s2D and s3D flow you have to make a separate input file s2D or s3D with ecosat file name Go to INPUT s2D FILE or INPUT s3D FILE See also 2 1 12 7 and 2 1 12 8 For time step a suggestion is given based on two different stability criteria One for dominant convective flow and one for dominant dispersive flow see appendix 3 Diffusion coefficients for species or gases and for suspended particles are set in this table Dispersivity can be set in the soil column data sets 2 1 12 2 See appendix 3 for information about the 2 possible boundary conditions Select output for different time steps and nodes Several options are available like ALL First LAST SEVERAL SELECT TIME or DEPT OUTPUT FILE tof or dof If you have a lot of specific output depths or moments you can use a data file tof or dof This might be very convenient in case of optimizing transport parameters with FIT See chapter 2 1 13 for optimization calculations for the diffusion coefficient with FIT ECOSAT EDIT FIT 2 1 12 2 Soil Column Soil column data is specified in the soil column edit
7. TWO _REG1 eco Transport combined with 2 region kinetic model Cim expressed in mol l immobile water View diagrams for total amount of the compound in the 2 regions TWO _REG2 eco Transport combined with 2 region kinetic model Cim expressed in mol l mobile water View diagrams for total amount of the compound in the 2 regions TWO_SITE eco Transport combined with the 2 site kinetic model View diagrams for the compound in the 2 sites 75 76
8. Cm and Q Cm are expressed in mol l mobile water and Cimt Cim and Q _Cim in mol l immobile water Schematically this system is presented in figure 1 1 In figure 1 1 the solid arrows between two species indicate that they are in equilibrium The dotted arrows indicate that mass transfer is rate limited m im The slow mass transfer equation can be formulated as 7 a C C 1 t with Sim 7 the total amount of the component in the immobile region dissolved and adsorbed Sim T OimCim 1 ApKgCim mol l soil 2 with fthe mobile water fraction Om 6 and Om 1 6 the immobile water fraction p is the soil bulk density kg l and Kg the distribution constant l kg a is the mass transfer rate constant d Cm in mol l mobile water and Cim in mol l immobile water 50 Kg Ge Sh gt K z gt Sim Figure 1 1 Schematic representation of the concept upon which the two region model is based linear sorption model The governing transport equations to describe the 2 region system mathematically are OC K OS mT Ta fe d oC i L C im T 3 A On a 0 0 a oe LIC v D 4 Jam Ze Da gt 4 Sr OC 0 1 K a C C 5 F On tA F Ka a G C 5 v local pore velocity m d Dm diffusion dispersion constant for the mobile water region m d In the mobile region transport of solutes is described by an advective dispersion equation In t
9. M F Benedetti and M J Avena lon binding to natural organic matter composition heterogeneity stoichiometry and thermodynamic consistency Colloids and Surfaces A 151 147 166 1999 Dzombak D A and F M M Morel Surface complexation modeling hydrous ferric oxide John Whiley amp Suns 1990 New York 39 40 Appendix 2 Reaction Kinetics In ECOSAT Reaction kinetics in ECOSAT Slow mass transfer reactions taking place in soil water systems like decay of organic compounds desorption from organic matter and dissolution of minerals are described according to the next general formulation Mass transfer reaction aA bB lt cC dD A is a component and B C and D are species a b c and d are stoichiometric coefficients d A Rate equation for component A a K A TB K C D K is the forward rate constant mol l day K the backward rate constant x y p and q are parameters related to the reaction order of A with respect to the species B C and D If B C and D are components rate equations have to be formulated for these components as well For example for component C AC Ex AIB Ex ICPD dt a a The partial differential equation is solved numerically using an integration method Several choices for the integration method are possible Euler explicit method Runge Kutta order 2 Runge Kutta order 4 with constant time step more accurate Runge Kutta order 4 with variable time step less accurate but pr
10. In most edit tables the first column is reserved for the name of the variable e g component or species The format of this column is of type 1 combined with type 2 In this case the available menu options are Select Item Select the variable from the specified database file in a second window you can make a selection from the active database set Not only the variable name but also all other data specific for the chosen variable present in the other columns is retrieved from the database file and added to the edit table Set Dbase file Select the active database file from a second window Edit name Edit the variable name use this only if the variable name is not available from the database file Changing a component name is equal to deleting the old one and inserting a new one This can mean that surface species become deleted Quit Quit the window without making any selection same as Esc 2 Input manager Start the program with ECO DOS or click on button ECOSAT Input Run in ECOSHELL Windows The program begins with displaying the ECOSAT start screen Press any key to continue The next screen displays several menu options in the ECOSAT main menu and an overview of the system description Use F1 to get on line help information anywhere in the program In the second row at the left the actual file name ECO is shown ECOSAT main menu options see also figure 4 File File handling retrieve save start a new fi
11. NICA_DON sof RADIALS3D eco Transport of chloride by semi 3 dimensional water flow radial symmetric Flux data and scaling factors in file radials3d s3d View diagram of total amount of Cl in the soil column Output RADIALS3D sof breakthrough curve of Cl at several nodes REL _MIN eco Zn adsorption on Fe oxide particle surface according to Freundlich model Total amount of Fe oxide equal to calculated amount of goethite related mineral Variable pH and constant ionic strength SPM_TRAN eco Transport of zinc via 1 dimensional water flow Adsorption of Zn according to the SPM model View diagrams for solid solution formation pH and Zn total amount in different phases Solution not stable SPM_PLOT eco Adsorption of Zn according to the SPM model Multiple run for Zn concentration Constant pH and constant ionic strength Output SPM_PLOT sof 74 TRA _ATRA eco Transport of atrazine combined with slow desorption according to the 2 site kinetic model View diagrams of fast and slow reacting atrazine TRA _CD H eco Transport of Cd H and DOC via 1 dimensional water flow Adsorption of Cd onto soil and suspended DOC according a pH dependent Freundlich model View diagrams for total amounts of relevant compounds TRA _PO4 eco Transport of phosphate via 1 D water flow Adsorption of PO on goethite according to the Tri plane model VC Langmuir Normal Plane Triple Layer View diagrams for phosphate in several phases
12. OC p p L C LK 1 P K C 4KS 19 A a K 9 19 EK 1 PK C K S 20 59 Note that the unit of S is in mol kg Using the transformation S oS it is expressed in mol l soil water We then get OC UC 7 K 1 PK C KS L C k C k S 21 amp TD K 1 F K C K S k C k S 22 Now we will show were to fill in the data into ECOSAT for this model The data we will use are given in tables 2 1 and 2 2 see also example TWO_SITE Table 2 2 Speciation and transport data for the two site kinetic model Seren OT omona ranson vp Darcy flux m d Fees concntaton mueres o 60 Components edit table Ecosat File Build Meis Run Dbase Tools Setup Quit j C ECOSAT EXAMPLES TWO SITE Edit Components onstant Calc Total amount ge mo1 1 Total amount 1 0000000E 01 Total amount 9 4400000E 02 1 000000 1 0000 The total amount of C is 0 1 mol mobile water The total amount for Q_S in the system has been calculated from the total amount for C assuming equilibrium at time 0 First calculate C for C 0 1 mol l Cr C QS C Fp K4 Cl O C 0 1 2 695 0 03711 Then calculate the concentration of Q_S Q_S 1 F p Kg C 6 mol l 0 6 x 1 5 x 10 x 0 03711 0 5 0 0944 mol l Species edit table Ecosat File j Dbase Tools Setup Quit j C ECOSAT EX O SITE Edit Species Molar mass teference KAKKAKKKE comment Ecosat File Build We Run Dbas
13. both H and OH will then be calculated With H2O gt Total amount we mean that total amount of component H or OH is constant and that the actual value will also be determined by water dissociation The total amount of components H and OH constant calculation type H2O gt Total amount does not include the total amount present in water 55 56 mol l at 25 C This value of 55 56 mol l will be added automatically by the program ECOCALC Thus for H and OH total amount in the components edit table can be zero while they still are present Total amount for H and OH given by the output manager does NOT include this 55 56 mol l In the H20 edit table select EDIT PHASES H20 it is possible to change the dissociation constant of water 2 1 7 Environment The environment parameters ionic strength temperature and gas volume have to be defined in the environment edit table select EDIT ENVIRONMENT lonic strength is necessary to calculate the activity coefficients which will be used to convert component and species activity into concentration ECOSAT uses a slightly adapted Davies equation for that purpose see help text for detailed information Parameters for the Davies equation can be set at SETUP 10 Temperature can be used to calculate log K for dissolved species gases minerals and organic liquids at temperature T with the given log K at T 298 15 K and delta H enthalpy change with the Van t Hoff equatio
14. content data in the soil column data sets is used For that purpose negative values 1 for water and gas content are given in file s3d 20 Parameter or variable value e g 1 and 2 Soil column data sets depth e Set name e g A e Depth e Components total amount or concentration or activity e Partial gas pressure e Particle surface total amount e lonic strength e Temperature e Volumetric water content e Volumetric gas content e Dispersivity nm Figure 5 Soil column data sets A B C D E F for different soil depths For example dashed line component total amount and dashed dotted line component activity pH Possible parameters and variables in the soil column data sets are indicated Parameter or variable value e g 1 and 2 Feed data sets Set name e g A Time period Component total amount or concentration or activity Partial gas pressure Particle total amount lonic strength Temperature Flux Figure 6 Feed data sets A B C D for different time periods For example solid line dark gray water flux and dashed line light gray component total amount Possible parameters and variables in the feed data sets are indicated 21 2 1 13 View In case of transport calculations it is possible at runtime to look at calculated results for components species gases minerals organic liquids particle surfaces surface components surface species ionic strength
15. data for components gases particle surfaces or environment parameters to fill feed data sets Go to EDIT TRANSPORT READ FEED FILE INPUT FILE and select the input data file e g with extension DAT or PRN Then specify the total number of text lines labels or blank at the top of the file option TEXT LINES Then specify in the edit table for column order option COLUMN ORDER which data types see chapter 3 can be found in the different columns Select then option READ FILE to compose the feed data sets 2 1 12 7 Input s2D File See also appendix 5 Semi 2D and semi 3D transport in ECOSAT Make s2D file for semi 2 dimensional transport Go to EDIT TRANSPORT INPUT s2D FILE The file s2d name of eco file contains for all nodes the following data flux m day scale factor 1 h1 scale factor 2 h2 volumetric water content and volumetric gas content Make this file with help of menu option INPUT s2D FILE READ s2D FILE The data will be read from a DOS ASCII text file e g prn with the relevant data ordered in columns Create this text file with help of menu option INPUT s2D FILE FILL s2D FILE or with option INPUT s2D FILE AXIAL SYMMETRIC or with any other DOS text editor If you want to use the volumetric water and gas content as given in the soil column data sets give negative values e g 1 for these parameters in file s2d Default values for the scale factors 1 For axial symmetric cylindrical flow f
16. exchange reaction into surface complexation reactions taking one of them as the reference reaction with log K 0 results in adapted log K values for all other ion exchange reactions see table 6 E n X0 K and X t p CEC l l ith p in kg l m XO 17 2 nd X t p mol l with p in kg Using the exchange coefficients for ion pairs the relevant surface reactions with their log K values are formulated automatically by the input manager of the ECOSAT program 36 Table 6 Table of species for Gaines Thomas ion exchange of components A and B Components Species mol l n log Krerr 0 m log Kg Totelamount mol xy aw ew Heterogeneous models Sorption of heavy metals onto organic matter is often only satisfactorily described if heterogeneity of the organic matter surface caused by different reactivity of reaction sites is taken into account Different models have been implemented in ECCOSAT The most important ones are Langmuir Freundlich 0 Ko KC KC l1 K Ch with m heterogeneity parameter which characterizes the width of the log K distribution function i ranges from 1 to the total number of all competing components K median affinity constant of component i for the surface site NICA non ideal competitive adsorption EC DECO ZG 1 R C ni and p are model parameters indicating ion specific and surface site specific heterogeneity inter actions respectivel
17. log K values adapted Mass balance formulations are changed sometimes and derivatives ofthe mass balance functions are determined analytically or numerically Some of the possible sorption models are discussed here in more detail For more information see the textbook on Chemical sorption in the soil water system Freundlich Heavy metal behaviour in soils is quite often reasonably well described with the empirical multi component Freundlich model For example for cadmium sorption interaction of pH zinc and calcium has been reported leading to formulations like 34 Qoa Keg Cd H Zn Ca with Qca in mol kg According to the standard speciation calculation the dimension of the surface species Qca has to be changed into mol l This makes adaptation of the log K value necessary K cp Kca with soil solution ratio in kg l The multicomponent Freundlich equation is not an expression for competitive sorption but includes only several interaction terms The most important one is the pH dependency of heavy metal sorption However in standard speciation programs this formulation should lead to wrong expressions for the mass balances of all components involved e g a mol Cd or c mol Zn per mol Qca To solve this problem parameter values are changed in the calculation of the mass balances a gets the value 1 in the mass balance for Cd and b c and d get the value 0 in the mass balances for H Zn and Ca respectively An example
18. output unchanged data saved by ECOCALC in sequential order menu option BASIC or ALL The column ordered output file can easily be imported into a spreadsheet program To run the output manager in a Windows environment click button ECOSAT Output in ECOSHELL see figure 2 To run the output manager in a DOS environment type OM OM BAT is a batch file with the command OUTMAN See chapter 3 for detailed information 1 4 ECOSAT edit tables System description is specified in so called edit tables saved in tmp files in subdirectory ecotmp There are edit tables for all different groups of variables such as components species gases minerals organic liquids particle surfaces surface components surface species environment ionic strength temperature gas volume for PC and program setup and for additional information used for the different calculation types Multiple run e g titration or reading measured data from file Cascade repeated soil extraction Kinetics slow mass transfer Transport 1 dimensional stationary water or gas flow also semi 2 or 3 dimensional transport using mathematical transformation to 1 dimensional transport e g axial or radial symmetric flow Fit parameter optimization with the program FIT version 2 5 In these tables input data can be specified for each variable or parameter in a separated table row Data in the different columns represent specific formatted information for
19. soil composition calculation but that for all next calculations the total amount is constant and thus concentration or activity variable Of course total amount will vary due to mass transport 18 For transport calculations we normally don t use constant calculation types Concentration and Activity Partial gas pressures are set in the gases edit table select TRANSPORT SOIL COLUMN EDIT GASES Total amount of particle surfaces is set in the soil column particle surfaces edit table select TRANSPORT SOIL COLUMN EDIT PARTICLE SURFACES Soil column parameters are set in the soil column parameters edit table select TRANSPORT SOIL COLUMN EDIT PARAMETERS Here parameters like calculation type for ionic strength ionic strength temperature volumetric water content volumetric gas content and dispersivity for species and suspended particles are set For s2D or s3D flow volumetric water content and volumetric gas content can also be set for each node in file s2d or s3d 2 1 12 3 Feed Feed data can be considered as input data for the upper boundary in the soil column They are specified in the feed edit tables For each time period a feed data set can be defined figure 6 Each data set contains information concerning the feed composition and flow characteristics The program creates always a default data set with the name Start default in which component concentrations particle surface amounts g
20. that variable see figure 3 Special function keys see Help text F1 for more information F1 on line help help index F2 Save the edit table and return to the ECOSAT main menu F3 Save edit table and go back to previous menu F4 Accelerator to PHASES menu F5 Accelerator to ADSORPTION menu F6 Accelerator to MULTIPLE RUN menu F7 Accelerator to KINETICS menu F8 Accelerator to TRANSPORT menu Esc Quit the edit table do not save Back to previous menu Ins Insert row in edit table Del Delete field in edit table Alt Y Delete row in edit table Alt CG Copy row in edit table Dbase Tools Setup Quit Components Charge onstant Ci Total amount Lmat lar mass comp comp ype mol 1 g mo 112 0000 6 000000 2 000000 35 4000 Select from Db 7 000000 1 0000 Edit name 7 000000 17 0000 Quit Save Quit Figure 3 Components edit table in the ECOSAT input manager selection from database The maximum number for most variables in the edit tables amounts 200 maximum of 200 rows in the tables However maximum amount of components and particle surfaces is limited to 25 in the database 200 For each particle surface maximum number of surface components and surface species amounts respectively 15 and 75 Limits depend also on your computer memory The columns in the edit tables have all a specific format Several format types are possible Select from menu Select from data set Integer value
21. the column Related Mineral Total amount of the mineral mol l is converted into kg l for the particle surface with the molar mass of the mineral The total amount for the particle surface specified in this edit table is then an initial estimate for the iteration procedure For maximum number of iteration steps and relative tolerance value default 0 5 see Setup 2 5 ECOCALC converts total amount of the sorbed components surface species from mol kg into mol l by adapting log K values to log K values For nvc models by using the particle surface total amount kg l and total amount of the surface component mol kg and for most vc models by using the number of sites nm specific surface area m kg see model parameters and particle surface total amount kg l Selection of sorption models occurs according to the following scheme press ENTER in the column Sorption model Non Variable Charge Freundlich Langmuir normal 1 site advanced 2 sites lon Exchange Gaines Thomas Donnan Heterogeneous NICA CONICA Langmuir Freundlich Generalized Freundlich Toth Variable Charge Langmuir normal 1 site gt GM VC advanced 2 sites gt GM VC Heterogeneous NICA gt GM VC CONICA gt GM VC Langmuir Freundlich gt GM VC Generalized Freundlich gt GM VC Toth gt GM VC Surface Precipitation Model SPM gt GM VC choose geometry and charge model Geometry
22. then log conc act has to be given as an estimated starting value The equilibrium concentration will be calculated then If concentration or activity is constant then total amount will be calculated no input value for total amount is necessary can be zero If total amount is constant known value constant calc data type Total amount or P gas gt Total amount or H2O gt Total amount you have to give a positive value for the total amount of the component present A total amount of zero means that the component is not present in the system for that calculation unless data type equals P gas gt Total amount or H2O gt Total amount In case of zero total amount and constant calc data type Total amount all concentrations of surface species and phases containing this component are set to zero For the components H and OH the program will automatically add the amount present in water 55 56 mol l for these two components Therefore data type equals H20 gt Total amount The constant calculation data type can also be P gas gt Total amount which indicates that total amount is constant and partly determined by the constant gas pressure of the gas species containing the component It is possible and convenient to select all components from the database file However it is also possible to add them directly into the components edit table If you want to add components to the components datab
23. 1 0 0 0 2 E 1 E 1 Concentration profile for file TWO REG2 ECOSAT transport Day 7 4400e 01 U Vo 3 720000 Concentration Concentration Cm C_in o E 0 m 1 0 0 0 3 0 0 0 3 0 E 2 E 2 Ads_Concentr Ads_Concentr Qx_Cm Oase Cim o E 0 mn 1 0 0 0 1 0 0 0 2 0 Two site kinetic model In the two site kinetic model Parker and Van Genuchten 1984 assume two different types of adsorption sites For one type of the sites adsorption will take place instantaneously and for the other type adsorption is rate limiting Since the surface species belonging to this rate limiting adsorption are not in chemical equilibrium with the rest of the system we have to define additional components for these species Table 2 1 describes the two site kinetic model that is used in Gaber et al 1995 TABLE 2 1 Table of species belonging to a simple two site kinetic model species C QS 0 15 Q S total amount Cr mol l 0 0944 B In this table of species we have defined a compound C which can adsorb onto two different sites The total amount of Q_S corresponds to the amount of the compound C that is initially adsorbed onto the slow reacting surface sites S2 Since Q_S is not in chemical equilibrium with C Q_S is also used as component For the fast reacting surface sites S a linear Freundlich isotherm is chosen However we may choose also a non linear Freundlich equation Other sorption models are not possible due to the fact that i
24. 13 2 1 8 3 Surface species All surface species present on the selected particle surface have to be defined in the surface species edit table go to EDIT ADSORPTION SURFACE SORPTION SURFACE SPECIES Here the surface species name and composition log K and depending on the chosen sorption model other parameters can be edited The surface species can be added automatically from the database file if the database auto fill parameter has been set to Yes default value It is very easy to select surface species from the database file However it is also possible to add them directly into the surface species edit table If you want to add new surface species for this particle surface to the database files go to DBASE ADSORPTION SURFACE SORPTION SURFACE SPECIES EDIT and edit the database file When editing is finished you have to save this edit table Quit and Save press Esc or F2 or F3 For the Freundlich model Log K values of the surface species are adapted to log K values by ECOCALC using total particle surface amounts and the correction for ionic strength only for the dissolved components present in the sorption model formulation For the Langmuir advanced sorption model bi dentate surface species are formed by complexation with two surface components A and B For all sorption models except Freundlich and ion exchange Log K values of the surface species are adapted to log K values by ECOCALC using the correction for ion
25. Ac Oxalate Ox and Citrate Cit species all amino acids ECO_ACTI dbB all U and UO species actinides ECOMIN1 dbD all minerals not present in ECOMIN2 or ECOMINS ECOMIN2 dbD all SiO4 MoO4 SeO4 Ag Se As and Hg minerals ECOMINS3 dbD all U and UO minerals The ECOPART dbS database for surface sorption data contains examples of data for different types of sorption models for particle surfaces mentioned in file ECOPART dbP Included is some recent data for NICA sorption of heavy metals on humic acid and sorption data of metals and oxy anions on HFO Hydrous Ferric Oxide Data from database files for a specific variable group can be selected in the corresponding edit table go to the first column and press ENTER choose Select from Dbase in the displayed window Automatic addition of surface species gases minerals or organic liquids for newly added surface components or particle surfaces from the database files is possible if the auto fill parameters for the relevant variable groups are enabled Building your own speciation system starts with selection of components from the components database file ECOCOMP After saving the components edit table the program will automatically search for other relevant variables e g species gases minerals organic liquids in the available database files When found they will be added to the edit tables However this automatic procedure is not recommended for gases and minerals You can
26. DIT GASES Total amount of suspended particle surfaces is set in the feed particle surfaces edit table Total amount of other particle types solid and biota is set to 0 0 TRANSPORT FEED EDIT PARTICLE SURFACES Feed parameters are set in the feed parameters edit table select TRANSPORT FEED EDIT PARAMETERS Here parameters like ionic strength calculation type ionic strength temperature and flux are set For s2D or s3D flow flux for each node is read from file s2d or s3d 2 1 12 4 Mobility Sometimes it might be useful to exclude certain components present in the form of dissolved species from transport In this edit table mobility of species in the water phase can be enabled This can be a useful option in case of transport in combination with reaction kinetics see 2 1 11 19 2 1 12 5 Read soil column file Read column ordered data for components gases particle surfaces or environment parameters to fill soil column data sets Go to EDIT TRANSPORT READ SOIL COLUMN FILE INPUT FILE and select the input data file e g with extension DAT or PRN Then specify the total number of text lines labels or blank at the top of the file option TEXT LINES Then specify in the edit table for column order option COLUMN ORDER which data types see chapter 3 can be found in the different columns Select then option READ FILE to compose the soil column data sets 2 1 12 6 Read feed file Read column ordered
27. DVC If there is no divergence V v 0 and if D depends only on r V vC V D r V C with v and D as function of r The data for the flux v r and for the scaling factors hi h2 h3 have to be given in a data file s2D or _s3D Example cylindrical flow v 1 at r 1 0 node 0 node v h h2 hs 1 1 11 1 0 9 1 2 1 25 1 0 8 1 3 1 43 1 0 7 1 4 1 67 1 0 6 1 5 2 1 0 5 1 6 2 5 1 0 4 1 7 3 33 1 0 3 1 8 5 1 0 2 1 9 10 1 0 1 1 10 100 1 0 01 1 At r 0 we take a small value for r otherwise zero division Available pore volume for flow water content or gas content can also be a function of r In that case add an extra column for 6 For radial symmetric spherical flow we get a more or less equal approach Scaling factors are then h 1 h2 r and hs r sing Mass transport equation in pole coordinates Knowing streamlines and equipotential surfaces the transport problem can be solved in a coordinates system determined by these streamlines and potential surfaces Bear and Verruyt 1987 If diffusion dispersion can be neglected we can solve the transport problem along the streamlines Note no diffusion dispersion at all If only transversal diffusion dispersion can be neglected we have to know the scaling factors for all nodes They have to be derived numerically from flow data Introducing the potential coordinates 8 8 we can solve this 3D problem in 1D in the flow direction or amp direction The potentia
28. Real value Log real value Character string Unit choice for variable or parameter value Toggle yes no CONOOoRWN The field width is an indication for the maximum number of characters that can be used for type 3 4 5 6 and 7 To find out which format for a column is applicable move the cursor to a field in a specific row and column using arrow keys and press key ENTER For type 1 and 2 a window appears with several menu options or with a specific data set e g all components present in the database Use arrow keys to move and press ENTER to select For selection of an item from the data set shown in the window you can also move the cursor to a certain item by typing the first character s of its name For type 3 4 5 and 6 the cursor will move into the field and you can start editing For those column format types it is not necessary to start editing always with ENTER You can also directly start editing by typing the first character of the number or string ECOSAT will check for the right format For type 7 a window appears with several menu options Use arrow keys to move and press ENTER to select You can choose a certain unit and add then the variable or parameter value e g mol l or mg l for the total amount of the component ECOSAT will automatically recalculate this value into the standard default unit e g mol l For type 8 the value in the field changes after pressing ENTER Yes gt No and No gt Yes
29. Table of species for benzene toluene no mixture present Components Benzene Toluene logkK Species mol l Benz w Tol w Benz g Tol g H H Qbenz Qioi log Ka roj Phases Benz L Tol L Total amount mol l For a mixture of both organic liquids introduce new components and adapt log K for all relevant species 33 Table 3 Table of species for benzene toluene mixture of organic liquids present Components Berl Toll logk Species mol l Benz w Tol w log Sbenz log Sroi a log Hg Benz Tol g Qbenz Quo Benz L Tol L Total amount mol l Benz t Calculate species concentrations by dividing log K with Benz L Tol L log Stoi log Hg Toi log Spenz 10g Ka Benz m Sto log Ka roi OOk ECOSAT adapts automatically the table of species in case of the presence of organic liquid mixtures Sorption models To describe adsorption or desorption different types of sorption models are available in ECOSAT Components adsorb to particle surfaces where surface sites surface components react with the component resulting in bound components surface species Taking electrostatic effects into account leads to the so called variable charge VC models Possible VC models are Diffuse Double Layer DDL Basic Stern BS Constant Capacitance CC Triple layer and Donnan The surface complexation reactions are described with the Langmuir
30. Y User manual 2009 M G Keizer W H van Riemsdijk Department of Soil Quality WAGENINGEN UNIVERSITY WAGENINGEN EGS ECOSAT A computer program for the calculation of Speciation and Transport in soil water systems 2009 version 4 9 M G Keizer amp W H van Riemsdijk Department of Soil Quality Wageningen University P O Box 47 6700 AA Wageningen The Netherlands WAGENINGEN UNIVERSITY WAGENINGEN IEN Table of Contents 1 Introduction 1 1 Installation 1 2 Program structure 1 3 Getting started 1 4 ECOSAT edit tables 2 Input manager 2 1 System description 2 1 1 Components 2 1 2 Species 2 1 3 Gases 2 1 4 Minerals 2 1 5 Organic liquids 2 1 6 H20 2 1 7 Environment 2 1 8 Adsorption 2 1 8 1 Particle surfaces 2 1 8 2 Surface components 2 1 8 3 Surface species 2 1 8 4 lon Exchange coefficients 2 1 8 5 Model parameters 2 1 9 Multiple run 2 1 10 Cascade 2 1 11 Reaction kinetics 2 1 12 Transport 2 1 12 1 Transport parameters 2 1 12 2 Soil column 2 1 12 3 Feed 2 1 12 4 Mobility 2 1 12 5 Read soil column file 2 1 12 6 Read feed file 2 1 12 7 Input s2D file 2 1 12 8 Input s3D file 2 1 13 View 2 1 14 Fit 2 1 14 1 Fit Ecosat 2 1 14 2 Data input 2 1 14 3 Procedure 2 2 Database files 2 3 Build 2 4 Tools 2 5 File 2 6 PC and program setup 3 Output manager Appendix 1 Speciation calculations in ECOSAT Appendix 2 Reaction kinetics in ECOSAT Appendix 3 Multicomponent transpo
31. ake by yourself a short cut to your pc desktop icon for ECOSHELL exe 1 2 Program structure The ECOSAT package consists of 4 different programs all related to each other Input manager ECOSAT Calculation program ECOCALC Output manager OUTMAN Windows shell ECOSHELL ECOSAT is the user input interface to compose and edit your own system Data is stored in file ECO ECOCALC is the main program doing the calculations reading data from file ECO Output results are stored in file ECO at the end of the system description OUTMAN is the user output interface which can be used to select specific output results Data from file ECO are read and used to make the selected output which is saved in file OUTMAN DAT see figure 1 To facilitate working with ECOSAT in a Windows environment you can run ECOSHELL exe These programs can run independently when their input files are available ECOSAT run ECO bat last ECO file as default input OUTMAN run OM bat last ECO file as default input ECOCALC type ECOCALC ECO ECO as input file only in DOS environment ECOSHELL run double click short cut icon on your desktop see figure 2 file name maximum of 8 characters ECOSAT Input manager ECOCALC niee OUT M AN Output manager Y outman dat Output file Figure 1 ECOSAT program and file structure Fit Ecosat shell ECOSAT Input Run ECOSAT Output Help Exit Work directory d ecosat Show Ou
32. akthrough curve combine columns and pile stack columns Make Make selected output and write data into file OUTMAN DAT save output selections in file OUTMANIN SOF 29 Basic Write basic output to file OUTMAN DAT basic output output from ECOCALC saved in file ECO This is the minimum output needed for OUTMAN to calculate all other output All Write basic output all species concentrations to file OUTMAN DAT Setup PC set up Quit Make file OUTMANIN SOF and quit program no output In stead of edit tables OUTMAN works with so called choice tables where different types of output for specific variables can be chosen from a menu displayed in a window figure 11 Basic All Setup Quit Components Output Outpu O Selection Selection all Dissolved Total all Save Back Save Quit Figure 11 Components output choice menu in the output manager OUTMAN uses the data in the edit tables of the input manager as input for the system description or creates these edit tables first on retrieving the selected ECO file For each variable group component species gas mineral organic liquid particle surface surface component surface species environment parameters you can select different types of output in these choice tables select CHOICE Delete all former choices with option Delete all After output selection you can select MAKE to create the selected output OUTMAN reads then the calculated o
33. ally the components species etc from the database files After selection of the variables present in the system you can define a certain calculation type e Multiple Run Single Run the default calculation type e Cascade e Kinetics e Transport e Fit parameter optimization combine with FIT exe If the system description is complete select menu option RUN The calculation starts then The output manager OUTMAN will get started automatically when calculation is finished Don t make your system too complicated at the first time but try to run the program first with a rather simple system To create a complete new system go to menu option FILE and select option NEW All edit tables will get cleared and you start with empty edit tables Select menu options EDIT or BUILD to formulate your new system 2 1 System description See also appendix 1 Speciation calculations in ECOSAT 2 1 1 Components First of all you have to select the components which will be present in the system select EDIT and then COMPONENTS in the edit menu In the components edit table you have to fill in the component names and further also data like constant calculation data type indicating what is constant total amount concentration or activity total amount estimated concentration or activity log value charge and molar mass see also figure 3 For each component only total amount or concentration or activity can be constant If total amount is constant
34. and temperature for the soil column in a diagram on the screen Several data output types in default units are possible depending on the variable group e g concentrations mol l activities total amounts mol l This can be specified in the view edit tables select EDIT VIEW There is a maximum of 10 diagrams possible See figure 7 and 8 for examples Figure 7 shows the screen for a reaction kinetics calculation see example file KIN_BT_1 eco and figure 8 for a transport calculation see example file TRA_CD_H eco ECOSAT kinetic Day 2 4400e 01 Total_A11 Total_Solution Benz Benz E 0 E 2 0 0 0 0 o 2 5 o 2 5 E 1 days E 1 days Total_A11 Total_Solution Tol Tol 1 0 1 0 E 0 E 2 0 0 0 0 o 2 5 o 2 5 E 1 days E 1 days Figure 7 Screen display of reaction kinetics calculation example file KIN_BT_1 eco Different time curves in the diagrams y axis variable value x axis time days Slow first order decay of a mixture of benzene and toluene in the water phase 22 ECOSAT transport Day 3 0800e 01 U Vo 0 205333 Concentration Ads_Concentr Ads_Concentr Cd Cd soil Cd DOC o Oo E 1 E 1 m m 5 0 5 0 5 0 0 0 1 0 0 0 1 0 0 0 5 0 E 4 E 3 E S Total_amount Total_amount logtAct gt poc Soil Fr H Figure 8 Screen display of a transport calculation example file TRA_CD_H eco Different soil column concentration profiles in the diagrams y axis soil depth x axis variable value Leaching of C
35. as pressures and flow parameters are initially set to 0 0 Environment parameters ionic strength and temperature for the feed get the same default value as in the environment edit table EDIT ENVIRONMENT First edit this default data set or define your own specific data set select TRANSPORT FEED DEFINE or EDIT Use other feed menu options to copy or delete specific feed data sets or to get an overview of all data sets defined for certain time periods option VIEW Feed composition will be calculated with the data in the feed edit tables Component data total amount concentrations activities have to be set in the feed components edit table select TRANSPORT FEED EDIT select data set COMPONENTS Constant values can be given However it is also possible to let ECOCALC calculate component total amount or concentration or activity as a function of time select calculation type Function in stead of Constant A linear or an exponential function can be chosen for each different component and their parameters can be set here Also the constant calculation type can be set constant Total Amount Concentration Activity P gas gt Total amount and H20 gt Total amount For gas flow constant partial gas pressure s constant calculation data type for components in the gas phase will be P gas gt Total amount Partial gas pressures are set in the gases edit table select TRANSPORT FEED E
36. ase file select DBASE COMPONENTS EDIT and edit the database file This file has the default name ECOCOMP dbA When all components are added to the edit table you have to save this components edit table Quit and Save press Esc or F2 or F3 Species gases minerals organic liquids etc can be added automatically from the database files to their respective edit tables depending on the settings of the database auto fill parameters go to DBASE DBASE GROUP AUTO FILL see chapter 2 2 It is also possible to add components automatically to the system via menu option BUILD see chapter 2 3 See chapter 2 1 9 for multiple run calculations with components total amount e g titration and or components concentration or activity e g pH range 2 1 2 Species The dissolved species in the system have to be defined in the species edit table select EDIT SPECIES They will be added automatically from the database files after selection of the components if the database auto fill parameter for species is set to Yes default value see chapter 2 2 In the edit table you can change or add delete species data like name composition delta H and log K values Molar mass of the species will be calculated automatically by the program after saving the edit table All components except e electron are added automatically to the species edit table It is easy to select all other species from the database files However it is also possible to a
37. ater Species edit table Ecosat File Build Jel Run Dbase Tools Setup Quit Reference comment Tools Setup Quit Ecosat File Build Mal Run Dbase Molar ma ce Coe 5 Comp e i Comp KEEKKEKEEKE 0 0000 0 0000 1 0000 E im 0 0000 0 0000 1 0000 Cm We have here only the 2 dissolved species C and Cim Mind that species Cim is not mobile Particle surfaces edit table Interactions Quit Geometry KEKEKEEKEEEESE Q Solid 3 0000E 00 Freundlich Q Solid 3 0000E 00 Freundlich We have defined two particle surfaces Q is the particle surface in the mobile region and Q is the particle surface in the immobile region The total amount we have to fill in is the soil solution ratio So here Q fp Om 0 4 x 1 5 0 2 3 0 kg mobile water and Q 1 f p Oiim 0 6 x 1 5 0 3 3 kg l immobile water 54 Freundlich surface species edit tables We have to fill in two Freundlich surface species tables because we have defined two particle surfaces Q and Q For both surface species Q _C_m and C _C_ im log Kp 0 15 Particle surface Reference comment Edit Freundlich surface spe Comp Surface sorption edit table for particle surface Q Surface species Q _C_m with log Kr 0 15 Adsorption Particle surfaces iaa Interactions Particle surface Comp Surface sorption edit table for particle surface Q Surface species Q _C_im with log Ke 0 15 Kinetics rate equatio
38. can add or edit the specific data in so called edit tables A lot of the data needed can be selected from database files Much attention has been given to an user friendly input and output interface The ECOSAT project on developing a speciation model started already in 1980 by the implementation of MINEQL Westall 1976 Addition of sorption models variable charge models Basic Stern Diffuse Double Layer Constant Capacitance Triple layer and non variable charge Freundlich Langmuir lon exchange made the speciation model much more useful for specific applications in the field of soil chemistry and soil pollution Since then much work has been done on more sophisticated models for the description of sorption of ions to clay s oxides and organic matter sorption models including surface heterogeneity e g on multi component transport models and on slow mass transfer reaction kinetics e g slow decay decomposition desorption dissolution and on transport in the gas phase e g important for volatile organic compounds in case of bioventing Speciation calculations were combined with slow reaction kinetics and transport Together with the FIT program Kinniburgh 1993 it is know possible to optimize a large number of model parameters Literature Keizer M G and W H van Riemsdijk Chemical interactions in soil water sediment PC practical Department of Soil Quality Wageningen University Wageningen 2005 Hiemstra Tj an
39. can start with a complete new system With option BATCH you can do several different ECOSAT runs after each other The ECO files are put in a batch file 2 5 PC and program setup PC and program setup parameters can be adjusted in the edit table SETUP These program parameters determine the maximum number of iteration steps and convergence criteria for various numerical procedures Time integration method can be chosen and the B parameter in the Davies equation can be set see also ENVIRONMENT ionic strength Factors for estimating transport time step F1 and F2 are set here For multiple run calculations a parameter can be set in order to use the previous calculated component results as estimates for the next calculation All these default values are saved in file ecosat48 ini which is a copy of eco_sat ini Ecosat48 ini is only active for the sub directory in which it resides To change eco_sat ini and thus all future ecosat48 ini files choose option save permanently 28 3 Output manager Start the program with OM DOS or click button ECOSAT output in ECOSHELL Windows The output manager OUTMAN can only be used for output selection of calculated data saved by ECOCALC in the ECO files The input manager ECOSAT only writes the system description to ECO files input for ECOCALC Calculated output data saved by ECOCALC in these files can be used as input for the output manager OUTMAN With the output manager you can
40. cted output is automatically saved in outmanin sof Start ECOSAT input manager again and edit Fit data EDIT FIT Select parameters to be optimized PARAMETER CHOICE Insert column position of Y calc in file outman dat DEPENDENT Y VAR and save replace file or run again Start FIT with FITECO here we assume that FIT is located in subdirectory C FIT and define parameter optimization problem create file def e Choose ECOSAT as model e Insert input data file dat with the Y known values and set the position column of the dependent variable e Insert initial values for the parameters e Insert output file name for the optimization results Run FIT FIT automatically starts ECOCALC reads Y calc from outman dat adapts parameter values which will be saved in fit and restarts ECOCALC again ECOCALC reads the parameter data in fit and of course all system data from file eco Parameter data in fit overrules parameter data in eco The ECOSAT output manager starts automatically with arguments M and F OUTMAN M F forcing OUTMAN to generate output automatically conforming the selected output stored in outmanin sof argument M and prevents output to the screen argument F View results of the parameter optimization in the FIT output file res 25 Parameter Optimization with FIT ECOSAT def lt FIT fit lt ECOSAT dat Y known 4 hd ECOSAT
41. d Ca total amounts in solid and water phase NICA_TES eco Adsorption of many heavy metals onto DOM GFA and GHA using NICA DONNAN model NICA 2CD eco Sorption of Cd and H onto humic acid GHA according to NICA Donnan model Gel volume as function of ionic strength Variable ionic strength and multiple run for pH and Cd concentration Output NICA 2CD sof NICA 2DH eco Sorption of H onto humic acid GHA according to NICA Donnan Initially adsorbed amount Q for H Multiple run for background electrolyte K NOz and added base NaOH Na and OH Gel volume function of ionic strength variable ionic strength Fitting parameter Q of H Output NICA 2DH sof NICA CD eco Sorption of Cd and H onto humic acid GHA Multiple run for Cd total amount and pH read from data file mrf Fitting parameters several parameters for surface species Variable ionic strength Gel volume function of ionic strength Output NICA_CD sof NICA DH eco Sorption of H onto humic acid GHA Multiple run for pH read from data file mrf Fit parameter choice for Q H surface components and surface species Variable ionic strength Gel volume function of ionic strength Initially adsorbed amount Q for H Output NICA_DH sof NICA DON eco Adsorption of H and Ca onto humic and fulvic acid according to the NICA Donnan model Variable gel volume as function of ionic strength variable ionic strength Multiple run for Ca and H concentration Output
42. d W H van Riemsdijk Chemical interactions in soil water sediment system Department of Soil Quality Wageningen University Wageningen 2005 Kinniburgh D G FIT User Guide Technical Report WD 93 23 British Geological Survey Keyworth 1993 J C L Meeussen Chemical speciation and behaviour of cyanide in contaminated soils Phd Thesis Wageningen Agricultural University Wageningen The Netherlands 1992 M M Nederlof Analysis of binding heterogeneity PhD thesis Wageningen Agricultural University Wagening en The Netherlands 1992 Westal J J Zachary and F Morel MINEQL a computer program for the calculation of chemical equilibria composition of aqueous systems Technical note no 18 Massachusetts Institute of Technology Cambridge Massachusetts USA 1976 J C M de Wit Proton and metal ion binding to humic substances Ph D thesis Wageningen Agricultural University Wageningen The Netherlands S E A T M van der Zee Transport of solutes in soils Department of Soil Science and Plant Nutrition Agricultural University Wageningen 1991 1 1 Installation To start working with ECOSAT for the very first time you have to copy all files to your hard disk using the installation program INSTALL bat The installation procedure creates the directory ECOSAT on your hard disk ca 4 Mb Read the READ ME file for the latest information ECOSAT is a DOS program which runs in a DOS window on a Windows PC M
43. d due to deposition of acid rain also leaching of DOC dissolved organic carbon 23 2 1 14 Fit Here you can arrange input data in order to combine ECOSAT with the parameter fitting program FIT Parameter choice and all necessary input data for the dependent variable can be set Kinniburgh D G 1993 FIT User Guide Technical Report WD 93 23 British Geological Survey Keyworth 2 1 14 1 FIT ECOSAT ECOSAT will calculate the value s for the dependent variable Y calc for a certain choice of parameters which have to be optimized The FIT program will adapt these parameters in an optimization process using known values for the dependent variable Y known and ECOSAT will automatically start again to calculate new values for the dependent variable Y calc This will be repeated until a predefined accuracy criterion in the FIT program related to the difference between Y known and Y calc has been reached For parameter optimization several more than 1 data points are required for both Y known and Y calc Therefore ECOSAT has to do a Multiple Run a Cascade a Kinetics or a Transport calculation ECOSAT produces calculated values for the dependent variable Y calc FIT compares these calculated values with the known values Y known and adapts the parameter values Y calc values are saved in file outman dat Y known values are stored in a file with any name and extension e g dat with eco file name Total number of Y calc va
44. dd them directly into the species edit table If you want to add species to the species database files select DBASE SPECIES EDIT and edit the database files When all species are added to the edit table you have to save this edit table Quit and Save press Esc or F2 or F3 It is possible to optimize log K values for species with FIT ECOSAT EDIT FIT see chapter 2 1 13 2 1 3 Gases The gas species in the system have to be defined in the gases edit table select EDIT GASES They can be added automatically from the database files after selection of the components if the database auto fill parameter for gases is set to Yes which is not the default value The default setting of this database auto fill parameter is No Selection of the components H OH and e electron should always result in automatic selection of the gases H and O However often you will not be interested in these gases Therefore select the gases manually press ENTER when the cursor is in the first column of the gases edit table and choose Select Item from the menu displayed in the window It is very easy to select all gases from the database files If you want to add new gases to the gases database files select DBASE GASES EDIT and edit the database files In the edit table you can change or add delete gases data name composition delta H log K gas pressure type constant or variable and gas pressure different units e g bar or Pa Molar mass
45. del Soil column data e p soil bulk density kg soil Om volumetric mobile water content Oim volumetric immobile water content L column length m os Cm initial total amount mol l mobile water Cim initial total amount mol l immobile water 0 1 on Fosdoononaten nmatmastowa jo We choose here to express Cim in mol l mobile water C im see also example TWO_REG2 See example TWO_REG1 for Cim in mol l immobile water Initially the system is in a state of chemical equilibrium Using the input manager of ECOSAT we have to fill in several input tables In the following the most relevant input tables are shown First we discuss the input for Cim in mol l immobile water file TWO_REG1 In file TWO_REG2 Cim is expressed in mol mobile water The latter is more convenient e g because total amounts in both regions can be added then without any correction in order to calculate total amount adsorbed See screen dumps on the next pages the files can be found in directory ECOSAT EXAMPLES 53 Components edit table Ecosat File Build Wei Run Dbase Tools Setup Quit ge Cc comp y g glo Total amount 1 000000 C_im 0 Total amount 1 5000000E 01 1 000000 1 0000 In the first column both components in the mobile and immobile region Cm and Cim are defined The total amount of Cm is 0 1 mol mobile water and for Cim r 0 15 mol l immobile water The value for C im r 0 1 x 0 3 0 2 0 15 mol l mobile w
46. e Tools Setup Quit Molar mass eference E Comp Coeff Comp ERARARAAAAA comment 0 0000 1 0000 1 0000 0 0000 1 0000 1 0000 Q 52 Here we have chosen for Q_S as a dissolved species This makes it easier because we do not have to specify a particular adsorption model for Q_S Since we define Q_S as a dissolved species we have to specify later that Q_S is not mobile Particle surfaces edit table Qo Interactions Quit Particle surfa article Related Total amount orption Geometry z Mineral kg 1 el AMARA 1 2000E 00 Freundlich Note that we have to fill in the data for only one particle surface The total amount of the particle surface belonging to the kinetic adsorption is accounted for in the total amount of Q_ So 61 Freundlich surface species table Adsorption Particle surfaces Sejam Eegen gon Interactions Quit Particle surface Ro 3 Edit Freundlich surface sp Reference Sorbec oeff Comp comment amp The surface species Q_Sz is already defined in the dissolved species table So in the Freundlich surface species table we have to define only the equilibrium surface species Q_S The soil solution ratio equals p 8 0 4 x 1 5 0 5 1 2 kg l Kinetic rate equations edit table Ecosat File Build Jeb Run Dbase Tools Setup Quit Rate equations Arrhenius log A ale 1 0000 Os 1761 1 0000 deE dt FOSSZ 1 0000 0 5814 1 0000 1 0000 Os 1761 1 0000
47. e equilibrium solution because mineral activity equals 1 For the case of equilibrium with a mixture of minerals special care has been taken in ECOSAT to ensure that all possible combinations of minerals are evaluated A special algorithm has been developed to find as fast as possible the correct mineral composition of the system The decision which minerals are present at equilibrium is based on comparison of ion activity products with solubility constants and on comparing calculated total amounts of components compared with the known total amounts Organic liquid mixture DNAPL or NAPL mixture If a mixture of pure organic liquids is present the distribution calculation becomes much more complicated due to the fact that the total amount of the components present in the mixture influences the concentration of the components in the water and gas phase Raoult s law This makes a different approach necessary from the normal solution scheme as used for minerals where total mineral amount is not important at all For example for a mixture of benzene and toluene the mass balances for the components benzene and toluene may be formulated as 32 Benz t Tol t Benz L Benz aq Benz g Benz ads Tol L Tol aq Tol g Tol ads L pure organic liquid form aq dissolved in water g gas form ads adsorbed onto soil particle surfaces The concentrations in the different phases water gas adsorbed can be ex
48. equation or with heterogeneous sorption models For more simplistic approaches non variable charge NVC models can be applied Freundlich including linear sorption Langmuir and Gaines Thomas for ion exchange A specific VC model is the Surface Precipitation Model SPM of Farley Dzombak and Morel in Dzombak and Morel 1990 For both VC and NVC sorption models also heterogeneity of the particle surface can be taken into account using specific surface site complexation models in stead of the standard Langmuir equation Possible heterogeneous sorption models are NICA CONICA Langmuir Freundlich Generalized Freundlich and Toth It is possible in ECOSAT to relate the total amount of the particle surface to the calculated total amount of a specific mineral Total amount of the mineral mol l is converted then into kg l using the molar mass of the mineral This might be interesting for e g oxides Sorption of suspended particles like DOC Dissolved Organic Carbon is important in modelling transport and bio availability of organic chemicals PHA pesticides and heavy metals At this moment ECOSAT can calculate transport of suspended particles but exclusive particle interactions Interaction of suspended particles with the soil matrix is a recent research topic and will be implemented in a later version The standard approach in solving chemical equilibria is followed as much as possible Often extra specific components are introduced and
49. erature K R gas constant 8 31 J mol K Depending on the chosen VC model other extra layers plus Boltzmann factors are defined B for DDL BS Triple layer Donnan and B for Triple layer These Boltzmann factors are introduced as extra electrostatic components making calculation of species concentration possible according to the standard procedure The total amount of this electrostatic component equals to the change of charge due to sorption in the surface layer Charge and potential are related via the chosen VC model An example of the formulation of VC sorption is given in table 7 Table 7 Table of species for sorption of component A according to the Langmuir DDL model Components Species mol l Total amount mol l pl oZeFN F S t p N S t total number of sites on the particle surface mol l Ns total number of sites mol kg p soil solution ratio kg l o Surface charge z charge of the surface component 1 F Faraday constant The charge calculated using the mass balance equation is compared with the charge calculated on basis of the electrostatic model In the ECOSAT model it is not necessary to take integer charges for the surface groups Z on the soil particle surface s In ECOSAT it is at this moment not possible to calculate the composition of the DDL For sorption of metals on organic matter the NICA Donnan is very appropriate In the Donnan model the potential in the Donnan vol
50. ersion coefficient local pore velocity time TSU Q In this equation we make use of the vector operations div divergence and grad gradient These vector operations are normally used for right Cartesian coordinates ee grado Vp divv V 2 14 Wv V The continuity equation can also be formulated in other coordinates like for instance cylindrical or spherical coordinates For mass transport where we can neglect diffusion dispersion it is rather easy to apply coordinate transformation using streamlines and equipotential lines Also if only transversal diffusion dispersion can be neglected 2 or 3 dimensional transport can be simplified using coordinates transformation In this way mass transport can be calculated along a streamline 1 dimensional flow assuming no interactions with other streamlines no mass transfer between streamlines Mathematical formulation Assume X X U V W y y U V w Z Z U V W A good view to the u v w coordinates offer the coordinate surfaces u u constant v v constant w w constant and the coordinate curves x X U V1 W1 X X U1 V w and x X U1 V w Each time two coordinates are kept constant x equals a certain vector function The 3 dinat h t t tivel Ox OX OX e 3 coordinate curves have as tangents respectively PEEN u a AW Ox OX OX The vectors are in general no unity vectors The length of these vectors equal to t
51. ever it is also possible to add them directly into the organic liquid edit table If you want to add new organic liquids to the database files select DBASE PHASES ORG LIQUIDS EDIT and edit the database files When all organic liquids are added to the edit table you have to save this edit table Quit and Save press Esc or F2 or F3 You can also add organic liquids to the system via menu option BUILD see chapter 2 3 For mixtures of organic liquids Raoult s law is used to calculate the equilibrium concentration in the water phase actual mole fraction times saturated water solubility and gas phase actual mole fraction times saturated vapour pressure See also appendix 1 2 1 6 H O Water is present in the system if both H and OH are chosen as components However the speciation calculations are mathematically possible even if water as separate phase is not present H or OH is not a component Water is only partly treated in the same way as minerals and organic liquids The difference is that the total amount of the components present in water H and OH have NOT to be added to the total amount of the components in the whole system If the constant calculation data type of component H or OH Activity or Concentration the constant calculation data type of the other component in water OH or H has to be Total amount or better H2O gt Total amount otherwise you will encounter a phase rule violation Total amount of
52. fault value 1 liter liter select EDIT CASCADE PARAMETERS Cascade calculations are nested within the multiple run dimensions loops Ns Ny N N Mi N file N cas 2 2 2 2 y gt 2 speciation with Neas total number of cascade steps m n 2 1 11 Reaction kinetics See also appendix 2 Reaction kinetics in ECOSAT and appendix 4 Two region and two site kinetic model in ECOSAT Slow reaction kinetics or mass transfer include processes like decay or decomposition adsorption or desorption precipitation or dissolution Kinetic speciation calculations can be combined with multiple run cascade and transport calculations See chapter 2 1 13 for optimization calculations of slow mass transfer parameters with FIT ECOSAT EDIT FIT Output parameters are the same as for transport EDIT KINETICS PARAMETERS For transport calculations it is not possible to edit here these parameters Instead you have to edit them at TRANSPORT PARAMETERS see chapter 2 1 12 1 In the rate equations edit table EDIT KINETICS RATE EQUATIONS differential equations for all time depending reacting components are formulated These rate equation terms are of the form ZT 0 i j b mass transfer coefficient k rate constant c species concentration x reaction order In each row of the edit table one term of this sum for component i has to be formulated See help files for detailed information Kinetic speciation calcula
53. he Ou OA Ww scaling factors h4 ha hs 5 OX h OX _ X Llar gt lar law We introduce now a new basis with unity vectors 66 1 Ox 1 Ox 1 Ox a BA na In the new coordinate system with the basic vectors e e ez we can give a formulation for vector v velocity V V l1 Vy 2 VWwE3 with Note that the scaling factors are not constants but are a function of place In the coordinate system given by u v w the formula s for the vector operations div and grad are different from the formula s for the operators in the standard Cartesian coordinate system un Htl Ann Arto A ga a vo LE 1 1 as h Gu h amp h dw Transport equation in cylindrical coordinates 2 or 3 dimensional mass transport with axial symmetrical cylindrical flow can be transformed to 1 dimensional flow using cylindrical coordinates If transversal diffusion dispersion can be neglected the solution of the mass transport problem only depends on the distance to the line source radius of the cylinder Introducing cylindrical coordinates r p z we can solve this 3 dimensional problem in 1 D in the r direction De cylindrical coordinates r p z depend on the Cartesian coordinates x y z according to X T COSQ y r sing z z r radius of the cylinder The scaling factors belonging to this transformation are hi 1 ho r h3 1 67 Continuity equation V vC V DVC C V v v VC V
54. he immobile region it is assumed that there are no advective diffusive and dispersive fluxes Furthermore it is assumed that the rate of solute exchange between the mobile and immobile region can be described by a first order process with mass transfer constant a 51 We will now rewrite equation 3 and 5 in a formulation that can be used by ECOSAT First we will substitute equation 5 into equation 3 We then get Ze K PE al patie Sen a O a lp e m with p f p Dividing equation 5 with Oim gives oC OS K Ze im T hs P d OC in a 5 a or 0 Ot 0 a 0 0 im im im T with p 1 f p a a Substitution with k a and k results into m im OC ze Jkt tice 8 a Cima EC Ea 9 Ot Cmr and Cim are the total amounts of the component C in the mobile and immobile region respectively Note that Cm is expressed in mol l mobile water and Cim in mol l immobile water Although not really necessary we can convert Cim into the more convenient unit mol l mobile water using C Onc with C im in mol l mobile water im m 10 and rewrite equations 8 and 9 EC mT He joc ee ING iC k C at 0 im 11 ac onee Ot On Om 12 Now we have to fill in the speciation and transport data into ECOSAT The data we will use are summarized in tables 1 1 and 1 2 Take 6 0 and D Dm 52 Table 1 2 Speciation and transport data for the two region mo
55. he minerals manually press ENTER when the cursor is in the first column of the minerals edit table and choose Select Item from the menu displayed in the window In the edit table you can change or add delete mineral data name composition delta H and log Ks values Molar mass of the minerals will be calculated automatically by the program after saving the edit table It is easy to select all minerals from the database files However it is also possible to add them directly into the minerals edit table If you want to add new minerals to the minerals database files select 9 DBASE PHASES MINERALS EDIT and edit the database files When all minerals are added to the edit table you have to save this edit table Quit and Save press Esc or F2 or F3 You can also add minerals to the system via menu option BUILD see chapter 2 3 2 1 5 Organic Liquids The organic liquids pure organic compounds or D NAPL s in the system have to be defined in the organic liquids edit table select EDIT PHASES ORG LIQUIDS Relevant organic liquids can be added automatically from the database file if the database auto fill parameter has been set to Yes default value In the edit table you can change or add delete organic liquid data name delta H and log S values Molar mass of the organic liquids will be calculated automatically by the program after saving the edit table It is easy to select all organic liquids from the database files How
56. ic strength only for the dissolved component For the ion exchange model surface species are automatically derived from the ion exchange coefficients data for which a separate edit table has to be used see chapter 2 1 8 4 See chapter 2 1 9 for multiple run calculations for several variables EDIT MULTIPLE RUN SURFACE SORPTION SPECIES See chapter 2 1 13 for optimization calculations with FIT ECOSAT EDIT FIT 2 1 8 4 lon Exchange coefficients The lon Exchange coefficients for the particle surface with Gaines Thomas ion exchange as sorption model have to be defined in the ion exchange coefficients edit table select EDIT ADSORPTION SURFACE SORPTION ION EXCHANGE COEFFICIENTS Surface species are generated automatically after saving this edit table Log K values are at that moment still incomplete formation constants Log K values are adapted to log K values by ECOCALC using total particle amount kg l total amount of the ion exchange surface components mol kg and the correction for ionic strength only for the dissolved components 2 1 8 5 Model parameters Only for particle surfaces with a variable charge sorption model additional parameter values have to be specified in the model parameters edit table go to EDIT ADSORPTION SURFACE SORPTION MODEL PARAMETERS These parameter data can be added automatically from the database file if the database auto fill parameter has been set to Yes default value It is not
57. icle surface kg l e asorption model describing sorption onto that particle surface including the model parameters e a certain amount of surface components on the particle surface mole kg Multiplied with the particle surface total amount this equals to the maximum binding capacity mol l in the system e Surface species representing the bound components In ECOSAT different sorption models are available e Several non variable charge nvc sorption models Freundlich Langmuir lon Exchange Gaines Thomas and Donnan e Heterogeneous sorption models like NICA Langmuir Freundlich Generalized Freundlich Toth These models can also be combined with electrostatic variable charge models e Several variable charge vc electrostatic models Diffuse Double Layer DDL Constant Capacitance CC Basic Stern BS Three planes TP and Donnan These models can be applied for different geometry of the particle surfaces plane DDL CC BS TP or gel Donnan e Specific models like the Surface Precipitation Model SPM To define sorption you have to add a certain amount of a particle surface into the system Assign a specific sorption model to that particle surface and define all other variables and parameters you need to describe sorption surface components not for the Freundlich model surface species and different model parameters 2 1 8 1 Particle surfaces The particle surfaces in the system have to be defined in the par
58. immobile stagnant Further they assume that diffusion in the immobile region is negligible Because species in the mobile region are not in local equilibrium with species in the immobile region we have to double the species table In table 1 1 this extended species table for the simple system that is described in Gaber et al 1995 is shown In this system we have only one component which can be present in both regions in dissolved and adsorbed form Although elaborated here for a mono component system it can be applied to a multicomponent system as well As adsorption model a linear Freundlich model is used Q_C KaG This is not a restriction the two region approach can be used in combination with any other adsorption model Table 1 1 Table of species belonging to a simple two region kinetic model oat I species i i I Cm 1 Cim it Q Cn Q _Cim L I TEE o B A To indicate in which region the species and components are present we have given them an index m or im for the mobile and immobile region respectively Sorption of the component Cm on particle surface Q in the mobile region and of Cim onto particle surface Q in the immobile region In each separate region the dissolved species Cm or Cim is in chemical equilibrium with the adsorbed species Q _ Cm or Q _Cim Mass transfer from one region to the other is assumed to be proportional with the difference in concentration of the dissolved species Cm Cim Cmr
59. l coordinates amp 0 are a function of the Cartesian coordinates x y Z 68 x f 0 9 y f 5 0 0 z f3 9 9 The scaling factors belonging to this transformation are aa CE OE OE 4 Gr 3 1 gt 60 00 60 Fi Tr Fs 3 2 Conservation equation ae V vC V DVC C V v v VO V DVC a If there is no divergence V v 0 and diffusion dispersion can be neglected OC NO with v v 0 0 If the coordinates in the amp direction are equidistant than the scaling factor h equals 1 OC OC a AS Fe Note that in this case the values of the other scaling factors are not important no diffusion dispersion 69 70 Appendix 6 Examples How to run example files Example files eco can be found in subdirectory ecosat examples To run an example file start ECOSAT eco and choose FILE RETRIEVE and select the specific file Inspect the edit tables to learn and press RUN to start the calculation Sometimes a specific selections output file sof is available This file is automatically retrieved by the Output manager and can be used to generate output If there is no specific selections output file you can make your own output with option CHOICE or use option BASIC or ALL Output is stored in file outman dat Examples overview ADS_FR eco Adsorption of Cd according to a pH dependent Freundlich model and a linear model on two particle surfaces Complexatio
60. le etc Build Build your system by adding chemicals minerals or organic liquids Edit Change the edit tables Run Start calculation Dbase Edit database files Tools several extra facilities Setup PC and program parameter settings Quit Quit program no calculation Dbase Tools Setup Quit System compilation Components E Species Gases Minerals Species Organic Liquids Gases Water Phases Adsorption Particle Surfaces Environment Multiple run Cascade Kinetics Transport View Fit Quit Surface Components Surface Species Boltzmann Factors Total components Total species Multiple run nr Cascade steps Fit parameter nr Kinetics Transport Kinetics Figure 4 ECOSAT input manager main and edit menu system compilation To do an ECOSAT calculation you have to create your own chemical system using the available variable groups e g components particle surfaces species etc Start always with defining the components Use as much as possible the available database files for easy selection of the variables you need If specific data is not present in the database files you can better add the new data immediately to the database file for later use Of course it is always possible to add new data only to the edit tables It is also possible to make your system using added total amounts of chemicals minerals or organic liquids Use in that case menu option BUILD ECOSAT selects automatic
61. le run calculations are possible for different data types and various units Often also log values can be used e g log activity Data types for which these multiple run calculations are possible Components Total amount mol l or mg l concentration mol l or mg l activity Log total amount Log concentration or activity Log activity Species log K Gases Partial gas pressure bar Pa mol l or mg l Log P gas Log K Minerals log Ksoi Organic liquids log Sw Sw Particle surfaces Total amount kg l initially adsorbed amount mol kg Surface components Total amount site density only vc models distribution parameters only for heterogeneous models Surface species log Ka non ideality parameter Freundlich coefficients Boltzmann factors for plane 0 1 and 2 Model parameters Specific surface area capacities gel volume Environment lonic strength temperature gas volume and their log values Up to 5 multiple run dimensions for the calculations of type A are available 5 nested loops Besides that all these data can be read from a data file type B multiple run calculations A constant volume change in case of for example a titration can also be specified The default value for volume change equals zero If data is read from file MRF no volume correction can be made Calculation order of the 6 multiple run loops dimensions 1 till 5 and file data Ns Ng N3 No N Npe y gt gt y De gt
62. low sorption with transport leads to the following formulation of the 1 dimensional convection diffusion dispersion equation 2 OCir _ D O Ci mobie 7 C i mobile Ot Ox Ox with Cir total amount of component i in the whole system mol l or mg l f speciation Ci mobile total amount of the component in the mobile phase mol l or mg l See appendix 4 for more information about the well known 2 site and 2 region models to describe slow mass transfer of components in soil column leaching studies 47 To solve the multicomponent transport equation next steps are followed att 0 Determine C r in all nodes of the numerical grid boundary condition for t 0 and x gt 0 Determine Cimobiie by speciation calculation att t At Calculate C in all nodes using the transport equation Determine Ci mobie by speciation calculation Determine Ci mobile for node O feed composition This equals the boundary condition for x O andt gt 0 Speciation and mass transport are thus calculated independently 48 Appendix 4 Two region and two site kinetic models in ECOSAT Two region and two site kinetic models in ECOSAT Two region kinetic model The two region kinetic model of Parker and Van Genuchten 1984 conceptually divides the porous medium into two domains Due to the heterogeneous pore size distribution pore water can be more or less mobile Parker and Van Genuchten assume that the pore water is either mobile or
63. lues has to be equal to total number of Y known values ECOCALC will calculate speciation using the parameter values chosen in the FIT edit tables and saved in file fit FIT will adapt these parameter values in an optimization process based on Weighted Residual Sum of Squares WRSS File fit contains also other information for the FIT program to start the whole optimization process Results of the optimization process are saved in the FIT program file res 2 1 14 2 Data input Both programs FIT and ECOSAT require their specific data input For FIT it is enough to see also the help information in the FIT program select ECOSAT nr as model set the total number of parameters their labels and their initial values set the total number of variables in the data input file minimum of 2 and set which variable is the dependent one Y known Set optimization parameters e g convergence criterion finite difference step size For ECOSAT the complete system for a speciation transport calculation has to be formulated in an eco file Extra data input has to be given in EDIT FIT Indicate which parameter has to be optimized see EDIT FIT Parameter choices and in which column of file outman dat the calculated values Y calc can be found see EDIT FIT Dependent Y var It is possible to use available datasets for more than one variable Y known values In that case you have to use option Piled Columns in the Output manage
64. lux and scale factors 1 and 2 are calculated using input data for discharge m day screen length and screen diameter INPUT s2D FILE AXIAL SYMMETRIC For the volumetric water and gas content data in the soil column data sets is used For that purpose negative values 1 for water and gas content are given in file s2d 2 1 12 8 Input s3D File See also appendix 5 Semi 2D and semi 3D transport in ECOSAT Make s3D file for semi 3 dimensional transport Go to EDIT TRANSPORT INPUT s3D FILE The file s3d name of eco file contains for all nodes the following data flux m day scale factor 1 h1 scale factor 2 h2 scale factor 3 h3 volumetric water content and volumetric gas content Make this file with help of menu option INPUT s3D FILE READ s3D FILE The data will be read from a DOS ASCII text file e g prn with the relevant data ordered in columns Create this text file with help of menu option INPUT s3D FILE FILL s3D FILE or with option INPUT s3D FILE RADIAL SYMMETRIC or with any other DOS text editor If you want to use the volumetric water and gas content as given in the soil column data sets give negative values e g 1 for these parameters in file s3D Default values for the scale factors 1 For radial symmetric spherical flow flux and scale factors 1 2 and 3 are calculated using input data for discharge m day and sphere diameter INPUT s3dFILE RADIAL SYMMETRIC For the volumetric water and gas
65. n Note delta H values are not yet compiled in the database files see HELP info for calculating delta H values If gas pressure is variable gas volume has to have a certain constant value With this volume the partial gas pressure can be calculated Also for a constant gas pressure a certain positive gas volume should be given although this is not necessary to calculate the speciation In this case the volume is only used to calculate the total amount of the components present in the system In case of a constant gas pressure total amount of the component s present in the gas species will be determined by the value of the partial gas pressure If constant calc data type of this component equals Total amount it will be converted automatically into P gas gt Total amount It means that total amount of the component is constant and that its value is also determined by the partial gas pressure of the gas species See chapter 2 1 9 for multiple run calculations with constant ionic strength temperature and gas volume 2 1 8 Adsorption The concept applied in ECOSAT to model adsorption and desorption of compounds is that this sorption takes place on soil particle surfaces according to a particular sorption model Depending on the chosen model sorption is described with the aid of surface components surface sites and surface species bound components on surface sites To describe sorption we need e acertain amount of a part
66. n of Cd with Cl and hydrolysis of Cd Variable ionic strength and pH variation in a multiple run calculation adsorption edge Output ADS_FR sof ADS _LANG eco Adsorption of Cd according to the Langmuir model nvc Complexation of Cd with Cl and hydrolysis of Cd Constant pH and ionic strength Multiple run calculation for total amount of Cd adsorption isotherm Output ADS_LANG sof AIOH eco Al hydrolysis multiple run calculation for pH ADSLAADV eco Adsorption of Cd according to the Langmuir Advanced model Multiple run calculation for Cd total amount Output ADSLAADV sof AXIALS2D eco Transport of chloride by semi 2 dimensional water flow axial symmetric Flux data and scaling factors in file axials2d s2d View diagram of total amount of Cl in the soil column Output AXIALS2D sof breakthrough curve of Cl at several nodes BTX eco Speciation for a mixture of organic liquids benzene toluene and xylene Adsorption onto organic matter according to a linear Freundlich model BT_VENT eco Transport of benzene and toluene via the gas phase venting Speciation organic liquids gases dissolved and adsorbed View diagrams for total amounts of benzene and toluene in gas phase organic liquid phase and adsorbed CASCADE eco Repeated CaCl extraction cascade treatment of soil containing Cd and Zn Adsorption of Cd and Zn according to a pH dependent Freundlich model Constant pH and variable ionic strength Outpu
67. ns edit table Now we have to define the kinetic part of the transport equation From the menu we choose the option Kinetics rate equation In this table we define the terms of the kinetic part of the transport equations These terms look like bk Lei 13 In each row of this table we can define one term of this sum The constant b is the transfer coefficient and can have the value of 1 The constant k is the rate constant at 298 15 K Values of this constant at other temperatures can be calculated using the Arrhenius constant according to In k Ea RT 1In a see ECOSAT help 14 The constant x is the order of the reaction with respect to the compound Cj We can choose as compounds any of the species in the system In this case the dissolved species C and Cim Ecosat File Build We Run Dbase Tools Setup Quit Order al 1 0000 0 6990 1 0000 dc dt C_im 1 0000 0 8751 1 0000 1 0000 0 6990 1 0000 55 Kinetics rate equations edit table continued Ecosat File Build jek Run Dbase Tools Setup Quit Kinetics Rate equations Group Part Surf Order KEEKEKKEEEEKEEKEE 1 0000 Cm species 1 0000 C im species 1 0000 Cm species 1 0000 im species In the first row of this table we have formulated the term a Bm Cm of equation 11 with log a 0m log 1 5 0 2 0 8751 K The second row represents the second kinetic term of equation 11 a 0im C im with log 0 0 m log 1 5 0 3
68. obably faster The default setting is Euler explicit Time integration method can be set at menu option SETUP Examples of slow mass transfer reactions e Decay of compound A A x O lt gt CO H20 dA Assume O2 dependend first order decay of component A K A 0 t with A the concentration of A in the water phase Atota equals the total amount of A in the system mol l For Os aoe xK A 0 with O2 the O gt concentration in the water phase x transfer coefficient number of moles O used per mol A e Slow desorption of component A see also appendix 4 The driving force for adsorption or desorption is the difference between the actually adsorbed amount and the adsorbed amount at equilibrium SA S A Ka soil water distribution constant asa K SAI K A S K SAF K SPL S 42 The driving force for slow mass transfer is the difference between the really adsorbed amount SA and what it should be at equilibrium often x p q 1 e Slow dissolution of the mineral A B AaBp gt aA bB Ks solubility constant Here the driving force is not the difference between actual total mineral amount and total mineral amount at equilibrium which will have minor influence on the dissolution rate but for instance the difference between ion activity product IAP and the solubility constant Ks for that mineral At equilibrium Ks IAP Of course this a rough approximation of the
69. of the gas species will be calculated automatically by the program after saving the edit table Log K equals here to the Henri constant in L bar mol Gas pressure is expressed in bar default unit Two different calculation types for gas pressure are possible Probably in most cases you want to do a single speciation calculation with a constant gas pressure gas pressure type Constant or with a variable gas pressure gas pressure type Variable For both situations you have to specify also the gas volume gas liquid ratio in the system select EDIT ENVIRONMENT The components edit table will be checked for the chosen gas type For multiple run calculations with constant gas pressures see chapter 2 1 9 When all gases are added to the edit table you have to save this edit table Quit and Save press Esc or F2 or F3 2 1 4 Minerals The minerals in the system have to be defined in the minerals edit table select EDIT PHASES MINERALS Relevant minerals can be added automatically from the database files if the database auto fill parameter has been set to Yes which is not the default value For available standard database files for minerals see chapter 2 2 The default setting of the database auto fill parameter for minerals is No The database files contain many minerals with the same chemical formula which cannot exist all together in the same system phase rule violation Therefore the default setting is aimed at selecting t
70. of 6 because otherwise it should not be dimensionless 35 In table 5 the table of species is given for competitive sorption of components A and B S t is the total number of sites available for sorption mol l S t p Qmax with Qmax equal to the total number of sorption sites in mol kg Table 5 Table of species for Langmuir sorption of components A and B components s a 8 og Species mol l 0 0 1 0 0 0 0 log K a 1 log K s Total amount mol l B t lon exchange lon exchange is calculated according to Gaines Thomas GT The exchange coefficient is defined as SEI AI Korx a gt x 8 Y 1 m E B based on the exchange reactions Gaines Thomas 1 n XA 1 m B o 1 mXmB 1 n A E sorbed equivalent fraction For the Gaines Thomas ion exchange model implementation in a standard speciation program is not straightforward This is due to the different dimensions used for the sorbed amount dimensionless in the exchange model versus mol l in the speciation model It implies recalculation of the value of the exchange coefficient into a value for the formation constant of the surface species The free surface site can be considered as an extra component of which the total amount is equal to the cation exchange capacity CEC in mol p kg This surface component will not be present in the form of a species as all sites are occupied by cations This in contrast to the Langmuir model Reformulating the
71. of this approach is presented in table 34with sorption of components A and B according to Qa K A B Os Kf5 B P Components log K Species mol l A 0 B 0 Qa m 0 log K 4 log p p 1 log K s log p Total amount mol l A t B t saan of rene chemicals can often be described with the most simple form of the Freundlich model K C with n 1 linear adsorption model and K Kg Fom Kom Ka distribution ear fom fraction organic matter and Koy organic matter water distribution constant In ECOSAT log Kom can be used if p fou is taken for the total amount of the soil particle surface present in the system Langmuir The Langmuir model describes sorption of components on the soil particle surface according to the surface complexation reaction S A lt gt SA Competition between components for the same surface sites is included in the formulation of the model multicomponent Langmuir KiC 0 bas YC i C concentration of component i Ki sorption affinity constant for component i i fraction of sites occupied by the adsorbed component i for component A SAJ S t with S t total number of sites The Langmuir model is easily incorporated in the standard formulation as the distribution constant K is dimensionless Calculations can be based on fractions or total amounts mol l For the Langmuir Advanced model bidentate sorption K has to be expressed in terms
72. possible to select them manually from the database file Depending on the sorption model it concerns data like specific surface area m kg capacities estimated potentials sphere cylinder radius gel volume also gel volume type and gel volume function parameters See chapter 2 1 9 for multiple run calculations for several variables EDIT MULTIPLE RUN SURFACE SORPTION PARAMETERS See chapter 2 1 13 for optimization calculations with FIT ECOSAT EDIT FIT 2 1 9 Multiple run Multiple run calculations repeated runs are set in the multiple run edit tables for the different possible variable groups components species gases minerals organic liquids particle surfaces surface components surface species and environment data select EDIT MULTIPLE RUN There are two types of multiple run calculations possible 14 A The variable value is increased each time with a specific step value new value old value step value 1 volume change In this case specify the start value and the step value in the edit table for the relevant variable group Select here also the multiple run dimension or calculation loop 1 2 3 4 or 5 in which the automatic data change takes place Total number of steps and volume change for each multiple run dimension are specified in the parameters edit table EDIT MULTIPLE RUN DIM FILE PARAM B The variable value for each step is read from data file MRF multiple run file Multip
73. pressed in terms of the total amount of the pure organic liquid In case of linear adsorption knowledge of the K is sufficient for describing sorption behaviour Further information about water solubility S and Henri s constant H is needed Assume Benz L x and Tol L y where x x y equals the mol fraction of benzene and y x y the molfraction of toluene in the mixture Benz t Tol t X X x Y Spenz X X y Senz Hpenz X X Y Spenz Ka Benz y y x y Sto y x y Sto Hro Y X y Sto Hro Katol S water solubility H Henry constant Kg soil water distribution constant These equations can be solved according to the standard procedure by taking x and y as components Derivatives for the elements of the Jacobian matrix in the Newton Raphson iteration method are determined numerically The decision on the presence of the organic liquid is based on comparison of the concentrations in the water phase with the water solubility S This might give some numerical inaccuracy In table 2 an example of the table of species for a system containing benzene and toluene is shown If total amounts of benzene and toluene are high enough to exceed water solubility a mixture of both aromatic compounds will be present and Raoult s law Cw n S n mole fraction has to be used to calculate speciation assuming ideal behaviour of the compounds benzene and toluene This is formulated in table 3 Table 2
74. r The trick is that all Y known values are placed on top of each other in one column The Output manager will do that also for the calculated Y values Possible parameter choices Components Total amount Species Formation constant log K Particle Surfaces Total amount kg l Initially adsorbed amount of a component mol kg 24 Surface Sorption Surface Components Total amount mol kg Site density heterogeneity parameter s e g for Surface Species log Ka non ideality parameter e g for Component coefficients Freundlich exponents Surface parameters Surface area Capacity Radius Gel volume Gel volume function parameters Kinetics Log K rate constant Reaction order coefficient Transport Transport parameters e g Diffusion coefficient or Dispersivity 2 1 14 3 Procedure Procedure for parameter optimization with FIT using ECOSAT as model see figure 9 4 Create ecosat file eco with Multiple Run Cascade Kinetics or Transport calculation Use a first estimate of the parameters to be optimized Be sure that the calculated values for the dependent variable Y calc correspond with the known measured values Y known Save or Run ECOSAT it creates FIT_ECO bat FITEXEC bat and fit Run ECOSAT to check the calculation and to select output Select output at least Y calc with the output manager OM Be sure that total number of Y calc values equals total number of Y known values Sele
75. r clay constant Ca concentration FEOH_KIN eco Slow dissolution of Fe OH s Fe hydrolysis variable pH constant ionic strength View diagrams for total amount and log IAP of Fe OH s s FLUOR eco Adsorption of F onto goethite according to the Basic Stern model VC Langmuir Normal Plane BS Constant ionic strength and multiple run for pH Output FLUOR sof IONSTR eco Calculation of ionic strength ION_EXCH eco Na Ca exchange with Gaines Thomas model Multiple run calculation for Ca total amount KIN_BT eco Decay of benzene toluene organic liquid mixture decay only in the water phase Speciation organic liquid gas dissolved and adsorbed linear model View diagrams for total amounts of benzene and toluene in all phases MIN NICA eco Combination of adsorption according to the VC NICA Donnan model and precipitation of minerals Constant pH and constant pe in multiple run calculation MINERALS eco Speciation of Cd Ca and CO formation of precipitates carbonates hydroxides Constant CO pressure constant pH variable ionic strength 73 MnOH_KIN eco Slow dissolution of MnO s Variable pH constant ionic strength View diagrams for total amount and log IAP of MnO s NACA_EXCH eco Transport of Ca and Na in the soil lon exchange according to Gaines Thomas First leaching of Ca in a Na soil followed by leaching of Na in the Ca soil after 3 pore volumes of leaching View diagrams with Na an
76. real process AABI x 1 AP dt K S A IAP and for example for component A a2 a K K a 43 44 Appendix 3 Multicomponent transport in ECOSAT Multicomponent transport in ECOSAT In ECOSAT transport is limited to 1 dimensional stationary water or gas flow 2 or 3 dimensional water or gas flow however can be simulated as if it is 1 dimensional using mathematical transformations This is called semi 2 dimensional or semi 3 dimensional flow see appendix 3 Gas flow is treated in the same way as water flow no local pressure influence on the gas flow and the gas is assumed to be incompressible ECOSAT needs input of the water or gas flux for the whole calculation period and for the whole soil column all nodes The 1 dimensional convection diffusion dispersion equation used is formulated as OC total un D Cs O Ci mobile Ot ox Ox Ci mobile a total amount of component i in the mobile phase water or gas Ci total total amount of component i in the system Ci mobile Ciimobile diffusion dispersion coefficient in the mobile phase same value for all species D Daittusion Dispersion Dait D v with DL longitudinal dispersivity m v pore velocity of the mobile phase v vo 8 with vp the Darcy flux and 6 the volumetric water or gas content x t distance and time For gas flow only gases and for water flow all dissolved species and components bound to suspended particles suspended
77. rrections are made with the Davies equation and the Van t Hoff equation The standard approach followed in solving chemical equilibria is based on formulation of the mass balances for all components and expressing the species concentrations in terms of component concentrations and formation constants An overview of all relevant equations can be given in a so called table of species For a system with only the components A and B and the species A Bm this is shown in table 1 Table 1 Table of aaa ES mol l A B m Kanem Reading this table in vertical direction gives an expression for the mass balances of the components For example A t A n A B In horizontal direction the expression for the species concentration is given For example A Bm A B K anem For all types of species and phases present in the system this approach is followed as much as possible Only in some specific cases special adaptations in the solution procedure have been made Some topics related to speciation calculations are discussed here in more detail For more information see the textbooks on Chemical equilibria in soil water sediment part B and on Chemical sorption in the soil water system Minerals mixture If a mineral is present in a system the solubility reaction is used as an extra equation leading to reduction of the number of independent mass balances As long as the mineral is present its total mineral amount is not important for th
78. rt in ECOSAT Appendix 4 Two region and two site kinetic models in ECOSAT Appendix 5 Semi 2D and semi 3D transport in ECOSAT Appendix 6 Examples page ARW 1 Introduction ECOSAT acronym for Equilibrium Calculation Of Speciation And Transport is a computer program which can be used to calculate the chemical equilibrium composition of soil water systems depending on speciation and transport With speciation we mean the distribution of total amounts of components in the system over all possible phases and forms including complexes gases minerals organic liquids pure organic compounds or D NAPL s and adsorbed components Besides speciation ECOSAT can compute 1 dimensional and semi 2 or 3 dimensional stationary water or gas flow multi component transport Both speciation and transport calculations can include slow mass transfer reaction kinetics For theoretical background of the processes involved reference is made to the course Soil Chemical Applications at Wageningen University The soil water system description in ECOSAT is based on the use of different groups of variables Components basic entities used to form dissolved species gases minerals organic liquids Particle surfaces used to define adsorption of components on the surface sites surface components in the form of surface species Environment ionic strength temperature and gas volume In ECOSAT you can build your own system with these variables You
79. select and compose specific output Output is saved in file OUTMAN DAT which can be read by a spreadsheet program or text editor The output selections are saved in a data file with extension SOF Selections Output File Default name OUTMANIN SOF see also figure 1 The introduction screen of OUTMAN is very similar to that of ECOSAT The same function keys are available In stead of the menu options EDIT and RUN OUTMAN has the menu options CHOICE and MAKE see figure 10 Make Basic All Setup Quit T ECO BMP DEMO Use arrow keys and ENTER to select Selections Components output Total amount Delete all Total amount mol l Components Concentration mg l Species Activity mol kg Gases Distribution mg kg Minerals Extracted Cascade distr Org Liquids Sorbed 00 log mol l Adsorption Sorbed Qo log mg l Environment log mol kg Transport Quit log mg kg Combine columns ee Ne ee Quit Quit Quit Help Figure 10 Components output choice menus in the output manager selection order Choice gt Components gt Sorbed gt mol kg Output manager main menu options File Select data file ECO or selections output file SOF The program uses default OUTMANIN SOF as selections input file Choice Selection of output for components dissolved species gases minerals organic liquids particle surfaces surface components surface species environment parameters transport data concentration profile or bre
80. sible To realize this select EDIT VIEW and edit the data in the view edit tables Probably you will find it difficult to estimate the maximum values for the soil column profiles Just try and look at the results in the diagrams or look at the output made with the output manager and adapt the maximum value for the next calculation press F2 save and go back to the ECOSAT main menu and select RUN to start the calculation Press space bar to break off transport calculations The transport equation is solved with a numerical integration method Several choices for the integration method are possible Euler explicit method Runge Kutta order 2 Runge Kutta order 4 with constant time step more accurate Runge Kutta order 4 with variable time step less accurate but probably faster The default setting is Euler explicit Time integration method can be set at menu option SETUP See appendix 3 for information about the formulation of multicomponent transport See appendix 4 for information about the two site and the two region kinetic transport sorption models See appendix 5 for information about semi 2 and 3 dimensional flow 17 2 1 12 1 Transport parameters Transport parameters like transport calculation type soil column length number of nodes time step and time length boundary condition type of diffusion dispersion coefficient output for different time steps and nodes are set in the transport parameters edit table EDIT TRANSPORT
81. speciation with N total number of runs in dimension x ijk l mon Nie total number of data sets in file mrf The input data for multiple run calculations can also be read from data file MRF Multiple Run File In this file all data is listed in a special sequential order This file can be made with menu option EDIT MULTIPLE RUN READ MR FILE using a spreadsheet file e g PRN as input In this spreadsheet file all data has to be ordered in columns only numeric data This column ordered input data file can be made with a spreadsheet program an DOS text editor and also with the aid of menu option EDIT MULTIPLE RUN FILL MR FILE To make the MRF file Go to EDIT MULTIPLE RUN READ MR FILE INPUT FILE and select the name of the input data file e g with extension PRN Then specify the total number of text lines labels or blank at the top of the file option TEXT LINES Then specify in the edit table for column order option COLUMN ORDER which data types can be found in the different columns Select then option MAKE FILE to compose the MRF file with the same name as the ECO file 15 2 1 10 Cascade In a cascade extraction calculation the total amount of components is adapted at each step by replace ment of a certain volume of the water phase To edit the extractant composition added solution select EDIT CASCADE EXTRACTANT COMPOSITION To edit total number of cascade steps and replaced volume de
82. surface species are taken as the mobile species Suspended particles are thus also transported The partial differential equation has to be solved for all components affected by transport and all suspended particles The 1 dimensional convection diffusion dispersion equation is solved numerically with the method of finite differences using the stream upwind scheme for the advection term and central differences for the dispersion diffusion term This is only possible if boundary conditions are given In ECOSAT 2 different formulations of the boundary conditions can be chosen Boundary Condition 1 BC1 Cimobie 0 t f t feed concentration OC L t G mobile eN S 0 Ox with x distance t time L column length Ci mobie mobile total amount of component i and f feed composition at time t in node 0 Boundary Condition 2 BC2 Cini 0 t 0 t ape 0 t a Vp a J C mobile 0 t G mobile LD C mobile Ox with x distance t time L column length Ci mobie mobile total amount of component i f feed composition at time t in node 0 6 volumetric water or gas content vp Darcy flux D diffusion dispersion coefficient Jo flux at node 0 46 BC1 is the default boundary condition applicable for most situations e g soil column leaching studies BC2 can be used in situations where at node O no mass transfer by diffusion dispersion is possible e g impermeable layer
83. surface species or the model parameters go to EDIT ADSORPTION SURFACE SORPTION and select the particle surface for which you want to edit the surface sorption data 2 1 8 2 Surface components All surface components present on the selected particle surface have to be defined in the surface components edit table go to EDIT ADSORPTION SURFACE SORPTION COMPONENTS SURF Here the surface component name and depending on the chosen sorption model several different parameters like total amount mol kg or number of sites m charge and the heterogeneity parameter can be edited The surface components can be added automatically from the database file if the database auto fill parameter has been set to Yes default value It is very easy to select the surface components from the database file However it is also possible to add them directly into the surface components edit table If you want to add new surface components for this particle surface to the database files go to DBASE ADSORPTION SURFACE SORPTION COMPONENTS SURF EDIT and edit the database file When editing is finished you have to save this edit table Quit and Save press Esc or F2 or F3 See chapter 2 1 9 for multiple run calculations for several variables EDIT MULTIPLE RUN SURFACE SORPTION COMPONENTS See chapter 2 1 13 for optimization calculations with FIT ECOSAT EDIT FIT Note For the Freundlich sorption model no surface components are required
84. switch off this automatic search and add procedure by disabling the auto fill parameter for the specific variable group go to DBASE DBASE GROUP AUTO FILL 27 2 3 Build Via menu option BUILD you can create a new system using total amounts of chemicals minerals or organic liquids as input ECOSAT will automatically generate the components species etc belonging to that system It is also possible to add total amounts of chemicals minerals or organic liquids to an existing system Specify the data in the build edit tables select BUILD CHEMICALS or MINERALS or ORG LIQUIDS Select then BUILD SYSTEM and make a new system or add the data to the existing system Check always the results of this procedure select menu option EDIT 2 4 Tools At menu option TOOLS you can find several extra facilities Calculation of log K or log K at a specific ionic strength for dissolved species gases or minerals select TOOLS K lt gt K The data in this edit table can be added to the selected database file In the edit tables NOT in the database files automatic replacement of a component by a dissolved species or gas select TOOLS REPLACE COMPONENT Check always the results of this procedure 2 4 File At menu option FILE several options to handle the ECO files can be found Retrieve Save Delete choose a new file etc With option NEW FILE all edit tables TMP files are cleared and you
85. t CASCADE sof CDCL eco Complexation of Cd with Cl and hydrolysis Variable pH and constant ionic strength CDCL_FIT eco Complexation of Cd with Cl Fit parameter choice for log K of a dissolved species CdCI Multiple run calculation for Cl total amount Output CDCL_FIT sof 72 CD NICA eco Cd adsorption according to the NICA non variable charge model CL BTC eco Calculation of the breakthrough curve for Cl Output time data from file CL_BTC tof View diagram for total amount of chloride in solution Output CL BTC sof CO2 eco Cd speciation complexation with Cl and COs hydrolysis Constant pH and variable ionic strength Constant gas pressure for CO in a multiple run calculation Output CO2 sof Cu Multi eco Multi site complexation for Cu in clay soil Particle surfaces SOM DOM Clay Components Cu Ca Al NO3 H and OH Sorption models NICA Donnan for SOM and DOM Donnan ion exchange for clay illite Al in equilibrium with gibbsite constant Ca concentration CYANIDE eco Cyanide speciation dissolved Fe CN s species and equilibrium with Prusian blue and ironhydroxide Constant pH in a multiple run calculation Constant ionic strength Electron as component Output CYANIDE sof Delta H eco CO gt H 0 CaCO s system with temperature variation in multiple run DonnanlE eco Donnan ion exchange nvc model for clay Particle surface clay illite Components Cu Ca NO3 H and OH Donnan volume 0 1 L fo
86. t has to be possible to calculate the adsorbed amount at equilibrium at any time step independent of the concentrations of all other components For the fast reacting surface sites a linear Freundlich isotherm is chosen S FK C For the equilibrium situation we use for S the same model as for S4 S2eq 1 F Kg C with S S S2 FS 1 F S Here we can only choose for the Freundlich model because the equilibrium situation S2 q has to be calculated independently from the actual composition of the system It is possible to include components which concentration is not influenced by the sorption process in the formulation for S eq e g pH dependent Freundlich 08 The slow mass transfer equation can be formulated as ae K s ae s f 15 with S the total amount of the component on the slow ad desorbing sites S2 1 F Kg C mol kg 16 with F the fraction fast reacting sites Ka the distribution constant l kg K is the mass transfer rate constant a 58 The governing equations for this two site kinetic model are 2 Ln Ne 17 a 0 a 04 x x B _x a PK C S 18 This system is represented schematically in figure 2 1 gt nen Figure 2 1 Schematic representation of the concept upon which the two site model is based We will now rewrite equation 17 and 18 in a formulation that is used in ECOSAT Substitution of equation 18 into 17 and rewriting the kinetic part gives
87. t the maximum value for the next calculation 2 1 12 Transport In order to do transport calculations you have to define transport calculation type and all other transport data in the transport edit tables EDIT TRANSPORT Transport of species in the gas phase or in the water phase are solved numerically for 1 dimensional or semi 2 or 3 dimensional stationary flow To start a transport calculation First build your system with components species gases minerals organic liquids particle surfaces surface components and surface species environment parameter data etc select EDIT Choose a transport calculation type select EDIT TRANSPORT PARAMETERS Possible choices 1D water flow 1 dimensional flow in the water phase 1D gas flow 1 dimensional flow in the gas phase s2D water flow semi 2 dimensional water flow s2D gas flow semi 2 dimensional gas flow s3D water flow semi 3 dimensional water flow s3D gas flow semi 3 dimensional gas flow Fill in all other transport parameter values select EDIT TRANSPORT PARAMETERS Define and edit soil column data sets see figure 5 select EDIT TRANSPORT SOIL COLUMN Define and edit feed data sets see figure 6 select EDIT TRANSPORT FEED To see something happening on your screen during the transport calculation you can get soil column data profiles in diagrams on your screen At every time step this screen will be renewed Several data types are pos
88. tables For each soil depth a soil column data set can be defined figure 5 Each data set contains information concerning soil column composition and characteristics The program creates always a default data set with the name Basic default in which component concentrations particle surface amounts gas pressures environment data and soil column parameters are initially set to the default values in the corresponding edit tables e g EDIT COMPONENTS and EDIT ADSORPTION PARTICLE SURFACES First edit this default data set or define your own specific data set select TRANSPORT SOIL COLUMN DEFINE or EDIT Use other soil column menu options to copy or delete specific soil column data sets or to get an overview of all data sets defined for certain soil column depths option VIEW Initial soil column composition will be calculated with the data in the soil column edit tables Component total amounts or concentrations are set in the soil column components edit table select TRANSPORT SOIL COLUMN EDIT COMPONENTS Also the constant calculation type can be set Besides the types constant Total Amount Concentration Activity P gas gt Total amount and H20 gt Total amount 2 additional types are available Concentration gt Total and Activity gt Total They mean that for the first speciation calculation in each node for the whole soil column component concentration or activity is constant initial
89. ticle surfaces edit table select EDIT ADSORPTION PARTICLE SURFACES In the particle surfaces edit table you have to fill in the particle surface name particle type total amount and the relevant sorption model Total amount can be related to the total amount of a mineral present in the system related mineral It is possible to select all particle surfaces from the available database file However it is also possible 11 to add them directly into the particle surface edit table If you want to add particle surfaces to the database file select DBASE ADSORPTION PARTICLE SURFACES EDIT and edit the database file This file has the default name ECOPART dbP Surface components surface species and model parameters can be added automatically to their edit tables depending on the setting of the database auto fill parameter select DBASE ADSORPTION SURFACE SORPTION AUTO FILL see chapter 2 2 The default setting for this parameter is Yes The particle surfaces can be of type Solid Suspended or Biota Suspended particles are subject to transport in the water phase e g dissolved organic carbon DOC or oxide colloids Uptake of components by soil organisms is simulated by adsorption In that case choose for particle type Biota to distinguish uptake from normal adsorption Solid is the default particle surface type Particle total amount kg l can be set equal to the total amount of a mineral present Select therefore a mineral in
90. tions are nested within the multiple run dimensions loops and cascade calculations Ns N N N N N fie N cas 2 2 2 2 2 2 2 kinetic speciation You have to formulate differential equations for all components which are affected by the slow mass transfer Thus the slow reacting surface species or phase mineral organic liquid has to be defined as a component In case of transport these components which are also present as dissolved species are not always mobile To disable mobility of species see 8 2 1 12 4 The partial differential equation is solved with a numerical integration method Several choices for the integration method are possible Euler explicit method Runge Kutta order 2 Runge Kutta order 4 with constant time step more accurate Runge Kutta order 4 with variable time step less accurate but 16 probably faster The default setting is Euler explicit Time integration method can be set at menu option SETUP To see something happening on your screen during the kinetics speciation calculation you can get time profiles of several variables in diagrams on your screen At every time step this screen will be renewed Several data types are possible To realize this select EDIT VIEW and edit the data in the view edit tables Probably you will find it difficult to estimate the maximum values for the time profiles Just try and look at the results in the diagrams or look at the output made with the output manager and adap
91. tman dat Run FIT Figure 2 Start up screen of ECOSHELL a Windows shell for ECOSAT Click on button ECOSAT Input Run for input of system data and starting the calculation actually you start then ECO bat Click on button Show Outman dat for displaying printing or saving the calculated output in file OUTMAN dat Click on button ECOSAT Output to generate output in file OUTMAN dat actually you start then OM bat With Help you get some more detailed information about this Ecosat shell With button Change ECOSAT work directory you can change the sub directory in which you want to save the files Button Run Fit starts the parameter fitting program FIT see chapter 2 1 14 1 3 Getting started To run the ECOSAT program in a Windows environment double click ECOSHELL exe make an icon on your desktop and click on button ECOSAT Input Run see figure 2 To run the ECOSAT program in a DOS environment type ECO ECO BAT is a batch file with respectively the commands ECOSAT ECOCALC ECO OUTMAN ECOSAT creates an user input data file ECO user name This data file contains the system description components species etc The results of a successful calculation are added at the end of this file Run time errors are reported in file ECOSAT LOG The output manager OUTMAN reads file ECO and creates after output selection the file OUTMAN DAT with the selected output ordered in columns menu option CHOICE or all basic
92. ume or gel volume By and the concentrations of the dissolved species are equal for the whole volume homogeneous system Given a certain gel volume it is rather easy to calculate the composition of the gel volume see table 8 The gel volume often depends on ionic strength In ECOSAT it is possible to calculate gel volume als function of variable ionic strength during runtime This function is a log linear relation for which both parameters a b can be adapted for each particle surface log Va a b log with ionic strength mol l Va gel volume I kg a b parameters 38 Table 8 Table of species for a system with sorption according to the NICA Donnan model comporens B TS AJS ek Aa mol l ara Ka se Kaos oo species log p Va log Ka EEE species log Ka SA 1 logKass Ka SB js Se jj nj zi ion valence a change of charge due to formation of the surface species relative to the charge of the free surface site S z t change of charge due to sorption z t p F N Za with i SA or SB S t total number of sites on the particle surface mol l Ns total number of sites mol kg p soil solution ratio kg l F Faraday constant Literature Hiemstra T and W H van Riemsdijk Environmental surface chemistry chemical sorption in the system soil water sediment Textbook Wageningen University 1998 Kinniburgh D W H van Riemsdijk L K Koopal M Borkovec
93. utput data of ECOCALC in file ECO calculates the selected output and writes the results to file OUTMAN DAT The output selection itself is stored in the default file OUTMANIN SOF Data in OUTMAN DAT is presented in columns for each output item not for option BASIC The first rows are reserved for labels Other rows contain calculated data for each step in the multiple run or cascade calculations and for each output moment or depth in the transport calculation and for each output moment in the kinetics speciation calculation For transport two different output formats are possible soil column profile data for specific time steps see also figure 9 breakthrough concentration curve data for specific nodes select CHOICE TRANSPORT XY FORMAT 30 Appendix 1 Speciation calculations in ECOSAT Speciation calculations in ECOSAT Speciation Speciation deals with the chemical equilibrium distribution of compounds over different forms and phases in the soil water system All distribution reactions are formulated in terms of reacting components and distribution constants For all components mass balance equations are formulated and solved numerically with a Newton Raphson algorithm Possible different types of species are dissolved species in the water phase ion pairs complexes free components gases minerals organic liquids D NAPL surface species adsorbed components onto soil particles lonic strength and temperature co
94. y NICA non ideal competitive adsorption Kinniburgh 1999 on Ko EEC Da ERC 1 ERC To follow the standard calculation procedure surface components are introduced to express the formulation of the surface species concentration in terms of the components and the median affinity constant It is not necessary to take the surface components also as surface species because the free surface sites are not included in the formulations of the heterogeneous models Variable charge models 37 Sorption of anions and cations onto organic matter or metal hydr oxides is often well described taking electrostatic effects into account In ECOSAT the charging behaviour can be described with well known models like Diffuse Double Layer DDL Constant Capacitance CC Basic Stern Triple Layer and Donnan Due to the presence of a charged field counter ions are accumulated in a double layer near the particle surface The surface complexation reaction can be described with the Langmuir model or with one of the heterogeneous models using the local component concentration in stead of the equilibrium bulk concentration The local component concentration and the equilibrium concentration in the bulk solution are related via the electrostatic potential at the surface o according to the Boltzmann equation For example for component A e A B B Boltzmann factor for the surface layer F Faraday constant 96491 C mol p T temp

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