Quick User Guide for MHEDYN INTERFACE
Contents
1. as shown in figure 4 Metal Diffusion Tapez une question a Number of Fulvic Sites chosen 15_ maximum 39 Populate the lt DEFAULT VALUES gt for the choosen METAL if available log K 0 lt 1 M gt Distance of closest approach lt m gt 5 00E 10 FS tot lt gC L gt 2 00E 03 5 20E 01 Diffusion Coefficient lt m2 s gt 2 80E 10 _log Kmin lt 1 M gt _9 50E 00 a lt mol KgC gt 2 00E 01 Y lt mV gt 9 13E 01 log Kmax lt 1 M gt 1 55E 01 Compute log K lt 1 M gt gt 1243 Computation of total site concentrations Name Concentration lt M gt Log k lt 1 M gt FAL 9 85E 11 15 30 FA2 1 59E 10 14 90 FA3 2 57E 10 14 50 FA4 4 1410 14 10 FAS 6 69E 10 13 70 l FAS 1 08E 09 13 30 FA7 17 09 12 90 FAB 2 82 09 12 50 FAS 4 5409 12 10 g i 5 0 sf oof a s cal ral I FA10 7 309 11 70 Ea u E au E eo O o FA12 1 91E 08 10 90 FA13 3 09E 08 10 50 FAI4 4 98608 10 10 FAIS 8 04 08 3 70 0 00E 00 0 00 R E MHEDYN User Figure 4 The fulvic sites screen The user must give the number of fulvic sites in the field at the top of the screen 39 sites is the maximum value permitted Then the user must populate the fulvic site parameter either by accepting the default value from the databas2. 12 2307 LOSE 12 l Tot Conc P lt m gt 24365 4 18E 07 T 5 866 13 fot Conc P lt M 7 48E 07 3 28E 13 0 00 00 0 00E 00 Figure 5 Aggregate classes screen First of all the user must enter the number of the aggregate size chosen at the top of the screen Then the user must choose a Major Component P from the list and at least one of the two minor component X or and Y P is the component related to the structure and the size distribution of aggregates It may also be complexing X and Y are complexing components adsorbed on P in minor proportions inside the aggregate For the moment the major component P is considered as not reactive with the metal therefore the user MUST add a minor component to see a complexation effect of the aggregate classes For each component a list of values of complexation parameters is proposed from the database but the user can change as he wishes any of the parameter On the right side of the screen the characteristic parameters for aggregate classes must be given In particular the user must give the minimum and the maximum aggregate radius in nm and in um respectively for the computation of the diffusion coefficient of the aggregate classes the fractal dimension Dy of the aggregates usually 1 lt D lt 3 and the exponent B usually 2 lt B lt 4 of the Pareto size distribution of aggregates The mass concentration of
3. lt M gt 0 01 pH 8 Total Concentration lt M gt Diffusion coefficient lt m2 s gt Electric charge kw lt 1 s gt Fulvic Sites Aggregate Classes Aggregate Classes e Matal for Fanilihrinm Concentration in MINTFO This is the bar where to click to TEE EP e added values The three buttons Simple Ligands Fulvic Sites and Aggregate Classes allows the user to make simulations with simple ligands fulvic sites and aggregate classes respectively Section 3 The last section is optional It allows the user to add up to 3 metals in the simulation called competitive metals because they may be important in the computation of the equilibrium concentration with MINTEQ They are not involved in the flux computations Simple Ligands By clicking on the button Simple Ligands a new window appears as shown in figure 3 DEX ax Humber of Simple Ligands chosen 2 er Total _Ligand Name area lt m2 s gt 2 00E 03 20E 2 00E 00 5 TEN j 1 00E 06 1 00E 00 5 00E 10 0 00E 00 l 0 00E 00 0 00E 00 Difusion lt m2 s gt 1 cuco3 aay 1 00E 00 7 14E 10 0 00E 2 curcosyz 2 6 70E 01 i 7 14610 E 3 0 00E 00 0 00E 00 0 00E 00 0 00E 00 0 00E 00 0 00E 00 Double kon the EMPTY lt Complr gt to ADD a component Double dick on the lt Complexe gt to ERASE the components Figure 3 The window of the Simple Ligands I
4. LIL MHEDYN_VXXX gt Double click on the SETUP EXE gt Follow the instructions gt This will install the MHEDYN Interface and the Access 2003 runtime 4 Double click on the icon the main menu of the MHEDYN interface will display 2 MhedynInterface MDB MHEDYN INTERFACE When you run the interface the screen shown in figure 1 will appear Metal Diffusion Figure 1 Initial screen when you first run the interface By clicking on the button General Parameters you will be redirected to the General Parameters screen as shown in figure 2 lt m gt _2 00E 05 Number of points in each subgrid 1 00E 01 Grid increasing factor 1 00E 08 7 14E 10 2 1 00E 10 2 00E 05 1 00E 03 CHIAN Figure 2 General Parameter screen Thi e MHEDYN UserGuide EE Menu Principal E General Parar g s is the starting point to create your experiment General Parameters Let s have a look at each section in the General Parameter screen Section 1 There are two fields the Creation date field and the Test n field Both are automatically updated by the system Section 2 This is the core section of the screen The user must fill all the fields It contains the following fields Owner The user must put a reference name which will appear as the owner of the experiment Diffusion layer thickness The user must put the d
5. Quick User Guide for MHEDYN INTERFACE WELCOME This guide is intended for people who already are familiar with environmental chemistry and associated subjects Welcome to the MHEDYN INTERFACE quick user guide This is a user manual to quickly get familiar with the possibilities offered you by the MHEDYN INTERFACE You will be able to use the interface to prepare and run experiment to compute metal ion flux at planar interface by considering aqueous solution containing simple ligands and or fulvic substances and or aggregate of particles for physicochemical discussions and dynamic parameters related to these complexes see 1 and 2 for examples of flux computations see 3 and 4 This is just a quick reference guide A more complete user guide will come soon Any suggestion to improve the interface is welcome REQUIREMENTS Please verify that the following components are installed on your computer Windows XP or any able to run access2003 Java installed GETTING STARTED The following procedure will help you in download and install the MHEDYN user interface from the page website http www unige ch cabe dynamic 1 Download the ZIP file CHIAM ZIP 2 Decompress the file on the C drive gt A directory called CHIAM will be created 3 1 If ACCESS 2003 is installed on your computer Go on CHIAM Double click on the access file 3 2 If ACCESS 2003 is NOT installed on your computer gt Go on C CHIAM INSTA
6. ay the DELETED record TPR SPECIAL RULES FOR DELETING RECORDS You cannot delete a MASTER RECORD without having deleted all the SLAVE RECORDS Each record has to be deleted one by one and a confirmation is asked To delete a record you have to place the cursor on any field of it and then press the delete button Example gt For instance in the screen below you have a master record of aggregate class and 10 slave records of Diffusion coefficients If you press the is DELETE button in the AGGREGATE CLASSES the system will remind you to delete first the 10 records as shown in the next picture Minor Minor R min lt nm gt R max lt pm gt A ean 0 00 00 of 2 50E 00 y 0 00E 00 Distance of closest 5 00E 10 _0 00E 00 _0 00E 00__ approach lt m gt log K lt 1 M gt 6 60E 00 7 21E 00 0 00E 00 B Component P reactive _ Number of reactive components 2 a gt t lt o t gt _ 20604 P t lt g L gt _1 00E 03 Compute Total Concentrations Tot Cone X lt M gt 8 31607 Tot Conc PeM gt 3 32E 06 N Here are the 10 records to be deleted DIFFERENCE BETWEEN displayed FIELDS AND FIELDS AVAILABLE FOR Input When fields are available for INPUT the background colour is WHITE When fields are NOT available for INPUT the background colour is GREEN as shown in the next screen picture When possible the fields are filled in with defau
7. d close to x 0 to the subdomain with the largest grid close to x 0 It must be given by the user Best values are between 2 and 5 Temperature The user must put the temperature in centigrade Celsius degrees at which the experiment is performed Ionic strength The user must put the ionic strength value in mol dm If the user leaves the field empty the default value of 0 zero is taken pH The user must put the pH value Metal The user must select one metal from the list for the computation of the flux Total Concentration The user must give a total concentration value in mol dm for the chosen metal Diffusion Coefficient The user must give the diffusion coefficient in m s of the chosen metal A value is proposed from the database Electric charge The user must give the electric charge of the metal A value is proposed from the database Kw The user must give a value of k in 1 s for the chosen metal A value is proposed from the database Once the user has filled in the above mentioned fields he must confirm the values by clicking on the vertical gray strip on the left as shown in the picture below E Mei General Parameter E a E Creation date __4 18 2007 __ Owner Davide Diffusion layer thickness lt m gt 2 00E 05 Number of points in each subgrid _____ 20 Total real simulation time lt s gt 1 00E 01 Grid increasing factor _ 4 Temperature lt C gt 25 Tonic strength
8. e by pressing the corresponding button or choosing values by himself The parameters to be introduced are the following for definitions discussion and values of these parameters see ref 1 Log K 0 Characteristic stability constant of the metal fulvic complexes provided by their Freundlich isotherm at given pH ionic strength and temperature T Characteristic parameter of the metal fulvic complexes provided by the slope of their Freundlich isotherm at given pH ionic strength and temperature I is representative of the chemical heterogeneity of the fulvics 0 lt T lt 1 x Total density of sites in mol KgC with fulvic mass expressed in Kg of carbon Distance of closest approach Minimum distance between metal and site to be given in meters Diffusion Coefficient To be given in m s Y electric potential difference between the inside of fulvics and the bulk solution in mV FS Total concentration of fulvic sites in gC L Log Kmin Minimun value of the equilibrium constant of fulvic sites used for the computation Log Kmax Maximum value of the equilibrium constant of fulvic sires used for the computation Then the user can compute the weighted average stability constant of the whole of fulvic complexes considered log K see 1 by clicking on the button Compute Log K If the user is happy with his choice he must confirm the values introduced by clicking on the grey strip on the left side of
9. iffusion layer thickness in meters This is the physical domain where concentration gradients will occur and where the computation will be done The flux is computed at the left hand side of the domain corresponding physically with the origin x 0 and with the position of the consuming interface The boundary conditions on the domain are already implemented in the code and are the following e Perfect sink condition for the metal ion at x 0 e At the right hand side of the domain x the concentration of each species is fixed to the initial concentration values as shown in the file initialconc txt corresponding to the bulk values e Nil flux condition are ensured for each ligand and each complex at x 0 e The initial concentrations of each species are set everywhere in the domain equal to the bulk values Total real simulation time The user must put an estimation of the total real simulation time in seconds Simulation will be stopped after that time Number of points in each subgrid This is a spatial discretization parameter The user must put the number of points within each sub domain Usually the larger this value is the more accurate the simulation is Best values are between 15 and 30 However too large value could compromise stability and or increase the computational time Grid increasing factor This is another spatial discretization parameter It defines the increasing factor from the subdomain with the smallest gri
10. lt values but the user can always modify them IMPORTANT TO KNOW When you quit a screen if no errors are detected the modifications will automatically be validated as if you press the vertical toolbar 3 Fulvic Sites Number of Fulvic Sites choosen maximum 39 Woks Populate the lt DEFAULT VALUES gt for the choosen METAL if available log K O lt 1 M gt 6 40E 00 T 6 00 01 A lt mol KgC gt 2 00E 01 Distance of closest approach lt m gt Diffusion Coefficient lt m2 s gt WY lt mv gt 5 00E 10 2 8E 10 9 13E 01 FS tot lt gC L gt 1 00E 05 log Kmin lt 1 M gt 3 20E 00 log Kmax lt 1 M gt 7 10E 00 Site Number _ 1 OW OB wo nT fiw hw 10 lum roAut Concentration lt M gt 1 75E 09 2 99E 09 5 13E 09 8 79E 09 1 51E 08 2 58E 08 4 43E 08 7 59E 08 1 30E 07 2 23E 07 0 00E 00 Log K lt 1 M gt 6 91 6 52 6 13 5 74 5 35 4 96 4 57 4 18 3 79 3 40 0 00 Aaditi Press the VERTICAL TOOLBAR to add or modify values in the database once pressed the PENCIL will change in an ARROW REFERENCES 1 Buffle J Zhang Z and Startchev K Metal flux and dynamic speciation at bio interfaces Part I critical evaluation and compilation of physicochemical parameters for complexes with simple ligands and fulvic humic substances Environ Sci Technol 41 7609 7620 2007 2 Zhang Z Buffle J and Alemani D Metal flux and dy
11. n this window the user can introduce the simple ligands It is made of 2 sections In the first section the user can choose the ligands he wants to add by giving the Ligand Name The user can introduce a ligand by picking up from a scroll list Total Concentration The user must give the total concentration in mol dm of the chosen ligand Diffusion Coefficient The user must give the diffusion coefficient in m7 s of the chosen ligand A value is proposed from the database when available Electric charge The user must give the electric charge of the chosen ligand A default value is proposed from the database Distance of closest approach The user must give the distance of closest approach in m of the selected ligand A default value is proposed When the user has chosen a ligand he must confirm its addition by clicking on the grey bar located just at the left of its name as shown in the picture below Total Diffusion Distance of Concentration Coefficient Electric closest approach Ligand Name lt M gt lt m2 s gt charge lt m gt 2 00E 03 9 20E 10 2 00E 00 5 00E 10 1 00E 06 5 27E 09 1 00E 00 1 00E 10 0 00E 00 0 00E 00 0 00E 00 0 00E 00 Click here to confirm the values for the simple ligand CO3 The user can at anytime remove one or more of the ligands he has introduced simply by selecting the ligand s he want to remove and clicking on the removal button as shown in the picture below lick here to remove
12. namic speciation at bio interfaces Part II evaluation and compilation of physicochemical parameters for complexes with particles and aggregates Environ Sci Technol 41 7621 7631 2007 3 Alemani D Buffle J Zhang Z Galceran J and Chopard B Metal flux and dynamic speciation at bio interfaces Part III MHEDYN a general code for metal flux computation application to simple and fulvic complexants Env Sci Technol 42 2021 2008 4 Alemani D Buffle J Zhang Z Galceran J and Chopard B Metal flux and dynamic speciation at bio interfaces Part IV MHEDYN a general code for metal flux computation application to particulate complexants and their mixtures with the other natural ligands Env Sci Technol 42 2028 2008
13. tant as reminder of input data and the lability degree of each complex generated by the metal with ligands fulvic sites and aggregates NOTE The lability degree is computed under the steady state conditions When the simulation has stopped the general output results are available at C CHIAM work chiam_xx where xx is the test number of the experiment In particular this file says whether or not the simulation has reached the steady state The file C CHIAM Mhedyn output summary txt gives a summary of the main parameters of the simulation It can be opened at any time after the simulation has started USING THE TOOLBAR When opening the application a toolbar is displayed on the top of each screen Depending of the context the buttons of the toolbar are available or not 1 Applying a filter in searching records Press the first button and put the screen in search mode nter any filter on any field i e search for owner beginning with A e bottom of the screen you can see the number of records returned and that you used a filter Jc cancel the filter and display ALL the records click on the third button Press this button to display the LAST record iaz K4 e am Press this button to display the PREVIOUS record i aly e MEZI Press this button to display the NEXT record iaz K Q y a 3 Create or Delete records Press this button to display the CREATED record Press this button to displ
14. the minor components X Y and of the major component P must also be given in g L The user must click on the button Compute Total Concentrations to compute the total molar concentration of sites of X Y and P Before to compute the diffusion coefficient by clicking the button Compute Diffusion Coefficients the user must confirm the values introduced by clicking on the grey strip on the left side of the screen as for fulvics Then the button Compute Diffusion Coefficients must be pressed to compute the diffusion coefficients of each size class RUN OF A SIMULATION When all the values have been introduced by the user it is possible to run a simulation by clicking on the button Launch the SIMULATION for MINTEQ MHEDYN in the General Parameters screen Note that the computation of the initial bulk equilibrium species distribution by MINTEQ is usually much faster than the following flux computation performed by MHEDYN The latter may take minutes to days or even more for steady state flux computations in particular when quickly reacting metals and large size slowly diffusing aggregates are considered For that reason the user can stop MHEDYN with the appropriate button at the right bottom of the General Parameter screen This may allow him her to check see results below that the species distribution computed by MINTEQ is the appropriate one before running an experiment requiring a long computer time
15. the screen as shown below E Fulvic Sites Numbe gt A log K 0 lt 1 M gt T 6 a lt mol KgC gt 2 Compute log V _ ill n it a N lick here to confirm the values introduced for the fulvics Now the user must click on the button Computation of total site concentrations to compute the total site concentrations of fulvics Aggregate Classes If the user wants to add classes of aggregate complexes he must click on the button Aggregate Classes in the General Parameters screen The Aggregate classes screen will appear as shown in figure 5 Complexes with aggregates as well as the corresponding dynamic parameters are discussed in 2 Davide vax Major R min lt nm gt R max lt pm gt component 3 00E 00 1 00E 00 Minor Name Solid Particles y n lt nm2 gt 1 00E 01 l h lt m gt 3 00E 09 Df 2 00 p lt kg L gt 2 00E 00 wy lt mV gt 0 00E 00 X 5 00E 10 log K lt 1 M gt 9 68E 00 2 00E 01 3 00 Component P reactive _ Number of reactive components 1 Compute Diffusion Coefficients X t lt g L gt 3 00E 05 Classes Radius lt m gt Diffusion Coefficient lt m2 s gt a i 4 01E 09 6 12E 11 7 17E 09 1 3 42E 11 P t lt a L gt 3 00E 03 eee poe Compute Total Concentrations 2 296 08 LOEAi aeos ZER Tot Conc X lt M gt 7 3208 3 35E 12 L31E07 187
16. the selected ligand s Once the user has introduced a ligand he must add at least one complex resulting from the reaction between the metal and the selected ligand In order to do that the user must use the second section starting with the label number of successive complexations by giving the Complexes By double clicking on the first line the first complex will appear By clicking on the following line the following complexes will appear until no more component has been found in the database To remove a complex double click from the last added complex It is possible to introduce up to 5 complexes per ligand Ratio of Coord N To each selected complex the ratio of coordination number is required This is the ratio of the metal free coordination number in the complex to the total metal coordination number Diffusion coefficient The user must give the diffusion coefficient in m s of the complex A value is proposed from the database when available Otherwise the value of diffusion coefficient of the free metal ion can be used as a first approximation Electric charge The user must give the electric charge of the complex Once the user has finished to add simpe ligands he can come back to the General parameters screen by closing the window Fulvic Sites If the user wants to add fulvic sites he must press the button Fulvic Sites in the General Parameter screen and the fulvic sites screen will appear
17. with MHEDYN In particular the user can check the file C CHIAM MINTEQA2 data out which is the output of MINTEQ Diffusion layer thickness lt m gt 2 00E 05 Number of points in each suborid Total real simulation time lt s gt 1 00E 01 Grid increasing factor Metals Total Concentration lt M gt 100608 E 7 Diffusion coefficient lt m2 s gt 714610 Jectric h a 2 if 1 006710 competitive Metal for re Metal Total concentration lt M gt Fez 2 00E 05 Fe3 1 00E 03 Click here to RUN a simulation Click here to STOP a simulation CHECK OF THE RESULTS Once the simulation is running the user can check the results by opening the file C CHIAM Mhedyn output site_flux txt The site_flux txt is a text file that summarizes the most relevant results of the simulation during the evolution time In particular it gives information on e The total flux and the real time of computation e The flux of the free metal ion and its proportion with respect to the total flux and the ratio between the free metal ion concentrations at x 0 and at x 0 e The flux of each complex and its proportion with respect to the total flux and the ratio between its concentrations at x 0 and at x 0 e The ratio between the concentrations at x 0 and at x for each ligand fulvic site and aggregate classes e The equilibrium cons
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