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1. MasSol g The mass of dry soil incubated in each jar VolLigSol mL Volume of liquid in the moist soil during incubation VolLigAdd mL Volume of liquid added to the soil after incubation i e the amount of liquid added to perform a conventional desorption equilibrium experiment CntOm kg kg Mass fraction of organic matter in the soil ConLigRef mg L Reference concentration in the liquid phase ExpFre Freundlich exponent use value taken from adsorption isotherm measured for this pesticide soil combination KomEal L kg coefficient of equilibrium sorption on organic matter use value taken from adsorption isotherm measured for this pesticide soil combination in case you have no organic matter content of the soil set the organic matter to 1 0 and specify the measured Freundlich equilibrium coefficient see Eqn 6 Masini ug The initial total mass of pesticide in each jar contrast to initial versions of PEARLNEO this parameter will be optimised There is no default value for this parameter FacSorNeqEal factor describing the ratio hye Arne Areg as defined by Eqn 4 7his parameter will be optimised but you have to specify an initial guess here The default value is 0 5 CofRatDes d the desorption rate coefficient 7his parameter will be optimised but you have to specify an initial guess here The default value is 0 01 d DT50Ref d the transformation half life under reference conditions applying to2. mg L 1 ValMin 0 1d0 Freundlich N call GetInput ExpFre ExpFre ValMin 0 01d0 ValMax 1 3d0 Equilibrium Kom call GetInput KomEql KomEql L kg 1 ValMin 0 d0 CofFreEql KomEql CntOm Ratio Kf neq Kf eq call GetInput FacSorNeqEql FacSorNeqEql Valmin 0 d0 CofFreNeq FacSorNeqEql CofFreEql Desorption rate coefficient call GetInput CofRatDes CofRatDes d 1 ValMin 0 d0 ValMax 0 5d0 Transformation parameters Molar activation energy call GetInput amp MolEntTra MolEntTra kJ mol 1 ValMin 0 d0 ValMax 200 d0 MolEntTra 1 d3 MolEntTra Pesticide half life call GetInput DT50Ref DT50Ref d ValMin 1 d 1 ValMax 1 d6 Reference temperature call GetInput TemRefTra TemRefTra C TemRefTra TemRefTra 273 15d0 Experimental temperatures Main part of programme RAEE ee write FilOut a write ErilOut ay y ss write FilOut a System properties write FilOut a f10 4 Mass of dry soil g MasSol write FilOut a f10 4 Volume of water in moist soil mL VolLiqSol write FilOut a f10 4 Volume of water added mL VolLiqAdd write FilOut a f10 4 Initial mass of pesticide ug MasIni write FilOut a f10 4 Reference concentration ug mL 1 ConLiqRef write FilOut a f10 4 Equilibrium sorption coeff mL g 1 CofFreEql write FilOut a f10 4 Non
3. Hotspots van biodiversiteit in Nederland op basis van broedvogelgegevens Didderen K en P F M Verdonschot Graadmeter Natuurwaarde aquatisch Typen indicatoren en monitoring van regionale wateren Wamelink G W W G J Reinas J P MolDijkstra J Kros H J Wieggers Verbeteringen voor de Natuurplanner Groeneveld R A amp I A M Schrijver FIONA 1 0 Technical description Luesink H H M J C de Bode P W G Groot Koerkamp H Klinker H A C Verkerk amp O Oenema Protocol voor monitoring landelijke mestmarkt onder een stelsel van gebruiksnormen Bakker Verdurmen M R L J W Eimers M A G Hinssen Haanen T J van der Zwaag van Hoorn Handboek secretariaat WOT Natuur amp Milieu Pleite M amp M A H J van Bavel Europees en gebiedsgericht beleid natuur tussen hamer en aambeeld Een verkennend onderzoek naar de relatie tussen Europees en gebiedsgericht beleid Kramer H G W Hazeu amp J Clement Basiskaart Natuur 2004 vervaardiging van een landsdekkend basisbestand terrestrische natuur in Nederland Koomen A J M W Nieuwenhuizen J Roos Klein Lankhorst D J Brus amp P F G Vereijken Monitoring landschap gebruik van steekproeven en landsdekkende bestanden Selnes T A M A H J van Bavel amp T van Rheenen Governance of biodiversity Vries S de 2007 Neranderende landschappen en hun beleving Broekmeyer M E A amp F H Kistenkas Bouwen en natuur Europese natuurwaarden op het ruimtelijk ordeningsspoor
4. 2003 2005 2006 2007 Model control Yes ScreenOutput 0 0 TimStart d Start time of experiment 500 0 TimEnd d End time of experiment 0 01 DelTim d Time step of Euler s integration procedure System characterization 54 64 MasIni ug Initial guess of initial mass 45 36 MasSol g Mass of soil in incubation jar 6 64 VolLigSol mL Volume of liquid in the moist soil 0 0 VolLigAdd mL Volume of liquid ADDED 0 047 CntOm kg kg 1 Organic matter content Sorption parameter 1 0 ConLiqRef mg L 1 Reference liquid concentration 0 87 ExpFre Freundlich exponent dd KomEql L kg 1 Coefficient for equilibrium sorption 0 5 FacSorNeqEql Initial guess of ration KfNeq KfEql 0 01 CofRatDes d 1 Initial guess of desorption rate constant Transformation parameters 14 00 DT50Ref d Initial guess of half life at ref temperature 20 0 TemRefTra C Reference temperature 110 0 MolEntTra kJ mol 1 Initial guess of molar activation energy Temperature at which the incubation experiments have been carried out table Tem C E 2920 2 15 0 Manual of PEARLNEQ v4 21 end table Provide the results of the measurements Tim Tem Mas ConLiq d C ug ug mL table Observations 2 5 51 6300 5 7285 OBS 10 5 50 5900 5 0560 OBS 42 5 46 0200 3 6635 OBS 87 5 38 6100 2 9320 OBS 157 5 32 8150 1 9280 OBS 244 5 25 8700 1 4650 OBS 358 5 20 3150 0 8820 OBS 451 5 9 4250 0 6015 OBS 2 5 51 3300 5 8955 OBS 6
5. 44 79 e mail info mnp nl The Working Documents series is published by the Statutory Research Tasks Unit for Nature amp the Environment WOT Natuur Milieu part of Wageningen UR This document is available from the secretary s office and can be downloaded from www wotnatuurenmilieu wur nl Wettelijke Onderzoekstaken Natuur amp Milieu Statutory Research Tasks Unit for Nature amp the Environment P O Box 47 6700 AA Wageningen Tel 0317 47 78 44 Fax 0317 42 49 88 e mail info wnm wur nl Internet www wotnatuurenmilieu wur nl Project WOT 04 003 5233523 01 Werkdocument 71 September 2007 F 0008 2007 Contents Summary 1 2 3 4 5 6 7 8 9 Introduction Precautionary remark Description of the incubation experiment Theoretical background Fitting procedure for parameters with PEST Installation of PEARLNEQ Running the example Run PEARL_Neq with your own data Concluding remark Literature Appendix 1 Example input file Appendix 2 Results of the default example Appendix 3 Comparison between an analytical solution and PearlNeq Appendix 4 Listing of Fortran program PearlNeq oO 0 N U 13 14 15 17 19 20 21 23 25 27 Summary This manual describes the PEARLNEQ v4 sofware package This package can estimate long term sorption parameters using results of aged sorption studies with soil using a submodel for sorption and transformation that is identical to the submodel used for
6. InFile status old IOStat IOS if IOS 0 then Error condition abort program execution Error Code 1 write Error ml Cannot find file a with status old trim InFile stop Illegal run id no error file generated end if rewind FilInp Open the error file Call OpenAfterDelete FilErr trim ErrFile Open the output file Call OpenAfterDelete FilOut trim OutFile Open the log file Call OpenAfterDelete FilLog trim LogFile rn my 1 Na a eae ae ee ee ee Ban PEARLNEQ c MNP RIVM Alterra ji p sine NOE TTA OUR AA ARR AC MONROE MTM ONE Lone AU dm ANCONA NE m mm write PEARLNEQ version 4 write write write write write write write write write PEARLNEQ created on a trim Model Date mjn UR MENTI c ree rte m1 ux u 1 NE US GO GR ap 0 Cab EEE Write the Run ID file names and date and time to the output file do F 21 22 write MEME SS SS A RA 5S S SSS See eee ss amp ir seri pina en 8t write F Results from PEARLNEQ c MNP RIVM Alterra write F PEARLNEQ version 4 write F PEARLNEQ created on a trim Model Date write F write F Run ID e aj trim GetRun write F Input file generated on a2 NEN 5257 a0 amp DateVal 7 8 DateVal 5 6 DateVal 1 4 WELLE EARTH 9559575555550 amp EE
7. PEST there are procedures available to do so but these have not yet been implemented in PEARLNEQ So the user has to average first all measurements for each point in time Manual of PEARLNEQ v4 13 6 Installation of PEARLNEQ PEARLNEQ is distributed in a zip file Unzip the file and specify a path e g c pearlneg Be sure there is no space within the specified path because this will cause of failure The package contains four directories i e Neq Bin Pest Neq fortran source files and Neq Example e The Neq Bin directory contains the PEARLNEQ executables PEARLNEQ EXE and PEARLMK EXE e The PEST optimisation software is available in the Pest directory As PEST is now available freeware http www sspa com pest we included the latest version as of 29 10 2003 version 7 0 1 Separate installation of PEST is not necessary e The Neq fortran source files directory contains the fortran source files used to generated the PEST input files and the programme that calculates the sorption kinetics e The Neq Example directory contains results from an example study as described in the FOCUS PEARL user manual version 1 1 1 8 3 2 10 page 51 54 14 WOtwerkdocument 71 7 Running the example The following steps must be followed 1 Run the example to check if everything works and get experience with the system Go to the Neq Example directory and run the example example bat e The batch file will first call PEARLMK This p
8. amp CofRatDes CofFreNeq ConLiqRef ConPor ConLiqRef ExpFre XNeq Increase time Tim Tim DelTim Steps Steps 1 if Tim dge TimeEnd exit end do TimeLoop write FilOut 2 1x f6 1 3 1x 20 8 Tem 273 15d0 Tim Mas ConSus XNeq end do Temperatures contains double precision function Freundlich Mas MasSol VolLiq CofFreEql ConLiqRef ExpFre This function calculates the equilibrium concentration in a system implicit none double precision parameter Err 1 d 4 double precision ConLiqOld ConLiq CofFre double precision intent in Mas MasSol VolLig CofFreEgl ConLigRef ExpFre Manual of PEARLNEQ v4 29 30 ConLiq ConLiqRef do ConLiqOld ConLiq CofFre amp CofFreEgl ConLiqRef 1 dQ ExpFre max ConLiq 1 d 30 ExpFre 1 d0 ConLiq Mas VolLiqtMasSol CofFre if abs ConLiq ConLiqOld lt Err abs ConLiq exit end do Freundlich ConLiq end function Freundlich subroutine SetModelStamp Set the model stamp implicit none Model ExtInp neq Model ExtOut out Model ExtLog log Model ExtErr err Call InitCh Model Date Call InitCh Model PearlVersion Call InitCh Model GeoVersion Call InitCh Model FocusVersion Model PearlVersion 3 3 3 Model Date 10 May 2007 end subroutine SetModelStamp subroutine OpenPearlNeqFiles ProgramPath Performs the following tasks 1 Opens the input and output files 2 Pri
9. equili sorption coeff mL g 1 CofFreNeq write FilOut a f10 4 Freundlich exponent ExpFre write FilOut a f10 4 Desorption rate coefficient d 1 CofRatDes write FilOut a f10 4 Half life transformation d DT50Ref WOt werkdocument 71 write FilOut a f10 4 Reference temperature K TemRefTra write PilOuty ayy IT TFT IT HET Hanne write FilOut a write FilOut a6 1x a6 3 1x a20 Temp Time Mas ConLiq XNeq write FilOut a6 1x a6 3 1x a20 C d ug ug mL 1 ug g 1 Temperatures do T 1 TemTab NumRow Calculate the coefficient at ambient temperature Tem TemTab Y 1 T 273 15d0 FacTem exp MolEntTra RGas 1 d0 Tem 1 d0 TemRefTra CofRatTra FacTem log 2 d0 DT50Ref Initialize the time loop Mas MasIni XNeq 0 d0 Tim TimeStart Steps 0 TimeLoop do MasEql Mas MasSol XNeq ConPor Freundlich MasEql MasSol VolLiqSol CofFreEql ConLiqRef ExpFre ConSus Freundlich MasEql MasSol VolLigSus CofFreEql ConLiqRef ExpFre if mod Steps StepsToPrint 0 then ConSus is always the only output concentration allowing direct fits of desorption measurements write FilOut 2 1x 6 1 3 1x 20 8 Tem 273 15d0 Tim Mas ConSus XNeq end if Integration of total mass Mas Mas DelTim 1 d0 CofRatTra Mas MasSol XNeq Integration of non equilibrium domain XNeq XNeq DelTim
10. input parameter Therefore we offer two options for weighing equal which gives a weight of 1 0 to all observations so equal weights inverse which gives a weight that is proportional to the inverse of the observed value If the observed value is zero the weight is set equal to 1 0 in any case The option equal implies that high observed values get more weight than low observed values As described above the fitting procedure considers two quantities mass of pesticide and the concentration in the liquid phase This may lead to completely different weights for these two types of quantities E g if the mass is initially 50 ug and the concentration in the liquid phase is in the order of 1 ug mL then the fitting procedure will be completely dominated by the decline of the mass of pesticide So if the option equal is used the user should choose a mass of solid phase such that the values of the mass of pesticide in ug should be in the same order of magnitude as the concentration in liquid phase in ug mL The option inverse implies that each measurement gets more or less equal weight for the parameter estimation This inverse option gave the best results in a few tests However we do not claim that this is the best choice for your dataset nor do we claim that the other PEST input parameters are the best choice for your dataset The provided package cannot handle duplicate or triplicate observations for each point in time Within
11. no_name no_name no_name no_name no_name no_name no_name no_name no_name no_name no_name no_name no_name no_name no_name no_name no_name no_name no_name no_name no_name no_name no_name no_name no_name 23 See file EXAMPLE RES for more details of residuals in graph ready format See file EXAMPLE SEO for composite observation sensitivities Objective function gt Sum of squared weighted residuals ie phi 0 4297 Correlation Coefficient gt Correlation coefficient 0 8997 Analysis of residuals gt All residuals Number of residuals with non zero weight 34 Mean value of non zero weighted residuals 1 3161E 02 Maximum weighted residual observation o13 0 3174 Minimum weighted residual observation o30 0 2677 Standard variance of weighted residuals 1 4816E 02 Standard error of weighted residuals 0 1217 Note the above variance was obtained by dividing the objective function by the number of system degrees of freedom i number of observations with non zero weight plus number of prior information articles with non zero weight minus the number of adjustable parameters If the degrees of freedom is negative the divisor becomes the number of observations with non zero weight plus the number of prior information items with non zero weight Parameter covariance matrix gt fsne crd dt50 masini met
12. start of the experiment the same initial mass of pesticide is added to the moist soil in all jars The jars are incubated at a fixed temperature or at a few temperatures At certain time points the remaining total amount of pesticide is measured via an extraction with organic solvent At the same time the concentration in the liquid phase of the moist soil is measured The liquid phase can be collected by centrifuging the moist soil over a filter As an alternative for centrifuging a desorption experiment can be carried out by adding a certain volume of water and subsequent shaking for about 24 h It is assumed that additionally an adsorption isotherm with an equilibration time of about 24 h has been measured for the same soil and pesticide Manual of PEARLNEQ v4 9 4 Theoretical background PEARLNEQ assumes a Freundlich two site sorption submodel one site for equilibrium sorption and the second site for long term sorption kinetics The operational definition for the equilibrium sorption sites is that they have reached equilibrium after about 24 h shaking of a well stirred suspension of the soil in water The long term sorption sites do not reach equilibrium within 24 h PEARLNEQ assumes first order degradation kinetics for the molecules present in liquid phase and sorbed to the equilibrium site however molecules sorbed on the kinetic site are assumed not to degrade This conceptual model is presented in Figure 1 The submodel for sorption and
13. that purpose in the FOCUS_PEARL v3 3 3 The submodel assumes two types of sorption sites equilibrium sites and non equilibrium sites The sorption isotherms for bot sites are described with Freundlich equations The content sorbed at the equilibrium site is assumed to be continuously at equilibrium and the content sorbed at the non equilibrium site is described with a pseudo first order sorption rate equation The transformation rate in soil is assumed to be proportional to the amount in the liquid phase plus the amount sorbed at the equilibrium site So the content sorbed at the non equilibrium site is not subject to transformation The mathematical equations describing the submodel are solved via a FORTRAN programme An additional FORTRAN programme generates the necessary input files for the PEST optimisation package Instructions are given how to obtain optimized parameters using an example dataset and subsequently instructions are given how to obtain parameters using your own data Manual of PEARLNEQ v4 5 1 Introduction This document describes a PEARLNEQ PEST combination which can be used to estimate the parameters for long term sorption kinetics in the PEARL model on the basis of an incubation experiment for a certain soil and a certain pesticide The combination provides also the transformation half life at reference temperature when long term sorption kinetics are included in PEARL the definition of this half life changes so it has t
14. the equilibrium domain 7hys parameter will be optimised but you have to specify an initial guess here As a default value you can use the classical half life which applies to the total soil system i e the equilibrium domain the non equilibrium domain TemRefTra C The reference temperature for which the half life will be provided set to incubation temperature if data for only one temperature are available and set to 20 C if you have data for multiple temperatures MolEntTra kJ mol the molar enthalpy of transformation This parameter will be optimised if you have carried out the experiment at multiple temperatures otherwise it is a model input In any case you have to specify a value e g 60 kJ mol which will be used as an initial guess in case of data for more than one temperature table Tem C List of temperatures at which the incubation experiment has been car ried out One temperature is OK if only data for one temperature are available table Observations List of observations The first column contains the time d the second column the temperature column 3 contains the total mass of pesticide in the system ug column 4 contains the concentration of pesticide ug mL measured in the pore water of moist soil then VolLigAdd 0 or in the water phase after a desorption experiment in which case VolLigAdd is not zero and column 5 contains the characters OBS Manual of PEARLNEQ v4 17 gt option Opt weig
15. 023 23 1400 024 1 64700 025 10 8950 026 0 671000 027 3 13500 028 0 152500 029 1 44000 030 3 050000E 02 031 0 450000 032 0 00000 033 0 150000 034 0 00000 Manual of PEARLNEQ v4 confidence limits themselves s EN for parameter sensitivities Calculated Residual value 55 5316 3 90156 5 39742 0 331082 53 4684 2 87844 5 08081 2 480823E 02 46 2635 0 243511 4 06320 0 399703 38 2669 0 343149 3 09390 0 161897 29 0458 3 76922 2 16483 0 236828 20 9646 4 90536 1 47675 1 175005E 02 13 8380 6 47702 0 932184 5 018437E 02 9 90684 0 481840 0 648450 4 694962E 02 53 3843 2 05426 5 17830 0 717199 48 4369 1 04190 4 62304 0 180537 43 9959 1 06909 4 12910 0 178099 21 3140 1 82600 1 70735 6 034768E 02 8 98367 1 91133 0 544736 0 126264 3 26320 0 128203 0 131795 2 070505E 02 1 24259 0 197406 3 866613E 02 8 166130E 03 0 399623 5 037676E 02 1 077987E 02 1 077987E 02 0 162574 1 257429E 02 4 019330E 03 4 019330E 03 Weigh 9000 1750 0000 1980 2000 2730 6000 3410 0000 5190 9000 6830 9000 1 134 0 1060 1 663 9000 1700 1000 2250 2000 2530 3000 6070 2000 1 490 0 3190 6 557 0 6940 923 NO 2 222 1 000 6 667 1 000 POWDOWONONON O OORONONOEH E 02 E 02 E 02 E 02 E 02 E 02 E 02 E 02 E 02 E 02 E 02 E 02 PEST manual Group no_name no_name no_name no_name no_name no_name no_name no_name no_name
16. 5 47 3950 4 4425 OBS 10 5 45 0650 3 9510 OBS 42 5 23 1400 1 6470 OBS 87 5 10 8950 0 6710 OBS 157 5 351350 0 1525 OBS 244 5 1 4400 0 0305 OBS 358 5 0 4500 0 0000 OBS 451 5 0 1500 0 0000 OBS end table Option for weights of observations equal gives equal weights to all measurements inverse gives weigth equal to inverse value of each measurement if measurement is zero then weight is 1 0 inverse Opt weights 22 WOtwerkdocument 71 Appendix 2 Results of the default example Results taken from last section of REC file These are the results of the defaultexample provided with the package OPTIMISATION RESULTS Parameters gt Parameter Estimated 95 percent confidence limits value lower limit upper limit fsne 0 600286 0 408681 0 791892 crd 1 226317E 02 9 886449E 03 1 463989E 02 dt50 13 0062 11 5100 14 5024 masini 56 0664 52 1243 60 0084 met 108 755 102 806 114 705 Note confidence limits provide only an indication of parameter uncertainty They rely on a linearity assumption which may not extend as far in parameter space as th See file EXAMPLE S Observations gt Observation Measured value ol 51 6300 02 5 72850 03 50 5900 o4 5 05600 05 46 0200 06 3 66350 07 38 6100 08 2 93200 09 32 8150 010 1 92800 oll 25 8700 012 1 46500 013 20 3150 o14 0 882000 o15 9 42500 o16 0 601500 017 51 3300 018 5 89550 019 47 3950 020 4 44250 o21 45 0650 022 3 951700
17. Achtergronddocument bij Natuurbalans 2006 Sollart K M amp F J P van den Bosch De provincies aan het werk Praktijkervaringen van provincies met natuur en landschapsbeleid in de periode 1990 2005 Achtergronddocument bij Natuurbalans 2006 Sollart K M amp R de Niet met bijdragen van M M M Overbeek Natuur en mens Achtergronddocument bij de Natuurbalans 2006 Manual of PEARLNEQ v4 33 2007 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 34 Ten Berge H F M A M van Dam B H Janssen amp G L Velthof Mestbeleid en bodemvruchtbaarheid in de Duin en Bollenstreek Advies van de CDM werkgroep Mestbeleid en Bodemvruchtbaarheid in de Duin en Bollenstreek Kruit J amp LE Salverda Spiegeltje spiegeltje aan de muur valt er iets te leren van een andere plannings cultuur Rijk PJ E J Bos amp E S van Leeuwen Nieuwe activiteiten in het landelijk gebied Een verkennende studie naar natuur en landschap als vestigingsfactor Ligthart S S H Natuurbeleid met kwaliteit Het Milieu en Natuurplanbureau en natuurbeleidsevaluatie in de periode 1998 2006 Kennismarkt 22 maart 2007 van onderbouwend onderzoek Wageningen UR naar producten MNP in 27 posters Kuindersma W Rl van Dam amp J Vreke Sturen op niveau Perversies tussen nationaal natuurbeleid en besluitvorming op gebiedsniveau Melman Th C P ed Indicatoren voor Convention on Biodive
18. Manual of PEARLNEQ v4 J J T Boesten A Tiktak R C van Leerdam Y Y Heu v X 5 ks talk de el WAGENINGEN TIEN Manual of PEARLNEQ v4 J J T I Boesten A Tiktak R C van Leerdam Werkdocument 71 Wettelijke Onderzoekstaken Natuur amp Milieu Wageningen september 2007 The Working Documents series presents interim results of research commissioned by the Statutory Research Tasks Unit for Nature amp the Environment WOT Natuur amp Milieu from various external agencies The series is intended as an internal channel of communication and is not being distributed outside the WOT Unit The content of this document is mainly intended as a reference for other researchers engaged in projects commissioned by the Unit As soon as tinal research results become available these are published through other channels The present series includes documents reporting research findings as well as documents relating to research management issues This Working document was produced in accordance with the Quality Manual of the Statutory Research Tasks for Nature and the Environment Unit Dit werkdocument is gemaakt conform het Kwallteitshandboek van de WOT Natuur amp Milieu 2007 Alterra P O Box 47 6700 AA Wageningen Tel 0317 47 47 00 fax 0317 41 90 00 e mail info alterra wur nl Milieu en Natuurplanbureau MNP P O Box 303 3720 AH Bilthoven Tel 030 274 27 45 fax 030 274
19. RE eee ln a in a my write E 1 mt end do end subroutine OpenPearlNEQFiles end program PearlNeq Manual of PEARLNEQ v4 31 WOt onderzoek Verschenen documenten in de reeks Werkdocumenten van de Wettelijke Onderzoekstaken Natuur amp Milieu vanaf mei 2005 Werkdocumenten zijn verkrijgbaar bij het secretariaat van Unit Wettelijke Onderzoekstaken Natuur amp Milieu te Wageningen T 0317 47 78 44 F 0317 41 90 00 E info wnm wur nl De werkdocumenten zijn ook te downloaden via de WOt website www wotnatuurenmilieu wur nl 2005 1 Eimers J W Samenstelling Projectverslagen 2004 2 Hinssen P J W Strategisch Plan van de Unit Wettelijke Onderzoekstaken Natuur amp Milieu 2005 2009 3 Sollart K M Recreatie Kennis en datavoorziening voor MNP producten Discussienotitie 4 Jansen M J W ASSA Algorithms for Stochastic Sensitivity Analysis Manual for version 1 0 5 Goossen C M amp S de Vries Beschrijving recreatie indicatoren voor de Monitoring en Evaluatie Agenda Vitaal Platteland ME AVP 6 Mol Diikstra J P Ontwikkeling en beheer van SMART2 SUMO Ontwikkelings en beheersplan en versiebeheerprotocol Oenema O How to manage changes in rural areas in desired directions Dykstra H Monitoring en Evaluatie Agenda Vitaal Platteland inventarisatie aanbod monitoringsystemen Ottens H F L amp H J A M Staats BelevingsGIS versie2 Auditverslag 10 Straalen F M van Lijnvormige beplanting Groene Woud Een stu
20. ching as calculated with the PEARL model for FOCUS scenarios BCPC Symposium Proceedings No 78 Pesticide behaviour in soils and water p 27 32 FOCUS 2006 Guidance document on estimating persistence and degradation kinetics from environmental fate studies on pesticides in EU registration EC Document Sanco 10058 2005 version 2 0 European Commission Brussels 434 pp Available at http viso ei jrc it focus Leistra M AMA van der Linden JJTI Boesten A Tiktak amp F van den Berg 2001 PEARL model for pesticide behaviour and emissions in soil plant systems description of the processes in FOCUS PEARL version 1 1 1 Alterra Report 013 Alterra Wageningen RIVM Report 711401009 RIVM Bilthoven Available at PEARL website to be found via Help button in main screen of PEARL Tiktak A F van den Berg JJTI Boesten D van Kraalingen M Leistra amp AMA van der Linden 2000 Manual of FOCUS PEARL version 1 1 1 RIVM report 711401008 RIVM Bilthoven the Netherlands Available at PEARL website to be found via Help button in main screen of PEARL 20 WOt werkdocument 71 Appendix 1 Example input file Example input file example mkn STANDARD FILE for pearlmk version 4 Program to fit the half life activation energy and parameters for long term sorption kinetics of pesticides in soil This file is intented for use with the PEST program Doherty et al 1991 Please see manual of PEARLNEQ c RIVM MNP Alterra
21. degradation kinetics used in PEARLNEQ can be described as follows Leistra et al 2001 M V Cy tM AX ig FX pyr 1 N C Kro KF go en 2 CLR dX 4 C Ts k Kr ve CLR E X 3 t CLR Kp ve fre K to 4 dM a k Vc M X 50 5 dt Keo Mou Konco 6 where M initial total mass of pesticide in each jar ug acronym Maslni Y the volume of water in the soil incubated in each jar mL acronym VolLiq M the mass of dry soil incubated in each jar g acronym MasSol c concentration in the liquid phase ug L acronym ConLiq C g reference concentration in the liquid phase ug L acronym ConLiqRef Xo content sorbed at equilibrium sites ug g Xng content sorbed at non equilibrium sites ug g Arco equilibrium Freundlich sorption coefficient mL g acronym CofFreEgl Arve non equilibrium Freundlich sorption coefficient mL g acronym CofFreNeq N Freundlich exponent acronym ExpFre k desorption rate coefficient d acronym CofRatDes fyc a factor for describing the ratio between the equilibrium and non equilibrium Freundlich coefficients acronym FacSorNeqEq k degradation rate coefficient d oy Mass fraction of organic matter in the soil kg kg acronym CntOm Komeo coefficient of equilibrium sorption on organic matter mL g acronym KomEq 10 WOt werkdocument 71 PEARLNEQ does not use the transformation rate coefficient k as input parameter but the half life at refe
22. die naar het verdwijnen van lanen en perceelsrandbegroeiing in de Meierij 11 Pogramma Commissie Natuur Onderbouwend Onderzoek voor de Natuurplanbureau functie van het MNP Thema s en onderzoeksvragen 2006 12 Velthof G L samenstelling Commissie van Deskundigen Meststoffenwet Taken en werkwijze 13 Sanders ME amp G W Lammers Lokaliseren kansen en knelpunten van de Ecologische Hoofdstructuur met informatie van de terreinbeheerders 14 Verdonschot P F M C H M Evers R C Nijboer amp K Didderen Graadmeters aquatische natuur Fase 1 Vergelijking van de graadmeter Natuurwaarde met de Natuurdoeltypen en KRW maatlatten 15 Hinssen PJW Wettelijke Onderzoekstaken Natuur amp Milieu Werkplan 2006 16 Melman Th C P R G Groeneveld R A M Schrijver amp H P J Huiskes Ontwikkeling economisch ecologisch optimaliseringmodel natuurbeheer in combinatie met agrarische bedrijfsvoering Studie in het licht van LNV beleidsombuiging van verwerving naar beheer 17 Vreke J Rl van Dam amp F LP van den Bosch De plaats van natuur in beleidsprocessen Casus Besluitvormingsproces POL aanvulling Bedrijventerrein Zuid Limburg 18 Gerritsen A L J Kruit amp W Kuindersma Ontwikkelen met kwaliteit Een verkenning van evaluatiecriteria 19 Bont C J A de M Boekhoff WA Rienks A Smit amp A E G Tonne jck Impact van verschillende wereldbeelden op de landbouw in Nederland Achtergronddocument bij Verkenning Duurzame Landbouw 20 Net
23. fsne 8 7787E 03 8 4444E 05 5 6502E 02 6 4073E 02 0 1016 crd 8 4444E 05 1 3507E 06 4 5078E 04 6 0200E 04 6 0023E 04 dt50 5 6502E 02 4 5078E 04 0 5353 0 5756 1 463 masini 6 4073E 02 6 0200E 04 0 5756 3 716 0 8663 met 0 1016 6 0023E 04 1 463 0 8663 8 463 Parameter correlation coefficient matrix gt fsne erd dt50 masini met fsne 1 000 0 7755 0 8242 0 3548 0 3727 crd 0 7755 1 000 0 5301 0 2687 OLAS dt50 0 8242 0 5301 1 000 0 4081 0 6872 masini 0 3548 0 2687 0 4081 1 000 0 1545 met 0 3727 041775 0 6872 0 1545 1 000 Normalized eigenvectors of parameter covariance matrix gt Vector 1 Vector 2 Vector 3 Vector 4 Vector 5 fsne 1 4335E 02 0 9842 0 1744 2 2879E 02 1 1198E 02 erd 0 9999 1 4279E 02 1 5744E 03 1 9999E 04 6 4642E 05 dt50 9 4905E 04 0 1745 0 9453 0 2229 0 1618 masini 7 8350E 05 1 4702E 02 0 2006 0 9685 0 1467 met 7 0894E 05 1 9859E 02 0 1889 0 1084 0 9758 Eigenvalues gt 4 7821E 07 1 7663E 03 0 1313 3 753 8 837 24 WOt werkdocument 71 Appendix 3 PearlNeq Comparison between an analytical solution and In this appendix an analytical solution for the remaining mass of pesticide is compared with the PearlNeq solution appendix 4 The system properties were Mass of dry soil MasSol g 1 0000 Volume of water in moist soil VolLiqsol mL Volume of water added VolLigAdd mL Initial mass of pesticide Masini ug 0 2000 0 0000 10 0000 Reference concentration Co
24. hts options for weights Two options for weighing are offered equal which gives a weight of 1 0 to all observations so equal weights and inverse which gives a weight that is proportional to the inverse of the observed value if the observed value is zero the weight is set equal to 1 0 in any case you can inspect the weigths in the pst file 2 Modify the contents of the example bat file with right mouse button replace example everywhere it occurs by the name of the copied input file and delete last line of the file which would generate the graph Repeat step 1 5 of chapter 7 3 If the optimization is not succesfull you can try re running PEARLNEQ with different initial guesses of Masini DT5ORef FacSorNeqEql and CofRatDes 18 WOtwerkdocument 71 9 Concluding remark While using PEARLNEQ we noticed that very regularly the results depend on the initial guesses of the parameters Therefore we advise you to perform always a number of runs with different initial guesses We advise you also to analyse the results very carefully especially the 95 confidence intervals of your parameters If the interval is wide for a certain parameter this indicates that the estimated variable is very uncertain As a consequence it is usually not meaningful to use it any further in the risk assessment Manual of PEARLNEQ v4 19 Literature Boesten JJTI amp AMA van der Linden 2001 Effect of long term sorption kinetics on lea
25. ion parameter TimeStart 0 d0 Start time double precision parameter DelTimPrint 1 d0 Print time step double precision CntOm CofFreEql CofFreNeq CofRatDes CofRatTra DelTim DT50Ref ExpFre Mas MasEql MasIni MasSol VolLiqAdd MolEntTra TimeEnd VolLigSol VolLigSus XNeg ConLigRef Tim Tem FacTem TemRefTra KomEql FacSorNegEql ConPor ConS us type TableType TemTab save IOMode IOMode Full ShowScreen false Initial part of program Set the model stamp Call SetModelStamp version numbers etc Open the input file call InitCh Path Call OpenPearlNeqFiles Path System properties Initial mass of pesticide call GetInput MasIni MasIni ug Valmin 0 d0 Mass of dry soil call GetInput MasSol MasSol g Valmin 0 d0 Volume of liquid in moist soil and volume of liquid added call GetInput VolLiqSol VolLiqSol mL Valmin 0 d0 call GetInput VolLiqAdd VolLigAdd mL Valmin 0 d0 Manual of PEARLNEQ v4 27 28 Calculate the volume of the suspension VolLiqSus VolLiqSol VolLigAdd Organic matter content call GetInput CntOm CntOm kg kg 1 ValMin 0 d0 End time call GetInput TimeEnd TimEnd d ValMin 0 d0 Time step call GetInput DelTim DelTim d ValMin 0 d0 StepsToPrint max 1 int DelTimPrint 1 d 10 DelTim Sorption parameters Reference concentration call GetInput ConLiqRef ConLiqRef
26. ly the operational definition of the equilibrium sorption site Assumption B is justifiable because desorption coefficients for long term kinetics are usually in the order of 0 01 d which implies that amounts desorbed within 1 day are negligibly small Using these assumptions the concentration in the liquid phase of the supernatant after desorption can be estimated by stating that i the total content of substance in the moist soil and the soil water suspension have to be equal and ii the content sorbed at the non equilibrium sites in the moist soil and in the soil water suspension are equal Using Equation 1 then results in the following equation y C ms M oss X ve E V V pp C sus M Xd X yep 9 where the subscript MS indicates the moist soil system the subscript SUS indicates the soil water suspension system and Vipp volume of liquid usually CaCl solution added to the soil at each sampling point just before starting the 24 h desorption experiment mL acronym VolLigAdd At each sampling point in time Equation 9 can be rewritten using Eqn 2 into an equation that contains only one unknown variable i e the concentration in the liquid phase of the soil suspension c sus PEARLNEQ provides as output always the concentration in the soil water suspension as a function of time If Vp O then this implies that the concentration in the moist soil is given PEARLNEQ solves the set of Eqn 1 to Eqn 9 numerically
27. nLiqRef ug mL 1 Equilibrium sorption coefficient CofFreEql mL g 1 Non equili sorption coefficient CofFreNeq mL g 1 1 0000 1 0000 0 5000 Freundlich exponent ExFre Desorption rate coefficient CofRatDes d 1 Half life transformation DT5ORef d Reference temperature TemRefTra K 1 0000 0 0100 69 3000 293 1500 The analytical solution was taken from Appendix 4 of FOCUS 2006 The figure shows that the PearlNeq solution coincides very well with the analytical solution PearlNeq analytical 12 o 2 10 amp 8 o 6 o E 4 5 2 me 0 0 100 200 400 500 600 Incubation time d Comparison between the analytical solution and the PearlNeg solution Manual of PEARLNEQ v4 25 Appendix 4 program PearlNeq Listing of Fortran program PearlNeq PEARLNEQ program simulates pesticide behaviour in a closed incubation system assuming a two site Freundlich sorption submodel and first order transformation kinetics Initial Version Version Version lt WN HH RWNRO FWN HH version for Pearl 1 1 compatible compatible compatible with FOCUS with FOCUS with FOCUS sion 4 of 10 May 2007 use Sishell use CompilerSpecific General routines Compiler specific statements implicit none character len LineLength Path integer T Steps StepsToPrint double precision parameter RGas 8 31432d0 Molar gas constant double precis
28. nts the date and time and the Run Id to all opened output files 3 Reads the start time and end time gets the print interval 5 Sets the begin CPU time in seconds The following input and output files are used by the model Unit FilInp The input file extension prl Unit FilOut The output file extension out Unit FilLog The log file extension log implicit none Declaration of local variables character len LineLength InFile OutFile LogFile SumFile ErrFile RunName integer IOS character len WordLength DateVal TimeVal ZoneVal character len LineLength ProgramName ProgramPath integer F integer dimension 8 TimArray Main part of procedure Create Memory Space for the Words variable Words Allocated false Call Create Words NumWords Date and time Call Date And Time Date DateVal Time TimeVal Zone ZoneVal Values TimArray WOtwerkdocument 71 Get the run ID Call InitCh RunName RunName GetRun Get the path for the program Call GetProgramName ProgramName Call GetPath ProgramName ProgramPath Construct the file names add the extensions call InitCh InFile call InitCh OutFile call InitCh LogFile call InitCh SumFile call InitCh ErrFile InFile trim RunName Model ExtInp OutFile trim RunName Model ExtOut LogFile trim RunName Model ExtLog ErrFile trim RunName ModelSExtErr Open the input file Open FilInp file trim
29. o be recalculated see Boesten and van der Linden 2001 If the incubation experiment has been carried out at multiple temperatures the Arrhenius activation energy for the transformation rate in soil can be optimised simultaneously Manual of PEARLNEQ v4 7 2 Precautionary remark This PEARLNEQ PEST software tool should be seen as an introduction to fitting results of experiments on long term sorption kinetics to the sorption submodel used in the PEARL model The tool shows you how PEST can be coupled to a fortran programme that contains this PEARL sorption submodel i e PEARLNEQ EXE but it should not be seen as a ready to use tool The tool provides you with example input files for the PEST optimisation package and shows you how to organise this optimisation We had to make a number of assumptions for generating these PEST input files e g upper and lower bounds of parameters weighing factors for each measurement etc etc We do not claim that these assumptions are defensible for your problem they are our best guesses but they may not be appropriate for your problem It is your responsibility to check the appropriateness of the result obtained We do not accept any responsibility for use of PEARLNEQ 8 WOt werkdocument 71 3 Description of the incubation experiment The PEARLNEQ PEST tool can be used to fit the results of the following experiment A number of jars is filled with soil Each jar contains the same mass of moist soil At the
30. re processing program generates the input files for PEST i e example pst example tpl and example ins see Figure 2 Runld example e Then the optimisation starts PEST calls PEARLNEQ several times see Figure 2 in the example 39 times e f you get an error message after the first step PEARLMK type control break to stop the process and check the error messages available in the example err file After successful optimisation read the results from the file example rec Choose select the program from the list and open with Notepad The relevant results including parameter values 95 confidence intervals and correlation matrices can be found at the end of this file Section OPTIMISATION RESULTS see Appendix 2 The meaning of the short acronyms in this rec file is as follows fsne FacSorNeqEal crd CofRatDes dt50 DT50Ref masini Maslni met MolEntTra PEST also generates parameter sensitivity files etc Details can be found in the PEST manual which is available in the PEST subdirectory of the package If you encounter errors during the second step you can try running PEARLNEQ directly PEARLMK has created a file example neq in Neq_Example which is the input file for pearlneg You can run PEARLNEQ by typing Neq_Bin pearlneq example in a DOS box PEARLNEQ will create an output file example out and a log file example log The output files are self explaining The output file contains the
31. rence temperature acronym DT5ORef af50 They are related as follows assuming first order kinetics at50 In 2 k 7 The effect of soil temperature on the transformation rate coefficient in soil is described by the Arrhenius equation sE 1 m 8 fr oaf R E B where f the multiplication factor for the rate coefficient E Arrhenius activation energy kJ mol 7 temperature of the soil K Traer the reference temperature for the specified D750 K R the gas constant kJ mol K equilibrium sorption subject to transformation o non equilibrium sorption Figure 1 Conceptual representation of the PEARL NEQ model Often no concentration measurements in the soil pore water are available but instead at each sampling point in time a certain volume of water usually a CaCl solution is added to soil and the suspension is shaken for about 24 h after which the concentration in the supernatant is measured In such a case the fit has to be based on these concentration measurements in the supernatant of the soil water suspension This is simulated in PEARLNEQ as follows A it is assumed that full equilibrium is reached for the equilibrium sorption site during the desorption experiment i e shaking for 24 h B it is assumed that desorption from the non equilibrium sorption site can be ignored during the desorption experiment Manual of PEARLNEQ v4 11 Assumption A is justifiable because this is exact
32. result of the last run which is in PEST by definition the run with the optimised parameters You can use the XyWin program to make a graph After running the example this will be done automatically XyWin is available in the neq_bin xypearl directory of PEARLNEQ you can also get the graph via typing in a DOS box Neq_Bin xypearl ixywin j example job W I However XyWin is not userfriendly so we recommend to use the results from the output file example out as the source for the best fit and create graphs with software of your own choice Manual of PEARLNEQ v4 15 Runld mkn y PearlMk Runld ins Runld tpl Runld pst If and bei Runld rec Runld neq PearlNeq Runld out Figure 2 Dataflow diagram for the PEARLNEQ PEST combination The acronym Runld s example for the example provided 16 WOt werkdocument 71 8 Run PEARL Neq with your own data We assume that you have carried out an appropriate incubation experiment as described before The first step of optimising your own data consists of editing the file example mkn which can be found in the example subdirectory of the PEARLNEQ di rectory Open the file with Notepad Please make a copy of this file before editing Make sure there is no space in the new name This will give an error An example of this input file is listed in Appendix 1 The following parameters must be provided VVVWV vvv TimEnd d The duration of the incubation experiment
33. rondeigenaren Uitkomsten van een marktonderzoek Didderen K P F M Verdonschot M Bleeker Basiskaart Natuur aquatisch Deel 1 Beleidskaarten en prototype Boesten J J T 1 A Tiktak amp R C van Leerdam Manual of PEARLNEQ v4 WOt werkdocument 71
34. rsity 2010 Broekmeyer MEA E P A G Schouwenberg amp ME Sanders amp R Pouwels Synergie Ecologische Hoofdstructuur en Natura 2000 gebieden Wat stuurt het beheer Bosch F J P van den Draagvlak voor het Natura 2000 gebiedenbeleid Onder relevante betrokkenen op regionaal niveau Jong JJ amp M N van Wijk LM Bouwma Beheerskosten van Natura 2000 gebieden Pouwels R amp M J S M Reinen amp M van Adrichem amp H Kuipers Ruimtelijke condities voor VHR soorten Bouwma I M Quickscan Natura 2000 en Programma Beheer Schouwenberg E P A G Huidige en toekomstige stikstofbelasting op Natura 2000 gebieden Hoogeveen M Herberekening Ammoniak 1998 werktitel Jaarrapportage 2006 WOT 04 001 ME AVP Jaarrapportage 2006 WOT 04 002 Onderbouwend Onderzoek Jaarrapportage 2006 WOT 04 003 Advisering Natuur amp Milieu Jaarrapportage 2006 WOT 04 385 Milieuplanbureaufunctie Jaarrapportage 2006 WOT 04 394 Natuurplanbureaufunctie Brasser E A M F van de Kerkhof A M E Groot L Bos Gorter M H Borgstein H Leneman Verslag van de Dialogen over Duurzame Landbouw in 2006 Hinssen P J W Wettelijke Onderzoekstaken Natuur amp Milieu Werkplan 2007 Nieuwenhuizen W amp J Roos Klein Lankhorst Landschap in Natuurbalans 2006 Landschap in verandering tussen 1990 en 2005 Achtergronddocument bij Natuurbalans 2006 Geelen J amp H Leneman Belangstelling motieven en knelpunten van natuuraanleg door g
35. using Euler s method for integration of the state variables M and Xy The time step for integration can be set as an input parameter we recommend 0 01 d The concentration in the liquid phase is calculated via an iteration procedure as described in Appendix 4 of FOCUS 2006 Appendix 3 shows a test of the PEARLNEQ results against an analytical solution for the case of a linear isotherm A1 indicating good correspondence between numerical and analytical results 12 WOtwerkdocument 71 5 Fitting procedure for parameters with PEST The provided package assumes that the following variables need to be optimized e the initial mass of the pesticide Masini e the ratio between the equilibrium and non equilibrium Freundlich coefficients FacSorNeqEq e the desorption rate coefficient CofRatDes e the half life at reference temperature DT50Ref e the molar activation energy MolEntTra this can only be optimized if the experiment has been carried out at multiple temperatures It is assumed that all other variables are known The provided package assumes that the measurements that are fitted consist for each point in time of e amass of pesticide in ug e a concentration in liquid phase in ug mL PEST needs a number of input parameters for the fitting procedure e g upper and lower bounds of parameters weighing factor for each measurement etc etc Our experience is that the weighing factor for each measurement is the most important
36. verschenen 32 WOt werkdocument 71 2006 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 Rienks W A Terluin amp P H Vereijken Towards sustainable agriculture and rural areas in Europe An assessment of four EU regions Knegt B de H W B Bredenoord J Wiertz amp M E Sanders Monitoringsgegevens voor het natuurbeheer anno 2005 Ecologische effectiviteit regelingen natuurbeheer Achtergrondrapport 1 Jaarrapportage 2005 WOT 04 001 Monitor en Evaluatiesysteem Agenda Vitaal Platteland Jaarrapportage 2005 WOT 04 002 Onderbouwend Onderzoek Natuurplanbureaufunctie Jaarrapportage 2005 WOT 04 385 Milieuplanbureaufunctie Jaarrapportage 2005 WOT 04 394 Natuurplanbureaufunctie Jaarrapportage 2005 WOT 04 Kennisbasis Verboom J R Pouwels J Wiertz amp M Vonk Strategisch Plan LARCH Van strategische visie naar plan van aanpak Velthof G L en LAM van Grinsven eds Inzet van modellen voor evaluatie van de meststoffenwet Advies van de CDM werkgroep Harmonisatie modellen Hinssen M A G R van Oostenbrugge amp K M Sollart Draaiboek Natuurbalans Herziene versie Swaay C A M van V Mensing amp M F Wallis de Vries Hotspots dagvlinder biodiversiteit Goossen C M amp F Langers Recreatie en groen in en om de stad Achtergronddocument bij Natuurbalans 2006 Turnhout Chr Van W B Loos R P B Foppen M J S M Reijnen
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