PRODUCTION' MODEL USER'S GUIDE
Contents
1. 10 2 2 Program FITSOLAR o o eee sn 11 2 3 Program PSPARMS 2 ws ee ne o 12 2 4 Programs YEARPROD and DAYPROD css rs ss ses 12 2 5 Programs YTOTALS and DTOTALS ss ss 13 3 DATA FORMATS oe dns nm ee 14 3 1 General eus sue 14 3 1 1 Disc file nomenclature ss 14 3 1 2 Header lines 0 ee 15 3 1 3 Dates ou sn me 15 3 1 4 Solar data o poo ee ees sr 15 3 1 5 Transparency chlorophy11 Ph and adata wee eel 3 1 6 Hypsographic data s oe ee 17 3 1 7 Mixing depth data sus es use 17 3 1 8 Organization of data in DAT files cnrs 18 3 2 Program FITSOLAR ae ee 18 3 3 Program PSPARMS esse ss mm e 18 3 4 Program YEARPROD esse mm mm 19 3 5 Program DAYPROD o et ee ee ess 20 3 6 Program YTOTALS ooo o 21 3 7 Program DTOTALS o een mm um 22 4 RUNNING THE MODEL 444444 23 4 1 Starting the Programs s ee 23 4 2 Error Handling o 4 ee ee a 24 4 3 Breakpointing Runs esse mu 24 4 4 Run time commands sers rs 25 A tmos Effect lt value gt cnrs ns ee 25 B reakpoint lt o o o 25 Check o o et ss us 25 I ntervals lt ndepths gt2. ss ss ee 26 L atitude lt degrees gt scs uses se 26 Ojutput lt drive gt ee eee 26 iv S olar lt drive gt o 26 Ujniform o P mu 26 Z max lt maxdepth gt 44 444440 26 5 EXAMPLES o o 27 5 1 Program FITSOLAR o ss e ew ew 27 5 2 Program PSPARMS son 28 5 3 Program YEARPROD ssa ss 29 5 4 Program DAYPROD a we ee eee Sl 5 5 Program YTOTALS o cone ee tw ee we we eee BI 5 6 Program DTOTALS es we 32 ACKNOWLEDGMENTS 2 sers e ss 33 REFERENCES eaaa ew es 33 APPENDIX cresson esse cnrs ss ss ss 35 LIST OF TABLES Table Page 1 The variables used in the model required units and which programs use 2 them ss mm 4 Comparison of annual primary production rates in Experimental Lakes Area ELA Takes calculated with the old incubator model Fee 1977 and with the new model presented in this report ssas eee ee Acceptable ranges of values for variables used in the primary production model s a ww we we 4 Summary of file types used in the model the uses of each type and the programs that use each type a 15 LIST OF FORMULAS Formula Page 1 Simpson s 3 point numerical integration rule o sa 0 10 2 Calculating cloudless solar
3. MAY 9 5 40 1594 1241 1361 1124 167 231 3 78E 009 3 12 009 27 02 2 2 MAY 10 5 40 1779 1383 1519 1253 187 258 4 22E 009 3 48 009 27 19 2 2 l totals gm 9 7 6 8 8 2 6 2 1 0 1 4 2 29E 010 1 73E 010 Maximum depth 12 00 Number of depth intervals 41 Cloudless Tight data for 1976 latitude 50 0 atmos effect 0 3563 Note that the uncorrected integrals col 4 do not exactly match the corresponding results in the file TESTYR OUT section 5 3 that was used as input to this program The reason for this is that the integrals reported by YTOTALS were calculated with 41 depth intervals while those calculated by YEARPROD were calculated with only 11 depth intervals The reason for using more depth intervals in the TOTALS programs was discussed in section 2 5 5 6 PROGRAM DTOTALS If the disc contains the TESTDAY OUT file produced by the example run in section 5 4 and if the example data shown in section 3 7 are contained in the file TESTDAY DAT then typing A gt dtotals testday i 41 should produce a file called TESTDAY TOT that contains 33 L Wpg Station 318 1976 Cloudless weather Uncorr Morphometry Corrected mean ligh Horror dao He Epi mg C m2 mg C m2 mg C m3 IMass Produced gm C mE m2 min Depth Total Epil Total EpilTotal Epi To zmax In Epi Epi Hyp JUN 6 10 00 137 137 133 133 17 17 3 69 008 3 69E 008 5 03 0 0 Maximum depth 10 00 Lake Winnipeg 1976 Cruise 3 Latitude 50
4. using empirical surface light data Enter values for the southern hemisphere as negative numbers O utput lt drive gt This command allows you to specify the disc drive A P on which the output file for this run will be written Normally the output files are written onto the default drive see the CP M manual for the definition of drive nomenclature S olar lt drive gt This command allows you to specify the disc drive A P on which the solar data for this run is to be found By putting the solar data on the second drive you can make more space available on the default drive for output files U niform This causes the input data values for chlorophyll and Pi to be applied uniformly over the input depths instead of being linearly interpolated An example will make this clear Suppose that the input data looked like IMAY 5 0 0 10 5 0 100 10 0 1000 1 If the Uniform command is given then ali depths between 0 and 4 99 meters will be assigned the value 10 depths between 5 and 9 99 meters will be assigned the value 100 and any depths greater than 10 meters will be assigned the value 1000 If you do not specify this command then values will be linearly interpolated if calculation depths are at 0 1 2 etc then the interpolated values for the above dataset would be 10 28 46 etc Z max lt maxdepth gt In a shallow lake the calculated euphotic zone depth might be greater than the actual maximum depth of the lake
5. 1 02 0 57 0 Chlorophy11 mg m 3 JUN 6 1 70 1 70 1 70 1 70 1 70 1 70 1 70 1 70 1 70 1 70 1 alpha mg C mg ch1 E m 2 JUN 6 5 40 5 40 5 40 5 40 5 40 5 40 5 40 5 40 5 40 5 40 5 PBm mg C mg chl hr JUN 6 4 70 4 70 4 70 4 70 4 70 4 70 4 70 4 70 4 70 4 70 4 Lake Winnipeg 1976 Cruise 3 Latitude 50 0 atmos effect 0 3563 The format of these results is the same as for YEARPROD section 5 3 5 5 PROGRAM YTOTALS If the disc contains the TESTYR OUT and CLDLSS SOL files produced by the example run in section 5 3 and if the example data shown in section 3 6 are contained in the file TESTYR DAT then typing A gt ytotals testyr i 41 32 should produce a file called TESTYR TOT that contains Lake Winnipeg 1976 Cruise 3 Uncorr Morphometry Corrected mean ligh Hon He Re 4 Epi mg C m2 mg C m2 mg C m3 Mass Produced gm C mE m2 min Depth Total Epil Total EpilTotal Epil To zmax In Epi Epi Hyp MAY 1 3 00 169 80 145 76 18 27 4 02E 008 2 10E 008 35 93 4 9 MAY 2 3 60 342 191 293 179 36 53 8 13E 008 4 96 008 32 97 4 0 MAY 3 3 60 518 288 442 269 54 80 1 23E 009 7 47E 008 33 21 4 0 MAY 4 4 20 693 443 592 409 73 106 1 65 009 1 14 009 30 62 3 3 MAY 5 4 20 871 557 745 515 91 133 2 07E 009 1 43E 009 30 83 3 3 MAY 6 4 80 1049 749 897 685 110 157 2 49E 009 1 90E 009 28 60 2 7 MAY 7 4 80 1229 875 1050 801 129 183 2 92E 009 2 23E 009 28 79 2 7 MAY 8 4 80 1412 1006 1206 920 148 210 3 35E 009 2 56E 009 28 97 2 7
6. GLO PRODN MTH PRODN REP TOTALS GLO ABORT PLI ADJDAT PLI BRKPOINT PLI CALCPARM PLI CALCZEUP PLI CALCZMAX PLI CALENDER PLI CHKDATA PLI CNVRTDRV PLI COPYF PLI DALYRATE PLI DATACHK PLI DAYPROD PLI DELREN PLI DTOTALS PLI ECHOYEAR PLI ERASE PLI FINSHDAY PLI FINSHTOT PLI FINSHYR PLI FITSOLAR PLI FMJULIAN PEI GENSOL PLI GETDATA PLI GETFILE PLI GETHYPSO PLI GETIZERO PLI GETPARM PLI GETZEPI PLI HEADER PLI INITDAY PLI INITDTOT PLI INITYEAR PLI INITYTOT PLI Global Declarations Files Numeric variables used by all programs Boolean variables Files Numeric variables used by YEARPROD and DAYPROD Calender variables Constants Variables used by YTOTALS and DTOTALS PL I Files Prints error message and stops Interpolates data for YTOTALS and DTOTALS Breakpoints the output file and stops Interpolates data for YEARPROD and DAYPROD Returns the depth of the euphotic zone Returns the depth of production profile calculations Sets up the Julian calender Determines data availability for YEARPROD and DAYPROD Converts a disc drive specifier CP M Copies a file then deletes it Computes daily production profile and integral Determines data availability for for YTOTALS and DTOTALS DAYPROD main program Deletes old disc file and names new file CP M DTOTALS main program Summarizes an input dataset for YEARPROD Deletes a disc file CP M Summarizes all input data for DAYPROD Summarizes totals for YTOTALS Summarizes
7. There must therefore be some way of forcing the program to use the maximum depth input in the transparency data as zmax rather than the maximum calculated euphotic zone depth This is accomplished with this command You can also force the program to use a predetermined maximum depth by specifying a value after the equal sign Some examples are A gt YEARPROD_ELA84 Z B 1 15 This run will use the maximum depth in the input transparency data as zmax it will calculate production at 15 depth intervals and it will automatically breakpoint itself after calculating the first days results 27 A gt YEARPROD WPG76 Z 10 5 L 53 C S B 0 B This run will use 10 5 meters as the maximum depth 53 degrees for the latitude if cloudless irradiances are calculated the solar irradiance data will be checked for errors before doing the calculations solar data will be read from disc drive B and the output file WPG76 0UT will be written on drive B 5 EXAMPLES This section shows the output produced by the model given the example datasets in section 3 as inputs 5 1 PROGRAM FITSOLAR This program is interactive with the terminal The output below shows a session with this program As before user inputs are underlined program output appears in bold typeface A gt fitsolar FITSOLAR Version 3 0 20 SEP 84 FWI Software Tools Enter year e g 1980 1984 Enter latitude in degrees 50 Enter date e g May 1 jun 21 Enter surface irradiance at
8. a signal that all data for that day have been entered Note that dates don t have to be on separate lines nor do successive tables have to start on new lines If data for more than one date are included in a SOL file is not necessary that the file contain data for each consecutive day i e the file can contain gaps in the dates However data that are present must be in chronological order Empirical measurements of solar radiation must be digitized for input to the model This can either be done with a data logger at the time that the data are collected or the data can be recorded on a strip chart and later digitized with a mechanical pen follower The model can also use simulated cloudless solar data The protocol that determines which of these two types of solar data are used is o If you want the program to use empirical solar data then you must put these data in a disc file whose first name is the year for which calculations are to be made and whose last name is SOL e g 1976 S0L o If a disc file containing empirical solar data cannot be found the model looks for cloudless solar data in a file called CLDLSS SOL o If neither of the above files can be found then the model generates cloudless solar data for the dates for which calculations are to be made If YEARPROD is the program generating these data then the generated data are saved in a file named CLDLSS SOL these data can then be used by YTOTALS or by subsequent runs of YEARPR
9. all input data for YEARPROD FITSOLAR main program Converts Julian date to day and month Generates cloudless solar irradiance data Gets depth profile data Gets a data file Gets hypsographic data Gets surface irradiance data Gets parameters Gets the depth of the epilimnion Prints depths of calculation Opens files and initializes variables for DAYPROD Opens files and initializes variables for DTOTALS Opens files and initializes variables for YEARPROD Opens files and initializes variables for YTOTALS 36 INPUTXY PLI Reads paired x y values from a file INTEGRAT PLI Integrates an array using Simpson s Rule MKTMPFIL PLI Puts input data into temporary files CP M NINDEX PLI Miscellaneous PL I string function NSUBSTR PLI Miscellaneous PL I string function OPENF PLI Opens a file PCLINE PLI Processes the control line CP M PRTTOTL PLI Splits production into mixed layer and hypolimnion totals PSPARMS PLT PSPARMS main program READDATA PLI Inputs raw data REGER PLI Linear regression SEPNAME PLI Separates CP M file name into its parts CP M SETOTOTL PLI Gets files for DTOTALS program SETUPFIL PLI Sets up output file for DAYPROD program TOJULIAN PLI Converts day and month to Julian date TRIM PLI Miscellaneous PL I string function TUPPER PLI Miscellaneous PL I string function VERSION PLI Displays version identifier WARN PLI Prints warning message WHCHLITE PLI Determines existence of solar irradiance data file WRAPUP PLI
10. as a single large program that tries to do everything Experience has shown that this software tools approach provides a more flexible data processing environment Individual tools are more easily modified for specialized research purposes and investigators must learn only the programs that they need for their specific application Some examples of applications where this toolkit approach pays off are o Those working with laboratory or in situ cultures may want to calculate photosynthesis parameters and will need only PSPARMS o Those who want to convert remotely sensed chlorophyll and transparency data into productivity estimates for large lakes will need only YEARPROD and or DAYPROD o Those who are using empirical solar irradiance data as input to the model will not have any need for FITSOLAR 1 2 SYSTEM REQUIREMENTS At the Freshwater Institute this model has been used on Zenith Data Systems Z 100 Z 90 and H 89 computers It will run as is on any microcomputer that has the following hardware o An 8080 8085 Z80 8086 or 8088 central processor o At least one disc drive o A minimum of 64K 8 bit machines or 128K 16 bit machines bytes of memory i You will also need the following software o CP M version 2 2 8 bit machines or CP M 86 16 bit machines These operating systems are supplied by Digital Research Pacific Grove Calif o A text editing program for entering data into disc files we use VEDIT Compuvi
11. disc files Surface solar irradiances for the period for which production is to be calculated These data are input as tables of instantaneous values at time intervals of 30 minutes If a disc file with these data in it can t be found cloudless irradiances will be automatically generated In situ transpagency The parameter Pm which is the rate of photosynthesis per unit of chlorophyll at optimal irradiance The parameter a which is the slope of the light limited part of the photosynthesis vs light curve per unit of chlorophy11 Chlorophy11 concentration YTOTALS and DTOTALS read the output disc files of YEARPROD and DAYPROD respectively and also read the following data from a disc file In situ transparency The depth of the mixed layer The hypsographic area vs depth curve If these data cannot be found the totals will not be morphometry corrected MODEL OUTPUTS FITSOLAR displays the fitted constant on the terminal screen PSPARMS records the fitted parameters in a disc file YEARPROD and DAYPROD record the following output in a disc file The depth profile of production for each day The depth profile of production for the entire time period for which calculations were made The integral of production for each day The integral of production for the entire time period for which calculations were made The values of the input data that were used at each depth where production was calculated
12. follow ext light extinction chi chlorophyll alp pbm Ph zep mixing depth hyp hypsographic data See sections 3 4 3 7 for examples The remainder of this line is ignored by the programs and can be used for notes about the data 3 2 PROGRAM FITSOLAR This program prompts the user to type the date and a measured value of midday irradiance on that date It displays the fitted value of ATMOS EFFECTS on the console monitor 3 3 PROGRAM PSPARMS This program reads incubator data from a disc file whose second name is INC This file contains a header line and a tables of incubator data one for each experiment The program is very flexible regarding the input of incubator data 20 or less distinct light levels and five or less replicates at each light level are allowed A file containing two sets of incubator data might look like Yellowknife Lake Study 1983 Data IStation 01 5 7 13 1 0 14 9 39 2 1 0 67 0 78 9 126 7 L 2 49 3 05 9 366 7 1 3 05 3 13 9 1 Station 75 2 6 10 1 12 4 1 0 11 9 27 3 1 0 57 0 57 9 57 5 1 1 49 1 62 9 125 6 1 5 36 3 57 9 289 2 1 4 80 9 1 Incubator data are interpreted in the following way o The first line in the file is a header line o Each incubator dataset starts with an identifier e g Station 01 If 19 this identifier contains blanks you must enclose it in single quotes o Following the identifier comes the chloroph
13. irradiances eee ee 10 3 Calculating photosynthesis vs depth profiles 13 ABSTRACT Fee E J 1984 Freshwater Institute primary production model user s guide Can Tech Rep Fish Aquat Sci 1328 v 36 p This report describes the numerical model that is used at the Freshwater Institute for estimating phytoplankton primary production This model runs on 8 or 16 bit personal computers controlled by the CP M operating system It is written in PL 1 and can therefore be transported to any computer that has a PL 1 compiler The theory of the model is presented in detail along with instructions for use Example data sets and resulting output are shown for each of the programs in the model Key words phytoplankton limnology oceanography trophic dynamics computer simulation RESUME Fee E J 1984 Freshwater Institute primary production model user s guide Can Tech Rep Fish Aquat Sci 1328 v 36 p Ce rapport d crit le mod le num rique utilis 1 Institut des eaux douces pour valuer la production primaire de phytoplancton Ce mod le fonctionne sur des ordinateurs individuels 8 ou 16 bits syst me d exploitation CP M 11 est r dig en PL 1 et peut par cons quent tre utilis sur tout ordinateur 4 compilateur PL 1 Le rapport pr sente en d tail la th orie du mod le ainsi que son mode d utilisation 11 pr sente des exemples de fichiers et le r sultat final
14. lake with depth you must supply hypsographic data The format of these data is the same as for depth profile data section 3 1 5 except that no date is attached to them A hypsographic dataset might look like 10 27 7E8 2 24 47E8 4 23 908 6 21 298 18 17 37E8 10 10 7468 12 0 65E8 1 The first number in each pair is the depth the second is the area of the lake at that depth 3 1 7 Mixing depth data YTOTALS and DTOTALS require mixing depths to be able to calculate the split production between the mixed layer and the hypolimnion A set of mixing depth data might look like lApr 1 5 May 1 3 May 5 6 May 30 10 Note that the programs do not need any negative end of data signal to tell where the input for a single date ends since only one value of mixing depth 18 can be input for each date Mixing depths can be greater than values in either the hypsographic data or the depths to which production was computed YTOTALS or DTOTALS wit extrapo late those data as necessary to obtain values for greater depths 3 1 8 Organization of data in DAT files YEARPROD YTOTALS DAYPROD and DTOTALS each read several types of data from a single DAT file These different data types transparency chlorophy11 a gt mixing depth hypsographic data can be entered in any order in a DAT file Each data type is separated from the others by a line which has a slash in column 1 followed by three letters which specify the type of data which
15. noon 125 5 ATMOS EFFECT 0 3635 Enter date e g May 1 may 2 Enter surface irradiance at noon 115 ATMOS EFFECT 0 3677 Enter date e g May 1 C The symbol C stands for Control C and is obtained by pressing C while holding down the control key This is the way that you terminate this program 28 5 2 PROGRAM PSPARMS If the data shown in section 3 3 are in a file called TESTPRM INC then typing A gt psparms_testprm should produce the following output in the file TESTPRM PRM Yellowknife Lake Study 1983 Data Identifier lter Chl PBm Alpha Sum Sq Est Err Station 01 30 5 7 0 55 1 48 0 011 0 077 Station 75 17 2 6 1 95 4 77 0 440 0 247 This output is interpreted in the following way o The first line is the header for the entire dataset o The second line shows what the columns of calculated results contain o The results follow Column 1 is the experiment identifier If this identifier is longer than 20 characters it will be truncated to this length Column 2 shows the number of iterations that were required for convergence to the best estimates Column 3 shows the chlorophyll concentration Column 4 shows the best estimate of Pm Column 5 shows the best estimate of a Column 6 shows the final sum of squares of the deviations between the best fit of the photosynthesis equation given in section 2 4 and the experimental data If this number is unusually large you should check your input da
16. the output of YEARPROD o DAT file that contains header line The beginning and ending dates for calculating totals and the year Light extinction data This will usually be identical to the data that were in the DAT file used by YEARPROD to compute the production profiles Mixing depth data see section 3 1 7 for the format of these data Hypsographic data see section 3 1 6 for the format of these data These are required only if you wish to have the totals morphometry corrected A DAT file for YTOTALS might look Tike 22 ILake Winnipeg 1976 Cruise 3 May 1 May 10 1976 ext May 5 0 100 10 1 1 hyp 10 27 78E8 2 25 5768 4 23 90E8 6 21 2968 18 17 37E8 10 10 7468 12 0 65E8 1 zep IMay 1 3 May 30 10 This DAT file is interpreted in the following way o The first line is a header o Next come the starting and ending dates for which totals are to be calculated o The year follows the dates o Transparency mixing depth and hypsographic data follow See section 3 1 8 for a description of the organization of these data in DAT files Note that this DAT file contains different data than the DAT file given as an example in section 3 4 However this is for purposes of illustration only In practice the same DAT file would usually be used as input to both YEARPROD AND YTOTALS with all data needed by both programs included Each program will simply ignore data in the file that it doesn t nee
17. 0 atmos_effect 0 3563 Number of depth intervals 41 ACKNOWLEDGMENTS Gordon Buchanan answered my questions about PL I and CP M with good cheer and great skill He also supplied the 8080 assembler routines described in Appendix 1 Susan Kasian suggested the organization of the manual Bob Hecky encouraged the project Dave Hayward and John Shearer tested the programs and made suggestions that shaped their design REFERENCES BANNISTER T T 1974 Production equations in terms of chlorophy11 concentration quantum yield and upper limit to production Limnol Oceanogr 19 1 12 BROCK T D 1981 Calculating solar radiation for ecological studies Ecol Modelling 14 1 19 CACECI M S and W P CACHERIS 1984 Fitting curves to data Byte 9 340 362 DAVIES J A 1981 Models for estimating incoming solar irradiance Can Climate Centre Report No 81 2 unpubl ms FEE E J 1969 A numerical model for the estimation of photosynthetic production integrated over time and depth in natural waters Limnol Oceanogr 14 906 911 FEE E J 1971 Digital computer programs for estimating primary production integrated over depth and time in water bodies Special Report No 14 Center for Great Lakes Studies Univ Wisc Milwaukee FEE E d 1973a A digital computer program for calculating integral 34 phytoplankton primary production in vertically stratified waterbodies Fish Res Board Can Tech Rep 376 14 p FEE E
18. 34221 cos f2 0 00128 sin F2 0 000719 cos 2 f2 0 000077 sin 2 f2 Finally using a value of 373 4 mE m min for the SOLAR_CONSTANT solar irradiance at the top of the atmosphere at the mean solar distance cloudless irradiances are calculated at 30 minute intervals with the formula ATMOS EFFECT SOLAR CONSTANT DSQ sin DECL sin LATITUDE cos DECL cos LATITUDE cos MIN_ANGLE where MIN_ANGLE is the angle of the sun from due south at any minute during the day 2 2 PROGRAM FITSOLAR a The upper and lower bounds for the search are set to 1 and 0 respectively b The upper and lower bounds for the search are averaged to obtain a test value t c A solar irradiance curve is generated using t d If the value of midday irradiance in the generated solar irradiance curve is greater than the observed value then the upper bound for the search is set to t otherwise the lower bound for the search is set to t 12 e steps b d are repeated until the difference between the upper and the Tower bounds is less than 0 001 2 3 PROGRAM PSPARMS The Simplex algorithm is used to find the best fit of the equation given in section 2 3 to the experimental production vs light data See Caceci and Cacheris 1984 for an explanation of this nonlinear curve fitting algorithm Starting values of the parameters are obtained in the following way o P is the maximum value of production in the dataset
19. 69 0 MAY 5 100 00 57 54 33 11 19 05 10 96 6 31 3 63 2 09 1 20 0 69 0 MAY 10 100 00 57 54 33 11 19 05 10 96 6 31 3 63 2 09 1 20 0 69 0 Chlorophy11 mg m 3 MAY 1 1 00 1 00 1 00 1 00 1 00 1 00 1 00 1 00 1 00 1 00 1 MAY 10 10 00 10 00 10 00 10 00 10 00 10 00 10 00 10 00 10 00 10 00 10 alpha mg C mg ch1 E m 2 JAN 1 5 00 5 00 5 00 5 00 5 00 5 00 5 00 5 00 5 00 5 00 5 MAY 10 5 00 5 00 5 00 5 00 5 00 5 00 5 00 5 00 5 00 5 00 5 PBm mg C mg chl hr MAY 1 1 98 1 98 1 98 1 98 1 98 1 98 1 98 1 98 1 98 1 98 1 DEC 31 1 98 1 98 1 98 1 98 1 98 1 98 1 98 1 98 1 98 1 98 1 Lake Winnipeg 1976 Cruise 3 Cloudless light data for 1976 latitude 50 0 atmos_effect 0 3563 gt TESTYR Light extinction data on MAY 5 extended to start date 31 gt TESTYR alpha data on JAN 1 extended to finish date gt TESTYR PBm data on DEC 31 extended to start date gt TESTYR Light extinction data on MAY 5 extended to finish date 5 4 PROGRAM DAYPROD If the example data sets in section 3 5 are in a disc file called TESTDAY DAT and 318 STA respectively and if there are no solar data on the disc then typing A gt dayprod testday should produce the following output in the file TESTDAY OUT L Wpg Station 318 1976 Cloudless weather Depths 0 00 0 30 0 60 0 90 1 20 1 50 1 80 2 10 2 40 2 70 3 o mg C m 3 day 80 51 29 14 6 2 0 INPUT DATA Light extinction of Surface Light JUN 6 100 00 56 37 31 78 17 91 10 10 5 69 3 21 1 81
20. 90 1 97 2 103 3 108 111 6 113 7 114 4 113 7 111 6 108 1 103 3 97 2 90 1 81 9 72 8 63 1 52 42 1 31 2 20 4 9 7 0 0 1 0 MAY 10 0 0 10 2 20 9 31 7 42 6 53 2 63 5 73 3 82 3 90 5 97 7 103 7 108 112 0 114 1 114 8 114 1 112 0 108 5 103 7 97 7 90 5 82 3 73 3 63 5 53 42 6 31 7 20 9 10 2 0 0 1 0 30 o Afile called TESTYR OUT that contains the computed productivity profiles for each day for the entire time period simulated and the integrals of all of these profiles The second half of the output contains the input data as interpolated at the depths where calculations were made and the warning messages for this run Lake Winnipeg 1976 Cruise 3 Depths 0 00 1 20 2 40 3 60 4 80 6 00 7 20 8 40 9 60 10 80 12 mg sqm mg C m 3 day MAY 1 171 28 27 26 24 20 14 8 5 2 1 MAY 2 343 56 55 52 49 41 28 17 9 4 2 MAY 3 517 85 82 79 73 62 43 26 14 7 3 MAY 4 693 114 110 106 98 83 57 35 19 9 3 MAY 5 870 143 139 133 123 104 72 43 24 12 4 MAY 6 1049 172 167 160 148 126 87 52 29 14 5 MAY 7 1229 201 195 187 173 148 102 62 34 16 6 MAY 8 1410 230 224 215 199 170 117 71 39 19 7 MAY 9 1593 259 253 242 225 192 133 80 44 21 8 MAY 10 1777 289 281 270 251 214 149 90 49 24 9 total 9 7 1 6 1 5 1 5 1 4 1 2 0 8 0 5 0 3 0 1 0 0 gm a new page starts here INPUT DATA Depths 0 00 1 20 2 40 3 60 4 80 6 00 7 20 8 40 9 60 10 80 12 Light extinction of Surface Light MAY 1 100 00 57 54 33 11 19 05 10 96 6 31 3 63 2 09 1 20 0
21. ARPROD DAYPROD YTOTALS and DTOTALS incorporate a standard set of constants see section 2 1 1 and default procedures You may not always want these programs to operate in these standard ways By appending special words commands to the NAME of the data file when you start one of these programs you can change their normal operation Run time commands are separated from the file NAME and from each other by spaces and or commas Note that you need type only the first letter of any command the rest of the command name is ignored In the following descriptions names enclosed in angle brackets lt gt are variables that are to be filled in with actual values e g you might type 11 where lt ndepths gt appears and anything enclosed in square brackets is optional The first letter of each command is enclosed in parentheses to indicate that only this letter is needed for the command to be recognized The currently implemented run time commands are A tmos Effect lt value gt This causes the value specified after the equal sign to be used as the value of ATMOS EFFECT see section 2 1 4 for this run B reakpoint This causes YEARPROD or DAYPROD to breakpoint itself see section 4 3 after checking the input data for errors and computing production for the first date for which production is to be calculated It allows you to check for bad input data to see the depths at which calculations are going to be made and to check the magn
22. Canadian Technical Report of Fisheries and Aquatic Sciences 1328 December 1984 FRESHWATER INSTITUTE PRIMARY PRODUCTION MODEL USER S GUIDE by E J Fee Western Region Department of Fisheries and Oceans Winnipeg Manitoba R3T 2N6 This is the 174th Technical Report from the Western Region Winnipeg 11 c Minister of Supply and Services Canada 1984 Cat no Fs 97 6 1328E ISSN 0706 6457 Correct citation for this publication is Fee E J 1984 Freshwater Institute primary production user s guide Can Tech Rep Fish Aquat Sci 1328 v 36 p 111 TABLE OF CONTENTS Page ABSTRACT RESUME 2 o o o v 1 INTRODUCTION sasso 0 4 sus se 1 1 1 Scope and design of the model nn ss 2 1 2 System requirements Co ms es em 3 1 3 Required inputs and units of the data ww tte ee 4 1 4 Model outputs ses coran sms 5 1 5 Time requirements nes sn sms es 6 1 6 Comparison to earlier versions e 6 1 7 Availability and transportability o 7 2 THEORY OF THE MODEL ns sms em 7 2 1 General ee ee ee nn sn ss sum me 7 2 1 1 Constants uses ss se sens sms 8 2 1 2 Missing data o ee ee 9 2 1 3 Integration method s s ee ee 10 2 1 4 Simulation of cloudless solar irradiances
23. Copies warning messages to end of output YEARPROD PLI YEARPROD main program YTOTALS PLI YTOTALS main program Assembler Files CONTO ASM Console character input output CP M DELFILE ASM Deletes a disc file CP M RENFILE ASM Renames a disc file CP M The four system specific primitives coded in assembler will have to be recoded for other operating systems The specifications of these procedures are o CONRDY returns 1 b if the user has pressed a key o CONIN returns a character from the keyboard o DELFILE erases the disc file whose name is sent to it as a character string o RENFILE accepts two character strings as input and renames the disc file that has the name of the first string to the name given in the second string The model needs these procedures so that you can interrupt it and later restart it at the place where it was interrupted On mainframe computers you won t need to or be allowed to breakpoint the program and you can simply remove all references to these procedures
24. J 1973b Modelling primary production in water bodies a numerical approach that allows vertical inhomogeneities J Fish Res Board Can 30 1469 1473 FEE E J 1977 A computer program for estimating annual primary production in vertically stratified water bodies with an incubator technique Can Fish Mar Serv Tech Rep 741 38 p FEE E J 1980 Important factors for estimating annual phytoplankton production in the Experimental Lakes Area Can J Fish Aquat Sci 37 513 522 HECKY R E and S GUILDFORD 1984 The primary production of Southern Indian Lake before during and after impoundment and Churchill River diversion Can J Fish Aquat Sci 41 591 604 JASSBY A D and T PLATT 1976 Mathematical formulation of the relationship between photosynthesis and light for phytoplankton Limnol Oceanogr 21 540 547 MARRA L 1978 Effect of short term variations in light intensity on photosynthesis of a marine phytoplankter laboratory simulation study Mar Biol N Y 46 191 202 WELSCHMEYER J A and C J LORENZEN 1981 Chlorophy11 specific photosynthesis and quantum efficiency at subsaturating light intensities J Phycol 17 283 293 35 APPENDIX This appendix lists the disc files that contain the source code for the productivity model Files with CP M in the right margin contain CP M specific code that will need modification for other operating systems GENERAL GLO PRODN BIT PRODN FIL PRODN
25. ME TYP The file s NAME is what you type when you start a program it tells the program where the data for it are to be found The NAME can contain eight or fewer characters When you create your data files you can make up whatever NAMEs that you wish e g LWPG69 The file TYP tells the model what kind of data the file contains e g files with a TYP of SOL contain solar radiation data The file TYP contains three characters When you create your data files you must give them the proper TYP or they will not be found by the model The TYPes of files used in the productivity model are given in the following table 15 Table 4 Summary of file types used in the model the uses of each type and the programs that use each type TYP Use Used b Contents SOL Input Output YEARPROD YTOTALS Solar data DAYPROD OTOTALS INC Imput PSPARMS Incubator data PRM Output PSPARMS Fitted parameters DAT Input YEARPROD YTOTALS Input data DAYPROD DTOTALS STA Input DAYPROD DTOTALS Input data for a station OUT Output YEARPROD DAYPROD Computed results TOT Output YTOTALS DTOTALS Computed results Output YEARPROD YTOTALS Fatal error messages DAYPROD DTOTALS 3 1 2 Header lines The first line in any disc file that contains input data can contain any information that you wish to be permanently recorded with the computed output This header usually describes the location dates instruments used etc Make sure that you don t have a blank l
26. OD without having to be regenerated i If a disc file containing solar data was found but production is to be calculated for a date for which no data exist in this file then cloudless weather wil be generated for the missing date s These newly generated data will not be saved or added to the disc file from which solar data are being read 17 3 1 5 Transparency chlorophyll Ph and a data All these data are input as depth profiles Each depth profile starts with the date Following the date are pairs of data the first value in each pair is a depth the second value is the value of the variable at the depth just specified A negative value for either the depth or for the value of the variable terminates data input for the profile For example a single depth profile of water transparency might look like duly 17 lo 100 11 50 12 25 13 12 5 14 6 25 1 1 Because data entry is free format these data could also be input as duly 17 0 100 1 50 2 25 3 12 5 4 6 25 1 Notice that no header lines are shown in these examples This is because depth profile data are always input as part of a DAT or STA file and it is only the first line of the entire file which contains a header Note further that the PRM output UR produced by PSPARMS is not in the proper format for input of chlorophy11 or a data 3 1 6 Hypsographic data If you want YTOTALS or DTOTALS to correct the production values for the decrease of the volume of the
27. RY OF THE MODEL The fundamental difference between the new model and previous versions is that the rate of production at a given irradiagce is calculated from an equation based on photosynthetic parameters Pm and a instead of being calculated by linear interpolation in the raw incubator data The use of these parameters in studies of phytoplankton ecology is relatively recent Bannister 1974 Jassby and Platt 1976 and the following considerations Jed to their incorporation in the new model o A model based on these parameters can be used to estimate primary production in lakes for which only chlorophy11 and transparency data are available o Calculation of these parameters makes it easier to spot errors in the input data and consequently model output is more reliable o By requiring them as input to the model a valuable database will be created over time This information will allow us to formulate and test hypotheses about how latitude turbidity lake size acidification nutrient loading and a multitude of other factors influence Pm and a I is only when we can predict the spatial and temporal variations of these parameters we will be able to reliably estimate productivity from remotely sensed chlorophyll and transparency data 2 1 GENERAL This subsection describes constants and algorithms used by more than one program in the model 2 1 1 Constants The following constants are incorporated into the model o DELTAT The t
28. TALS and DTOTALS do not check their input data before starting calculations as YEARPROD and DAYPROD do if any fatal errors are encountered they also record them in a file with the TYPe of 4 3 BREAKPOINTING RUNS YEARPROD and DAYPROD have a built in breakpoint facility that allows you to interrupt the calculations at any point without losing the results that have already been obtained when you restart the run This is handy if you want to check for data errors before committing the program to a long calculation see section 4 3 or if you want to use the computer for something else You breakpoint a run by typing the letter B anytime after the message 25 Press B to breakpoint run appears on the screen see example in section 4 1 When you do this the intermediate results are stored on a disc file with a TYPe of OUT and the same NAME as the NAME which you typed to start the run At the point where the run was breakpointed the OUT disc file will have a backslash in column 1 This character is a signal to the program that this is the output from an incomplete run Restart the run by typing in the same command line that was used when the run was first initiated If the Program finds the backslash character the calculations resume at the point where they were interrupted If it does not find the backslash the OUT file will be erased if it exists and calculations will start over from the beginning 4 4 RUN TIME COMMANDS YE
29. Warning messages if any YTOTALS and DTOTALS record the following output in a disc file The depth of the mixed layer for each day Uncorrected and optionally morphometry corrected production integrals and averages for the mixed layer and for the hypolimnion for each day Uncorrected and optionally morphometry corrected production integrals and averages for the mixed layer and for the hypolimnion for the entire time period for which calculations were made The mean irradiances in the mixed layer and the hypolimnion for each day 1 5 TIME REQUIREMENTS The times quoted below are for a Z 100 microcomputer 8085 chip running at 4 MHz FITSOLAR and PSPARMS use 15 25 seconds for processing a single dataset DAYPROD requires about the same amount of time to calculate daily production for a single station YEARPROD takes about 15 minutes to calculate annual production for a lake with a seven month ice free season OTOTALS uses about 20 seconds to morphometry correct production totals for a single station YTOTALS takes about 10 minutes to morphometry correct production totals for a seven month ice free season 1 6 COMPARISON TO EARLIER VERSIONS The new model was used to calculate annual production for lakes at the Experimental Lakes Area for the period 1976 1982 The following table compares the values given by the new model with those given by the old model Table 2 Comparison of annual primary production rates in Experime
30. ance I is obtained by multiplying the value of surface irradiance by the fraction of surface light that reaches that depth Production P as a function of irradiance is calculated with the equations 13 Let I Ph a Then if I lt 0 u Ik 20 then P 0 else if 1 gt 2 1 then P chi Ph else P chl a I 1 a I 4 f where I I Ik 20 Note that I Les 1 chl a and Ph are all functions of depth The daily total of production at that depth is updated o The daily profile is integrated with Simpson s Rule section 2 1 3 to obtain the daily integral and this value is added to the annual total The equation relating production to available light is adapted from one given in Jassby and Platt 1976 it was chosen over their recommended hyperbolic tangent function because it gives identical integral values while requiring only one fifth of the computer time to evaluate Production is forced through zero at an irradiance of 1 205 thispconstant was determined empirically and corresponds to Jassby and Platt s R Note that inhibition of production by high surface irradiances that occur at shallow depths on sunny days is ignored Marra 1978 and Welschmeyer and Lorenzen 1981 have shown that such inhibition probably does not occur in nature and Fee 1980 showed that it is of little quantitative importance even if it does occur The model implicitly assumes that a oh and transparency do not vary ov
31. ated Cloudless jtght data for 1976 latitude 50 0 atmos effect 0 3563 MAY 1 0 0 5 4 16 2 27 1 38 0 48 8 59 2 69 0 78 1 86 4 93 6 99 7 104 108 1 110 2 110 9 110 2 108 1 104 6 99 7 93 6 86 4 78 1 69 0 59 2 48 38 0 27 1 16 2 5 4 0 0 1 0 MAY 2 0 0 6 0 16 7 27 6 38 6 49 3 59 7 69 5 78 6 86 9 94 1 100 2 105 108 6 110 7 111 4 110 7 108 6 105 0 100 2 94 1 86 9 78 6 69 5 59 7 49 38 6 27 6 16 7 6 0 0 0 1 0 MAY 3 0 0 6 5 17 3 28 2 39 1 49 8 60 2 70 0 79 1 87 4 94 6 100 7 105 109 0 111 2 111 9 111 2 109 0 105 5 100 7 94 6 87 4 79 1 70 0 60 2 49 39 1 28 2 17 3 6 5 0 0 1 0 MAY 4 0 0 7 1 17 8 28 7 39 6 50 4 60 7 70 5 79 6 87 8 95 0 101 1 106 109 5 111 6 112 3 111 6 109 5 106 0 101 1 95 0 87 8 79 6 70 5 60 7 50 39 6 28 7 17 8 7 1 0 0 1 0 MAY 5 0 0 7 6 18 3 29 2 40 1 50 9 61 2 71 0 80 1 88 3 95 5 101 6 106 109 9 112 1 112 8 112 1 109 9 106 4 101 6 95 5 88 3 80 1 71 0 61 2 50 40 1 29 2 18 3 7 6 0 0 1 0 MAY 6 0 0 8 1 18 9 29 7 40 6 51 3 61 7 71 5 80 6 88 8 96 0 102 0 106 110 4 112 5 113 2 112 5 110 4 106 8 102 0 96 0 88 8 80 6 71 5 61 7 51 40 6 29 7 18 9 8 1 0 0 1 0 MAY 7 0 0 8 7 19 4 30 2 41 1 51 8 62 2 71 9 81 0 89 2 96 4 102 5 107 110 8 112 9 113 6 112 9 110 8 107 3 102 5 96 4 89 2 81 0 71 9 62 2 51 41 1 30 2 19 4 8 7 0 0 1 0 MAY 8 0 0 9 2 19 9 30 7 41 6 52 3 62 6 72 4 81 5 89 6 96 8 102 9 107 111 2 113 3 114 0 113 3 111 2 107 7 102 9 96 8 89 6 81 5 72 4 62 6 52 41 6 30 7 19 9 9 2 0 0 1 0 MAY 9 0 0 9 7 20 4 31 2 42 1 52 8 63 1 72 8 81 9
32. d 3 7 PROGRAM DTOTALS This program requires four input data files o The SOL file that was used by DAYPROD to calculate the production profiles that are to be totalled o The OUT file produced by DAYPROD that contains the computed production profiles that are to be totalled o A STA file that contains A header line A list of station names o A DAT file one for each station named in the STA file that contains A header line for that station The date and year Light extinction data These will normally be identical to the transparency data that were used by DAYPROD to produce the production profiles that are to be totalled o The mixing depth see section 3 1 7 for the format of these data o Hypsographic data see section 3 1 6 for the format of these data 23 These are required only if you want the totals to be morphometry corrected A STA file for use with DTOTALS would look exactly like the example given in section 3 5 The file 318 DAT pointed to by this example might look like IL Wpg Station 318 1976 Cloudless weather Jun 6 1976 ext Jun 6 lo hyp 10 27 78E8 2 25 57E8 4 23 9068 6 21 2958 18 17 37E8 10 10 74 8 12 0 65E8 1 zep Jun 6 10 0 100 2 2 19 1 These data are interpreted in the following way o The first line is a header for this station o Next comes the date and year o Light extinction mixing depth and hypsographic data follow See section 3 1 8 for a
33. de chacun des programmes du mod le Mots cl s phytoplancton limnologie oc anographie dynamique trophique ordinateur simulation 1 INTRODUCTION Estimating phytoplankton primary production is an important part of several research projects at the Freshwater Institute The method that we use is based on the measurement of the relation between photosynthesis and Tight under controlled laboratory conditions A computer model combines these incubator data with in situ transparency and solar irradiance data to yield in situ production estimates see Fee 1973a for a general description of the method The computer model that is the core of this method has been rewritten several times during the last 15 years Fee 1969 1973b 1977 The version currently in use at the Freshwater Institute has a number of new features which include o It runs on inexpensive personal computers Previous versions required mainframe computers o It is written in PL I and is consequently easier to understand and modify than the previous FORTRAN versions o It generates cloudless surface irradiance data for any location on the eapth previous versions had to be reprogrammed for latitudes other than 50 N o It provides separate estimates of production in the mixed layer and the hypolimnion o It provides estimates of the daily mean irradiances in the mixed layer and in the hypolimnion These values are useful for determining the degree to whic
34. description of the organization of these data in STA files Note that this DAT file contains different data than the DAT file given as an example in section 3 4 However this is for purposes of illustration only In practice the same DAT file would usually be used as input to both DAYPROD AND DTOTALS with all data needed by both programs included Each program will simply ignore data in the file that it doesn t need 4 RUNNING THE MODEL This section describes how to run the programs in the model 4 1 STARTING THE PROGRAMS All of the programs in the model are started by typing the name of the program a space and then the NAME of the disc file see section 3 1 1 that contains input data for that program For example to start the program YEARPROD and tell it that the input data are to be found in the disc file ELA84 DAT you would type A gt yearprod ela84 The symbols A gt are the CP M system prompt you type the rest in this and all examples which follow text that you type is underlined and text that the computer prints on the screen is printed in bold typeface 24 Each program starts by printing a banner its name the version number and the date on which this version was created For example the following text would appear on the screen if you typed the line above Annual Primary Production Program FWI Software Tools Version 2 8 26 JUN 84 While the program is running it may print informative messages on the
35. divided by the chlorophy11 concentration o a is taken as 5 0 mg C mg ch1 E m 2 The reason for taking a fixed value as the starting estimate for this parameter is that unusual datapoints outliers can give very bad initial estimates that will prevent the program from converging 2 4 PROGRAMS YEARPROD AND DAYPROD These programs begin by calculating the depth of the euphotic zone the depth where in situ light is 0 5 of surface light from the input transparency data The euphotic zone is then divided into discrete layers of equal thickness Before in situ production can be simulated values for the following variables must be known at the calculation depths the surface the bottom of the euphotic zone and at the depths where the layers meet o The fraction of the surface solar irradiance that reaches that depth o The chlorophyll concentration ch1 o PR O g The values of these variables are linearly interpolated for the required depths from the input data Transparency data are linearized by converting them to logarithms before the interpolation is done and are converted back to linear units after being interpolated Linear interpolation is also used to obtain values for dates between sampling dates After the data are interpolated daily production is simulated in the following way o For each value of surface irradiance during the day the following steps are performed for all calculation depths The absolute irradi
36. e the course of the day These kinds of variation are of secondary importance and for routine purposes are best ignored Fee 1980 2 5 PROGRAMS YTOTALS AND DTOTALS Reasons for not incorporating the functions of these programs into YEARPROD and DAYPROD are o It would make those programs very complex and hard to modify o Not every application requires production totals split between the mixed layer and the hypolimnion o It it advantageous to be able to specify more depth intervals in the euphotic zone when calculating the split of production between the mixed layer and the hypolimnion than were used in the original calculations of production section 4 4 shows how to do this For example suppose that you calculated production at 11 depths the default and the euphotic zone depth was 10 meters Thus production would be calculated at depth intervals of 1 meter However if the depth of the mixed layer was two meters only three production values would be available for calculating the integral in the mixed layer Such an integration would be very inaccurate However if you specify that you want 41 depth intervals when you run the totais program there will be nine data points for 14 integrating production in the mixed layer This will result in similar accuracy for the 0 2 m integral as was obtained for the whole water column by the original production program Like YEARPROD and DAYPROD these programs divide the euphotic zone int
37. ess than the tabled minimum the program prints a warning message at the end of the computed output and continues with the calculations NN o LATITUDE The degrees from the equator north positive of the _ waterbody It is used when the model calculates cloudless solar irradiances see section 2 1 4 and if you always use empirical solar data you don t have to worry about its value The default value is 50 N o ATMOS EFFECT This is an empirical constant that specifies the fraction of solar irradiance at the top of the atmosphere that reaches the surface of the earth at the location of the waterbody under cloudless conditions It is used when the model calculates cloudless solar irradiances see section 2 1 4 and if you always use empirical solar data you don t have to worry about its value The default value is 0 3563 and was measured at the Experimental Lakes Area in NW Ontario The program FITSOLAR is used to fit values of this constant for other locations f The default values of the constants DELTAT NDEPTHS LATITUDE and ATMOS_EFFECT can be altered at the time that the programs are run see section 4 3 To alter the other constants EUPI MAXDATA NIZERO MINCHL you must change the value s in the file PRODN REP see Appendix 1 and recompile the programs 2 1 2 Missing data YEARPROD DAYPROD YTOTALS and DTOTALS use linear interpolation to obtain values of variables for dates between sampling dates For example if you i
38. ew Products Ann Arbor Michigan o If you plan to modify the programs you will need the Digital Research PL I 80 8 bit machines or PL 1 86 16 bit machines compiler 1 3 REQUIRED INPUTS AND UNITS OF THE DATA The following table shows which variables are used by which programs and the required units of the data Table 1 The variables used in the model required units and which programs use them Variable Units Used By Latitude degrees north positive FITSOLAR Midday Cloudless Irradiance milliEinsteins m2 min FITSOLAR Chlorophyll mg m PSPARMS YEARPROD DAYPROD YTOTALS DTOTALS Incubator Irradiance microEinsteins m sec PSPARMS Incubator Photosynthesis Rate mg C m hr PSPARMS Solar Irradiances mil 1iEinsteins m min YEARPROD DAYPROD YTOTALS DTOTALS In situ Transparency any units YEARPROD DAYPROD YTOTALS DTOTALS a mg C mg chl Einstein m 2 YEARPROD DAYPROD Ph mg C mg chl hr YEARPROD DAYPROD Mixing depth meters o YTOTALS DTOTALS Hypsographic data meters YTOTALS DTOTALS 1 4 FITSOLAR needs the latitude the date year month day and values of midday solar irradiance This program is interactive and reads input from the terminal PSPARMS reads the following incubator data from a disc file Chlorophyll concentration for the sample Incubator irradiances Rates of photosynthesis at the specified irradiances YEARPROD and DAYPROD read the following data from
39. h light limits primary production Hecky and Guildford 1984 o It calculates the total mass of carbon produced in a lake correcting for the fact that the volume of the lake decreases as a function of depth see Fee 1980 for a discussion of the importance of morphometry correction o It is based on input of photosynthetic parameters rather than tables of raw photosynthesis vs light data This reduces the probability of inputting bad data and makes it suitable for estimating production from remotely sensed chlorophy11 data o Data entry is greatly simplified from previous versions and all input data are checked for plausibility o It can be interrupted at any point and later restarted without losing intermediate results o It can estimate production for any number of isolated dates and any number of different stations in a single run This manual describes this primary production model It is assumed that you know how to turn on your computer insert floppy discs etc In order to effectively use these programs you will also need a rudimentary knowledge of the CP M operating system how to enter data into disc files display the contents of a disc file on the screen display the disc directory etc All of this information is contained in the operators manual and the CP M manual for your personal computer 1 1 SCOPE AND DESIGN OF THE MODEL These programs are used by limnologists and oceanographers engaged in research on t
40. he dynamics of phytoplankton populations Six programs are included in the model o FITSOLAR Estimates a constant that describes how atmospheric factors e g haze altitude locally modify the global cloudless irradiance equation o PSPARMS Calculates photosynthetic parameters from incubator data o YEARPROD Calculates production at one station for a range of dates usually an entire year o DAYPROD Calculates production at any number of stations for individual dates o YTOTALS Calculates the split of production between the mixed layer and the hypolimnion optionally corrected for morphometry and the mean light in these layers at one station for a range of dates usually an entire year o DTOTALS Calculates the split of production between the mixed layer and the hypolimnion optionally corrected for morphometry and the mean Tight in these layers for single dates at any number of stations At the Freshwater Institute these programs are used in the context of research programs that operate in the following way o Integrated water samples are taken from a waterbody at time intervals of approximately two weeks If the waterbody is stratified the mixed layer the thermocline and the hypolimnion are sampled separately The transparency of the waterbody is measured at approximately 2 week intervals with a quantum sensor Fitted with a flat late cosine corrected collector Surface solar irradiances are measured co
41. ime interval between successive values of surface solar irradiance A value of 30 minutes is used Previous versions of the program used five minutes but test runs showed no differences in daily production for time steps between five and 40 minutes there were significant differences with a time steps greater than 40 minutes o NDEPTHS The number of layers that the euphotic zone is divided into The program uses eleven layers Previous versions of the model used 21 layers but tests with actual data showed that there is no loss of accuracy with eleven o EUPI The fraction of surface light at the bottom of the euphotic zone The program uses a value of 0 005 0 5 o MAXDATA The maximum number of data point pairs that can be input in a single depth profile of transparency chlorophy11 Pm or The program uses 50 for this limit o NIZERO The maximum number of dat points in a single solar irradiance curve The program uses 150 which is sufficient for a time step of 10 minutes o MINCHL MAXCHL MINPARM MAXPARM MAXZEUP As data are read they are checked for plausibility by seeing if they exceed the maxima or minima in the following table Table 3 Acceptable ranges of values for variables used in the primary production mode Variable Minimum Maximum Chlorophy11 0 5 350 a 0 5 10 ph E 0 5 10 Euphotic Zone Depth none 20 If an input datum is greater than the tabled maximum or l
42. ine at the start of a data file or it will be taken to be the header line and what you intended to be the header will be read unsuccessfully as data 3 1 3 Dates Most inputs must be dated All dates are input as Month day pairs where the month is alphabetic and the day is numeric e g May 10 Month names can be shortened to their first three letters e g Aug The model assumes that all dates are from the same year 3 1 4 Solar data Solar data are input as tables one for each day that give the instantaneous flux of solar radiation at time intervals of 30 minutes Data are required only for times when the sun is above the horizon but including zeros for the dark periods does no harm A solar file containing data for two days might look like 16 JELA Cloudless solar irradiance data IMay 1 0 0 11 9 18 8 27 0 36 2 46 0 56 2 66 5 76 4 85 9 194 4 101 7 107 7 112 2 114 9 115 8 114 9 112 2 107 7 101 7 194 4 85 9 76 4 66 5 56 2 46 0 36 2 27 0 18 8 11 9 0 0 1 0 May 2 0 11 8 18 4 26 3 35 1 44 6 54 5 64 4 74 2 83 6 192 1 99 7 106 1 111 0 114 4 116 1 116 1 114 4 111 0 106 1 199 7 92 1 83 6 74 2 64 4 54 5 44 6 35 1 26 3 18 4 111 8 0 0 1 0 In this example and in those which follow the vertical line represents the left edge of each line in the input file The file starts with a header line The table for each day begins with the date Following the date come the data for that day A negative light value is interpreted as
43. ise 3 May 1 May 10 1976 ext May 5 0 100 10 1 1 ehd May 1 0 1 1 May 10 0 10 1 atp Jan 1 0 5 1 pbm Dec 31 0 1 98 1 This file is interpreted in the following way o The first line is a header o The starting and ending dates for which production is to be calculated 20 are entered next These dates must both be in the same year This means that separate runs must be made if the period for which production is to be calculated extends past the end of a year e g production for the period Oct 20 1976 to Mar 31 1977 would have to be done in two runs Oct 20 Dec 31 1976 and Jan 1 Mar 31 1977 o The year for which production is to be calculated is input next o Depth profiles of transparency chlrophy11 a and Pht follow See sectio 3 1 8 for a description of the organization of these data in DAT files 3 5 PROGRAM DAYPROD This program reads data from three files o A SOL file that contains solar data see section 3 1 4 o A STA file that contains a header line for the entire run and a list of station identifiers o A DAT file one for each station named in the STA file that contains the input for that station Each DAT file contains A header line for that station The date for which production is to be calculated The year Depth profiles of transparency chlorophyll a and Ph A STA file for DAYPROD might look Tike ILake Winnipeg 1976 Cruise 3 1318 This data is inter
44. itude of the calculated values on the first day before committing the machine to a long calculation C heck YEARPROD and DAYPROD do not normally check the solar data for errors as they do all of the other input data You force them to check for errors with this command The reason for not normally checking these data is that a single solar radiation dataset is typically used for many different stations or for many different lakes It takes about five times as long to read and check these data during the preliminary error checking phase of the program than it does to check all the other input data combined Moreover it is only necessary to check them once or indeed to not check them at all e g when the program has generated simulated cloudless weather 26 I ntervals lt ndepths gt This sets the number of depths at which production will be calculated to lt ndepths gt If this command is not specified ndepths defaults to 11 Because of the integration algorithm used see section 2 1 3 lt ndepths gt must be an odd number To assure reasonable accuracy values less than five are not allowed If more than 41 intervals are needed then the program must be recompiled after changing the value of MAXINTR in the file PRODN REP L atitude lt degrees gt This sets the latitude of the waterbody to the value specified after the equal sign The value of latitude is used to calculate cloudless surface irradiances and is irrelevant if you are
45. ne are used to compute values at greater depths than were input For the transparency data if five or more data points were input the first three data points that were input are not used in fitting the straight line since the log of transparency vs depth is usually highly nonlinear near the surface 10 If you only enter one profile or value it will be extrapolated forward and or backward in time as needed For example if you input an a value date 1 June and request production for the period 1 May through 1 October the 1 June value will be used for the entire period Whenever input data are extrapolated in this manner a warning message is recorded along with the output 2 1 3 Integration method YEARPROD DAYPROD YTOTALS and DTOTALS integrate functions over depth All integrations are done with Simpson s 3 point numerical integration rule This algorithm consists of fitting parabolas to successive groups of three points on the curve to be integrated and summing the areas under the individual parabolas The formula for Simpson s Rule is Zb f f z dz Zb Zt Ly t4yat2y sty q 2Y ga a 2 Y y gt 1 3 n 1 Zt where f z is the function being integrated over depth Zt is the depth where the integration starts Zb is the depth where the integration ends Ye is the k th value of the function f z i e F Zt y etc n is the number of points at which the function is known in the interval Zb Zt Note that this algorithm require
46. nput a chlorophy11 value of 1 0 on June 1 and a value of 2 0 on July 1 then the value used on June 10 will be 1 333 on June 15 will be 1 5 and so on Certain variables transparency chlorophyll Ph a and hypsographic data are input as depth profiles values as a function of depth If the maximum depth to which production is to be calculated is less than or equal to the maximum depth of the input data then values for the depths where production is to be calculated are obtained by interpolation in the input data However if an input profile does not include data for all depths where values are needed then the available data are extrapolated in the following way o Chlorophyll ph and a data If the input does not include a value for the surface then the value at the shallowest depth that was input is used from the surface down to that depth If the input must be extrapolated to greater depths than were input then the value at the greatest depth that was input is used uniformly at all greater depths o Transparency and hypsographic data If a value is not input for a depth of O m or if only one value is input the program prints an error message and stops At least two data points must be input for each profile because a line must be fit to these data in order to extrapolate them A straight line is Fit to the available data transparency data are linearized by converting them to logarithms The slope and intercept of this li
47. ntal Lakes Area ELA lakes calculated with the old incubator mode Fee 1977 and with the new model presented in this report Reported values are percentages new old 1976 1977 1978 1979 1980 1981 1982 Lake a II 114 97 112 94 107 103 222 98 i 96 105 98 223 94 96 100 97 105 107 109 224 93 102 107 104 226N 97 106 92 98 101 104 101 226S 102 102 100 95 100 106 112 227 97 95 98 97 94 104 102 239 91 101 98 98 99 105 102 261 99 100 302N 101 98 96 108 101 3025 98 100 96 102 97 304 96 99 91 111 382 104 98 99 92 103 3828 99 91 103 383 100 99 cn kkkkE mean 97 100 98 99 96 106 104 gt 100 1 7 AVAILABILITY AND TRANSPORTABILITY The programs are available from the author on two floppy disc formats o 8 single sided single density standard CP M o 5 1 4 double sided double density Heath Zenith CP M specify 48 tpi or 96 tpi Please specify whether you want the 8 bit or 16 bit version The source code of the model is contained in 73 disc files The names of these files and a brief description of their contents are given in Appendix 1 Listings of these files about 100 pages will be supplied to users that need to adapt the model to other machines All but four procedures are written in PL I Because the Digital Research compilers conform to the specifications of subset G of the full PL I language there will be few problems transporting the code to other machines See Appendix 1 for more details 2 THEO
48. ntinuously with a quantum sensor located at the central laboratory o In the laboratory the following analyses are made on each water sample Subsamples are taken for determination of dissolved inorganic carbon and chlorophy11 concentrations 12 or more ground glass stoppered bottles are filled by siphoning from the remaining sample C is added to these bottles and they are placed in the dark and at five or more light levels in an artificial light incubator for 2 4 hr Light levels in the different chambers of the incubator are measured with a spherical quantum sensor 2 3 times during the incubation At the end of the incubation five mL aliquots from each bottle are placed in scintillation vials and inorganic C is stripped out by lowering the pH to 2 3 with HCl and bubbling with air for 15 20 minutes 14 Fluor is added to the vials and the C activity is determined in a liquid scintillation spectrometer o Photosynthesis rates are calculated from data on the the 14 uptake rates and dissolved inorganic carbon concentrations o PSPARMS is used to estimate the photosynthesis parameters o YEARPROD or DAYPROD are used to generate in situ productivity profiles o YTOTALS or DTOTALS are used to morphometry correct the productivity profiles and to determine the split of production between the mixed layer and the hypolimnion The model was implemented as a collection of separate programs that perform distinct jobs rather than
49. o discrete layers of equal thickness and calculate values for the following variables at the surface at the bottom of the euphotic zone and at each of the depths where these layers meet o The fraction of solar irradiance that reaches that depth o The daily production at that depth o The area of the lake at that depth if morphometry correction is desired In addition the depth of the mixed layer must be known Given all of the required variables it is straightforward to calculate the various totals with Simpson s Rule section 2 1 3 3 DATA FORMATS This section describes how input data must be organized for the different programs in the primary production model All programs read their inputs in free format This means that it doesn t matter where you type data on an input line successive values are separated by blanks commas tabs or the ends of lines Further alphabetic data can be entered in either upper or lower case Free format does not mean that data can be entered in any order For example although it doesn t matter where on a line you type a date it is very important whether you type the date as May 1 or 1 May 3 1 GENERAL This subsection describes formats that are used by more than one program in the model 3 1 1 Disc file nomenclature Except for FITSOLAR all programs read their input from disc files and write their output into other disc files Disc files are named in the following way NA
50. preted in the following way o The first line is a header o The NAME s that follow they don t have to be on separate lines point to separate DAT disc files each of which has a TYPe of DAT DAT files for DAYPROD contain data which is identical in format to DAT files used by YEARPROD except that only one date is specified instead of a range of dates Note to provide a simple example only one station is shown normally many stations would be listed in this file The above STA file points to the file 318 DAT which might look like 21 IL Wpg Station 318 1976 Cloudless weather dun 6 1976 ext Jun 6 10 100 2 2 19 1 ch1 Jun 6 0 1 7 1 alp Jun 6 0 5 4 1 pbm Jun 6 0 4 7 1 The STA file is interpreted in the following way o The first line is a header o The date and year follow o Depth profiles of light extinction chlorophy11 concentration a and Ph follow see section 3 4 for description of the way these data are organized in DAT files If a date on any of these profiles do not match the date for which production is to be calculated then a warning message will be recorded along with the computed results 3 6 PROGRAM YTOTALS This program reads data from three files o A SOL file that contains the solar data that were used to calculate the production results that are to be split into mixed layer and hypolimnion totals a The OUT file which contains the computed production profiles This is
51. s n to be an odd numb 2 1 4 Simulation of cloudless solar irradiances Solar data ggnerated by the model are scaled in units of milliEinsteins m min and are made specific for each waterbody by the parameters LATITUDE and ATMOS EFFECT LATITUDE is the location of the waterbody in units of degrees from the equator negative for the southern hemisphere ATMOS_EFFECT is the fraction of the irradiance at the top of the atmosphere that reaches the earth at the location of the waterbody under typical cloudless conditions Its value depends on air pollution altitude and other factors The following formulas were adapted from Brock 1981 and Davies 1981 The declination of the earth during the year the angle between the sun and the equator at solar noon north positive is calculated with the formula DECL 23 44803 sin 2 x 284 qd Yq where m is 3 1415927 11 da is the Julian date y is the number of days in the year n The angle of the sun from due south at sunset is calculated with the formulas let f1 tan LATITUDE tan DECL Then if fl gt 1 then SUNSET_ANGLE 0 else if f1 lt 1 then SUNSET ANGLE 1 else SUNSET ANGLE acos f1 The minutes of sunlight during the day is given by the formula d 8 SUNSET ANGLE 7 180 1 The square of the deviation of the earth from its mean distance from the sun is calculated with the formulas let f2 2 vm d Ya Then DSQ 1 00011 0 0
52. screen For example YEARPROD may print Generating cloudless light data done Press B to breakpoint run The next to the last line indicates that a disc file with solar data could not be found so it generated these data Only messages such as this appear on the screen all warning and error messages are permanently recorded in disc file s see section 4 2 4 2 ERROR HANDLING When YEARPROD and DAYPROD start up they look through all input data for errors before they actually do any calculations This ensures that the data are acceptable before the machine starts on a long series of calculations If questionable data using the criteria in section 2 1 1 are encountered the run will continue after a warning message has been recorded However if the model cannot recover from the data error a message will be printed into a disc file with the same NAME as the input data file and a TYP see section 3 1 1 for definitions of NAME and TYP of The reason for having a special file TYP of is that typically many runs are batched together for submission to CP M as a single unit see the CP M manual for documentation of the SUBMIT utility that is used for this purpose When all of the runs have finished you will want to find out which of the runs failed because of data errors without having to print out all of the output for all of the runs You do this by simply looking at the disc directory for files with TYPes of H Although YTO
53. ta for errors Column 7 shows the estimated error the standard deviation divided by the number of data points minus the number of parameters that were fit 2 If this number is unusually large you should check your input data for errors While this program is running it displays on the screen the values of Ph a and the sum or squares for each iteration This is done primarily to assure you that the machine is not dead You can also use this information to speed up the parameter estimation procedure Because of arithmetic round off errors it is possible for the program to get stuck after it has converged to an acceptable solution This is what is happening when the parameter values that appear on successive iterations alternate between two very slightly different values and the sum of squares doesn t change If you aren t concerned with wasting computer time you can just let the program go on and it will stop itself after 100 iterations However you can keep it from making unnecessary iterations by pressing the B key This causes the program to give up on the current dataset and go on to the next 29 5 3 PROGRAM YEARPROD If the data shown in section 3 4 are in a file called TESTYR DAT and if neither 1969 SOL nor CLDLSS SOL exist on the disc then typing A gt yearprod testyr should produce two disc files o A file called CLDLSS SOL that contains simulated cloudless irradiances for the period for which production was simul
54. y11 concentration o Light values for the first incubator chamber follow the chlorophy11 concentration Any number of replicate measurements can be entered the end of a set of replicates is signalled by a negative value The replicate light measurements are averaged to obtain a single value that is paired with the photosynthesis rates that were measured at this light level This allows you to enter all light measurements for a single incubator chamber without having to manually average them beforehand o Following the light measurements come the corresponding photosynthesis measurements The program keeps reading successive photosynthesis values for a chamber until a number less than or equal to 5 is entered The replicates of photosynthesis are not averaged before being used in the parameter fitting procedure o The above format light values followed by production values is repeated for each chamber in the incubator It doesn t matter whether the incubator data are entered from low irradiances to high or vice versa A negative value for light terminates input for a single incubator dataset 3 4 PROGRAM YEARPROD This program reads data from two disc files o A SOL file that contains solar data see section 3 1 4 o A DAT file that contains The starting and ending dates for which calculations are to be made Depth profiles of chlorophyll transparency a and Ph DAT file for YEARPROD might look like Lake Winnipeg 1976 Cru
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