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Module 4: experimental data files, soil and plant nitrogen, N-limited production

This notebook follows the fourth day of a DSSAT training course, exercise by exercise:

  1. Creating crop measurement files: the 1976 peanut shading study. Build its experiment file (UFGA7609.PNX, with an environmental modification that shades the crop), write its FileA and FileT from the course’s spreadsheets (what the ATCreate tool does), and evaluate the simulation. Then the whole published study, and a sweep over when and how strongly the crop is shaded.
  2. Nitrogen-limited production: the maize experiment UFGA8213.MZX with the water and nitrogen balances on, built as the exercise specifies, and its three self tests (N rate, soil type, residue and initial N).

Data. Course data in notebooks/course-data/: PN_1976_Summary.xls and PN_1976_TimeSeriesData.xls (Hang et al. 1984). From DSSAT/dssat-csm-data (BSD-3): peanut UFGA7601 and UFGA7604, maize UFGA8201, weather and soils.

engine   : C:\TEMP\dsn\dssat\dscsm048.exe
csm-data : C:\Users\benny\OneDrive\Documents\Github\dssat-csm-data @ 99c95b34

1. Creating crop measurement files

A FileA holds one line per treatment of what was measured at the end of the season; a FileT holds one line per treatment and sampling date. The columns are DSSAT variable codes, defined in the engine’s DATA.CDE, and the files are fixed-format: 6 characters per column, right-aligned under the code.

The shading study’s data

The course gives the final harvest (FileA) and the growth analysis (FileT) of a control and a shaded treatment as two spreadsheets. Their header row already holds the DSSAT codes:

TRNO PWAM H#AM HWAM CWAM HWUM
0 1 6718 942 5283 14240 0.5608
1 2 5037 658 3611 11431 0.5488
TRNO DATE PWAD G#AD GWAD P#AD CWAD GWGD
0 1 76161 10 0 0 0 1407 0.0
1 1 76168 28 0 0 0 2268 0.0
2 1 76175 99 0 0 11 3032 0.0
3 1 76182 362 0 0 69 4365 0.0
4 1 76189 727 85 99 192 6498 116.5
5 1 76196 1305 313 448 329 7426 143.1
code label description file
0 PWAM Pod/Ear w kg/ha Pod/Ear/Panicle weight at maturity (kg [dm]/ha) FileA
1 H#AM Number #/m2 Number at maturity (no/m2) FileA
2 HWAM Mat Yield kg/ha Yield at harvest maturity (kg [dm]/ha) FileA
3 CWAM Biomass kg/ha Biomass at maturity (total crop minus roots) (... FileA
4 HWUM Weight g/unit Unit wt at maturity (g [dm]/unit) FileA
5 PWAD Pod wt kg/ha Pod weight (kg [dm]/ha) FileT
6 G#AD Grain no #/m2 Grain number (no/m2) FileT
7 GWAD Grain wt kg/ha Grain weight (kg [dm]/ha) FileT
8 P#AD Pod no #/m2 Pod number (no/m2) FileT
9 CWAD Biomass kg/ha Total crop weight minus roots (kg [dm]/ha) FileT
10 GWGD Grain wt mg Unit grain weight (mg [dm]/grain) FileT

Building the experiment: UFGA7609.PNX

The exercise starts from the 1976 Florunner experiment UFGA7601.PNX and changes only what differs: the experiment number (9), the planting and simulation start date (22 April 1976), automatic irrigation, and a second treatment with an environmental modification: solar radiation set to 20% of normal for 21 days, from 4 to 24 August 1976, and back to normal on 25 August. The notebook makes the same edits to the text of the file, section by section, as XBuild would.

*TREATMENTS                        -------------FACTOR LEVELS------------
@N R O C TNAME.................... CU FL SA IC MP MI MF MR MC MT ME MH SM
 1 1 0 0 CONTROL, NO SHADE          1  1  0  1  1  0  1  0  0  0  0  1  1
 2 1 0 0 SHADE 20%, 4-24 AUG        1  1  0  1  1  0  1  0  0  0  1  1  1


*ENVIRONMENT MODIFICATIONS
@E ODATE EDAY  ERAD  EMAX  EMIN  ERAIN ECO2  EDEW  EWIND ENVNAME
 1 76217 A   0 M .20 A   0 A   0 A 0.0 A   0 A   0 A   0
 1 76238 A   0 M   1 A   0 A   0 A 0.0 A   0 A   0 A   0

In the ERAD column, M .20 multiplies radiation by 0.20 from 4 August (day 217); M 1 restores it on 25 August (day 238). A modification stays in force until another one replaces it, which is why the second row is needed.

Writing the FileA and FileT

learnlib.write_observed writes both files from the spreadsheets. The engine reads them by column position, so the alignment has to be exact: a first version of this writer put every name one character to the left of its values; read back by whitespace the file looked fine, but the engine’s evaluation reported anthesis about 11,000 days after planting. Comparing the engine’s Evaluate output with the spreadsheet is the check.

*EXP.DATA (A): UFGA7609PN Environmental Modification

@TRNO   PWAM  H#AM  HWAM  CWAM  HWUM
     1  6718   942  5283 14240 .5608
     2  5037   658  3611 11431 .5488

*EXP.DATA (T): UFGA7609PN Environmental Modification

@TRNO   DATE  PWAD  G#AD  GWAD  P#AD  CWAD  GWGD
     1 76161    10     0     0     0  1407     0
     1 76168    28     0     0     0  2268     0
     1 76175    99     0     0    11  3032     0
TRNO code simulated measured description sim/obs
0 1 HWAM 5115.0000 5283.0000 Yield at harvest maturity (kg [dm]/ha) 0.968200
1 1 PWAM 6438.0000 6718.0000 Pod/Ear/Panicle weight at maturity (kg [dm]/ha) 0.958321
2 1 CWAM 14118.0000 14240.0000 Biomass at maturity (total crop minus roots) (... 0.991433
3 1 H#AM 873.0000 942.0000 Number at maturity (no/m2) 0.926752
4 1 HWUM 0.5859 0.5608 Unit wt at maturity (g [dm]/unit) 1.044757
5 2 HWAM 4170.0000 3611.0000 Yield at harvest maturity (kg [dm]/ha) 1.154805
6 2 PWAM 5266.0000 5037.0000 Pod/Ear/Panicle weight at maturity (kg [dm]/ha) 1.045464
7 2 CWAM 12017.0000 11431.0000 Biomass at maturity (total crop minus roots) (... 1.051264
8 2 H#AM 775.0000 658.0000 Number at maturity (no/m2) 1.177812
9 2 HWUM 0.5381 0.5488 Unit wt at maturity (g [dm]/unit) 0.980503
TRNO variable n rmse d
0 1 CWAD 13 1168.345543 0.979878
1 1 G#AD 13 146.599664 0.963029
2 1 GWAD 13 447.629139 0.986172
3 1 GWGD 13 29.257332 0.994307
4 1 P#AD 13 127.975659 0.928809
5 1 PWAD 13 764.970537 0.975743
6 2 CWAD 4 506.247469 0.889125
7 2 G#AD 4 89.262254 0.390711
8 2 GWAD 4 503.647694 0.792966
9 2 GWGD 4 81.832422 0.757863
10 2 P#AD 4 43.809246 0.408153
11 2 PWAD 4 472.626174 0.847008

The whole study, and when shade hurts most

The published experiment UFGA7604.PNX of dssat-csm-data has the full study: a control and four 21-day shade periods at 25% of normal radiation, from early in the season to pod filling. And with the shade exercise’s experiment as a template, the notebook moves a 21-day window through the season in steps of a week, at two strengths, in one FileX with one environmental-modification level per treatment.

*ENVIRONMENT MODIFICATIONS
@E ODATE EDAY  ERAD  EMAX  EMIN  ERAIN ECO2  EDEW  EWIND ENVNAME
 1 76154 A   0 M .25 A   0 A   0 A 0.0 A   0 A   0 A   0
 1 76175 A   0 M   1 A   0 A   0 A 0.0 A   0 A   0 A   0
TRNO TNAM HWAM CWAM H#AM HWUM HWAM_obs CWAM_obs H#AM_obs
0 1 CONTROL- NO SHADE 5034 13162 871 0.577839 5283 14240 942
1 2 21D SHADE- 154-174 4143 11742 842 0.492103 5344 13724 967
2 3 21D SHADE- 175-195 2845 11963 653 0.435442 4511 13143 795
3 4 21D SHADE- 196-216 2684 12245 592 0.453101 3597 10786 720
4 5 21D SHADE- 217-237 3975 11211 780 0.509775 3611 11431 658
radiation 0.25 0.50 1.00
start
NaN NaN NaN 5115.0
154.0 4527.0 4930.0 NaN
161.0 4293.0 4855.0 NaN
168.0 3875.0 4573.0 NaN
175.0 3273.0 4225.0 NaN
182.0 2540.0 3979.0 NaN
189.0 2385.0 3557.0 NaN
196.0 2794.0 3418.0 NaN
203.0 3367.0 3612.0 NaN
210.0 3964.0 3977.0 NaN
217.0 4204.0 4398.0 NaN
224.0 4220.0 4709.0 NaN
231.0 4306.0 4805.0 NaN
238.0 4593.0 5027.0 NaN 
WindowsPath('C:/Users/benny/OneDrive/Documents/Github/xdssat/docs/learn/data/module4/shade_files.csv')

2. Nitrogen-limited production: UFGA8213.MZX

The exercise builds on the water-limited maize experiment of module 3 and adds what the nitrogen balance needs:

  • initial conditions measured on 25 February 1982: previous crop maize, 100 kg/ha of roots, no nodules or rhizobia, 1000 kg/ha of crop residue with 0.8% N, fully incorporated to 15 cm;
  • the initial ammonium and nitrate of each soil layer (1.5 g/Mg of NH4 in the top four layers, 0.6 in the next two and 0.5 in the last two; 0.6 g/Mg of NO3 throughout), with the same soil water as before;
  • water and nitrogen simulated; nitrogen fertilizer on reported dates;
  • four treatments: rainfed and automatically irrigated (30 cm, 50%), each without N and with 60 kg N/ha on 15 March plus 75 kg N/ha on 12 April as ammonium nitrate, broadcast and incorporated at 10 cm.

The soil N model keeps ammonium and nitrate in every layer; they change with fertilizer, mineralization, nitrification, leaching and uptake (Soil/Inorganic_N/SOILNI.for). In the plant, CERES-Maize compares the N concentration of the tops with a critical (TCNP) and a minimum (TMNC) concentration: NFAC = 1 - (TCNP - TANC) / (TCNP - TMNC) (MZ_NFACTO.for:61).

*TREATMENTS                        -------------FACTOR LEVELS------------
@N R O C TNAME.................... CU FL SA IC MP MI MF MR MC MT ME MH SM
 1 1 0 0 RAINFED, NO N              1  1  0  1  1  0  0  0  0  0  0  0  1
 2 1 0 0 AUTO IRRIGATED, NO N       1  1  0  1  1  0  0  0  0  0  0  0  2
 3 1 0 0 RAINFED, 135 KG N          1  1  0  1  1  0  1  0  0  0  0  0  1
 4 1 0 0 AUTO IRRIGATED, 135 KG N   1  1  0  1  1  0  1  0  0  0  0  0  2


*INITIAL CONDITIONS
@C   PCR ICDAT  ICRT  ICND  ICRN  ICRE  ICWD ICRES ICREN ICREP ICRIP ICRID ICNAME
 1    MZ 82056   100     0     0     0   -99  1000    .8     0   100    15 -99
@C  ICBL  SH2O  SNH4  SNO3
 1     5 0.086   1.5   0.6
 1    15 0.086   1.5   0.6
 1    30 0.086   1.5   0.6
 1    60 0.086   1.5   0.6
 1    90 0.076   0.6   0.6
 1   120 0.076   0.6   0.6
 1   150 0.130   0.5   0.6
 1   180 0.258   0.5   0.6


*PLANTING DETAILS
@P PDATE EDATE  PPOP  PPOE  PLME  PLDS  PLRS  PLRD  PLDP  PLWT  PAGE  PENV  PLPH  SPRL                        PLNAME
 1 82057   -99   7.2   7.2     S     R    61     0     7   -99   -99   -99   -99     0                        -99


*FERTILIZERS (INORGANIC)
@F FDATE  FMCD  FACD  FDEP  FAMN  FAMP  FAMK  FAMC  FAMO  FOCD FERNAME
 1 82074 FE001 AP002    10    60     0     0     0     0   -99 -99
 1 82102 FE001 AP002    10    75     0     0     0     0   -99 -99


 1 OP              Y     Y     N     N     N     N     N     Y     M
 1 MA              R     R     R     N     M
 2 OP              Y     Y     N     N     N     N     N     Y     M
 2 MA              R     A     R     N     M
TRNO treatment HWAM CWAM NICM NUCM NLCM NIAM NMINC CNAM GNAM PRCM IRCM DRCM
0 1 rainfed, no N 547 2505 0 25 44 13 47 21 6 661 0 411
1 2 irrigated, no N 882 2992 0 27 46 13 50 23 9 661 74 451
2 3 rainfed, 135 kg N 2268 7086 135 114 66 34 44 85 39 661 0 321
3 4 irrigated, 135 kg N 8436 16373 135 130 70 21 51 110 80 661 200 370
NSTD CNAD GNAD VNAD GN%D VN%D NUPC
TRNO
1 0.60 20.69 6.41 15.29 1.05 4.4 24.95
2 0.58 23.12 9.66 15.81 1.01 4.4 27.18
3 0.05 92.48 42.56 92.48 1.74 4.4 114.08
4 0.60 109.80 79.61 102.00 1.27 4.4 129.81

Two soil organic matter models

DSSAT has two ways to simulate soil organic matter, chosen with the MESOM switch of the simulation controls: G, the original CERES approach (Godwin), and P, the CENTURY-based model (Parton). The four treatments of the exercise under both:

HWAM NMINC
model CENTURY (Parton) CERES (Godwin) CENTURY (Parton) CERES (Godwin)
treatment
irrigated, 135 kg N 8097 8436 33 51
irrigated, no N 368 882 29 50
rainfed, 135 kg N 2600 2268 24 44
rainfed, no N 250 547 27 47

Self test 1: the response to the N rate

0, 50, 100, 150 and 200 kg N/ha in total, in the two applications of the exercise (in the same 60:75 proportion), rainfed and automatically irrigated.

water irrigated rainfed
rate
0 882 547
50 3195 1374
100 6205 2309
150 9140 2161
200 10389 1530

Self test 2: three soils

The four treatments on a clay, a silt loam and a sand from the generic profiles of the soil file (the deep ones, 210 cm), next to the Millhopper fine sand. For those three soils the initial soil water is rebuilt at 100% of their plant-available range (ic_water=1.0); ammonium and nitrate keep the exercise’s values by depth.

treatment irrigated, 135 kg N irrigated, no N rainfed, 135 kg N rainfed, no N
soil
Millhopper fine sand 8436 882 2268 547
deep sand 8392 351 4773 301
deep silt loam 11875 2837 4466 2091
deep silty clay 12752 5599 11352 5161

Self test 3: residue and initial nitrogen

The fertilized treatments (3 and 4) with the crop residue, its N content and the initial nitrate changed one at a time, through the initial-conditions columns ICRES, ICREN and SNO3 (the nitrate value is then the same in every layer).

treatment irrigated, 135 kg N rainfed, 135 kg N
scenario
3000 kg/ha residue 8821 2303
NO3 10 g/Mg in every layer 8541 2290
NO3 3 g/Mg in every layer 8462 2306
as in the exercise 8436 2268
no residue 8233 2310
residue 0.4% N 8270 2289
residue 1.6% N 8684 2326

Nitrogen fixation in a legumeGrain legumes add a source of nitrogen that cereals lack: symbiotic fixation by root nodules. CROPGRO growsnodules when the crop’s nitrogen demand exceeds what roots take up from the soil and mobilize from old tissue,and the nodules fix nitrogen at a rate set by their mass and by temperature, the crop’s water status, flooding,nodule age and the carbohydrate they receive (Plant/CROPGRO/NFIX.for). The SYMBI switch in the simulation controls turns fixation on or off.Bragg soybean at Gainesville in 1978 (UFGA7801.SBX, a sandy soil without fertilizer), with the nitrogen balanceon and fixation on or off, and with the nitrogen balance off for comparison:

case treatment HWAM CWAM NUCM NFXM NLCM
0 no fixation irrigated 75 119 9 0 39.0
1 no fixation rainfed 85 146 10 0 36.0
2 fixation irrigated 2806 5988 14 276 34.0
3 fixation rainfed 1088 3363 10 180 33.0
4 nitrogen not limiting irrigated 2849 6016 0 0 NaN
5 nitrogen not limiting rainfed 1115 3400 0 0 NaN

3. Things to try

  • Write your own FileT for a field you know: one row per sampling date, the codes from DATA.CDE.
  • In the shade sweep, find the 21 days when shade costs most. What is the crop doing then?
  • Move all the nitrogen of treatment 4 to planting. What happens to leaching and to yield?
0
engine C:\TEMP\dsn\dssat\dscsm048.exe
csm_data_commit 99c95b340acb9515c2d0a8ab582f5fbbf076f345
csm_os_commit 25c93b9a2f73f8ec45bf441b198dac5fb7b22849
run_on 2026-11-07 10:53
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