Settings defined for instruction files are listed below. Most settings are compulsory but some (*) are required only in cohort mode.
You may edit the settings (with care), for example using the inbuilt text editor in the LPJ-GUESS Windows Shell. The editor may be invoked by choosing Open in editor ... in the File menu, or by clicking on the View/edit ... button on the Simulation settings form. Any changes to the instruction file should be made only in a copy in the current workspace folder. Do not edit the master copies found in the LPJ-GUESS Education folder in the Windows Program Files folder (or equivalent, depending on your Windows version).
Restoring default settings
If your instruction file becomes corrupted or you want to go back to the original settings, the easiest way is to create a new workspace by choosing Change workspace ... on the File menu of the LPJ-GUESS Windows Shell. Fresh copies of the default instruction files cohort.inz and population.inz will appear in the new workspace folder. You may then continue working in the new workspace, or replace the corrupted instruction files in the old workspace with the fresh copies in the new workspace. You can return to your old workspace by clicking on File|Change workspace ... and choosing the Browse ... option.
Output settings
See File output and Available output variables.
General settings
* = cohort mode only, ignored in population mode.
| title | Title for run |
| vegmode | Vegetation mode ("cohort", "population") |
| npatch | Number of replicate patches to simulate* |
| patcharea | Patch area (m2)* |
| ifdisturb | Whether generic patch-destroying disturbances enabled (0,1)* |
| distinterval | Generic patch-destroying disturbance interval (years)* |
| iffire | Whether wildfire disturbance enabled (0,1) |
| ifcalcsla | Whether to calculate SLA from leaf longevity |
| ifcalcton | Whether to calculate leaf minimum C:N ratio from leaf longevity |
| ifcdebt | Whether to allow labile carbon storage by plants (0,1) |
| estinterval | Interval for establishment of new cohorts (years)* |
| ifbgestab | Whether background establishment enabled (0,1)* |
| ifsme | Whether spatial mass effect enabled for establishment (0,1)* |
| ifstochestab | Whether establishment stochastic (0,1)* |
| ifstochmort | Whether mortality stochastic (0,1)* |
| ifsmoothgreffmort | Whether stress mortality is gradual (1) or sudden (0)* |
| ifdroughtlimitedestab | Whether (1) or not (0) establishment declines at low soil water |
| ifrainonwetdaysonly | Whether precipitation occurs on rain days (1) or every day (0) |
| ifbvoc | Whether to calculate BVOC emissions (not available in LPJ-GUESS Education) |
| wateruptake | Mode for plant water uptake ("rootdist", "wcont", "smart", "speciesspecific") |
| ifcentury | Whether to use CENTURY soil carbon dynamics (mandatory if N cycling enabled) (0,1) |
| ifnlim | Whether nitrogen cycling and N-limitation of plant production enabled (0,1) |
| freenyears | Number of initial spinup years without N-limitation (should be fixed at 100) |
| nfix_a | Term in N fixation equation |
| nfix_b | Term in N fixation equation |
| nrelocfrac | Fraction of plant N retranslocated prior to leaf and root shedding |
| runlandcover | Whether to use landcover input (0,1) (not available in LPJ-GUESS Education) |
PFT settings
* = cohort mode only, ignored in population mode.
| include | Whether to include PFT in analysis (0,1) |
| preferredrgb | RGB colour for screen output |
| lifeform | Lifeform ("tree", "grass") |
| leafphysiognomy | Leaf physiognomy ("broadleaf", "needleleaf") |
| phenology | Phenology ("evergreen", "summergreen", "raingreen", "any") |
| phengdd5ramp | Growing degree days on 5°C base to attain full leaf cover |
| wscal_min | Water stress threshold for leaf abscission (raingreen PFTs) |
| pathway | Biochemical pathway for photosynthesis ("C3", "C4") |
| pstemp_min | Approximate low temperature limit for photosynthesis (°C) |
| pstemp_low | Approximate lower range of temperature optimum for photosynthesis (°C) |
| pstemp_high | Approximate higher range of temperature optimum for photosynthesis (°C) |
| pstemp_max | Maximum temperature limit for photosynthesis (°C) |
| lambda_max | Non-water-stressed ratio of intercellular to ambient CO2 partial pressure |
| cton_leaf_min | Minimum leaf C:N mass ratio |
| cton_root | Reference fine root C:N mass ratio |
| cton_sap | Reference sapwood C:N mass ratio |
| nuptoroot | Maximum nitrogen uptake per fine root |
| km_volume | Half-saturation concentration for N uptake (kgN l−1) |
| fnstorage | Fraction of sapwood (trees) or fine roots (grasses) scaling plant N storage capacity |
| rootdist | Fraction of roots in upper and lower soil layer |
| gmin | Canopy conductance not associated with photosynthesis (mm s−1) |
| emax | Maximum evapotranspiration rate (mm day−1) |
| respcoeff | Respiration scalar in range 0-1 |
| reprfrac | Fraction of NPP allocated to reproduction |
| sla | Specific leaf area (m2 kgC−1) |
| leaflong | Leaf longevity (years) |
| turnover_leaf | Leaf turnover (fraction year−1), must be min(1,1/leaflong) |
| turnover_root | Fine root turnover (fraction year−1) |
| turnover_sap | Sapwood turnover (fraction year−1) |
| wooddens | Sapwood and heartwood density (kgC m−3) |
| crownarea_max | Maximum tree crown area (m2) |
| k_allom1 | Constant in allometry equations |
| k_allom2 | Constant in allometry equations |
| k_allom3 | Constant in allometry equations |
| k_rp | Constant in allometry equations |
| k_latosa | Tree leaf to sapwood cross-sectional area ratio |
| ltor_max | Non-water-stressed leaf:fine root mass ratio |
| intc | interception scalar |
| litterme | Litter moisture flammability threshold (fraction of soil upper layer AWC) |
| fireresist | Fire resistance in range 0-1 |
| tcmin_surv | Minimum 20-year coldest month mean temp for survival (°C) |
| tcmin_est | Minimum 20-year coldest month mean temp for establishment (°C) |
| tcmax_est | Maximum 20-year coldest month mean temp for establishment (°C) |
| twmin_est | Minimum warmest month mean temp for establishment (°C) |
| gdd5min_est | Minimum growing degree days on 5°C base for establishment |
| drought_tolerance | Drought sensitivity factor in range 0-1 where 1 signifies maximum sensitivity |
| k_chilla | Constant in equation for budburst chilling time requirement* |
| k_chillb | Coefficient in equation for budburst chilling time requirement* |
| k_chillk | Exponent in equation for budburst chilling time requirement* |
| parff_min | Minimum forest floor PAR for grass growth/tree establishment (J m−2 day−1)* |
| alphar | Shape parameter for recruitment-juvenile growth rate relationship* |
| est_max | Maximum sapling establishment rate (indiv m−2 yr−1)* |
| kest_repr | Constant in equation for tree establishment rate* |
| kest_bg | Constant in equation for tree establishment rate* |
| kest_pres | Constant in equation for tree establishment rate* |
| longevity | Expected longevity under lifetime non-stressed conditions (yr)* |
| greff_min | Threshold for growth suppression mortality (kgC m−2 leaf yr−1)* |
| ga | Aerodynamic conductance (ms−1) (used in BVOC calculations, not available in LPJ-GUESS Education) |
| eps_iso | Isoprene emission capacity (μgC g−1 hr−1) (used in BVOC calculations, not available in LPJ-GUESS Education) |
| eps_mon | Monoterpene emission capacity (μgC g−1 hr−1) (used in BVOC calculations, not available in LPJ-GUESS Education) |
| seas_iso | Whether isoprene emissions show seasonality (0,1) (used in BVOC calculations, not available in LPJ-GUESS Education) |
| storfrac_mon | Fraction of monoterpene production assigned to storage pool (used in BVOC calculations, not available in LPJ-GUESS Education) |