Regeneration during the dormant period cause model crash

[trotsiuk]

Description

If there is a new cohort regenerated of broadleaf species during the dormant period it seems to cause the model crash. This issue is occurring most likely due to the correct_bias part, where we have the log(age). At this point in time the age is 0 which case the issue.

https://github.com/trotsiuk/r3PG/blob/master/src/md_3PG.f95#L1643

This issue seems not to be a problem if the regeneration occurs during the growing period (not dormant).

Another explanation can be that there are some further allocations related to it.

Code

This is very specific issue. With the code below everything works well those. Need more tests for the code

library(r3PG)
library(dplyr)
library(ggplot2)

# Run with regeneration ---------------------------------------------------

# create a regeneration part

d_species_r <- d_species %>%
  dplyr::mutate( species = paste0(species, '_r'),
                 planted = '2006-01',
                 stems_n = 1000,
                 biom_stem = 1,
                 biom_root = 1,
                 biom_foliage = 1) %>%
  # dplyr::bind_rows(dplyr::mutate(d_species, dplyr::across( c(stems_n, biom_stem, biom_root, biom_foliage), ~.*0.2)), .)
  dplyr::bind_rows( d_species, .)

d_thinning_r <- d_thinning %>%
  dplyr::mutate(stems_n = stems_n * 0.2)

d_parameters_r <- d_parameters %>%
  dplyr::rename_at( vars(-parameter),function(x) paste0(x,"_r") ) %>%
  dplyr::inner_join( d_parameters, ., by = 'parameter')

d_sizeDist_r <- d_sizeDist %>%
  dplyr::rename_at( vars(-parameter),function(x) paste0(x,"_r") ) %>%
  dplyr::inner_join( d_sizeDist, ., by = 'parameter')

out_3PG <- run_3PG(
  site        = d_site, 
  species     = d_species_r, 
  climate     = d_climate, 
  # thinning    = NULL,
  thinning    = d_thinning_r,
  parameters  = d_parameters_r, 
  size_dist   = d_sizeDist_r,
  settings    = list(light_model = 2, transp_model = 2, phys_model = 2, 
                     height_model = 1, correct_bias = 1, calculate_d13c = 0),
  check_input = TRUE, df_out = TRUE)

i_var <- c('stems_n',  'dbh', 'height', 'biom_stem', 'biom_root', 'biom_foliage')
i_lab <- c('Stem density', 'DBH', 'Height', 'Stem biomass', 'Root biomass', 'Foliage biomass')

out_3PG %>%
  filter(variable %in% i_var) %>%
  mutate(variable = factor(variable, levels = i_var)) %>%
  ggplot( aes(date, value))+
  geom_line( aes(color = species), size = 0.5)+
  facet_wrap( ~ variable, scales = 'free_y', ncol = 3, 
              labeller = labeller(variable = setNames(i_lab, i_var) )) +
  scale_color_brewer('', palette = 'Dark2') +
  theme_classic()+
  theme(legend.position="bottom")+
  xlab("Calendar date") + ylab('Value')  

explore.data <- out_3PG %>%
  dplyr::filter( date %in% c(as.Date('2006-12-31'), as.Date('2006-01-31'), as.Date('2006-02-28'), as.Date('2006-03-31'), as.Date('2006-04-30'), as.Date('2006-05-31'))) %>%
  tidyr::pivot_wider( names_from = 'date', values_from = 'value')