Bug in Continue functionality

[maringos]

Dear All,
I have realized that if I simulate only the diffusion for one step and then add the bacteria, the sim object does not contain information about the first step (i.e. it must be zero, but the counting must be there). Please revise the functionality of the argument continue.
Regards and thanks for your efforts,
@maringos

 library(BacArena)
 data("Ec_core")
 
 bac  <- Bac(Ec_core)
[1] "Median lower bound for non-zero and non-Inf exchanges is:-106"
 arena <- Arena(n=20, m=20)
 arena <- addSubs(arena, smax=0.05, mediac="EX_glc(e)", unit="mM", addAnyway = T)
 sim   <- simEnv(arena, time=1, with_shadow = T, continue = T)
Substances 1 / 1
iteration: 1 	 organisms: 0 	 biomass: 0 pg 
	time total:  0.106 	diffusion:  0.003  ( 2.8 %)

--------------------------------------------------------------------
 sim@simlist
[[1]]
[1] biomass   type      phenotype x         y        
<0 rows> (or 0-length row.names)

[[2]]
[1] biomass   type      phenotype x         y        
<0 rows> (or 0-length row.names)

 sim <- addOrg(sim,bac,amount=30)
 sim   <- simEnv(sim, time=1, with_shadow = T, continue = T)
Substances 20 / 20
iteration: 1 	 organisms: 30 	 biomass: 11.14464 pg 
                 count  biomass   %
ecoli_core_model    30 11.14464 -21
	time total:  0.277 	diffusion:  0.07  ( 25.3 %)

--------------------------------------------------------------------
Warning message:
In simEnv(sim, time = 1, with_shadow = T, continue = T) :
  If growth is limited by maximum weight for an organism (max_weight=TRUE) it is recommended to use minimize total flux (sec_obj='mtf').
 sim@simlist
[[1]]
     biomass type phenotype  x  y
1  0.5129950    1        NA  3  3
2  0.3250450    1        NA  8 20
3  0.5211150    1        NA  7 10
4  0.5912180    1        NA  1  6
5  0.3209694    1        NA  6  3
6  0.4763702    1        NA 20  9
7  0.5972710    1        NA  1 13
8  0.5766454    1        NA 19  6
9  0.4619492    1        NA 18 13
10 0.3786961    1        NA  5  4
11 0.4502750    1        NA 19 14
12 0.3904994    1        NA 18  6
13 0.7807046    1        NA 20 10
14 0.3214857    1        NA 12 12
15 0.4597189    1        NA 10 13
16 0.3531474    1        NA 14 14
17 0.2979755    1        NA 10 10
18 0.3092325    1        NA  3  8
19 0.6280822    1        NA 17 15
20 0.5742473    1        NA 11  7
21 0.2554119    1        NA  3  7
22 0.3475802    1        NA  2 20
23 0.6343229    1        NA 14 19
24 0.6444364    1        NA 17 14
25 0.1874060    1        NA  5 12
26 0.5307558    1        NA  9 16
27 0.6477503    1        NA  6  8
28 0.5163725    1        NA  4 12
29 0.5137511    1        NA 12 17
30 0.5017057    1        NA  9  9

[[2]]
     biomass type phenotype  x  y
3  0.4116808    1         0  5  9
22 0.2745883    1         0  3 18
17 0.2354006    1         0 10 12
23 0.5011151    1         0 13 19
9  0.3649398    1         0 19 15
20 0.4536554    1         0 10  7
7  0.4718441    1         0  3 12
14 0.2539737    1         0 13 14
6  0.3763324    1         0 19  7
26 0.4192971    1         0 11 16
5  0.2535658    1         0  7  5
8  0.4555499    1         0 20  6
1  0.4052661    1         0  4  5
2  0.2567855    1         0 10 18
12 0.3084946    1         0 19  5
28 0.4079343    1         0  6 10
13 0.6167566    1         0 20  8
18 0.2442937    1         0  1 10
16 0.2789864    1         0 13 15
30 0.3963475    1         0  8  9
21 0.2017754    1         0  3  6
11 0.3557173    1         0 18 16
4  0.4670622    1         0  3  8
29 0.4058634    1         0 11 19
25 0.1480508    1         0  5 11
10 0.2991699    1         0  7  4
27 0.5117228    1         0  8  8
19 0.4961850    1         0 15 14
15 0.3631780    1         0 12 15
24 0.5091048    1         0 16 13