CHU Pan revised @ SIAT
SUN Hui provided the source code.
MIT Licence

This code is based on the work that published in $Elife$.

Warren, M. R. et al. Spatiotemporal establishment of dense bacterial colonies growing on hard agar. Elife 8, e41093 (2019).

(1) compile the code:
$> cd run_sim
$> g++ ../*.cpp -fopenmp -O3 -o [file name]
(2) run the code:
$> [file name] [parameter file] [core number] /Direcotry/To/Output/Folder [field file output flag] > /Redirect/Console/Output &
The command line argument [parameter file] is the input txt file.
The command line argument [core number] means we run this code using how much cores. You can change it to some other numbers.
The command line argument [field file output flag] means whether outputing filed data, if set 0, we will disable field data out put.
The command line argument /Direcotry/To/Output/Folder is the directory to output the data.
The command line argument > /Redirect/Console/Output & means console outpout gets redirected to /Redirect/Console/Output, and the program runs in background.
Note: When perform long-term simulation, specially, time limit is extended to more than 12 hrs. The lineage files can be more than 100 Giga bits. Make sure that there is sufficient free disk space left.

We provide an easy way to compile and run the code with the help of python script.
$> python CellMD3D_compile_run.py -n [path for compiled file] -i [path for parameter file] -o [directory for output files] --core_num [core number]

Cells: containing .txt files that recording the cells' info;
The output format has been defined in InputOutput.cpp.

t, ID, cell.Type, cell.Position.p.x, cell.Position.p.y, cell.Position.p.z, cell.Position.q.x, cell.Position.q.y, cell.Position.q.z, cell.Length, T.xx, T.yy, T.zz, cell.Velocity.x, cell.Velocity.y, cell.Velocity.z, cell.GrowthRate, cell.DynFric.x, cell.DynFric.y, cell.DynFric.z, cell.StaFric.x, cell.StaFric.y, cell.StaFric.z, cell.Position.time_p, cell.Position.time_q, cell.Position.age_p, cell.Position.age_q, cell.Ancestor, cell.G, cell.R
0.4002 0 1 1.0151 2.8463 0.4718 0.0211 0.2836 0.4718 2.7487 0.0000 0.0000E+00 0.0000E+00 4.9329E-15 1.2738E-14 1.2576E+00 1.5140E+00 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0 0 1 3.8623 4.6081

The position of cells was described by a sphero-cylinder model, p and q characterize the two centers of the two hemispheres. Notice, the radius of cells, i.e. the radius of the two hemispheres, is defined in Constants.cpp and the unit is microns.

The toggle switch within cells was defined in file integrate.cpp, updateToggle function is used for update the state of the toggle. $$ \dot{G} = \alpha_G \cdot H_{G}(R) - \lambda \cdot G \ \dot{R} = \alpha_R \cdot H_{R}(G) - \lambda \cdot R
$$

$$ \O \overset{\alpha_G \cdot H_{G}(R) }{\rightarrow} G \\ \O \overset{\alpha_R \cdot H_{R}(G) }{\rightarrow} R \\ G \overset{\lambda G}{\rightarrow} \O \\ R \overset{\lambda R}{\rightarrow} \O $$

$$ \pmb{\lambda}(\pmb{r}, t) = \lambda_s \frac{\pmb{C}(\pmb{r}, t)}{\pmb{C}(\pmb{r}, t) + K_s} $$

$$ V_{cell}= \frac{1}{4} \pi w_0^2 l + \frac{1}{6} \pi w_0^3, M_{cell}=\rho_{cell}V_{cell} $$

$$ \dot l = \tilde{\lambda} l $$

$$ l_1 = \frac{1}{2} l_{div} - \frac{w_0}{2} + \eta l_{rand}, l_2 = \frac{1}{2} l_{div} - \frac{w_0}{2} - \eta l_{rand}, $$

$$ t_d = \frac{\ln 2}{\lambda}, l_{div} = l_0 \exp( \tilde{\lambda} t_d) $$

$$ \frac{\tilde{\lambda}}{\lambda} = \sigma = \frac{\ln(2 l_{div} / (l_{div} - w_0))}{\ln 2} $$

Note: $w_0$ is the diameter of the hemisphere.

UpdateEnvArray: Update the nutrient concentration

s0: Calculate the field, nutrient conc.
s1: Calculate forces and move cells
s2: Output fields,cells,density
s3: Cell division
s4: switch cells location between olds and news
s00: get colony height

8/2/2022

• the code can be compiled under windows platform;
  Note: When running codes in Windows platform may incur
  terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc \
• Create the lineage file automatically.

8/9/2022

• The proteins in toggle have a basic decay rate deltaP.

8/11/2022 V0.12

• Update the toggle switch states by cell mass gowth rate, rather elongation rate;
• Add parameter SigmaMoL replace the fixed dividing cell aspect ratio log(3)/log(2).

10/9/2022 V0.20

• SSA version

/home/fulab/colony_agent_based/InputOutput.cpp: In function ‘int LoadCells(char*, Cell*, UniformGrid&, double&, double&)’: /home/fulab/colony_agent_based/InputOutput.cpp:423:7: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 423 | fread(&t, sizeof(double), 1, FID); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/fulab/colony_agent_based/InputOutput.cpp:424:7: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 424 | fread(&dt, sizeof(double), 1, FID); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/fulab/colony_agent_based/InputOutput.cpp:431:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 431 | fread (cells, sizeof(Cell), cell_count, FID); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/fulab/colony_agent_based/InputOutput.cpp: In function ‘Inputs ReadParameters(char*)’: /home/fulab/colony_agent_based/InputOutput.cpp:475:7: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 475 | fread(buffer, fileLen, 1, FID); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /home/fulab/colony_agent_based/InputOutput.cpp: In function ‘void CreateOutputFileLineage(int, OutputFiles&, bool)’: /home/fulab/colony_agent_based/InputOutput.cpp:107:36: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size between 0 and 499 [-W$/home/fulab/colony_agent_based/InputOutput.cpp: In function ‘void CreateOutputFileLineage(int, OutputFiles&, bool)’: [102/374]/home/fulab/colony_agent_based/InputOutput.cpp:107:36: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size between 0 and 499 [-Wformat-overflow=] 107 | (void)sprintf(lineage_name,"%s/%d",lineage_name,OutputID); | ^~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/9/cstdio:42, from /usr/include/c++/9/ext/string_conversions.h:43, from /usr/include/c++/9/bits/basic_string.h:6496, from /usr/include/c++/9/string:55, from /usr/include/c++/9/bits/locale_classes.h:40, from /usr/include/c++/9/bits/ios_base.h:41, from /usr/include/c++/9/ios:42, from /usr/include/c++/9/ostream:38, from /usr/include/c++/9/iostream:39, from /home/fulab/colony_agent_based/InputOutput.h:7, from /home/fulab/colony_agent_based/InputOutput.cpp:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 3 and 512 bytes into a destination of size 500 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

• Invalid index

t = 11.005550, 1060805 cells;      sim time =   3:30:57;      time cost = 627.799 2.35591 626.019 24.3967 5.64741 0.000171.

Colony_V0.2.4.7: /home/fulab/PycharmProjects/colony_agent_based_SSA/tools.h:24: void MyAssert(bool, const char*): Assertion `false' failed.
Invalid index into array

Aborted (core dumped)

[CellsMD3D ssa_in23_Colony_V0.2.4.7] -> Simulation failed

parameters

t_max       15
dt          0.00005
Cdt         0.1
Box_x       64
Box_y       64
Box_z       40
Box_z_agar	16
maxLevels	4
FilterLen	5

Size is small?

New parameters

t_max       15
dt          0.00005
Cdt         0.1
Box_x       72
Box_y       72
Box_z       52
Box_z_agar	20
maxLevels	4
FilterLen	5