#include <param.h>
Definition at line 35 of file param.h.
◆ BoundSpaceMode
| Enumerator |
|---|
| kOpen | The simulation space grows to encapsulate all agents.
|
| kClosed | Enforce an artificial cubic bound around the simulation space. The dimensions of this cube are determined by parameter min_bound and max_bound.
If agents move outside the cube they are moved back inside.
|
| kTorus | Enforce an artificial cubic bound around the simulation space. The dimensions of this cube are determined by parameter min_bound and max_bound.
Agents that move outside the cube are moved back in on the opposite side.
|
Definition at line 196 of file param.h.
◆ ExecutionOrder
| Enumerator |
|---|
| kForEachAgentForEachOp | |
| kForEachOpForEachAgent | |
Definition at line 439 of file param.h.
◆ MappedDataArrayMode
MappedDataArrayMode options: kZeroCopy: access agent data directly only if it is requested.
kCache: Like kZeroCopy but stores the results in contiguous array, to speed up access if it is used again.
kCopy: Copy all data elements to a contiguous array at initialization time. Serves requests from the cache.
| Enumerator |
|---|
| kZeroCopy | |
| kCopy | |
| kCache | |
Definition at line 545 of file param.h.
◆ NumericalODESolver
Variable which specifies method using for solving differential equation {"Euler", "RK4"}.
Definition at line 103 of file param.h.
◆ ThreadSafetyMechanism
List of thread-safety mechanisms
kNone:
kUserSpecified: The user has to define all agent that must not be processed in parallel.
- See also
Agent::CriticalRegion.
kAutomatic: The simulation automatically locks all agents of the microenvironment.
| Enumerator |
|---|
| kNone | |
| kUserSpecified | |
| kAutomatic | |
Definition at line 273 of file param.h.
◆ Param() [1/2]
◆ ~Param()
◆ Param() [2/2]
| bdm::Param::Param |
( |
const Param & |
other | ) |
|
◆ AssignFromConfig()
| void bdm::Param::AssignFromConfig |
( |
const std::shared_ptr< cpptoml::table > & |
config | ) |
|
Assign values from config file to variables.
Definition at line 220 of file param.cc.
◆ BDM_CLASS_DEF_NV()
| bdm::Param::BDM_CLASS_DEF_NV |
( |
Param |
, |
|
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1 |
|
|
) |
| |
|
private |
◆ Get() [1/2]
template<typename TParamGroup >
| TParamGroup* bdm::Param::Get |
( |
| ) |
|
|
inline |
◆ Get() [2/2]
template<typename TParamGroup >
| const TParamGroup* bdm::Param::Get |
( |
| ) |
const |
|
inline |
◆ MergeJsonPatch()
| void bdm::Param::MergeJsonPatch |
( |
const std::string & |
patch | ) |
|
◆ RegisterParamGroup()
| void bdm::Param::RegisterParamGroup |
( |
ParamGroup * |
param | ) |
|
|
static |
◆ Restore()
| void bdm::Param::Restore |
( |
Param && |
other | ) |
|
◆ ToJsonString()
| std::string bdm::Param::ToJsonString |
( |
| ) |
const |
◆ DiffusionTest_CopyOldData_Test
| friend class DiffusionTest_CopyOldData_Test |
|
friend |
◆ backup_file
| std::string bdm::Param::backup_file = "" |
Backup file name for full simulation backups
Path is relative to working directory.
Default value: "" (no backups will be made)
TOML config file:
[simulation]
backup_file = <path>/<filename>.root
Command line argument: -b, --backup
Definition at line 159 of file param.h.
◆ backup_interval
| uint32_t bdm::Param::backup_interval = 1800 |
Specifies the interval (in seconds) in which backups will be performed.
Default Value: 1800 (every half an hour)
TOML config file:
[simulation]
backup_interval = 1800 # backup every half an hour
Definition at line 177 of file param.h.
◆ bound_space
Default value: open (simulation space is "infinite")
- See also
- BoundSpaceMode TOML config file:
[simulation]
bound_space = "open"
Definition at line 218 of file param.h.
◆ cache_neighbors
| bool bdm::Param::cache_neighbors = false |
Neighbors of an agent can be cached so to avoid consecutive searches. This of course only makes sense if there is more than one ForEachNeighbor* operation.
Default value: false
TOML config file:
[performance]
cache_neighbors = false
Definition at line 480 of file param.h.
◆ calculate_gradients
| bool bdm::Param::calculate_gradients = true |
Calculate the diffusion gradient for each substance.
TOML config file: Default value: true
[simulation]
calculate_gradients = true
Definition at line 265 of file param.h.
◆ compute_target
| std::string bdm::Param::compute_target = "cpu" |
Run the simulation partially on the GPU for improved performance. Possible values: "cpu", "cuda", "opencl" Default value: "cpu"
TOML config file: [experimental] compute_target = false
Definition at line 625 of file param.h.
◆ debug_numa
| bool bdm::Param::debug_numa = false |
Automatically track changes in the simulation and BioDynaMo repository. If set to true, BioDynaMo scans the simulation directory and the BioDynaMo repository for changes and saves the information of the git repositories in the output directory.
Default Value: true
Output debugging info related to running on NUMA architecture.
- See also
ThreadInfo, ResourceManager::DebugNuma Default Value: false
TOML config file: [development]
debug_numa = false
Definition at line 586 of file param.h.
◆ detect_static_agents
| bool bdm::Param::detect_static_agents = false |
Calculation of the displacement (mechanical interaction) is an expensive operation. If agents do not move or grow, displacement calculation is omitted if detect_static_agents is turned on. However, the detection mechanism introduces an overhead. For dynamic simulations where agents move and grow, the overhead outweighs the benefits.
Default value: false
TOML config file:
[performance]
detect_static_agents = false
Definition at line 470 of file param.h.
◆ diffusion_boundary_condition
| std::string bdm::Param::diffusion_boundary_condition = "Neumann" |
Define the boundary condition of the diffusion grid [open, closed, Neumann, Dirichlet, Periodic]
Default value: "Neumann"
TOML config file:
[simulation]
diffusion_boundary_condition = "Neumann"
Definition at line 244 of file param.h.
◆ diffusion_method
| std::string bdm::Param::diffusion_method = "euler" |
A string for determining diffusion type within the simulation space. Currently, only the method "euler" implementing a FTCS scheme is supported. See for instance here: https://en.wikipedia.org/wiki/FTCS_scheme (accessed 2023-07-17) Default value: "euler"
TOML config file:
[simulation]
diffusion_method = <diffusion method>
Definition at line 257 of file param.h.
◆ environment
| std::string bdm::Param::environment = "uniform_grid" |
The method used to query the environment of a simulation object. Default value: "uniform_grid"
Other allowed values: "kd_tree", "octree"
TOML config file:
[simulation]
environment = "uniform_grid"
Definition at line 122 of file param.h.
◆ execution_order
| ExecutionOrder bdm::Param::execution_order = ExecutionOrder::kForEachAgentForEachOp |
This parameter determines whether to execute kForEachAgentForEachOp
for (auto* agent : agents) {
for (auto* op : agent_ops) {
(*op)(agent);
}
}
or kForEachOpForEachAgent
for (auto* op : agent_ops) {
for (auto* agent : agents) {
(*op)(agent);
}
}
Definition at line 457 of file param.h.
◆ export_visualization
| bool bdm::Param::export_visualization = false |
Write data to file for post-simulation visualization Default value: false
TOML config file:
[visualization]
export = false
Definition at line 312 of file param.h.
◆ groups_
◆ insitu_visualization
| bool bdm::Param::insitu_visualization = false |
Use ParaView Catalyst for insitu visualization.
Insitu visualization supports live visualization and rendering without writing files to the harddisk.
Default value: false
TOML config file:
[visualization]
insitu = false
Definition at line 304 of file param.h.
◆ mapped_data_array_mode
Initial value:=
MappedDataArrayMode::kZeroCopy
This parameter sets the operation mode in bdm::MappedDataArray.
Allowed values are defined in MappedDataArrayMode
Possible values: zero-copy, cache, copy
Default value: zero-copy
TOML config file:
[performance]
mapped_data_array_mode = "zero-copy"
Definition at line 555 of file param.h.
◆ max_bound
| real_t bdm::Param::max_bound = 100 |
Maximum allowed value for x-, y- and z-position if simulation space is bound (
- See also
bound_space).
Default value: 100
TOML config file: [simulation]
max_bound = 100
Definition at line 236 of file param.h.
◆ mem_mgr_aligned_pages_shift
| uint64_t bdm::Param::mem_mgr_aligned_pages_shift = 5 |
The BioDynaMo memory manager allocates N page aligned memory blocks. The bigger N, the lower the memory overhead due to metadata storage if a lot of memory is used.
N must be a number of two.
Therefore, this parameter specifies the shift for N. N = 2 ^ shift
Default value: 5 -> N = 32
TOML config file:
[performance]
mem_mgr_aligned_pages_shift = 5
Definition at line 499 of file param.h.
◆ mem_mgr_growth_rate
| real_t bdm::Param::mem_mgr_growth_rate = 1.1 |
The BioDynaMo memory manager allocates memory in increasing sizes using a geometric series. This parameter specifies the growth rate. Default value: 2.0
TOML config file:
[performance]
mem_mgr_growth_rate = 1.1
Definition at line 508 of file param.h.
◆ mem_mgr_max_mem_per_thread_factor
| uint64_t bdm::Param::mem_mgr_max_mem_per_thread_factor = 1 |
The BioDynaMo memory manager can migrate memory between thread pools to avoid memory leaks.
This parameter influences the maximum memory size in bytes before migration happens.
The size in bytes depends on the system's page size and the parameter mem_mgr_aligned_pages_shift and is calculated as follows: PAGE_SIZE * 2 ^ mem_mgr_aligned_pages_shift * mem_mgr_max_mem_per_thread_factor
Default value: 1
TOML config file:
[performance]
mem_mgr_max_mem_per_thread_factor = 1
Definition at line 522 of file param.h.
◆ min_bound
| real_t bdm::Param::min_bound = 0 |
Minimum allowed value for x-, y- and z-position if simulation space is bound (
- See also
bound_space).
Default value: 0
TOML config file: [simulation]
min_bound = 0
Definition at line 227 of file param.h.
◆ minimize_memory_while_rebalancing
| bool bdm::Param::minimize_memory_while_rebalancing = true |
This parameter is used inside ResourceManager::LoadBalance. If it is set to true, the function will reuse existing memory to rebalance agents to NUMA nodes. (A small amount of additional memory is still required.)
If this parameter is set to false, the balancing function will first create new objects and delete the old ones in a second step. In the worst case this will real_t the required memory for agents for. Default value: true
TOML config file:
[performance]
minimize_memory_while_rebalancing = true
Definition at line 536 of file param.h.
◆ nanoflann_depth
| uint32_t bdm::Param::nanoflann_depth = 10 |
◆ numerical_ode_solver
◆ opencl_debug
| bool bdm::Param::opencl_debug = false |
Compile OpenCL kernels with debugging symbols, for debugging on CPU targets with GNU gdb. Default value: false
TOML config file: [experimental] opencl_debug = false
Definition at line 633 of file param.h.
◆ output_dir
| std::string bdm::Param::output_dir = "output" |
Output Directory name used to store visualization and other files.
Path is relative to working directory.
Default value: "output"
TOML config file:
[simulation]
output_dir = "output"
Definition at line 113 of file param.h.
◆ plot_memory_layout
| bool bdm::Param::plot_memory_layout = false |
Determines if agents' memory layout plots should be generated during load balancing.
Definition at line 645 of file param.h.
◆ preferred_gpu
| int bdm::Param::preferred_gpu = -1 |
Set the index of the preferred GPU you wish to use. In GpuHelper we set the default to whichever GPU supports double precision Default value: 0
TOML config file: [experimental] preferred_gpu = <GPU with double precision support>
Definition at line 641 of file param.h.
◆ progress_bar_time_unit
| std::string bdm::Param::progress_bar_time_unit = "s" |
Time unit of the progress bar. Possible values: "ms", "s", "min", "h" Default value: "s"
TOML config file: [development] progress_bar_time_unit = "s"
Definition at line 614 of file param.h.
◆ pv_insitu_pipeline
| std::string bdm::Param::pv_insitu_pipeline |
Initial value:=
"/include/core/visualization/paraview/default_insitu_pipeline.py")
Enable insitu visualization with a custom python pipeline Default value: "<path-to-bdm>/include/core/visualization/paraview/default_insitu_pipeline.py"
TOML config file: [visualization] pv_insitu_pipeline = ""
Definition at line 328 of file param.h.
◆ pv_insitu_pipelinearguments
| std::string bdm::Param::pv_insitu_pipelinearguments = "" |
Arguments that will be passed to the python ParaView insitu pipeline specified in Param::pv_insitu_pipeline.
The arguments will be passed to the ExtendDefaultPipeline function def ExtendDefaultPipeline(renderview, coprocessor, datadescription, script_args): as fourth argument.
Default value: ""
TOML config file:
[visualization]
pv_insitu_pipelinearguments = ""
Definition at line 343 of file param.h.
◆ random_seed
| uint64_t bdm::Param::random_seed = 4357 |
Set random number seed.
The pseudo random number generator (prng) of each thread will be initialized as follows: prng[tid].SetSeed(random_seed * (tid + 1));
Default value: 4357
TOML config file:
[simulation]
random_seed = 4357
Definition at line 90 of file param.h.
◆ registered_groups_
◆ remove_output_dir_contents
| bool bdm::Param::remove_output_dir_contents = true |
If set to true (default), BioDynaMo will automatically delete all contents inside Param::output_dir at the beginning of the simulation. Use with caution in combination with Param::output_dir. If you do not want to delete the content, set this parameter to false. BioDynaMo then organizes your simulation outputs in additional subfolders labelled with the date-time of your simulation YYYY-MM-DD-HH:MM:SS. Note that you will inevitably use more disk space with this option.
Definition at line 149 of file param.h.
◆ restore_file
| std::string bdm::Param::restore_file = "" |
File name to restore simulation from
Path is relative to working directory.
Default value: "" (no restore will be made)
TOML config file:
[simulation]
restore_file = <path>/<filename>.root
Command line argument: -r, --restore
Definition at line 169 of file param.h.
◆ root_visualization
| bool bdm::Param::root_visualization = false |
Use ROOT for enable visualization.
Default value: false
TOML config file:
[visualization]
root = false
Definition at line 320 of file param.h.
◆ scheduling_batch_size
| uint64_t bdm::Param::scheduling_batch_size = 1000 |
Batch size used by the Scheduler to iterate over agents
Default value: 1000
TOML config file:
[performance]
scheduling_batch_size = 1000
Definition at line 437 of file param.h.
◆ show_simulation_step
| uint64_t bdm::Param::show_simulation_step = 0 |
Display the simulation step in the terminal output with a defined frequency.\nThe value 0 shows no output, a value of 1 prints all steps, a value of 2 prints every second step, and so on.
Default value: 0
TOML config file: [development] show_simulation_step = 0
Definition at line 595 of file param.h.
◆ simulation_max_displacement
| real_t bdm::Param::simulation_max_displacement = 3.0 |
Maximum jump that a point mass can do in one time step. Useful to stabilize the simulation
Default value: 3.0
TOML config file:
[simulation]
max_displacement = 3.0
Definition at line 194 of file param.h.
◆ simulation_time_step
| real_t bdm::Param::simulation_time_step = 0.01 |
Time between two simulation steps, in hours. Default value: 0.01
TOML config file:
[simulation]
time_step = 0.0125
Definition at line 185 of file param.h.
◆ statistics
| bool bdm::Param::statistics = false |
Statistics of profiling data; keeps track of the execution time of each operation at every timestep.
If set to true it prints simulation data at the end of the simulation to std::cout and a file.
Default Value: false
TOML config file:
[development]
statistics = false
Definition at line 568 of file param.h.
◆ thread_safety_mechanism
Initial value:=
ThreadSafetyMechanism::kUserSpecified
Select the thread-safety mechanism.
Possible values are: none, user-specified, automatic.
TOML config file:
[simulation]
thread_safety_mechanism = "none"
Definition at line 281 of file param.h.
◆ unibn_bucketsize
| uint32_t bdm::Param::unibn_bucketsize = 16 |
◆ unschedule_default_operations
| std::vector<std::string> bdm::Param::unschedule_default_operations |
List of default operation names that should not be scheduled by default Default value: {}
TOML config file:
[simulation]
unschedule_default_operations = ["mechanical forces", "load
balancing"]
Definition at line 99 of file param.h.
◆ use_bdm_mem_mgr
| bool bdm::Param::use_bdm_mem_mgr = true |
Default value: true
TOML config file:
[performance]
use_bdm_mem_mgr = true
Definition at line 487 of file param.h.
◆ use_progress_bar
| bool bdm::Param::use_progress_bar = false |
Use a progress bar to visualize the simulation progress. The progress bar also gives an estimate of the remaining simulation time assuming that the following simulations steps are as computationally expensive as the previous ones. It is not recommended to use the ProgressBar when you write information to std::cout in Simulate() because the ProgressBar uses '\r' in its print statements. Default value: false
TOML config file: [development] use_progress_bar = false
Definition at line 607 of file param.h.
◆ visualization_compress_pv_files
| bool bdm::Param::visualization_compress_pv_files = true |
Specifies if the ParView files that are generated in export mode should be compressed.
Default value: true
TOML config file:
[visualization]
export = true
compress_pv_files = true
Definition at line 427 of file param.h.
◆ visualization_engine
| std::string bdm::Param::visualization_engine = "paraview" |
Name of the visualization engine to use for visualizaing BioDynaMo simulations
Default value: "paraview"
TOML config file:
[visualization]
adaptor = <name_of_adaptor>
Definition at line 293 of file param.h.
◆ visualization_export_generate_pvsm
| bool bdm::Param::visualization_export_generate_pvsm = true |
If export_visualization is set to true, this parameter specifies if the ParaView pvsm file will be generated!
Default value: true
TOML config file:
[visualization]
export_generate_pvsm = true
Definition at line 362 of file param.h.
◆ visualization_interval
| uint32_t bdm::Param::visualization_interval = 1 |
If export_visualization is set to true, this parameter specifies how often it should be exported. 1 = every timestep, 10: every 10 time steps.
Default value: 1
TOML config file:
[visualization]
interval = 1
Definition at line 353 of file param.h.
◆ visualize_agents
| std::map<std::string, std::set<std::string> > bdm::Param::visualize_agents |
JSON_object.
Specifies which agents should be visualized.
Every agent defines the minimum set of data members which are required to visualize it. (e.g. Cell: position_ and diameter_).
With this parameter it is also possible to extend the number of data members that are sent to the visualization engine. Default value: empty (no agent will be visualized)
NB: This data member is not backed up, due to a ROOT error. TOML config file:
[visualization]
# turn on insitu or export
export = true
[[visualize_agent]]
name = "Cell"
# the following entry is optional
additional_data_members = [ "density_" ]
# The former block can be repeated for further agents
[[visualize_agent]]
name = "Neurite"
Definition at line 386 of file param.h.
◆ visualize_diffusion
Specifies for which substances extracellular diffusion should be visualized.
Default value: empty (no diffusion will be visualized)
TOML config file:
[visualization]
# turn on insitu or export
export = true
[[visualize_diffusion]]
# Name of the substance
name = "Na"
# the following two entries are optional
# default value for concentration is true
concentration = true
# default value for gradient is false
gradient = false
# The former block can be repeated for further substances
[[visualize_diffusion]]
name = "K"
# default values: concentration = true and gradient = false
Definition at line 416 of file param.h.
The documentation for this struct was generated from the following files:
