Parameters | |
| num_phys_regions <Int> | |
| Description | The number of physics regions. FIELD_COUNT_LEGACY |
| Default value | (Int)(0) |
| Validation | Value must be greater than (Int)(0) |
| Description | Array containing the defined physics regions. |
Parameters | |
| ptype <Int> | |
| Description | Defines the type of physics. |
| Default value | (Int)(0) |
| Validation |
Possible values are
|
| required parameter: |
|
| name <String> | |
| Description | Symbolic name for the physics region |
| Default value | (String)("") |
| required parameter: |
|
| num_IDs <Int> | |
| Description | Defines the number of IDs (equivalent to element tags) listed under 'ID'. FIELD_COUNT_LEGACY |
| Default value | (Int)(0) |
| required parameter: |
|
| ID <Int> | |
| Description | Define the set of tags forming a mesh region. Notation supports lists and ranges such as 100:200,203,300:2:400. Indexed assignments remain supported for compatibility. |
| Default value | (Int)(0) |
| required parameters: |
|
Parameters | |
| num_gregions <Int> | |
| Description | Defines the total number of regions with respectively different conductivity settings. FIELD_COUNT_LEGACY |
| Default value | (Int)(1) |
| Validation | Value must be greater than (Int)(1) |
| Description | Sets the conductivity for different regions (or conduction velocities when using the DREAM). The array index allows enumeration of all gregions. |
Parameters | |
| g_mult <Float> | |
| Description | Defines the factor by which all conductivities in the region should be multiplied (after all other modifications are performed). |
| Default value | (Float)(1.0) |
| Validation | Value must be greater than (Float)(0) |
| required parameter: |
|
| g_il <Double> | |
| Description | Defines the intracellular conductivity along the fiber direction (longitudinal). |
| Unit | S/m |
| Default value | (Double)(0.174) |
| Validation | Value must be greater than (Double)(0) |
| required parameter: |
|
| g_el <Double> | |
| Description | Defines the extracellular conductivity along the fiber direction (longitudinal). |
| Unit | S/m |
| Default value | (Double)(0.625) |
| Validation | Value must be greater than (Double)(0) |
| required parameter: |
|
| g_it <Double> | |
| Description | Defines the intracellular conductivity in sheet direction (transversal). |
| Unit | S/m |
| Default value | (Double)(0.019) |
| Validation | Value must be greater than (Double)(0) |
| required parameter: |
|
| g_et <Double> | |
| Description | Defines the extracellular conductivity in sheet direction (transversal). |
| Unit | S/m |
| Default value | (Double)(0.236) |
| Validation | Value must be greater than (Double)(0) |
| required parameter: |
|
| g_in <Double> | |
| Description | Defines the intracellular conductivity in the sheet-normal direction (normal). |
| Unit | S/m |
| Default value | (Double)(0.019) |
| Validation | Value must be greater than (Double)(0) |
| required parameter: |
|
| g_en <Double> | |
| Description | Defines the extracellular conductivity in the sheet-normal direction (normal). |
| Unit | S/m |
| Default value | (Double)(0.236) |
| Validation | Value must be greater than (Double)(0) |
| required parameter: |
|
| g_bath <Double> | |
| Description | Defines the isotropic conductivity for non-myocardium domain, e.g blood. The absence of anisotropy is assumed for this region. If anisotropy is required use a negative tag for the mesh elements in the .elem file and set fibre direction in the .lon file. |
| Unit | S/m |
| Default value | (Double)(1.) |
| Validation | Value must be greater than (Double)(0) |
| required parameter: |
|
| name <String> | |
| Description | Symbolic description of this conductive region (e.g. bath, cavity etc.) |
| Default value | (String)("") |
| required parameter: |
|
| num_IDs <Int> | |
| Description | Shows how many model regions use this conductivity setting. FIELD_COUNT_LEGACY |
| Default value | (Int)(0) |
| required parameter: |
|
| ID <Int> | |
| Description | Specify the set of model regions (equivalent to mesh element tags, non-negative) using this conductivity setting. Notation supports lists and ranges such as 100:200,203,300:2:400. Indexed assignments remain supported for compatibility. |
| Default value | (Int)(-1) |
| required parameters: |
|
| Description | Specify the conduction velocities for the Diffusion Reaction Eikonal Alternant Model. |
Parameters | |
| vel_l <Double> | |
| Description | Defines the conduction velocity along the fiber direction (longitudinal) for the eikonal model |
| Unit | mm/s |
| Default value | (Double)(1000) |
| Validation | Value must be greater than (Double)(0) |
| required parameter: |
|
| vel_t <Double> | |
| Description | Defines the transversal conduction velocity for the eikonal model. |
| Unit | mm/s |
| Default value | (Double)(600) |
| Validation | Value must be greater than (Double)(0) |
| required parameter: |
|
| vel_n <Double> | |
| Description | Defines the normal conduction velocity for the eikonal model. |
| Unit | mm/s |
| Default value | (Double)(400) |
| Validation | Value must be greater than (Double)(0) |
| required parameter: |
|
Parameters | |
| gi_scale_vec <RFile> | |
| Description | Path to element-wise intracellular conductivity scaling file. Supports n=1 (one scalar per element) and n=3 (sl st sn, one triplet per element in the fiber frame). Format: optional header line containing n (1 or 3), followed by g_numelem lines each with n whitespace-separated floats. If no header is present, n is inferred from the number of values on the first data line. For n=3, sl/st/sn scale eVals[0..2] in the fiber/sheet/normal frame; bath elements (no fiber) are scaled isotropically using sl. Note (monodomain): with bidm_eqv_mono=1 (default) the intra grid uses the effective conductivity D_eff = sigma_i*sigma_e/(sigma_i+sigma_e); gi_scale_vec then scales D_eff directly, not sigma_i alone. |
| Default value | (RFile)("") |
Parameters | |
| ge_scale_vec <RFile> | |
| Description | Path to element-wise extracellular conductivity scaling file. Supports n=1 (one scalar per element) and n=3 (sl st sn, one triplet per element in the fiber frame). Format: optional header line containing n (1 or 3), followed by g_numelem lines each with n whitespace-separated floats. If no header is present, n is inferred from the number of values on the first data line. For n=3, sl/st/sn scale eVals[0..2] in the fiber/sheet/normal frame; bath elements (no fiber) are scaled isotropically using sl. Note (bidomain): the extracellular stiffness matrix is assembled with the bulk conductivity tensor (sigma_i + sigma_e). ge_scale_vec therefore scales this sum, not sigma_e alone. The intracellular stiffness (parabolic equation) is unaffected. Note (monodomain): the extracellular grid is not initialised for monodomain simulations; ge_scale_vec has no effect. Use gi_scale_vec instead. |
| Default value | (RFile)("") |
Parameters | |
| num_imp_regions <Int> | |
| Description | Number of different region definitions. FIELD_COUNT_LEGACY |
| Default value | (Int)(1) |
| Validation | Value must be greater than (Int)(1) |
| Description | Sets the ionic model for different regions. The array index allows enumeration of all imp_region[]. |
Parameters | |
| im <String> | |
| Description | Defines the ionic model to be used in the simulation. Query for available ionic models by calling 'bench' with the command list-imps. |
| Default value | (String)(TO_STRING(LuoRudy91)) |
| required parameter: |
|
| im_sv_init <RFile> | |
| Description | Name of the file containing the initial of state variable values. |
| Default value | (RFile)("") |
| required parameter: |
|
| plugins <String> | |
| Description | Specify a colon separated list of plug-ins to use with the ionic model. Query for available plug-ins by calling 'bench --plugin-outputs'. |
| Default value | (String)("") |
| required parameter: |
|
| name <String> | |
| Description | Defines the symbolic name of region. This helps with structuring extensive parameter lists and makes them more human readable. |
| Default value | (String)(strncmp(TO_STRING([[Father]]),TO_STRING(PurkIon),7)? TO_STRING(Myocardium):TO_STRING(Purkinje)) |
| required parameter: |
|
| num_IDs <Int> | |
| Description | Number of elements tags listed in 'imp_region[].ID[]'. FIELD_COUNT_LEGACY |
| Default value | (Int)(0) |
| required parameter: |
|
| ID <Int> | |
| Description | Set of non-negative element tags associated with this model region. Notation supports lists and ranges such as 100:200,203,300:2:400. Indexed assignments remain supported for compatibility. |
| Default value | (Int)(-1) |
| required parameters: |
|
| im_param <String> | |
| Description | Specify a comma separated list of changes from default values, e.g. 'APDshorten*4,Gks*1.29,...'. |
| Default value | (String)(strcmp([[Father]].im,TO_STRING(DiFranNoble))? TO_STRING():TO_STRING(G_Na*3)) |
| required parameters: |
|
| im_sv_dumps <String> | |
| Description | Specify a comma separated list of state variables of an ionic model to be dumped into the simulation folder. Use bench --imp=XXX --imp-info to get a list of SVs for imp XXX. |
| Default value | (String)("") |
| required parameter: |
|
| plug_sv_dumps <String> | |
| Description | This produces a colon separated lists of state variables of a plugin to dump (use bench --imp=XXX --plug-in=YYY --imp-info to get a list of SVs for imp XXX and plug-in YYY) |
| Default value | (String)("") |
| required parameter: |
|
| plug_param <String> | |
| Description | User can modify the values for various ionic model parameters. Every PARAMETER=VALUE modification needs to be separated with a comma. |
| Default value | (String)("") |
| required parameter: |
|
| volFrac <Float> | |
| Description | Defines the portion of the volume occupied by cells. |
| Default value | (Float)(1.) |
| Validation | Value must be between (Float)(0) and (Float)(1) |
| required parameter: |
|
| cellSurfVolRatio <Float> | |
| Description | Defines the default single cell surface-to-volume-ratio used if it is not specified by the ionic model plugin (IMP). |
| Unit | um^-1 |
| Default value | (Float)(0.14) |
| Validation | Value must be greater than (Float)(0) |
| required parameter: |
|
| Description | Settings for IMP specific CV restitution and diffusion current approximation used in the DREAM. |
Parameters | |
| Description | Specify CV restitution properties for the eikonal model using the DREAM. Default parameters are set for healthy Courtemanche IMP model. |
Parameters | |
| rho <Double> | |
| Description | Defines the parameter rho of the CV restitution formula: 'v_ref * (1 - rho * exp(-log(rho)/psi * (DI + kappa))), if DI > theta' |
| Default value | (Double)(811) |
| Validation | Value must be greater than (Double)(0) |
| required parameter: |
|
| kappa <Double> | |
| Description | Defines the parameter kappa of the CV restitution formula: 'v_ref * (1 - rho * exp(-log(rho)/psi * (DI + kappa))), if DI > theta' |
| Default value | (Double)(53) |
| Validation | Value must be greater than (Double)(-100000) |
| required parameter: |
|
| theta <Double> | |
| Description | Defines the parameter theta of the CV restitution formula: 'v_ref * (1 - rho * exp(-log(rho)/psi * (DI + kappa))), if DI > theta' |
| Default value | (Double)(137) |
| Validation | Value must be greater than (Double)(0) |
| required parameter: |
|
| psi <Double> | |
| Description | Defines the parameter psi of the CV restitution formula: 'v_ref * (1 - rho * exp(-log(rho)/psi * (DI + kappa))), if DI > theta' |
| Default value | (Double)(159) |
| Validation | Value must be greater than (Double)(0) |
| required parameter: |
|
| Description | Diffusion current approximation for RE+, RE-, and DREAM solution methods. |
Parameters | |
| model <Short> | |
| Description | Defines the equation used for diffusion current approximation in reaction-eikonal or DREAM models. - Foot current: '-A_F/tau_F exp((t - t_a)/tau_F) e_on e_off' - Triple Gaussian: 'sum_i (a_i exp(-((t - t_a) - b_i)^2/c_i^2)) i = 1,2,3' |
| Default value | (Short)(0) |
| Validation |
Possible values are
|
| required parameter: |
|
| A_F <Double> | |
| Description | Constant A_F of the foot current '-A_F/tau_F exp((t - t_a)/tau_F) e_on e_off' |
| Unit | mV |
| Default value | (Double)(0.91) |
| required parameter: |
|
| tau_F <Double> | |
| Description | Time constant tau_F of the foot current '-A_F/tau_F exp((t - t_a)/tau_F) e_on e_off' |
| Unit | ms |
| Default value | (Double)(0.25) |
| required parameter: |
|
| V_th <Double> | |
| Description | Intrinsic excitation threshold of the cellular dynamics model used for foot current |
| Unit | mV |
| Default value | (Double)(-30) |
| required parameter: |
|
| alpha_i <Double> | |
| Description | Parameter 'a_i' of triple Gaussian: 'sum_i (a_i exp(-(x - b_i)^2/c_i^2)) i = 1,2,3' |
| Unit | muA/cm^2 |
| Default value | (Double)(149.5)(Double)(41.2)(Double)(-192.2) |
| required parameter: |
|
| beta_i <Double> | |
| Description | Parameter 'b_i' of triple Gaussian: 'sum_i (a_i exp(-(x - b_i)^2/c_i^2)) i = 1,2,3' |
| Unit | ms |
| Default value | (Double)(2.383)(Double)(2.07)(Double)(2.56) |
| required parameter: |
|
| gamma_i <Double> | |
| Description | Parameter 'c_i' of triple Gaussian: 'sum_i (a_i exp(-(x - b_i)^2/c_i^2)) i = 1,2,3' |
| Unit | ms |
| Default value | (Double)(0.22)(Double)(0.56)(Double)(0.29) |
| required parameter: |
|
| Description | Sets the ionic model for different regions when using the EMI model. The array index allows enumeration of all imp_region_emi[]. |
Parameters | |
| im <String> | |
| Description | Defines the ionic model to be used in a simulation with the EMI physics. Query for available ionic models by calling 'bench --list-imps' |
| Default value | (String)(TO_STRING(LuoRudy91)) |
| required parameter: |
|
| im_sv_init <RFile> | |
| Description | Name of the file containing the initial of state variable values. |
| Default value | (RFile)("") |
| required parameter: |
|
| plugins <String> | |
| Description | Specify a colon separated list of plug-ins to use with the ionic model. Query for available plug-ins by calling 'bench --plugin-outputs'. |
| Default value | (String)("") |
| required parameter: |
|
| name <String> | |
| Description | Defines the symbolic name of region. This helps with structuring extensive parameter lists and makes them more human readable. |
| Default value | (String)(strncmp(TO_STRING([[Father]]),TO_STRING(PurkIon),7)? TO_STRING(Myocardium):TO_STRING(Purkinje)) |
| required parameter: |
|
| num_IDs <Int> | |
| Description | Number of elements tags listed in 'imp_region[].ID[]'. FIELD_COUNT_LEGACY |
| Default value | (Int)(0) |
| required parameter: |
|
| ID <String> | |
| Description | Array of element tags associated with this model region. |
| Default value | (String)(0) |
| required parameters: |
|
| im_param <String> | |
| Description | Specify a comma separated list of changes from default values, e.g. 'APDshorten*4,Gks*1.29,...'. |
| Default value | (String)(strcmp([[Father]].im,TO_STRING(DiFranNoble))? TO_STRING():TO_STRING(G_Na*3)) |
| required parameters: |
|
| im_sv_dumps <String> | |
| Description | Specify a comma separated list of state variables of an ionic model to be dumped into the simulation folder. Use bench --imp=XXX --imp-info to get a list of SVs for imp XXX. |
| Default value | (String)("") |
| required parameter: |
|
| plug_sv_dumps <String> | |
| Description | This produces a colon separated lists of state variables of a plugin to dump (use bench --imp=XXX --plug-in=YYY --imp-info to get a list of SVs for imp XXX and plug-in YYY) |
| Default value | (String)("") |
| required parameter: |
|
| plug_param <String> | |
| Description | User can modify the values for various ionic model parameters. Every PARAMETER=VALUE modification needs to be separated with a comma. |
| Default value | (String)("") |
| required parameter: |
|
Parameters | |
| dump_imp_region <Int> | |
| Description | flag controlling whether to dump nodal ionic region indices. output file name is 'imp_region.dat' |
| Default value | (Int)(0) |
| Validation |
Possible values are
|
Parameters | |
| num_external_imp <Int> | |
| Description | Defines the number of models to read in from external libraries. FIELD_COUNT_LEGACY |
| Default value | (Int)(0) |
Parameters | |
| external_imp <RFile> | |
| Description | Defines external imp modules to read into openCARP. Multiple imps can be grouped using a comma seperated list which can be used here. |
| required parameter: |
|
Parameters | |
| num_stim <Int> | |
| Description | Defines the number of stimuli. FIELD_COUNT_LEGACY |
| Default value | (Int)(0) |
| Validation | Value must be greater than (Int)(0) |
| Description | Array of stimuli |
Parameters | |
| name <String> | |
| Description | Definition of the label for a single electrode. !!!! The stimulus[] parameter was declared legacy. Please use stim[] !!!! |
| Default value | (String)("") |
| required parameter: |
|
| vtx_file <RFile> | |
| Description | File name allowing a vertex based electrode definition. Using a non-empty string switches to vertex-based definition and ignores other settings. For file format specifications check the first chapters of the openCARP manual. !!!! The stimulus[] parameter was declared legacy. Please use stim[] !!!! |
| Default value | (RFile)("") |
| required parameter: |
|
| dump_vtx_file <Short> | |
| Description | For volume based electrode definitions, vertices of this electrode are dumped to a file. The output file name is electrode_num.stim !!!! The stimulus[] parameter was declared legacy. Please use stim[] !!!! |
| Default value | (Short)(0) |
| Validation | Value must be between (Short)(0) and (Short)(1) |
| required parameter: |
|
| x0 <Float> | |
| Description | Lower x ordinate of electrode volume (xd defines the spatial electrode extension in x) !!!! The stimulus[] parameter was declared legacy. Please use stim[] !!!! |
| Unit | um |
| Default value | (Float)(0) |
| required parameter: |
|
| y0 <Float> | |
| Description | Lower y ordinate of electrode volume (yd defines the spatial electrode extension in y) !!!! The stimulus[] parameter was declared legacy. Please use stim[] !!!! |
| Unit | um |
| Default value | (Float)(0) |
| required parameter: |
|
| z0 <Float> | |
| Description | Lower z ordinate of electrode volume (zd defines the spatial electrode extension in z) !!!! The stimulus[] parameter was declared legacy. Please use stim[] !!!! |
| Unit | um |
| Default value | (Float)(0) |
| required parameter: |
|
| xd <Float> | |
| Description | x dimension of electrode volume. This will give the limits [x0,x0+xd]. To change this to [x0-xd/2,x0+xd/2] use stimulus.ctr_def !!!! The stimulus[] parameter was declared legacy. Please use stim[] !!!! |
| Unit | um |
| Default value | (Float)(100) |
| Validation | Value must be greater than (Float)(0) |
| required parameter: |
|
| yd <Float> | |
| Description | y dimension of electrode volume. This will give the limits [y0,y0+yd]. To change this to [y0-yd/2,y0+yd/2] use stimulus.ctr_def !!!! The stimulus[] parameter was declared legacy. Please use stim[] !!!! |
| Unit | um |
| Default value | (Float)(100) |
| Validation | Value must be greater than (Float)(0) |
| required parameter: |
|
| zd <Float> | |
| Description | z dimension of electrode volume. This will give the limits [z0,z0+zd]. To change this to [z0-zd/2,z0+zd/2] use stimulus.ctr_def !!!! The stimulus[] parameter was declared legacy. Please use stim[] !!!! |
| Unit | um |
| Default value | (Float)(100) |
| Validation | Value must be greater than (Float)(0) |
| required parameter: |
|
| ctr_def <Flag> | |
| Description | setting this to 1 yields limits in the form of [x0-xd/2,x0+xd/2] for x,y and z. Setting to 0 yields [x0,x0+xd] for x,y and z. !!!! The stimulus[] parameter was declared legacy. Please use stim[] !!!! |
| Default value | (Flag)(0) |
| required parameter: |
|
| geometry <Int> | |
| Description | Refers to a region ID to be used as geometry definition for the stimulus electrode !!!! The stimulus[] parameter was declared legacy. Please use stim[] !!!! |
| Default value | (Int)(-1) |
| required parameter: |
|
| start <Double> | |
| Description | Defines the start time when the stimulationpulse is introduced !!!! The stimulus[] parameter was declared legacy. Please use stim[] !!!! |
| Unit | ms |
| Default value | (Double)(0) |
| Validation | Value must be between (Double)(0) and (Double)(tend) |
| required parameters: |
|
| bcl <Float> | |
| Description | Defines the basic cycle length for repetitive stimulation. Duration must be smaller than bcl, as it specifies the duration of a single stimulation event. The full protocol duration is npls * bcl. This is derived automatically from the user input. !!!! The stimulus[] parameter was declared legacy. Please use stim[] !!!! |
| Unit | ms |
| Default value | (Float)(tend-[[Father]].start) |
| Validation | Value must be between (Float)(stimulus.duration) and (Float)(tend-stimulus.start) |
| required parameters: |
|
| npls <Int> | |
| Description | Defines the number of pulses in the stimulation protocol. The period of pulses can be set with bcl in ms. If set to 0, the stimulus will have a single instance. !!!! The stimulus[] parameter was declared legacy. Please use stim[] !!!! |
| Default value | (Int)(tend > 0 ? 1 : 0) |
| Validation | Value must be between (Int)(0) and (Int)(tend > 0 ? 1+tend/stimulus.bcl : 0) |
| required parameters: |
|
| duration <Float> | |
| Description | Defines the duration of one a single stimulation event. !!!! The stimulus[] parameter was declared legacy. Please use stim[] !!!! |
| Unit | ms |
| Default value | (Float)(tend-[[Father]].start) |
| Validation | Value must be between (Float)(0) and (Float)(tend-stimulus.start) |
| required parameters: |
|
| d1 <Float> | |
| Description | This parameter is used to introduce biphasic stimulation pulses. It specifies the duration of the first part of the pulse relative to the duration of the entire pulse (1.0 = monophasic). Further parameters to define biphasic stimuli are: stimulus.strength, stimulus.s2, stimulus.tau_edge and stimulus.tau_plateau !!!! The stimulus[] parameter was declared legacy. Please use stim[] !!!! |
| Default value | (Float)(1.0) |
| Validation | Value must be between (Float)(0.) and (Float)(1.0) |
| required parameter: |
|
| strength <Float> | |
| Description | Defines strength of prescribed stimulation. Strength is defined as amplitude of signal. If dealing with currents it is defined as uA/volume. If dealing with voltages it is defined as mV. To create a stimulation the minimum requirement is a given stimulus.duration and stimulus.strength. This creates a monophasic stimulus. For biphasic stimuli check stimulus.s2 and stimulus.d1. For more advanced pulsesignals introduce them using a pulse file with stimulus.pulse_file !!!! The stimulus[] parameter was declared legacy. Please use stim[] !!!! |
| Unit | uA/cm^2(2D current), uA/cm^3(3D current), or mV |
| Default value | (Float)(0.) |
| required parameter: |
|
| s2 <Float> | |
| Description | This value is only used for defining a biphasic pulse. This value is a relative value and defines the stimulus strength of the trailing pulse (after zero crossing) relative to leading pulse (from start to zero crossing). Giving the value 0 will result in a flip of polarity Other important parameters for stimulus form definition are: stimulus.tau_edge, stimulus.tau_plateau, stimulus.strength, stimulus.duration !!!! The stimulus[] parameter was declared legacy. Please use stim[] !!!! |
| Default value | (Float)(0) |
| Validation | Value must be between (Float)(0) and (Float)(10) |
| required parameter: |
|
| tau_edge <Float> | |
| Description | Defines the time constant governing leading and trailing edge of pulse. The formulation used resembles the equation: Amp * (1 - exp( -t/tau_edge)) * exp( -t/tau_plateau ). A larger tau_edge will result in a fast drop, while a smaller tau_edge will have a longer exponentialy decreasing flank. Other important parameters for stimulus form definition are: stimulus.tau_edge, stimulus.tau_plateau, stimulus.strength, stimulus.duration !!!! The stimulus[] parameter was declared legacy. Please use stim[] !!!! |
| Unit | ms |
| Default value | (Float)(0.01) |
| Validation | Value must be between (Float)(0.) and (Float)(1000) |
| required parameter: |
|
| tau_plateau <Float> | |
| Description | Defines a time constant governing plateau of pulse (>10^5 is infinite) A larger tau_plateau will result in a longer plateauphase. Other important parameters for stimulus form definition are: stimulus.tau_edge, stimulus.tau_plateau, stimulus.strength, stimulus.duration !!!! The stimulus[] parameter was declared legacy. Please use stim[] !!!! |
| Unit | ms |
| Default value | (Float)(1000.) |
| Validation | Value must be between (Float)(0.1) and (Float)(1000000.) |
| required parameter: |
|
| bias <Float> | |
| Description | Defines a constant term which is added to the stimuluspulse. !!!! The stimulus[] parameter was declared legacy. Please use stim[] !!!! |
| Default value | (Float)(0.0) |
| required parameter: |
|
| stimtype <Short> | |
| Description | Defines the stimulus type. Closed loop stimuli return to ground (0 mV) when expired. Open loop stimuli are removed entirely when expired. !!!! The stimulus[] parameter was declared legacy. Please use stim[] !!!! |
| Default value | (Short)(0) |
| Validation |
Possible values are
|
| required parameter: |
|
| balance <Int> | |
| Description | Defines whether the electrode is balancing another electrode. The balance value is interpreted as the electrode index to balance. The waveform is mirrored, but with opposite polarity. If the balance value is -1, no balancing is applied. !!!! The stimulus[] parameter was declared legacy. Please use stim[] !!!! |
| Default value | (Int)(-1) |
| Validation | Value must be between (Int)(-1) and (Int)(num_stim-1) |
| required parameters: |
|
| total_current <Short> | |
| Description | Treat strengths as total current (uA) and not density !!!! The stimulus[] parameter was declared legacy. Please use stim[] !!!! |
| Default value | (Short)(0) |
| Validation | Value must be between (Short)(0) and (Short)(1) |
| required parameter: |
|
| pulse_file <RFile> | |
| Description | Reads in pulse definition from an external file. For file format specifications check the first chapters of the openCARP manual. !!!! The stimulus[] parameter was declared legacy. Please use stim[] !!!! |
| Default value | (RFile)("") |
| required parameter: |
|
| data_file <RFile> | |
| Description | Stimulus dependent auxiliary data. Used for presribed takeoff and prescribed phie. !!!! The stimulus[] parameter was declared legacy. Please use stim[] !!!! |
| Default value | (RFile)("") |
| required parameter: |
|
| vtx_fcn <Short> | |
| Description | Set true to specify stimulation strengths on a nodal basis. The specific values need to be provided in the stimulus.vtx_file. For file format specifications check the first chapters of the openCARP manual. !!!! The stimulus[] parameter was declared legacy. Please use stim[] !!!! |
| Default value | (Short)(0) |
| required parameter: |
|
| Description | Definition of stimuli |
Parameters | |
| name <String> | |
| Description | Definition of the label for a single electrode |
| Default value | (String)("") |
| required parameter: |
|
| Description | Definition of stimulation pulse |
Parameters | |
| name <String> | |
| Description | Definition of the Label for the prescribed pulse waveform |
| Default value | (String)("") |
| required parameter: |
|
| shape <Short> | |
| Description | Defines the shape of the prescribed pulse if an implemented pulseform is chosen (see choices below). To impose a manually created stimulus use the pulse.file functionality. By default, the pulse shape is defined as a monophasic pulse of square-like shape of a certain duration and strength. There are two time constants: - tau_edge, governs the leading and trailing edges of the pulse. - tau_plateau, governs the plateau phase. By default, these time constants are set to yield essentially a square-like pulse shape, but can be easily adjusted to generate truncated exponential-like pulses. Biphasic shapes are specified by two additional parameters, the duration of the first part of the pulse relative to the duration of the entire pulse (specified by pulse.d1 in range of [0,1] ), and the strength of the second part of the pulse relative to the strength of the first part (specified by pulse.s2 in range of [0,1] ). To create a stimulation the minimum requirement is a given ptcl.duration and pulse.strength |
| Default value | (Short)(1) |
| Validation |
Possible values are
|
| required parameter: |
|
| file <RFile> | |
| Description | Reads in pulse definition from external file. Strength of external pulse shape definition can be adjusted with pulse.strength. For file format specifications check the first chapters of the openCARP manual. |
| Default value | (RFile)("") |
| required parameter: |
|
| strength <Float> | |
| Description | Defines strength of prescribed stimulation. Strength is defined as amplitude of signal. If dealing with currents it is defined as uA/volume. If dealing with voltages it is defined as mV. To create a stimulation the minimum requirement is a given ptcl.duration and pulse.strength |
| Unit | uA/cm^2(2D current), uA/cm^3(3D current), or mV |
| Default value | (Float)(0.) |
| required parameter: |
|
| d1 <Float> | |
| Description | This parameter is used to introduce biphasic stimulation pulses. It specifies the duration of the first part of the pulse relative to the duration of the entire pulse (1.0 = monophasic). Further parameters to define biphasic stimuli are: pulse.s2, pulse.tau_edge, pulse.tau_plateau, pulse.strength, pulse.bias, ptcl.duration |
| Default value | (Float)(1.0) |
| Validation | Value must be between (Float)(0.) and (Float)(1.0) |
| required parameter: |
|
| s2 <Float> | |
| Description | This value is only used for defining a biphasic pulse. This value is a relative value and defines the stimulus strength of the trailing pulse (after 0 crossing) relative to leading pulse (from start to 0 crossing). Giving the value 0 will result in a flip of polarity. Further parameters to define biphasic stimuli are: pulse.d1, pulse.tau_edge, pulse.tau_plateau, pulse.strength, pulse.bias, ptcl.duration |
| Default value | (Float)(0.) |
| Validation | Value must be between (Float)(0) and (Float)(10) |
| required parameter: |
|
| tau_edge <Float> | |
| Description | Defines the time constant governing leading and trailing edge of pulse. The formulation used resembles the equation: Amp * (1 - exp( -t/tau_edge)) * exp( -t/tau_plateau ). A larger tau_edge will result in a fast drop, while a smaller tau_edge will have a longer exponentialy decreasing flank. Further parameters to define biphasic stimuli are: pulse.d1, pulse.s2, pulse.tau_plateau, pulse.strength, pulse.bias, ptcl.duration |
| Unit | ms |
| Default value | (Float)(0.01) |
| Validation | Value must be between (Float)(0.) and (Float)(1000) |
| required parameter: |
|
| tau_plateau <Float> | |
| Description | Defines a time constant governing plateau of pulse (>10^5 is infinite). A larger tau_plateau will result in a longer plateauphase. Further parameters to define biphasic stimuli are: pulse.d1, pulse.s2, pulse.tau_edge, pulse.strength, pulse.bias, ptcl.duration |
| Unit | ms |
| Default value | (Float)(1000.) |
| Validation | Value must be between (Float)(0.1) and (Float)(1000000.) |
| required parameter: |
|
| bias <Float> | |
| Description | Defines a constant term which is added to the stimulus pulse.shape = 1. |
| Default value | (Float)(0.) |
| required parameter: |
|
| trig <Float> | |
| Description | Defines the time relative to ptcl.start at which the square wave is triggered (pulse.shape = 0). |
| Unit | ms |
| Default value | (Float)(0.0) |
| Validation | Value must be greater than (Float)(0.) |
| required parameter: |
|
| phase <Float> | |
| Description | Defines the phase shift of the sine wave when used with pulse.shape = 2. Phase shift is calculated by `pulse.phase/180*PI`. |
| Default value | (Float)(0.) |
| Validation | Value must be between (Float)(0.) and (Float)(2*3.1415926) |
| required parameter: |
|
| freq <Float> | |
| Description | Defines the frequency (not angular frequency!) of the sine wave when used with pulse.shape = 2. |
| Unit | mHz |
| Default value | (Float)(1.) |
| Validation | Value must be greater than (Float)(0.00001) |
| required parameter: |
|
| dumpTrace <Short> | |
| Description | Can be enabled to write out trace data of the stimuli pulse wave. |
| Default value | (Short)(0) |
| Validation | Value must be between (Short)(0) and (Short)(1) |
| required parameter: |
|
| Description | Definition of stimulation protocol |
Parameters | |
| name <String> | |
| Description | Label of protocol used (S1-S2, restitution, etc). This helps with structuring extensive parameter lists and makes them more human readable. |
| Default value | (String)("") |
| required parameter: |
|
| start <Double> | |
| Description | Defines the start time of the stimulation protocol |
| Unit | ms |
| Default value | (Double)(0) |
| Validation | Value must be between (Double)(0) and (Double)(tend) |
| required parameters: |
|
| duration <Float> | |
| Description | Defines the duration of one a single stimulation event. |
| Unit | ms |
| Default value | (Float)(tend-[[Father]].start) |
| Validation | Value must be between (Float)(0) and (Float)(tend-stim.start) |
| required parameters: |
|
| npls <Int> | |
| Description | Defines the number of pulses in the stimulation protocol. The period of pulses can be set with bcl in ms.If set to 0, the stimulus will have a single instance. |
| Default value | (Int)(tend > 0 ? 1 : 0) |
| Validation | Value must be greater than (Int)(0) |
| required parameters: |
|
| bcl <Float> | |
| Description | Defines the basic cycle length for repetitive stimulation. protocol.duration must be smaller than protocol.bcl, as it specifies the duration of a single stimulation event.The full protocol duration is protocol.npls * protocol.bcl. This is derived automatically from the user input. |
| Unit | ms |
| Default value | (Float)(tend-[[Father]].start) |
| Validation | Value must be between (Float)(stim.duration) and (Float)(tend-stim.start) |
| required parameters: |
|
| stimlist <String> | |
| Description | List of activation times (float), defining the stim protocol. Entries are separated by a comma (,). The list should be surrounded by quotes. An activation time can also be expressed as an increment to the previous activation, by starting with a '+', e.g.: '0,+240' |
| Unit | ms |
| Default value | (String)("") |
| required parameter: |
|
| Description | Definition of electrode geometry |
Parameters | |
| geomID <Int> | |
| Description | region ID defining an electrode's geometry, standard block defs are used if set to -1. |
| Default value | (Int)(-1) |
| required parameter: |
|
| domain <Int> | |
| Description | tissue domains affected |
| Default value | (Int)(1) |
| Validation |
Possible values are
|
| required parameter: |
|
| vtx_file <RFile> | |
| Description | File name allowing a vertex based electrode definition. Using a non-empty stringswitches to vertex-based definition and ignores other settings. For file format specifications check the first chapters of the openCARP manual. |
| Default value | (RFile)("") |
| required parameter: |
|
| vtx_fcn <Short> | |
| Description | Whether the electrode is spatially constant (homogenous) or varying (inhomogenous).Spatially inhomogenous stimulations need to be defined via a .vtx file that includes nodes and nodal scaling. |
| Default value | (Short)(0) |
| Validation |
Possible values are
|
| required parameter: |
|
| p0 <Float> | |
| Description | Used to describe the profile chosen in electrode.geom_type. - If sphere was chosen, this value describes the center of the sphere. - If box was chosen, this value describes the lower left corner of box. - If cylinder was chosen, this value describes the start of the cylinders main axis. - For sphere & cylinder the additional parameter electrode.radius is needed. - For box & cylinder the additional parameter electrode.p1 is needed. |
| Unit | micrometers |
| Default value | (Float)(0)(Float)(0)(Float)(0) |
| required parameter: |
|
| p1 <Float> | |
| Description | Used to describe the profile chosen in electrode.geom_type. - If sphere was chosen, this value is not necessary/ignored. Use TagRegion.radius instead. - If box was chosen, this value describes the upper right corner of box. - If cylinder was chosen, this value describes the end of the cylinders main axis. - For sphere & cylinder the additional parameter electrode.radius is needed. - For box & cylinder the additional parameter electrode.p0 is needed. |
| Unit | micrometers |
| Default value | (Float)(100)(Float)(100)(Float)(100) |
| required parameter: |
|
| radius <Float> | |
| Description | Used to describe the profile chosen in electrode.geom_type. - If sphere was chosen, this value is sets the radius of the sphere. - If box was chosen, this value is not necessary/ignored. Use TagRegion.p1 & TagRegion.p0 instead. - If cylinder was chosen, this value is sets the radius of the cylinder. |
| Unit | micrometers |
| Default value | (Float)(100) |
| required parameter: |
|
| geom_type <Int> | |
| Description | This value defines the geometry used for the electrode. For now only predefined geometries are supported. |
| Default value | (Int)(2) |
| Validation |
Possible values are
|
| required parameter: |
|
| dump_vtx_file <Short> | |
| Description | For volume based electrode definitions, vertices of this electrode are dumped to a file. |
| Default value | (Short)(0) |
| Validation | Value must be between (Short)(0) and (Short)(1) |
| required parameter: |
|
| Description | Definition of setup and wiring of stimulation circuit |
Parameters | |
| type <Short> | |
| Description | Defines the physics of the actual source used for stimulation and in some cases also the wiring of the electric stimulation circuit. |
| Default value | (Short)(0) |
| Validation |
Possible values are
|
| required parameter: |
|
| balance <Int> | |
| Description | Defines whether the electrode is balancing another electrode. The balance value is interpreted as the electrode index to balance. The waveform is mirrored, but with opposite polarity. The volume/surface current is balanced exactly independent of the specific element arrangement around the stimulus node(s). If the balance value is -1, no balancing is applied. |
| Default value | (Int)(-1) |
| Validation | Value must be between (Int)(-1) and (Int)(num_stim-1) |
| required parameters: |
|
| total_current <Short> | |
| Description | Treat strengths as total current (uA) |
| Default value | (Short)(0) |
| Validation | Value must be between (Short)(0) and (Short)(1) |
| required parameter: |
|
Parameters | |
| simID <String> | |
| Description | Defines the Simulation ID to generate output directory. A good practice is to include date and time of the simulation in the 'simID'to avoid overwriting simulations. If 'simID' already exists, e.g the directory was created in a previous run, the user needs to decide on how to proceed (overwrite, append, abort) the simulation. |
| Default value | (String)("OUTPUT_DIR") |
Parameters | |
| dt <Double> | |
| Description | Defines the time step size to solve the numeric equations for. Check the first chapters of the openCARP manual for a comprehensive explanation on how to choose 'dt'. |
| Unit | microseconds |
| Default value | (Double)(5.) |
| Validation | Value must be greater than (Double)(0.) |
Parameters | |
| tend <Double> | |
| Description | Defines the point in time when the simulation stops. To get a rough estimation for 'tend', multiply the number of stimulation pulses 'stimulation.npls' with the basic cycle length 'stimulation.bcl'. 'tend' then needs to be larger than 'stimulation.npls * stimulation.bcl' to cover your entire stimulation protocol. |
| Unit | ms |
| Default value | (Double)(100.) |
| Validation | Value must be greater than (Double)(dt/1000.) |
| required parameter: |
|
Parameters | |
| num_io_nodes <Int> | |
| Description | The number of nodes to dedicate to doing IO |
| Default value | (Int)(0) |
Parameters | |
| buildinfo <Flag> | |
| Description | (deprecated) the build info is now shown by default. hence this flag has no effect. |
Parameters | |
| output_level <Int> | |
| Description | Defines the level of verbosity [0, 10] to the terminal output. 0 is considered minimal feedback to the user on the terminal. |
| Default value | (Int)(1) |
| Validation | Value must be between (Int)(0) and (Int)(10) |
Parameters | |
| dump2MatLab <Flag> | |
| Description | Dumps stiffness and mass matrices, mappings and stimulation vectors to be used with MatLab to the simulation folder |
| Default value | (Flag)(0) |
Parameters | |
| dump_basename <String> | |
| Description | Defines the basename for dumped files. Different endings will be attached to specify different variables: - _Ki & _Kie ... for the intra- & extracellular stiffness matrices - _Mi & _Me ... for the intra- & extracellular mass matrices - _i2e & _e2i ... for the intracellular-to-extracellular and vice-versa mappings - _Itr & _Ie ... for the transmembrane- & extracellular currents |
| Default value | (String)("MatLabDump") |
Parameters | |
| vofile <WFile> | |
| Description | IGB formatted file of transmembrane voltages. |
| Default value | (WFile)("vm") |
Parameters | |
| phiefile <WFile> | |
| Description | IGB formatted file of extracellular potential (phi). |
| Default value | (WFile)("phie") |
Parameters | |
| phieifile <WFile> | |
| Description | IGB formatted file of extracellular potential (phie) on intracellular grid (only in presence of bath required). |
| Default value | (WFile)("phie_i") |
Parameters | |
| gridout_i <Int> | |
| Description | Defines if intracellular grid is outputted in simulation directory. Settings: 0=none, 1=surface, 2=volumetric mesh, 3=surface & volumetric mesh. |
| Default value | (Int)(0) |
| Validation | Value must be greater than (Int)(0) |
Parameters | |
| gridout_e <Int> | |
| Description | Defines if extracellular grid is outputted in simulation directory. Settings: 0=none, 1=surface, 2=volumetric mesh, 3=surface & volumetric mesh. |
| Default value | (Int)(0) |
| Validation | Value must be greater than (Int)(0) |
Parameters | |
| gridout_emi <Int> | |
| Description | Defines if EMI-generated grids are outputted in simulation directory. Settings: 0=none, 1=membrane surface mesh, 2=volumetric EMI mesh, 3=membrane surface & volumetric EMI mesh. |
| Default value | (Int)(3) |
| Validation | Value must be between (Int)(0) and (Int)(3) |
Parameters | |
| gridout_tags <String> | |
| Description | Set of region tags to include in output mesh and IGB output. An empty set outputs all IDs. Notation supports lists and ranges such as 100:200,203,300:2:400. Indexed assignments remain supported for compatibility. |
| Default value | (String)("") |
Parameters | |
| gridout_p <Int> | |
| Description | If not 0, writes partition index of each element as .dat file in simulation directory. |
| Default value | (Int)(0) |
Parameters | |
| dataout_i <Short> | |
| Description | Defines how intracellular grid data is outputted. |
| Default value | (Short)(2) |
| Validation |
Possible values are
|
Parameters | |
| dataout_i_vtx <RFile> | |
| Description | if option dataout_i == 3, intracellular output is restricted to the provided vertices. |
| Default value | (RFile)("") |
Parameters | |
| dataout_e <Short> | |
| Description | Defines how extracellular grid data is outputted. |
| Default value | (Short)(2) |
| Validation |
Possible values are
|
Parameters | |
| dataout_e_vtx <RFile> | |
| Description | if option dataout_e == 3, extracellular output is restricted to the provided vertices. |
| Default value | (RFile)("") |
Parameters | |
| spacedt <Double> | |
| Description | Defines the temporal interval to output data to files. It can only be as small as 'dt/1000'. For long simulations outputting every single calculated value, would yield terrabytes of data. So here you can reduce the outputted values. |
| Unit | ms |
| Default value | (Double)(3.) |
| Validation | Value must be between (Double)(dt/1000.) and (Double)(tend) |
| required parameters: |
|
Parameters | |
| timedt <Double> | |
| Description | Defines the temporal interval between progress updates made to the terminal. (For informational purposes only). |
| Unit | ms |
| Default value | (Double)(1.) |
| Validation | Value must be between (Double)(dt/1000.) and (Double)(tend) |
| required parameters: |
|
Parameters | |
| dump_data <Short> | |
| Description | Flag to dump auxiliary simulation data. Can be combined (summed) to dump multiple data entries. 0 = Turned off. 1 = Dump membrance currents as Iion.igb and Ic.igb [uA/cm^2] to the simulation folder. 2 = Dump volumetric current, i.e. Ki Vm, as Ivol.igb [uA] to the simulation folder. 4 = Dump activating current, i.e. Ki Phie_i, as Iact.igb [uA] to the simulation folder. |
| Default value | (Short)(0) |
| Validation | Value must be between (Short)(0) and (Short)(7) |
Parameters | |
| output_setup <Flag> | |
| Description | If set outputs all the parameters. |
| Default value | (Flag)(0) |
Parameters | |
| num_trace <Int> | |
| Description | Number of nodes at which to gather trace info. FIELD_COUNT_LEGACY |
| Default value | (Int)(0) |
Parameters | |
| trace_node <Int> | |
| Description | Nodes at which to gather trace information. |
| required parameter: |
|
Parameters | |
| tracedt <Double> | |
| Description | Time resolution to print out trace info. |
| Unit | ms |
| Default value | (Double)(timedt) |
| Validation | Value must be greater than (Double)(dt/1000.) |
| required parameters: |
|
Parameters | |
| dump_protocol <Short> | |
| Description | If set to 1, the overall stimulation protocol will be outputted as a trace file. |
| Default value | (Short)(0) |
| Validation | Value must be between (Short)(0) and (Short)(1) |
Parameters | |
| num_tsav <Int> | |
| Description | Defines the number of states to be saved. Each time instant of the simulation progression needs to be specified in 'tsav'. FIELD_COUNT_LEGACY |
| Default value | (Int)(0) |
| Validation | Value must be between (Int)(0) and (Int)(50) |
Parameters | |
| tsav <Double> | |
| Description | Defines the times at which to save the simulation state. Multiple saves for different times can be defined by adding the times to this array. |
| Unit | ms |
| Default value | (Double)(tend-dt/1000.) |
| Validation | Value must be between (Double)(0) and (Double)(num_tsav>1?tend:1.0e50) |
| required parameters: |
|
Parameters | |
| tsav_ext <WFile> | |
| Description | Defines the filename for each saved state file. For multiple save states of the simulation, add the names for all savetimes in respective order to this array. |
| Default value | (WFile)(opencarp::stringify(tsav[$Index])) |
| required parameters: |
|
Parameters | |
| write_statef <WFile> | |
| Description | Defines the basename of the output file in which to write a single saved state. Each saved state will have a timestamp appended to the basename. |
| Default value | (WFile)("state") |
Parameters | |
| start_statef <RFile> | |
| Description | Loads a statefile and continues the simulation from there. |
| Default value | (RFile)("") |
Parameters | |
| chkpt_start <Float> | |
| Description | Defines the start time to trigger interval-based checkpointing (saving of the simulation progress). |
| Unit | ms |
| Default value | (Float)(0) |
| Validation | Value must be between (Float)(0) and (Float)(tend) |
| required parameter: |
|
Parameters | |
| chkpt_intv <Float> | |
| Description | Defines the interval for checkpointing (saving of the simulation progress) in ms. 0 means no checkpointing. |
| Unit | ms |
| Default value | (Float)(0) |
| Validation | Value must be between (Float)(0) and (Float)(tend) |
| required parameter: |
|
Parameters | |
| chkpt_stop <Float> | |
| Description | Defines the time to stop interval-based checkpointing (saving of the simulation progress). |
| Unit | ms |
| Default value | (Float)(tend) |
| Validation | Value must be between (Float)(0) and (Float)(tend) |
| required parameter: |
|
Parameters | |
| num_adjustments <Int> | |
| Description | Size of the adjustment array. FIELD_COUNT_LEGACY |
| Default value | (Int)(0) |
| Validation | Value must be greater than (Int)(0) |
| Description | file of adjustments |
Parameters | |
| variable <String> | |
| Description | Defines the name of the variable that should be adjusted on initialization. The variable name should be defined as an external variable like 'Lambda', or an ionic model variable like 'LR1.tau_f_factor' in the cellmodel file. |
| Default value | (String)("") |
| required parameter: |
|
| file <RFile> | |
| Description | Defines the filename filled with nodal adjustments for the state variable |
| Default value | (RFile)("") |
| required parameter: |
|
| dump <Short> | |
| Description | Dump nodal adjustments for state variables for display on intra grid |
| Default value | (Short)(0) |
| Validation | Value must be between (Short)(0) and (Short)(1) |
| required parameter: |
|
Parameters | |
| num_gvecs <Int> | |
| Description | Specify the number of global state variable vector definitions. FIELD_COUNT_LEGACY |
| Default value | (Int)(0) |
| Description | Gives the global state variable vectors of each model region |
Parameters | |
| name <WFile> | |
| Description | Defines the name of the output file for the global state variable. |
| Default value | (WFile)("sv") |
| required parameter: |
|
| ID <String> | |
| Description | Defines the list of state variable names in a region, which are combined into a global vector. For example gvec[0].ID[0] = 'Cai' |
| Default value | (String)([[Father]].name) |
| required parameters: |
|
| units <String> | |
| Description | Units of the state variables to be written in the header of the ouput igb file. |
| Default value | (String)("") |
| required parameter: |
|
| imp <String> | |
| Description | If the state variable is defined in a plugin, specify the plugin name here. |
| Default value | (String)("") |
| required parameter: |
|
| bogus <Float> | |
| Description | Set to 1 if the state variable is not in a region. |
| Default value | (Float)(0) |
| required parameter: |
|
Parameters | |
| LAT_ID <String> | |
| Description | a variable |
| Default value | (String)("vm_act")(String)("phie_act")(String)("-thresh")(String)("-deriv") |
Parameters | |
| num_LATs <Int> | |
| Description | Defines the number of local activation measurements. FIELD_COUNT_LEGACY |
| Default value | (Int)(0) |
| Validation | Value must be greater than (Int)(0) |
Parameters | |
| prepacing_lats <RFile> | |
| Description | Tissue activation times to guide state set-up for prepacing |
| Default value | (RFile)("") |
Parameters | |
| prepacing_beats <Int> | |
| Description | Defines the number of beats to pre-pace using a single-cell model. Prepacing of a single cell is used to put the single-cell models into a preconditioned state. This state is then given all cells in a tissue simulation as a better initial starting point than a completly unstimulated cell |
| Default value | (Int)(0) |
Parameters | |
| prepacing_bcl <Float> | |
| Description | Sets the basic cycle length for the prepacing stimulus. |
Parameters | |
| prepacing_stimdur <Float> | |
| Description | Stimulation duration for single cells during prepacing. |
| Unit | ms |
| Default value | (Float)(1.0) |
Parameters | |
| prepacing_stimstr <Float> | |
| Description | Stimulation strength for single cells during prepacing. |
| Unit | uA/uF |
| Default value | (Float)(60.0) |
| Description | Array containing LATs. Index of array corresponds to LAT measurement. |
Parameters | |
| method <Int> | |
| Description | Describes the method used to determine the instant of local activation. Define the threshold using structure.threshold. Choose if you want to evaluate during the rising or falling slope of the signal using structure.mode. |
| Default value | (Int)(1) |
| Validation |
Possible values are
|
| required parameter: |
|
| threshold <Float> | |
| Description | Defines the crossing threshold (for method 1) or the derivative threshold (for method 2) |
| Default value | (Float)(-10) |
| required parameter: |
|
| mode <Short> | |
| Description | Toggles between detecting max derivative or positive(+) slope threshold crossing and detecting minimum derivative and negative(-) slope threshold crossing. |
| Default value | (Short)(0) |
| Validation |
Possible values are
|
| required parameter: |
|
| all <Int> | |
| Description | Defines that all activations should be detected (1) or only the first one (0). Detecting 'all' is the default. |
| Default value | (Int)(1) |
| Validation | Value must be between (Int)(0) and (Int)(1) |
| required parameter: |
|
| start <Float> | |
| Description | Activations earlier than this time (ms) are not recorded. 0 records all. |
| Default value | (Float)(0) |
| Validation | Value must be greater than (Float)(0) |
| required parameter: |
|
| measurand <Int> | |
| Description | Defines the quantity to measure, e.g. the signal (transmembrane voltage or extracellular potential) to use the thresholds on. |
| Default value | (Int)(0) |
| Validation |
Possible values are
|
| required parameter: |
|
| ID <WFile> | |
| Description | Defines the output filename. |
| Default value | (WFile)([[Father]].measurand ? LAT_ID[1] : LAT_ID[0]) |
| required parameters: |
|
Parameters | |
| t_sentinel <Float> | |
| Description | Sentinel checks for activations, based on LATs. If none are found, exits simulation, else continues. t_sentinel should always be >0 . t_sentinel describes the time sentinel is run for from the t_sentinel_start time. If during this time period no lats[] are detected, savequit() cleanly. |
| Default value | (Float)(-1) |
Parameters | |
| t_sentinel_start <Float> | |
| Description | Defines the time instant when checking for quiescence is started |
| Default value | (Float)(0) |
Parameters | |
| sentinel_ID <Int> | |
| Description | Sentinel will check the LAT ID specified here as a reference to quit or continue the simulation. |
| Default value | (Int)(-1) |
| Validation | Value must be smaller than (Int)(num_LATs-1) |
| required parameter: |
|
Parameters | |
| compute_APD <Flag> | |
| Description | Defines if the actionpotential duration should be computed - If is set to 1 = computes action potential durations - If is set to 0 = action potential durations are not calculated |
Parameters | |
| actthresh <Float> | |
| Description | Defines the threshold to determine if element was activated, e.g the threshold where an action potential was triggered. The magnitude is used from the signal to be thresholded. |
| Unit | mV |
| Default value | (Float)(30) |
Parameters | |
| recovery_thresh <Float> | |
| Description | Defines the threshold to determine if element wich was activated recovered back to its steadystate. The magnitude is used from the signal to be thresholded. |
| Unit | mV |
| Default value | (Float)(-60) |
| Description | Simulation setup for the Diffusion Reaction Eikonal Alternant Model solved using the cyclical fast iterative method. |
Parameters | |
| solve <Short> | |
| Description | Defines if the simulation is solved using the eikonal model, reaction-eikonal+ model, reaction-eikonal- model or DREAM. - Eikonal. Fast solver for activation times. - Reaction-eikonal+. Diffusion is taken into account. Depolarization is initiated by a foot current. Only available with parabolic solver. - Reaction-eikonal-. Diffusion is neglected. Depolarization is initiated by a foot current. Only available with parabolic solver. - Diffusion reaction eikonal alternant model (DREAM). Enables reactivation of nodes in the eikonal solver and supports reentries. |
| Default value | (Short)(2) |
| Validation |
Possible values are
|
| required parameter: |
|
| tau_s <Double> | |
| Description | Minimum allowed difference between min activation time and simulation time. |
| Default value | (Double)(10.0) |
| required parameter: |
|
| tau_inc <Double> | |
| Description | Maximum allowed increment of min activation time in every DREAM cycle. |
| Default value | (Double)(100.0) |
| required parameter: |
|
| tau_max <Double> | |
| Description | Maximum allowed difference of activation time values among nodes in the active list of fast iterative method. |
| Default value | (Double)(10.0) |
| required parameter: |
|
| repol_time_thresh <Double> | |
| Description | Threshold for annotating repolarization time when crossed with negative slope |
| Unit | mV |
| Default value | (Double)(-40) |
| required parameter: |
|
| Description | Settings for the (cyclical) fast iterative method. |
Parameters | |
| tol <Double> | |
| Description | Fast iterative method solver tolerance for eikonal problem. |
| Unit | ms |
| Default value | (Double)(0.1) |
| required parameter: |
|
| max_iter <Int> | |
| Description | Eikonal/RE: maximum number of FIM iterations. Larger, more complex meshes need more iterations. Otherwise, there might be non-activated nodes left. DREAM: maximum number of list iterations that each node is allowed to stay in the list per cycle. |
| Default value | (Int)(50) |
| required parameter: |
|
| max_addpt <Int> | |
| Description | Maximum number of times a node can be added to the list per cycle (DREAM only). |
| Default value | (Int)(50) |
| required parameter: |
|
| max_coh <Int> | |
| Description | Maximum number of allowed coherence iterations (DREAM only). |
| Default value | (Int)(5) |
| required parameter: |
|
| Description | Control data output for the DREAM model. |
Parameters | |
| atfile <WFile> | |
| Description | IGB formatted file of activation times. Updated only after every eikonal cycle, hence 'time steps' in the file should be interpreted as cycles. |
| Default value | (WFile)("act") |
| required parameter: |
|
| rtfile <WFile> | |
| Description | IGB formatted file of recovery times. Updated only after every eikonal cycle, hence 'time steps' in the file should be interpreted as cycles. |
| Default value | (WFile)("rpt") |
| required parameter: |
|
| idifffile <WFile> | |
| Description | IGB formatted file of approx. diffusion current (optional). Output is foot current or triple gaussian NOT actual diffusion. |
| Default value | (WFile)("") |
| required parameter: |
|
| debugNode <Int> | |
| Description | Log detailed solver data for specified node ID. Should only be used for debugging. |
| Default value | (Int)(-1) |
| required parameter: |
|
Parameters | |
| meshname <String> | |
| Description | Defines the basename for mesh files |
| Default value | (String)("project") |
Parameters | |
| numtagreg <Int> | |
| Description | Defines the number of regions to retag |
| Default value | (Int)(0) |
| Validation | Value must be greater than (Int)(0) |
| Description | Defines the regions to which to assign new tags |
Parameters | |
| tag <Int> | |
| Description | New tag for a region in the mesh. Each element in this region is re-assigned this tag. In general, each element in a mesh is designated as part of a region. Electrical or mechanical properties are assigned based on region definitions. |
| Default value | (Int)(321) |
| required parameter: |
|
| name <String> | |
| Description | Label for a region in the mesh. This helps with structuring extensive parameter lists and makes them more human readable. |
| Default value | (String)("") |
| required parameter: |
|
| type <Int> | |
| Description | Defines profile of region. 1-3 are predefined shapes while 4 can be used to create own region profile. |
| Default value | (Int)(1) |
| Validation |
Possible values are
|
| required parameter: |
|
| no_elem_split <Short> | |
| Description | Defines whether a mesh element needs to be fully enclosed by the tagreg.type definition to become part of this region. 1 = all nodes of each element need to be fully contained inside tagreg.type 0 = a single node of an element within tagreg.type is sufficient to become a member of this region |
| Default value | (Short)(0) |
| Validation | Value must be between (Short)(0) and (Short)(1) |
| required parameter: |
|
| elemfile <RFile> | |
| Description | Name of file with list of elements to be assigned to this region. The file needs the extension .regele with the format being the number of elements followed by one element number per line |
| Default value | (RFile)("") |
| required parameter: |
|
| p0 <Float> | |
| Description | Used to describe the profile chosen in tagregion.type in more detail. - If sphere was chosen, this value describes the center of the sphere. - If box was chosen, this value describes the lower left corner of the box. - If cylinder was chosen, this value describes the center of the cylinders' base. - For sphere & cylinder the additional parameter tagregion.radius is needed. - For box & cylinder the additional parameter tagregion.p1 is needed. |
| Unit | micrometers |
| Default value | (Float)(0)(Float)(0)(Float)(0) |
| required parameter: |
|
| p1 <Float> | |
| Description | Used to describe the profile chosen in tagregion.type in more detail. - If sphere was chosen, this value is not necessary/ignored. Use tagregion.radius instead. - If box was chosen, this value describes the upper right corner of the box. - If cylinder was chosen, this value describes the center of the cylinders' top. - For sphere & cylinder the additional parameter tagregion.radius is needed. - For box & cylinder the additional parameter tagregion.p0 is needed. |
| Unit | micrometers |
| required parameter: |
|
| radius <Float> | |
| Description | Used to describe the profile chosen in tagregion.type in more detail. - If sphere was chosen, this value is the radius of the sphere. - If box was chosen, this value is not necessary/ignored. Use tagregion.p0 & tagregion.p1 instead. - If cylinder was chosen, this value is the radius of the cylinder. |
| Unit | micrometers |
| Default value | (Float)(100) |
| required parameter: |
|
Parameters | |
| tagfile <RFile> | |
| Description | Optional ASCII file with one integer tag per element, in the same global element order as .elem. Format: n tag_1 ... tag_n When set, overrides the tags embedded in .elem before any dynamic retagging (numtagreg). The header n must match the mesh element count. |
| Default value | (RFile)("") |
Parameters | |
| retagfile <WFile> | |
| Description | Defines an output file storing the element labels after applying all 'dynamic' tagreg choices to the input mesh. |
| Default value | (WFile)("") |
Parameters | |
| ppID <String> | |
| Description | Defines the name of the output directory in post processing mode. - It comes into play when choosing 'experiment 4'. - If it is specified, it must not already exist. - A folder with the default name will be created, if it is not specified. |
| Default value | (String)("POSTPROC_DIR") |
Parameters | |
| experiment <Short> | |
| Description | Defines how the simulation will be solved and what will be outputted |
| Default value | (Short)(0) |
| Validation |
Possible values are
|
Parameters | |
| post_processing_opts <Short> | |
| Description | Post-processing Options, add up option numbers to use multiple options |
| Default value | (Short)(0) |
| Validation |
Possible values are
|
Parameters | |
| phie_rec_ptf <WFile> | |
| Description | Defines the basename for the phie recovery file. This file specifies the phie recovery points. Use the same convention and format as for the mesh points file (see the first chapters of the openCARP manual file format section). Provide the filename without extension. |
| Default value | (WFile)("") |
Parameters | |
| phie_recovery_file <WFile> | |
| Description | Defines the file name used to output recovered extracellular potentials. Output granularity is defined by 'spacedt'. |
| Default value | (WFile)("phie_recovery") |
Parameters | |
| lf_dir <String> | |
| Description | Directory in which the leadfields are stored. |
| Default value | (String)("") |
Parameters | |
| lf_vmfile <String> | |
| Description | Path to the transmembrane voltage file used for ECG calculation. |
| Default value | (String)("") |
Parameters | |
| ecg_timedt <Float> | |
| Description | Time resolution stride for ECG output. |
| Unit | ms |
| Default value | (Float)(1) |
Parameters | |
| bidomain <Short> | |
| Description | Defines if the simulation is solved using the monodomain, bidomain or pseudo-bidomain approach. - Monodomain model (less costly). Dervied from bidomain under the assumption that intracellular and extracellular tensors are related. - Bidomain model solves for both the intra- & extracellular space. - Pseudo-bidomain model (monodomain model with adjustments to account for bath loading effects). |
| Default value | (Short)(0) |
| Validation |
Possible values are
|
Parameters | |
| pstrat <Short> | |
| Description | Defines the partitioning strategy. |
| Default value | (Short)(2) |
| Validation |
Possible values are
|
Parameters | |
| renumbering <Short> | |
| Description | Algebraic node renumbering to reduce matrix bandwidth. Affects PETSc and Ginkgo backends. Option 1 is a reversed breadth-first (Cuthill-McKee style) ordering: it seeds at the first local node and visits neighbours in ascending index order. Clustering the nonzeros near the diagonal may improve cache locality of the sparse matrix-vector product, but the gain depends on mesh, backend and rank count: it is largest when the per-rank block is much larger than cache, and vanishes or reverses when the block is already cache resident. It also changes the ILU fill pattern, so the iteration count can move in either direction; It is off by default and worth benchmarking on your own setup before enabling. |
| Default value | (Short)(0) |
| Validation |
Possible values are
|
Parameters | |
| pstrat_imbalance <Float> | |
| Description | Amount of imbalance to tolerate in parmetis partitioning |
| Default value | (Float)(1.0001) |
Parameters | |
| ellip_solve <Short> | |
| Description | Defines the solving method for elliptic problems. - Direct is typically more accurate but memory consuming. - Iterative methods are more suitable for large problems. |
| Default value | (Short)(0) |
| Validation |
Possible values are
|
Parameters | |
| flavor <String> | |
| Description | String defining the backend to be used |
| Default value | (String)("petsc") |
Parameters | |
| ginkgo_exec <String> | |
| Description | Defines the hardware backend used by Ginkgo. |
| Default value | (String)("ref") |
| Validation |
Possible values are
|
Parameters | |
| device_id <Int> | |
| Description | Device ID used for the Ginkgo backend. |
| Default value | (Int)(0) |
| Validation | Value must be greater than (Int)(0) |
Parameters | |
| ellip_options_file <RFile> | |
| Description | File containing PETSc or Ginkgo options for elliptic solver. For all available solver options, refer to the documentation of the respective library. |
| Default value | (RFile)("") |
Parameters | |
| parab_solve <Short> | |
| Description | Defines the solution method for the parabolic problem |
| Default value | (Short)(1) |
| Validation |
Possible values are
|
Parameters | |
| parab_solve_emi <Short> | |
| Description | Defines the solution method for the EMI parabolic problem |
| Default value | (Short)(0) |
| Validation |
Possible values are
|
Parameters | |
| theta <Float> | |
| Description | Defines the weight given to solution at t(n+1) when using Crank-Nicolson (theta) method |
| Default value | (Float)(0.5) |
| Validation | Value must be between (Float)(0.1) and (Float)(0.99) |
Parameters | |
| parab_options_file <RFile> | |
| Description | File containing PETSc or Ginkgo options for parabolic solver. For all available solver options, refer to the documentation of the respective library. |
| Default value | (RFile)("") |
Parameters | |
| bidm_eqv_mono <Short> | |
| Description | Use monodomain conductivities that are equivalent to the bidomain. |
| Default value | (Short)(1) |
| Validation |
Possible values are
|
Parameters | |
| ode_fac <Short> | |
| Description | Defines the number of ode solves per global dt |
| Default value | (Short)(1) |
| Validation | Value must be between (Short)(1) and (Short)(10) |
Parameters | |
| extracell_monodomain_stim <Flag> | |
| Description | When bidomain mode is turned off, i.e. '-bidomain=0', set phi_e to be utterly determined by the extracellular stimuli. |
| Default value | (Flag)(0) |
Parameters | |
| cg_tol_ellip <Double> | |
| Description | conjugate gradient solver tolerance for elliptic problem |
| Default value | (Double)(1.0e-8) |
Parameters | |
| cg_norm_ellip <Short> | |
| Description | Pick a norm for checking convergence of elliptic solve for PETSc solvers |
| Default value | (Short)(0) |
| Validation |
Possible values are
|
Parameters | |
| cg_maxit_ellip <Int> | |
| Description | Defines the maximum number of iterations for iterative solver of elliptic PDE. |
| Default value | (Int)(500) |
| Validation | Value must be between (Int)(0) and (Int)(10000) |
Parameters | |
| cg_tol_parab <Double> | |
| Description | conjugate gradient solver tolerance for parabolic problem |
| Default value | (Double)(1.0e-8) |
Parameters | |
| cg_norm_parab <Short> | |
| Description | Pick a norm for checking convergence of parabolic solve (PETSc solvers only, ignored with PT) |
| Default value | (Short)(0) |
| Validation |
Possible values are
|
Parameters | |
| cg_maxit_parab <Int> | |
| Description | maximum number of iterations for iterative solver of parabolic PDE. |
| Default value | (Int)(100) |
| Validation | Value must be between (Int)(0) and (Int)(1000) |
Parameters | |
| mass_lumping <Short> | |
| Description | toggles mass matrix lumping |
| Default value | (Short)(1) |
| Validation |
Possible values are
|
Parameters | |
| operator_splitting <Short> | |
| Description | toggles operator splitting |
| Default value | (Short)(1) |
| Validation |
Possible values are
|