Parameters | |
| num_external_imp <Int> | |
| Description | Defines the number of models to read in from external libraries |
| Default value | (Int)(0) |
| required parameter: |
|
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. |
| Default value | (RFile)("") |
Parameters | |
| rt_lib <String> | |
| Description | Gives a colon separated list of runtime shared object libraries |
| Default value | (String)("") |
Parameters | |
| rt_lib_args <String> | |
| Description | Gives colon separated list of parameters for objects |
| Default value | (String)("") |
Parameters | |
| num_trace <Int> | |
| Description | Number of nodes at which to gather trace info. |
| Default value | (Int)(0) |
| required parameter: |
|
Parameters | |
| trace_node <Int> | |
| Description | Nodes at which to gather trace information. |
| Default value | (Int)(0) |
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.) |
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 | |
| 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 | |
| phie_rec_meth <Int> | |
| Description | Defines the method for recovering phie with monodomain runs. |
| Default value | (Int)(1) |
| Validation |
Possible values are
|
Parameters | |
| dump_ecg_leads <Int> | |
| Description | Dump recovered phie data from nodes stored in 'phie_rec_ptf'. The stated node file may contain arbitrary nodes of interest. In the case of an ecg recording, the spatial coordinates of LA, RA, LF, V1-V6 need to be provided. |
| Default value | (Int)(strlen(phie_rec_ptf)>0?0:1) |
| Validation | Value must be between (Int)(0) and (Int)(1) |
Parameters | |
| num_gregions <Int> | |
| Description | Defines the total number of regions with respectively different conductivity settings. |
| Default value | (Int)(1) |
| Validation | Value must be greater than (Int)(1) |
| required parameters: |
|
| Description | Sets the conductivity for different regions. The array index allows enumeration of all gregions. |
Parameters | |
| ID <Int> | |
| Description | Specify a list of model regions (equivalent to mesh element tags) using this conductivity setting. |
| Default value | (Int)(0) |
| required parameters: |
|
| num_IDs <Int> | |
| Description | Shows how many model regions use this conductivity setting |
| Default value | (Int)(0) |
| required parameter: |
|
| name <String> | |
| Description | Symbolic description of this conductive region (e.g. bath, cavity etc.) |
| Default value | (String)("") |
| 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: |
|
| g_en <Double> | |
| Description | Defines the extracellular conductivity in the local sheet direction, i.e. perpendicular to the longitudinal fiber 'g_el' and transversal fiber directions 'g_et'. |
| 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 local sheet direction, i.e. perpendicular to the longitudinal fiber 'g_il' and transversal fiber 'g_it' directions. |
| 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 transverse to the fiber direction i.e. perpendicular to the longitudinal fiber 'g_il' and local sheet 'g_it' direction. |
| Unit | S/m |
| Default value | (Double)(0.236) |
| Validation | Value must be greater than (Double)(0.) |
| required parameter: |
|
| g_it <Double> | |
| Description | Defines the intracellular conductivity transverse to the fiber direction i.e. perpendicular to the longitudinal fiber 'g_il' and local sheet 'g_it' direction. |
| Unit | S/m |
| Default value | (Double)(0.019) |
| 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_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_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: |
|
Parameters | |
| gi_scale_vec <RFile> | |
| Description | Path to element-wise vector with intra-cellular conductivity scaling |
| Default value | (RFile)("") |
Parameters | |
| ge_scale_vec <RFile> | |
| Description | Path to element-wise vector with extra-cellular conductivity scaling |
| Default value | (RFile)("") |
Parameters | |
| num_gvecs <Int> | |
| Description | Specify the number of global state variable vector definitions. |
| Default value | (Int)(0) |
| required parameters: |
|
| Description | Gives the global state variable vectors of each model region |
Parameters | |
| bogus <Float> | |
| Description | Set to 1 if the state variable is not in a region. |
| Default value | (Float)(0.) |
| required parameter: |
|
| imp <String> | |
| Description | If the state variable is defined in a plugin, specify the plugin name here. |
| Default value | (String)("") |
| required parameter: |
|
| units <String> | |
| Description | Units of the state variables to be written in the header of the ouput igb file. |
| Default value | (String)("") |
| 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: |
|
| name <WFile> | |
| Description | Defines the name of the output file for the global state variable. |
| Default value | (WFile)("sv") |
| required parameter: |
|
Parameters | |
| num_imp_regions <Int> | |
| Description | Number of different region definitions. |
| Default value | (Int)(1) |
| Validation | Value must be greater than (Int)(1) |
| required parameters: |
|
| Description | Sets the ionic model for different regions. The array index allows enumeration of all imp_regions. |
Parameters | |
| 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: |
|
| 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: |
|
| 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: |
|
| 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: |
|
| 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: |
|
| 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: |
|
| ID <Int> | |
| Description | Array of element tags associated with this model region. |
| Default value | (Int)(0) |
| required parameters: |
|
| num_IDs <Int> | |
| Description | Number of elements tags listed in 'imp_region[].ID[]'. |
| Default value | (Int)(0) |
| 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: |
|
| 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: |
|
| im_sv_init <RFile> | |
| Description | Name of the file containing the initial of state variable values. |
| Default value | (RFile)("") |
| required parameter: |
|
| 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: |
|
Parameters | |
| dump_imp_region <Int> | |
| Description | flag controling whether to dump nodal ionic region indices. output file name is 'imp_region.dat' |
| Default value | (Int)(0) |
| Validation |
Possible values are
|
Parameters | |
| rseed <Int> | |
| Description | Defines the seed for the random generator |
| Default value | (Int)(1) |
Parameters | |
| fluct <Float> | |
| Description | Defines the conductivity fluctuation in percent. |
| Unit | % |
| Default value | (Float)(0.) |
| Validation | Value must be between (Float)(0.0) and (Float)(100.0) |
Parameters | |
| num_adjustments <Int> | |
| Description | Size of the adjustment array. |
| Default value | (Int)(0) |
| Validation | Value must be greater than (Int)(0) |
| required parameters: |
|
| Description | file of adjustments |
Parameters | |
| 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: |
|
| file <RFile> | |
| Description | Defines the filename filled with nodal adjustments for the state variable |
| Default value | (RFile)("") |
| required parameter: |
|
| 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: |
|
Parameters | |
| mesh_statistics <Flag> | |
| Description | Compute mesh statistic parameters (only edge lengths at this point). |
| Default value | (Flag)(PrMFALSE) |
Parameters | |
| meshname <String> | |
| Description | Defines the basename for mesh files |
| Default value | (String)("project") |
Parameters | |
| orthoname <String> | |
| Description | Basename for lon file holding orthotropy data !!!! This parameter is unsupported in openCARP, but kept for compatibility with CARPentry !!!! |
| Default value | (String)("") |
Parameters | |
| orthogonalize <Short> | |
| Description | Toggle automatic fiber orthogonalization |
| Default value | (Short)(0) |
| Validation | Value must be between (Short)(0) and (Short)(1) |
Parameters | |
| orthoname_output <WFile> | |
| Description | Basename for .lon file holding orthotropy data that is used for output purposed, e.g. strain in this fiber direction. !!!! This parameter is unsupported in openCARP, but kept for compatibility with CARPentry !!!! |
| Default value | (WFile)("") |
Parameters | |
| meshformat <Short> | |
| Description | Mesh format ID |
| Default value | (Short)(2) |
| Validation |
Possible values are
|
Parameters | |
| numtagreg <Int> | |
| Description | Defines the number of regions to retag |
| Default value | (Int)(0) |
| Validation | Value must be greater than (Int)(0) |
| required parameters: |
|
| Description | Defines the regions to which to assign new tags |
Parameters | |
| 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: |
|
| 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 |
| Default value | (Float)(0.) |
| 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: |
|
| 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: |
|
| 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: |
|
| 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: |
|
| 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: |
|
| 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: |
|
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 | |
| 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 | |
| pstrat_i <Short> | |
| Description | Defines the partitioning strategy for the intracellular grid !!!! This parameter is unsupported in openCARP, but kept for compatibility with CARPentry !!!! |
| Default value | (Short)(1) |
| 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 PETSc options refer to the PETSc documentation. |
| Default value | (RFile)("") |
Parameters | |
| floating_ground <Short> | |
| Description | Enforces average extracellular potential to be zero. !!!! This parameter is unsupported in openCARP, but kept for compatibility with CARPentry !!!! |
| Default value | (Short)(0) |
| Validation | Value must be between (Short)(0) and (Short)(1) |
Parameters | |
| floating_ground_refnode <Int> | |
| Description | Reference node which is clamped to zero for elliptic solve prior to shifting phie average to zero. !!!! This parameter is unsupported in openCARP, but kept for compatibility with CARPentry !!!! |
| Default value | (Int)(0) |
| Validation | Value must be greater than (Int)(0) |
Parameters | |
| parab_solve <Short> | |
| Description | Defines the solution method for the parabolic problem |
| Default value | (Short)(1) |
| 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 |
| 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 | |
| stimactivedelay <Float> | |
| Description | Time after stimulus ends to continue FEM solve. |
| Unit | ms |
| Default value | (Float)(0.) |
Parameters | |
| vm_per_phie <Short> | |
| Description | Defines the number of Vm solves per phi_e solve |
| Default value | (Short)(1) |
| Validation | Value must be between (Short)(1) and (Short)(1000) |
Parameters | |
| par_fac <Short> | |
| Description | Defines the number of parabolic solves per global dt |
| Default value | (Short)(1) |
| Validation | Value must be between (Short)(1) and (Short)(100) |
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 | |
| ellip_use_pt <Short> | |
| Description | Choose solvers for the elliptic PDE from: - PETSc, then set to 0, or - PT, then set to 1. |
| Default value | (Short)(0) |
| Validation | Value must be between (Short)(0) and (Short)(1) |
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 | |
| parab_use_pt <Short> | |
| Description | Choose solvers for the parabolic PDE from: - PETSc, then set to 0, or - PT, then set to 1. |
| Default value | (Short)(0) |
| Validation | Value must be between (Short)(0) and (Short)(1) |
Parameters | |
| cg_precond <Int> | |
| Description | Defines the preconditioning method to ensure fast convergence of the conjugate gradient method. |
| Default value | (Int)(2) |
| Validation |
Possible values are
|
Parameters | |
| mat_entries_per_row <Short> | |
| Description | Assumed average number of entries per PETSc matrix row timportant for memory preallocation. !!!! This parameter is unsupported in openCARP, but kept for compatibility with CARPentry !!!! |
| Default value | (Short)(27) |
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
|
Parameters | |
| num_stim <Int> | |
| Description | Defines the number of stimuli. |
| Default value | (Int)(2) |
| Validation | Value must be greater than (Int)(0) |
| required parameters: |
|
| Description | Array of stimuli |
Parameters | |
| 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: |
|
| 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: |
|
| 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: |
|
| 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: |
|
| 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: |
|
| 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: |
|
| 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: |
|
| 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: |
|
| 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: |
|
| 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: |
|
| 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: |
|
| 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: |
|
| 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: |
|
| 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: |
|
| 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: |
|
| 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: |
|
| 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: |
|
| 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: |
|
| 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)(cell_length) |
| Validation | Value must be greater than (Float)(0.) |
| required parameters: |
|
| 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)(cell_length) |
| Validation | Value must be greater than (Float)(0.) |
| required parameters: |
|
| 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)(cell_length) |
| Validation | Value must be greater than (Float)(0.) |
| required parameters: |
|
| 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: |
|
| 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: |
|
| 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: |
|
| 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: |
|
| 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: |
|
| 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: |
|
| Description | Definition of stimuli |
Parameters | |
| name <String> (default=(String)("")) | |
| Description | "Definition of the label for a single electrode" |
| required parameter: |
|
| Description | "Definition of setup and wiring of stimulation circuit" |
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: |
|
| 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. |
| Default value | (Int)(-1) |
| Validation | Value must be between (Int)(-1) and (Int)(num_stim-1) |
| required 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: |
|
| Description | "Definition of electrode geometry" |
Parameters | |
| 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: |
|
| 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: |
|
| 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: |
|
| 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)(0.) |
| 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: |
|
| 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: |
|
| 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: |
|
| domain <Int> | |
| Description | tissue domains affected |
| Default value | (Int)(1) |
| Validation |
Possible values are
|
| required parameter: |
|
| 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: |
|
| Description | "Definition of stimulation protocol" |
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: |
|
| 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: |
|
| 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: |
|
| 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: |
|
| 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: |
|
| 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: |
|
| Description | "Definition of stimulation pulse" |
Parameters | |
| bias <Float> | |
| Description | Defines a constant term which is added to the stimulus pulse. |
| Default value | (Float)(0.) |
| 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: pulse.tau_edge, pulse.tau_plateau, pulse.strength, pulse.duration |
| Unit | ms |
| Default value | (Float)(1000.) |
| Validation | Value must be between (Float)(0.1) and (Float)(1000000.) |
| 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: pulse.tau_edge, pulse.tau_plateau, pulse.strength, pulse.duration |
| Unit | ms |
| Default value | (Float)(0.01) |
| Validation | Value must be between (Float)(0.) and (Float)(1000.) |
| 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. Other important parameters for stimulus form definition are: pulse.tau_edge, pulse.tau_plateau, pulse.strength, pulse.duration |
| Default value | (Float)(0.) |
| Validation | Value must be between (Float)(0.) and (Float)(10.) |
| required parameter: |
|
| tilt_ampl <Float> | |
| Description | prescribe fixed tilt amplitude (as in real shock delivery devices by capacitive discharge) |
| Default value | (Float)(1.0) |
| Validation | Value must be between (Float)(0.) and (Float)(1.0) |
| required parameter: |
|
| tilt_time <Float> | |
| Description | prescribe fixed tilt time (not value) relative to pulse duration |
| 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 pulse.duration and pulse.strength |
| Unit | uA/cm^2(2D current), uA/cm^3(3D current), or mV |
| Default value | (Float)(0.) |
| required parameter: |
|
| file <RFile> | |
| Description | Reads in pulse definition from external file. For file format specifications check the first chapters of the openCARP manual. |
| Default value | (RFile)("") |
| 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 pulse.duration and pulse.strength |
| Default value | (Short)(0) |
| Validation |
Possible values are
|
| required parameter: |
|
| name <String> | |
| Description | Definition of the Label for the prescribed pulse waveform |
| Default value | (String)("") |
| 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.) |
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. |
| Default value | (Flag)(PrMFALSE) |
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_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) |
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) |
Parameters | |
| spacetol <Float> | |
| Description | Defines the spatial tolerance when searching for a node. |
| Unit | um |
| Default value | (Float)(100.) |
| Validation | Value must be greater than (Float)(0.) |
Parameters | |
| display_meminfo <Short> | |
| Description | Turns on/off displaying memory malloc info. |
| Default value | (Short)(0) |
| Validation |
Possible values are
|
Parameters | |
| cell_length <Float> | |
| Description | Defines the default cell length. |
| Unit | um |
| Default value | (Float)(100.) |
| Validation | Value must be greater than (Float)(0.) |
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'. |
| Default value | (Int)(0) |
| Validation | Value must be between (Int)(0) and (Int)(50) |
| required parameters: |
|
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) |
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[PrMelem1])) |
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) |
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) |
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) |
Parameters | |
| queue_time <Float> | |
| Description | Defines the reserved queue time when running in batch mode |
| Unit | hours |
| Default value | (Float)(168.) |
| Validation | Value must be between (Float)(0.) and (Float)(168.) |
Parameters | |
| shrimp_pipe <String> | |
| Description | Defines the path to file where info should be dumped when openCARP receives SIGIO (in general, this should be a named pipe) |
| Default value | (String)("") |
Parameters | |
| state_dump_buffer <Long> | |
| Description | Defines the dump buffer size |
| Default value | (Long)(100000000) |
| Validation | Value must be greater than (Long)(1000) |
Parameters | |
| LAT_ID <String> | |
| Description | a variable |
| Default value | default_value[PrMelem1] |
Parameters | |
| num_LATs <Int> | |
| Description | Defines the number of local activation measurements. |
| Default value | (Int)(0) |
| Validation | Value must be greater than (Int)(0) |
| required parameters: |
|
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. |
| Default value | (Float)(0.) |
| Description | Array containing LATs. Index of array corresponds to LAT measurement. |
Parameters | |
| ID <WFile> | |
| Description | Defines the output filename. |
| Default value | (WFile)([[Father]].measurand ? LAT_ID[1] : LAT_ID[0]) |
| required parameters: |
|
| 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: |
|
| 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: |
|
| 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: |
|
| threshold <Float> | |
| Description | Defines the crossing threshold (for method 1) or maximum derivative threshold (for method 2) |
| Default value | (Float)(-10.) |
| required parameter: |
|
| 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: |
|
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) |
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 |
| Default value | (Flag)(PrMFALSE) |
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.) |
Parameters | |
| num_phys_regions <Int> | |
| Description | The number of physics regions |
| Default value | (Int)(0) |
| Validation | Value must be greater than (Int)(0) |
| required parameters: |
|
| Description | Array containing the defined physics regions. |
Parameters | |
| ID <Int> | |
| Description | Define a list of tags forming a mesh region. |
| Default value | (Int)(0) |
| required parameters: |
|
| num_IDs <Int> | |
| Description | Defines the number of IDs (equivalent to element tags) listed under 'ID'. |
| Default value | (Int)(0) |
| required parameter: |
|
| name <String> | |
| Description | Symbolic name for the physics region |
| Default value | (String)("") |
| required parameter: |
|
| ptype <Int> | |
| Description | Defines the type of physics. |
| Default value | (Int)(0) |
| Validation |
Possible values are
|
| required parameter: |
|