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CvSys

Introduction

This tutorial guides through using the 0D Cardiovascular system simulator. The code is based on the CircAdapt model, see [Arts2005], [Lumens2009], [Arts2012], and [Walmsley2015].

Usage

(Requires the cvsys package)

Basic Options

To see the full option list run

cvstool
  --help

The following basic options are available:

-h,
  --help              Display this information

  -s,
  --solver <solver>   Choose
  ODE solver

                          Choices:

                            forw-euler: forward Euler method

                            rfk45: Runge-Kutta-Fehlberg 45

                            cvode: Sundials CVode solver

  -d,
  --duration <float>  Duration
  of the simulation in (s)

                            default: 0.85 s

  -o,
  --output <dir>      Place
  the output into the directory <dir>

  --create-opts
  <file>    Create options file
  with default values

                            format choices are `json` and `prm`

                            default: `cvs_options.json`

  --opts
  <file>           Use input
  options in <file>

The following command computes the heartbeat of a healthy adult over 60 seconds:

cvstool
  -d 60 \

          -o
  healthy_adult

Parameters of the cardiovascular systems can be changed using specific option files. First, generate options with

cvstool
  --create-opts cvs_options.json

Second, modify the options file cvs_options.json, e.g., set Aortic valve stenosis [pct.] to 70.

And third, simulate the heartbeat with a 70% aortic stenosis using the options file with

cvstool
  -d 60 \

          -o
  aortic_stenosis \

          --opts
  cvs_options.json

Post-processing

The cvsys experiment output information file on the cardiovascular system in the chosen output folder in csv format. Depending on the cardiovascular component these contain pressure information, volume information, flow rates and many other additional informations. These files can be used for a post-processing analysis using the tool cavplot. Call

cavplot
  --help

for a detailed description of the usage.

The default output containts pressure-volume loops as well as pressure and volume traces

cavplot
  ./healthy_adult/cav.LV.csv

To plot a time interval of the output use --time-interval or --time For example to plot the last two seconds of the simulation call

cavplot
  ./healthy_adult/cav.LV.csv --time-interval 58 60

To change the unit to mmHg use the flag --mmHg. To show PV loop and pressure traces for the aortic stenosis case call

cavplot
  ./aortic_stenosis/cav.LV.csv --time 58 --mmHg

This should give you a plot similar to

The options l+= and l= allow to add labels to the output. To compare the pvloops for the healthy case and the case with 70% aortic stenosis call

cavplot
  healthy_adult/cav.LV.csv:l="Healthy" \

          aortic_stenosis/cav.LV.csv:l="Aortic Stenosis" \

          --time
  55 --pvloop

The option ls= in {dotted, dashdot, dashed, solid} allows to change the linestyle. E.g., plot the pressure drop over the aortic valve:

cavplot
  aortic_stenosis/cav.LV.csv \

          aortic_stenosis/tube.AO.csv:ls=dashed \

          --time
  55 --pressure

The options v*=, p*=, and f*= allows to scale the volume(v), pressure(p), and flux(f), respectively. The same also works for \=, and +=, -= for a translation. E.g. plot the flux over the pulmonary outlet, the mitral valve, volume change of the left atrium in one plot:

cavplot
  aortic_stenosis/valve.PO.csv:f*=-1 \

          aortic_stenosis/valve.MV.csv
  \

          aortic_stenosis/cav.LA.csv:ls=dashed:l="LA Volume Change"
  \

          --flux
  --time 56.7 58.7

Advanced Options

The following more advanced options are available:

--version
  <version>  Specify CircAdapt
  version to use (`2012`,
  `2015`)

                         default: `2015`

  --no-peri            Run
  simulation without pericardium

  --stiff-av-valves    Run
  simulation without updating leak area

                       of atrio-ventricular valves

  --mass-conservation  Enable
  mass conservation

  --allow-negative-p   Allow
  negative pressures in cavities

The different versions (2012, 2015) correspond to the publications [Arts2012] and [Walmsley2015], see also http://www.circadapt.org/downloads/files.

For example we can allow negative pressures in the cavities using

cvstool
  -d 60 -o healthy_adult_np --allow-negative-p

We plot the difference in the left atrial PV loop using the plotting option c= that allows to change the color using RGB-HEX format

cavplot
  healthy_adult/cav.LA.csv:l="standard":c=#000 \

          healthy_adult_np/cav.LA.csv:l="allow-negative-p":c=#ff0000 \

          --pvloop
  --time 55 --mmHg

References

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09_bivslice