profile
viewpoint

maierbn/opendihu 3

Simulation framework for a multi-scale skeletal muscle model, for computing EMG signals and muscle contraction.

qres/HowToSimtech 2

List of useful tools and things I should have known earlier.

qres/arbor 0

The Arbor multi-compartment neural network simulation library.

qres/gfx-rs 0

A high-performance, bindless graphics API for Rust.

qres/miri 0

An experimental interpreter for Rust MIR

qres/NumSim 0

Nothing to see here, just an university exercise

qres/rust 0

a safe, concurrent, practical language

push eventmaierbn/opendihu

Felix Huber

commit sha 543f60c7e674c5a49a372ea6e53bfee7b23c074c

scorep warnings if modules are not loaded and correct face-scorep.sh location

view details

push time in a month

push eventmaierbn/opendihu

Felix Huber

commit sha ff77eb3e1c1c41b28bc8883dd8c998fbcee15e45

scorep warnings if modules are not loaded

view details

push time in a month

push eventmaierbn/opendihu

Felix Huber

commit sha 410453fafb19a730c20c0c2f1f58fab34d94d863

support Extrae with static linking

view details

push time in a month

push eventmaierbn/opendihu

Felix Huber

commit sha c26e23aebc388085ad4256781ab01d7460f48e31

dont'r reset libary file name if compillation failed so we can still try to load an existing library. This is needed for extrae, where the compilation fails.

view details

Felix Huber

commit sha b23e9a379f3bd4e07002c0a75def5c77ad18f8e2

support Extrae with static linking

view details

push time in a month

push eventmaierbn/opendihu

Felix Huber

commit sha c99be5dcd7b8cbf7c0192c9228199a216d022297

documentation on "meshName" and "solverName"

view details

Felix Huber

commit sha 8ab67e16f7d0b59616a5175c303ee8b452bf8bb3

delete misleading config entries inline mesh and solver settings are ignored if "meshName" or "solverName" are given.

view details

push time in 2 months

push eventmaierbn/opendihu

Felix Huber

commit sha 555e938939240a6679d03cf52f2760c2a84d0407

add "timeStepWidthRelativeTolerance" to all configs

view details

push time in 3 months

push eventmaierbn/opendihu

Felix Huber

commit sha b62010f8618fcfba5b5e684b3ad5e85f44310745

fix formula in documentation

view details

push time in 3 months

push eventmaierbn/opendihu

Felix Huber

commit sha 772db71df50bf55865afb3293fd3174b85d9dbde

allow the CellML model not to set initial values so the outer time stepping scheme can set them

view details

Felix Huber

commit sha 0e27c8e9e9440f4e6f534129eac84f08d7bd3dc6

use "initialValues" to specify initial values in multiple fibers

view details

Felix Huber

commit sha a0239eb641bdbec833cf829e1a43365be3d9de78

more details on when the setSpecificStatesFunction is called in documentation

view details

push time in 3 months

push eventmaierbn/opendihu

Felix Huber

commit sha e6df6eb611dab5c97ff5096c1859369541dddab3

fixup! fix computation of system matrix and integration matrix rhs

view details

Felix Huber

commit sha 151403d5687b96e21b9b0ede8efc9db0eb7120cb

add setting for implicit methods to control the relative tolerance for the time step size before the system matrix gets recomputed

view details

Felix Huber

commit sha 34740f41a065aa8c613d98569951d77aadcb6aca

add log key to measure time and number of reinitializations

view details

push time in 3 months

push eventmaierbn/opendihu

Felix Huber

commit sha f1aa323255b7152ced98309f56521649464fc5df

fix memory leak on repeated calls to `setSystemMatrix` and `setIntegrationMatrixRightHandSide`

view details

Felix Huber

commit sha f627d8e44af68d6e4f4b25a89b380d3d3b8da602

fix time step width computation In the previous version, the time step size fitting (+10% or refine the time step, or dt = inteval_length / n_steps) was already applied during construction when the time interval is not known. Therefore it was applied to the default [0,1] interval which resulted in wrong time step sizes. This lead to errors in the systemMatrix. Especially when setting a fixed number of time steps per interval, the results were very wrong. We now store the step size given in the settings file and recompute the time step correctly every time the integration interval changes. A follow up commit will fix the systemMatrix setup, to use the correct time step size.

view details

Felix Huber

commit sha b04e582f35f09c25d1cdc5c602498a35a15ccbfd

fix computation of system matrix and integration matrix rhs Move the construction of the matrices from `initialization` to the beginning of `advanceTimeStep`, because the time step width depends on the integration interval, which is not known until the integration start. Without this fix, a wrong time step size was used, especially if the integrator was based on 'number of steps per interval'. Therefore we initialize the matrices with the correct time step width in the first call to `advanceTimeStep`. The matrices are only recomputed if the time step changes. This, also fixes the problem, that different time step sizes lead to different results with 'multiple fibers' (and probably all other simulations, too).

view details

push time in 3 months

push eventmaierbn/opendihu

Felix Huber

commit sha 367be0be84b135b7f284f60fec99e2a3383ed5cf

ensure that the output writer don't count the initial value output so that the time values for different output intervals are aligned

view details

push time in 3 months

push eventmaierbn/opendihu

Felix Huber

commit sha 03d92cb0827095d7afc2fc1f0caadff582b05006

fix warning message if numberTimeSteps is zero

view details

push time in 3 months

push eventmaierbn/opendihu

Felix Huber

commit sha 0f7dfa130bf478816f9f79f778ed2d2c255dfd48

add arguments to multiple_fibers to specify number of time steps

view details

push time in 3 months

push eventmaierbn/opendihu

Felix Huber

commit sha e2c35f7864e0ec28646339f99059979b8175580c

more convenient usage of numberTimeSteps if numberTimeSteps is zero it is ignored

view details

Felix Huber

commit sha 41a980b7686d658150cd6449febe8f57840c376b

formatting

view details

push time in 3 months

push eventmaierbn/opendihu

Felix Huber

commit sha 6520a73d46bd34b94b213b29481440d85b47dc5c

fix format of python error output

view details

push time in 3 months

push eventmaierbn/opendihu

Felix Huber

commit sha c4b4ffe5b5bb712378fd210e3f750afb9be2493f

show warning if a python script gets arguments it does not know about

view details

push time in 3 months

push eventmaierbn/opendihu

Felix Huber

commit sha 2a91839c0bf0c556afb4acd2e6adc2f17aace591

output stderr of python config file

view details

push time in 3 months

push eventmaierbn/opendihu

Felix Huber

commit sha ecaa4e28af9566236036c23e03e18dfe7d0e9f73

add argument to multiple fibers to load initial values from file and disable stimuli

view details

Felix Huber

commit sha d5cf20ea1c0b603d74259deeb9b0b7c4c00416f3

remove file which should not have been in git

view details

push time in 3 months

more