Activity for RBCsimulation

  • Siva Siva committed [r109]

    getMembraneTractionNonTensor modified to use neo-Hookean constitutive equation for membrane stress.

  • Siva Siva committed [r108]

    Sign error corrected in getMembraneTractionNonTensor.m

  • Siva Siva committed [r107]

    Bending component included in getMembraneTractionNonTensor.m

  • Siva Siva committed [r106]

    getMembraneTractionNonTensor.m modified to use the "singularity-free" formulation.

  • Siva Siva committed [r105]

    VesicleInfFlow runs through with getMembraneTractionNonTensor that uses divgcm. Haven't tested things like area/volume/force balance with the results.

  • Siva Siva committed [r104]

    Non-debug versions of mex files (had debug flags on in last commit)

  • Siva Siva committed [r103]

    Just a small error in vhagcm, pu and pv were switched around.

  • Siva Siva committed [r102]

    vhagc working in from fortran test code (see DivergenceTest.f90), but not from MEX. Why?

  • Siva Siva committed [r101]

    divgcm.mexw64 committed

  • Siva Siva committed [r100]

    getMembraneTractionNonTensor.m added, but not working because it seems like divergence is not being computed correctly.

  • Siva Siva committed [r99]

    Building mex for vhagcm and divgcm to calculate divergence. These two mexes have not been tested yet.

  • Siva Siva committed [r98]

    never committed integrateForce.m and testForceIntegral.m

  • Siva Siva committed [r97]

    getVolumeArea.m was never committed

  • Siva Siva committed [r96]

    MATLAB 2019a with Intel Fortran 19.0 has default /integer-size:64 option. This is a problem for spherepack (where variables are not explicitly declared) and other places where variables are declared as "integer" to mean "integer*4". There is no way to override this (see discussion in https://www.mathworks.com/matlabcentral/answers/474520-overriding-compiler-switch-in-mex?s_tid=prof_contriblnk). So had to write a Makefile to do this.

  • Siva Siva committed [r95]

    Two more mex binaries added; this is not good, need a better way for this.

  • Siva Siva committed [r94]

    number of longitude points changed to 2*nlat - 1 (i.e., nlat = N+1, nlon = 2*N + 1) in

  • Siva Siva committed [r93]

    Error corrections in get_9NodeQuad_GtKu_nonsingular.F90 and get_9NodeQuad_GtKu_singular.F90

  • Siva Siva committed [r92]

    In BEM direct, instead of forming matrices and then multiplying, we try to multiply the kernel by vector then integrate. get_9nodeQuad_BEM_GtKu.m is only partly done. Ali is going to complete this.

  • Siva Siva committed [r91]

    Updated check_conservation.m for parallelization

  • Siva Siva committed [r90]

    Tried to use parfor to parallelize in solveBIE.m; this actually hurts performance. Probably MATLAB was doing enough multithreading that using parfor in fact hurt. Going to revert to non-parallel version after this commit.

  • Siva Siva committed [r89]

    Created

  • Siva Siva committed [r88]

    Bug fix: In VesicleInfFlow.m, was using undeformed geometry to calculate uinf; corrected to use deformed geometry.

  • Siva Siva committed [r87]

    Fixed a bug in VesicleInfFlow.m (was passing undeformed instead of deformed configuration to solveBIE).

  • Siva Siva committed [r86]

    Modify solveBIE.m to rotations the new way.

  • Siva Siva committed [r85]

    Modifying to avoid multiple masks speeds up a bit more. For N = 20, speedup is 10x. For N = 40, speedup is about 6x.

  • Siva Siva committed [r84]

    Rotation of SH coefficients is the most time-consuming part. Try new organization for doing this calculation in testSHCoeffRotation.m. A bit better (2-3x faster), but may be avoiding multiple masks can give further speedup.

  • Siva Siva committed [r83]

    VesicleInfFlow.m modified: rotation matrices can be computed once upfront (and stored in a cell array)

  • Siva Siva committed [r82]

    Radical changes...

  • Siva Siva committed [r81]

    Correction: Added minus sign in getSHBIEGK.f90

  • Siva Siva committed [r80]

    A long time since the last commit. Apparently, ...

  • Siva Siva committed [r79]

    A brute force implementation of the constant vo...

  • Siva Siva committed [r78]

    Monitor volume conservation in visualizeRBC.m. ...

  • Siva Siva committed [r77]

    Runs to 1s with 1e-2 time step when ED is set t...

  • Siva Siva committed [r76]

    Activated dealiasing because computation was no...

  • Siva Siva committed [r75]

    Modified runRBCsimulation.m to work with Stress...

  • Siva Siva committed [r74]

    Modified StressResultantShell.m so that undefor...

  • Siva Siva committed [r73]

    G computation is modified (in getSHBIEGK.F90) s...

  • Siva Siva committed [r72]

    Error fixed in nullspace (normal vector) calcul...

  • Siva Siva committed [r71]

    Put constitutive equations in. Results for

  • Siva Siva committed [r70]

    Forgot to save changes in ShellFormulation.tex ...

  • Siva Siva committed [r69]

    Modified stress-resultant shell implementation ...

  • Siva Siva committed [r68]

    Tried to do derivative of (sqrt(a) s_ll) becaus...

  • Siva Siva committed [r67]

    Christoffel symbol for ellipsoid does not work ...

  • Siva Siva committed [r66]

    Computing Christoffel symbol using derivative o...

  • Siva Siva committed [r65]

    Got an idea to test, at least computation of a_...

  • Siva Siva committed [r64]

    Stress resultant shell formulation added. Not t...

  • Siva Siva committed [r63]

    Reverted get_9nodequad_solid_angle.m to revisio...

  • Siva Siva committed [r62]

    committed from CCR machine, put timing in diffe...

  • Siva Siva committed [r61]

    There were 2 problems.

  • Siva Siva committed [r60]

    Moved matrix rearranging into spmd, doing distr...

  • Siva Siva committed [r59]

    Modified runRBCsimulation.m to use spmd instead...

  • Siva Siva committed [r58]

    Using a 3 parfor structure with 2 sets of cell ...

  • Siva Siva committed [r57]

    Tried to break the construction of G and K into...

  • Siva Siva committed [r56]

    Modified runRBCsimulation.m with revised call t...

  • Siva Siva committed [r55]

    ABAQUS test works correctly, so KK appears to b...

  • Siva Siva committed [r54]

    Modified shagsd.f, actually quite simple. Gives...

  • Siva Siva committed [r53]

    The plan is to make a new version of shags, cal...

  • Siva Siva committed [r52]

    Added shagsim and shagsm for precomputing assoc...

  • Siva Siva committed [r51]

    Made a new mex, shagsm. Changed shagcm call to ...

  • Siva Siva committed [r50]

    Modified getSHBIEGK.F90 to compute only lower t...

  • Siva Siva committed [r49]

    Wrote computation of G and K matrices in mex.

  • Siva Siva committed [r48]

    Modified ExtStokesFlow.m and getSHBIEmatrices.m...

  • Siva Siva committed [r47]

    Reverted ExtStokesFlow.m and getSHBIEmatrices.m...

  • Siva Siva committed [r46]

    Added some plotting in getSHBIEmatrices.m to vi...

  • Siva Siva committed [r45]

    Reverted ExtStokesFlow.m and getSHBIEmatrices.m...

  • Siva Siva committed [r44]

    Using shagcm does not work well. Since G is no ...

  • Siva Siva committed [r43]

    getSHBIEmatrices.m modified and checked that us...

  • Siva Siva committed [r42]

    Took ExtStokesFlow.m and getSHBIEmatrices.m to ...

  • Siva Siva committed [r41]

    Still messing around with getSHBIEmatrices.m.

  • Siva Siva committed [r40]

    Modified only ExtStokesFlow.m. Using Gauss quad...

  • Siva Siva committed [r39]

    SparseGrid doesn't work for the RBC geometry (o...

  • Siva Siva committed [r38]

    Modified runRBCsimulation.m to run one time ste...

  • Siva Siva committed [r37]

    Everything works in CCR. Ran on CCR, got rbcsim...

  • Siva Siva committed [r36]

    modifications to run on CCR cluster, commited f...

  • Siva Siva committed [r35]

    getSHBIEmatrices.m was screwed up in the last c...

  • Siva Siva committed [r34]

    Went back to Matlab version of getSHBIEmatrices...

  • Siva Siva committed [r33]

    Tried to rewrite getSHBIEmatricesMEX.F90, still...

  • Siva Siva committed [r32]

    Revised getSHBIEmatrices.m in an attempt to mak...

  • Siva Siva committed [r31]

    PuttingItTogether works (just had the wrong sig...

  • Siva Siva committed [r30]

    Put the RBC forces in as well, but the RBC is d...

  • Siva Siva committed [r29]

    Started PuttingItTogether!

  • Siva Siva committed [r28]

    Rewrote computing G and K in getSHBIEmatrices.m...

  • Siva Siva committed [r27]

    Tested ExtStokesFlow.m with undeformed/deformed...

  • Siva Siva committed [r26]

    Modified ExtStokesFlow.m in BIEsphere to also c...

  • Siva Siva committed [r25]

    ExtStokesFlow.m modified to use SHRotateMEX -> ...

  • Siva Siva committed [r24]

    1. SHRotate mexed to SHRotateMEX.f90; speedup m...

  • Siva Siva committed [r23]

    New traction conditions for inlet and outlet ed...

  • Siva Siva committed [r22]

    Fortan for both singular and nonsingular parts ...

  • Siva Siva committed [r21]

    The nested functions in get_9nodeQuad_BEM_matri...

  • Siva Siva committed [r20]

    Orienting normal vectors made general in BEMdir...

  • Siva Siva committed [r19]

    Boundary integral with spherical harmonics is w...

  • Siva Siva committed [r18]

    Committing for solid angle stuff.

  • Siva Siva committed [r17]

    Added solid angle computation

  • Siva Siva committed [r16]

    1. Checked RBC force calculation using finite d...

  • Siva Siva committed [r15]

    Number of major changes in shell formulation (R...

  • Siva Siva committed [r14]

    Working on LearnSphericalHarmonics directory, n...

  • Siva Siva committed [r13]

    Did force balance check

  • Siva Siva committed [r12]

    Modified BEMdirect to treat traction unknowns a...

  • Siva Siva committed [r11]

    PatranImport modified --- reads INLET, OUTLET a...

  • Siva Siva committed [r10]

    PatranImport modified --- reads INLET and OUTLE...

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