Commits June 2014

commits@lists.einsteintoolkit.org

5 participants
36 discussions

[svn:einsteintoolkit] NullConstr/trunk/ (Rev. 20)
by rhaas＠tapir.caltech.edu 18 Jun '14

18 Jun '14

User: rhaas Date: 2014/06/18 03:53 PM Modified: /trunk/ README Log: NullConstr: respect Cactus' IO::truncate parameter File Changes: Directory: /trunk/ ================== File [modified]: README Delta lines: +2 -2 =================================================================== --- trunk/README 2014-05-21 15:49:56 UTC (rev 19) +++ trunk/README 2014-06-18 20:53:29 UTC (rev 20) @@ -35,8 +35,8 @@ Title: Characteristic Extraction Tool for Gravitational Waveforms Authors: M.C. Babiuc, B. Szilagyi, J. Winicour, Y. Zlochower - arXiv:1011.4223 - submitted to Physical Review D + arXiv:1011.4223, Phys Rev D 84, 044057, + doi: http://dx.doi.org/10.1103/PhysRevD.84.044057 Title: Cauchy-characteristic matching Authors: N. Bishop, R. Isaacson, R. Gomez, L. Lehner, B. Szilagyi, J.

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[svn:einsteintoolkit] NullEvolve/trunk/ (Rev. 27)
by rhaas＠tapir.caltech.edu 18 Jun '14

18 Jun '14

User: rhaas Date: 2014/06/18 03:23 PM Modified: /trunk/ README Log: NullEvolve: update publication information of CCE paper add published paper reference File Changes: Directory: /trunk/ ================== File [modified]: README Delta lines: +2 -2 =================================================================== --- trunk/README 2014-05-21 15:50:02 UTC (rev 26) +++ trunk/README 2014-06-18 20:23:35 UTC (rev 27) @@ -37,8 +37,8 @@ Title: Characteristic Extraction Tool for Gravitational Waveforms Authors: M.C. Babiuc, B. Szilagyi, J. Winicour, Y. Zlochower - arXiv:1011.4223 - submitted to Physical Review D + arXiv:1011.4223, Phys Rev D 84, 044057, + doi: http://dx.doi.org/10.1103/PhysRevD.84.044057 Title: Cauchy-characteristic matching Authors: N. Bishop, R. Isaacson, R. Gomez, L. Lehner, B. Szilagyi, J.

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[svn:einsteintoolkit] TOVSolver/ (Rev. 153)
by knarf＠cct.lsu.edu 17 Jun '14

17 Jun '14

User: knarf Date: 2014/06/17 11:11 AM Added: /trunk/src/util/ mode_spectrum.py Log: add script to generate a mode spectum Directory Changes: Directory: /svn:executable/ =========================== + * File Changes: Directory: /trunk/src/util/ =========================== File [added]: mode_spectrum.py Delta lines: +73 -0 =================================================================== --- trunk/src/util/mode_spectrum.py (rev 0) +++ trunk/src/util/mode_spectrum.py 2014-06-17 16:10:59 UTC (rev 153) @@ -0,0 +1,73 @@ +#!/usr/bin/python +# -*- coding: utf-8 -*- + +# Â© Frank LÃ¶ffler <knarf(a)cct.lsu.edu> +# License: GPLv2+ + +# Compute power spectral density of given data +from plot_defaults import * +from matplotlib.mlab import detrend_linear + +xlim = (0,10) +ylim = (-140,-100) + +# load data +Fx, Fy = np.loadtxt("hydrobase::rho.maximum.asc.bz2", comments="#", usecols=(1,2), unpack=True) +dt = M_to_ms/(Fx[1]-Fx[0]) + +# slice data if wanted +start = 0.0 +end = 1. +Fx = Fx[int(start*len(Fx)): int(end*len(Fx))] +Fy = Fy[int(start*len(Fy)): int(end*len(Fy))] + +# Plot basics +fig = plt.figure(figsize=(6, 3)) +fig.subplots_adjust(top=0.92,bottom=0.16, left=0.11,right=0.98) +ax = fig.add_subplot(1,1,1) + +# mode names and frequencies for non-rotating Gamma=2 K=100 TOV stars +modes = { +"F" : 1.44252691528028, +"H1": 3.95408396916149, +"H2": 5.91494894170517, +"H3": 7.77382493405710, +"H4": 9.58768293806276, +"H5": 11.3772129983097, +"H6": 13.1520241905666, +"H7": 14.9172321735655, +} + +# plot modes as vertical lines and label them +for mode, freq in modes.items(): + ax.plot((freq,freq), ylim, 'b--') + ax.text(freq-0.1, ylim[1]+1, mode, fontsize=fontsize) +#ax.plot((2*modes["F"], 2*modes["F"]), (-200,0), 'g--') +#ax.plot((3*modes["F"], 3*modes["F"]), (-200,0), 'g--') +#ax.plot((4*modes["F"], 4*modes["F"]), (-200,0), 'g--') + +# plot PSD +frac = 0.5 * len(Fy) +ax.psd(Fy, NFFT=int(frac), pad_to=5*int(frac), noverlap=int(frac*0.5), detrend=detrend_linear, Fs=dt, linestyle='-', color='black', scale_by_freq=False) +#ax.psd(Fy, NFFT=int(len(Fy)*frac), pad_to=10*int(len(Fy)*frac), noverlap=int(len(Fy)*frac*0.50), detrend=detrend_linear, Fs=M_to_ms/(Fx[1]-Fx[0]), linestyle='-', marker='x', color='red') + +# plot properties +ax.set_xlim(xlim) +ax.set_ylim(ylim) + +#plt.title('PSD', fontsize=fontsize) +ax.set_xlabel(r'$f$ [kHz]') +ax.set_ylabel(r'PSD [dB/Hz]') + +ax.xaxis.set_major_locator(mticker.MaxNLocator(10)) +ax.xaxis.set_minor_locator(mticker.MaxNLocator(20)) +ax.xaxis.grid(False) +ax.yaxis.set_major_locator(mticker.MaxNLocator(5)) +ax.yaxis.set_minor_locator(mticker.MaxNLocator(9)) +ax.yaxis.grid(False) +set_tick_sizes(ax, 8, 4) + + +#plt.show() +plt.savefig('mode_spectrum.pdf') + Property changes on: trunk/src/util/mode_spectrum.py ___________________________________________________________________

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[svn:einsteintoolkit] AHFinderDirect/trunk/src/ (Rev. 1586)
by schnetter＠cct.lsu.edu 11 Jun '14

11 Jun '14

User: eschnett Date: 2014/06/11 06:27 PM Modified: /trunk/src/driver/ mask.cc /trunk/src/gr/ gr.hh Log: Change cGH* to const cGH* File Changes: Directory: /trunk/src/driver/ ============================= File [modified]: mask.cc Delta lines: +1 -1 =================================================================== --- trunk/src/driver/mask.cc 2014-05-21 15:53:14 UTC (rev 1585) +++ trunk/src/driver/mask.cc 2014-06-11 23:27:37 UTC (rev 1586) @@ -78,7 +78,7 @@ namespace { struct mask_grid_info { - cGH *GH; // --> Cactus grid hierarchy + const cGH *GH; // --> Cactus grid hierarchy // Cactus coordinate system // (for the *current* grid if we are doing mesh refinement) Directory: /trunk/src/gr/ ========================= File [modified]: gr.hh Delta lines: +1 -1 =================================================================== --- trunk/src/gr/gr.hh 2014-05-21 15:53:14 UTC (rev 1585) +++ trunk/src/gr/gr.hh 2014-06-11 23:27:37 UTC (rev 1586) @@ -129,7 +129,7 @@ // struct cactus_grid_info { - cGH *GH; // --> Cactus grid hierarchy + const cGH *GH; // --> Cactus grid hierarchy int coord_system_handle; // Cactus coordinate system handle // this describes the semantics of the Cactus gij gridfns:

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[svn:einsteintoolkit] manifest/trunk/ (Rev. 289)
by schnetter＠cct.lsu.edu 10 Jun '14

10 Jun '14

User: eschnett Date: 2014/06/10 06:45 PM Modified: /trunk/ einsteintoolkit.th Log: Don't mention MemSpeed, which is not part of the ET File Changes: Directory: /trunk/ ================== File [modified]: einsteintoolkit.th Delta lines: +1 -1 =================================================================== --- trunk/einsteintoolkit.th 2014-06-10 23:44:40 UTC (rev 288) +++ trunk/einsteintoolkit.th 2014-06-10 23:45:07 UTC (rev 289) @@ -86,7 +86,7 @@ !TARGET = $ARR !TYPE = svn !URL = https://svn.cactuscode.org/arrangements/$1/$2/trunk -!CHECKOUT = CactusElliptic/EllPETSc CactusExamples/HelloWorldCUDA CactusExamples/HelloWorldOpenCL CactusExamples/WaveToyOpenCL CactusTest/TestAllTypes CactusUtils/Accelerator CactusUtils/MemSpeed CactusUtils/OpenCLRunTime +!CHECKOUT = CactusElliptic/EllPETSc CactusExamples/HelloWorldCUDA CactusExamples/HelloWorldOpenCL CactusExamples/WaveToyOpenCL CactusTest/TestAllTypes CactusUtils/Accelerator CactusUtils/OpenCLRunTime CactusBase/Boundary CactusBase/CartGrid3D CactusBase/CoordBase

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[svn:einsteintoolkit] manifest/trunk/ (Rev. 288)
by schnetter＠cct.lsu.edu 10 Jun '14

10 Jun '14

User: eschnett Date: 2014/06/10 06:44 PM Modified: /trunk/ einsteintoolkit.th Log: Enable PAPI by default File Changes: Directory: /trunk/ ================== File [modified]: einsteintoolkit.th Delta lines: +3 -3 =================================================================== --- trunk/einsteintoolkit.th 2014-06-10 23:43:29 UTC (rev 287) +++ trunk/einsteintoolkit.th 2014-06-10 23:44:40 UTC (rev 288) @@ -289,7 +289,7 @@ !TARGET = $ARR !TYPE = svn !URL = https://svn.cactuscode.org/projects/$1/$2/trunk -!CHECKOUT = ExternalLibraries/OpenCL ExternalLibraries/PAPI ExternalLibraries/pciutils ExternalLibraries/PETSc +!CHECKOUT = ExternalLibraries/OpenCL ExternalLibraries/PETSc ExternalLibraries/BLAS ExternalLibraries/FFTW3 ExternalLibraries/GSL @@ -301,8 +301,8 @@ ExternalLibraries/MPI #DISABLED ExternalLibraries/OpenCL ExternalLibraries/OpenSSL -#DISABLED ExternalLibraries/PAPI -#DISABLED ExternalLibraries/pciutils +ExternalLibraries/PAPI +ExternalLibraries/pciutils #DISABLED ExternalLibraries/PETSc ExternalLibraries/zlib

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[svn:einsteintoolkit] manifest/trunk/ (Rev. 287)
by schnetter＠cct.lsu.edu 10 Jun '14

10 Jun '14

User: eschnett Date: 2014/06/10 06:43 PM Modified: /trunk/ einsteintoolkit.th Log: Mark all disabled thorns with DISABLED File Changes: Directory: /trunk/ ================== File [modified]: einsteintoolkit.th Delta lines: +15 -15 =================================================================== --- trunk/einsteintoolkit.th 2014-06-02 13:48:00 UTC (rev 286) +++ trunk/einsteintoolkit.th 2014-06-10 23:43:29 UTC (rev 287) @@ -105,14 +105,14 @@ CactusDoc/CoreDoc CactusElliptic/EllBase -#CactusElliptic/EllPETSc +#DISABLED CactusElliptic/EllPETSc CactusElliptic/EllSOR CactusExamples/DemoInterp CactusExamples/FleshInfo CactusExamples/HelloWorld -#CactusExamples/HelloWorldCUDA -#CactusExamples/HelloWorldOpenCL +#DISABLED CactusExamples/HelloWorldCUDA +#DISABLED CactusExamples/HelloWorldOpenCL CactusExamples/IDWaveMoL CactusExamples/SampleBoundary CactusExamples/SampleIO @@ -120,7 +120,7 @@ CactusExamples/WaveMoL CactusExamples/WaveToy1DF77 CactusExamples/WaveToy2DF77 -#CactusExamples/WaveToyOpenCL +#DISABLED CactusExamples/WaveToyOpenCL CactusIO/IOJpeg @@ -149,7 +149,7 @@ CactusPUGHIO/IOHDF5 CactusPUGHIO/IOHDF5Util -#CactusTest/TestAllTypes +#DISABLED CactusTest/TestAllTypes CactusTest/TestArrays CactusTest/TestComplex CactusTest/TestCoordinates @@ -173,12 +173,12 @@ CactusTest/TestTimers CactusTest/TestTypes -#CactusUtils/Accelerator +#DISABLED CactusUtils/Accelerator CactusUtils/Formaline CactusUtils/NaNChecker CactusUtils/Nice CactusUtils/NoMPI -#CactusUtils/OpenCLRunTime +#DISABLED CactusUtils/OpenCLRunTime CactusUtils/TerminationTrigger CactusUtils/TimerReport @@ -212,8 +212,8 @@ EinsteinAnalysis/WeylScal4 EinsteinBase/ADMBase -EinsteinBase/ADMCoupling # deprecated -EinsteinBase/ADMMacros # to be deprecated, don't use for new code +EinsteinBase/ADMCoupling # deprecated +EinsteinBase/ADMMacros # deprecated EinsteinBase/Constants EinsteinBase/CoordGauge EinsteinBase/EOS_Base @@ -299,15 +299,15 @@ ExternalLibraries/libjpeg ExternalLibraries/LORENE ExternalLibraries/MPI -#ExternalLibraries/OpenCL +#DISABLED ExternalLibraries/OpenCL ExternalLibraries/OpenSSL -#ExternalLibraries/PAPI -#ExternalLibraries/pciutils -#ExternalLibraries/PETSc +#DISABLED ExternalLibraries/PAPI +#DISABLED ExternalLibraries/pciutils +#DISABLED ExternalLibraries/PETSc ExternalLibraries/zlib TAT/TATelliptic -#TAT/TATPETSc +#DISABLED TAT/TATPETSc @@ -362,7 +362,7 @@ McLachlan/ML_CCZ4_Helper McLachlan/ML_CCZ4_Test McLachlan/ML_WaveToy -#McLachlan/ML_WaveToy_CL +#DISABLED McLachlan/ML_WaveToy_CL McLachlan/ML_WaveToy_Test

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[svn:einsteintoolkit] IllinoisGRMHD/trunk/ (Rev. 33)
by knarf＠cct.lsu.edu 03 Jun '14

03 Jun '14

User: knarf Date: 2014/06/03 10:13 AM Modified: /trunk/ TODO Log: add a todo item File Changes: Directory: /trunk/ ================== File [modified]: TODO Delta lines: +1 -0 =================================================================== --- trunk/TODO 2014-06-03 02:03:26 UTC (rev 32) +++ trunk/TODO 2014-06-03 15:13:03 UTC (rev 33) @@ -6,6 +6,7 @@ * extreneous checks and code lines that never executa in MoL_registration * all externally visible functions should be prefixed by IllinoisGRMHD_ (or put in an IllinoisGRMHD namespace -- note that this does not work for the extern "C" ones) * (personal choice): you use very long lines, this is ok (your code, your style). Usually we prefer shorter lines (80 chars) but that is really each author's decision +* Please don't use tab characters in source files. This just messes up the code display for users that use a different length for tabs than you. Replace them with spaces. * don't use explicitly spelled out decimals. The compiler will evaluate fractions at compile time anyway, ie use: (1./3.)*x instead of 0.3333*x * consider passing CCTK_PASS_CTOC and DECLARE_CCTK_ARGUMENTS (may be slower though) rather than passing cctkGH and cctk_lsh * gettimeofday may not exist, don' rely on it

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[svn:einsteintoolkit] IllinoisGRMHD/trunk/ (Rev. 32)
by rhaas＠tapir.caltech.edu 02 Jun '14

02 Jun '14

User: rhaas Date: 2014/06/02 09:03 PM Added: /trunk/ TODO Log: IllinoisGRMHD: add TODO file File Changes: Directory: /trunk/ ================== File [added]: TODO Delta lines: +19 -0 =================================================================== --- trunk/TODO (rev 0) +++ trunk/TODO 2014-06-03 02:03:26 UTC (rev 32) @@ -0,0 +1,19 @@ +General comments: +* use CCTK_REAL for floating point Cactus variables, not double since CCTK_REAL can be float or long double +* don't use exit(1) and printf() to report errors, instead use CCTK_VError (eg. stdout of non-rank0 procs is often lost) +* use CCTK_VInfo to report status not printf (CCTK_VInfo supports hooks) +* (optional) add "const" qualifier to constants defined outside of omp parallel regions +* extreneous checks and code lines that never executa in MoL_registration +* all externally visible functions should be prefixed by IllinoisGRMHD_ (or put in an IllinoisGRMHD namespace -- note that this does not work for the extern "C" ones) +* (personal choice): you use very long lines, this is ok (your code, your style). Usually we prefer shorter lines (80 chars) but that is really each author's decision +* don't use explicitly spelled out decimals. The compiler will evaluate fractions at compile time anyway, ie use: (1./3.)*x instead of 0.3333*x +* consider passing CCTK_PASS_CTOC and DECLARE_CCTK_ARGUMENTS (may be slower though) rather than passing cctkGH and cctk_lsh +* gettimeofday may not exist, don' rely on it +* only pass by (non-const) reference objects that are actually going to be modified. Best is to pass by value. +* there are some unused functions with CCTK_FNAME() ie Fortran names defined. If they are not actually used I'd remove them. + +Obsolete code/methods: +* support symmetries using SymBase rather than cartgrid3f (ie remove SetCartSymGN) +* don't use "magic" numbers for Symmetry +* use CCTK_ERROR instead of CCTK_WARN(0, +

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[svn:einsteintoolkit] IllinoisGRMHD/trunk/ (Rev. 31)
by rhaas＠tapir.caltech.edu 02 Jun '14

02 Jun '14

User: rhaas Date: 2014/06/02 09:03 PM Added: /trunk/ README Log: IllinoisGRMHD: add README file license informatin is still missing File Changes: Directory: /trunk/ ================== File [added]: README Delta lines: +16 -0 =================================================================== --- trunk/README (rev 0) +++ trunk/README 2014-06-03 02:03:11 UTC (rev 31) @@ -0,0 +1,16 @@ +Cactus Code Thorn IllinoisGRMHD +Author(s) : Zachariah B. Etienne +Maintainer(s): Zachariah B. Etienne +Licence : TBD +-------------------------------------------------------------------------- + +1. Purpose + +IllinoisGRMHD employs a conservative, high-resolution shock capturing +scheme to evolve the general relativistic magnetohydrodynamics (GRMHD) +equations in a dynamical spacetime context. It is based on the +original code of the Illinois numerical relativity group, but has been +rewritten for the benefit of beginners, with complete documentation +and code comments, as well as a new, highly modular interface. This +code has been released as an open-source module in the latest version +of the Einstein Toolkit.

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Commits June 2014