[gmx-developers] question for gromacs-5.0 source code

[Mark Abraham]

On Thu, Aug 21, 2014 at 10:12 AM, David van der Spoel <spoel at xray.bmc.uu.se>
wrote:

> On 2014-08-21 10:08, xiexiaobin at sjtu.edu.cn wrote:
>
>> Dose these functions will be called when mdrun?
>>
> No. If you want to learn more go to your build directory and run
> make doc-all
> this will build the development documentation, accessible using your
> browser from doxygen/index.html
>

Or, as auto-built by Gerrit -
http://jenkins.gromacs.org/job/Doxygen_Gerrit_5_0/javadoc/html-lib/page_unittesting.xhtml

Mark


>
>> ------------------------------------------------------------------------
>> xiexiaobin at sjtu.edu.cn
>>
>>     *From:* David van der Spoel <mailto:spoel at xray.bmc.uu.se>
>>     *Date:* 2014-08-21 16:00
>>
>>     *To:* gmx-developers <mailto:gmx-developers at gromacs.org>
>>     *Subject:* Re: [gmx-developers] question for gromacs-5.0 source code
>>     On 2014-08-21 09:57, xiexiaobin at sjtu.edu.cn wrote:
>>      > The functions in this file are like this:
>>     It is googletest code to test the FFT routines.
>>      >
>>      > //TODO: test with threads and more than 1 MPI ranks
>>      > TEST_F(FFFTest3D, Real5_6_9)
>>      > {
>>      > int ndata[] = {5, 6, 9};
>>      > MPI_Comm comm[] = {MPI_COMM_NULL, MPI_COMM_NULL};
>>      > real * rdata;
>>      > t_complex* cdata;
>>      > ivec local_ndata, offset, rsize, csize, complex_order;
>>      >
>>      > gmx_parallel_3dfft_init(&fft_, ndata, &rdata, &cdata,
>>      > comm, TRUE, 1);
>>      >
>>      > gmx_parallel_3dfft_real_limits(fft_, local_ndata, offset, rsize);
>>      > gmx_parallel_3dfft_complex_limits(fft_, complex_order,
>>      > local_ndata, offset, csize);
>>      > checker_.checkVector(rsize, "rsize");
>>      > checker_.checkVector(csize, "csize");
>>      > int size = csize[0]*csize[1]*csize[2];
>>      >
>>      > memcpy(rdata, inputdata, size*sizeof(t_complex));
>>      > gmx_parallel_3dfft_execute(fft_, GMX_FFT_REAL_TO_COMPLEX, 0,
>> NULL);
>>      > //TODO use std::complex and add checkComplex for it
>>      > checker_.checkSequenceArray(size*2,
>>      > reinterpret_cast<real*>(cdata), "forward");
>>      >
>>      > memcpy(cdata, inputdata, size*sizeof(t_complex));
>>      > gmx_parallel_3dfft_execute(fft_, GMX_FFT_COMPLEX_TO_REAL, 0,
>> NULL);
>>      > for (int i = 0; i < ndata[0]*ndata[1]; i++) //check sequence but
>> skip
>>      > unused data
>>      > {
>>      > checker_.checkSequenceArray(ndata[2], rdata+i*rsize[2],
>>      > gmx::formatString("backward %d", i).c_str());
>>      > }
>>      > }
>>      >
>>      >
>>     ------------------------------------------------------------
>> ------------
>>      > xiexiaobin at sjtu.edu.cn
>>      >
>>      >     *From:* David van der Spoel <mailto:spoel at xray.bmc.uu.se>
>>      >     *Date:* 2014-08-21 15:53
>>      >     *To:* gmx-developers <mailto:gmx-developers at gromacs.org>
>>      >     *Subject:* Re: [gmx-developers] question for gromacs-5.0
>>     source code
>>      >     On 2014-08-21 09:35, xiexiaobin at sjtu.edu.cn wrote:
>>      >      > Hi,
>>      >      >
>>      >      > I saw a source file fft.cpp that contains some test
>> functions
>>      >     under the
>>      >      > path gromacs-5.0\src\gromacs\fft\tests.What is it used
>>     for?Dose any
>>      >      > functions in other files will use this file's functions?
>>      >     What does it look like? Testing. So the answer is probably no.
>>      >      >
>>      >      > BR,
>>      >      > Steve
>>      >      >
>>      >      >
>>      >
>>     ------------------------------------------------------------
>> ------------
>>      >      > xiexiaobin at sjtu.edu.cn <mailto:xiexiaobin at sjtu.edu.cn>
>>      >      >
>>      >      >
>>      >     --
>>      >     David van der Spoel, Ph.D., Professor of Biology
>>      >     Dept. of Cell & Molec. Biol., Uppsala University.
>>      >     Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
>>      >     spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
>>      >     --
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>>      >
>>     --
>>     David van der Spoel, Ph.D., Professor of Biology
>>     Dept. of Cell & Molec. Biol., Uppsala University.
>>     Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
>>     spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
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>>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
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> Gromacs Developers mailing list
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