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I see. Thank you for the feedback Matthew! Thanks, Miguel On 1 Apr 2024, at 18: 32, Matthew Knepley <knepley@ gmail. com> wrote: On Mon, Apr 1, 2024 at 11: 13 AM MIGUEL MOLINOS PEREZ <mmolinos@ us. es> wrote: Dear Matthew, Thank you for
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I see. Thank you for the feedback Matthew!
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<div>Thanks,</div>
<div>Miguel<br id="lineBreakAtBeginningOfMessage">
<div><br>
<blockquote type="cite">
<div>On 1 Apr 2024, at 18:32, Matthew Knepley <knepley@gmail.com> wrote:</div>
<br class="Apple-interchange-newline">
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<div dir="ltr">On Mon, Apr 1, 2024 at 11:13 AM MIGUEL MOLINOS PEREZ <<a href="mailto:mmolinos@us.es">mmolinos@us.es</a>> wrote:<br>
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<div>Dear Matthew,
<div><br>
</div>
<div>Thank you for your suggestion. I tried to update the vector with the information coming from the hdf5 file inside the main function. Then I print the vector two times (see the lines below), the first time it has the correct data. However, the second time,
it has the same values like I never updated it with VecLoad. </div>
<div><br>
</div>
<div>It is an alternative way of initialise a vector coming from DMSWarm with previously stored information (keeping the parallel structure)? </div>
</div>
</blockquote>
<div><br>
</div>
<div>Oh, you cannot use the Swarm vectors for VecLoad(). They are just a view into the particle data, and that view is destroyed on restore. Swarm data is stored in a particle-like data structure, not in Vecs. If you want to load this Vec, you have to duplicate
exactly as you did. This interface is likely to change in the next year to make this problem go away.</div>
<div><br>
</div>
<div> Thanks,</div>
<div><br>
</div>
<div> Matt</div>
<div> </div>
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<div>Miguel</div>
<div><br>
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<div>
<div style="color: rgb(212, 212, 212); background-color: rgb(30, 30, 30); font-family: Menlo, Monaco, "Courier New", monospace; line-height: 18px; white-space: pre-wrap;">
<div><span style="color: rgb(106, 153, 85);">//! Load Hdf5 viewer</span></div>
<div><span style="color: rgb(78, 201, 176);">PetscViewer</span> <span style="color: rgb(156, 220, 254);">
viewer_hdf5</span>;</div>
<div><span style="color: rgb(86, 156, 214);">REQUIRE_NOTHROW</span>(<span style="color: rgb(220, 220, 170);">PetscViewerHDF5Open</span>(MPI_COMM_WORLD, Output_hdf5_file,</div>
<div>FILE_MODE_READ, &viewer_hdf5));</div>
<div><span style="color: rgb(86, 156, 214);">REQUIRE_NOTHROW</span>(<span style="color: rgb(220, 220, 170);">PetscViewerHDF5PushTimestepping</span>(<span style="color: rgb(156, 220, 254);">viewer_hdf5</span>));</div>
<br>
<div><span style="color: rgb(106, 153, 85);">//! Load the vector and fill it with the information from the .hdf5 file</span></div>
<div><span style="color: rgb(78, 201, 176);">Vec</span> <span style="color: rgb(156, 220, 254);">
stdv_q</span>;</div>
<div><span style="color: rgb(86, 156, 214);">REQUIRE_NOTHROW</span>(<span style="color: rgb(220, 220, 170);">DMSwarmCreateGlobalVectorFromField</span>(</div>
<div><span style="color: rgb(156, 220, 254);">Simulation</span>.<span style="color: rgb(156, 220, 254);">atomistic_data</span>,
<span style="color: rgb(206, 145, 120);">"stdv-q"</span>, &<span style="color: rgb(156, 220, 254);">stdv_q</span>));</div>
<br>
<div><span style="color: rgb(86, 156, 214);">REQUIRE_NOTHROW</span>(<span style="color: rgb(220, 220, 170);">PetscViewerHDF5PushGroup</span>(<span style="color: rgb(156, 220, 254);">viewer_hdf5</span>,
<span style="color: rgb(206, 145, 120);">"/particle_fields"</span>));</div>
<div><span style="color: rgb(86, 156, 214);">REQUIRE_NOTHROW</span>(<span style="color: rgb(220, 220, 170);">VecLoad</span>(<span style="color: rgb(156, 220, 254);">stdv_q</span>,
<span style="color: rgb(156, 220, 254);">viewer_hdf5</span>));</div>
<div><span style="color: rgb(86, 156, 214);">REQUIRE_NOTHROW</span>(<span style="color: rgb(220, 220, 170);">VecView</span>(stdv_q,
<span style="color: rgb(86, 156, 214);">PETSC_VIEWER_STDOUT_WORLD</span>));</div>
<div><span style="color: rgb(86, 156, 214);">REQUIRE_NOTHROW</span>(<span style="color: rgb(220, 220, 170);">PetscViewerHDF5PopGroup</span>(<span style="color: rgb(156, 220, 254);">viewer_hdf5</span>));</div>
<br>
<div><span style="color: rgb(86, 156, 214);">REQUIRE_NOTHROW</span>(<span style="color: rgb(220, 220, 170);">DMSwarmDestroyGlobalVectorFromField</span>(</div>
<div><span style="color: rgb(156, 220, 254);">Simulation</span>.<span style="color: rgb(156, 220, 254);">atomistic_data</span>,
<span style="color: rgb(206, 145, 120);">"stdv-q"</span>, &<span style="color: rgb(156, 220, 254);">stdv_q</span>));</div>
<br>
<div><span style="color: rgb(106, 153, 85);">//! Destoy HDF5 context</span></div>
<div><span style="color: rgb(86, 156, 214);">REQUIRE_NOTHROW</span>(<span style="color: rgb(220, 220, 170);">PetscViewerDestroy</span>(&<span style="color: rgb(156, 220, 254);">viewer_hdf5</span>));</div>
<br>
<div><span style="color: rgb(106, 153, 85);">//! Load the vector again and print</span></div>
<div><span style="color: rgb(86, 156, 214);">REQUIRE_NOTHROW</span>(<span style="color: rgb(220, 220, 170);">DMSwarmCreateGlobalVectorFromField</span>(</div>
<div><span style="color: rgb(156, 220, 254);">Simulation</span>.<span style="color: rgb(156, 220, 254);">atomistic_data</span>,
<span style="color: rgb(206, 145, 120);">"stdv-q"</span>, &<span style="color: rgb(156, 220, 254);">stdv_q</span>));</div>
<br>
<div><span style="color: rgb(86, 156, 214);">REQUIRE_NOTHROW</span>(<span style="color: rgb(220, 220, 170);">VecView</span>(stdv_q,
<span style="color: rgb(86, 156, 214);">PETSC_VIEWER_STDOUT_WORLD</span>));</div>
<br>
<div><span style="color: rgb(86, 156, 214);">REQUIRE_NOTHROW</span>(<span style="color: rgb(220, 220, 170);">DMSwarmDestroyGlobalVectorFromField</span>(</div>
<div><span style="color: rgb(156, 220, 254);">Simulation</span>.<span style="color: rgb(156, 220, 254);">atomistic_data</span>,
<span style="color: rgb(206, 145, 120);">"stdv-q"</span>, &<span style="color: rgb(156, 220, 254);">stdv_q</span>));</div>
</div>
</div>
<div><br>
</div>
<div>Best,</div>
<div>Miguel</div>
<div><br id="m_-5709158563722898845lineBreakAtBeginningOfMessage">
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Miguel Molinos<br>
Investigador postdoctoral <br>
Juan de la Cierva<br>
Dpto. Mecánica de Medios Continuos y Teoría de Estructuras - ETSI<br>
Universidad de Sevilla<br>
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<div>On 1 Apr 2024, at 16:28, Matthew Knepley <<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>> wrote:</div>
<br>
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<div style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none;">
>From the description, my guess is that this is pointer confusion. The vector inside the function is different from the vector outside the function.</div>
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