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A variable 'arecomplex' which is by default set to false inside PetscBinaryRead() overrides 'complex', true in PetscBinaryRead(file, "complex", true) thus giving real valued output unless one manually changes arecomplex=true
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<div dir="ltr">A variable 'arecomplex' which is by default set to false inside PetscBinaryRead() overrides 'complex', true in PetscBinaryRead(file, "complex", true) thus giving real valued output unless one manually changes arecomplex=true inside the function.</div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Jul 1, 2024 at 5:40 PM Pierre Jolivet <<a href="mailto:pierre@joliv.et">pierre@joliv.et</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div><br id="m_-6671829671767901193lineBreakAtBeginningOfMessage"><div><br><blockquote type="cite"><div>On 1 Jul 2024, at 4:37 PM, maitri ksh <<a href="mailto:maitri.ksh@gmail.com" target="_blank">maitri.ksh@gmail.com</a>> wrote:</div><br><div><div dir="ltr" id="m_-6671829671767901193pfptBanneracnmlir" style="writing-mode:revert;color:revert;font-family:revert;font-feature-settings:revert;font-kerning:revert;font-size:revert;font-stretch:revert;font-variant-alternates:revert;font-variant-caps:revert;font-variant-east-asian:revert;font-variant-ligatures:revert;font-variant-numeric:revert;font-weight:revert;text-orientation:revert;zoom:revert;letter-spacing:revert;background-blend-mode:revert;background-image:revert;background-position:revert;background-repeat:revert;background-size:revert;border-collapse:revert;box-sizing:revert;break-after:revert;break-before:revert;break-inside:revert;caption-side:revert;clear:revert;columns:revert;column-fill:revert;column-gap:revert;column-rule:revert;column-span:revert;empty-cells:revert;float:revert;image-orientation:revert;isolation:revert;line-break:revert;line-height:revert;list-style:revert;mix-blend-mode:revert;object-fit:revert;object-position:revert;outline:revert;overflow:revert;quotes:revert;table-layout:revert;text-align:left;text-align-last:revert;text-decoration:revert;text-emphasis:revert;text-indent:revert;text-overflow:revert;text-transform:revert;text-underline-position:revert;vertical-align:revert;white-space:revert;word-break:revert;border-spacing:revert;word-spacing:revert;background-clip:revert;background-origin:revert;text-combine-upright:revert;display:block;opacity:revert;background-color:rgb(208,216,220);border-bottom:revert;border-left:revert;border-right:revert;height:revert;max-height:revert;max-width:revert;min-height:revert;width:revert;margin:16px 0px;padding:8px 16px;border-radius:4px;min-width:200px;border-top:4px solid rgb(144,164,174)"><div id="m_-6671829671767901193pfptBanneracnmlir" 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0px 1px;max-width:600px"><div id="m_-6671829671767901193pfptBanneracnmlir" style="writing-mode:unset;font-family:Arial,sans-serif;font-feature-settings:unset;font-kerning:unset;font-size:14px;font-stretch:unset;font-variant-alternates:unset;font-variant-caps:unset;font-variant-east-asian:unset;font-variant-ligatures:unset;font-variant-numeric:unset;font-weight:bold;text-orientation:unset;zoom:unset;letter-spacing:unset;background-blend-mode:unset;background-image:unset;background-position:unset;background-repeat:unset;background-size:unset;border-collapse:unset;border:unset;box-sizing:unset;break-after:unset;break-before:unset;break-inside:unset;caption-side:unset;clear:unset;columns:unset;column-fill:unset;column-gap:unset;column-rule:unset;column-span:unset;empty-cells:unset;float:unset;image-orientation:unset;isolation:unset;line-break:unset;line-height:18px;list-style:unset;mix-blend-mode:unset;object-fit:unset;object-position:unset;outline:unset;overflow:unset;quotes:unset;table-layout:unset;text-align:unset;text-align-last:unset;text-decoration:unset;text-emphasis:unset;text-indent:unset;text-overflow:unset;text-transform:unset;text-underline-position:unset;vertical-align:unset;white-space:unset;word-break:unset;border-spacing:unset;word-spacing:unset;background-clip:unset;background-origin:unset;text-combine-upright:unset;display:block;opacity:unset;background-color:rgb(208,216,220);border-radius:unset;height:unset;margin:unset;max-height:unset;max-width:unset;min-height:unset;min-width:unset;padding:unset;width:unset">This Message Is From an External Sender</div><div id="m_-6671829671767901193pfptBanneracnmlir" style="writing-mode:unset;font-family:Arial,sans-serif;font-feature-settings:unset;font-kerning:unset;font-size:12px;font-stretch:unset;font-variant-alternates:unset;font-variant-caps:unset;font-variant-east-asian:unset;font-variant-ligatures:unset;font-variant-numeric:unset;font-weight:unset;text-orientation:unset;zoom:unset;letter-spacing:unset;background-blend-mode:unset;background-image:unset;background-position:unset;background-repeat:unset;background-size:unset;border-collapse:unset;border:unset;box-sizing:unset;break-after:unset;break-before:unset;break-inside:unset;caption-side:unset;clear:unset;columns:unset;column-fill:unset;column-gap:unset;column-rule:unset;column-span:unset;empty-cells:unset;float:unset;image-orientation:unset;isolation:unset;line-break:unset;line-height:18px;list-style:unset;mix-blend-mode:unset;object-fit:unset;object-position:unset;outline:unset;overflow:unset;quotes:unset;table-layout:unset;text-align:unset;text-align-last:unset;text-decoration:unset;text-emphasis:unset;text-indent:unset;text-overflow:unset;text-transform:unset;text-underline-position:unset;vertical-align:unset;white-space:unset;word-break:unset;border-spacing:unset;word-spacing:unset;background-clip:unset;background-origin:unset;text-combine-upright:unset;display:block;opacity:unset;background-color:rgb(208,216,220);border-radius:unset;height:unset;margin-bottom:unset;margin-left:unset;margin-right:unset;max-height:unset;max-width:unset;min-height:unset;min-width:unset;padding:unset;width:unset;margin-top:2px">This message came from outside your organization.</div></div><div style="height:0px;clear:both;display:block;line-height:0;font-size:0.01px"></div></div><div dir="ltr" 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">I need to export complex vectors data from PETSc and read them in MATLAB. However, I am encountering some issues with the data format and interpretation in MATLAB. <br><div><br></div><div>code-snippet of the vector data export section:</div><div>// Assemble the vectors before exporting<br>ierr = VecAssemblyBegin(f); CHKERRQ(ierr);<br>ierr = VecAssemblyEnd(f); CHKERRQ(ierr);<br><br>PetscViewer viewerf;<br>// Save the complex vectors to binary files<br>ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD, "output_f.dat", FILE_MODE_WRITE, &viewerf); CHKERRQ(ierr);<br>ierr = VecView(f, viewerf); CHKERRQ(ierr);<br>ierr = PetscViewerDestroy(&viewerf); CHKERRQ(ierr);<br><br>// Create vectors to store the magnitudes<br>Vec f_magnitude;<br>ierr = VecDuplicate(f, &f_magnitude); CHKERRQ(ierr);<br><br>// Get local portion of the vectors<br>const PetscScalar *f_array;<br>PetscScalar *f_magnitude_array;<br>PetscInt n_local;<br><br>ierr = VecGetLocalSize(f, &n_local); CHKERRQ(ierr);<br>ierr = VecGetArrayRead(f, &f_array); CHKERRQ(ierr);<br>ierr = VecGetArray(f_magnitude, &f_magnitude_array); CHKERRQ(ierr);<br><br>// Compute the magnitude for each element<br>for (int i = 0; i < n_local; i++) {<br> f_magnitude_array[i] = PetscAbsScalar(f_array[i]);<br>}<br><br>// Restore arrays<br>ierr = VecRestoreArrayRead(f, &f_array); CHKERRQ(ierr);<br>ierr = VecRestoreArray(f_magnitude, &f_magnitude_array); CHKERRQ(ierr);<br><br>// Assemble the magnitude vectors<br>ierr = VecAssemblyBegin(f_magnitude); CHKERRQ(ierr);<br>ierr = VecAssemblyEnd(f_magnitude); CHKERRQ(ierr);<br><br>// Save the magnitude vectors to binary files<br>PetscViewer viewerfmag;<br>ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD, "output_f_mag.dat", FILE_MODE_WRITE, &viewerfmag); CHKERRQ(ierr);<br>ierr = VecView(f_magnitude, viewerfmag); CHKERRQ(ierr);<br>ierr = PetscViewerDestroy(&viewerfmag); CHKERRQ(ierr);<br></div><div><br></div><div>In MATLAB, I am using<span> </span><code>petscBinaryRead</code><span> </span>to read the data. The complex vectors are read, but only the real part is available. The magnitude vectors are however read as alternating zero and non-zero elements. What went wrong?<br></div><div>How can I export the data correctly to MATLAB-accessible format? (I have not configured PETSc with Matlab as I was encountering library conflict issues)</div></div></div></blockquote><br></div><div><br></div><div>How are you reading complex-valued binary files in MATLAB?</div><div>It is not the same as real-valued files, in particular, you must add the parameters 'complex', true to the PetscBinaryRead() call, type help PetscBinaryRead in the MATLAB console.</div><div><br></div><div>Thanks,</div><div>Pierre</div><br></div></blockquote></div>