<div dir="ltr">Hi Wang,<div><br></div><div>I don't have experience using Laserslab simulations, so I don't quite understand the workflow.</div><div><br></div><div>I recommended including a logfile for the case restart = .false. to confirm your initial run was successful. That may help others chime in for you to get the help you need.</div><div><br></div><div>Are you saying that the checkpoint file is corrupted? Or is the "empty image" from looking at <span style="font-variant-ligatures:no-common-ligatures;color:rgb(0,0,0);font-family:Menlo;font-size:11px">modu3d_forced_hdf5_plt_cnt_0000?</span></div>
<div><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><br></div><div>If you're concerned the plt_cnt file is empty, note this warning message: </div><div>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space"> </span>WARNING you have called IO_writePlotfile but no plot_vars are defined.</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space"> </span>put the vars you want in the plotfile in your flash.par (plot_var_1 = "dens")</span></p></div><div dir="ltr"><br></div><div>You also have some runs end with:</div><div>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space"> </span>[ 07-12-2020<span class="gmail-Apple-converted-space"> </span>16:42:22.879 ] [DRIVER_ABORT]: Driver_abort() called by PE <span class="gmail-Apple-converted-space"> </span>0</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space"> </span>[ 07-12-2020<span class="gmail-Apple-converted-space"> </span>16:42:22.879 ] abort_message: pi_createProtons3DRec: proton does not hit domain boundary!</span></p></div><div dir="ltr"><br></div><div>There were 19 runs in the logfile that you sent. What are the differences between the runs?</div><div dir="ltr"><br></div><div>Best,</div><div dir="ltr">--------<div>Ryan</div></div></div></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sun, Jul 12, 2020 at 2:05 PM Wang <<a href="mailto:astrowjz@mail.bnu.edu.cn">astrowjz@mail.bnu.edu.cn</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 style="overflow-wrap: break-word;">Hi Ryan,<div><br></div><div>Thanks for your advice!<br><div><br></div><div>I run with restart = .false. before, it will produce a new checkpoint file, but I want to use the checkpoint file that I have obtained from Laserslab simulation, so that I can get magnetic information from proton image.</div><div><br></div><div>If I run with restart = .false., I can get an image of uniform proton distribution, otherwise, if I run with restart = .true. to load data, I can only get an empty image.</div><div><br></div><div>Do you mean I should run first time with <span style="color:rgb(0,0,0)">restart = .false. </span>to rewrite the checkpoint file and run second time with <span style="color:rgb(0,0,0)">restart = .true. to obtain proton image?</span></div><div><span style="color:rgb(0,0,0)"><br></span></div><div><span style="color:rgb(0,0,0)">Best,</span></div><div><span style="color:rgb(0,0,0)">Wang</span></div><div>
<div><br><blockquote type="cite"><div>On Jul 13, 2020, at 00:30, Ryan Farber <<a href="mailto:rjfarber@umich.edu" target="_blank">rjfarber@umich.edu</a>> wrote:</div><br><div><div dir="ltr">Hi Wang,<div><br></div><div>It looks like you accidentally left restart = .true. in flash.par. If that was intentional, it would be helpful to see the logfile of the run with restart = .false. that produces the checkpoint file you're trying to restart from.</div><div><br></div><div>Best,<br clear="all"><div><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div dir="ltr">--------<div>Ryan</div></div></div></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sun, Jul 12, 2020 at 6:22 AM Wang <<a href="mailto:astrowjz@mail.bnu.edu.cn" target="_blank">astrowjz@mail.bnu.edu.cn</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><span>Hi all,</span><div><br></div><div>Recently I am using FLASH to simulate proton images. I have already run a simulation and generated a 3D check point file. And I tended to use proton imaging unit and let a proton beam pass through the simulation region of the check point files. If everything’s ok, I can obtain a txt file which records proton’s position.<br><br></div><div>But now, I can only obtain an empty file, I don’t know how to fix it. </div><div>Thank you for your help, and<span style="font-family:Calibri,sans-serif"> any suggestions would be greatly appreciated.</span></div><div><br></div><div>This is the setup of protonimaging:</div><div><div style="margin:0px;font-stretch:normal;line-height:normal;font-family:"Helvetica Neue"">./setup ProtonImaging -auto -3d -geometry=cartesian -parfile=flash.par -nxb=32 -nyb=32 -nzb=32 +protonImaging --without-unit=physics/Hydro --without-unit=physics/Eos -objdir=astrowjz/protonimaging pi_maxBeams=1 pi_maxDetectors=1 threadProtonTrace=True</div></div><div style="margin:0px;font-stretch:normal;line-height:normal;font-family:"Helvetica Neue""><br></div><div style="margin:0px;font-stretch:normal;line-height:normal;font-family:"Helvetica Neue""><br></div><div style="margin:0px;font-stretch:normal;line-height:normal;font-family:"Helvetica Neue"">Best,</div><div style="margin:0px;font-stretch:normal;line-height:normal;font-family:"Helvetica Neue"">Wang</div><div style="margin:0px;font-stretch:normal;line-height:normal;font-family:"Helvetica Neue""><br></div><div style="margin:0px;font-stretch:normal;line-height:normal;font-family:"Helvetica Neue""><br></div><div style="margin:0px;font-stretch:normal;line-height:normal;font-family:"Helvetica Neue""><br></div><div style="margin:0px;font-stretch:normal;line-height:normal;font-family:"Helvetica Neue""></div></div><div><div style="margin:0px;font-stretch:normal;line-height:normal;font-family:"Helvetica Neue""></div></div><div><div style="margin:0px;font-stretch:normal;line-height:normal;font-family:"Helvetica Neue""></div></div><div><div style="margin:0px;font-stretch:normal;line-height:normal;font-family:"Helvetica Neue""></div></div><div><div style="margin:0px;font-stretch:normal;line-height:normal;font-family:"Helvetica Neue""></div></div><div><br>
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