From ljhwang at ucdavis.edu Wed Oct 3 14:08:56 2018 From: ljhwang at ucdavis.edu (Lorraine Hwang) Date: Wed, 3 Oct 2018 14:08:56 -0700 Subject: [aspect-devel] CIG Wanted: Your 2018 Fall AGU Abstract Message-ID: Congratulations to all CIG community members with accepted abstracts for this year’s 2018 Fall AGU Meeting. Help your colleagues and attendees find your research by listing it on the CIG website: https://geodynamics.org/cig/events/calendar/agu-2018/2018-agu-abstracts/ To do so, please reply to this email events at geodynamcis.org by simply cutting and pasting your acceptance information AND your link to your abstract. e.g., https://agu.confex.com/agu/fm18/meetingapp.cgi/Paper/419977 Abstract ID: 419977 Abstract Title: A Decade+ of Open Software Practice at CIG Final Paper Number: IN43C-2835 Presentation Type: Poster Session Date and Time: Thursday, 13 December 2018; 13:40 - 18:00 Session Number and Title: IN43C: FAIR Data Is Not Enough: Communicating Data Quality and Making Analytical Code FAIR Posters Best, -Lorraine ***************************** Lorraine Hwang, Ph.D. Associate Director, CIG 530.752.3656 -------------- next part -------------- An HTML attachment was scrubbed... URL: From ljhwang at ucdavis.edu Fri Oct 5 15:22:09 2018 From: ljhwang at ucdavis.edu (Lorraine Hwang) Date: Fri, 5 Oct 2018 15:22:09 -0700 Subject: [aspect-devel] We are moving ... the mailing list Message-ID: <81EAFD61-E7B9-4B71-9D26-54BA160A3C9D@ucdavis.edu> 5 October 2018 Dear aspect-devel Community, In an effort to improve the service we provide to the CIG community, the aspect-devel mailing list will be moved to a discussion forum. The discussion forum will provide a searchable and open interface for you to locate discussion topics and provide help to members of our community. This action is part of our slow roll out of the forum for the entire CIG community. Hence, as beta testers, we encourage you to provide feedback on what can be improved. We have chosen the open source discourse platform as a civilized place to hold discussion. You can find out more about the platform by navigating here: https://www.discourse.org/ Beginning sometime next week, all emails to the mailing list will be forwarded to the forum. You will be notified when this happens. As we are in beta testing, the forum is currently hidden from public view. You will need to register as a user to receive replies and see all discussions on the topic. The forum supports login from GitHub or you can create a new account To begin: 1, Sign up by navigating to: https://community.geodynamics.org/login 2. Check your email and spam folder. User accounts are automatically approved upon registering. Follow instructions to activate your account. 3. Login in with your new account. 4. Read the header on the page that begins with “Welcome … “, the FAQs and the About the ASPECT Category (this is the pinned topic in the ASPECT category). At this point you should see the available forum categories including the ASPECT category. This is where all aspect-devel emails will be listed. Don’t forget to set your notifications! There are quite a number of settings and features you can tweak so we encourage you to explore. You may wish to check your user settings Emails and Notifications. We anticipate continuing the forwarding for several weeks to ensure a smooth transition and encourage you all to sign up early and help us make this a robust platform for our community. Thanks for your participation! Best, -Lorraine ***************************** Lorraine Hwang, Ph.D. Associate Director, CIG 530.752.3656 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2018-10-05 at 2.36.07 PM.png Type: image/png Size: 48640 bytes Desc: not available URL: From kneumiller at opendap.org Fri Oct 5 12:50:16 2018 From: kneumiller at opendap.org (Kodi Neumiller) Date: Fri, 5 Oct 2018 13:50:16 -0600 Subject: [aspect-devel] Calling a parameter value in utilities Message-ID: I created a new global parameter that takes a boolean value and I am trying to pass it in to the read_and_distribute_file_content function. Is there already something in place that can be called from utilities to check the value of a global parameter or do I need to implement something new? Thanks, Kodi -------------- next part -------------- An HTML attachment was scrubbed... URL: From rene.gassmoeller at mailbox.org Fri Oct 5 16:58:40 2018 From: rene.gassmoeller at mailbox.org (Rene Gassmoeller) Date: Fri, 5 Oct 2018 16:58:40 -0700 Subject: [aspect-devel] Calling a parameter value in utilities In-Reply-To: References: Message-ID: <25952162-8986-d554-a4f8-4204bf126ae9@mailbox.org> Hi Kodi, can you give a bit more information about how you implemented this global parameter? Is it a member of the `Parameters` class? Then it would probably be easiest to hand over this variable to the `read_and_distribute_file_content` function as a parameter from the calling plugin. Many calling plugins can already access global parameters using the `SimulatorAccess` class. Try accessing `this->get_parameters().your_variable_name` in the calling plugin, and check if this gives you the parameter you are looking for. Out of curiosity: What does this parameter do? How would it modify the behavior of the function? And from where do you call the function? Best, Rene On 10/05/2018 12:50 PM, Kodi Neumiller wrote: > I created a new global parameter that takes a boolean value and I am > trying to pass it in to the read_and_distribute_file_content function. > Is there already something in place that can be called from utilities > to check the value of a global parameter or do I need to > implement something new? > > Thanks, > Kodi > > > _______________________________________________ > We are MOVING… this mailing list to a discussion forum: community.geodynamics.org in the coming weeks. More information coming soon! > _______________________________________________ > Aspect-devel mailing list > Aspect-devel at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel -- Rene Gassmoeller https://gassmoeller.github.io/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From rene.gassmoeller at mailbox.org Fri Oct 5 17:47:05 2018 From: rene.gassmoeller at mailbox.org (Rene Gassmoeller) Date: Fri, 5 Oct 2018 17:47:05 -0700 Subject: [aspect-devel] We are moving ... the mailing list In-Reply-To: <81EAFD61-E7B9-4B71-9D26-54BA160A3C9D@ucdavis.edu> References: <81EAFD61-E7B9-4B71-9D26-54BA160A3C9D@ucdavis.edu> Message-ID: <46d43ea4-4622-def0-9c5c-cca124adacea@mailbox.org> Hi all, Wow. So now the secret development is out there :-). As discussed on Tuesday at the last online user meeting we would like to test how this transition will work, and want to make sure everything transitions as smoothly as possible. All our tests suggest that it will be a much more convenient and nicer interaction, and will allow for easier communication than a mailing list. Additionally, past discussions will be simpler to search and reference, especially for users that are not part of the mailing list. But do not worry if you prefer to have all messages in your mail inbox, there is a mailing list mode that will allow you to keep everything as is, receive emails for every post, and directly reply to them. If you want to be one of the first posters on the new forum, then feel free to register at https://community.geodynamics.org/login (e.g. using your github account), and familiarize yourself with the new interface. I created a feedback post at https://community.geodynamics.org/t/asking-for-feedback-about-the-new-forum/100/2 and would appreciate any feedback about design, the process, or your concerns. Since the forum is highly configurable, it is most likely we can incorporate constructive suggestions. Let us know what you think, Best, Rene On 10/05/2018 03:22 PM, Lorraine Hwang wrote: > > 5 October 2018 > > Dear aspect-devel Community, > > In an effort to improve the service we provide to the CIG community, > the aspect-devel mailing list will be* moved* to a discussion forum. >  The discussion forum will provide a searchable and open interface for > you to locate discussion topics and provide help to members of our > community. This action is part of our slow roll out of the forum for > the entire CIG community. Hence, as beta testers, we encourage you to > provide feedback on what can be improved. > > We have chosen the open source /discourse/ platform as a civilized > place to hold discussion. You can find out more about the platform by > navigating here: > https://www.discourse.org/ > > Beginning sometime next week, all emails to the mailing list will be > forwarded to the forum. You will be notified when this happens. As we > are in beta testing, the forum is currently hidden from public view. > You will need to register as a user to receive replies and see all > discussions on the topic.  The forum supports login from GitHub or you > can create a new account > > To begin: > 1, Sign up by navigating to: > > https://community.geodynamics.org/login > > 2. Check your email and spam folder. User accounts are automatically > approved upon registering. Follow instructions to activate your account. > 3. Login in with your new account. > 4. Read the header on the page that begins with “Welcome … “,  the > FAQs and the About the ASPECT Category (this is the pinned topic in > the ASPECT category). > > At this point you should see the available forum categories including > the ASPECT category.  This is where all aspect-devel emails will be > listed. Don’t forget to set your notifications! > > There are quite a number of settings and features you can tweak so we > encourage you to explore. You may wish to check your user settings > Emails and Notifications. > > We anticipate continuing the forwarding for several weeks to ensure a > smooth transition and encourage you all to sign up early and help us > make this a robust platform for our community. > > Thanks for your participation! > > Best, > -Lorraine > > ***************************** > Lorraine Hwang, Ph.D. > Associate Director, CIG > 530.752.3656 > > > > > > _______________________________________________ > We are MOVING… this mailing list to a discussion forum: community.geodynamics.org in the coming weeks. More information coming soon! > _______________________________________________ > Aspect-devel mailing list > Aspect-devel at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel -- Rene Gassmoeller https://gassmoeller.github.io/ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2018-10-05 at 2.36.07 PM.png Type: image/png Size: 48640 bytes Desc: not available URL: From rene.gassmoeller at mailbox.org Tue Oct 9 11:38:11 2018 From: rene.gassmoeller at mailbox.org (Rene Gassmoeller) Date: Tue, 9 Oct 2018 11:38:11 -0700 Subject: [aspect-devel] We are moving ... the mailing list In-Reply-To: <46d43ea4-4622-def0-9c5c-cca124adacea@mailbox.org> References: <81EAFD61-E7B9-4B71-9D26-54BA160A3C9D@ucdavis.edu> <46d43ea4-4622-def0-9c5c-cca124adacea@mailbox.org> Message-ID: Hi all, as mentioned, we (thanks, Tyler!) now activated the automatic forwarding from the mailing list to the new forum. A few things to keep in mind during the transition: - Every email on the mailing list will create a discussion on the forum so that the conversation can happen on either platform. Answers on the forum will unfortunately not be forwarded to the mailing list to prevent mails bouncing back and forth between the platforms (complicated solutions to this have been considered and we opted for the simple way out). We encourage you to use the forum as much as possible, but keep in mind that users who are exclusively subscribed to the mailing list will not see your reply until they transition to the forum. - Every email on the mailing list will generate an auto-reply to the sender that explains the transition. - We currently plan to keep the mailing list active until the end of October and switch off the delivery of emails by Oct 31st. It will still send the auto-reply afterwards to let everyone know about the change. Of course if we discover severe problems with the forum this date could be extended. Do not forget after you signed up for the forum to click on the ASPECT category, and set it to 'Watching' or at least 'Watching first post'. Otherwise you will not be notified about new discussions. You can change this setting by clicking on the little circle next to the 'New Topic' button on the top right, above the list of all ASPECT topics. https://community.geodynamics.org/c/aspect Looking forward to seeing you on the forum. Best, Rene On 10/05/2018 05:47 PM, Rene Gassmoeller wrote: > > Hi all, > > Wow. So now the secret development is out there :-). As discussed on > Tuesday at the last online user meeting we would like to test how this > transition will work, and want to make sure everything transitions as > smoothly as possible. All our tests suggest that it will be a much > more convenient and nicer interaction, and will allow for easier > communication than a mailing list. Additionally, past discussions will > be simpler to search and reference, especially for users that are not > part of the mailing list. But do not worry if you prefer to have all > messages in your mail inbox, there is a mailing list mode that will > allow you to keep everything as is, receive emails for every post, and > directly reply to them. > > If you want to be one of the first posters on the new forum, then feel > free to register at https://community.geodynamics.org/login (e.g. > using your github account), and familiarize yourself with the new > interface. I created a feedback post at > https://community.geodynamics.org/t/asking-for-feedback-about-the-new-forum/100/2 > and would appreciate any feedback about design, the process, or your > concerns. Since the forum is highly configurable, it is most likely we > can incorporate constructive suggestions. > > Let us know what you think, > > Best, > > Rene > > > On 10/05/2018 03:22 PM, Lorraine Hwang wrote: >> >> 5 October 2018 >> >> Dear aspect-devel Community, >> >> In an effort to improve the service we provide to the CIG community, >> the aspect-devel mailing list will be* moved* to a discussion forum. >>  The discussion forum will provide a searchable and open interface >> for you to locate discussion topics and provide help to members of >> our community. This action is part of our slow roll out of the forum >> for the entire CIG community. Hence, as beta testers, we encourage >> you to provide feedback on what can be improved. >> >> We have chosen the open source /discourse/ platform as a civilized >> place to hold discussion. You can find out more about the platform by >> navigating here: >> https://www.discourse.org/ >> >> Beginning sometime next week, all emails to the mailing list will be >> forwarded to the forum. You will be notified when this happens. As we >> are in beta testing, the forum is currently hidden from public view. >> You will need to register as a user to receive replies and see all >> discussions on the topic.  The forum supports login from GitHub or >> you can create a new account >> >> To begin: >> 1, Sign up by navigating to: >> >> https://community.geodynamics.org/login >> >> 2. Check your email and spam folder. User accounts are automatically >> approved upon registering. Follow instructions to activate your account. >> 3. Login in with your new account. >> 4. Read the header on the page that begins with “Welcome … “,  the >> FAQs and the About the ASPECT Category (this is the pinned topic in >> the ASPECT category). >> >> At this point you should see the available forum categories including >> the ASPECT category.  This is where all aspect-devel emails will be >> listed. Don’t forget to set your notifications! >> >> There are quite a number of settings and features you can tweak so we >> encourage you to explore. You may wish to check your user settings >> Emails and Notifications. >> >> We anticipate continuing the forwarding for several weeks to ensure a >> smooth transition and encourage you all to sign up early and help us >> make this a robust platform for our community. >> >> Thanks for your participation! >> >> Best, >> -Lorraine >> >> ***************************** >> Lorraine Hwang, Ph.D. >> Associate Director, CIG >> 530.752.3656 >> >> >> >> >> >> _______________________________________________ >> We are MOVING… this mailing list to a discussion forum: community.geodynamics.org in the coming weeks. More information coming soon! >> _______________________________________________ >> Aspect-devel mailing list >> Aspect-devel at geodynamics.org >> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel > > -- > Rene Gassmoeller > https://gassmoeller.github.io/ > > > _______________________________________________ > Aspect-devel is MOVING… to a discussion forum: > community.geodynamics.org in the coming weeks. More information coming soon! > _______________________________________________ > Aspect-devel mailing list > Aspect-devel at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel -- Rene Gassmoeller https://gassmoeller.github.io/ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2018-10-05 at 2.36.07 PM.png Type: image/png Size: 48640 bytes Desc: not available URL: From rene.gassmoeller at mailbox.org Tue Oct 9 12:00:18 2018 From: rene.gassmoeller at mailbox.org (Rene Gassmoeller) Date: Tue, 09 Oct 2018 19:00:18 -0000 Subject: [aspect-devel] ASPECT Newsletter #65 Message-ID: <20181009185118.26F99AC1B02@geodynamics.org> Hello everyone! This is ASPECT newsletter #65. It automatically reports recently merged features and discussions about the ASPECT mantle convection code. ## Below you find a list of recently proposed or merged features: #2681: www: update Timo's affiliation (proposed by tjhei; merged) https://github.com/geodynamics/aspect/pull/2681 #2680: update Timo's affiliation (proposed by tjhei; merged) https://github.com/geodynamics/aspect/pull/2680 #2679: Fix multiple additional named outputs postprocessor (proposed by gassmoeller; merged) https://github.com/geodynamics/aspect/pull/2679 #2678: Implement maximum first timestep parameter. (proposed by MFraters) https://github.com/geodynamics/aspect/pull/2678 #2677: design a structure for interpolating material model outputs onto comp... (proposed by jdannberg) https://github.com/geodynamics/aspect/pull/2677 #2676: update parameters (proposed by tjhei; merged) https://github.com/geodynamics/aspect/pull/2676 #2675: [WIP] implement consistent boundary heat flux computation (proposed by gassmoeller) https://github.com/geodynamics/aspect/pull/2675 #2674: Move a comment (proposed by bartniday; merged) https://github.com/geodynamics/aspect/pull/2674 #2673: Fix some typos (proposed by gassmoeller; merged) https://github.com/geodynamics/aspect/pull/2673 #2672: Fix typo in documentation (proposed by bartniday; merged) https://github.com/geodynamics/aspect/pull/2672 #2671: Fix bound preserving limiter in 3d (proposed by gassmoeller; merged) https://github.com/geodynamics/aspect/pull/2671 #2667: Fix reference temperature for discontinuous element face terms (proposed by gassmoeller; merged) https://github.com/geodynamics/aspect/pull/2667 #2661: allow /rebuild in Jenkins (proposed by tjhei; merged) https://github.com/geodynamics/aspect/pull/2661 #2650: Use the max of physical and artificial viscosity. (proposed by bangerth; merged) https://github.com/geodynamics/aspect/pull/2650 #2574: World builder3 add plugins (proposed by MFraters; merged) https://github.com/geodynamics/aspect/pull/2574 #2525: Create CODE_OF_CONDUCT.md (proposed by lkellogg; merged) https://github.com/geodynamics/aspect/pull/2525 #2419: [Bugfix] add an option that fixes temperature/composition only on inflow/close... (proposed by jdannberg; merged) https://github.com/geodynamics/aspect/pull/2419 ## And this is a list of recently opened or closed discussions: #2682: Update all references to the mailing list by the new forum address (opened) https://github.com/geodynamics/aspect/issues/2682 #2658: How could I get 'composition' in the prescribed_velocity.cc? (closed) https://github.com/geodynamics/aspect/issues/2658 #2611: Fix bibtex entry in citing.html (closed) https://github.com/geodynamics/aspect/issues/2611 #903: Investigate compositional boundary conditions at in/outflow parts of the boundary (closed) https://github.com/geodynamics/aspect/issues/903 A list of all major changes since the last release can be found at https://aspect.geodynamics.org/doc/doxygen/changes_current.html. Thanks for being part of the community! Let us know about questions, problems, bugs or just share your experience by writing to aspect-devel at geodynamics.org, or by opening issues or pull requests at https://www.github.com/geodynamics/aspect. Additional information can be found at https://aspect.geodynamics.org/, and https://geodynamics.org/cig/software/aspect/. -------------- next part -------------- An HTML attachment was scrubbed... URL: From kneumiller at opendap.org Thu Oct 11 08:25:07 2018 From: kneumiller at opendap.org (Kodi Neumiller) Date: Thu, 11 Oct 2018 09:25:07 -0600 Subject: [aspect-devel] Including a separate directory in Aspect Message-ID: <43B4481D-E7BD-4798-B413-4E6911CFFB21@opendap.org> Hello, I am trying to include a header file in one of the Aspect files and I am wondering what the best approach is? I was looking into using include_directories inside the cmake file, but I am not very familiar with cmake itself. Any help is appreciated Thank you, Kodi Neumiller From ljhwang at ucdavis.edu Thu Oct 11 11:31:33 2018 From: ljhwang at ucdavis.edu (Lorraine Hwang) Date: Thu, 11 Oct 2018 14:31:33 -0400 Subject: [aspect-devel] This is a test Message-ID: <8093862D-477B-4B8F-9392-80BB608EF810@ucdavis.edu> Test Sorry for the spam! Best, -Lorraine ***************************** Lorraine Hwang, Ph.D. Associate Director, CIG 530.752.3656 out of office: October 9-24 -------------- next part -------------- An HTML attachment was scrubbed... URL: From kneumiller at opendap.org Thu Oct 11 09:09:28 2018 From: kneumiller at opendap.org (Kodi Neumiller) Date: Thu, 11 Oct 2018 10:09:28 -0600 Subject: [aspect-devel] Calling a parameter value in utilities In-Reply-To: References: Message-ID: <5945037A-092A-48DD-ADEB-97573F5F4B6D@opendap.org> Rene, Thanks for the help, passing the value as a parameter in the read_and_distribute_file_content function from the calling plugin seemed to work! The parameter is used to determine if the file to be read is coming from a url or is a local file. It would affect the way the function reads in the file if it needs to get said file from a url. Otherwise if it is a local file the function will read in the file as usual. The function is still being called from the appropriate plugins, except now it has the option to read files from a url or from the local system. > On Oct 5, 2018, at 1:50 PM, Kodi Neumiller wrote: > > I created a new global parameter that takes a boolean value and I am trying to pass it in to the read_and_distribute_file_content function. Is there already something in place that can be called from utilities to check the value of a global parameter or do I need to implement something new? > > Thanks, > Kodi -------------- next part -------------- An HTML attachment was scrubbed... URL: From rene.gassmoeller at mailbox.org Fri Oct 19 15:00:21 2018 From: rene.gassmoeller at mailbox.org (Rene Gassmoeller) Date: Fri, 19 Oct 2018 15:00:21 -0700 Subject: [aspect-devel] ASPECT online user meeting, Oct 24th, 9am PT In-Reply-To: <608819df-ae5d-7ed5-7b76-94866b762a35@mailbox.org> References: <608819df-ae5d-7ed5-7b76-94866b762a35@mailbox.org> Message-ID: Hi all, this is an early reminder that we will have our ASPECT user meeting next week, Oct 24th at 9 am PT. As always the meeting will be available using the Zoom software, at: https://zoom.us/j/887502259 Topics we could discuss are feedback to our new forum, questions regarding the transition from the mailing list, setting a day for our ASPECT dinner during AGU, and any open issue you are interested in. As always, if you are interested in a certain feature of ASPECT, or want to present one of your works related to ASPECT then let us know until Tuesday so that we can schedule it. Looking forward to seeing you next week. Best, Rene From rene.gassmoeller at mailbox.org Wed Oct 24 12:00:23 2018 From: rene.gassmoeller at mailbox.org (Rene Gassmoeller) Date: Wed, 24 Oct 2018 19:00:23 -0000 Subject: [aspect-devel] ASPECT Newsletter #66 Message-ID: <20181024185120.6DFAFAC0360@geodynamics.org> Hello everyone! This is ASPECT newsletter #66. It automatically reports recently merged features and discussions about the ASPECT mantle convection code. ## Below you find a list of recently proposed or merged features: #2692: remove broken badge from readme (proposed by tjhei) https://github.com/geodynamics/aspect/pull/2692 #2691: [bugfix] fix restarting melt models (proposed by jdannberg) https://github.com/geodynamics/aspect/pull/2691 #2690: Instantiate additional dislocation viscosities output object (proposed by gassmoeller) https://github.com/geodynamics/aspect/pull/2690 #2689: Balto plugin (proposed by kneumiller) https://github.com/geodynamics/aspect/pull/2689 #2688: Replace aspect-devel references (proposed by naliboff; merged) https://github.com/geodynamics/aspect/pull/2688 #2687: fix doxygen formatting (proposed by tjhei; merged) https://github.com/geodynamics/aspect/pull/2687 #2686: change mailing list link and contact section (proposed by tjhei; merged) https://github.com/geodynamics/aspect/pull/2686 #2685: Remove reference to mailing list from website (proposed by gassmoeller; merged) https://github.com/geodynamics/aspect/pull/2685 #2684: Fix typo in website title. (proposed by gassmoeller; merged) https://github.com/geodynamics/aspect/pull/2684 #2683: Remove link to legal notice of deal.ii on website (proposed by gassmoeller; merged) https://github.com/geodynamics/aspect/pull/2683 #2677: design a structure for interpolating material model outputs onto comp... (proposed by jdannberg; merged) https://github.com/geodynamics/aspect/pull/2677 ## And this is a list of recently opened or closed discussions: #2657: how do I get stress tensor of some mesh point? (closed) https://github.com/geodynamics/aspect/issues/2657 A list of all major changes since the last release can be found at https://aspect.geodynamics.org/doc/doxygen/changes_current.html. Thanks for being part of the community! Let us know about questions, problems, bugs or just share your experience by writing to aspect-devel at geodynamics.org, or by opening issues or pull requests at https://www.github.com/geodynamics/aspect. Additional information can be found at https://aspect.geodynamics.org/, and https://geodynamics.org/cig/software/aspect/. -------------- next part -------------- An HTML attachment was scrubbed... URL: From bangerth at colostate.edu Tue Oct 30 10:11:14 2018 From: bangerth at colostate.edu (Wolfgang Bangerth) Date: Tue, 30 Oct 2018 17:11:14 +0000 Subject: [aspect-devel] Postprocessing scripts In-Reply-To: <07d5114e-12f4-7d30-2e70-1c7f7d74e5a4@elsi.jp> References: <351e8e64-96ef-22c3-006b-613b0b8bcba9@elsi.jp> <53d2e5d3-100b-7576-4358-333314aa5047@colostate.edu> <07d5114e-12f4-7d30-2e70-1c7f7d74e5a4@elsi.jp> Message-ID: <5538ac12-1835-74ba-9134-c3d936f19764@colostate.edu> Marine, I'm not sure anyone ever answered this email -- so let me do this 3 months late... > But to be able to do a good comparisons with existing results, I'll need > things like horizontal averages (of composition, temperature, > velocities) and difference between the field and the horizontal average > (of composition, temperature). But the horizontal here is average over a > sphere, so I am guessing the post-processors are not so easy. (to get > average radial profiles) This is actually what our 'depth average' postprocessor does -- average over all points at a certain depth where depth is defined differently for each geometry. > I'm definitely not used to paraview, and I'm more used to do all my data > processing by hand... So a good tutorial on how to implement that with > paraview or equivalent, with a scripting (I usually have several dozens > of runs to process at a time) would be nice :-) But so far, I think that > a way to obtain a list of the points and values in the volume (without > duplicates), and maybe something to do the interpolation at required > points would be nice. This isn't going to be efficient. There may be tens of millions of points in a simulation, and they are stored by maybe hundreds of processors, and the interpolation between individual points is really quite complicated if you have a non-trivial geometry. There are really only two efficient ways to deal with this much data: by outputting the data in specialized file formats for visualization, and by implementing postprocessors within ASPECT. I know that you'd like to do this by hand in some scripting language, but don't do it -- you won't be happy this way if the data just becomes too large. Best W. -- ------------------------------------------------------------------------ Wolfgang Bangerth email: bangerth at colostate.edu www: http://www.math.colostate.edu/~bangerth/ From jperryh2 at uoregon.edu Tue Oct 30 11:32:44 2018 From: jperryh2 at uoregon.edu (Jonathan Perry-Houts) Date: Tue, 30 Oct 2018 11:32:44 -0700 Subject: [aspect-devel] Postprocessing scripts In-Reply-To: <5538ac12-1835-74ba-9134-c3d936f19764@colostate.edu> References: <351e8e64-96ef-22c3-006b-613b0b8bcba9@elsi.jp> <53d2e5d3-100b-7576-4358-333314aa5047@colostate.edu> <07d5114e-12f4-7d30-2e70-1c7f7d74e5a4@elsi.jp> <5538ac12-1835-74ba-9134-c3d936f19764@colostate.edu> Message-ID: <9c5a2f60-0124-8f26-42a4-524c06f88c01@uoregon.edu> Perhaps a repository of paraview filters would be useful. It's possible to save a "pipeline" as a filter, and expose certain variables to the user through it. Marine: I agree with Wolfgang that this is not an efficient way to do things, but it does come in handy sometimes. For what it's worth, here's a script to convert vtk output to csv, which you can then handle with the usual python tools: ``` import glob from paraview import simple as pvsimple for ifname in glob('output/solution/*.pvtu'): ofname = ifname.rsplit('.', 1)[0]+'.csv' reader = pvsimple.OpenDataFile(ifname) writer = pvsimple.CreateWriter(ofname, reader) writer.FieldAssociation = 'Points' writer.UpdatePipeline() ``` I also highly recommend compressing those files, because they'll probably be enormous: ``` import gzip, os, shutil with open(ofname, 'rb') as f_in, \ gzip.open(ofname+'.gz', 'wb') as f_out: shutil.copyfileobj(f_in, f_out) os.remove(ofname) ``` numpy (and probably Pandas and whatnot) automatically recognize gzipped data and treat it transparently as a plain csv file. Hope that helps someone, -JPH On 10/30/18 10:11 AM, Wolfgang Bangerth wrote: > Marine, > I'm not sure anyone ever answered this email -- so let me do this 3 > months late... > > >> But to be able to do a good comparisons with existing results, I'll need >> things like horizontal averages (of composition, temperature, >> velocities) and difference between the field and the horizontal average >> (of composition, temperature). But the horizontal here is average over a >> sphere, so I am guessing the post-processors are not so easy. (to get >> average radial profiles) > > This is actually what our 'depth average' postprocessor does -- average > over all points at a certain depth where depth is defined differently > for each geometry. > > >> I'm definitely not used to paraview, and I'm more used to do all my data >> processing by hand... So a good tutorial on how to implement that with >> paraview or equivalent, with a scripting (I usually have several dozens >> of runs to process at a time) would be nice :-) But so far, I think that >> a way to obtain a list of the points and values in the volume (without >> duplicates), and maybe something to do the interpolation at required >> points would be nice. > > This isn't going to be efficient. There may be tens of millions of > points in a simulation, and they are stored by maybe hundreds of > processors, and the interpolation between individual points is really > quite complicated if you have a non-trivial geometry. There are really > only two efficient ways to deal with this much data: by outputting the > data in specialized file formats for visualization, and by implementing > postprocessors within ASPECT. I know that you'd like to do this by hand > in some scripting language, but don't do it -- you won't be happy this > way if the data just becomes too large. > > Best > W. > From jbnaliboff at ucdavis.edu Tue Oct 30 13:29:28 2018 From: jbnaliboff at ucdavis.edu (John Naliboff) Date: Tue, 30 Oct 2018 13:29:28 -0700 Subject: [aspect-devel] Postprocessing scripts In-Reply-To: <9c5a2f60-0124-8f26-42a4-524c06f88c01@uoregon.edu> References: <351e8e64-96ef-22c3-006b-613b0b8bcba9@elsi.jp> <53d2e5d3-100b-7576-4358-333314aa5047@colostate.edu> <07d5114e-12f4-7d30-2e70-1c7f7d74e5a4@elsi.jp> <5538ac12-1835-74ba-9134-c3d936f19764@colostate.edu> <9c5a2f60-0124-8f26-42a4-524c06f88c01@uoregon.edu> Message-ID: Hi all, I agree with Jonathan that a repository containing post processing scripts (Paraview, Visit, Python, etc, etc) would be incredibly useful.  In fact, Max Rudolph raised this question on the mailing with respect to post processing scripts developed at CIDER. I believe the consensus was that we should include this type of script collection in the main repository. Marine - If you prefer to work outside of Paraview, you can also import unstructured VTK data into numpy arrays in python.  Here is a link to an example of doing this data conversion (VTK to numpy): https://stackoverflow.com/questions/23138112/vtk-to-maplotlib-using-numpy Happy to send over some of my own scripts as well. However, as Wolfgang noted for very large data sets this will be prohibitively time consuming and memory intensive. Perhaps there are way to speed this up through cython and  python's openmp functionality, but I have not looked into it. Paraview can be run in parallel and it really is the most efficient way to process and explore large data sets. Cheers, John On 10/30/18 11:32 AM, Jonathan Perry-Houts wrote: > Perhaps a repository of paraview filters would be useful. It's possible > to save a "pipeline" as a filter, and expose certain variables to the > user through it. > > Marine: I agree with Wolfgang that this is not an efficient way to do > things, but it does come in handy sometimes. For what it's worth, here's > a script to convert vtk output to csv, which you can then handle with > the usual python tools: > > ``` > import glob > from paraview import simple as pvsimple > > for ifname in glob('output/solution/*.pvtu'): > ofname = ifname.rsplit('.', 1)[0]+'.csv' > > reader = pvsimple.OpenDataFile(ifname) > writer = pvsimple.CreateWriter(ofname, reader) > writer.FieldAssociation = 'Points' > writer.UpdatePipeline() > ``` > > I also highly recommend compressing those files, because they'll > probably be enormous: > > ``` > import gzip, os, shutil > > with open(ofname, 'rb') as f_in, \ > gzip.open(ofname+'.gz', 'wb') as f_out: > shutil.copyfileobj(f_in, f_out) > > os.remove(ofname) > ``` > > numpy (and probably Pandas and whatnot) automatically recognize gzipped > data and treat it transparently as a plain csv file. > > Hope that helps someone, > -JPH > > On 10/30/18 10:11 AM, Wolfgang Bangerth wrote: >> Marine, >> I'm not sure anyone ever answered this email -- so let me do this 3 >> months late... >> >> >>> But to be able to do a good comparisons with existing results, I'll need >>> things like horizontal averages (of composition, temperature, >>> velocities) and difference between the field and the horizontal average >>> (of composition, temperature). But the horizontal here is average over a >>> sphere, so I am guessing the post-processors are not so easy. (to get >>> average radial profiles) >> This is actually what our 'depth average' postprocessor does -- average >> over all points at a certain depth where depth is defined differently >> for each geometry. >> >> >>> I'm definitely not used to paraview, and I'm more used to do all my data >>> processing by hand... So a good tutorial on how to implement that with >>> paraview or equivalent, with a scripting (I usually have several dozens >>> of runs to process at a time) would be nice :-) But so far, I think that >>> a way to obtain a list of the points and values in the volume (without >>> duplicates), and maybe something to do the interpolation at required >>> points would be nice. >> This isn't going to be efficient. There may be tens of millions of >> points in a simulation, and they are stored by maybe hundreds of >> processors, and the interpolation between individual points is really >> quite complicated if you have a non-trivial geometry. There are really >> only two efficient ways to deal with this much data: by outputting the >> data in specialized file formats for visualization, and by implementing >> postprocessors within ASPECT. I know that you'd like to do this by hand >> in some scripting language, but don't do it -- you won't be happy this >> way if the data just becomes too large. >> >> Best >> W. >> > _______________________________________________ > Aspect-devel has MOVED to our new forum. Please head to https://community.geodynamics.org. > > This mailing address will be disabled at the end of October. > _______________________________________________ > Aspect-devel mailing list > Aspect-devel at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel -------------- next part -------------- An HTML attachment was scrubbed... URL: From maxrudolph at ucdavis.edu Tue Oct 30 13:35:17 2018 From: maxrudolph at ucdavis.edu (Max Rudolph) Date: Tue, 30 Oct 2018 13:35:17 -0700 Subject: [aspect-devel] Postprocessing scripts In-Reply-To: References: <351e8e64-96ef-22c3-006b-613b0b8bcba9@elsi.jp> <53d2e5d3-100b-7576-4358-333314aa5047@colostate.edu> <07d5114e-12f4-7d30-2e70-1c7f7d74e5a4@elsi.jp> <5538ac12-1835-74ba-9134-c3d936f19764@colostate.edu> <9c5a2f60-0124-8f26-42a4-524c06f88c01@uoregon.edu> Message-ID: I am happy to open a pull request containing my python scripts to interpolate output. They won't work for all conceivable cases, especially DG elements where nodal values can be multiply defined. Max On Tue, Oct 30, 2018 at 1:29 PM John Naliboff wrote: > Hi all, > > I agree with Jonathan that a repository containing post processing scripts > (Paraview, Visit, Python, etc, etc) would be incredibly useful. In fact, > Max Rudolph raised this question on the mailing with respect to post > processing scripts developed at CIDER. I believe the consensus was that we > should include this type of script collection in the main repository. > > Marine - If you prefer to work outside of Paraview, you can also import > unstructured VTK data into numpy arrays in python. > > Here is a link to an example of doing this data conversion (VTK to numpy): > > https://stackoverflow.com/questions/23138112/vtk-to-maplotlib-using-numpy > > Happy to send over some of my own scripts as well. > > However, as Wolfgang noted for very large data sets this will be > prohibitively time consuming and memory intensive. Perhaps there are way to > speed this up through cython and python's openmp functionality, but I have > not looked into it. Paraview can be run in parallel and it really is the > most efficient way to process and explore large data sets. > > Cheers, > John > > On 10/30/18 11:32 AM, Jonathan Perry-Houts wrote: > > Perhaps a repository of paraview filters would be useful. It's possible > to save a "pipeline" as a filter, and expose certain variables to the > user through it. > > Marine: I agree with Wolfgang that this is not an efficient way to do > things, but it does come in handy sometimes. For what it's worth, here's > a script to convert vtk output to csv, which you can then handle with > the usual python tools: > > ``` > import glob > from paraview import simple as pvsimple > > for ifname in glob('output/solution/*.pvtu'): > ofname = ifname.rsplit('.', 1)[0]+'.csv' > > reader = pvsimple.OpenDataFile(ifname) > writer = pvsimple.CreateWriter(ofname, reader) > writer.FieldAssociation = 'Points' > writer.UpdatePipeline() > ``` > > I also highly recommend compressing those files, because they'll > probably be enormous: > > ``` > import gzip, os, shutil > > with open(ofname, 'rb') as f_in, \ > gzip.open(ofname+'.gz', 'wb') as f_out: > shutil.copyfileobj(f_in, f_out) > > os.remove(ofname) > ``` > > numpy (and probably Pandas and whatnot) automatically recognize gzipped > data and treat it transparently as a plain csv file. > > Hope that helps someone, > -JPH > > On 10/30/18 10:11 AM, Wolfgang Bangerth wrote: > > Marine, > I'm not sure anyone ever answered this email -- so let me do this 3 > months late... > > > > But to be able to do a good comparisons with existing results, I'll need > things like horizontal averages (of composition, temperature, > velocities) and difference between the field and the horizontal average > (of composition, temperature). But the horizontal here is average over a > sphere, so I am guessing the post-processors are not so easy. (to get > average radial profiles) > > > This is actually what our 'depth average' postprocessor does -- average > over all points at a certain depth where depth is defined differently > for each geometry. > > > > I'm definitely not used to paraview, and I'm more used to do all my data > processing by hand... So a good tutorial on how to implement that with > paraview or equivalent, with a scripting (I usually have several dozens > of runs to process at a time) would be nice :-) But so far, I think that > a way to obtain a list of the points and values in the volume (without > duplicates), and maybe something to do the interpolation at required > points would be nice. > > > This isn't going to be efficient. There may be tens of millions of > points in a simulation, and they are stored by maybe hundreds of > processors, and the interpolation between individual points is really > quite complicated if you have a non-trivial geometry. There are really > only two efficient ways to deal with this much data: by outputting the > data in specialized file formats for visualization, and by implementing > postprocessors within ASPECT. I know that you'd like to do this by hand > in some scripting language, but don't do it -- you won't be happy this > way if the data just becomes too large. > > Best > W. > > > _______________________________________________ > Aspect-devel has MOVED to our new forum. Please head to https://community.geodynamics.org. > > This mailing address will be disabled at the end of October. > _______________________________________________ > Aspect-devel mailing listAspect-devel at geodynamics.orghttp://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel > > > _______________________________________________ > Aspect-devel has MOVED to our new forum. Please head to > https://community.geodynamics.org. > > This mailing address will be disabled at the end of October. > _______________________________________________ > Aspect-devel mailing list > Aspect-devel at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel -------------- next part -------------- An HTML attachment was scrubbed... URL: From jbnaliboff at ucdavis.edu Tue Oct 30 16:00:02 2018 From: jbnaliboff at ucdavis.edu (John Naliboff) Date: Tue, 30 Oct 2018 16:00:02 -0700 Subject: [aspect-devel] Postprocessing scripts In-Reply-To: References: <351e8e64-96ef-22c3-006b-613b0b8bcba9@elsi.jp> <53d2e5d3-100b-7576-4358-333314aa5047@colostate.edu> <07d5114e-12f4-7d30-2e70-1c7f7d74e5a4@elsi.jp> <5538ac12-1835-74ba-9134-c3d936f19764@colostate.edu> <9c5a2f60-0124-8f26-42a4-524c06f88c01@uoregon.edu> Message-ID: <8d4477fb-5eb1-a678-ca44-1395b58ab655@ucdavis.edu> Hi Max, That would be great, thank you! Cheers, John On 10/30/18 1:35 PM, Max Rudolph wrote: > I am happy to open a pull request containing my python scripts to > interpolate output. They won't work for all conceivable cases, > especially DG elements where nodal values can be multiply defined. > > Max > > On Tue, Oct 30, 2018 at 1:29 PM John Naliboff > wrote: > > Hi all, > > I agree with Jonathan that a repository containing post processing > scripts (Paraview, Visit, Python, etc, etc) would be incredibly > useful.  In fact, Max Rudolph raised this question on the mailing > with respect to post processing scripts developed at CIDER. I > believe the consensus was that we should include this type of > script collection in the main repository. > > Marine - If you prefer to work outside of Paraview, you can also > import unstructured VTK data into numpy arrays in python. > >  Here is a link to an example of doing this data conversion (VTK > to numpy): > https://stackoverflow.com/questions/23138112/vtk-to-maplotlib-using-numpy > > Happy to send over some of my own scripts as well. > > However, as Wolfgang noted for very large data sets this will be > prohibitively time consuming and memory intensive. Perhaps there > are way to speed this up through cython and  python's openmp > functionality, but I have not looked into it. Paraview can be run > in parallel and it really is the most efficient way to process and > explore large data sets. > > Cheers, > John > > On 10/30/18 11:32 AM, Jonathan Perry-Houts wrote: >> Perhaps a repository of paraview filters would be useful. It's possible >> to save a "pipeline" as a filter, and expose certain variables to the >> user through it. >> >> Marine: I agree with Wolfgang that this is not an efficient way to do >> things, but it does come in handy sometimes. For what it's worth, here's >> a script to convert vtk output to csv, which you can then handle with >> the usual python tools: >> >> ``` >> import glob >> from paraview import simple as pvsimple >> >> for ifname in glob('output/solution/*.pvtu'): >> ofname = ifname.rsplit('.', 1)[0]+'.csv' >> >> reader = pvsimple.OpenDataFile(ifname) >> writer = pvsimple.CreateWriter(ofname, reader) >> writer.FieldAssociation = 'Points' >> writer.UpdatePipeline() >> ``` >> >> I also highly recommend compressing those files, because they'll >> probably be enormous: >> >> ``` >> import gzip, os, shutil >> >> with open(ofname, 'rb') as f_in, \ >> gzip.open(ofname+'.gz', 'wb') as f_out: >> shutil.copyfileobj(f_in, f_out) >> >> os.remove(ofname) >> ``` >> >> numpy (and probably Pandas and whatnot) automatically recognize gzipped >> data and treat it transparently as a plain csv file. >> >> Hope that helps someone, >> -JPH >> >> On 10/30/18 10:11 AM, Wolfgang Bangerth wrote: >>> Marine, >>> I'm not sure anyone ever answered this email -- so let me do this 3 >>> months late... >>> >>> >>>> But to be able to do a good comparisons with existing results, I'll need >>>> things like horizontal averages (of composition, temperature, >>>> velocities) and difference between the field and the horizontal average >>>> (of composition, temperature). But the horizontal here is average over a >>>> sphere, so I am guessing the post-processors are not so easy. (to get >>>> average radial profiles) >>> This is actually what our 'depth average' postprocessor does -- average >>> over all points at a certain depth where depth is defined differently >>> for each geometry. >>> >>> >>>> I'm definitely not used to paraview, and I'm more used to do all my data >>>> processing by hand... So a good tutorial on how to implement that with >>>> paraview or equivalent, with a scripting (I usually have several dozens >>>> of runs to process at a time) would be nice :-) But so far, I think that >>>> a way to obtain a list of the points and values in the volume (without >>>> duplicates), and maybe something to do the interpolation at required >>>> points would be nice. >>> This isn't going to be efficient. There may be tens of millions of >>> points in a simulation, and they are stored by maybe hundreds of >>> processors, and the interpolation between individual points is really >>> quite complicated if you have a non-trivial geometry. There are really >>> only two efficient ways to deal with this much data: by outputting the >>> data in specialized file formats for visualization, and by implementing >>> postprocessors within ASPECT. I know that you'd like to do this by hand >>> in some scripting language, but don't do it -- you won't be happy this >>> way if the data just becomes too large. >>> >>> Best >>> W. >>> >> _______________________________________________ >> Aspect-devel has MOVED to our new forum. Please head tohttps://community.geodynamics.org. >> >> This mailing address will be disabled at the end of October. >> _______________________________________________ >> Aspect-devel mailing list >> Aspect-devel at geodynamics.org >> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel > > _______________________________________________ > Aspect-devel has MOVED to our new forum.  Please head to > https://community.geodynamics.org. > > This mailing address will be disabled at the end of October. > _______________________________________________ > Aspect-devel mailing list > Aspect-devel at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel > > > _______________________________________________ > Aspect-devel has MOVED to our new forum. Please head to https://community.geodynamics.org. > > This mailing address will be disabled at the end of October. > _______________________________________________ > Aspect-devel mailing list > Aspect-devel at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel -------------- next part -------------- An HTML attachment was scrubbed... URL: