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hoomd-users is read-only. Please post questions about HOOMD-blue in GitHub discussions:
https://github.com/glotzerlab/
hoomd-blue/discussions/
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Joshua Anderson
2
12/11/23
HOOMD-blue support is moving to GitHub discussions!
This mailing list is now read-only. Post all new questions to the HOOMD-blue discussion board on
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HOOMD-blue support is moving to GitHub discussions!
This mailing list is now read-only. Post all new questions to the HOOMD-blue discussion board on
12/11/23
Nikhil Menda
, …
Saurav Varma
4
12/11/23
Need Guidance: Implementing Depletion Interaction for Beginners in HPMC Tutorial
Dear Nikhil and Joshua, I am also new to HOOMD and wanted to simulate spherocylinders with depletion
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Need Guidance: Implementing Depletion Interaction for Beginners in HPMC Tutorial
Dear Nikhil and Joshua, I am also new to HOOMD and wanted to simulate spherocylinders with depletion
12/11/23
Xinyan Yang
12/10/23
hoomd.custom.Action issue with MPI
Hi, I wrote a hoomd.custom.Action and updater. Here is a simpler version of my action code: ---------
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hoomd.custom.Action issue with MPI
Hi, I wrote a hoomd.custom.Action and updater. Here is a simpler version of my action code: ---------
12/10/23
Anna Ashkinazi
,
Joshua Anderson
8
12/8/23
Particle with unique tag ABCD has NaN for its position [recurring error]
Joshua — thank you, this should resolve my question (I was manipulating the Li parameters to set
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Particle with unique tag ABCD has NaN for its position [recurring error]
Joshua — thank you, this should resolve my question (I was manipulating the Li parameters to set
12/8/23
Xiaotian Li
,
Joshua Anderson
4
12/8/23
[BUG]particles move out of box
Thank you for confirming that you found a fix. ------ Joshua A. Anderson, Ph.D. Research Area
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[BUG]particles move out of box
Thank you for confirming that you found a fix. ------ Joshua A. Anderson, Ph.D. Research Area
12/8/23
koji iwa
,
Joshua Anderson
5
12/6/23
Query Regarding Specifying Time Steps (W) for Viscosity Measurement Using hoomd.md.update.ReversePerturbationFlow
I cannot speak for Ludwig. ------ Joshua A. Anderson, Ph.D. Research Area Specialist, Chemical
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Query Regarding Specifying Time Steps (W) for Viscosity Measurement Using hoomd.md.update.ReversePerturbationFlow
I cannot speak for Ludwig. ------ Joshua A. Anderson, Ph.D. Research Area Specialist, Chemical
12/6/23
peaches liang
,
Joshua Anderson
2
12/6/23
Trouble in measuring the viscosity using hoomd.md.update.muller_plathe_flow
I answer support questions only for the latest major version of HOOMD-blue (currently 4.x). That
unread,
Trouble in measuring the viscosity using hoomd.md.update.muller_plathe_flow
I answer support questions only for the latest major version of HOOMD-blue (currently 4.x). That
12/6/23
Joshua Anderson
12/6/23
HOOMD-blue 4.4.0 release
All, HOOMD-blue 4.4.0 is now available. Thanks to all who reviewed changes, submitted bug reports,
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HOOMD-blue 4.4.0 release
All, HOOMD-blue 4.4.0 is now available. Thanks to all who reviewed changes, submitted bug reports,
12/6/23
Xinyan Yang
,
Joshua Anderson
5
12/5/23
BoxResize MPI
I see. Thank you! On Tue, Dec 5, 2023 at 1:56 PM Joshua Anderson <joaa...@umich.edu> wrote:
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BoxResize MPI
I see. Thank you! On Tue, Dec 5, 2023 at 1:56 PM Joshua Anderson <joaa...@umich.edu> wrote:
12/5/23
Joshua Anderson
2
12/4/23
New members must request to join
Apparently, Google does not notify group owners when members request to join. I have adjusted the
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New members must request to join
Apparently, Google does not notify group owners when members request to join. I have adjusted the
12/4/23
Ramalingam Kailasham
,
Avishek Kumar
3
11/20/23
Error while initializing particle types with unequal number
Hi Avishek Thank you very much for the updated code and providing an explanation for what was wrong
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Error while initializing particle types with unequal number
Hi Avishek Thank you very much for the updated code and providing an explanation for what was wrong
11/20/23
Anthony Trubiano
,
Joshua Anderson
7
11/20/23
Interactions stop working in long simulations
Thanks for the update, Anthony. I can't name a single change between 3.9.0 and 4.0 that might
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Interactions stop working in long simulations
Thanks for the update, Anthony. I can't name a single change between 3.9.0 and 4.0 that might
11/20/23
Xinyan Yang
, …
Joshua Anderson
4
11/14/23
superlinear speedup?
I see. I did not measure number os trial moves per second. Will have a look at it. Thank you! Best,
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superlinear speedup?
I see. I did not measure number os trial moves per second. Will have a look at it. Thank you! Best,
11/14/23
Xinyan Yang
, …
Joshua Anderson
4
11/13/23
Install GPU version HOOMD 4.3.0
The components of HOOMD that perform run time compilation require linking to the CUDA driver library
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Install GPU version HOOMD 4.3.0
The components of HOOMD that perform run time compilation require linking to the CUDA driver library
11/13/23
Avishek Kumar
, …
Joshua Anderson
4
11/10/23
Acessing the function of source file (C++) in the python script
Avishek, Please read the **extensive** documentation that we have provided in ARCHITECTURE.md and in
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Acessing the function of source file (C++) in the python script
Avishek, Please read the **extensive** documentation that we have provided in ARCHITECTURE.md and in
11/10/23
Xinyan Yang
,
Joshua Anderson
2
11/10/23
Steered Molecular Dynamics Simulation
Xinyan, Yes. I am aware of users that have implemented this in Python using HOOMD's API. ------
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Steered Molecular Dynamics Simulation
Xinyan, Yes. I am aware of users that have implemented this in Python using HOOMD's API. ------
11/10/23
Bojana Zivkovic
, …
Xinyan Yang
8
11/9/23
making rigid bodies -beginner - please help
Great! Thank you! Best, On Thu, Nov 9, 2023 at 2:18 PM Joshua Anderson <joaa...@umich.edu>
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making rigid bodies -beginner - please help
Great! Thank you! Best, On Thu, Nov 9, 2023 at 2:18 PM Joshua Anderson <joaa...@umich.edu>
11/9/23
Avishek Kumar
11/8/23
Accessing the internal C++ function
Hi, I have added a new function in NeighbourList.cc which modifies the h_nlist array and h_headlist
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Accessing the internal C++ function
Hi, I have added a new function in NeighbourList.cc which modifies the h_nlist array and h_headlist
11/8/23
Joshua Anderson
,
Work Ren
3
11/3/23
HOOMD-blue 4.3.0 release
Ren, If there is a particular electrostatics model you are interested in, you are welcome to
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HOOMD-blue 4.3.0 release
Ren, If there is a particular electrostatics model you are interested in, you are welcome to
11/3/23
Xinyan Yang
,
Joshua Anderson
2
11/1/23
Hybrid HPMC and MD
Xinyan Yang, When you switch from MC to MD, you need to add the constituent particles to the system
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Hybrid HPMC and MD
Xinyan Yang, When you switch from MC to MD, you need to add the constituent particles to the system
11/1/23
Ryan Collanton
,
Joshua Anderson
2
10/31/23
bond breaking during a simulation
Ryan, HOOMD does not currently support breaking individual bonds. ------ Joshua A. Anderson, Ph.D.
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bond breaking during a simulation
Ryan, HOOMD does not currently support breaking individual bonds. ------ Joshua A. Anderson, Ph.D.
10/31/23
Spencer Xu
,
Joshua Anderson
2
10/31/23
Error compile generating code
Spencer, Use sqrtf. ------ Joshua A. Anderson, Ph.D. Research Area Specialist, Chemical Engineering,
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Error compile generating code
Spencer, Use sqrtf. ------ Joshua A. Anderson, Ph.D. Research Area Specialist, Chemical Engineering,
10/31/23
Avishek Kumar Avishek Kumar
,
Brandon Butler
2
10/31/23
Is there get_net_virial() of particle group in HOOMD v4.1.0
Hello Avishek, If you want to compute the sum of a particular group of particles you can use local
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Is there get_net_virial() of particle group in HOOMD v4.1.0
Hello Avishek, If you want to compute the sum of a particular group of particles you can use local
10/31/23
Remya Ann
, …
Joshua Anderson
4
10/26/23
Units of temperature and length
Dear Antonia and Dr. Anderson, Thank you for your email. I'm sorry I wasn't very clear
unread,
Units of temperature and length
Dear Antonia and Dr. Anderson, Thank you for your email. I'm sorry I wasn't very clear
10/26/23
Trung Nguyen
,
Joshua Anderson
4
10/19/23
Undefined symbols in the _md module (v4.2.1)
Trung, Good that you got it working. I'm not surprised. You mentioned you are using an anacnoda
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Undefined symbols in the _md module (v4.2.1)
Trung, Good that you got it working. I'm not surprised. You mentioned you are using an anacnoda
10/19/23
Bryan VanSaders
,
Lourens Veen
3
10/19/23
cuda test compile fails with denied access to /local/scratch on cluster
Lourens, That was exactly my problem, thank you -Bryan On Thursday, October 19, 2023 at 1:04:02 PM
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cuda test compile fails with denied access to /local/scratch on cluster
Lourens, That was exactly my problem, thank you -Bryan On Thursday, October 19, 2023 at 1:04:02 PM
10/19/23
Bryan VanSaders
,
Chris Jones
3
10/19/23
Incremental gsd frame writing in 4.2
Thanks Chris, I missed that in the docs. On Wednesday, October 18, 2023 at 6:25:00 PM UTC-4 Chris
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Incremental gsd frame writing in 4.2
Thanks Chris, I missed that in the docs. On Wednesday, October 18, 2023 at 6:25:00 PM UTC-4 Chris
10/19/23
Xuan Feng
,
Joshua Anderson
3
10/19/23
HPMC with implicit depletant
Hi Anderson, I get it. Thanks very much! Regards, Feng Xuan Joshua Anderson <joaa...@umich.edu
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HPMC with implicit depletant
Hi Anderson, I get it. Thanks very much! Regards, Feng Xuan Joshua Anderson <joaa...@umich.edu
10/19/23
岩瀬晃司
,
Joshua Anderson
10
10/17/23
Warning Message Regarding MuellerPlatheFlow with WCA Particles in 2D System
Joshua Thanks, warnings disappeared. 2023年10月3日火曜日 20:54:39 UTC+9 Joshua Anderson: I think you should
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Warning Message Regarding MuellerPlatheFlow with WCA Particles in 2D System
Joshua Thanks, warnings disappeared. 2023年10月3日火曜日 20:54:39 UTC+9 Joshua Anderson: I think you should
10/17/23
岩瀬晃司
10/14/23
Inquiry about Method for Creating Particle Flow
I am working on a simulation of a Karman vortex and need to generate a flow of WCA particles in the
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Inquiry about Method for Creating Particle Flow
I am working on a simulation of a Karman vortex and need to generate a flow of WCA particles in the
10/14/23