hoomd-users

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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 Anderson2

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 Varma4

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

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 Anderson8

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 Anderson4

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 Anderson5

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 Anderson2

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

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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 Anderson5

12/5/23

I see. Thank you! On Tue, Dec 5, 2023 at 1:56 PM Joshua Anderson <joaa...@umich.edu> wrote:

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I see. Thank you! On Tue, Dec 5, 2023 at 1:56 PM Joshua Anderson <joaa...@umich.edu> wrote:

12/5/23

Joshua Anderson2

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 Kumar3

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 Anderson7

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 Anderson4

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 Anderson4

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 Anderson4

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 Anderson2

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 Yang8

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

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 Ren3

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 Anderson2

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 Anderson2

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 Anderson2

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 Butler2

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 Anderson4

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

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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 Anderson4

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 Veen3

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 Jones3

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 Anderson3

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 Anderson10

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

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

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