Dear Chandra,
your packing fraction seems to be very small. Usually chain formation can be expected for higher fractions. Try using phi=0.05 or even phi=0.1 for seeing the effect. Of course the real value should apply to the system you actually want to simulate, but for the sake of creating chain formation you can try with the above values. Your graphic may be a bit misleading because the points are not drawn in the correct scale and are in fact a lot smaller.
Also, in my experience, your alpha value seems a bit large. lambda=4 particles dont usually experience that high zemann forces for experimentally achievable magnetic fields. But i may be corrected on that.
Best,
Martin
On Oct 26, 2020 13:57, chandra shekhar maurya <chandra15294@gmail.com> wrote:
Dear users,I am using Gay_berne potential for ellipsoid shape magnetic particles for tutorial "11-ferrofluid_part2".Input parameters are-# Lennard-Jones parameters
lj_sigma = 1.
lj_eps = 1.
lj_cut = 2**(1./6.) * lj_sigma
k = 1.2
# Particles
N = 1000
# Area fraction of the mono-layer
phi = 0.0000001
# Dipolar interaction parameter lambda = mu_0 m^2 /(4 pi sigma^3 kT)
dip_lambda = 4.
# Temperature
kT = 1.0
# Friction coefficient
gamma = 1.0
# Time step
dt = 0.01
# Langevin parameter alpha = mu_0 m H / kT
alpha = 1000.
# vacuum permeability
mu_0 = 1.#Gay berne potentialsystem.non_bonded_inter[0,0].gay_berne.set_params(eps=lj_eps,sig=lj_sigma,cut=lj_cut, k1=k, k2=5, mu=2, nu=1)Your help will be highly appreciated.Thanks & RegardsChandra Shekhar MauryaMechanical Eng. Dept.Indian Institute of Technology PatnaContact No:9793572837On Mon, Oct 19, 2020 at 9:39 PM <espressomd-users-request@nongnu.org> wrote:Send Espressomd-users mailing list submissions to
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Today's Topics:
1. Re: Espressomd-users Digest, Vol 117, Issue 3 (Kai Szuttor)
----------------------------------------------------------------------
Message: 1
Date: Mon, 19 Oct 2020 08:51:33 +0200
From: Kai Szuttor <kai@icp.uni-stuttgart.de>
To: chandra shekhar maurya <chandra15294@gmail.com>
Cc: espressomd-users@nongnu.org
Subject: Re: Espressomd-users Digest, Vol 117, Issue 3
Message-ID: <20201019065133.GB17973@bongo.icp.uni-stuttgart.de">20201019065133.GB17973@bongo.icp.uni-stuttgart.de>
Content-Type: text/plain; charset="iso-8859-1"
Please note that the visualization tool always only shows spherical particles.
Best,
Kai
On Mon, Oct 19, 2020 at 11:17:18AM +0530, chandra shekhar maurya wrote:
> Dear users,
> I used Gay-Berene interaction for ellipsoidal particles, but i am still
> getting spherical particles. As you can see in attached figures.
> Thanks & Regards
> Chandra Shekhar Maurya
> Mechanical Eng. Dept.
> Indian Institute of Technology Patna
> Contact No:9793572837
> On Sat, Oct 17, 2020 at 9:32 PM <espressomd-users-request@nongnu.org>
> wrote:
>
> Send Espressomd-users mailing list submissions to
> Â Â Â Â espressomd-users@nongnu.org
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> than "Re: Contents of Espressomd-users digest..."
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> Today's Topics:
>
> Â Â 1. Re: Espressomd-users Digest, Vol 117, Issue 1
> Â Â Â (chandra shekhar maurya)
> Â Â 2. Re: Espressomd-users Digest, Vol 117, Issue 1
> Â Â Â (=?UTF-8?Q?Jean-No=C3=ABl_Grad?=)
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 17 Oct 2020 10:44:11 +0530
> From: chandra shekhar maurya <chandra15294@gmail.com>
> To: espressomd-users@nongnu.org
> Subject: Re: Espressomd-users Digest, Vol 117, Issue 1
> Message-ID:
> Â Â Â Â
> <CALf1gEy6wDdV8Jj8tMVwM9hzcqSo7bPY8ACd_su7hrG6A8PaNw@mail.gmail.com">CALf1gEy6wDdV8Jj8tMVwM9hzcqSo7bPY8ACd_su7hrG6A8PaNw@mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear users,
> During using Gay-Berne interactio, i am geting bellow error. Please
> suggetme , how can i correct i?
>
> Box size 88.6226925452758
> Traceback (most recent call last):
> Â File "test.py", line 51, in <module>
>
> system.non_bonded_inter[0,0].gay_berne.set_params(eps=lj_eps,sig=lj_sig,cutoff=lj_cut,
> k1=k)
> AttributeError: 'NoneType' object has no attribute 'set_params'
>
> *Thanks & Regards*
> Chandra Shekhar Maurya
> Mechanical Eng. Dept.
> Indian Institute of Technology Patna
> Contact No:9793572837
>
> On Tue, Oct 13, 2020 at 9:33 PM <espressomd-users-request@nongnu.org>
> wrote:
>
> > Send Espressomd-users mailing list submissions to
> >Â Â Â Â Â espressomd-users@nongnu.org
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> >Â Â Â Â
> Â https://lists.nongnu.org/mailman/listinfo/espressomd-users
> > or, via email, send a message with subject or body 'help' to
> >Â Â Â Â Â espressomd-users-request@nongnu.org
> >
> > You can reach the person managing the list at
> >Â Â Â Â Â espressomd-users-owner@nongnu.org
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of Espressomd-users digest..."
> >
> >
> > Today's Topics:
> >
> >Â Â 1. Regarding dealing with non-spherical particles in Ferrofluid
> >Â Â Â Â - Part I (chandra shekhar maurya)
> >Â Â 2. Re: Regarding dealing with non-spherical particles in
> >Â Â Â Â Ferrofluid - Part I (Rudolf Weeber)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Tue, 13 Oct 2020 19:30:12 +0530
> > From: chandra shekhar maurya <chandra15294@gmail.com>
> > To: espressomd-users-request@nongnu.org,
> >Â Â Â Â Â espressomd-users-owner@nongnu.org,Â
> espressomd-users@nongnu.org
> > Subject: Regarding dealing with non-spherical particles in Ferrofluid
> >Â Â Â Â Â - Part I
> > Message-ID:
> >Â Â Â Â Â <
> > CALf1gEwsVKt4AtCbqeDe0V2iN710x8aKZ_1+a8Gufw3wha8GvQ@mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Dear users,
> >Â I am trying to do simulation for "Ferrofluid - Part I", using
> > non-spherical particles.
> > So how can I deal with non-spherical particles like ellipsoid, flake
> shape.
> > Your help will be highly obliged.
> >
> >
> >
> > *Thanks & Regards*
> > Chandra Shekhar Maurya
> > Mechanical Eng. Dept.
> > Indian Institute of Technology Patna
> > Contact No:9793572837
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL: <
> >
> https://lists.nongnu.org/archive/html/espressomd-users/attachments/20201013/d4cd6fa4/attachment.html
> > >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Tue, 13 Oct 2020 16:31:20 +0200
> > From: Rudolf Weeber <weeber@icp.uni-stuttgart.de>
> > To: chandra shekhar maurya <chandra15294@gmail.com>
> > Cc: espressomd-users@nongnu.org
> > Subject: Re: Regarding dealing with non-spherical particles in
> >Â Â Â Â Â Ferrofluid - Part I
> > Message-ID: <20201013143120.GA1918947@icp.uni-stuttgart.de">20201013143120.GA1918947@icp.uni-stuttgart.de>
> > Content-Type: text/plain; charset=us-ascii
> >
> > Hi Chandra,
> > On Tue, Oct 13, 2020 at 07:30:12PM +0530, chandra shekhar maurya
> wrote:
> > >Â I am trying to do simulation for "Ferrofluid - Part I", using
> > > non-spherical particles.
> > > So how can I deal with non-spherical particles like ellipsoid, flake
> > shape.
> > > Your help will be highly obliged.
> > For ellipsoidal particles, you can use the Gay-Berne interaction,
> which is
> > available in Espresso.
> > For other cases, you can make use of the raspberry model as an
> > approximation (using Espresso's VirtualSitesRelative feature).
> > See e.g., the works on magnetic cube-like particles by Kantorovich et
> al.
> >
> > Regards, Rudolf
> >
> >
> >
> >
> > ------------------------------
> >
> > Subject: Digest Footer
> >
> > _______________________________________________
> > Espressomd-users mailing list
> > Espressomd-users@nongnu.org
> > https://lists.nongnu.org/mailman/listinfo/espressomd-users
> >
> >
> > ------------------------------
> >
> > End of Espressomd-users Digest, Vol 117, Issue 1
> > ************************************************
> >
> -------------- next part --------------
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> <https://lists.nongnu.org/archive/html/espressomd-users/attachments/20201017/4280e549/attachment.html>
>
> ------------------------------
>
> Message: 2
> Date: Sat, 17 Oct 2020 14:46:45 +0200
> From: "=?UTF-8?Q?Jean-No=C3=ABl_Grad?=" <jgrad@icp.uni-stuttgart.de>
> To: chandra shekhar maurya <chandra15294@gmail.com>
> Cc: espressomd-users@nongnu.org, Espressomd-users
> Â Â Â Â
> <espressomd-users-bounces+jgrad=icp.uni-stuttgart.de@nongnu.org>
> Subject: Re: Espressomd-users Digest, Vol 117, Issue 1
> Message-ID: <b6490cc19d143c0a41a67a93b3f7b82f@icp.uni-stuttgart.de">b6490cc19d143c0a41a67a93b3f7b82f@icp.uni-stuttgart.de>
> Content-Type: text/plain; charset=US-ASCII; format=flowed
>
> Dear Chandra Shekhar Maurya,
>
> Maybe the feature GAY_BERNE is missing from your myconfig.hpp file. If
> you didn't provide a custom myconfig.hpp file when compiling ESPResSo,
> then it used the default one which is missing GB.
>
> Best,
> JN
>
> On 2020-10-17 07:14, chandra shekhar maurya wrote:
> > Dear users,
> > During using Gay-Berne interactio, i am geting bellow error. Please
> > suggetme , how can i correct i?
> >
> > Box size 88.6226925452758
> > Traceback (most recent call last):
> >Â Â File "test.py", line 51, in <module>
> >
> >
> system.non_bonded_inter[0,0].gay_berne.set_params(eps=lj_eps,sig=lj_sig,cutoff=lj_cut,
> > k1=k)
> > AttributeError: 'NoneType' object has no attribute 'set_params'
> >
> > Thanks & Regards
> >
> > Chandra Shekhar Maurya
> > Mechanical Eng. Dept.
> > Indian Institute of Technology Patna
> >
> > Contact No:9793572837
> >
> > On Tue, Oct 13, 2020 at 9:33 PM <espressomd-users-request@nongnu.org>
> > wrote:
> >
> >> Send Espressomd-users mailing list submissions to
> >> espressomd-users@nongnu.org
> >>
> >> To subscribe or unsubscribe via the World Wide Web, visit
> >> https://lists.nongnu.org/mailman/listinfo/espressomd-users
> >> or, via email, send a message with subject or body 'help' to
> >> espressomd-users-request@nongnu.org
> >>
> >> You can reach the person managing the list at
> >> espressomd-users-owner@nongnu.org
> >>
> >> When replying, please edit your Subject line so it is more specific
> >> than "Re: Contents of Espressomd-users digest..."
> >>
> >> Today's Topics:
> >>
> >> 1. Regarding dealing with non-spherical particles in Ferrofluid
> >> - Part I (chandra shekhar maurya)
> >> 2. Re: Regarding dealing with non-spherical particles in
> >> Ferrofluid - Part I (Rudolf Weeber)
> >>
> >>
> > ----------------------------------------------------------------------
> >>
> >> Message: 1
> >> Date: Tue, 13 Oct 2020 19:30:12 +0530
> >> From: chandra shekhar maurya <chandra15294@gmail.com>
> >> To: espressomd-users-request@nongnu.org,
> >> espressomd-users-owner@nongnu.org,
> >> espressomd-users@nongnu.org
> >> Subject: Regarding dealing with non-spherical particles in
> >> Ferrofluid
> >> - Part I
> >> Message-ID:
> >>
> >> <CALf1gEwsVKt4AtCbqeDe0V2iN710x8aKZ_1+a8Gufw3wha8GvQ@mail.gmail.com>
> >> Content-Type: text/plain; charset="utf-8"
> >>
> >> Dear users,
> >> I am trying to do simulation for "Ferrofluid - Part I", using
> >> non-spherical particles.
> >> So how can I deal with non-spherical particles like ellipsoid, flake
> >> shape.
> >> Your help will be highly obliged.
> >>
> >> *Thanks & Regards*
> >> Chandra Shekhar Maurya
> >> Mechanical Eng. Dept.
> >> Indian Institute of Technology Patna
> >> Contact No:9793572837
> >> -------------- next part --------------
> >> An HTML attachment was scrubbed...
> >> URL:
> >>
> >
> <https://lists.nongnu.org/archive/html/espressomd-users/attachments/20201013/d4cd6fa4/attachment.html>
> >>
> >> ------------------------------
> >>
> >> Message: 2
> >> Date: Tue, 13 Oct 2020 16:31:20 +0200
> >> From: Rudolf Weeber <weeber@icp.uni-stuttgart.de>
> >> To: chandra shekhar maurya <chandra15294@gmail.com>
> >> Cc: espressomd-users@nongnu.org
> >> Subject: Re: Regarding dealing with non-spherical particles in
> >> Ferrofluid - Part I
> >> Message-ID: <20201013143120.GA1918947@icp.uni-stuttgart.de">20201013143120.GA1918947@icp.uni-stuttgart.de>
> >> Content-Type: text/plain; charset=us-ascii
> >>
> >> Hi Chandra,
> >> On Tue, Oct 13, 2020 at 07:30:12PM +0530, chandra shekhar maurya
> >> wrote:
> >>> I am trying to do simulation for "Ferrofluid - Part I", using
> >>> non-spherical particles.
> >>> So how can I deal with non-spherical particles like ellipsoid,
> >> flake shape.
> >>> Your help will be highly obliged.
> >> For ellipsoidal particles, you can use the Gay-Berne interaction,
> >> which is available in Espresso.
> >> For other cases, you can make use of the raspberry model as an
> >> approximation (using Espresso's VirtualSitesRelative feature).
> >> See e.g., the works on magnetic cube-like particles by Kantorovich
> >> et al.
> >>
> >> Regards, Rudolf
> >>
> >> ------------------------------
> >>
> >> Subject: Digest Footer
> >>
> >> _______________________________________________
> >> Espressomd-users mailing list
> >> Espressomd-users@nongnu.org
> >> https://lists.nongnu.org/mailman/listinfo/espressomd-users
> >>
> >> ------------------------------
> >>
> >> End of Espressomd-users Digest, Vol 117, Issue 1
> >> ************************************************
>
> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
> Espressomd-users mailing list
> Espressomd-users@nongnu.org
> https://lists.nongnu.org/mailman/listinfo/espressomd-users
>
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>
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