Hello everyone,

I have a working script of sph= eres diffusing from a source to a sink through a pore with pore walls simul= ated by particles that are fixed in space. The box size is (30*sigma)^3. Ra= ther than partial periodic conditions (x and y periodic, z not periodic), t= he system has another wall of fixed particles at z =3D 29*sigma so there is= no diffusion from source to sink except through the pore. The thermostat a= nd solvent are simulated through dissipative particle dynamics. I would lik= e to add the Lattice Boltzmann system to the simulation to model the hydrod= ynamic interactions and I have a few questions.

1) Are there reasonable parameters to use as a starting point for=
lbfluid? The fluid should be quiescent water with no external force. The w=
all particle size is (2.55*sigma) and the diffusing sphere size is=20
(0.1*sigma) as dictated by the LJ interaction parameters which might influe=
nce the choice for the agrid parameter. The time step for MD is 0.001. I am=
confused by the term "LB units" in the user guide which is why I=
don't know where to start. I have a working script of sph= eres diffusing from a source to a sink through a pore with pore walls simul= ated by particles that are fixed in space. The box size is (30*sigma)^3. Ra= ther than partial periodic conditions (x and y periodic, z not periodic), t= he system has another wall of fixed particles at z =3D 29*sigma so there is= no diffusion from source to sink except through the pore. The thermostat a= nd solvent are simulated through dissipative particle dynamics. I would lik= e to add the Lattice Boltzmann system to the simulation to model the hydrod= ynamic interactions and I have a few questions.

2) Will the walls (fixed particles) serve as hydrodynami=
c boundaries for the fluid or do I need to add the LB boundaries as dictate=
d by the pore dimensions?

Any advice you can g=
ive is greatly appreciated!

Thanks,

--Vincent Ustac=
h

Stefan,

Thanks for your re= ply! I have the code running but of course I still have a lot of work to do= . I did not want the discussion to get stale, however, so I am replying now= with the info that I have.

I am abandoning the DPD thermostat and using LB for a thermostat and fo= r the HIs. I was not using inter_dpd. Sorry that I was not clear.

I will look into the pore constraint, but I don't want to restrict myse= lf to cylindrical and conical pores.

This is indeed a concentr=
ation gradient driven diffusion, however electrostatics will be involved la=
ter. Viscosity seems to be (0.8 Pa * s) *10^-3. What are the units for fric=
tion?Thanks for your re= ply! I have the code running but of course I still have a lot of work to do= . I did not want the discussion to get stale, however, so I am replying now= with the info that I have.

I am abandoning the DPD thermostat and using LB for a thermostat and fo= r the HIs. I was not using inter_dpd. Sorry that I was not clear.

I will look into the pore constraint, but I don't want to restrict myse= lf to cylindrical and conical pores.

Vincent

<=
br clear=3D"all">

--047d7bf19840742a9504dc18a011--
From MAILER-DAEMON Tue May 07 03:14:10 2013
Received: from list by lists.gnu.org with archive (Exim 4.71)
id 1UZc6E-0008E8-Ks
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(envelope-from --Vincent Ustach

=A0 University of California, Dav= is

=A0 University of California, Dav= is

On Mon, May 6, 2013 at 12:05 AM, Stefan =
Kesselheim <kessel@icp.uni-stuttgart.de> wrote:

Dear Vincent,

I' like to ask a few questions back:

* Why would u use DPD+LB? Are you referring to the (conservative) sof= t particle interaction of DPD type or the thermostat? Is it clear to you th= at inter_dpd is not the conservative DPD interaction?

On May 6, 2013, at 3:12 AM, Vincent Ustach <vustach@ucdavis.edu> wrote:

> Hello everyone,

>

> I have a working script of spheres diffusing from a source to a sink t= hrough a pore with pore walls simulated by particles that are fixed in spac= e. The box size is (30*sigma)^3. Rather than partial periodic conditions (x= and y periodic, z not periodic), the system has another wall of fixed part= icles at z =3D 29*sigma so there is no diffusion from source to sink except= through the pore. The thermostat and solvent are simulated through dissipa= tive particle dynamics. I would like to add the Lattice Boltzmann system to= the simulation to model the hydrodynamic interactions and I have a few que= stions.

* Are you familiar with the pore constraint? It might be a replacement for = your particles. The wall constraint can probably replace the other walls.LB intrinsically uses a different unit system, in which the (LB time-= step is 1), however the interface is always made so that you interact with = it in (usual) MD units.

> 1) Are there reasonable parameters to use as a starting point for lbfl= uid? The fluid should be quiescent water with no external force. The wall p= article size is (2.55*sigma) and the diffusing sphere size is (0.1*sigma) a= s dictated by the LJ interaction parameters which might influence the choic= e for the agrid parameter. The time step for MD is 0.001. I am confused by = the term "LB units" in the user guide which is why I don't kn= ow where to start.

The right choice of LB parameters however is a tricky thing. It depends on = the effects you expect in your system. Are you expecting collective transpo= rt (e.g. diffusophoretic effects), such as fluid transport due to a concent= ration gradient? Or are pairwise interactions important?

>From my experience a good starting point are the LB parameters:

density 1 viscosity 0.8 friction 10 agrid 1 tau 0.01

Then the hydrodynamic radius of the particles will be 0.45 sigma. I'd r= ecommend to scale up the rest of the system.

This is not clear yet. lbboundaries use the link bounce back method, = which is considered a "good" method for boundaries. If a set of p= articles is a "good" boundary depends e.g. on the friction, on th= e density etc. Usually the combination of a "constraint" and an i= dentical "lbboundary" is the way to go, but implementing own shap= es is tedious.

> 2) Will the walls (fixed particles) serve as hydrodynamic boundaries f= or the fluid or do I need to add the LB boundaries as dictated by the pore = dimensions?

Cheers and good luck

Stefan

Stefan,

>>What is your mass and you= r Diffusion coefficient? Most likely you'll=20 find out that if you put in the numbers, both your viscosity and your=20 friction will be incredibly high.<<

Do you mean what are=
the empirical mass and Diffusion coefficients of the particles I am simula=
ting? Indeed for the parameters>>What is your mass and you= r Diffusion coefficient? Most likely you'll=20 find out that if you put in the numbers, both your viscosity and your=20 friction will be incredibly high.<<

density 1 viscosity 0.8 friction 10 = agrid 1 tau 0.01

the spheres moved extremely slowly.

--Vincent Ustach

=A0 University of California, Da= vis

=A0 University of California, Da= vis

On Tue, May 7, 2013 at 12:14 AM, Stefan =
Kesselheim <kessel@icp.uni-stuttgart.de> wrote:

Hi,

That means that you also plan to throw out the DPD particles? OK. Tha= t sounds fair. Have you tried the GPU version of LB? It is incredibly fast!=

On May 7, 2013, at 5:43 AM, Vincent Ustach <vustach@ucdavis.edu> wrote:

> Stefan,

>

> Thanks for your reply! I have the code running but of course I still h= ave a lot of work to do. I did not want the discussion to get stale, howeve= r, so I am replying now with the info that I have.

>

> I am abandoning the DPD thermostat and using LB for a thermostat and f= or the HIs. I was not using inter_dpd. Sorry that I was not clear.

That makes sense. However it is probably better to use the bounce bac= k method for walls. One thing that we always wanted to do, is making it pos= sible to flag single nodes as boundary nodes, but this is not implemented a= t the moment. Though quite easy, both for GPU and CPU. However I'm rath= er busy with my thesis right now, and thus would prefer to do it later :-).= You can do it quite easily.

> I will look into the pore constraint, but I don't want to restrict= myself to cylindrical and conical pores.

What is your mass and your Diffusion coefficient? Most likely you'= ;ll find out that if you put in the numbers, both your viscosity and your f= riction will be incredibly high.

> This is indeed a concentration gradient driven diffusion, however elec= trostatics will be involved later. Viscosity seems to be (0.8 Pa * s) *10^-= 3. What are the units for friction?

You can try. It depends on your system, if it is. This I can tell you= for sure. And on you definition of "adequate" :-).

> I am working on printing the fluid velocity field to an output file an= d then hopefully it will shed some light on if the wall of particles serves= as an adequate LB boundary.

Please don't think that you can get LB for free (not computationally, b= ut in terms of carefully thinking about your system). Just as in DPD you ha= ve to worry seriously about getting parameters right. I have spent quite so= me time learning about that and I'm quite sure I can get helpful advice= now. But you need to know: Will you have "macroscopic" fluid mot= ion in your system, or is just correlations that matter? Probably in both c= ases it is necessary to fit the "effective particle radius" 1/(6 = pi eta D) to the other lengths scales in you system. But in the first case = it is OK if the radius is small, while in the second case it is important t= o have a high resolution to get the near field right.

Don't worry about the discussion getting stale, we can revive it later = :-). =A0My desk is also quite full.

Cheers and good luck

Stefan

Dear All,=A0

I have a one-dimensional s=
ystem of spherical particles of diameter sigma move along a line.=A0

<=
div>I am using

=A0# =A0 --- The simulation Box is =
periodic in only one direction

setmd periodic 1 0 0

setmd box_l $bl $bl $bl

and the interaction potential is either the WCA, hertzian or Gaussian pote=
ntial

My compilation of ESPresSo is as f=
ollows:

ESPResSo-3.2.0

{ Compilation status { FFTW =
} { CONSTRAINTS } { ROTATIONAL_INERTIA } { BOND_ANGLE_HARMONIC } { GAY_BERN=
E } { GAUSSIAN } { COMFIXED } { HERTZIAN } { PARTIAL_PERIODIC } { LENNARD_J=
ONES } { VIRTUAL_SITES_RELATIVE } { EXTERNAL_FORCES } { TABULATED } { ROTAT=
ION } { SOFT_SPHERE } { VIRTUAL_SITES_NO_VELOCITY } { LENNARD_JONES_GENERIC=
} { ROTATION_PER_PARTICLE } { BOND_VIRTUAL } }

=A0

I am running the simulation with:

{ lang=
evin 1.0 1.0 }=A0

=A0However=
, with the current version of ESPresSo 3.2.0, I have problems to control th=
e temperature with any of the above mentioned potentials.

WCA-Potencial

{0 0 lennard-=
jones 1.0 0.5 0.5612310241546865 0.25 0.0 0.0 0.0 }=A0

=

=A0t=3D1.000000000000001 E=3D1.784989386884216, T=3D3.5299316707096 (L=
J cap =3D 20)

=A0t=3D2.000000000000001 E=3D2.105429430274374, T=3D4.149024028202554 =
(LJ cap =3D 30)

However, for the same =
script with the same set of parameters using version 3.1.1, I get the follo=
wing

{0 0 lennard-jones 1.0 0.5 0.5612310241546865 0.25 0.0 0.0 0.0 }=
=A0

{ langevin 1.0 1.0 }=A0

=A0

=A0t=3D2.000000000000001 E=3D0.5662738721667048, T=3D1.071506110193384=
(LJ cap =3D 30)

I observe the same pr=
oblem with both WCA and Hertzian potentials. Correct temperature in 3.1.1 b=
ut not in 3.2.0

Does any body could shed some light? =A0Any sugge=
stion would be greatly appreciated.

Th=
anks a lot in advance,

Salvador

Hi Olaf,=A0

Thanks for your quickly rep=
ly.

You were right, turning off the rotation=
(I also turned off virtual sites) solve the "problem".

Now the compilation of ESPresSo is as follows:

ESPResSo-3.2.0

{ Compilation status { FFTW } { CONS=
TRAINTS } { BOND_ANGLE_HARMONIC } { GAUSSIAN } { HERTZIAN } { PARTIAL_PERIO=
DIC } { LENNARD_JONES } { MODES } { EXTERNAL_FORCES } { TABULATED } { SOFT_=
SPHERE } { LENNARD_JONES_GENERIC } { MASS } { ELECTROSTATICS } { BOND_CONST=
RAINT } { EXCLUSIONS } }

=A0

The control of temperature is ok for the three potential=
s (WCA, Hertzian and Gaussian).

Thanks a lot,=A0

Salvador

On Mon, May 1=
3, 2013 at 1:48 PM, Olaf Lenz <olenz@icp.uni-stuttgart.de>=
wrote:

Hi!

Could you try whether this also happens when you turn off

ROTATION_PER_PARTICLE?

In general, when you just do a standard simulation, DO NOT turn on

ROTATION, as this will make ESPResSo significantly slower.

Anyway, this is a problem that should be solved.

Olaf

--

On 05/13/2013 08:43 PM, Salvador H-V wrote:

> Dear All,

>

> I have a one-dimensional system of spherical particles of diameter

> sigma move along a line.

>

> I am using # =A0 --- The simulation Box is periodic in only one

> direction setmd periodic 1 0 0 setmd box_l $bl $bl $bl and the

> interaction potential is either the WCA, hertzian or Gaussian

> potential

>

> My compilation of ESPresSo is as follows: ESPResSo-3.2.0 {

> Compilation status { FFTW } { CONSTRAINTS } { ROTATIONAL_INERTIA } {> BOND_ANGLE_HARMONIC } { GAY_BERNE } { GAUSSIAN } { COMFIXED } {

> HERTZIAN } { PARTIAL_PERIODIC } { LENNARD_JONES } {

> VIRTUAL_SITES_RELATIVE } { EXTERNAL_FORCES } { TABULATED } { ROTATION<= br> > } { SOFT_SPHERE } { VIRTUAL_SITES_NO_VELOCITY } {

> LENNARD_JONES_GENERIC } { ROTATION_PER_PARTICLE } { BOND_VIRTUAL } }>

> I am running the simulation with: { langevin 1.0 1.0 }

>

> However, with the current version of ESPresSo 3.2.0, I have problems> to control the temperature with any of the above mentioned

> potentials.

>

> WCA-Potencial {0 0 lennard-jones 1.0 0.5 0.5612310241546865 0.25 0.0> 0.0 0.0 } t=3D1.000000000000001 E=3D1.784989386884216, T=3D3.529931670= 7096

> (LJ cap =3D 20) t=3D2.000000000000001 E=3D2.105429430274374,

> T=3D4.149024028202554 (LJ cap =3D 30)

>

> However, for the same script with the same set of parameters using

> version 3.1.1, I get the following {0 0 lennard-jones 1.0 0.5

> 0.5612310241546865 0.25 0.0 0.0 0.0 } { langevin 1.0 1.0 }

>

> t=3D1.000000000000001 E=3D0.4317609210550725, T=3D0.8207101850023056 (= LJ

> cap =3D 20) t=3D2.000000000000001 E=3D0.5662738721667048,

> T=3D1.071506110193384 (LJ cap =3D 30)

>

> I observe the same problem with both WCA and Hertzian potentials.

> Correct temperature in 3.1.1 but not in 3.2.0

>

> Does any body could shed some light? =A0Any suggestion would be

> greatly appreciated.

>

> Thanks a lot in advance,

>

> Salvador

>

>

>

Dr. rer. nat. Olaf Lenz

Institut f=FCr Computerphysik, Allmandring 3, D-70569 Stuttgart

Phone: +49-711-685-63607

Dr. Salvador Herrera-Velarde

Simulacion Computacional de Mat= eria Condensada Blanda

Sub-Direccion de Investigacion y Posgrado

Instituto Tecnologico Superior de Xalapa (ITSX)

Instituto Tecnol=F3gico Superior de Xalapa=

Secci=F3n 5A Reserva Terr= itorial s/n,=A0

Col. Santa B=E1rbara,=A0

CP 91096

Xalapa, Ver. Mexico

=3Do=3Do=3Do=3Do=3Do=3Do=3Do=3Do=3Do=3Do=3Do=3Do=3Do=3Do=3Do= =3Do=3Do=3Do=3Do

Este correo ha sido editado para evitar el uso de a= centos y guardar compatibilidad entre

diferentes distribuciones

Xalapa, Ver. Mexico

=3Do=3Do=3Do=3Do=3Do=3Do=3Do=3Do=3Do=3Do=3Do=3Do=3Do=3Do=3Do= =3Do=3Do=3Do=3Do

Este correo ha sido editado para evitar el uso de a= centos y guardar compatibilidad entre

diferentes distribuciones

Hi!

If that works, the problem is probably rather that you make some assumption on the degrees of freedom in your script, which are no longer true. In previous versions of Espresso, if ROTATION was compiled in, the DOF per particle were 6. Now, if ROTATION_PER_PARTICLE is on, it is still 3 for all particles that are still rotationally invariant, so in your case, all. Best is, that you get rid of this assumption in the script.

Best regards,

Axel

On 05/13/2013 09:50 PM, Salvador H-V wrote:

If that works, the problem is probably rather that you make some assumption on the degrees of freedom in your script, which are no longer true. In previous versions of Espresso, if ROTATION was compiled in, the DOF per particle were 6. Now, if ROTATION_PER_PARTICLE is on, it is still 3 for all particles that are still rotationally invariant, so in your case, all. Best is, that you get rid of this assumption in the script.

Best regards,

Axel

On 05/13/2013 09:50 PM, Salvador H-V wrote:

Hi Olaf,

Thanks for your quickly reply.

You were right, turning off the rotation (I also turned off virtual sites) solve the "problem".

Now the compilation of ESPresSo is as follows:ESPResSo-3.2.0{ Compilation status { FFTW } { CONSTRAINTS } { BOND_ANGLE_HARMONIC } { GAUSSIAN } { HERTZIAN } { PARTIAL_PERIODIC } { LENNARD_JONES } { MODES } { EXTERNAL_FORCES } { TABULATED } { SOFT_SPHERE } { LENNARD_JONES_GENERIC } { MASS } { ELECTROSTATICS } { BOND_CONSTRAINT } { EXCLUSIONS } }The control of temperature is ok for the three potentials (WCA, Hertzian and Gaussian).

Thanks a lot,

Salvador

On Mon, May 13, 2013 at 1:48 PM, Olaf Lenz <olenz@icp.uni-stuttgart.de> wrote:

Hi!

Could you try whether this also happens when you turn off

ROTATION_PER_PARTICLE?

In general, when you just do a standard simulation, DO NOT turn on

ROTATION, as this will make ESPResSo significantly slower.

Anyway, this is a problem that should be solved.

Olaf

--

On 05/13/2013 08:43 PM, Salvador H-V wrote:

> Dear All,

>

> I have a one-dimensional system of spherical particles of diameter

> sigma move along a line.

>

> I am using # --- The simulation Box is periodic in only one

> direction setmd periodic 1 0 0 setmd box_l $bl $bl $bl and the

> interaction potential is either the WCA, hertzian or Gaussian

> potential

>

> My compilation of ESPresSo is as follows: ESPResSo-3.2.0 {

> Compilation status { FFTW } { CONSTRAINTS } { ROTATIONAL_INERTIA } {

> BOND_ANGLE_HARMONIC } { GAY_BERNE } { GAUSSIAN } { COMFIXED } {

> HERTZIAN } { PARTIAL_PERIODIC } { LENNARD_JONES } {

> VIRTUAL_SITES_RELATIVE } { EXTERNAL_FORCES } { TABULATED } { ROTATION

> } { SOFT_SPHERE } { VIRTUAL_SITES_NO_VELOCITY } {

> LENNARD_JONES_GENERIC } { ROTATION_PER_PARTICLE } { BOND_VIRTUAL } }

>

> I am running the simulation with: { langevin 1.0 1.0 }

>

> However, with the current version of ESPresSo 3.2.0, I have problems

> to control the temperature with any of the above mentioned

> potentials.

>

> WCA-Potencial {0 0 lennard-jones 1.0 0.5 0.5612310241546865 0.25 0.0

> 0.0 0.0 } t=1.000000000000001 E=1.784989386884216, T=3.5299316707096

> (LJ cap = 20) t=2.000000000000001 E=2.105429430274374,

> T=4.149024028202554 (LJ cap = 30)

>

> However, for the same script with the same set of parameters using

> version 3.1.1, I get the following {0 0 lennard-jones 1.0 0.5

> 0.5612310241546865 0.25 0.0 0.0 0.0 } { langevin 1.0 1.0 }

>

> t=1.000000000000001 E=0.4317609210550725, T=0.8207101850023056 (LJ

> cap = 20) t=2.000000000000001 E=0.5662738721667048,

> T=1.071506110193384 (LJ cap = 30)

>

> I observe the same problem with both WCA and Hertzian potentials.

> Correct temperature in 3.1.1 but not in 3.2.0

>

> Does any body could shed some light? Any suggestion would be

> greatly appreciated.

>

> Thanks a lot in advance,

>

> Salvador

>

>

>

Dr. rer. nat. Olaf Lenz

Institut für Computerphysik, Allmandring 3, D-70569 Stuttgart

Phone: +49-711-685-63607

--

=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o

Dr. Salvador Herrera-Velarde

Simulacion Computacional de Materia Condensada Blanda

Sub-Direccion de Investigacion y Posgrado

Instituto Tecnologico Superior de Xalapa (ITSX)

Instituto Tecnológico Superior de Xalapa

Sección 5A Reserva Territorial s/n,Col. Santa Bárbara,CP 91096

Xalapa, Ver. Mexico

=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o

Este correo ha sido editado para evitar el uso de acentos y guardar compatibilidad entre

diferentes distribuciones

-- JP Dr. Axel Arnold ICP, Universität Stuttgart Pfaffenwaldring 27 70569 Stuttgart, Germany Email: arnolda@icp.uni-stuttgart.de Tel: +49 711 685 67609--------------030809070905020205090709-- From MAILER-DAEMON Tue May 14 02:03:56 2013 Received: from list by lists.gnu.org with archive (Exim 4.71) id 1Uc8L6-000530-6W for mharc-espressomd-users@gnu.org; Tue, 14 May 2013 02:03:56 -0400 Received: from eggs.gnu.org ([208.118.235.92]:46561) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from

Hi,

set temp [expr [analyze energy kinetic]/(0.5*$np)]

Thanks for the suggestions and obse=
rvations.

However, in my script I am not making as=
sumptions about the number degrees of freedom.

I just obtain the system temperature with:

<= /div>

What I found is that only when I turn off the Rotation, Rot=
ational_Inertia, Rotation_Per_Particle and Virtual_Sites I get=A0

puts "The degrees of freedom is [degre=
es_of_freedom] " =3D 3!

If I unde=
rstand well, if some of the virtual_sites features are activated, then rota=
tion feature is automatically activated, then=A0

% [code_info]

invalid command name=
"ESPResSo-3.2.0

{ Compilation status { FFTW } { CONSTRAINTS=
} { BOND_ANGLE_HARMONIC } { GAUSSIAN } { COMFIXED } { HERTZIAN } { PARTIAL=
_PERIODIC } { LENNARD_JONES } { VIRTUAL_SITES_RELATIVE } { EXTERNAL_FORCES =
} { TABULATED } { ROTATION } { SOFT_SPHERE } { VIRTUAL_SITES_NO_VELOCITY } =
{ LENNARD_JONES_GENERIC } { BOND_VIRTUAL } }"

% [degrees_of_freedom]

invalid command name "6"

All the best,

Salvador