Re: [ESPResSo-users] Espressomd-users Digest, Vol 71, Issue 7

On Wed, Sep 28, 2016 at 5:22 AM, Georg Rempfer <address@hidden> wrote:

I'm not familiar with the internals of MMM2D. From our institute Michael Kuron was the last one to work on MMM2D, and Jonas Landsgesell and Tobias Richter recently implemented the pressure contribution due to P3M. I blieve these people are more qualified to answer that question.

They should be on this mailing list. Guys?

On Tue, Sep 27, 2016 at 7:48 PM, padidela uday <address@hidden> wrote:
Thank you Georg for your response.

Can you give me an idea how to include the pressure in this calculation?

Thank you

Uday

On Tue, Sep 27, 2016 at 9:30 PM, <address@hiddennu.org> wrote:
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Today's Topics:

1. Re: WARNING: pressure calculated, but MMM2D pressure not
implemented (Georg Rempfer)

----------------------------------------------------------------------

Message: 1
Date: Mon, 26 Sep 2016 19:10:09 +0200
From: Georg Rempfer <address@hidden>
To: padidela uday <address@hidden>
Cc: "address@hidden" <address@hidden>
Subject: Re: [ESPResSo-users] WARNING: pressure calculated, but MMM2D
pressure not implemented
Message-ID:
<CAA6P0aKo=5UZNA-H-Ua1cY+X+scFaddress@hiddenail.com>
Content-Type: text/plain; charset="utf-8"

Hello Padidela,

this just means that when you run 'analyze pressure total', the resulting
value does not contain the pressure contribution due to the electrostatic
interactions. There is nothing wrong with the dynamics of the system, this
only influences this calculated observable.

Do you need to know the pressure? I assume it's not a problem in principle
to include this contribution in the calculation, but so far no one has
implemented the necessary code.

Greetings,
Georg

On Fri, Sep 16, 2016 at 3:39 PM, padidela uday <address@hidden>
wrote:

>
> Dear all,
>
> I am trying to implement charged wall constraints in one of my scripts
> along with the particles between the constraints. But however I land up in
> few troubles with it.
>
> After equilibrating the system a warning is displayed on screen during
> sampling
>
>
> *calculating pressure for electrostatics method that does have it
> implemented*
> *WARNING: pressure calculated, but MMM2D pressure not implemented*
>
> Is there something wrong with the code could you help me to handle this?
>
> Thank you for your time
>
> set n_solute 200
> set n_solvent 200
> set top_wall 100
> set bottom_wall 100
> set n_wall 200
> set n_part [expr ($n_solute + $n_solvent + $top_wall + $bottom_wall)]
> set box_l 200
> set sig1 2.0
> set box_lxy [expr sqrt(2) * $box_l]
> set box_lz [expr 0.5*$box_l]
>
> setmd box_l $box_lxy $box_lxy [expr $box_lz + $sig1]
> setmd periodic 1 1 0
>
> for {set i 0} { $i < 200 } {incr i} {
> set posx [expr $box_lxy*[t_random]]
> set posy [expr $box_lxy*[t_random]]
> set posz [expr $box_lz*[t_random] + $sig1]
> set vx [gauss_random]
> set vy [gauss_random]
> set vz [gauss_random]
> part $i pos $posx $posy $posz type 0 v $vx $vy $vz q -2 mass 1.0
> }
>
> for {set i 200} { $i < 400 } {incr i} {
> set posx [expr $box_lxy*[t_random]]
> set posy [expr $box_lxy*[t_random]]
> set posz [expr $box_lz*[t_random] + $sig1]
> set vx [gauss_random]
> set vy [gauss_random]
> set vz [gauss_random]
> part $i pos $posx $posy $posz type 1 v $vx $vy $vz q 1 mass 1.0
> }
>
> #wall at top
> constraint wall normal 0 0 1 dist $sig1 type 2
>
> for {set i 400} { $i < 500 } {incr i} {
> set posx [expr $box_lxy*[t_random]]
> set posy [expr $box_lxy*[t_random]]
> set posz [expr ($box_lz + $sig1)]
>
> part [expr $i + $one_wall] pos $posx $posy $posz type 2 q 1
> }
>
> constraint wall normal 0 0 -1 dist [expr -$box_lz - $box_lz] type 2
>
> #wall at bottom
>
> for {set i 500} { $i < 600 } {incr i} {
> set posx [expr $box_lxy*[t_random]]
> set posy [expr $box_lxy*[t_random]]
> set posz [expr ($box_lz - $box_lz)*[t_random]]
> part [expr $i + $two_wall] pos $posx $posy $posz type 2 q 1
> }
>
> set sigma [expr -0.25*$n_wall/($box_lxy*$box_lxy)]
> constraint plate height 0 sigma $sigma
> constraint plate height [expr $box_lz + $sig1] sigma $sigma
>
> setmd time_step 0.00002624
> setmd skin 0.3
> set temp 4.9576
> set gamma 1
> thermostat langevin $temp $gamma
>
> # POTENTIAL
> set sig1 2.0
> set sig2 1.15
> set sig3 0.3
> set eps1 1.0
> set eps2 0.7
> set eps3 0.5
> set cut1 [expr 1.12246*$sig1]
> set cut2 [expr 1.12246*$sig2]
> set cut3 [expr 1.12246*$sig3]
> set shift1 [expr 0.25*$eps3]
> set shift2 [expr 0.25*$eps3]
> set shift3 [expr 0.25*$eps3]
> inter 0 0 lennard-jones $eps3 $sig1 $cut1 $shift1 0
> inter 1 0 lennard-jones $eps3 $sig2 $cut2 $shift2 0
> inter 1 1 lennard-jones $eps3 $sig3 $cut3 $shift3 0
> inter 2 0 lennard-jones $eps3 $sig1 $cut1 $shift1 0
> inter 2 1 lennard-jones $eps3 $sig2 $cut2 $shift2 0
> #inter 2 2 lennard-jones $eps3 $sig3 $cut3 $shift3 0
>
> cellsystem layered 3
> inter coulomb 1.0 mmm2d 1e-4
>
> if { [regexp "ROTATION" [code_info]] } {
> set deg_free 6
> } {
> set deg_free 3
> }
>
> # prepare vmd connection
> if { $vmd_output=="yes" } {
> prepare_vmd_connection "vmd"
> imd listen 10000
> }
>
> inter ljforcecap individual
> set inter_steps 10000
> for {set cap 10} {$cap < 100} {incr 10} {
> set rad [expr 1.0 - 0.5*$cap/10.0]
> set lb [expr 1.0 * $cap / 10.0]
> inter 0 0 lennard-jones $eps3 $sig1 $cut1 $shift1 0 $rad
> inter 1 0 lennard-jones $eps3 $sig2 $cut2 $shift2 0 $rad
> inter 1 1 lennard-jones $eps3 $sig3 $cut3 $shift3 0 $rad
> inter coloumb $lb mmm2d 1e-4
> set temp [expr [analyze energy kinetic]/(($deg_free/2.0)*$n_part)]
> puts "t=[setmd time] E=[analyze energy total] T=$temp"
> if {$vmd_output=="yes"} {imd positions}
> inter ljforcecap $cap;
> integrate $inter_steps
> }
> inter ljforcecap 0
> inter coulomb 1.0 mmm2d 1e-4
>
> set h [open "production.data" "w"]
> set g [open "analysis.data" "w"]
> set n_part [expr ($n_solute + $n_solvent + $top_wall + $bottom_wall)]
> for {set i 0} { $i <4000 } {incr i} {
> set temp [expr [analyze energy kinetic]/(($deg_free/2.0)*$n_part)]
> puts $h " $i [setmd time] [analyze energy kinetic] $temp"
> integrate 200
>
> set f [open "config_$i" "w"]
> blockfile $f write tclvariable {box_lxy box_lz}
> blockfile $f write variable box_l
> blockfile $f write particles {id pos type v f}
> set temp [expr [analyze energy kinetic]/(($deg_free/2.0)*$n_part)]
> puts $f " \ { energy [analyze energy total] $temp}"
> puts $g " [analyze energy kinetic] [analyze pressure total] [analyze
> energy total] $temp"
>
> close $f
> }
> close $g
>
>
>
>
> With Kind Regards
>
> Uday
>
>
>
>
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End of Espressomd-users Digest, Vol 71, Issue 7
***********************************************

--
Uday Kumar Padidela
PhD Scholar
Department Of Chemistry,
BITS Pilani, Goa,
Mobile: +91-9850973742

From:	Lei Liu
Subject:	Re: [ESPResSo-users] Espressomd-users Digest, Vol 71, Issue 7
Date:	Wed, 28 Sep 2016 09:29:24 +0900