<div dir="ltr"><div><div><div><div><div><div><div>Hi Berk,<br><br></div>Yes, I think I was calling that after the coordinate communication. The place where I code it in is after the command:<br><br> if (bDoForces)<br> {<br> post_process_forces(fplog, cr, step, nrnb, wcycle,<br> top, box, x, f, vir_force, mdatoms, graph, fr, vsite,<br> flags);<br> }<br><br></div>After that I use a <br></div>if(bNS){<br></div> if (DOMAINDECOMP(cr)){<br><br></div>to make sure it is done every neighboring list step.<br><br></div>Is this correct? BTW, I was coding that in gromacs4.6.3 version (this is for historical reason because I have coded other unrelated things in other files).<br><br></div>I have checked that the ga2la_get_home in the first loop find all ai atoms, but the second loop ga2la_get missed some aj atoms. One of the reasons I guess is because the missing atom pairs
are too far apart (but less than 6 angstroms) in Cartesian space from
each other, so that even by including all cells of the home node it still could not find it. That could be a problem, but I don't know exactly how -dd find this pair partner in its neighboring cells. <div><div><div><div><div><div><div><br></div><div>Thank you,<br></div><div>Xingcheng<br></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Aug 28, 2015 at 11:28 AM, <span dir="ltr"><<a href="mailto:gromacs.org_gmx-developers-request@maillist.sys.kth.se" target="_blank">gromacs.org_gmx-developers-request@maillist.sys.kth.se</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Send gromacs.org_gmx-developers mailing list submissions to<br>
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Today's Topics:<br>
<br>
1. Re: dhdl expanded ensemble<br>
(Mirabzadeh, Christopher (<a href="mailto:mira2978@vandals.uidaho.edu">mira2978@vandals.uidaho.edu</a>))<br>
2. Re: Increase the scope of dd domains (Berk Hess)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Fri, 28 Aug 2015 16:17:40 +0000<br>
From: "Mirabzadeh, Christopher (<a href="mailto:mira2978@vandals.uidaho.edu">mira2978@vandals.uidaho.edu</a>)"<br>
<<a href="mailto:mira2978@vandals.uidaho.edu">mira2978@vandals.uidaho.edu</a>><br>
To: "<a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a>" <<a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a>>,<br>
"<a href="mailto:michael.shirts@virginia.edu">michael.shirts@virginia.edu</a>" <<a href="mailto:michael.shirts@virginia.edu">michael.shirts@virginia.edu</a>><br>
Subject: Re: [gmx-developers] dhdl expanded ensemble<br>
Message-ID: <<a href="mailto:3686D140-78FF-4961-80B0-C13B05A36EF7@vandals.uidaho.edu">3686D140-78FF-4961-80B0-C13B05A36EF7@vandals.uidaho.edu</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Thank you! I will look into redmine and I will also look at those variables closer.<br>
<br>
Thanks,<br>
<br>
-ChrisM<br>
<br>
Mirabzadeh, Christopher<br>
Graduate Research Assistant/Physics Instructor<br>
Department of Physics<br>
University of Idaho<br>
Moscow, Id<br>
<a href="tel:%28509%29339-5647" value="+15093395647">(509)339-5647</a><br>
<br>
<br>
<br>
> On Aug 28, 2015, at 5:58 AM, Shirts, Michael R. (mrs5pt) <<a href="mailto:mrs5pt@eservices.virginia.edu">mrs5pt@eservices.virginia.edu</a>> wrote:<br>
><br>
> Yeah, apologies, checking 5.1 in the in the debugger for a binding free<br>
> energy change, then there are some differences between the dhdl output<br>
> file when nstdhdl = 20, and the terms in the enerd->term dhdl components<br>
> at step = 10 matched what the output was in the dhdl file when nstdhdl =<br>
> 10. So don't rely on that dhdl, since it is missing some terms.<br>
><br>
> In any case, it would be relatively easy to change the existing machinery<br>
> to force it do the full calculation dhdl calculation every step. If you<br>
> wanted to make it very easy, just set nstdhdl = 1, and introduce a new<br>
> variable that controls the printing of dhdl to the file alone.<br>
><br>
> ~~~~~~~~~~~~<br>
> Michael Shirts<br>
> Associate Professor<br>
> Department of Chemical Engineering<br>
> University of Virginia<br>
> <a href="mailto:michael.shirts@virginia.edu">michael.shirts@virginia.edu</a><br>
> <a href="tel:%28434%29%20243-1821" value="+14342431821">(434) 243-1821</a><br>
><br>
><br>
><br>
> On 8/28/15, 3:11 AM, "Berk Hess" <<a href="mailto:hess@kth.se">hess@kth.se</a>> wrote:<br>
><br>
>> No. To be more precise dhdl is only (fully) calculated at each step<br>
>> where free energies are calculated, i.e. every nstdhdl steps.<br>
>> To find where the final values are stored, it's often easiest to look in<br>
>> mdebin.c, in this case at line 1244.<br>
>><br>
>> Cheers,<br>
>><br>
>> Berk<br>
>><br>
>> On 2015-08-28 03:52, Shirts, Michael R. (mrs5pt) wrote:<br>
>>> Dhdl is automatically calculated at every step if free energies are<br>
>>> calculated. Look in sum_dhdl -- difference components are stored in<br>
>>> enerd->term.<br>
>>><br>
>>> Unless it's a new development you would rather keep private for now, you<br>
>>> should consider posting the proposed enhancement on redmine. You would<br>
>>> likely get some tips about how to do it in a way that could be more<br>
>>> easily<br>
>>> included in later gromcs versions.<br>
>>><br>
>>> Best,<br>
>>> ~~~~~~~~~~~~<br>
>>> Michael Shirts<br>
>>> Associate Professor<br>
>>> Department of Chemical Engineering<br>
>>> University of Virginia<br>
>>> <a href="mailto:michael.shirts@virginia.edu">michael.shirts@virginia.edu</a><br>
>>> <a href="tel:%28434%29%20243-1821" value="+14342431821">(434) 243-1821</a><br>
>>><br>
>>><br>
>>> From: <Mirabzadeh>, "Christopher (<a href="mailto:mira2978@vandals.uidaho.edu">mira2978@vandals.uidaho.edu</a>)"<br>
>>> <<a href="mailto:mira2978@vandals.uidaho.edu">mira2978@vandals.uidaho.edu</a>><br>
>>> Reply-To: "<a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a>" <<a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a>><br>
>>> Date: Thursday, August 27, 2015 at 12:20 PM<br>
>>> To: "<a href="mailto:gromacs.org_gmx-developers@maillist.sys.kth.se">gromacs.org_gmx-developers@maillist.sys.kth.se</a>"<br>
>>> <<a href="mailto:gromacs.org_gmx-developers@maillist.sys.kth.se">gromacs.org_gmx-developers@maillist.sys.kth.se</a>><br>
>>> Subject: [gmx-developers] dhdl expanded ensemble<br>
>>><br>
>>><br>
>>><br>
>>> Hello,<br>
>>><br>
>>> What I'm trying to do;<br>
>>><br>
>>> I'm attempting to add functionality to expanded ensemble.<br>
>>><br>
>>><br>
>>> What I've done so far;<br>
>>><br>
>>> I've added functionality to accept my mdp options and found pre-written<br>
>>> functions to take advantage of.<br>
>>><br>
>>> Where I'm stuck;<br>
>>><br>
>>> I need the derivative of the Hamiltonian with respect to lambda at every<br>
>>> md step. I'm having a hard time narrowing down this variable. I know<br>
>>> it's<br>
>>> calculated and I see in mdebin.c there is a line that says "/* store_dh<br>
>>> is<br>
>>> dE */". Is the derivative "store_dhdl[]=enerd->term[F_DVDL]"?<br>
>>> Or, is this already being called somewhere in expanded.c that I can<br>
>>> take<br>
>>> advantage of, maybe dfhist?<br>
>>><br>
>>> Is the dhdl automatically calculated? Where is it stored? If dhdl isn?t<br>
>>> being calculated automatically, is there an mdp option or mdrun flag<br>
>>> that<br>
>>> I need?<br>
>>><br>
>>> I appreciate any advice that can be offered.<br>
>>><br>
>>><br>
>>> -ChrisM<br>
>>><br>
>>> Mirabzadeh, Christopher<br>
>>> Graduate Research Assistant/Physics Instructor<br>
>>> Department of Physics<br>
>>> University of Idaho<br>
>>> Moscow, Id<br>
>>> <a href="tel:%28509%29339-5647" value="+15093395647">(509)339-5647</a><br>
>>><br>
>>><br>
>>><br>
>>><br>
>>><br>
>><br>
><br>
> --<br>
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<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Fri, 28 Aug 2015 18:38:25 +0200<br>
From: Berk Hess <<a href="mailto:hess@kth.se">hess@kth.se</a>><br>
To: <a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a><br>
Subject: Re: [gmx-developers] Increase the scope of dd domains<br>
Message-ID: <<a href="mailto:55E08E81.2020207@kth.se">55E08E81.2020207@kth.se</a>><br>
Content-Type: text/plain; charset="windows-1252"; Format="flowed"<br>
<br>
Hi,<br>
<br>
I don't see why your current code doesn't work with 1D DD.<br>
<br>
You do call this code after the coordinate communication has been done?<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 08/28/2015 05:45 PM, Xingcheng Lin wrote:<br>
> Hi Berk,<br>
><br>
> The 1D dd where I used 2 MPI processes with -dd 1 1 2 can only work if<br>
> I do not turn on the -dlb yes. It seems the problem will always exist<br>
> if I have atom pairs separated in two domains.<br>
><br>
> You mentioned I could get all pairs by only looking at home atoms for<br>
> the i-atoms. Does it mean I can even make the code like this, by<br>
> changing ga2la_get for aj to ga2la_get_home?<br>
><br>
> // NP is number of tested pairs recorded in an array;<br>
> // If atom ai is one of the home atoms in a node, we start testing if<br>
> aj is<br>
> available by the same node;<br>
> // rlist = 1.0nm, Coulombtype = Cut-off, cutoff-scheme = Verlet, ns_type<br>
> = grid, pbc = xyz;<br>
><br>
> int Npairs = 0;<br>
> for (i=0; i<NP; ++i)<br>
> {<br>
> int ai = datai[i] ;<br>
> int localai;<br>
> // Examine if ai it is within the home atoms index;<br>
> if (ga2la_get_home(cr->dd->ga2la, ai, &localai))<br>
> {<br>
> aj = dataj[i] ;<br>
> // Examine if aj is available by local node;;<br>
> if (ga2la_get_home(cr->dd->ga2la, aj, &localaj))<br>
> {<br>
> FILE *fp;<br>
> fp = fopen("pairs.dat","a");<br>
><br>
> fprintf(fp, "%d\t%d\n", ai, aj);<br>
> fclose(fp);<br>
><br>
> r_N = 0.6 ;<br>
> pbc_dx(&pbc, x[localai], x[localaj], dx) ;<br>
> dr2 = iprod( dx, dx ) ;<br>
> dr = sqrt( dr2 ) ;<br>
> if (dr < r_N)<br>
> {<br>
> Npairs += 1;<br>
> }<br>
> }<br>
> }<br>
> }<br>
><br>
><br>
> On Fri, Aug 28, 2015 at 2:22 AM,<br>
> <<a href="mailto:gromacs.org_gmx-developers-request@maillist.sys.kth.se">gromacs.org_gmx-developers-request@maillist.sys.kth.se</a><br>
> <mailto:<a href="mailto:gromacs.org_gmx-developers-request@maillist.sys.kth.se">gromacs.org_gmx-developers-request@maillist.sys.kth.se</a>>> wrote:<br>
><br>
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> than "Re: Contents of gromacs.org_gmx-developers digest..."<br>
><br>
><br>
> Today's Topics:<br>
><br>
> 1. Increase the scope of dd domains (Xingcheng Lin)<br>
> 2. Re: energy group computation (Berk Hess)<br>
> 3. Re: dhdl expanded ensemble (Berk Hess)<br>
> 4. Re: Increase the scope of dd domains (Berk Hess)<br>
><br>
><br>
> ----------------------------------------------------------------------<br>
><br>
> Message: 1<br>
> Date: Thu, 27 Aug 2015 23:35:30 -0500<br>
> From: Xingcheng Lin <<a href="mailto:linxingcheng50311@gmail.com">linxingcheng50311@gmail.com</a><br>
> <mailto:<a href="mailto:linxingcheng50311@gmail.com">linxingcheng50311@gmail.com</a>>><br>
> To: <a href="mailto:gromacs.org_gmx-developers@maillist.sys.kth.se">gromacs.org_gmx-developers@maillist.sys.kth.se</a><br>
> <mailto:<a href="mailto:gromacs.org_gmx-developers@maillist.sys.kth.se">gromacs.org_gmx-developers@maillist.sys.kth.se</a>><br>
> Subject: [gmx-developers] Increase the scope of dd domains<br>
> Message-ID:<br>
><br>
> <CAPugp-HQjXb8hYKJO9i-1fMSfpzQxe=<a href="mailto:qZCOo8tPwPQrFraKEmw@mail.gmail.com">qZCOo8tPwPQrFraKEmw@mail.gmail.com</a> <mailto:<a href="mailto:qZCOo8tPwPQrFraKEmw@mail.gmail.com">qZCOo8tPwPQrFraKEmw@mail.gmail.com</a>>><br>
> Content-Type: text/plain; charset="utf-8"<br>
><br>
> Hi,<br>
><br>
> I am trying to encode a "on the fly" calculation for the number of<br>
> atom<br>
> pairs within some distance (for example here, 6 angstroms).<br>
><br>
> The problem happens when doing parallel domain decomposition.<br>
> Specifically,<br>
> when two particles reside in different domains, gromacs is not able to<br>
> recognize this pair. I am trying to use ga2la_get_home and<br>
> ga2la_get for<br>
> calculation, here is the code:<br>
><br>
> // NP is number of tested pairs recorded in an array;<br>
> // If atom ai is one of the home atoms in a node, we start testing<br>
> if aj is<br>
> available by the same node;<br>
> // rlist = 1.0nm, Coulombtype = Cut-off, cutoff-scheme = Verlet,<br>
> ns_type<br>
> = grid, pbc = xyz;<br>
><br>
> int Npairs = 0;<br>
> for (i=0; i<NP; ++i)<br>
> {<br>
> int ai = datai[i] ;<br>
> int localai;<br>
> // Examine if ai it is within the home atoms index;<br>
> if (ga2la_get_home(cr->dd->ga2la, ai, &localai))<br>
> {<br>
> aj = dataj[i] ;<br>
> // Examine if aj is available by local node;;<br>
> if (ga2la_get(cr->dd->ga2la, aj, &localaj, &localcell))<br>
> {<br>
> FILE *fp;<br>
> fp = fopen("pairs.dat","a");<br>
><br>
> fprintf(fp, "%d\t%d\n", ai, aj);<br>
> fclose(fp);<br>
><br>
> r_N = 0.6 ;<br>
> pbc_dx(&pbc, x[localai], x[localaj], dx) ;<br>
> dr2 = iprod( dx, dx ) ;<br>
> dr = sqrt( dr2 ) ;<br>
> if (dr < r_N)<br>
> {<br>
> Npairs += 1;<br>
> }<br>
> }<br>
> }<br>
> }<br>
><br>
> The results show some atom pairs, while atoms less than 6<br>
> angstroms apart,<br>
> are missing here. I increase rlist, but it doesn't help. Is there<br>
> any way<br>
> to increase the scope of atoms available in each domain so that<br>
> the missing<br>
> atoms can be detected?<br>
><br>
> Or are there any mistakes out of my notice in this code?<br>
><br>
> Thank you,<br>
> Xingcheng<br>
> -------------- next part --------------<br>
> An HTML attachment was scrubbed...<br>
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><br>
> ------------------------------<br>
><br>
> Message: 2<br>
> Date: Fri, 28 Aug 2015 09:04:56 +0200<br>
> From: Berk Hess <<a href="mailto:hess@kth.se">hess@kth.se</a> <mailto:<a href="mailto:hess@kth.se">hess@kth.se</a>>><br>
> To: <a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a> <mailto:<a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a>><br>
> Subject: Re: [gmx-developers] energy group computation<br>
> Message-ID: <<a href="mailto:55E00818.1060601@kth.se">55E00818.1060601@kth.se</a> <mailto:<a href="mailto:55E00818.1060601@kth.se">55E00818.1060601@kth.se</a>>><br>
> Content-Type: text/plain; charset="windows-1252"; Format="flowed"<br>
><br>
> Hi,<br>
><br>
> This is a use, not a development question. Please post such<br>
> questions to<br>
> gmx-users.<br>
><br>
> But the quick answer is that although it's technically possible to<br>
> calculate this number, this number is useless (and indeed high).<br>
><br>
> Cheers,<br>
><br>
> Berk<br>
><br>
> On 2015-08-27 19:00, ANTHONY C MANSON wrote:<br>
> > Hello:<br>
> ><br>
> > I am trying to estimate the polar solvation energy of a 76 residue<br>
> > protein at standard conditions. I am using the gromacs 4.5.3 dp<br>
> release.<br>
> > I have set up a simulation with the solvated (using spce water)<br>
> protein.<br>
> > I have defined two energygrps: Protein SOL in the *.mdp file.<br>
> > I have run the simulation and have then run g_energy on the<br>
> *.edr file.<br>
> > I get the following choices from g_energy:<br>
> ><br>
> > 1 Bond 2 Angle 3 Proper-Dih. 4<br>
> Improper-Dih.<br>
> > 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8<br>
> Disper.-corr.<br>
> > 9 Coulomb-(SR) 10 Coul.-recip. 11 Potential 12<br>
> > Kinetic-En.<br>
> > 13 Total-Energy 14 Temperature 15 Pres.-DC 16<br>
> Pressure<br>
> > 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX<br>
> > 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY<br>
> > 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ<br>
> > 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX<br>
> > 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 Mu-X<br>
> > 37 Mu-Y 38 Mu-Z<br>
> > 39 Coul-SR:Protein-Protein 40 LJ-SR:Protein-Protein<br>
> > 41 Coul-14:Protein-Protein 42 LJ-14:Protein-Protein<br>
> > 43 Coul-SR:Protein-SOL 44 LJ-SR:Protein-SOL<br>
> > 45 Coul-14:Protein-SOL 46 LJ-14:Protein-SOL<br>
> > 47 Coul-SR:SOL-SOL 48 LJ-SR:SOL-SOL<br>
> > 49 Coul-14:SOL-SOL 50 LJ-14:SOL-SOL<br>
> > 51 T-System<br>
> ><br>
> > I pick Coul-SR:Protein-SOL as a component of the polar solvation<br>
> energy.<br>
> > I note that the energy magnitude seems extremely high:<br>
> ><br>
> > Energy Average Err.Est. RMSD Tot-Drift<br>
> ><br>
> -------------------------------------------------------------------------------<br>
> > Coul-SR:Protein-SOL -8343.86 46 193.457 -192.93<br>
> > (kJ/mol)<br>
> ><br>
> > This seems unreasonable to me. I wanted to understand how mdrun<br>
> > was calculating this value. Perhaps it is accumulating energies<br>
> over<br>
> > many frames. What part of the code (force.c ...) handles this<br>
> > calculation so I can verify its action.<br>
> ><br>
> > Also, I tried running g_enemat on this with the following<br>
> groups.dat file.<br>
> ><br>
> > 2<br>
> > Protein<br>
> > SOL<br>
> ><br>
> > I use the command:<br>
> ><br>
> > g_enemat -f ub_short.edr -e 100<br>
> ><br>
> > and get:<br>
> ><br>
> > Opened ub_short.edr as double precision energy file<br>
> > Will read groupnames from in! putfile<br>
> > Read 2 groups<br>
> > group 0WARNING! could not find group (null):Protein-Protein (0,0)in<br>
> > energy file<br>
> > WARNING! could not find group (null):Protein-SOL (0,1)in energy file<br>
> > group 1WARNING! could not find group (null):SOL-SOL (1,1)in<br>
> energy file<br>
> ><br>
> > Will select half-matrix of energies with 6 elements<br>
> > Read frame: 1000, Time: 100.000e 100.000<br>
> > Will build energy half-matrix of 2 groups, 6 elements, over 1001<br>
> frames<br>
> > Segmentation fault<br>
> ><br>
> ><br>
> > Cheers<br>
> > Anthony Manson Ph.D.<br>
> ><br>
> ><br>
><br>
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> ------------------------------<br>
><br>
> Message: 3<br>
> Date: Fri, 28 Aug 2015 09:09:49 +0200<br>
> From: Berk Hess <<a href="mailto:hess@kth.se">hess@kth.se</a> <mailto:<a href="mailto:hess@kth.se">hess@kth.se</a>>><br>
> To: <a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a><br>
> <mailto:<a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a>>, "<a href="mailto:michael.shirts@virginia.edu">michael.shirts@virginia.edu</a><br>
> <mailto:<a href="mailto:michael.shirts@virginia.edu">michael.shirts@virginia.edu</a>>"<br>
> <<a href="mailto:michael.shirts@virginia.edu">michael.shirts@virginia.edu</a><br>
> <mailto:<a href="mailto:michael.shirts@virginia.edu">michael.shirts@virginia.edu</a>>><br>
> Subject: Re: [gmx-developers] dhdl expanded ensemble<br>
> Message-ID: <<a href="mailto:55E0093D.2000804@kth.se">55E0093D.2000804@kth.se</a> <mailto:<a href="mailto:55E0093D.2000804@kth.se">55E0093D.2000804@kth.se</a>>><br>
> Content-Type: text/plain; charset=windows-1252; format=flowed<br>
><br>
> No. To be more precise dhdl is only (fully) calculated at each step<br>
> where free energies are calculated, i.e. every nstdhdl steps.<br>
> To find where the final values are stored, it's often easiest to<br>
> look in<br>
> mdebin.c, in this case at line 1244.<br>
><br>
> Cheers,<br>
><br>
> Berk<br>
><br>
> On 2015-08-28 03:52, Shirts, Michael R. (mrs5pt) wrote:<br>
> > Dhdl is automatically calculated at every step if free energies are<br>
> > calculated. Look in sum_dhdl -- difference components are stored in<br>
> > enerd->term.<br>
> ><br>
> > Unless it's a new development you would rather keep private for<br>
> now, you<br>
> > should consider posting the proposed enhancement on redmine.<br>
> You would<br>
> > likely get some tips about how to do it in a way that could be<br>
> more easily<br>
> > included in later gromcs versions.<br>
> ><br>
> > Best,<br>
> > ~~~~~~~~~~~~<br>
> > Michael Shirts<br>
> > Associate Professor<br>
> > Department of Chemical Engineering<br>
> > University of Virginia<br>
> > <a href="mailto:michael.shirts@virginia.edu">michael.shirts@virginia.edu</a> <mailto:<a href="mailto:michael.shirts@virginia.edu">michael.shirts@virginia.edu</a>><br>
> > <a href="tel:%28434%29%20243-1821" value="+14342431821">(434) 243-1821</a> <tel:%28434%29%20243-1821><br>
> ><br>
> ><br>
> > From: <Mirabzadeh>, "Christopher (<a href="mailto:mira2978@vandals.uidaho.edu">mira2978@vandals.uidaho.edu</a><br>
> <mailto:<a href="mailto:mira2978@vandals.uidaho.edu">mira2978@vandals.uidaho.edu</a>>)"<br>
> > <<a href="mailto:mira2978@vandals.uidaho.edu">mira2978@vandals.uidaho.edu</a> <mailto:<a href="mailto:mira2978@vandals.uidaho.edu">mira2978@vandals.uidaho.edu</a>>><br>
> > Reply-To: "<a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a><br>
> <mailto:<a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a>>" <<a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a><br>
> <mailto:<a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a>>><br>
> > Date: Thursday, August 27, 2015 at 12:20 PM<br>
> > To: "<a href="mailto:gromacs.org_gmx-developers@maillist.sys.kth.se">gromacs.org_gmx-developers@maillist.sys.kth.se</a><br>
> <mailto:<a href="mailto:gromacs.org_gmx-developers@maillist.sys.kth.se">gromacs.org_gmx-developers@maillist.sys.kth.se</a>>"<br>
> > <<a href="mailto:gromacs.org_gmx-developers@maillist.sys.kth.se">gromacs.org_gmx-developers@maillist.sys.kth.se</a><br>
> <mailto:<a href="mailto:gromacs.org_gmx-developers@maillist.sys.kth.se">gromacs.org_gmx-developers@maillist.sys.kth.se</a>>><br>
> > Subject: [gmx-developers] dhdl expanded ensemble<br>
> ><br>
> ><br>
> ><br>
> > Hello,<br>
> ><br>
> > What I'm trying to do;<br>
> ><br>
> > I'm attempting to add functionality to expanded ensemble.<br>
> ><br>
> ><br>
> > What I've done so far;<br>
> ><br>
> > I've added functionality to accept my mdp options and found<br>
> pre-written<br>
> > functions to take advantage of.<br>
> ><br>
> > Where I'm stuck;<br>
> ><br>
> > I need the derivative of the Hamiltonian with respect to lambda<br>
> at every<br>
> > md step. I'm having a hard time narrowing down this variable. I<br>
> know it's<br>
> > calculated and I see in mdebin.c there is a line that says "/*<br>
> store_dh is<br>
> > dE */". Is the derivative "store_dhdl[]=enerd->term[F_DVDL]"?<br>
> > Or, is this already being called somewhere in expanded.c that<br>
> I can take<br>
> > advantage of, maybe dfhist?<br>
> ><br>
> > Is the dhdl automatically calculated? Where is it stored? If<br>
> dhdl isn?t<br>
> > being calculated automatically, is there an mdp option or mdrun<br>
> flag that<br>
> > I need?<br>
> ><br>
> > I appreciate any advice that can be offered.<br>
> ><br>
> ><br>
> > -ChrisM<br>
> ><br>
> > Mirabzadeh, Christopher<br>
> > Graduate Research Assistant/Physics Instructor<br>
> > Department of Physics<br>
> > University of Idaho<br>
> > Moscow, Id<br>
> > <a href="tel:%28509%29339-5647" value="+15093395647">(509)339-5647</a> <tel:%28509%29339-5647><br>
> ><br>
> ><br>
> ><br>
> ><br>
> ><br>
><br>
><br>
><br>
> ------------------------------<br>
><br>
> Message: 4<br>
> Date: Fri, 28 Aug 2015 09:20:44 +0200<br>
> From: Berk Hess <<a href="mailto:hess@kth.se">hess@kth.se</a> <mailto:<a href="mailto:hess@kth.se">hess@kth.se</a>>><br>
> To: <a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a> <mailto:<a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a>><br>
> Subject: Re: [gmx-developers] Increase the scope of dd domains<br>
> Message-ID: <<a href="mailto:55E00BCC.4040506@kth.se">55E00BCC.4040506@kth.se</a> <mailto:<a href="mailto:55E00BCC.4040506@kth.se">55E00BCC.4040506@kth.se</a>>><br>
> Content-Type: text/plain; charset="windows-1252"; Format="flowed"<br>
><br>
> Hi,<br>
><br>
> Gromacs uses a neutral-territory eighth-shell domain decomposition<br>
> method. So you can get all pairs by only looking at home-atoms for the<br>
> i-atoms. You code should work though for 1D decomposition, is that<br>
> the case?<br>
><br>
> To get this to work with 2D or 3D decomposition, you need to replace<br>
> ga2la_get_home by ga2la_get and then only consider i-j pairs where the<br>
> cell values are in the cell pair list given by dd->comm->zones. cell_i<br>
> should be < zones->nizone and zones->izone[cell_i].j0 <= cell_j <<br>
> zones->izone[cell_j].j1 When the DD cells get smaller than the cutoff,<br>
> you need to use cell % zones->n.<br>
><br>
> Note that since the ga2la_get calls are expensive, such an approach is<br>
> only efficient when you have only few atoms / atom pairs.<br>
> For improving performance, it can help to first lookup locala and cell<br>
> for all atoms and store them and then do the pair double loop after<br>
> that. And instead of using sqrt, check dr2 < r_N*r_N.<br>
><br>
> Cheers,<br>
><br>
> Berk<br>
><br>
> On 2015-08-28 06:35, Xingcheng Lin wrote:<br>
> > Hi,<br>
> ><br>
> > I am trying to encode a "on the fly" calculation for the number of<br>
> > atom pairs within some distance (for example here, 6 angstroms).<br>
> ><br>
> > The problem happens when doing parallel domain decomposition.<br>
> > Specifically, when two particles reside in different domains,<br>
> gromacs<br>
> > is not able to recognize this pair. I am trying to use<br>
> ga2la_get_home<br>
> > and ga2la_get for calculation, here is the code:<br>
> ><br>
> > // NP is number of tested pairs recorded in an array;<br>
> > // If atom ai is one of the home atoms in a node, we start<br>
> testing if<br>
> > aj is available by the same node;<br>
> > // rlist = 1.0nm, Coulombtype = Cut-off, cutoff-scheme = Verlet,<br>
> > ns_type = grid, pbc = xyz;<br>
> ><br>
> > int Npairs = 0;<br>
> > for (i=0; i<NP; ++i)<br>
> > {<br>
> > int ai = datai[i] ;<br>
> > int localai;<br>
> > // Examine if ai it is within the home atoms index;<br>
> > if (ga2la_get_home(cr->dd->ga2la, ai, &localai))<br>
> > {<br>
> > aj = dataj[i] ;<br>
> > // Examine if aj is available by local node;;<br>
> > if (ga2la_get(cr->dd->ga2la, aj, &localaj, &localcell))<br>
> > {<br>
> > FILE *fp;<br>
> > fp = fopen("pairs.dat","a");<br>
> ><br>
> > fprintf(fp, "%d\t%d\n", ai, aj);<br>
> > fclose(fp);<br>
> ><br>
> > r_N = 0.6 ;<br>
> > pbc_dx(&pbc, x[localai], x[localaj], dx) ;<br>
> > dr2 = iprod( dx, dx ) ;<br>
> > dr = sqrt( dr2 ) ;<br>
> > if (dr < r_N)<br>
> > {<br>
> > Npairs += 1;<br>
> > }<br>
> > }<br>
> > }<br>
> > }<br>
> ><br>
> > The results show some atom pairs, while atoms less than 6 angstroms<br>
> > apart, are missing here. I increase rlist, but it doesn't help. Is<br>
> > there any way to increase the scope of atoms available in each<br>
> domain<br>
> > so that the missing atoms can be detected?<br>
> ><br>
> > Or are there any mistakes out of my notice in this code?<br>
> ><br>
> > Thank you,<br>
> > Xingcheng<br>
> ><br>
> ><br>
> ><br>
> ><br>
><br>
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