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<div class="moz-cite-prefix">Hi,<br>
<br>
No, that code is correct.<br>
<br>
I ran 4.6.7 on a water slab in the middle of a box with vacuum on
top and bottom and I don't observe any issue with OpenMP only
parallelization.<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 06/07/2016 05:03 PM, Sheng Bi wrote:<br>
</div>
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<p class="MsoNormal"><span style="font-size:12.0pt">Hi Berk,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">
Thanks for your response!<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">
However, my question is still there. In fact, I run
simulation in one core (with multi-threadings), so domain
decomposition could not be the reason for this phenomenon.
Meanwhile, we use a quite large box (due to 3DC, Z length
usually need a huge vacuum), so I think the water is within
the box.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">
Actually, I have printed dipcorrA for both gmx331 and gmx467
and find that there is no difference. So it wouldn’t be the
</span><span style="font-size:12.0pt">PBC trouble.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">
I think <b>you are right about ewald_LRcorrection().</b> I
check this function further and think it works fine. <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">
However, I think there is <b>something wrong in
forcerec_set_excl_load() function (in forcerec.c file).</b>
We know in ewald_LRcorrection(), for each thread, we loop
over (i = fr->excl_load[t]; i < fr->excl_load[t+1])
to do dipole correction. The excl_load array is calculated
in forcerec_set_excl_load(), as shown in following:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">/ ******
line 3018 ********* /<o:p></o:p></span></p>
<div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt"> for
(t = 1; t <= fr->nthreads; t++)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt"> {<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">
ntarget = (ntot*t)/fr->nthreads;<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">
<b>while (i < top->excls.nr && n <
ntarget)<o:p></o:p></b></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">
{<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">
for (j = ind[i]; j < ind[i+1]; j++)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">
{<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">
if (a[j] > i)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">
{<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">
n++;<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">
}<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">
}<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">
i++;<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">
}<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">
fr->excl_load[t] = i;<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt"> }<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><span style="font-size:12.0pt">
</span><span style="font-size:12.0pt"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">
Suppose we have a system consisted by <b>2 types of
molecules</b>. The whole system contains 2 <b>atoms</b>,
1 for molecule <b>A(positively charged)</b> and 1 for
molecule <b>B(negatively charged)</b>. We perform
simulation in one core with one thread. So, for code above,
we can deduce parameters like following:<o:p></o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:12.0pt">
</span></b><b><span style="font-size:12.0pt">top->excls.nr
= 2<o:p></o:p></span></b></p>
<p class="MsoNormal"><b><span style="font-size:12.0pt">
fr->nthreads = 1 <o:p></o:p></span></b></p>
<p class="MsoNormal"><b><span style="font-size:12.0pt">
ntarget = ntot =1<o:p></o:p></span></b></p>
<p class="MsoNormal"><span style="font-size:12.0pt">
Since it <b>use while() statement here</b>, we can deduce
that:<o:p></o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:12.0pt">
fr->excl_load[0] =0<o:p></o:p></span></b></p>
<p class="MsoNormal"><b><span style="font-size:12.0pt">
fr->excl_load[1] =1<o:p></o:p></span></b></p>
<p class="MsoNormal"><span style="font-size:12.0pt">
However, <b>fr->excl_load[1] should be 2</b>. </span><span
style="font-size:12.0pt">This wrong value lead to <b>missing
a dipole correction on the 2<sup>th</sup> atom</b> in </span><span
style="font-size:12.0pt">ewald_LRcorrection()</span><span
style="font-size:12.0pt">. Because in </span><span
style="font-size:12.0pt">ewald_LRcorrection()</span><span
style="font-size:12.0pt">, we loop from </span><span
style="font-size:12.0pt">fr->excl_load[0]</span><span
style="font-size:12.0pt">=0 to </span><span
style="font-size:12.0pt">fr->excl_load[1] =1 </span><span
style="font-size:12.0pt">using for statement.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">
I think this is the direct reason for wrong additional force
on water molecule in my system. This error might result big
trouble when someone using umbrella sampling in a system
with </span><span style="font-size:12.0pt">system dipole.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">
</span><span style="font-size:12.0pt">Please correct me if I
am wrong.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">Best
regards!<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">Sheng <o:p></o:p></span></p>
<p class="MsoNormal">--<br>
PhD student<br>
State Key Laboratory of Coal Combustion,<br>
School of Energy and Power Engineering,<br>
Huazhong University of Science and Technology (HUST),<br>
Room 302 Power Building, <br>
1037 Luoyu Road, Wuhan, Hubei 430074 China<br>
Email: <a class="moz-txt-link-abbreviated" href="mailto:chrishengbee@hust.edu.cn">chrishengbee@hust.edu.cn</a><br>
Phone: (86)27-87548122 <br>
<a class="moz-txt-link-freetext" href="http://itp.energy.hust.edu.cn">http://itp.energy.hust.edu.cn</a> </p>
<p class="MsoNormal"><span
style="font-size:12.0pt;font-family:"Times New
Roman",serif"><o:p> </o:p></span></p>
<div
style="mso-element:para-border-div;border:none;border-top:solid
#E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal" style="border:none;padding:0in"><b>From:
</b><a moz-do-not-send="true" href="mailto:hess@kth.se">Berk
Hess</a><br>
<b>Sent: </b>Tuesday, June 7, 2016 5:49 PM<br>
<b>To: </b><a moz-do-not-send="true"
href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a><br>
<b>Subject: </b>Re: [gmx-developers] Question about
ewald_LRcorrection() function</p>
</div>
<p class="MsoNormal"><span
style="font-size:12.0pt;font-family:"Times New
Roman",serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:12.0pt;font-family:"Times New
Roman",serif">Hi,<br>
<br>
I think you misinterpreted the code in ewald_LRcorrection.
It does the same things in 3.3.1 and 4.6.7.<br>
My guess is that the issue you are observing is due to
periodic boundary conditions. With group cut-off scheme
charge groups are whole (not split by PBC), so water
molecules are usually whole. Then the 3DC correction always
works correctly when you have charge groups with zero net
charge. In the Verlet cut-off scheme with domain
decomposition, or with charged charge groups, (partial)
charges moving over PBC change the system dipole. To get
your system to run correctly you need to ensure that no
water molecule moves over the periodic boundary in along the
z-dimension. I think grompp will print a warning for this
issue.<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 2016-06-07 10:12, Sheng Bi wrote:</span><span
style="font-size:12.0pt;font-family:"Times New
Roman",serif"><o:p></o:p></span></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal">Sorry, some type-offs in previous
question.<o:p></o:p></p>
<p class="MsoNormal">In gmx-4.6.7, ewald_LRcorrection()<b>.</b>
We loop over excluded neighbours only in condition <b>calc_excl_corr=1</b>.
But when using Verlet cut-off scheme, <b>calc_excl_corr
will be 0</b>.<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">--<br>
PhD student<br>
State Key Laboratory of Coal Combustion,<br>
School of Energy and Power Engineering,<br>
Huazhong University of Science and Technology (HUST),<br>
Room 302 Power Building, <br>
1037 Luoyu Road, Wuhan, Hubei 430074 China<br>
Email: <a moz-do-not-send="true"
href="mailto:chrishengbee@hust.edu.cn">chrishengbee@hust.edu.cn</a><br>
Phone: (86)27-87548122 <br>
<a moz-do-not-send="true"
href="http://itp.energy.hust.edu.cn">http://itp.energy.hust.edu.cn</a>
<o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size:12.0pt;font-family:"Times New Roman
,serif",serif"> </span></p>
<div style="border:none;border-top:solid #E1E1E1
1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b>From: </b><a moz-do-not-send="true"
href="mailto:chrishengbee@hust.edu.cn">Sheng Bi</a><br>
<b>Sent: </b>Tuesday, June 7, 2016 1:28 AM<br>
<b>To: </b><a moz-do-not-send="true"
href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a><br>
<b>Subject: </b>[gmx-developers] Question about
ewald_LRcorrection() function<o:p></o:p></p>
</div>
<p class="MsoNormal"><span
style="font-size:12.0pt;font-family:"Times New Roman
,serif",serif"> </span></p>
<p class="MsoNormal">Dear GMX developers:</p>
<p class="MsoNormal"> I find a abnormal
phenomenon when using <b>gromacs-4.6.7</b>. I set up a
system containing two walls(consist of freeze atoms), one
wall has positively charges on atoms, another has negatively
charges. I put an water molecule(rigid spc/spce/tip3p
model) between these two walls. <b>Whole system seems like
below</b>:</p>
<p class="MsoNormal">
****************************************</p>
<p class="MsoNormal"> * -
H
+ * </p>
<p class="MsoNormal"> * - \
+
vacuum *</p>
<p class="MsoNormal"> * -
O
+ *</p>
<p class="MsoNormal"> * -
/
+ *</p>
<p class="MsoNormal"> * - H
+ *</p>
<p class="MsoNormal">
****************************************</p>
<p class="MsoNormal"> I use <b>Verlet cut-off
scheme, PME method, and ewald-geometry=3DC</b>.
Temperature of whole system is at <b>0K</b>, controlled by
<b>v-rescale method</b>. I run whole simulation <b>only in
OPENMP parallel</b>.</p>
<p class="MsoNormal"> One can have following
expected behavior of water molecule without MD simulation:
Since it can be seen as an infinite panel capacitor, <b>there
is constant electric field between two walls. So the water
will change it orientation, but won’t change it’s
position(Since 0K)</b>.</p>
<p class="MsoNormal"> This phenomenon can be <b>confirmed
by gromcas-3.3.1</b> (although there is position shift,
but quite small). Also, if one use higher version of
gromacs, such as 4.6.7 or higher <b>with ewald-geometry=3D,
either no problem</b>. However, if one use <b>3DC</b>
(and it should be), you can see <b>an obvious force on
water molecule</b>.</p>
<p class="MsoNormal"> I hacked into source code,
and find this might due to <b>ewald_LRcorrection()</b>
function:</p>
<p class="MsoNormal"> Firstly, in gmx-4.6.7,
ewald_LRcorrection()<b>.</b> We <b>loop over excluded
neighbours only in condition calc_excl_corr=0. But when
using verlet cut-off scheme, calc_excl_corr will be 1</b>.
In gmx-3.3.1, we do loop over excluded neighbours without
additional if() statement.</p>
<p class="MsoNormal"> Secondly, in gmx-4.6.7, ,
ewald_LRcorrection(). When do dipole correction on force, we
loop over <b>excl_load</b> (Exclusion load distribution
over the threads). In fact, most water model will have
nrexel=2. So, as a result, we <b>only do dipole correction
on O atom, but do nothing on H atoms</b> and we will see
an obvious force on the whole water molecule. I think this
is not purpose of 3DC<span style="font-family:DengXian"
lang="ZH-CN">。</span></p>
<p class="MsoNormal"> Best regards<span
style="font-family:DengXian" lang="ZH-CN">！</span></p>
<p class="MsoNormal">Sheng Bi</p>
<p class="MsoNormal"><b> </b></p>
<p class="MsoNormal">---<br>
PhD student<br>
State Key Laboratory of Coal Combustion,<br>
School of Energy and Power Engineering,<br>
Huazhong University of Science and Technology (HUST),<br>
Room 302 Power Building, <br>
1037 Luoyu Road, Wuhan, Hubei 430074 China<br>
Email: <a moz-do-not-send="true"
href="mailto:chrishengbee@hust.edu.cn">chrishengbee@hust.edu.cn</a><br>
Phone: (86)27-87548122 <br>
<a moz-do-not-send="true"
href="http://itp.energy.hust.edu.cn">http://itp.energy.hust.edu.cn</a>
<o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size:12.0pt;font-family:"Times New Roman
,serif",serif"> </span><o:p></o:p></p>
<p class="MsoNormal"> </p>
<p class="MsoNormal"><span style="font-family:"Times New
Roman",serif"><br>
<br>
<o:p></o:p></span></p>
</blockquote>
<p class="MsoNormal"><span style="font-family:"Times New
Roman",serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:black"><o:p> </o:p></span></p>
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