<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<meta name="Generator" content="Microsoft Word 15 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Consolas;
panose-1:2 11 6 9 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman",serif;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
p
{mso-style-priority:99;
mso-margin-top-alt:auto;
margin-right:0cm;
mso-margin-bottom-alt:auto;
margin-left:0cm;
font-size:12.0pt;
font-family:"Times New Roman",serif;}
p.msonormal0, li.msonormal0, div.msonormal0
{mso-style-name:msonormal;
mso-margin-top-alt:auto;
margin-right:0cm;
mso-margin-bottom-alt:auto;
margin-left:0cm;
font-size:12.0pt;
font-family:"Times New Roman",serif;}
span.gmaildefault
{mso-style-name:gmail_default;}
span.EmailStyle20
{mso-style-type:personal-reply;
font-family:"Calibri",sans-serif;
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:70.85pt 70.85pt 2.0cm 70.85pt;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang="EN-US" link="blue" vlink="purple">
<div class="WordSection1">
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Hi Mostafa<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">You can also try the (stand-alone) program xyz2dcd (<a href="https://github.com/cp2k/cp2k/blob/master/src/motion/xyz2dcd.F">https://github.com/cp2k/cp2k/blob/master/src/motion/xyz2dcd.F</a>)
from the current cp2k trunk which dumps the frames from a CP2K xyz trajectory file in dcd format optionally with wrapped coordinates (flags –pbc and –pbc0) using either fixed cell parameters (flags –abc and –cell) or the actual cell information for each frame
from the corresponding CP2K cell file of the same NpT run, e.g. by running<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas;color:#1F497D">xyz2dcd –pbc –cell_file project-1.cell project-pos-1.xyz >project-pos-1_wrapped.dcd<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">The generated binary file
</span><span style="font-size:10.0pt;font-family:Consolas;color:#1F497D">project-pos-1.dcd</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> in DCD format with wrapped coordinates and the corresponding cell information for
each frame can be loaded into VMD or converted again back to xyz (XMOL) format using</span><span style="font-size:10.0pt;font-family:Consolas;color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas;color:#1F497D">dumpdcd -xyz project-pos-1.xyz –of XMOL –o project-pos-1_wrapped.xyz project-pos-1_wrapped.dcd<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">xyz2dcd and dumpdcd are compiled automatically with the current CP2K trunk version and can be found then in folder cp2k/exe/<arch>/, but they can also be compiled
independently, e.g. using<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas;color:#1F497D">gfortran –ffree-form –o xyz2dcd xyz2dcd.F<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">The flag –h provides further usage info.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">HTH<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Matthias<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> cp...@googlegroups.com <...@googlegroups.com>
<b>On Behalf Of </b>Abedi, Mostafa<br>
<b>Sent:</b> Mittwoch, 22. Juli 2020 17:29<br>
<b>To:</b> cp...@googlegroups.com<br>
<b>Subject:</b> Re: [CP2K:13657] Re: AIMD under PBC<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<p class="MsoNormal"><span style="color:black">Dear Marcella,<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="color:black">Many thanks for your help. Now, I understand it. I've found a way to wrap the coordinate into the box using VMD:
<o:p></o:p></span></p>
</div>
<div>
<div>
<p class="MsoNormal"><span style="color:black">pbc set {xxx xxx xxx} -all <span class="gmaildefault"> # the "xxx" is the length of the box
</span><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="color:black">pbc box<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="color:black">pbc wrap -all <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span class="gmaildefault"><span style="font-family:"Arial",sans-serif;color:black">This works well for the NVE and NVT simulations that the length of the box is fixed, but it is not a case for the NpT simulation box, where the volume changes.
Do you have any idea how that would be for the NpT one? I greatly appreciate your help.
</span></span><span style="color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span class="gmaildefault"><span style="font-family:"Arial",sans-serif;color:black">Thanks,</span></span><span style="color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span class="gmaildefault"><span style="font-family:"Arial",sans-serif;color:black">Mostafa</span></span><span style="color:black"><o:p></o:p></span></p>
</div>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<p class="MsoNormal">On Wed, Jul 22, 2020 at 10:25 AM Marcella Iannuzzi <<a href="mailto:marci...@gmail.com">marci...@gmail.com</a>> wrote:<o:p></o:p></p>
</div>
<blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm">
<p class="MsoNormal">Dear Mostafa<o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">CP2K does not wrap the coordinates into the primary box, but works with the absolute coordinates.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">The PBC are anyway internally applied by calculating energy and forces, hence the interaction field in which your molecules move is correct. <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">To verify the actual situation within the simulation box just apply PBC when using the visualisation tool of your choice.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Regards<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Marcella<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><o:p> </o:p></p>
</div>
<div>
<div>
<p class="MsoNormal">On Wednesday, July 22, 2020 at 3:47:52 PM UTC+2 <a href="mailto:mos...@brown.edu" target="_blank">
mos...@brown.edu</a> wrote:<o:p></o:p></p>
</div>
<blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm">
<div>
<div>
<p class="MsoNormal"><span style="color:black">Hi Everyone,<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="color:black">I am trying to perform AIMD for a periodic system containing 8 CH4 molecules. Everything goes well, but after a few hundred steps, methane molecules start to leave the box. This is really strange behavior because
the simulation is running under PBC and if one molecule leaves the box, one of its images must enter through the opposite face with exactly the same way and direction. But this is not happening in my simulations. So, it seems PBC is not working. I believe
something is wrong in my input file, but I can not figure out what it is. I greatly appreciate it if someone could help me to fix this issue. Many thanks.
<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="color:black">&GLOBAL<br>
PROJECT methane<br>
RUN_TYPE MD <br>
WALLTIME 1000000<br>
PRINT_LEVEL MEDIUM<br>
&END GLOBAL<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="color:black">&FORCE_EVAL<br>
METHOD Quickstep<br>
&DFT<br>
BASIS_SET_FILE_NAME BASIS_MOLOPT<br>
POTENTIAL_FILE_NAME GTH_POTENTIALS <br>
CHARGE 0<br>
MULTIPLICITY 1<br>
&MGRID<br>
CUTOFF [Ry] 400 <br>
&END<br>
&QS<br>
METHOD GPW <br>
EPS_DEFAULT 1.0E-10 <br>
EXTRAPOLATION ASPC <br>
&END<br>
&POISSON<br>
PERIODIC XYZ <br>
POISSON_SOLVER PERIODIC<br>
&END<br>
&SCF<br>
&PRINT<br>
&RESTART OFF<br>
&END<br>
&END <br>
SCF_GUESS ATOMIC <br>
MAX_SCF 30<br>
EPS_SCF 1.0E-6 <br>
&OT<br>
PRECONDITIONER FULL_SINGLE_INVERSE<br>
MINIMIZER CG<br>
&END OT<br>
&OUTER_SCF <br>
MAX_SCF 10<br>
EPS_SCF 1.0E-6 <br>
&END<br>
&END SCF<br>
&XC<br>
&XC_FUNCTIONAL<br>
&PBE<br>
&END<br>
&END XC_FUNCTIONAL<br>
&VDW_POTENTIAL<br>
POTENTIAL_TYPE PAIR_POTENTIAL <br>
&PAIR_POTENTIAL<br>
PARAMETER_FILE_NAME dftd3.dat<br>
TYPE DFTD3<br>
REFERENCE_FUNCTIONAL PBE<br>
R_CUTOFF [angstrom] 16<br>
&END<br>
&END VDW_POTENTIAL<br>
&END XC<br>
&END DFT<br>
&SUBSYS<br>
&CELL <br>
ABC [angstrom] 9.2 9.2 9.2<br>
PERIODIC XYZ<br>
&END CELL<br>
&TOPOLOGY<br>
COORD_FILE_NAME <a href="http://methane.xyz" target="_blank">methane.xyz</a><br>
COORD_FILE_FORMAT XYZ<br>
&END<br>
&KIND H<br>
ELEMENT H<br>
BASIS_SET SZV-MOLOPT-GTH<br>
POTENTIAL GTH-PBE-q1<br>
&END KIND<br>
&KIND C<br>
ELEMENT C<br>
BASIS_SET SZV-MOLOPT-GTH<br>
POTENTIAL GTH-PBE-q4<br>
&END KIND<br>
&END SUBSYS<br>
&PRINT<br>
&FORCES ON<br>
FILENAME forces <br>
&END<br>
&END<br>
&END FORCE_EVAL<br>
<br>
&MOTION<br>
&GEO_OPT<br>
OPTIMIZER BFGS <br>
MAX_ITER 1000<br>
MAX_DR [bohr] 0.003 <br>
&BFGS<br>
&END<br>
&END<br>
&MD<br>
ENSEMBLE NVE<br>
STEPS 10000<br>
TIMESTEP 0.5<br>
TEMPERATURE 500<br>
&END MD<br>
&PRINT<br>
&CELL<br>
FILENAME cell <br>
&END<br>
&END<br>
&END MOTION<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="color:black">Best,<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="color:black">Mostafa<o:p></o:p></span></p>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="color:black"><o:p> </o:p></span></p>
</div>
</div>
</div>
</div>
</blockquote>
</div>
<p class="MsoNormal">-- <br>
You received this message because you are subscribed to the Google Groups "cp2k" group.<br>
To unsubscribe from this group and stop receiving emails from it, send an email to
<a href="mailto:cp2k+unsu...@googlegroups.com" target="_blank">cp2k+unsu...@googlegroups.com</a>.<br>
To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/717d7834-fa56-4517-933c-7447156d3100n%40googlegroups.com?utm_medium=email&utm_source=footer" target="_blank">
https://groups.google.com/d/msgid/cp2k/717d7834-fa56-4517-933c-7447156d3100n%40googlegroups.com</a>.<o:p></o:p></p>
</blockquote>
</div>
<p class="MsoNormal">-- <br>
You received this message because you are subscribed to the Google Groups "cp2k" group.<br>
To unsubscribe from this group and stop receiving emails from it, send an email to
<a href="mailto:cp2k+unsu...@googlegroups.com">cp2k+unsu...@googlegroups.com</a>.<br>
To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/CAG%3DTvs0s4GARLBc-nf5zAq8xGsvxm3Hac%2B8ZiiGdBjwJKqJfsA%40mail.gmail.com?utm_medium=email&utm_source=footer">
https://groups.google.com/d/msgid/cp2k/CAG%3DTvs0s4GARLBc-nf5zAq8xGsvxm3Hac%2B8ZiiGdBjwJKqJfsA%40mail.gmail.com</a>.<o:p></o:p></p>
</div>
</body>
</html>