
<html><head><meta http-equiv="content-type" content="text/html; charset=ISO-8859-1"><style>body { line-height: 1.5; }blockquote { margin-top: 0px; margin-bottom: 0px; margin-left: 0.5em; }div.foxdiv20151027155809350957 { }body { font-family: 'Segoe UI'; color: rgb(0, 0, 0); line-height: 1.5; }</style></head><body>

    

  

<div><span></span>Dear Matic,&nbsp;</div><div><br></div><div>Thanks for your patient explanation!</div><div>There are only two very small negative values in the final coordinates. My crystal is a kind of amino acid. &nbsp;In one unit cell, there are two molecules.&nbsp;<span style="line-height: 1.5;">In my input file, there is no negative values in atomic coordinates, but the boundary still can&nbsp;</span><span style="background-color: window; line-height: 1.5;">apparently</span><span style="line-height: 1.5;">&nbsp;break the chemical bonds.</span></div>

<div><br></div><div>Input:</div><div><span style="font-family: &quot;" segoe="" ui'";="" font-size:="" 16px;="" color:="" rgb(0,="" 0,="" 0);="" background-color:="" rgba(0,="" font-weight:="" normal;="" font-style:="" normal;text-decoration:="" none;'="">&amp;CONTROL<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;title&nbsp;=&nbsp;'2015971-Asparticacid'<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;calculation&nbsp;=&nbsp;'vc-relax'<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;restart_mode&nbsp;=&nbsp;'from_scratch'<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;outdir&nbsp;=&nbsp;'/home/yinli/aspartic_acid/vc-relax/test1'&nbsp;,<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;wfcdir&nbsp;=&nbsp;'/home/yinli/aspartic_acid/vc-relax/test1'&nbsp;,<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;pseudo_dir&nbsp;=&nbsp;'/home/yinli/espresso-5.1.1/pseudo/'&nbsp;,<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;prefix&nbsp;=&nbsp;'2015971-Asparticacid'<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;etot_conv_thr&nbsp;=&nbsp;5.0d-7&nbsp;,<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;forc_conv_thr&nbsp;=&nbsp;5.0d-4&nbsp;,<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;nstep&nbsp;=&nbsp;1500<br>&nbsp;/<br>&nbsp;&amp;SYSTEM<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;ibrav&nbsp;=&nbsp;-12<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;celldm(1)&nbsp;=&nbsp;&nbsp;&nbsp;9.663114537963445<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;celldm(2)&nbsp;=&nbsp;&nbsp;&nbsp;1.350523125061113,&nbsp;celldm(3)&nbsp;=&nbsp;&nbsp;&nbsp;1.484795150092891<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;celldm(5)&nbsp;=&nbsp;&nbsp;-0.185014881113262<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;nat&nbsp;=&nbsp;32<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;ntyp&nbsp;=&nbsp;4<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;ecutwfc&nbsp;=&nbsp;60<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;ecutrho&nbsp;=&nbsp;600<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;occupations&nbsp;=&nbsp;'fixed'<br>&nbsp;/<br>&nbsp;&amp;ELECTRONS<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;electron_maxstep&nbsp;=&nbsp;200<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;conv_thr&nbsp;=&nbsp;1.0D-10<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;diago_thr_init&nbsp;=&nbsp;1e-4<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;startingpot&nbsp;=&nbsp;'atomic'<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;startingwfc&nbsp;=&nbsp;'atomic'<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;mixing_mode&nbsp;=&nbsp;'plain'<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;mixing_beta&nbsp;=&nbsp;0.5<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;mixing_ndim&nbsp;=&nbsp;8<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;diagonalization&nbsp;=&nbsp;'david'<br>&nbsp;/<br>&amp;IONS<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;ion_dynamics&nbsp;=&nbsp;'bfgs'<br>&nbsp;/<br>&amp;CELL<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;cell_dynamics&nbsp;=&nbsp;'bfgs'<br>&nbsp;/<br>ATOMIC_SPECIES<br>&nbsp;&nbsp;&nbsp;&nbsp;H&nbsp;&nbsp;&nbsp;&nbsp;1.00794&nbsp;&nbsp;H.blyp-van_ak.UPF&nbsp;<br>&nbsp;&nbsp;&nbsp;&nbsp;C&nbsp;&nbsp;&nbsp;12.01070&nbsp;&nbsp;C.blyp-van_ak.UPF&nbsp;<br>&nbsp;&nbsp;&nbsp;&nbsp;N&nbsp;&nbsp;&nbsp;14.00670&nbsp;&nbsp;N.blyp-van_ak.UPF&nbsp;<br>&nbsp;&nbsp;&nbsp;&nbsp;O&nbsp;&nbsp;&nbsp;15.99940&nbsp;&nbsp;O.blyp-van_ak.UPF&nbsp;<br><br>ATOMIC_POSITIONS&nbsp;crystal<br>&nbsp;N&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.858300000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.978000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.316200000000000<br>&nbsp;H&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.029000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.914000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.388000000000000<br>&nbsp;H&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.810000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.100000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.389000000000000<br>&nbsp;H&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.900000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.022000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.188000000000000<br>&nbsp;C&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.634800000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.836000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.295200000000000<br>&nbsp;C&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.560500000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.796000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.478600000000000<br>&nbsp;C&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.715600000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.644000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.219800000000000<br>&nbsp;C&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.793000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.659000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.037800000000000<br>&nbsp;O&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.749700000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.784000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.609500000000000<br>&nbsp;O&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.318400000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.771000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.481700000000000<br>&nbsp;O&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.002000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.593000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.008500000000000<br>&nbsp;O&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.612500000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.744000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.916100000000000<br>&nbsp;H&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.468000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.898000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.207000000000000<br>&nbsp;H&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.881000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.578000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.313000000000000<br>&nbsp;H&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.541000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.556000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.207000000000000<br>&nbsp;H&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.679000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.750000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.797000000000000<br>&nbsp;N&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.141700000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.478000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.683800000000000<br>&nbsp;H&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.971000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.414000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.612000000000000<br>&nbsp;H&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.190000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.600000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.611000000000000<br>&nbsp;H&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.100000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.522000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.812000000000000<br>&nbsp;C&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.365200000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.336000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.704800000000000<br>&nbsp;C&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.439500000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.296000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.521400000000000<br>&nbsp;C&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.284400000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.144000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.780200000000000<br>&nbsp;C&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.207000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.159000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.962200000000000<br>&nbsp;O&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.250300000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.284000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.390500000000000<br>&nbsp;O&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.681600000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.271000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.518300000000000<br>&nbsp;O&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.998000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.093000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.991500000000000<br>&nbsp;O&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.387500000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.244000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.083900000000000<br>&nbsp;H&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.532000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.398000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.793000000000000<br>&nbsp;H&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.119000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.078000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.687000000000000<br>&nbsp;H&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.459000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.056000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.793000000000000<br>&nbsp;H&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.321000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.250000000000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0.203000000000000<br><br>K_POINTS&nbsp;automatic<br>3&nbsp;&nbsp;2&nbsp;&nbsp;2&nbsp;&nbsp;&nbsp;0&nbsp;0&nbsp;0<br><br></span></div><div><br></div><hr style="width: 210px; height: 1px;" color="#b5c4df" size="1" align="left">

<div><span><div style="margin: 10px; font-family: verdana; font-size: 15px;"><span style="color: rgb(0, 0, 0); background-color: rgba(0, 0, 0, 0);">Dr.&nbsp;Yin&nbsp;Li&nbsp;<br>Department&nbsp;of&nbsp;Biophysics,Medical&nbsp;School,&nbsp;University&nbsp;of&nbsp;Pecs,<br>No.12&nbsp;Szigeti&nbsp;Street,&nbsp;Pecs,&nbsp;H-7624,&nbsp;HUNGARY<br>Phone:&nbsp;+36-72-535271/36271</span></div></span></div>

<blockquote style="margin-top: 0px; margin-bottom: 0px; margin-left: 0.5em;"><div>&nbsp;</div><div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm"><div style="PADDING-RIGHT: 8px; PADDING-LEFT: 8px; FONT-SIZE: 12px;FONT-FAMILY:tahoma;COLOR:#000000; BACKGROUND: #efefef; PADDING-BOTTOM: 8px; PADDING-TOP: 8px"><div><b>From:</b>&nbsp;<a href="mailto:matic.poberznik@gmail.com">Matic Poberznik</a></div><div><b>Date:</b>&nbsp;2015-10-27&nbsp;16:51</div><div><b>To:</b>&nbsp;<a href="mailto:xcrysden@democritos.it">XCrySDen mailing list</a></div><div><b>Subject:</b>&nbsp;Re: [xcrysden] How to display a whole molecule in unit cell with good connection?</div></div></div><div><div class="FoxDiv20151027155809350957">

  

    

  

  

    <span style="line-height: 1.5; background-color: window;"><br>

      &gt;&gt;Actually, I don't want to modify the relative distance

      between atoms and boundaries. I think journals &gt;&gt;would not

      accept this.</span><br>

    <br>

    I think that modifying the relative distance, as far as the figure

    is concerned, should not be a problem. The only limitation I see is

    that all atoms defined in the ATOMIC_POSITIONS card should be

    translated by the same vector; due to periodicity both structures

    are equal, what will change is the way the program reads the

    structure. Without seeing the actual output I am assuming that your

    optimized coordinates contain atoms with negative values in

    coordinates, for example let's say the initial positions were 0.0,

    0.0, 0.0, but after optimization they changed to -0.1,-0.1,-0.1, so

    assuming a cubic structure of length "1" the program draws the

    optimized coordinates at 0.9, 0.9, 0.9 (equivalent position in the

    crystal cell), the result being the molecule "breaks" in the unit

    cell. By shifiting all positions (to positive values) by a specific

    vector this problem should disappear and as stated both structures

    are equivalent, so this representation should be acceptable. <br>

    <br>

    Both the xsf and pwscf formats are supported by openbabel, so

    converting it to other formats shouldn't be a problem, though I have

    no experience regarding the dynamic matrix, so&nbsp; I really have no

    idea if information will be lost or not.<br>

    <br>

    Best regards,<br>

    <br>

    Matic<br>

    <br>

    <div class="moz-cite-prefix">On 10/27/2015 01:47 PM,

      <a class="moz-txt-link-abbreviated" href="mailto:liyincumt@gmail.com">liyincumt@gmail.com</a> wrote:<br>

    </div>

    <blockquote cite="mid:2015102714473692451475@gmail.com" type="cite" style="margin-top: 0px; margin-bottom: 0px; margin-left: 0.5em;">

      

      

      <div><span></span>Dear Matic,</div>

      <div><br>

      </div>

      <div><span style="line-height: 1.5; background-color: window;">Thank

          you very much for your help!</span></div>

      <div><span style="line-height: 1.5; background-color: window;">Actually,

          I don't want to modify the relative distance between atoms and

          boundaries. I think journals would not accept this.&nbsp;</span><span style="background-color: window; line-height: 1.5;">I was

          thinking on whether Molden could display it properly as the

          dynamic matrix file can be read by Molden as well. I tried

          many options in molden but it still can't work. So far I just

          found material studio (Display style: Default) can display it

          properly.&nbsp;</span></div>

      <div><span style="background-color: window; line-height: 1.5;">I

          wonder whether I can convert quantum espresso files including

          dynamic matrix file and pwo into cif or any other format which

          could be read by material studio. Even it can be converted, I

          am still worried about the loss of the information of the

          forces on atoms.</span></div>

      <div><span style="background-color: window; line-height: 1.5;"><br>

        </span></div>

      <div><span style="background-color: window; line-height: 1.5;">Best

          Regards,</span></div>

      <div><span style="background-color: window; line-height: 1.5;">Yin</span></div>

      <div><br>

      </div>

      <hr style="width: 210px; height: 1px;" align="left" size="1" color="#b5c4df">

      <div><span>

          <div style="margin: 10px; font-family: verdana; font-size:

            15px;"><span style="color: rgb(0, 0, 0); background-color:

              rgba(0, 0, 0, 0);">Dr.&nbsp;Yin&nbsp;Li&nbsp;<br>

Department&nbsp;of&nbsp;Biophysics,Medical&nbsp;School,&nbsp;University&nbsp;of&nbsp;Pecs,<br>

              No.12&nbsp;Szigeti&nbsp;Street,&nbsp;Pecs,&nbsp;H-7624,&nbsp;HUNGARY<br>

              Phone:&nbsp;+36-72-535271/36271</span></div>

        </span></div>

      <blockquote style="margin-top: 0px; margin-bottom: 0px; margin-left: 0.5em;">

        <div>&nbsp;</div>

        <div style="border:none;border-top:solid #B5C4DF

          1.0pt;padding:3.0pt 0cm 0cm 0cm">

          <div style="PADDING-RIGHT: 8px; PADDING-LEFT: 8px; FONT-SIZE:

            12px;FONT-FAMILY:tahoma;COLOR:#000000; BACKGROUND: #efefef;

            PADDING-BOTTOM: 8px; PADDING-TOP: 8px">

            <div><b>From:</b>&nbsp;<a moz-do-not-send="true" href="mailto:matic.poberznik@gmail.com">Matic Poberznik</a></div>

            <div><b>Date:</b>&nbsp;2015-10-27&nbsp;14:27</div>

            <div><b>To:</b>&nbsp;<a moz-do-not-send="true" href="mailto:xcrysden@democritos.it">XCrySDen mailing

                list</a></div>

            <div><b>Subject:</b>&nbsp;Re: [xcrysden] How to display a whole

              molecule in unit cell with good connection?</div>

          </div>

        </div>

        <div>

          <div class="FoxDiv20151027143411640253"> Modifying this in the

            pwscf output file is impossible, so I suggest you convert

            the output file to xsf format using the pwo2xsf.sh tool. It

            can be found in the Quantum Espresso installation directory

            in my case it is in <br>

            <br>

            /esspreso-5.1.1/PW/tools/pwo2xsf.sh<br>

            <br>

            To write the optimized coordinates to the xsf file the

            syntax would be :<br>

            <br>

            bash pwo2xsf.sh -oc name_of_pwout.out &gt; name_of_xsf.xsf <br>

            <br>

            Once you have the xsf file I suggest you shift the

            coordinates of the atoms so that the molecule is in the

            center of the cell; If the molecule atoms are , for

            instance, at 0.0, 0.0, 0.0 you should shift them so that the

            coordinates correspond to 1/2a+1/2b+1/2c where a,b,c are

            vectors of the unit cell. You should shift all atomic

            positions accordingly and the result will hopefully be

            better. <br>

            <br>

            Best regards,<br>

            <br>

            Matic<br>

            <br>

            <div class="moz-cite-prefix">On 10/27/2015 11:25 AM, <a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:liyincumt@gmail.com">liyincumt@gmail.com</a>

              wrote:<br>

            </div>

            <blockquote cite="mid:2015102712253113411864@gmail.com" type="cite" style="margin-top: 0px; margin-bottom: 0px; margin-left: 0.5em;">

              <div><span></span>Dear&nbsp;<span style="line-height: 1.5;

                  background-color: window;">Matic,</span></div>

              <div><span style="line-height: 1.5; background-color:

                  window;"><br>

                </span></div>

              <div><span style="line-height: 1.5; background-color:

                  window;">Thanks for your kind help!&nbsp;</span></div>

              <div><span style="line-height: 1.5; background-color:

                  window;">After setting the number of units drawn, some

                  molecules inside the supercell are displayed

                  correctly. But there are too many molecules inside the

                  supercell. The figure would be hardly accepted by

                  journal.</span></div>

              <div><span style="line-height: 1.5; background-color:

                  window;">Is it possible to just display the molecules

                  correctly in one unit cell? I have tried buttons of

                  the display which are located in the bottom center of

                  the screen, none of them can work properly.&nbsp;</span></div>

              <div><br>

              </div>

              <div><span style="line-height: 1.5; background-color:

                  window;">Best Regards,</span></div>

              <div>Yin</div>

              <hr style="width: 210px; height: 1px;" align="left" size="1" color="#b5c4df">

              <div><span>

                  <div style="margin: 10px; font-family: verdana;

                    font-size: 15px;"><span style="color: rgb(0, 0, 0);

                      background-color: rgba(0, 0, 0, 0);">Dr.&nbsp;Yin&nbsp;Li&nbsp;<br>

Department&nbsp;of&nbsp;Biophysics,Medical&nbsp;School,&nbsp;University&nbsp;of&nbsp;Pecs,<br>

                      No.12&nbsp;Szigeti&nbsp;Street,&nbsp;Pecs,&nbsp;H-7624,&nbsp;HUNGARY<br>

                      Phone:&nbsp;+36-72-535271/36271</span></div>

                </span></div>

              <blockquote style="margin-top: 0px; margin-bottom: 0px; margin-left: 0.5em;">

                <div>&nbsp;</div>

                <div style="border:none;border-top:solid #B5C4DF

                  1.0pt;padding:3.0pt 0cm 0cm 0cm">

                  <div style="PADDING-RIGHT: 8px; PADDING-LEFT: 8px;

                    FONT-SIZE: 12px;FONT-FAMILY:tahoma;COLOR:#000000;

                    BACKGROUND: #efefef; PADDING-BOTTOM: 8px;

                    PADDING-TOP: 8px">

                    <div><b>From:</b>&nbsp;<a moz-do-not-send="true" href="mailto:matic.poberznik@gmail.com">Matic

                        Poberznik</a></div>

                    <div><b>Date:</b>&nbsp;2015-10-27&nbsp;12:14</div>

                    <div><b>To:</b>&nbsp;<a moz-do-not-send="true" href="mailto:xcrysden@democritos.it">XCrySDen

                        mailing list</a></div>

                    <div><b>Subject:</b>&nbsp;Re: [xcrysden] How to display a

                      whole molecule in unit cell with good connection?</div>

                  </div>

                </div>

                <div>

                  <div class="FoxDiv20151027121916502830"> Dear Yin,<br>

                    <br>

                    If I understood your problem correctly, I think the

                    best solution is to open the Modify menu and choose

                    the Atomic Radius (Shift+R) option. Once there you

                    can modify the Covalent Radius and Connectivity

                    Factor for each atom type to suit your needs. <br>

                    <br>

                    In order to load your custom parameters when

                    xcrysden starts you should add a line in

                    $HOME/.xcrysden/custom-definitions file, an example:<br>

                    <br>

                    #<br>

                    # this line changes the default atomic radius for

                    aluminum to 1.6<br>

                    #<br>

                    <br>

                    set atmRad(13) 1.6<br>

                    <br>

                    The custom definitions file is described on this

                    link: <a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://www.xcrysden.org/doc/custom.html">http://www.xcrysden.org/doc/custom.html</a><br>

                    <br>

                    If the problem stems from the periodic boundary

                    conditions then first try the different display

                    modes of unit cells, i. e. click the button for the

                    display of the translational asymmetric unit (bottom

                    center of the screen).&nbsp; Then try Modify =&gt; Number

                    of units drawn (Shift+N), if the covalent radius is

                    correct at least some molecules should be displayed

                    correctly. If that is not enough let me know, there

                    is one more workaround but it is a bit more

                    complicated.<br>

                    <br>

                    Best regards,<br>

                    <br>

                    Matic<br>

                    <br>

                    <br>

                    <br>

                    <div class="moz-cite-prefix">On 10/27/2015 09:19 AM,

                      <a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:liyincumt@gmail.com">liyincumt@gmail.com</a>

                      wrote:<br>

                    </div>

                    <blockquote cite="mid:2015102710192009085257@gmail.com" type="cite" style="margin-top: 0px; margin-bottom: 0px; margin-left: 0.5em;">

                      <div><span style="line-height: 1.5;

                          background-color: window;">Dear Xcrysden

                          developers,</span></div>

                      <div><br>

                      </div>

                      <div>Thanks for sharing this excellent

                        visualization software for free!&nbsp;</div>

                      <div><span style="line-height: 1.5;

                          background-color: window;">I am using xcrysden

                          to visualize the input and output files of

                          quantum espresso. I have a problem with

                          visualization of crystals. Due to the presence

                          of periodic boundary condition, some of atoms

                          which are outside of the boundary look like

                          being non-covalently connected. Is it possible

                          to display a whole molecule with good covalent

                          connections in Xcrysden.</span></div>

                      <div><span style="line-height: 1.5;

                          background-color: window;"><br>

                        </span></div>

                      <div><span style="line-height: 1.5;

                          background-color: window;">Thank you very

                          much!</span></div>

                      <div><span style="line-height: 1.5;

                          background-color: window;"><br>

                        </span></div>

                      <div><span style="line-height: 1.5;

                          background-color: window;">Best Regards,</span></div>

                      <div><span style="line-height: 1.5;

                          background-color: window;">Yin</span></div>

                      <div><br>

                      </div>

                      <hr style="width: 210px; height: 1px;" align="left" size="1" color="#b5c4df">

                      <div><span>

                          <div style="margin: 10px; font-family:

                            verdana; font-size: 15px;"><span style="color: rgb(0, 0, 0);

                              background-color: rgba(0, 0, 0, 0);">Dr.&nbsp;Yin&nbsp;Li&nbsp;<br>

Department&nbsp;of&nbsp;Biophysics,Medical&nbsp;School,&nbsp;University&nbsp;of&nbsp;Pecs,<br>

No.12&nbsp;Szigeti&nbsp;Street,&nbsp;Pecs,&nbsp;H-7624,&nbsp;HUNGARY<br>

                              Phone:&nbsp;+36-72-535271/36271</span></div>

                        </span></div>

                      <br>

                      <fieldset class="mimeAttachmentHeader"></fieldset>

                      <br>

                      <pre wrap="">_______________________________________________

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<a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:XCrySDen@democritos.it">XCrySDen@democritos.it</a>

<a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://www.democritos.it/mailman/listinfo/xcrysden">http://www.democritos.it/mailman/listinfo/xcrysden</a>

</pre>

                    </blockquote>

                    <br>

                  </div>

                </div>

              </blockquote>

              <br>

              <fieldset class="mimeAttachmentHeader"></fieldset>

              <br>

              <pre wrap="">_______________________________________________

XCrySDen mailing list

<a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:XCrySDen@democritos.it">XCrySDen@democritos.it</a>

<a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://www.democritos.it/mailman/listinfo/xcrysden">http://www.democritos.it/mailman/listinfo/xcrysden</a>

</pre>

            </blockquote>

            <br>

            <pre class="moz-signature" cols="72">-- 

Matic Poberznik

J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia </pre>

          </div>

        </div>

      </blockquote>

      <br>

      <fieldset class="mimeAttachmentHeader"></fieldset>

      <br>

      <pre wrap="">_______________________________________________

XCrySDen mailing list

<a class="moz-txt-link-abbreviated" href="mailto:XCrySDen@democritos.it">XCrySDen@democritos.it</a>

<a class="moz-txt-link-freetext" href="http://www.democritos.it/mailman/listinfo/xcrysden">http://www.democritos.it/mailman/listinfo/xcrysden</a>

</pre>

    </blockquote>

    <br>

    <pre class="moz-signature" cols="72">-- 

Matic Poberznik

J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia </pre>

  

</div></div></blockquote>

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