<table cellspacing="0" cellpadding="0" border="0"><tr><td valign="top"><div>I have tried to run pp.x on series and parallel but still getting the same error.</div></td></tr></table> <div id="_origMsg_">
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<span style="font-weight:bold">From:</span>
</b>
Jaret Qi <jaretqi@yahoo.com>; <br>
<b>
<span style="font-weight:bold">To:</span>
</b>
Giuseppe Mattioli <giuseppe.mattioli@ism.cnr.it>; <br>
<b>
<span style="font-weight:bold">Subject:</span>
</b>
Re: Re: Charge accumulation and depletion <br>
<b>
<span style="font-weight:bold">Sent:</span>
</b>
Tue, Dec 15, 2015 3:49:08 PM <br>
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<td valign="top"><div style="color:#000;background-color:#fff;font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:16px;"><div id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_4570" face="times new roman, new york, times, serif" size="2">I just did this;</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_4723" face="times new roman, new york, times, serif" size="2">First run input:</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_5255" face="times new roman, new york, times, serif" size="2">&INPUTPP</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_5249" face="times new roman, new york, times, serif" size="2"> prefix = 'interface' ,</font></div><div
class="" id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_5284" face="times new roman, new york, times, serif" size="2"> outdir = './',</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_5285" face="times new roman, new york, times, serif" size="2"> filplot = 'interface.dat' ,</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_5560" face="times new roman, new york, times, serif" size="2"> plot_num = 0,</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font face="times new roman, new york, times, serif" size="2"><br clear="none" class="" id="yui_3_16_0_1_1450192011307_4406"></font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_5289" face="times new roman, new york,
times, serif" size="2"> /</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_5290" face="times new roman, new york, times, serif" size="2"> EOF</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font face="times new roman, new york, times, serif" size="2">------------------------------------</font></div><div class="" dir="ltr" id="yui_3_16_0_1_1450192011307_4278"><font class="" id="yui_3_16_0_1_1450192011307_5589" face="times new roman, new york, times, serif" size="2">second run input</font></div><div class="" dir="ltr" id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_5589" face="times new roman, new york, times, serif" size="2"> &inputpp </font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_5630" face="times new roman, new york, times, serif" size="2"> prefix = 'A'
,</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_5635" face="times new roman, new york, times, serif" size="2"> outdir = './',</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_5634" face="times new roman, new york, times, serif" size="2"> filplot = 'A.dat' ,</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_5733" face="times new roman, new york, times, serif" size="2"> plot_num = 0,</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font face="times new roman, new york, times, serif" size="2"> /</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_5631" face="times new roman, new york, times, serif" size="2"> EOF</font></div><div
class="" id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_5699" face="times new roman, new york, times, serif" size="2">------------------------------------</font></div><div class="" dir="ltr" id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_5632" face="times new roman, new york, times, serif" size="2">third run input</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_5633" face="times new roman, new york, times, serif" size="2"> &INPUTPP</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_5697" face="times new roman, new york, times, serif" size="2"> prefix = 'B' ,</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_5350" face="times new roman, new york, times, serif" size="2"> outdir
= './',</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_5349" face="times new roman, new york, times, serif" size="2"> filplot = 'B.dat' ,</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font face="times new roman, new york, times, serif" size="2"> plot_num = 0,</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font face="times new roman, new york, times, serif" size="2"> /</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_5662" face="times new roman, new york, times, serif" size="2"> EOF</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_5352" face="times new roman, new york, times, serif" size="2"> ----------------------------- </font></div><div class=""
id="yui_3_16_0_1_1450192011307_4278"><font class="" id="yui_3_16_0_1_1450192011307_5382" face="times new roman, new york, times, serif" size="2">I run all of the above inputs using pp.x < input.in | tee input.out</font></div><div class="" dir="ltr" id="yui_3_16_0_1_1450192011307_4278"><b id="yui_3_16_0_1_1450192011307_5668"><font class="" id="yui_3_16_0_1_1450192011307_5384" face="times new roman, new york, times, serif" size="2">All finished but after each input run I got this: </font><span class="" id="yui_3_16_0_1_1450192011307_5369" style="font-family:'times new roman', 'new york', times, serif;font-size:small;">>>> namelist plot not found or invalid, exiting!!</span></b></div><div class="" dir="ltr" id="yui_3_16_0_1_1450192011307_4278"><b><span class="" style="font-family:'times new roman', 'new york', times, serif;font-size:small;"><br clear="none"></span></b></div><div class="" dir="ltr"
id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_5351" face="times new roman, new york, times, serif" size="2">then, I did the fourth pp.x run: </font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_5471" face="times new roman, new york, times, serif" size="2">&inputpp</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font face="times new roman, new york, times, serif" size="2">/</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_5485" face="times new roman, new york, times, serif" size="2">&plot</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_5486" face="times new roman, new york, times, serif" size="2"> nfile = 3</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_5487" face="times new roman, new york,
times, serif" size="2"> filepp(1) = 'interface.dat'</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_5488" face="times new roman, new york, times, serif" size="2"> weight(1) = 1.0</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_5489" face="times new roman, new york, times, serif" size="2"> filepp(2) = 'B.dat'</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_5490" face="times new roman, new york, times, serif" size="2"> weight(2) = -1.0</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_5491" face="times new roman, new york, times, serif" size="2"> filepp(3) = 'A.dat'</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_5492" face="times new roman, new york,
times, serif" size="2"> weight(3) = -1.0</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_5493" face="times new roman, new york, times, serif" size="2"> iflag = 3</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_4708" face="times new roman, new york, times, serif" size="2"> output_format = 5</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font face="times new roman, new york, times, serif" size="2"> fileout = ‘ALL.plot'</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_4707" face="times new roman, new york, times, serif" size="2"> e1(1) =1.0, e1(2)=1.0, e1(3) = 0.0,</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font face="times new roman, new york, times, serif" size="2"> e2(1) =0.0, e2(2)=0.0, e2(3) = 1.0,</font></div><div class=""
id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_4706" face="times new roman, new york, times, serif" size="2"> nx=56, ny=40</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font face="times new roman, new york, times, serif" size="2">/</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font face="times new roman, new york, times, serif" size="2">EOF</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_4705" face="times new roman, new york, times, serif" size="2">but I got this error:</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_5526" face="times new roman, new york, times, serif" size="2">forty: severe (174): SIGSEGV, segmentation fault occurred</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_4704" face="times new roman, new york, times, serif"
size="2">Image PC Routine Line Source </font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_4703" face="times new roman, new york, times, serif" size="2">pp.x 00000000008DA9A9 Unknown Unknown Unknown</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_5494" face="times new roman, new york, times, serif" size="2">pp.x 00000000008DAFED Unknown Unknown Unknown</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_4702" face="times new roman, new york, times, serif" size="2">pp.x 00000000008D9963 Unknown Unknown Unknown</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font
id="yui_3_16_0_1_1450192011307_4573" face="times new roman, new york, times, serif" size="2">pp.x 00000000008D9027 Unknown Unknown Unknown</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_4574" face="times new roman, new york, times, serif" size="2">pp.x 00000000007C63B2 plot_io_ 84 plot_io.f90</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_4653" face="times new roman, new york, times, serif" size="2">pp.x 0000000000446238 chdens_ 291 chdens.f90</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_4654" face="times new roman, new york, times, serif" size="2">pp.x 00000000004444E1 MAIN__ 44
postproc.f90</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_4655" face="times new roman, new york, times, serif" size="2">pp.x 0000000000443D0C Unknown Unknown Unknown</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_4656" face="times new roman, new york, times, serif" size="2">libc.so.6 00002BA147C5323D Unknown Unknown Unknown</font></div><div class="" id="yui_3_16_0_1_1450192011307_4278"><font id="yui_3_16_0_1_1450192011307_4657" face="times new roman, new york, times, serif" size="2">pp.x 0000000000443C09 Unknown Unknown Unknown</font></div><div id="yui_3_16_0_1_1450192011307_5532"><font id="yui_3_16_0_1_1450192011307_5530"
size="2">--------------------------------------------------------------------------------------</font></div><div id="yui_3_16_0_1_1450192011307_5765"><font id="yui_3_16_0_1_1450192011307_5766" size="2">Best</font></div><div id="yui_3_16_0_1_1450192011307_5765"><font id="yui_3_16_0_1_1450192011307_5767" size="2">Jaret</font></div><div id="yui_3_16_0_1_1450192011307_5768"><font id="yui_3_16_0_1_1450192011307_5769" size="2">ASU</font></div> <font size="2"><br clear="none"></font><div class="qtdSeparateBR" id="yui_3_16_0_1_1450192011307_5187"><font size="2"><br clear="none"><br clear="none"></font></div><div class="yqt6721680509" id="yqt28487"><div class="yahoo_quoted" id="yui_3_16_0_1_1450192011307_5191" style="display:block;"> <div id="yui_3_16_0_1_1450192011307_5190" style="font-family:HelveticaNeue, 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif;"> <div id="yui_3_16_0_1_1450192011307_5189" style="font-family:HelveticaNeue, 'Helvetica
Neue', Helvetica, Arial, 'Lucida Grande', sans-serif;"> <div dir="ltr" id="yui_3_16_0_1_1450192011307_5188"><font id="yui_3_16_0_1_1450192011307_5192" size="2" face="Arial"> On Tuesday, December 15, 2015 2:20 AM, Giuseppe Mattioli <giuseppe.mattioli@ism.cnr.it> wrote:<br clear="none"></font></div> <font size="2"><br clear="none"><br clear="none"> </font><div class="y_msg_container" id="yui_3_16_0_1_1450192011307_5193"><font id="yui_3_16_0_1_1450192011307_5528" size="2"><br clear="none">Dear Jaret<br clear="none">You must run pp.x *four times*, three times to extract the densities from the wfc files for your three systems, and the fourth time to produce the <br clear="none">difference plot. I do not see in your script the pp.x run that produces the 'interface.dat' file. if you look at my script there are indeed four calls <br clear="none">to pp.x...<br clear="none"><br clear="none">> > export FILEA="molecule+surface"<br
clear="none">> > export INPFILE=$FILEA-cha.inp<br clear="none">> > export OUTFILE=$FILEA-cha.out<br clear="none">> > echo " $FILEA"<br clear="none">> > echo " $INPFILE"<br clear="none">> > echo " $OUTFILE"<br clear="none">> > cat > $INPFILE << EOF<br clear="none">> ><br clear="none">> > &inputpp<br clear="none">> ><br clear="none">> > prefix = '$FILEA'<br clear="none">> > outdir = '$TMP_DIR/'<br clear="none">> > filplot = '$FILEA-cha.dat'<br clear="none">> > plot_num= 0<br clear="none">> ><br clear="none">> > /<br clear="none">> ><br clear="none">> > EOF<br clear="none">> > $PARA_PREFIX $ESPRESSO/pp.x $PARA_POSTFIX < $INPFILE >> $OUTFILE<br clear="none">> > <br clear="none">> > export FILEB="molecule"<br clear="none">>
> export INPFILE=$FILEB-cha.inp<br clear="none">> > export OUTFILE=$FILEB-cha.out<br clear="none">> > echo " $FILEB"<br clear="none">> > echo " $INPFILE"<br clear="none">> > echo " $OUTFILE"<br clear="none">> > cat > $INPFILE << EOF<br clear="none">> ><br clear="none">> > &inputpp<br clear="none">> ><br clear="none">> > prefix = '$FILEB'<br clear="none">> > outdir = '$TMP_DIR/'<br clear="none">> > filplot = '$FILEB-cha.dat'<br clear="none">> > plot_num= 0<br clear="none">> ><br clear="none">> > /<br clear="none">> ><br clear="none">> > EOF<br clear="none">> > $PARA_PREFIX $ESPRESSO/pp.x $PARA_POSTFIX < $INPFILE >> $OUTFILE<br clear="none">> > <br clear="none">> > <br clear="none">> > export FILEC="surface"<br
clear="none">> > export INPFILE=$FILEC-cha.inp<br clear="none">> > export OUTFILE=$FILEC-cha.out<br clear="none">> > echo " $FILEC"<br clear="none">> > echo " $INPFILE"<br clear="none">> > echo " $OUTFILE"<br clear="none">> > cat > $INPFILE << EOF<br clear="none">> ><br clear="none">> > &inputpp<br clear="none">> ><br clear="none">> > prefix = '$FILEC'<br clear="none">> > outdir = '$TMP_DIR/'<br clear="none">> > filplot = '$FILEC-cha.dat'<br clear="none">> > plot_num= 0<br clear="none">> ><br clear="none">> > /<br clear="none">> ><br clear="none">> > EOF<br clear="none">> > $PARA_PREFIX $ESPRESSO/pp.x $PARA_POSTFIX < $INPFILE >> $OUTFILE<br clear="none">> > <br clear="none">> > export FILE="rho-int-$FILEA"<br
clear="none">> > export INPFILE=$FILE.inp<br clear="none">> > export OUTFILE=$FILE.out<br clear="none">> > echo " $FILE"<br clear="none">> > echo " $INPFILE"<br clear="none">> > echo " $OUTFILE"<br clear="none">> > cat > $INPFILE << EOF<br clear="none">> ><br clear="none">> > &inputpp<br clear="none">> > /<br clear="none">> > &plot<br clear="none">> ><br clear="none">> > nfile = 3<br clear="none">> > filepp(1) = '$FILEA-cha.dat'<br clear="none">> > weight(1) = 1.0<br clear="none">> > filepp(2) = '$FILEB-cha.dat'<br clear="none">> > weight(2) = -1.0<br clear="none">> > filepp(3) = '$FILEC-cha.dat'<br clear="none">> > weight(3) = -1.0<br clear="none">> > iflag = 3<br clear="none">> > output_format = 5<br
clear="none">> > fileout = '$FILE.plot'<br clear="none">> > e1(1) =1.0, e1(2)=1.0, e1(3) = 0.0,<br clear="none">> > e2(1) =0.0, e2(2)=0.0, e2(3) = 1.0,<br clear="none">> > nx=56, ny=40<br clear="none">> ><br clear="none">> > /<br clear="none">> ><br clear="none">> > EOF<br clear="none">> > $PARA_PREFIX $ESPRESSO/pp.x $PARA_POSTFIX < $INPFILE >> $OUTFILE<br clear="none"><br clear="none">HTH<br clear="none">Giuseppe<br clear="none"><br clear="none">On Tuesday, December 15, 2015 03:15:24 AM you wrote:<br clear="none">> Dear Giuseppe,The charge densities plots you have on your paper is really what I'm looking to get for my system. Now, I tried the recipe you sent<br clear="none">> before but I failed to produce it. See what I did: I run three different pp.x for all of the below input files;system A: &INPUTPP<br clear="none">>
prefix = 'lsmo' ,<br clear="none">> outdir = './',<br clear="none">> filplot = 'lsmo.dat' ,<br clear="none">> plot_num = 0,system B:<br clear="none">> &INPUTPP<br clear="none">> prefix = 'PZT' ,<br clear="none">> outdir = './',<br clear="none">> filplot = 'pzt.dat' ,<br clear="none">> plot_num = 0,system A+B: &inputpp<br clear="none">> /<br clear="none">> &plot<br clear="none">> nfile = 3<br clear="none">> filepp(1) = 'interface.dat'<br clear="none">> weight(1) = 1.0<br clear="none">> filepp(2) = 'lsmo.dat'<br clear="none">> weight(2) = -1.0<br clear="none">>
filepp(3) = 'pzt.dat'<br clear="none">> weight(3) = -1.0<br clear="none">> iflag = 3<br clear="none">> output_format = 5<br clear="none">> fileout = 'all.plot'<br clear="none">> e1(1) =1.0, e1(2)=1.0, e1(3) = 0.0,<br clear="none">> e2(1) =0.0, e2(2)=0.0, e2(3) = 1.0,<br clear="none">> nx=56, ny=40<br clear="none">> /<br clear="none">> EOF <br clear="none">> but it did not work, I am bad in script so I think I did not understand the procedure.<br clear="none">> <br clear="none">> <br clear="none">> <br clear="none">> On Monday, December 14, 2015 4:54 AM, Giuseppe Mattioli <<a rel="nofollow" shape="rect" ymailto="mailto:giuseppe.mattioli@ism.cnr.it" target="_blank" href="javascript:return">giuseppe.mattioli@ism.cnr.it</a>> wrote:<br clear="none">> <br clear="none">> <br clear="none">> <br clear="none">> Dear Jaret<br
clear="none">> <br clear="none">> > 1) You said the spilling parameter has to be the same in all systems,<br clear="none">> <br clear="none">> Not "the same", only "similar"<br clear="none">> <br clear="none">> > in my case this is what I got:system A : spilling<br clear="none">> > parameter=0.0031system B : spilling parameter=0.0021interface(A+B) :<br clear="none">> > spilling parameter=0.0027,they are close but not the same, is this<br clear="none">> > fine?<br clear="none">> <br clear="none">> Yes, it is fine in my opinion. You can compare the values. If you want<br clear="none">> to be very diligent you can add the charge spilt out by adding 0.31%,<br clear="none">> 0.27%, 0.21% to all the atoms (this is an arbitrary but wise choice)<br clear="none">> of your three systems, respectively. However, I suppose that this will<br clear="none">> not change your results very
much so you can safely skip.<br clear="none">> <br clear="none">> > 2) To get the charge accumulation and depletion, is there a formula<br clear="none">> > to each on of them or what?I have calculate the charge difference of<br clear="none">> > each atom like this :<br clear="none">> > Charge diff.=Lowdin charge (atom in the interface)-Lowdin charge<br clear="none">> > (atom in the separate system A(B))<br clear="none">> > Using this, I've got positive and negative values, does the positive<br clear="none">> > means accumulation and the negative means depletion?<br clear="none">> <br clear="none">> The reply is yes to both questions, with only one further note:<br clear="none">> three-dimensional deltarho maps help you to see if there is a<br clear="none">> consistent interfacial charge accumulation, which is not always easy<br clear="none">> to fit into the Lowdin partitioning. You might
like to be inspired by<br clear="none">> the theoretical results "just accepted" for publication (see also the<br clear="none">> supporting information). The calculation has been applied to<br clear="none">> oligothiophenes in contact with a silver surface.<br clear="none">> <br clear="none">> <a rel="nofollow" shape="rect" target="_blank" href="http://pubs.acs.org/doi/abs/10.1021/acs.jpcc.5b08733">http://pubs.acs.org/doi/abs/10.1021/acs.jpcc.5b08733</a><br clear="none">> <br clear="none">> This information generally completes that contained in the Lowdin<br clear="none">> analysis of accumulation and depletion of charge in single atoms.<br clear="none">> <br clear="none">> HTH<br clear="none">> Giuseppe<br clear="none">> <br clear="none">> Quoting Jaret Qi <<a rel="nofollow" shape="rect" ymailto="mailto:jaretqi@yahoo.com" target="_blank" href="javascript:return">jaretqi@yahoo.com</a>>:<br
clear="none">> > Hello Mattioli,I tried the second case to calculate the charge<br clear="none">> > accumulation and depletion. Now I have some concerns:1) You said the<br clear="none">> > spilling parameter has to be the same in all systems, in my case<br clear="none">> > this is what I got:system A : spilling parameter=0.0031system B :<br clear="none">> > spilling parameter=0.0021interface(A+B) : spilling<br clear="none">> > parameter=0.0027,they are close but not the same, is this fine? if<br clear="none">> > not how one can get same values?<br clear="none">> > 2) To get the charge accumulation and depletion, is there a formula<br clear="none">> > to each on of them or what?I have calculate the charge difference of<br clear="none">> > each atom like this :<br clear="none">> > Charge diff.=Lowdin charge (atom in the interface)-Lowdin charge<br clear="none">> > (atom in the
separate system A(B))<br clear="none">> > Using this, I've got positive and negative values, does the positive<br clear="none">> > means accumulation and the negative means depletion?<br clear="none">> > ----------------------------------------------<br clear="none">> ><br clear="none">> > On Friday, October 23, 2015 1:36 AM, Giuseppe Mattioli<br clear="none">> ><br clear="none">> > <<a rel="nofollow" shape="rect" ymailto="mailto:giuseppe.mattioli@ism.cnr.it" target="_blank" href="javascript:return">giuseppe.mattioli@ism.cnr.it</a>> wrote:<br clear="none">> > <br clear="none">> > <br clear="none">> > <br clear="none">> > Dear Jaret<br clear="none">> > You may do two (complementary) things:<br clear="none">> > <br clear="none">> > 1) a Deltarho map. a) Calculation of your whole system and usage of<br clear="none">> > pp.x to extract the charge density
(plot_num=0). b) two separate scf<br clear="none">> > calculations<br clear="none">> > of the insulator slab and metal slab in the same atomic position of<br clear="none">> > the previous one and usage of pp.x to extract the charge densities.<br clear="none">> > c) Subtract<br clear="none">> > the charge densities calculated in b) to the charge densities<br clear="none">> > calculated in a). If you open the obtained file with xcrysden you<br clear="none">> > can visualize the<br clear="none">> > charge displacement at the interface (menu tools --> data grid).<br clear="none">> > <br clear="none">> > Something like this, which has been set up for a molecule/surface system...<br clear="none">> > <br clear="none">> > export FILEA="molecule+surface"<br clear="none">> > export INPFILE=$FILEA-cha.inp<br clear="none">> > export OUTFILE=$FILEA-cha.out<br
clear="none">> > echo " $FILEA"<br clear="none">> > echo " $INPFILE"<br clear="none">> > echo " $OUTFILE"<br clear="none">> > cat > $INPFILE << EOF<br clear="none">> ><br clear="none">> > &inputpp<br clear="none">> ><br clear="none">> > prefix = '$FILEA'<br clear="none">> > outdir = '$TMP_DIR/'<br clear="none">> > filplot = '$FILEA-cha.dat'<br clear="none">> > plot_num= 0<br clear="none">> ><br clear="none">> > /<br clear="none">> ><br clear="none">> > EOF<br clear="none">> > $PARA_PREFIX $ESPRESSO/pp.x $PARA_POSTFIX < $INPFILE >> $OUTFILE<br clear="none">> > <br clear="none">> > export FILEB="molecule"<br clear="none">> > export INPFILE=$FILEB-cha.inp<br clear="none">> > export OUTFILE=$FILEB-cha.out<br clear="none">>
> echo " $FILEB"<br clear="none">> > echo " $INPFILE"<br clear="none">> > echo " $OUTFILE"<br clear="none">> > cat > $INPFILE << EOF<br clear="none">> ><br clear="none">> > &inputpp<br clear="none">> ><br clear="none">> > prefix = '$FILEB'<br clear="none">> > outdir = '$TMP_DIR/'<br clear="none">> > filplot = '$FILEB-cha.dat'<br clear="none">> > plot_num= 0<br clear="none">> ><br clear="none">> > /<br clear="none">> ><br clear="none">> > EOF<br clear="none">> > $PARA_PREFIX $ESPRESSO/pp.x $PARA_POSTFIX < $INPFILE >> $OUTFILE<br clear="none">> > <br clear="none">> > <br clear="none">> > export FILEC="surface"<br clear="none">> > export INPFILE=$FILEC-cha.inp<br clear="none">> > export OUTFILE=$FILEC-cha.out<br
clear="none">> > echo " $FILEC"<br clear="none">> > echo " $INPFILE"<br clear="none">> > echo " $OUTFILE"<br clear="none">> > cat > $INPFILE << EOF<br clear="none">> ><br clear="none">> > &inputpp<br clear="none">> ><br clear="none">> > prefix = '$FILEC'<br clear="none">> > outdir = '$TMP_DIR/'<br clear="none">> > filplot = '$FILEC-cha.dat'<br clear="none">> > plot_num= 0<br clear="none">> ><br clear="none">> > /<br clear="none">> ><br clear="none">> > EOF<br clear="none">> > $PARA_PREFIX $ESPRESSO/pp.x $PARA_POSTFIX < $INPFILE >> $OUTFILE<br clear="none">> > <br clear="none">> > export FILE="rho-int-$FILEA"<br clear="none">> > export INPFILE=$FILE.inp<br clear="none">> > export OUTFILE=$FILE.out<br clear="none">> >
echo " $FILE"<br clear="none">> > echo " $INPFILE"<br clear="none">> > echo " $OUTFILE"<br clear="none">> > cat > $INPFILE << EOF<br clear="none">> ><br clear="none">> > &inputpp<br clear="none">> > /<br clear="none">> > &plot<br clear="none">> ><br clear="none">> > nfile = 3<br clear="none">> > filepp(1) = '$FILEA-cha.dat'<br clear="none">> > weight(1) = 1.0<br clear="none">> > filepp(2) = '$FILEB-cha.dat'<br clear="none">> > weight(2) = -1.0<br clear="none">> > filepp(3) = '$FILEC-cha.dat'<br clear="none">> > weight(3) = -1.0<br clear="none">> > iflag = 3<br clear="none">> > output_format = 5<br clear="none">> > fileout = '$FILE.plot'<br clear="none">> > e1(1) =1.0, e1(2)=1.0, e1(3) =
0.0,<br clear="none">> > e2(1) =0.0, e2(2)=0.0, e2(3) = 1.0,<br clear="none">> > nx=56, ny=40<br clear="none">> ><br clear="none">> > /<br clear="none">> ><br clear="none">> > EOF<br clear="none">> > $PARA_PREFIX $ESPRESSO/pp.x $PARA_POSTFIX < $INPFILE >> $OUTFILE<br clear="none">> > <br clear="none">> > 2) Use projwfc.x to obtain (Lowdin) atomic charges of your whole<br clear="none">> > system and of the separate slabs (you may also relax the slabs, in<br clear="none">> > this case, to<br clear="none">> > account for surface effects). Then you compare the atomic charges to<br clear="none">> > look for charge displacement. Be aware that there is a spilling<br clear="none">> > parameter at the<br clear="none">> > end of the projwfc output which indicates how much of your charge<br clear="none">> > density does not fit into the Lowding
atomic partitioning. Your<br clear="none">> > results are<br clear="none">> > reasonably meaningful only if the spilling parameter is similar for<br clear="none">> > all your calculations... You may also use the external Bader post<br clear="none">> > processing to<br clear="none">> > estimate atomic charges, but it requires (to be reliable) PAW or NC<br clear="none">> > pseudopotentials and hand-adjusted very dense FFT grids. You may<br clear="none">> > like to have a<br clear="none">> > look here if you want to try<br clear="none">> > <br clear="none">> > <a rel="nofollow" shape="rect" target="_blank" href="http://theory.cm.utexas.edu/henkelman/code/bader/">http://theory.cm.utexas.edu/henkelman/code/bader/</a><br clear="none">> > <br clear="none">> > HTH<br clear="none">> > Giuseppe<br clear="none">> > <br clear="none">> > On Friday, October 23, 2015 06:12:17 AM
you wrote:<br clear="none">> >> Dear Giuseppe,My system is an interface between an insulator and half-metal.<br clear="none">> >> -Jaret<br clear="none">> >> AST, USA>Dear mahmoudASU<br clear="none">> >> <br clear="none">> >> >First of all sign always your posts to this Forum with name and<br clear="none">> >> <br clear="none">> >> affiliation, please.<br clear="none">> >> <br clear="none">> >> >There are many ways to calculate charge displacements (Deltarho<br clear="none">> >> <br clear="none">> >> plots, atomic charge calculations, ...), but their best usage<br clear="none">> >> depends on >the kind<br clear="none">> >> <br clear="none">> >> >of charge displacement occurring in your system (molecule-surface<br clear="none">> >> <br clear="none">> >> interaction, charge transfer affecting
dopants or defects in a<br clear="none">> >> <br clear="none">> >> >semiconductor<br clear="none">> >> >matrix, ...). Impossible to say more without knowing more...<br clear="none">> >> ><br clear="none">> >> >HTH<br clear="none">> >> ><br clear="none">> >> >Giuseppe <br clear="none">> >> ><br clear="none">> >> >On Wednesday, October 21, 2015 11:42:37 PM Jaret Qi wrote:<br clear="none">> >> >> Hello QE users,Is there a way to calculate Charge accumulation<br clear="none">> >> <br clear="none">> >> and depletion in quantum espresso, if so then how?<br clear="none">> >> <br clear="none">> >> >> -mahmoudASU<br clear="none">> > <br clear="none">> > ********************************************************<br clear="none">> > - Article premier - Les hommes naissent et demeurent<br
clear="none">> > libres et ègaux en droits. Les distinctions sociales<br clear="none">> > ne peuvent être fondèes que sur l'utilitè commune<br clear="none">> > - Article 2 - Le but de toute association politique<br clear="none">> > est la conservation des droits naturels et<br clear="none">> > imprescriptibles de l'homme. Ces droits sont la libertè,<br clear="none">> > la propriètè, la sùretè et la rèsistance à l'oppression.<br clear="none">> > ********************************************************<br clear="none">> > <br clear="none">> > Giuseppe Mattioli <br clear="none">> > CNR - ISTITUTO DI STRUTTURA DELLA MATERIA <br clear="none">> > v. Salaria Km 29,300 - C.P. 10 <br clear="none">> > I 00015 - Monterotondo Stazione (RM), Italy <br clear="none">> > Tel + 39 06 90672836 -
Fax +39 06 90672316 <br clear="none">> > E-mail: <<a rel="nofollow" shape="rect" ymailto="mailto:giuseppe.mattioli@ism.cnr.it" target="_blank" href="javascript:return">giuseppe.mattioli@ism.cnr.it</a>><br clear="none">> > <a rel="nofollow" shape="rect" target="_blank" href="http://www.ism.cnr.it/english/staff/mattiolig">http://www.ism.cnr.it/english/staff/mattiolig</a><br clear="none">> > ResearcherID: F-6308-2012<br clear="none">> <br clear="none">> --<br clear="none">> ********************************************************<br clear="none">> - Article premier - Les hommes naissent et demeurent<br clear="none">> libres et ègaux en droits. Les distinctions sociales<br clear="none">> ne peuvent être fondèes que sur l'utilitè commune<br clear="none">> - Article 2 - Le but de toute association politique<br clear="none">> est la conservation des droits naturels et<br clear="none">>
imprescriptibles de l'homme. Ces droits sont la libertè,<br clear="none">> la propriètè, la sùretè et la rèsistance à l'oppression.<br clear="none">> ********************************************************<br clear="none">> <br clear="none">> Giuseppe Mattioli<br clear="none">> CNR - ISTITUTO DI STRUTTURA DELLA MATERIA<br clear="none">> v. Salaria Km 29,300 - C.P. 10<br clear="none">> I 00015 - Monterotondo Stazione (RM)<br clear="none">> Tel + 39 06 90672836 - Fax +39 06 90672316<br clear="none">> E-mail: <<a rel="nofollow" shape="rect" ymailto="mailto:giuseppe.mattioli@ism.cnr.it" target="_blank" href="javascript:return">giuseppe.mattioli@ism.cnr.it</a>><br clear="none"><br clear="none">********************************************************<br clear="none">- Article premier - Les hommes naissent et demeurent<br clear="none">libres et égaux en droits. Les
distinctions sociales<br clear="none">ne peuvent être fondées que sur l'utilité commune<br clear="none">- Article 2 - Le but de toute association politique<br clear="none">est la conservation des droits naturels et <br clear="none">imprescriptibles de l'homme. Ces droits sont la liberté,<br clear="none">la propriété, la sûreté et la résistance à l'oppression.</font><div class="yqt3103551482" id="yqtfd70470"><font id="yui_3_16_0_1_1450192011307_5451" size="2"><br clear="none">********************************************************<br clear="none"><br clear="none"> Giuseppe Mattioli <br clear="none"> CNR - ISTITUTO DI STRUTTURA DELLA MATERIA <br clear="none"> v. Salaria Km 29,300 - C.P. 10 <br clear="none"> I 00015 - Monterotondo Stazione (RM), Italy <br clear="none"> Tel + 39 06 90672836 - Fax +39 06 90672316 <br clear="none"> E-mail:
<<a rel="nofollow" shape="rect" ymailto="mailto:giuseppe.mattioli@ism.cnr.it" target="_blank" href="javascript:return">giuseppe.mattioli@ism.cnr.it</a>><br clear="none"> <a rel="nofollow" shape="rect" id="yui_3_16_0_1_1450192011307_5862" target="_blank" href="http://www.ism.cnr.it/english/staff/mattiolig">http://www.ism.cnr.it/english/staff/mattiolig</a><br clear="none"> ResearcherID: F-6308-2012</font></div><font id="yui_3_16_0_1_1450192011307_5239" size="2"><br clear="none" id="yui_3_16_0_1_1450192011307_5238"></font><br clear="none"></div> </div> </div> </div></div></div></td>
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