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<div class="moz-cite-prefix">On 23/12/2015 11:53, Ridwan Agbaoye
wrote:<br>
</div>
<blockquote
cite="mid:1610648291.2191599.1450868014652.JavaMail.yahoo@mail.yahoo.com"
type="cite">
<div style="color:#000; background-color:#fff;
font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial,
Lucida Grande, sans-serif;font-size:16px">
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<div
style="color:#000;background-color:#fff;font-family:HelveticaNeue,
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id="yui_3_16_0_1_1450866594342_3867">
<div class="yiv9628606616qtdSeparateBR"
id="yui_3_16_0_1_1450866594342_3866"><br clear="none">
Does this answers work for all systems be it FCC or
monoclinic or Hexagonal</div>
</div>
</div>
</div>
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</blockquote>
which part of the answer ? the first part about definition of alat
yes.<br>
<blockquote
cite="mid:1610648291.2191599.1450868014652.JavaMail.yahoo@mail.yahoo.com"
type="cite">
<div style="color:#000; background-color:#fff;
font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial,
Lucida Grande, sans-serif;font-size:16px">
<div id="yiv9628606616">
<div id="yui_3_16_0_1_1450866594342_3868">
<div
style="color:#000;background-color:#fff;font-family:HelveticaNeue,
Helvetica Neue, Helvetica, Arial, Lucida Grande,
sans-serif;font-size:16px;"
id="yui_3_16_0_1_1450866594342_3867">
<div class="yiv9628606616qtdSeparateBR"
id="yui_3_16_0_1_1450866594342_3866"><br
id="yui_3_16_0_1_1450866594342_6746">
</div>
<div class="yiv9628606616qtdSeparateBR"
id="yui_3_16_0_1_1450866594342_3866" dir="ltr"><span
style="font-family: 'Helvetica Neue', 'Segoe UI',
Helvetica, Arial, 'Lucida Grande', sans-serif;
font-size: 13px;" id="yui_3_16_0_1_1450866594342_6748"
class="">"final_alat = input_alat * 0.487685488 / 0.5
= 10,345371472 bohr " where does 0.5 come from </span><br
style="font-family: 'Helvetica Neue', 'Segoe UI',
Helvetica, Arial, 'Lucida Grande', sans-serif;
font-size: 13px;" id="yui_3_16_0_1_1450866594342_6750"
class="" clear="none">
</div>
<div class="yiv9628606616qtdSeparateBR"
id="yui_3_16_0_1_1450866594342_3866" dir="ltr"><span
style="font-family: 'Helvetica Neue', 'Segoe UI',
Helvetica, Arial, 'Lucida Grande', sans-serif;
font-size: 13px;" class=""><br>
</span></div>
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</blockquote>
from the comparison of your final cell and the common definition of
fcc Bravais lattice.<br>
<br>
<blockquote
cite="mid:1610648291.2191599.1450868014652.JavaMail.yahoo@mail.yahoo.com"
type="cite">
<div style="color:#000; background-color:#fff;
font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial,
Lucida Grande, sans-serif;font-size:16px">
<div id="yiv9628606616">
<div id="yui_3_16_0_1_1450866594342_3868">
<div
style="color:#000;background-color:#fff;font-family:HelveticaNeue,
Helvetica Neue, Helvetica, Arial, Lucida Grande,
sans-serif;font-size:16px;"
id="yui_3_16_0_1_1450866594342_3867">
<div class="yiv9628606616qtdSeparateBR"
id="yui_3_16_0_1_1450866594342_3866" dir="ltr"><span
style="font-family: 'Helvetica Neue', 'Segoe UI',
Helvetica, Arial, 'Lucida Grande', sans-serif;
font-size: 13px;" class=""
id="yui_3_16_0_1_1450866594342_6786">If i am working
on a monoclinic or Hexagonal crystal structure do i
still use the 0.5 or how do i calculate the 0.5</span></div>
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id="yui_3_16_0_1_1450866594342_3866" dir="ltr"><span
style="font-family: 'Helvetica Neue', 'Segoe UI',
Helvetica, Arial, 'Lucida Grande', sans-serif;
font-size: 13px;" class=""><br>
</span></div>
<div class="yiv9628606616qtdSeparateBR"
id="yui_3_16_0_1_1450866594342_3866" dir="ltr"><span
style="font-family: 'Helvetica Neue', 'Segoe UI',
Helvetica, Arial, 'Lucida Grande', sans-serif;
font-size: 13px;" class=""
id="yui_3_16_0_1_1450866594342_6845">
For the atomic position i got</span></div>
<div class="yiv9628606616qtdSeparateBR"
id="yui_3_16_0_1_1450866594342_3866" dir="ltr"><span
style="font-family: 'Helvetica Neue', 'Segoe UI',
Helvetica, Arial, 'Lucida Grande', sans-serif;
font-size: 13px;" class=""
id="yui_3_16_0_1_1450866594342_6912">
<blockquote type="cite"
id="yui_3_16_0_1_1450866594342_4518" class="">
<div class="" role="gridcell" tabindex="0"
id="yui_3_16_0_1_1450866594342_6888"
style="transition: none; outline: none 0px;">
<div id="yui_3_16_0_1_1450866594342_6889"
style="font-family: HelveticaNeue, 'Helvetica
Neue', Helvetica, Arial, 'Lucida Grande',
sans-serif; font-size: 16px;" class="">
<div class=""
id="yiv8580693823yui_3_16_0_1_1450677059337_4051"
style="margin: 1.2pt 0in;"><span class=""
id="yiv8580693823yui_3_16_0_1_1450677059337_9769"
style="font-size: 11pt; font-family:
Helvetica, sans-serif;">ATOMIC
POSITIONS(alat)</span></div>
<div class=""
id="yiv8580693823yui_3_16_0_1_1450677059337_4051"
style="margin: 1.2pt 0in;"><span class=""
id="yiv8580693823yui_3_16_0_1_1450677059337_9774"
style="font-size: 11pt; font-family:
Helvetica, sans-serif;">si -0.035697193
-0.035697193 -0.035697193</span></div>
<div class=""
id="yiv8580693823yui_3_16_0_1_1450677059337_4051"
style="margin: 1.2pt 0in;" dir="ltr"><span
class=""
id="yiv8580693823yui_3_16_0_1_1450677059337_9779"
style="font-size: 11pt; font-family:
Helvetica, sans-serif;">si 0.208182292
0.208182292 0.208182292</span></div>
</div>
</div>
</blockquote>
</span></div>
<div class="yiv9628606616qtdSeparateBR"
id="yui_3_16_0_1_1450866594342_3866" dir="ltr"><span
style="font-family: 'Helvetica Neue', 'Segoe UI',
Helvetica, Arial, 'Lucida Grande', sans-serif;
font-size: 13px;" class="">is there a rule to use in
converting to </span></div>
<div class="yiv9628606616qtdSeparateBR"
id="yui_3_16_0_1_1450866594342_3866" dir="ltr"><span
style="font-family: 'Helvetica Neue', 'Segoe UI',
Helvetica, Arial, 'Lucida Grande', sans-serif;
font-size: 13px;" class=""
id="yui_3_16_0_1_1450866594342_7181">0 0 0 and 1/4 1/4
1/4 <br>
</span></div>
<div class="yiv9628606616qtdSeparateBR"
id="yui_3_16_0_1_1450866594342_3866" dir="ltr"><span
style="font-family: 'Helvetica Neue', 'Segoe UI',
Helvetica, Arial, 'Lucida Grande', sans-serif;
font-size: 13px;" class=""><br>
</span></div>
</div>
</div>
</div>
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</blockquote>
read and understand the documentation.<br>
Ask yourself how would you have defined the atomic positions and
check in a few cases that you understand the way the code does it.
it's just geometry.<br>
<blockquote
cite="mid:1610648291.2191599.1450868014652.JavaMail.yahoo@mail.yahoo.com"
type="cite">
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font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial,
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<div
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Helvetica, Arial, 'Lucida Grande', sans-serif;
font-size: 13px;" class=""
id="yui_3_16_0_1_1450866594342_7464">Agbaoye Ridwan
Olamide</span></div>
<div class="yiv9628606616qtdSeparateBR"
id="yui_3_16_0_1_1450866594342_3866" dir="ltr"><span
style="font-family: 'Helvetica Neue', 'Segoe UI',
Helvetica, Arial, 'Lucida Grande', sans-serif;
font-size: 13px;" class=""
id="yui_3_16_0_1_1450866594342_7183">Federal
University of Agriculture, Abeokuta</span></div>
<div class="yiv9628606616qtdSeparateBR"
id="yui_3_16_0_1_1450866594342_3866" dir="ltr"><span
style="font-family: 'Helvetica Neue', 'Segoe UI',
Helvetica, Arial, 'Lucida Grande', sans-serif;
font-size: 13px;" class=""
id="yui_3_16_0_1_1450866594342_7465">M.Sc. (in view)</span></div>
</div>
</div>
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<div class=".yiv9628606616yahoo_quoted">
<div style="font-family:HelveticaNeue, Helvetica Neue,
Helvetica, Arial, Lucida Grande, sans-serif;font-size:16px;">
<div style="font-family:HelveticaNeue, Helvetica Neue,
Helvetica, Arial, Lucida Grande,
sans-serif;font-size:16px;">
<div dir="ltr"><font face="Arial" size="2"> On Monday,
December 21, 2015 1:18 AM, stefano de gironcoli
<a class="moz-txt-link-rfc2396E" href="mailto:degironc@sissa.it"><degironc@sissa.it></a> wrote:<br clear="none">
</font></div>
<br clear="none">
<br clear="none">
<div class="yiv9628606616y_msg_container">
<div id="yiv9628606616">
<div>
<div class="yiv9628606616moz-cite-prefix">if nor
celldm(1) [in Bohr] nor A [in \AA] are given in
input and the CELL_PARAMETERS card is given then
alat is defined as the length (in bohr) of the
first vector in CELL_PARAMETERS<br clear="none">
in your case 7.5*sqrt(2.0)=10.60660172 bohr<br
clear="none">
<br clear="none">
if celldm(1) or A are given then the
CELL_PARAMETERS are interpreted as given in those
units.<br clear="none">
In input atomic positions are given in the
selected units, in output they are always given in
unit of the alat value computed/defined in input.<br
clear="none">
<br clear="none">
If you want to use AA as your input/output length
unit the easiest way is to define<br clear="none">
<br clear="none">
A=1.0 or celldm(1)=1.889726878 in the &system
namelist<br clear="none">
CELL_PARAMETERS<br clear="none">
...<br clear="none">
ATOMIC_POSITIONS Angstrom [or alat since they are
the same] <br clear="none">
...<br clear="none">
<br clear="none">
in output the positions and cell information will
be given in (input) alat units, that is in AA
again.<br clear="none">
<br clear="none">
HTH<br clear="none">
<br clear="none">
stefano<br clear="none">
<br clear="none">
PS <br clear="none">
in your case the silicon cell contracted by<br
clear="none">
0.487685488 * alat / 7.5 = 0.487685488 * sqrt(2) <br
clear="none">
the final cell corresponds to an FCC with<br
clear="none">
final_alat = input_alat * 0.487685488 / 0.5 =
10,345371472 bohr<br clear="none">
<br clear="none">
In these units the atomic coordinates are just <br
clear="none">
0 0 0 and 1/4 1/4 1/4 (plus a small shift away
from the origin due to the fact that the center of
mass remains fixed during relaxation)<br
clear="none">
<br clear="none">
<br clear="none">
<br clear="none">
On 21/12/2015 07:30, Ridwan Agbaoye wrote:<br
clear="none">
</div>
<blockquote type="cite">
<div class="yiv9628606616yqt0889623001"
id="yiv9628606616yqt00984">
<div
style="color:#000;background-color:#fff;font-family:HelveticaNeue,
Helvetica Neue, Helvetica, Arial, Lucida
Grande, sans-serif;font-size:16px;">
<div class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_9717"
style="margin-top:1.2pt;margin-right:0in;margin-bottom:1.2pt;margin-left:0in;"><span
class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_9719"
style="font-size:11pt;font-family:Helvetica,
sans-serif;">Good Morning Everybody,</span></div>
<div class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_4526"
style="margin:1.2pt 0in;"><span
class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_9724"
style="font-size:11pt;font-family:Helvetica,
sans-serif;"> </span></div>
<div class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_4557"
style="margin:1.2pt 0in;"><span
class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_9729"
style="font-size:11pt;font-family:Helvetica,
sans-serif;">I need some help with the
interpretation of vc-relax output and
conversion from alat to bohr</span></div>
<div class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_4557"
style="margin:1.2pt 0in;"><span
class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_10896"
style="font-size:11pt;font-family:Helvetica,
sans-serif;">I want to do vc-relax
calculation for a monoclinic system but i
decide to start with silicon a
face-centered cubic system to understand
the concept of vc-relax properly </span></div>
<div class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_4525"
style="margin:1.2pt 0in;"><span
class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_9734"
style="font-size:11pt;font-family:Helvetica,
sans-serif;">I tried vc-relax for silicon
and i got the following output </span></div>
<div class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_4200"
style="margin:1.2pt 0in;"><span
class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_9739"
style="font-size:11pt;font-family:Helvetica,
sans-serif;">Begin Final Coordinate</span></div>
<div class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_4051"
style="margin:1.2pt 0in;"><span
class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_9744"
style="font-size:11pt;font-family:Helvetica,
sans-serif;">New Unit Cell volume =
276.90769au^3</span></div>
<div class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_4051"
style="margin:1.2pt 0in;"><span
class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_9749"
style="font-size:11pt;font-family:Helvetica,
sans-serif;">CELL
PARAMETERS(alat=10.60660172)</span></div>
<div class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_4051"
style="margin:1.2pt 0in;"><span
class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_9754"
style="font-size:11pt;font-family:Helvetica,
sans-serif;">-0.487685488 -0.000000000
0.487685488</span></div>
<div class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_4051"
style="margin:1.2pt 0in;"><span
class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_9759"
style="font-size:11pt;font-family:Helvetica,
sans-serif;"> 0.000117363 0.487685488
0.487685488</span></div>
<div class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_4051"
style="margin:1.2pt 0in;"><span
class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_9764"
style="font-size:11pt;font-family:Helvetica,
sans-serif;">-0.487685488 0.487685488
-0.000000000</span></div>
<div class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_4051"
style="margin:1.2pt 0in;"><span
class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_9769"
style="font-size:11pt;font-family:Helvetica,
sans-serif;">ATOMIC POSITIONS(alat)</span></div>
<div class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_4051"
style="margin:1.2pt 0in;"><span
class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_9774"
style="font-size:11pt;font-family:Helvetica,
sans-serif;">si -0.035697193
-0.035697193 -0.035697193</span></div>
<div class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_4051"
style="margin:1.2pt 0in;"><span
class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_9779"
style="font-size:11pt;font-family:Helvetica,
sans-serif;">si 0.208182292
0.208182292 0.208182292</span></div>
<div class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_4051"
style="margin:1.2pt 0in;"><span
class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_9784"
style="font-size:11pt;font-family:Helvetica,
sans-serif;">End of Final coordinate</span></div>
<div class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_4051"
style="margin:1.2pt 0in;"><span
class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_9789"
style="font-size:11pt;font-family:Helvetica,
sans-serif;"> </span></div>
<div class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_4051"
style="margin:1.2pt 0in;"><span
class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_9794"
style="font-size:11pt;font-family:Helvetica,
sans-serif;">My input file has </span></div>
<div class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_4051"
style="margin:1.2pt 0in;"><span
class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_9799"
style="font-size:11pt;font-family:Helvetica,
sans-serif;"> </span></div>
<div class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_4051"
style="margin:1.2pt 0in;"><span
class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_9804"
style="font-size:11pt;font-family:Helvetica,
sans-serif;">ibrav=0 nat=2 ntyp=2</span></div>
<div class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_4051"
style="margin:1.2pt 0in;"><span
class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_9809"
style="font-size:11pt;font-family:Helvetica,
sans-serif;"> </span></div>
<div class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_4051"
style="margin:1.2pt 0in;"><span
class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_9814"
style="font-size:11pt;font-family:Helvetica,
sans-serif;">CELL PARAMETER cubic</span></div>
<div class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_4051"
style="margin:1.2pt 0in;"><span
class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_9819"
style="font-size:11pt;font-family:Helvetica,
sans-serif;">-7.5000 0.0000 7.5000</span></div>
<div class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_4051"
style="margin:1.2pt 0in;"><span
class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_9824"
style="font-size:11pt;font-family:Helvetica,
sans-serif;">0.0000 7.5000 7.5000</span></div>
<div class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_4051"
style="margin:1.2pt 0in;"><span
class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_9829"
style="font-size:11pt;font-family:Helvetica,
sans-serif;">-7.5000 7.5000 0.0000</span></div>
<div class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_4051"
style="margin:1.2pt 0in;"><span
class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_9834"
style="font-size:11pt;font-family:Helvetica,
sans-serif;"> </span></div>
<div class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_4051"
style="margin:1.2pt 0in;"><span
class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_9839"
style="font-size:11pt;font-family:Helvetica,
sans-serif;">How exactly do we derive our
celldm(1) and how do we convert to bohr</span></div>
<div class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_4051"
style="margin:1.2pt 0in;"><span
class="yiv9628606616"
style="font-size:11pt;font-family:Helvetica,
sans-serif;"><br clear="none">
</span></div>
<div class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_4051"
style="margin:1.2pt 0in;"><span
class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_9844"
style="font-size:11pt;font-family:Helvetica,
sans-serif;">Do we need to convert the
atomic position from alat to Bohr or
Angstrom</span></div>
<div class="yiv9628606616"
id="yiv9628606616yui_3_16_0_1_1450677059337_4051"
style="margin:1.2pt 0in;"><span
class="yiv9628606616"
style="font-size:11pt;font-family:Helvetica,
sans-serif;"><br clear="none">
</span></div>
<div class="yiv9628606616" dir="ltr"
id="yiv9628606616yui_3_16_0_1_1450677059337_4051"
style="margin:1.2pt 0in;"><font
id="yiv9628606616yui_3_16_0_1_1450677059337_11772"
face="Helvetica, sans-serif"><span
id="yiv9628606616yui_3_16_0_1_1450677059337_11773"
style="font-size:14.6666669845581px;">must
i use bohr as the unit of CELL
PARAMETERS or i can use Angstrom and
declare it as CELL PARAMETER(angstrom) </span></font></div>
<div class="yiv9628606616" dir="ltr"
id="yiv9628606616yui_3_16_0_1_1450677059337_4051"
style="margin:1.2pt 0in;"><font
face="Helvetica, sans-serif"><span
style="font-size:14.6666669845581px;"><br
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</span></font></div>
<div> </div>
<div class="yiv9628606616" dir="ltr"
id="yiv9628606616yui_3_16_0_1_1450677059337_9848"><br
clear="none">
</div>
<div class="yiv9628606616" dir="ltr"
id="yiv9628606616yui_3_16_0_1_1450677059337_9848">
Agbaoye Ridwan Olamide</div>
<div class="yiv9628606616" dir="ltr"
id="yiv9628606616yui_3_16_0_1_1450677059337_9848">
Federal University of Agriculture, Abeokuta</div>
<div class="yiv9628606616" dir="ltr"
id="yiv9628606616yui_3_16_0_1_1450677059337_9848">
M.Sc.(in view)</div>
<div class="yiv9628606616" dir="ltr"
id="yiv9628606616yui_3_16_0_1_1450677059337_9848"><a
moz-do-not-send="true" rel="nofollow"
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class="yiv9628606616moz-txt-link-abbreviated"
ymailto="mailto:agbaoyeridwan@yahoo.com"
target="_blank"
href="mailto:agbaoyeridwan@yahoo.com"><a class="moz-txt-link-abbreviated" href="mailto:agbaoyeridwan@yahoo.com">agbaoyeridwan@yahoo.com</a></a></div>
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<pre>_______________________________________________
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