<div dir="ltr">Dear Prof. Gavin,<div><br></div><div> Thanks a lot for your help. It is working now. However, I have another query. After x optimize with the struct file a message comes as: SPACE GROUP CONTAINS INVERSION</div><div><b> alpha(3) .gt. 91.0; reset to 90.1. </b>However, the struct file remains the same after this message. Hence, should we ignore the message?</div><div><br></div><div>with regards,</div><div><br></div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, 25 Aug 2020 at 11:57, Gavin Abo <<a href="mailto:gsabo@crimson.ua.edu">gsabo@crimson.ua.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<p><font color="#0000ff">I took your attached
Nb2Se3_all_min_initial.struct at [1], kept the structure the
same but swapped the lattice angles (beta<->gamma),
lattice constants (b<->c), and atomic positions
(y<->z) in StructGen of w2web and generated the new
symmetry operations for it with "x symmetry" which gave the
attached Nb2Se3_all_min.struct following the advice at:</font></p>
<p><font color="#0000ff"><a href="https://urldefense.com/v3/__https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg12124.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!FEEtwhA5ust8qZ33lpDr8XYIkrrX9Q-5dJZwtsegrpZeCBDX0vBodglHQ7hv6bvcYwvi9Q$" rel="noreferrer" target="_blank">https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg12124.html</a></font></p>
<p><font color="#0000ff">I then ran the 4D "x optimize" on it using
WIEN2k 19.2 as given below. I'm not able to reproduce what you
have described as instead it looks like the "x optimize" script
changes the gamma angle just fine from the original 104.153240
degrees to other angles such as 102.070175 and 106.236305 in
some of the .struct files.<br>
</font></p>
<p><font color="#c0c0c0">username@computername:~/wiendata/Nb2Se3_all_min$
<font color="#000000">ls</font><br>
Nb2Se3_all_min.struct<br>
username@computername:~/wiendata/Nb2Se3_all_min$ <font color="#000000">x optimize</font><br>
********************************************<br>
GENERATES STRUCT-FILES AND optimize.job<br>
PLEASE CHOOSE ONE OF THE FOLLOWING FEATURES:<br>
<br>
[1] VARY VOLUME with CONSTANT RATIO A:B:C<br>
[2] VARY C/A RATIO with CONSTANT VOLUME (tetr and hex
lattices)<br>
[3] VARY C/A RATIO with CONSTANT VOLUME and B/A (orthorh
lattice)<br>
[4] VARY B/A RATIO with CONSTANT VOLUME and C/A (orthorh
lattice)<br>
[5] VARY A and C (2D-case) (tetragonal or hexagonal lattice)<br>
[6] VARY A, B and C (3D-case) (orthorhombic lattice)<br>
[7] VARY A, B, C and Gamma (4D-case) (monoclinic lattice)<br>
[8] VARY C/A RATIO and VOLUME (2D-case) (tetr and hex
lattices)<br>
<br>
********************************************<br>
<br>
<font color="#000000">7</font><br>
<br>
***************************************************<br>
Generating
Nb2Se3_all_min_initial.struct
<br>
next time this file will be used as template unless you remove
it explicitly.<br>
***************************************************<br>
number of structures: 15, 81 (3x3x3x3), 256 (4x4x4x4)<br>
<font color="#000000">15</font><br>
PLEASE enter a percentage change of a<br>
<font color="#000000">2</font><br>
Nb2Se3_all_min_mon____1.00.struct
<br>
12.153492 17.398148 6.478929104.153240<br>
Nb2Se3_all_min_mon____2.00.struct
<br>
12.401522 17.398148 6.478929104.153240<br>
Nb2Se3_all_min_mon____3.00.struct
<br>
12.649552 17.398148 6.478929104.153240<br>
Nb2Se3_all_min_mon____4.00.struct
<br>
12.401522 17.050185 6.478929104.153240<br>
Nb2Se3_all_min_mon____5.00.struct
<br>
12.401522 17.746111 6.478929104.153240<br>
Nb2Se3_all_min_mon____6.00.struct
<br>
12.401522 17.398148 6.349350104.153240<br>
Nb2Se3_all_min_mon____7.00.struct
<br>
12.401522 17.398148 6.608508104.153240<br>
Nb2Se3_all_min_mon____8.00.struct
<br>
12.153492 17.050185 6.478929104.153240<br>
Nb2Se3_all_min_mon____9.00.struct
<br>
12.153492 17.398148 6.349350104.153240<br>
Nb2Se3_all_min_mon___10.00.struct
<br>
12.401522 17.050185 6.349350104.153240<br>
Nb2Se3_all_min_mon___11.00.struct
<br>
12.401522 17.398148 6.478929102.070175<br>
Nb2Se3_all_min_mon___12.00.struct
<br>
12.401522 17.398148 6.478929106.236305<br>
Nb2Se3_all_min_mon___13.00.struct
<br>
12.153492 17.398148 6.478929102.070175<br>
Nb2Se3_all_min_mon___14.00.struct
<br>
12.401522 17.050185 6.478929102.070175<br>
Nb2Se3_all_min_mon___15.00.struct
<br>
12.401522 17.398148 6.349350102.070175<br>
Now run optimize.job<br>
0.0u 0.0s 0:09.80 0.0% 0+0k 0+264io 0pf+0w</font><br>
<br>
<font color="#c0c0c0">username@computername:~/wiendata/Nb2Se3_all_min$
<font color="#000000">awk 'FNR==4 {print FILENAME, substr($5,
length($5)-9, length($5))}'</font> <font color="#000000">*.struct</font><br>
Nb2Se3_all_min_initial.struct 104.153240<br>
Nb2Se3_all_min_mon___10.00.struct 104.153240<br>
Nb2Se3_all_min_mon____1.00.struct 104.153240<br>
<font color="#0000ff">Nb2Se3_all_min_mon___11.00.struct
102.070175</font><br>
<font color="#0000ff">Nb2Se3_all_min_mon___12.00.struct
106.236305</font><br>
Nb2Se3_all_min_mon___13.00.struct 102.070175<br>
Nb2Se3_all_min_mon___14.00.struct 102.070175<br>
Nb2Se3_all_min_mon___15.00.struct 102.070175<br>
Nb2Se3_all_min_mon____2.00.struct 104.153240<br>
Nb2Se3_all_min_mon____3.00.struct 104.153240<br>
Nb2Se3_all_min_mon____4.00.struct 104.153240<br>
Nb2Se3_all_min_mon____5.00.struct 104.153240<br>
Nb2Se3_all_min_mon____6.00.struct 104.153240<br>
Nb2Se3_all_min_mon____7.00.struct 104.153240<br>
Nb2Se3_all_min_mon____8.00.struct 104.153240<br>
Nb2Se3_all_min_mon____9.00.struct 104.153240<br>
<font color="#0000ff">Nb2Se3_all_min.struct 104.153240</font></font><br>
</p>
<p>[1]
<a href="https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg20403.html" target="_blank">https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg20403.html</a><br>
</p>
<div>On 8/24/2020 11:25 AM, shamik
chakrabarti wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Dear Prof. Laurence Marks Sir,
<div><br>
</div>
<div> I have changed
the atomic coordinates & reduced the symmetry to 1_P with
the help of the Bilbao crystallographic server. The
calculation is still running & 3 structures are already
generated without showing any error. However, the value of
Gamma is still not changing. Why so?</div>
<div><br>
</div>
<div>Thanks & Regards,</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Mon, 24 Aug 2020 at 18:03,
Laurence Marks <<a href="mailto:laurence.marks@gmail.com" target="_blank">laurence.marks@gmail.com</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="auto">You have to also change the positions, and
symmetry of course!<br>
<br>
<div>_____<br>
Professor Laurence Marks<br>
"Research is to see what everybody else has seen, and to
think what nobody else has thought", Albert Szent-Gyorgi<br>
<a href="http://www.numis.northwestern.edu" target="_blank">www.numis.northwestern.edu</a></div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Mon, Aug 24, 2020,
07:29 shamik chakrabarti <<a href="mailto:shamik15041981@gmail.com" target="_blank">shamik15041981@gmail.com</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">Dear Prof. Gavin,<br>
<div><br>
</div>
<div> If I change a to b, b to c
& c to a to make alpha to beta, beta to gamma
& gamma to alpha the produced structure shows
unphysical RMTs for all the atoms.: 1 for Nb &
0.51 for Se. What to do?</div>
<div><br>
</div>
<div>with regards,</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Mon, 24 Aug 2020 at
16:07, Gavin Abo <<a href="mailto:gsabo@crimson.ua.edu" rel="noreferrer" target="_blank">gsabo@crimson.ua.edu</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<p>The 4D is option 7 [
<a href="https://urldefense.com/v3/__https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg04931.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!FEEtwhA5ust8qZ33lpDr8XYIkrrX9Q-5dJZwtsegrpZeCBDX0vBodglHQ7hv6bvLE6WOCw$" rel="noreferrer" target="_blank">https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg04931.html</a>
,
<a href="https://urldefense.com/v3/__https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg14255.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!FEEtwhA5ust8qZ33lpDr8XYIkrrX9Q-5dJZwtsegrpZeCBDX0vBodglHQ7hv6btgMniYYw$" rel="noreferrer" target="_blank">https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg14255.html</a>
]:<br>
</p>
<p>[7] VARY A, B, C and Gamma (4D-case) (monoclinic
lattice)</p>
<p>I think that only worked correctly when the gamma
angle was the one that was greater than 90 (e.g.,
in your case it would likely need to be alpha=90
degrees, beta = 90 degrees, Gamma=104.15 degrees),
refer to:<br>
</p>
<p><a href="https://urldefense.com/v3/__https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg12124.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!FEEtwhA5ust8qZ33lpDr8XYIkrrX9Q-5dJZwtsegrpZeCBDX0vBodglHQ7hv6bvcYwvi9Q$" rel="noreferrer" target="_blank">https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg12124.html</a><br>
</p>
<p><br>
</p>
<div>On 8/23/2020 11:42 AM, shamik chakrabarti
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Dear wien2k users,
<div><br>
</div>
<div> During 4D
optimization of a monoclinic system (file
attached) I have obtained an error as
described below;</div>
<div><br>
</div>
<div>'FERMI' - EFERMI OUT OF ENERGY RANGE<br>
'FERMI' - STOP IN EFI<br>
'FERMI' - ENERGY OF LOWER BOUND
: -4.50517 <br>
'FERMI' - NUMBER OF STATES AT THE LOWER BOUND
: 0.00000 <br>
'FERMI' - ENERGY OF UPPER BOUND
:3003.00451 <br>
'FERMI' - NUMBER OF STATES AT THE UPPER BOUND
: 112.00000 <br>
'FERMI' - ADD 112.00000
<br>
'FERMI' - SOS
0.0000.0000.0000.0000.0000.0000.0000.0000.0003.156
<br>
'FERMI' - NOS
**************************************************
</div>
<div> <br>
<div> What is the meaning of this error &
how to get out of it?</div>
<div><br>
</div>
<div>I have two more queries:</div>
<div>(1) During 4D optimization, I am also
expecting the change in the value of Gamma,
but it remains the same along with all
structures produced by x optimize & also
in the case_default.struct the Gamma is not
changing. why so?</div>
<div><br>
</div>
<div>(2) In my structure, I have alpha=90
degree, beta = 104.15 degrees, Gamma=90
degree. Whether the code will change the
beta of my structure or I have to change the
lattice parameter a to b, b to c & c to
a to produce alpha to beta, beta to gamma
& gamma to alpha?</div>
<div><br>
</div>
<div>Looking forward to your reply in this
regard. Thanks in advance.</div>
<div><br>
</div>
<div>with regards, </div>
-- <br>
<div dir="ltr">
<div dir="ltr">
<div>
<div dir="ltr">
<div dir="ltr">
<div dir="ltr">
<div dir="ltr">
<div style="font-size:small">Dr.
Shamik Chakrabarti</div>
<div style="font-size:small">Research
Fellow </div>
<div style="font-size:small">Department
of Physics</div>
<div style="font-size:small">Indian
Institute of Technology Patna</div>
<div style="font-size:small">Bihta-801103</div>
<div style="font-size:small">Patna</div>
<div style="font-size:small">Bihar,
India</div>
</div>
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<div>
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<div dir="ltr">
<div dir="ltr">
<div style="font-size:small">Dr. Shamik
Chakrabarti</div>
<div style="font-size:small">Research
Fellow </div>
<div style="font-size:small">Department of
Physics</div>
<div style="font-size:small">Indian
Institute of Technology Patna</div>
<div style="font-size:small">Bihta-801103</div>
<div style="font-size:small">Patna</div>
<div style="font-size:small">Bihar, India</div>
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<div dir="ltr">
<div style="font-size:small">Dr. Shamik Chakrabarti</div>
<div style="font-size:small">Research Fellow </div>
<div style="font-size:small">Department of Physics</div>
<div style="font-size:small">Indian Institute of
Technology Patna</div>
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<div style="font-size:small">Patna</div>
<div style="font-size:small">Bihar, India</div>
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</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div style="font-size:small">Dr. Shamik Chakrabarti</div><div style="font-size:small">Research Fellow </div><div style="font-size:small">Department of Physics</div><div style="font-size:small">Indian Institute of Technology Patna</div><div style="font-size:small">Bihta-801103</div><div style="font-size:small">Patna</div><div style="font-size:small">Bihar, India</div></div></div></div></div></div></div></div>