Dear all,<br><br>Sorry for last arbitrary question. I found there was a code called cppp.x.<br><br>But now I encounter another serious problem with the information from pp.x of "ortho went bananas", when I try to add nose thermostat to the system at 150th step. <br>
<br>the process as follows,<br>First, I get the optimized geometry from the pw.x. Then I use that geometry as the initial input to pp.x.<br>During the first 19 of cp calculation, I did a few electronic steps with ions fixed and dt=1<br>
From 20th step to 79th step, I enlarge the dt to 3;<br>From 80th step to 149th step, I allow the ions to move and set dt to 5, with no thermostat.<br>When I tried to add nose thermostat, the "econt" of the system became to NaN and the vnhp became to Inf.<br>
And then the program crashed with the information that "ortho went bananas"<br> <br>here is a part of my input files,<br> &CONTROL <br>
title = 'CPMD' , <br> calculation = 'cp' , <br> restart_mode = 'from_scratch' , <br>
outdir = '/tmp/' , <br> wfcdir = '/tmp/' , <br> pseudo_dir = '/home/vega/espresso-4.0/pseudo/' , <br>
prefix = 'cp_dissociation1' ,<br> nstep = 99999 ,<br> dt = 1, <br> / <br>
&SYSTEM <br> ibrav = 8, <br> celldm(1) =24.8624,<br>
celldm(2) = 0.8520,<br> celldm(3) = 1.6964,<br> nat = 147, <br> ntyp = 3,<br> nr1b = 20,<br>
nr2b = 20, <br> nr3b = 20, <br> nosym = .true. , <br>
ecutwfc = 30,<br> ecutrho = 300,<br> / <br> <br> &ELECTRONS <br>
mixing_mode ='local-TF',<br> mixing_beta = 0.4, <br> electron_dynamics = 'damp', <br> / <br>
&IONS <br> ion_dynamics = 'none',<br> ion_temperature = 'not_controlled', <br>
/ <br>AUTOPILOT<br> on_step = 20 : dt=3<br> on_step = 20 : electron_dynamics = 'damp'<br> on_step = 80 : dt=5<br> on_step = 80 : ion_dynamics = 'damp'<br> on_step = 150 : ion_temperature = 'nose'<br>
ENDRULES <br>ATOMIC_SPECIES <br><span class="word"></span>......<br>
......<br>......<br><br>could you please do me a favor to tell me what is going wrong.<br><br>best wishes,<br><br>vega<br><br><div class="gmail_quote">On Wed, Nov 18, 2009 at 7:53 PM, vega lew <span dir="ltr"><<a href="mailto:quantumdft@gmail.com">quantumdft@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Dear sir,<br><br>thank you for your information.<br><br>could anyone tell me something about how to visualize the geometry of the output file?<br>
Is there a small tool to read the output file directly instead of converting the XYZ coordinations into another format and feeding it to VMD or VEGAZZ?<div class="im"><br>
<br>thank you in advance.<br><br>best wishes.<br><br>vega <br><br></div><div><div></div><div class="h5"><div class="gmail_quote">On Wed, Nov 18, 2009 at 3:00 PM, Paolo Giannozzi <span dir="ltr"><<a href="mailto:giannozz@democritos.it" target="_blank">giannozz@democritos.it</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><br>
On Nov 18, 2009, at 6:17 , vega lew wrote:<br>
<br>
> I have a question about the option "nr1b, nr2b, nr3b" in &SYSTEM<br>
> namelist.<br>
> Could you please tell me something more about it?<br>
<br>
</div><a href="http://www.quantum-espresso.org/user_guide/node30.html" target="_blank">http://www.quantum-espresso.org/user_guide/node30.html</a><br>
<div><div></div><div>><br>
<br>
<br>
P.<br>
---<br>
Paolo Giannozzi, Dept of Physics, University of Udine<br>
via delle Scienze 208, 33100 Udine, Italy<br>
Phone +39-0432-558216, fax +39-0432-558222<br>
<br>
<br>
<br>
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</div></div></blockquote></div><br><br clear="all"><br></div></div><div><div></div><div class="h5">-- <br>==================================================================================<br>Vega Lew ( weijia liu)<br>Graduate student<br>
State Key Laboratory of Materials-oriented Chemical Engineering<br>
College of Chemistry and Chemical Engineering<br>Nanjing University of Technology, 210009, Nanjing, Jiangsu, China<br>******************************************************************************************************************<br>
Email: <a href="mailto:vegalew@gmail.com" target="_blank">vegalew@gmail.com</a><br>Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing, Jiangsu, China <br>****************************************************************************************************************** <br>
</div></div></blockquote></div><br><br clear="all"><br>-- <br>==================================================================================<br>Vega Lew ( weijia liu)<br>Graduate student<br>State Key Laboratory of Materials-oriented Chemical Engineering<br>
College of Chemistry and Chemical Engineering<br>Nanjing University of Technology, 210009, Nanjing, Jiangsu, China<br>******************************************************************************************************************<br>
Email: <a href="mailto:vegalew@gmail.com">vegalew@gmail.com</a><br>Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing, Jiangsu, China <br>****************************************************************************************************************** <br>