[Pw_forum] Setup problems with espresso-3.2
On Feb 9, 2007, at 18:59 , Amos Leffler wrote: > I wonder if this problem and solution should be added to the user > problems. the solution will be included in the next version. P. --- Paolo Giannozzi, Democritos and University of Udine, Italy
[Pw_forum] Output and parallelization problem in pw.x
Dear all, I have serveral problems about pw.x. The performance of pw.x running in parallel under inter-node, is unreasonbly poor (about 25%). Later, I type sar to check, and find that something called "contextswitch" appears very frequently. But when pw.x is run under intra-node process, the problem did not occur and the performance become very good (>90%). I think that "contextswitch" cause the problem. But why did it occur and how to fix the problem? The second problem is about output file of pw.x. I want to get the stress tensor of each step of a pw.x (not cp.x) molecular dynamic run. I know that they exist in the standard output file. But the format is very inconvenient for further proccessing. Do anyone know is there any flag which can be specified to output a file of stress? Thanks a lot! Lawrence ___ YM - ??? http://messenger.yahoo.com.hk -- next part -- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070212/49d2989e/attachment.htm
[Pw_forum] Output and parallelization problem in pw.x
Lawrence Lee wrote: > The second problem is about output file of pw.x. I want to get the > stress tensor of each step of a pw.x (not cp.x) molecular dynamic run. > I know that they exist in the standard output file. But the format is > very inconvenient for further proccessing. Do anyone know is there any > flag which can be specified to output a file of stress? > grep -e "P=" --after 3 pw-vc.out hope it helps stefano
[Pw_forum] Output and parallelization problem in pw.x
On Feb 12, 2007, at 10:40 , Lawrence Lee wrote: > The performance of pw.x running in parallel under inter-node, > is unreasonably poor (about 25%). it is a well-known problem of Intel motherboards. See for instance: http://www.democritos.it/pipermail/pw_forum/2006-December/005540.html Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy
[Pw_forum] problem on "vc-relax" issue
Dear members,
I got a little problem on "vc-relax" issue.This is
part of input file below:
&CONTROL
calculation = 'vc-relax' ,
restart_mode = 'from_scratch' ,
outdir =
'/home/max/espresso-3.0/tmp/' ,
pseudo_dir =
'/home/max/espresso-3.0/pseudo/' ,
prefix = 'sc0.001' ,
tstress = .true. ,
tprnfor = .true. ,
/
&SYSTEM
ibrav = 0, celldm(1) =6.62,
nat = 4, ntyp = 2, ecutwfc = 64.0,
occupations='smearing',
smearing='gaussian',degauss=0.01
/
&ELECTRONS
conv_thr = 1.0d-8 ,
mixing_mode = 'plain' ,
mixing_beta = 0.7 ,
diagonalization = 'cg' ,
/
&CELL
cell_dynamics = "damp-w",
/
&IONS
pot_extrapolation = "second_order",
wfc_extrapolation = "second_order",
/
CELL_PARAMETERS {hexagonal}
1.0 0.0 0.0
-0.5 0.866025404 0.0
0.0 0.0 1.60900
But output file showed that:
%%
from read_namelists : error # 1
reading namelist cell
%%
So what I missing setup (necessary) in namelist cell
?(I had try several settings but got the same error
message above)
max
___
??? ?
http://messenger.yahoo.com.tw/
[Pw_forum] problem on "vc-relax" issue
the namelists are read in a specific order: &ions must come before &cell
stefano
? ?? wrote:
>Dear members,
>I got a little problem on "vc-relax" issue.This is
>part of input file below:
>
> &CONTROL
> calculation = 'vc-relax' ,
>restart_mode = 'from_scratch' ,
> outdir =
>'/home/max/espresso-3.0/tmp/' ,
> pseudo_dir =
>'/home/max/espresso-3.0/pseudo/' ,
> prefix = 'sc0.001' ,
> tstress = .true. ,
> tprnfor = .true. ,
> /
> &SYSTEM
>ibrav = 0, celldm(1) =6.62,
> nat = 4, ntyp = 2, ecutwfc = 64.0,
> occupations='smearing',
>smearing='gaussian',degauss=0.01
> /
> &ELECTRONS
>conv_thr = 1.0d-8 ,
> mixing_mode = 'plain' ,
> mixing_beta = 0.7 ,
> diagonalization = 'cg' ,
> /
>&CELL
> cell_dynamics = "damp-w",
>/
>&IONS
> pot_extrapolation = "second_order",
> wfc_extrapolation = "second_order",
>/
>CELL_PARAMETERS {hexagonal}
> 1.0 0.0 0.0
> -0.5 0.866025404 0.0
> 0.0 0.0 1.60900
>
>
>But output file showed that:
>
>
>%%
> from read_namelists : error # 1
> reading namelist cell
>
>%%
>
>So what I missing setup (necessary) in namelist cell
>?(I had try several settings but got the same error
>message above)
>
>max
>
>
>
>
>___
> ??? ?
> http://messenger.yahoo.com.tw/
>___
>Pw_forum mailing list
>Pw_forum at pwscf.org
>http://www.democritos.it/mailman/listinfo/pw_forum
>
>
[Pw_forum] How to get atomic partial charge for MD
Dear pwscf users, I am trying to get effective atomic charges of Bi2Te3 and apply them in my molecular dynamics simulation. Does any one know how to get this? I recognize that the definition of partial charge is arbitrary since the boundary of electron density is not distinct. I would like to know which kinds of partial charge can be obtained in PWSCF except Born charge. I was told that the charges derived from effective electrostatic potential (ESP) might be the most appropriate for MD calculation. I don't if I could get the effective electrostatic potential since ESP normally is obtained in Wan der Waals regimes, which may be not applicable for crystals. Any help will be greatly appreciated. Thanks very much Baoling Huang _ Laugh, share and connect with Windows Live Messenger http://clk.atdmt.com/MSN/go/msnnkwme002001msn/direct/01/?href=http://imagine-msn.com/messenger/launch80/default.aspx?locale=en-us&source=hmtagline
[Pw_forum] Re: About espresso on Mac with x86
Dear Carlos, few months ago I had succeeded in compiling QE on my mac laptop (intel proc, mac os X, intel compilers and mkl libraries) and I attach the make.sys I had used to this message. I was using however a now-old version of QE (3.1) so you may need some fixing here and there. Hope this helps. Good luck! Matteo On Feb 11 2007, Stefano Baroni wrote: >Hi Carlos: > >I have not found any posts of yours in the forum. >I think it does. I do not see any reasons why it shouldn't. >If you have trouble installing espresso on mac os x, please report to >the mailing list. > >Cheers >Stefano > >On Feb 7, 2007, at 6:09 PM, Carlos L?pez wrote: > >> Hello, I've been trying to compile espresso, and I've sent emails >> to the >> list but I haven't received any answer yet, just wanted to ask you if >> you know if it will compile well eventually on the mac with macos X >> with >> intel processors and fortran and c compilers from Intel. >> >> Thank you very much. >> Carlos L?pez > >--- >Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - >Trieste >[+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) > >Please, if possible, don't send me MS Word or PowerPoint attachments >Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > -- %%% Matteo Cococcioni Department of Chemical Engineering and Materials Science University of Minnesota 151 Amundson Hall 421 Washington Av. SE Minneapolis, MN 55455 Tel. +1 612 624 9056Fax +1 612 626 7246 %%% -- next part -- A non-text attachment was scrubbed... Name: make.sys_mac Type: application/octet-stream Size: 2359 bytes Desc: make.sys_mac Url : /pipermail/attachments/20070212/74310aa5/attachment.obj
[Pw_forum] How to get atomic partial charge for MD
Dear Baoling, I do not have much to offer, but you could look at some very recent (last few weeks) work of Paul Madden (Edinburgh), or some older work (2003-4) from Celeste Sagui. nicola naivebamboo Huang wrote: > Dear pwscf users, > I am trying to get effective atomic charges of Bi2Te3 and > apply them in my molecular dynamics simulation. Does any one know how to > get this? I recognize that the definition of partial charge is arbitrary > since the boundary of electron density is not distinct. I would like to > know which kinds of partial charge can be obtained in PWSCF except Born > charge. I was told that the charges derived from effective electrostatic > potential (ESP) might be the most appropriate for MD calculation. I > don't if I could get the effective electrostatic potential since ESP > normally is obtained in Wan der Waals regimes, which may be not > applicable for crystals. > Any help will be greatly appreciated. > > Thanks very much > > Baoling Huang > > _ > Laugh, share and connect with Windows Live Messenger > http://clk.atdmt.com/MSN/go/msnnkwme002001msn/direct/01/?href=http://imagine-msn.com/messenger/launch80/default.aspx?locale=en-us&source=hmtagline > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- - Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu
