[Pw_forum] difference between molecular dynamics of PW and that of CPMD
Dear sir / madam, I am a new user of pwscf. I know that pw can do molecular dynamics. What is the difference between that and CPMD? Besides, do you know how to restart the run in pw.x? For example, if I have made a run of 400 steps with dt = 20 atomic time unit, but now I find it insufficient. I need the run to have 2000 steps, say. Do I have any method to proceed the run without doing it from the first step again? Lawrence. ___ YM - ??? http://messenger.yahoo.com.hk -- next part -- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070104/f365bc2a/attachment.htm
[Pw_forum] average.x
Suppose your input is like this -input like this--- 1 out.dat 1 400 number of points 3 3 means along z direction 2.351833 window size -- ? ?? wrote: >Hi >I want to calculate the work function for slab ,Iread >every thing abuot it in the fourm and made pp.x and >average .x but I have some questions please answer me >:1- what is the difference between column 1 and 2 in >the output of average.x > > There are 3 columns in the output: column1 is the z direction (in bohr), column2 is the planner average and column3 is the average of column2 (the average of every n points in column2, n is determined by the "window size"). >2- In which units the potentials in the output of >average.x is it Ryd > > Yes. >3-What is the difference between planner average and >macroscopic average ,how we can calculate planner >average . > >4-Regfering to J.phy.condens.matter >11(1999),2689-2696 ,how can I choose the mean >electrostatic potential as areference for Efermi and >macroscopic potential . please answer me ,thanks. > >__ >Do You Yahoo!? >Tired of spam? Yahoo! Mail has the best spam protection around >http://mail.yahoo.com >___ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > > >
[Pw_forum] ph.x v3.2 on NEC SX-8
On Jan 4, 2007, at 12:17 , wlyim at puccini.che.pitt.edu wrote: >> There is also a division by another quantity (dz) that is never >> smaller >> than 1.d-6 by construction. actually I misinterpreted the definition of dz: dz is never LARGER then 1.d-6 by construction. You can simply set dz to a fixed value: 1.d-6, or 1.d-4 . Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy
[Pw_forum] How does PWSCF deal with charged solids?
Hi, guys, Recently, I have been working on some charged solids (like diamond). I think the Makov-Payne correction only is used for isolated molecules. So I just wonder how PWSCF deals with charged solids? I calculated diamond with one more electron per unit cell through PWSCF. Is the total energy correct? Thank you very much. Xiangqian -- next part -- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070104/094f8d83/attachment.htm
[Pw_forum] ph.x v3.2 on NEC SX-8
On Dec 28, 2006, at 23:00 , wlyim at puccini.che.pitt.edu wrote: > the NEC executables pass a larger "nrxx" value, 22200 in NEC vs 20736 > in Intel, given that nr1=24,nr2=24,nr3=36. So in NEC, some zero "zeta" > were passed to dmxc_spin subroutine which led to "divide by zero" > error > at line 1192 in Modules/functionals.f90. this is very unlikely. At line 1192 there is a division by rho (= rho up + rho down), but rho > small = 1.d-30 (there is a check at the beginning of the function). There is also a division by another quantity (dz) that is never smaller than 1.d-6 by construction. You may try to increase the value of "small" to something less small, e.g. 1.d-10 Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy
[Pw_forum] average.x
On Thu, 4 Jan 2007, ? ?? wrote: ??> Hi hi ??, ??> I want to calculate the work function for slab ,Iread ??> every thing abuot it in the fourm and made pp.x and ??> average .x but I have some questions please answer me ??> :1- what is the difference between column 1 and 2 in ??> the output of average.x please have a look at the corresponding sourcecode in the file average.f90. it is pretty well documented. ??> 2- In which units the potentials in the output of ??> average.x is it Ryd if you read the sourcecode, you'll see that this program does not care about units. so output units will be the same as what you put into it. ??> 3-What is the difference between planner average and ??> macroscopic average ,how we can calculate planner ??> average . see under 1). ??> 4-Regfering to J.phy.condens.matter ??> 11(1999),2689-2696 ,how can I choose the mean ??> electrostatic potential as areference for Efermi and you get a good approximation of the mean electrostatic potential by taking the average of the potential over all grid points (which should be equivalent to the average over all planar averages). axel ??> macroscopic potential . please answer me ,thanks. ??> ??> __ ??> Do You Yahoo!? ??> Tired of spam? Yahoo! Mail has the best spam protection around ??> http://mail.yahoo.com ??> ___ ??> Pw_forum mailing list ??> Pw_forum at pwscf.org ??> http://www.democritos.it/mailman/listinfo/pw_forum ??> -- === Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 === If you make something idiot-proof, the universe creates a better idiot.
[Pw_forum] difference between molecular dynamics of PW and that of CPMD
On Thu, 4 Jan 2007, Lawrence Lee wrote: LL> Dear sir / madam, hi lawrence, LL> I am a new user of pwscf. I know that pw can do molecular dynamics. LL> What is the difference between that and CPMD? please be a bit more precise. do you refer to the CPMD package or the CPMD method (as implemented in cp.x )? in the first case you have two packages that implement first principles calculations using DFT and plane wave basis sets with pseudopotentials. due to differences in the interests of the developers, those two packages (quantum espresso and CPMD) have different strenghts and weaknesses. those can be mostly deduced from looking at the descriptions of the input file syntax (plus a few undocumented features, for which you have to read the source code ;-) ). in the second case you have to distinguish between the born-oppenheimer MD in pw.x, where the ground state wavefunction is fully computed in each MD step, and car-parrinello MD in cp.x where, starting from a ground state wavefunction, the wavefunction for subsequent steps is propagated along the trajectory of the atoms by means of an extenden lagrangian scheme (i.e. it is not exactly the ground state wavefunction, but 'oszillates around it'). strictly speaking, CP-dynamics are also using the born-oppenheimer approximation, but BO-MD vs CP-MD is the established nomenclature. historically, CP-MD used to be much more efficient than BO-MD, even though you have to use an about 5 times shorter time step, but more efficient diagonalization and extrapolation and the availability of more cpu power make BO-MD competitive. on top of that, CP-dynamics put a number of restrictions on the system you want to investigate (it needs a band gap, your atom dynamics is modified by the fictitious electron dynamics). LL> Besides, do you know how to restart the run in pw.x? For example, if LL> I have made a run of 400 steps with dt = 20 atomic time unit, but LL> now I find it insufficient. I need the run to have 2000 steps, say. LL> Do I have any method to proceed the run without doing it from the LL> first step again? have you tried using restart_mode='restart' instead of 'from_scratch' ?? axel. LL> LL> Lawrence. LL> LL> ___ LL> YM - ???u?T?? LL> ?N???A?S???W???A?A???B?i?H?d?U?T?A?A???A?W?N?Y?A???N?C LL> http://messenger.yahoo.com.hk -- === Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 === If you make something idiot-proof, the universe creates a better idiot.
[Pw_forum] ph.x v3.2 on NEC SX-8
On Thu, 4 Jan 2007 wlyim at puccini.che.pitt.edu wrote: WY> ** WY> WY> Is there any benchmark test on NEC machine for the latest version of WY> espresso? william, there are a bunch of examples for all kinds of calculations in the example subdirectory. those are regularly tested on a few platforms. please try a few of those (see the README files for descriptions) and see if they work reasonably. this might help to identify the source of the problem. cheers, axel. WY> WY> Best regards, WY> William WY> WY> -- === Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 === If you make something idiot-proof, the universe creates a better idiot.
[Pw_forum] ph.x v3.2 on NEC SX-8
On Thu, 4 Jan 2007, Paolo Giannozzi wrote: > On Jan 4, 2007, at 12:17 , wlyim at puccini.che.pitt.edu wrote: > > >> There is also a division by another quantity (dz) that is never > >> smaller > >> than 1.d-6 by construction. > > actually I misinterpreted the definition of dz: dz is never LARGER then > 1.d-6 by construction. You can simply set dz to a fixed value: 1.d-6, or > 1.d-4 . > Dear Prof. Giannozzi, I tried your suggestion and set dz = 1.d-6 in functionals.f90: dz = min (1.d-6, 1.d-4 * abs (zeta) ) if (dz <= small) dz = 1.d-6 ! added line call xc_spin (rho, zeta - dz, ex, ec, vxupm, vxdwm, vcupm, vcdwm) call xc_spin (rho, zeta + dz, ex, ec, vxupp, vxdwp, vcupp, vcdwp) I hope I added it at the right point. Unfortunately, ph.x still gave wrong results: q = (0.0 0.0 0.0 ) ** omega( 1) = -40.084193 [THz] = -1337.073655 [cm-1] omega( 2) = -39.071262 [THz] = -1303.285663 [cm-1] omega( 3) = -39.071262 [THz] = -1303.285663 [cm-1] omega( 4) = -38.838931 [THz] = -1295.535888 [cm-1] omega( 5) = -38.070039 [THz] = -1269.888241 [cm-1] omega( 6) = -38.070039 [THz] = -1269.888241 [cm-1] ** ph-2.1.4, complied with INTEL and LINUX64 flags and internal FFTW, gave the results below (which is reasonable): q = (0.0 0.0 0.0 ) ** omega( 1) = -0.439781 [THz] = -14.669624 [cm-1] omega( 2) = 0.344752 [THz] = 11.499781 [cm-1] omega( 3) = 0.344752 [THz] = 11.499781 [cm-1] omega( 4) = 3.590255 [THz] = 119.758805 [cm-1] omega( 5) = 3.590255 [THz] = 119.758805 [cm-1] omega( 6) = 7.870822 [THz] = 262.544104 [cm-1] ** Is there any benchmark test on NEC machine for the latest version of espresso? Best regards, William -- Dr. Wai-Leung Yim Institut fuer Reine und Angewandte Chemie, Theoretische Chemie, Carl von Ossiezky Universtaet Oldenburg, 26129 Oldenburg, Germany Email: wlyim at puccini.che.pitt.edu Phone: +49-441-798-3950 (office) +49-441-798-5102 (home) Fax:+49-441-798-3964
[Pw_forum] average.x
Hi I want to calculate the work function for slab ,Iread every thing abuot it in the fourm and made pp.x and average .x but I have some questions please answer me :1- what is the difference between column 1 and 2 in the output of average.x 2- In which units the potentials in the output of average.x is it Ryd 3-What is the difference between planner average and macroscopic average ,how we can calculate planner average . 4-Regfering to J.phy.condens.matter 11(1999),2689-2696 ,how can I choose the mean electrostatic potential as areference for Efermi and macroscopic potential . please answer me ,thanks. __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com
[Pw_forum] ph.x v3.2 on NEC SX-8
On Thu, 4 Jan 2007, Paolo Giannozzi wrote: > > On Dec 28, 2006, at 23:00 , wlyim at puccini.che.pitt.edu wrote: > > > the NEC executables pass a larger "nrxx" value, 22200 in NEC vs 20736 > > in Intel, given that nr1=24,nr2=24,nr3=36. So in NEC, some zero "zeta" > > were passed to dmxc_spin subroutine which led to "divide by zero" > > error > > at line 1192 in Modules/functionals.f90. > > this is very unlikely. At line 1192 there is a division by rho > (= rho up + rho down), but rho > small = 1.d-30 (there is a check > at the beginning of the function). There is also a division by another > quantity (dz) that is never smaller than 1.d-6 by construction. > You may try to increase the value of "small" to something less > small, e.g. 1.d-10 I've checked, from ir=20737 to 22200, dz is zero. I've also tried to add a line in functionals.f90: zeta = (rhoup - rhodw) / rhotot if (zeta <= small) return ! added line ph.x can continue but give wrong result. > > Paolo > --- > Paolo Giannozzi, Democritos and University of Udine, Italy > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Dr. Wai-Leung Yim Institut fuer Reine und Angewandte Chemie, Theoretische Chemie, Carl von Ossiezky Universtaet Oldenburg, 26129 Oldenburg, Germany Email: wlyim at puccini.che.pitt.edu Phone: +49-441-798-3950 (office) +49-441-798-5102 (home) Fax:+49-441-798-3964
